BIOMARKER DLEC1 FOR CANCER
1. A method for assessing risk for esophageal squamous cell carcinoma (ESCC) in a subject, comprising the steps of:
- (a) measuring expression level of DLEC1 in a sample taken from the subject,(b) comparing the expression level obtained in step (a) with a standard control, and(c) determining the subject, who has a reduced DLEC1 expression level compared with the standard control, as having an increased risk for ESCC.
The present invention provides a method for diagnosing and determining prognosis of certain cancers (e.g., esophageal squamous cell carcinoma or ESCC) in a subject by detecting suppressed expression of the DLEC1 gene, which in some cases is due to elevated methylation level in the genomic sequence of this gene. A kit and device useful for such a method are also provided. In addition, the present invention provides a method for treating cancer by increasing DLEC1 gene expression or activity.
- 1. A method for assessing risk for esophageal squamous cell carcinoma (ESCC) in a subject, comprising the steps of:
(a) measuring expression level of DLEC1 in a sample taken from the subject, (b) comparing the expression level obtained in step (a) with a standard control, and (c) determining the subject, who has a reduced DLEC1 expression level compared with the standard control, as having an increased risk for ESCC.
- View Dependent Claims (2, 3, 4)
- 5-12. -12. (canceled)
- 13. A method for assessing risk for ESCC in a subject, comprising the steps of:
(a) treating DNA from an esophageal epithelial tissue sample taken from the subject with an agent that differentially modifies methylated and unmethylated DNA; (b) determining number of methylated CpGs in a genomic sequence, which is SEQ ID NO;
5 or 6 or a fragment thereof comprising at least 10 CpGs, and
(c) comparing the number of methylated CpGs from step (b) with the number of methylated CpGs in the genomic sequence from a non-ESCC sample and processed through steps (a) and (b); and (d) determining the subject, whose sample contains more methylated CpGs in the genomic sequence determined in step (b) compared to the number of methylated CpGs with the number of methylated CpGs in the genomic sequence from a non-ESCC sample and processed through steps (1) to (3), as having an increased risk for ESCC compared with a healthy subject not diagnosed with ESCC.
- View Dependent Claims (14, 15, 16)
- 17. (canceled)
- 18. A method for assessing likelihood of mortality from ESCC in an ESCC patient, comprising the steps of:
(a) treating DNA from an ESCC sample taken from a first ESCC patient with an agent that differentially modifies methylated and unmethylated DNA;
5 or 6 or a fragment thereof comprising at least 10 CpGs, and
(c) comparing the number of methylated CpGs from step (b) with the number of methylated CpGs in the genomic sequence from another ESCC sample of the same type obtained from a second ESCC patient and processed through steps (a) and (b); and (d) determining the first patient, whose ESCC sample contains more methylated CpGs in the genomic sequence determined in step (b) compared to the number of methylated CpGs with the number of methylated CpGs in the genomic sequence from the ESCC sample obtained from the second patient and processed through steps (1) to (3), as having an increased likelihood of mortality from ESCC compared with the second ESCC patient.
- View Dependent Claims (19, 20, 21)
- 22. (canceled)
- 23. A kit for detecting ESCC in a subject, comprising (1) a standard control that provides an average amount of DLEC1 protein or DLEC1 mRNA;
- and (2) an agent that specifically and quantitatively identifies DLEC1 protein or DLEC1 mRNA.
- View Dependent Claims (24, 25, 26)
- 27-28. -28. (canceled)
- 29. A method for inhibiting growth of an ESCC cell, comprising contacting the ESCC cell with an effective amount of a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:
- 4 or a nucleic acid comprising a polynucleotide sequence encoding SEQ ID NO;
- View Dependent Claims (30, 31, 32)
- 4 or a nucleic acid comprising a polynucleotide sequence encoding SEQ ID NO;
- 33. (canceled)
This application claims priority to U.S. Provisional Patent Application No. 62/714,506, filed Aug. 3, 2018, the contents of which are hereby incorporated by reference in the entirety for all purposes.
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Nov. 20, 2019, is named 080015-1148963-024410US_SL.txt and is 153,945 bytes in size.
Cancer-related causes are among the top reasons of death in developed countries. In the US alone, the number of new cases of cancer of any site averages about 450 per 100,000 men and women per year, and the number of deaths averages about 170 per 100,000 men and women per year. Cancer is a disease with a high mortality rate: while about 1,700,000 newly diagnosed cancer cases are expected each year, over 600,000 deaths annually are attributable to various types of cancer. Based on data from recent years, it is estimated that over 38% of men and women will be diagnosed with cancer at some point during their lifetime.
Esophageal cancer, for example, is the 8th most common cancer world-wide with nearly 500,000 new cases diagnosed each year. Globally, it is responsible for approximately 400,000 deaths annually. While its incidence varies significantly from country to country, nearly half of esophageal cancer consistently occurs in China. Due to its lack of early symptoms and therefore often late diagnosis, this disease has a grim prognosis with only 13-18% patient is surviving beyond 5 years after the initial diagnosis.
Because of the prevalence of cancer and its enormous social and economical impact globally, there exists an urgent need for new and more effective methods to diagnose, monitor, and treat cancer. This invention fulfills this and other related needs.
The present inventors have identified DLEC1 as a novel tumor suppressor and diagnostic/prognostic marker for various types of human cancer, especially esophageal cancer such as esophageal squamous cell carcinoma (ESCC). More specifically, the inventors show that, compared with normal individuals, CpG islands of DLEC1 gene are hypermethylated in biological samples of cancer tissues taken from cancer patients. Such hypermethylation leads to DLEC1 silencing at both mRNA and protein levels. Re-expression of DLEC1 inhibits cancer cell growth and induces programmed cell death. Protein/mRNA expression level of DLEC1 and promoter methylation level of DLEC1 genetic sequence closely correlate with the survival of cancer patients and are therefore also useful as prognostic markers for cancer.
Thus, in the first aspect, the present invention provides a method for (1) assessing risk for later developing esophageal squamous cell carcinoma (ESCC) in a subject who may not have exhibited any symptoms of ESCC or (2) diagnosing ESCC in a patient who has manifested one or more clinical symptoms suspected of ESCC. The method includes these steps: (a) measuring expression level of DLEC1 in a sample taken from the subject; (b) comparing the expression level obtained in step (a) with a standard control; and (c) determining the subject, who has a reduced DLEC1 expression level compared with the standard control, as having an increased risk for ESCC.
In some embodiments, the sample used for practicing the method is a esophageal epithelial tissue sample. In some embodiments, the expression level of DLEC1 is DLEC1 protein level. In some embodiments, the expression level of DLEC1 is DLEC1 mRNA level. In some embodiments, step (a) comprises an immunoassay using an antibody that specifically binds the DLEC1 protein; or step (a) may comprise an amplification reaction, such as a polymerase chain reaction (PCR), especially a reverse transcriptase-PCR (RT-PCR). In some embodiments, step (a) comprises a polynucleotide hybridization assay, such as a Southern Blot analysis or Northern Blot analysis, or an in situ hybridization assay. In some embodiments, when the subject is indicated as having an increased risk for ESCC, the method is further includes repeating step (a) at a later time using the sample type of sample from the subject, wherein an increase in the expression level of DLEC1 at the later time as compared to the amount from the original step (a) indicates a lessened risk of ESCC, and a decrease indicates a heightened risk for ESCC.
In the second aspect, the present invention provides a method for assessing risk for later developing ESCC in a subject who may not have exhibited any symptoms of ESCC or (2) diagnosing ESCC in a patient who has manifested one or more clinical symptoms suspected of ESCC. The method includes these steps: (a) treating DNA from an esophageal epithelial tissue sample taken from the subject with an agent that differentially modifies methylated and unmethylated DNA; (b) determining number of methylated CpGs in a genomic sequence, which is SEQ ID NO:5 or 6 or a fragment thereof comprising at least 10 CpGs, and (c) comparing the number of methylated CpGs from step (b) with the number of methylated CpGs in the genomic sequence from a non-ESCC sample and processed through steps (a) and (b); and (d) determining the subject, whose sample contains more methylated CpGs in the genomic sequence determined in step (b) compared to the number of methylated CpGs with the number of methylated CpGs in the genomic sequence from a non-ESCC sample and processed through steps (1) to (3), as having an increased risk for ESCC compared with a healthy subject not diagnosed with ESCC.
In some embodiments, the genomic sequence is SEQ ID NO:5 or SEQ ID NO:6. In embodiments, the agent that differentially modifies methylated DNA and unmethylated DNA is an enzyme that preferentially cleaves methylated DNA, an enzyme that preferentially cleaves unmethylated DNA, or a bisulfite. In some embodiments, step (b) comprises an amplification reaction, such as a PCR.
In the third aspect, the present invention provides a method for assessing likelihood of mortality from ESCC in an ESCC patient. The method comprises the steps of: (a) treating DNA from an ESCC sample taken from a first ESCC patient with an agent that differentially modifies methylated and unmethylated DNA; (b) determining number of methylated CpGs in a genomic sequence, which is SEQ ID NO:5 or 6 or a fragment thereof comprising at least 10 CpGs, and (c) comparing the number of methylated CpGs from step (b) with the number of methylated CpGs in the genomic sequence from another ESCC sample of the same type obtained from a second ESCC patient and processed through steps (a) and (b); and (d) determining the first patient, whose ESCC sample contains more methylated CpGs in the genomic sequence determined in step (b) compared to the number of methylated CpGs with the number of methylated CpGs in the genomic sequence from the ESCC sample obtained from the second patient and processed through steps (1) to (3), as having an increased likelihood of mortality from ESCC compared with the second ESCC patient.
In some embodiments, the genomic sequence is SEQ ID NO:5 or SEQ ID NO:6. In some embodiments, the agent that differentially modifies methylated DNA and unmethylated DNA is an enzyme that preferentially cleaves methylated DNA, an enzyme that preferentially cleaves unmethylated DNA, or a bisulfite. In some embodiments, step (b) comprises an amplification reaction such as a PCR.
In the fourth aspect, the present invention provides a kit for detecting ESCC in a subject. The kit includes (1) a standard control that provides an average amount of DLEC1 protein or DLEC1 mRNA; and (2) an agent that specifically and quantitatively identifies DLEC1 protein or DLEC1 mRNA. In some embodiments, the agent in (2) is an antibody that specifically binds the DLEC1 protein. In some embodiments, the agent in (2) is a polynucleotide probe that hybridizes with the DLEC1 mRNA. In some embodiments, the agent comprises a detectable moiety. In some embodiments, the kit may further include two oligonucleotide primers for specifically amplifying at least a segment of SEQ ID NO:3 or its complement in an amplification reaction. Optionally, the kit in some cases may further include an instruction manual to provide instructions for the users.
In the fifth aspect, the present invention provides a method for inhibiting growth of an ESCC cell, comprising contacting the ESCC cell with an effective amount of a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:4 or a nucleic acid comprising a polynucleotide sequence encoding SEQ ID NO:4. In some embodiments, the nucleic acid is an expression cassette comprising a promoter (e.g., an epithelium-specific promoter) operably linked to the polynucleotide sequence encoding SEQ ID NO:4. In some embodiments, the nucleic acid comprises the polynucleotide sequence set forth in SEQ ID NO:1 or 3. In some embodiments, the method is practiced to inhibit the growth of ESCC cells within a patient'"'"'s body, when the patient may or may not have exhibited clinical symptoms of ESCC.
The term “DLEC1 gene” or “DLEC1 protein,” as used herein, refers to any naturally occurring variants or mutants, interspecies homologs or orthologs, or man-made variants of human DLEC1 gene or DLEC1 protein. The human DLEC1 is localized on chromosome 3p21-22. The genomic DNA sequence for the gene is set forth in SEQ ID NO: 1, and the cDNA sequence corresponding to a human wild-type DLEC1 mRNA is set forth in GenBank Accession No. NM_007335.3 (provided herein as SEQ ID NO:2), which translate to a coding sequence (provided herein as SEQ ID NO:3) for a 1755-amino acid DLEC1 protein (GenBank Accession No. NP_031361, provided herein as SEQ ID NO:4). A DLEC1 protein within the meaning of this application typically has at least 80%, or 90%, or 95% or higher sequence identity to the human wild-type DLEC1 protein.
In this disclosure the term “esophageal squamous cell carcinoma” or “ESCC” refer to a type of cancer of the esophagus. Such cancer arises from the epithelial cells that line the esophagus and is usually (but not always) found in the higher portion of the esophagus. In contrast, a second type of esophagus cancer, esophageal adenocarcinoma (EAC), arises from the glandular cells that are typically present in the lower third of the esophagus. An “ESCC” cell is a esophageal epithelial cell possessing characteristics of ESCC and encompasses a precancerous cell, which is in the early stages of conversion to a cancer cell or which is predisposed for conversion to a cancer cell. Such cells may exhibit one or more phenotypic traits characteristic of the cancerous cells.
In this disclosure the term “or” is generally employed in its sense including “and/or” unless the content clearly dictates otherwise.
As used herein, the term “gene expression” is used to refer to the transcription of a DNA to form an RNA molecule encoding a particular protein (e.g., human DLEC1 protein) or the translation of a protein encoded by a polynucleotide sequence. In other words, both mRNA level and protein level encoded by a gene of interest (e.g., human DLEC1 gene) are encompassed by the term “gene expression level” in this disclosure.
In this disclosure the term “biological sample” or “sample” includes sections of tissues such as biopsy and autopsy samples, and frozen sections taken for histologic purposes, or processed forms of any of such samples. Biological samples include blood and blood fractions or products (e.g., serum, plasma, platelets, red blood cells, and the like), sputum or saliva, lymph and tongue tissue, cultured cells, e.g., primary cultures, explants, and transformed cells, stool, urine, esophagus biopsy tissue etc. A biological sample is typically obtained from a eukaryotic organism, which may be a mammal, may be a primate and may be a human subject.
In this disclosure the term “biopsy” refers to the process of removing a tissue sample for diagnostic or prognostic evaluation, and to the tissue specimen itself. Any biopsy technique known in the art can be applied to the diagnostic and prognostic methods of the present invention. The biopsy technique applied will depend on the tissue type to be evaluated (e.g., tongue, colon, prostate, kidney, bladder, lymph node, liver, bone marrow, blood cell, stomach tissue, esophagus, etc.) among other factors. Representative biopsy techniques include, but are not limited to, excisional biopsy, incisional biopsy, needle biopsy, surgical biopsy, and bone marrow biopsy and may comprise colonoscopy or endoscopy. A wide range of biopsy techniques are well known to those skilled in the art who will choose between them and implement them with minimal experimentation.
In this disclosure the term “isolated” nucleic acid molecule means a nucleic acid molecule that is separated from other nucleic acid molecules that are usually associated with the isolated nucleic acid molecule. Thus, an “isolated” nucleic acid molecule includes, without limitation, a nucleic acid molecule that is free of nucleotide sequences that naturally flank one or both ends of the nucleic acid in the genome of the organism from which the isolated nucleic acid is derived (e.g., a cDNA or genomic DNA fragment produced by PCR or restriction endonuclease digestion). Such an isolated nucleic acid molecule is generally introduced into a vector (e.g., a cloning vector or an expression vector) for convenience of manipulation or to generate a fusion nucleic acid molecule. In addition, an isolated nucleic acid molecule can include an engineered nucleic acid molecule such as a recombinant or a synthetic nucleic acid molecule. A nucleic acid molecule existing among hundreds to millions of other nucleic acid molecules within, for example, a nucleic acid library (e.g., a cDNA or genomic library) or a gel (e.g., agarose, or polyacrylamine) containing restriction-digested genomic DNA, is not an “isolated” nucleic acid.
The term “nucleic acid” or “polynucleotide” refers to deoxyribonucleic acids (DNA) or ribonucleic acids (RNA) and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologs, single nucleotide polymorphisms (SNPs), and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); and Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The term nucleic acid is used interchangeably with gene, cDNA, and mRNA encoded by a gene.
The term “gene” means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) involved in the transcription/translation of the gene product and the regulation of the transcription/translation, as well as intervening sequences (introns) between individual coding segments (exons).
In this application, the terms “polypeptide,” “peptide,” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymers. As used herein, the terms encompass amino acid chains of any length, including full-length proteins (i.e., antigens), wherein the amino acid residues are linked by covalent peptide bonds.
The term “amino acid” refers to refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, γ-carboxyglutamate, and O-phosphoserine. For the purposes of this application, amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. For the purposes of this application, amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.
Amino acids may include those having non-naturally occurring D-chirality, as disclosed in WO01/12654, which may improve the stability (e.g., half-life), bioavailability, and other characteristics of a polypeptide comprising one or more of such D-amino acids. In some cases, one or more, and potentially all of the amino acids of a therapeutic polypeptide have D-chirality.
Amino acids may be referred to herein by either the commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
As used in herein, the terms “identical” or percent “identity,” in the context of describing two or more polynucleotide or amino acid sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (for example, a variant DLEC1 protein used in the method of this invention (e.g., for treating esophageal cancer, especially ESCC) has at least 80% sequence identity, preferably 85%, 90%, 91%, 92%, 93, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity, to a reference sequence, e.g., a wild-type human DLEC1 protein), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Such sequences are then said to be “substantially identical.” With regard to polynucleotide sequences, this definition also refers to the complement of a test sequence. Preferably, the identity exists over a region that is at least about 50 amino acids or nucleotides in length, or more preferably over a region that is 75-100 amino acids or nucleotides in length.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters. For sequence comparison of nucleic acids and proteins, the BLAST and BLAST 2.0 algorithms and the default parameters discussed below are used.
A “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'"'"'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 1995 supplement)).
Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., (1990) J Mol. Biol. 215: 403-410 and Altschul et al. (1977) Nucleic Acids Res. 25: 3389-3402, respectively. Software for performing BLAST analyses is publicly available at the National Center for Biotechnology Information website, ncbi.nlm.nih.gov. The algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits acts as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a word size (W) of 28, an expectation (E) of 10, M=1, N=−2, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a word size (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).
The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul, Proc. Nat'"'"'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.
An indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the antibodies raised against the polypeptide encoded by the second nucleic acid, as described below. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions, as described below. Yet another indication that two nucleic acid sequences are substantially identical is that the same primers can be used to amplify the sequence.
In this disclosure the terms “stringent hybridization conditions” and “high stringency” refer to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acids, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993) and will be readily understood by those skilled in the art. Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength pH. The Tm is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, preferably 10 times background hybridization. Exemplary stringent hybridization conditions can be as following: 50% formamide, 5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS, incubating at 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C.
Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary “moderately stringent hybridization conditions” include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 1×SSC at 45° C. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency. Additional guidelines for determining hybridization parameters are provided in numerous references, e.g., Current Protocols in Molecular Biology, ed. Ausubel, et al.
An “expression cassette” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular polynucleotide sequence in a host cell. An expression cassette may be part of a plasmid, viral genome, or nucleic acid fragment. Typically, an expression cassette includes a polynucleotide to be transcribed, operably linked to a promoter. “Operably linked” in this context means two or more genetic elements, such as a polynucleotide coding sequence and a promoter, placed in relative positions that permit the proper biological functioning of the elements, such as the promoter directing transcription of the coding sequence. Other elements that may be present in an expression cassette include those that enhance transcription (e.g., enhancers) and terminate transcription (e.g., terminators), as well as those that confer certain binding affinity or antigenicity to the recombinant protein produced from the expression cassette.
The term “bisulfite” as used herein encompasses all types of bisulfites, such as sodium bisulfite, that are capable of chemically converting a cytosine (C) to a uracil (U) without chemically modifying a methylated cytosine and therefore can be used to differentially modify a DNA sequence based on the methylation status of the DNA.
As used herein, a reagent that “differentially modifies” methylated or non-methylated DNA encompasses any reagent that reacts differentially with methylated and unmethylated DNA in a process through which distinguishable products or quantitatively distinguishable results (e.g. degree of binding or precipitation) are generated from methylated and non-methylated DNA, thereby allowing the identification of the DNA methylation status. Such processes may include, but are not limited to, chemical reactions (such as an unmethylated C→U conversion by bisulfite), enzymatic treatment (such as cleavage by a methylation-dependent endonuclease), binding, and precipitation. Thus, an enzyme that preferentially cleaves methylated DNA is one capable of cleaving a DNA molecule at a much higher efficiency when the DNA is methylated, whereas an enzyme that preferentially cleaves unmethylated DNA exhibits a significantly higher efficiency when the DNA is not methylated. In the context of the present invention, a reagent that “differentially modifies” methylated and unmethylated DNA also refers to any reagent that exhibits differential ability in its binding to DNA sequences or precipitation of DNA sequences depending on their methylation status. One class of such reagents consists of methylated DNA binding proteins.
A “CpG-containing genomic sequence” as used herein refers to a segment of DNA sequence at a defined location in the genome of an individual. Typically, a “CpG-containing genomic sequence” is at least 15 contiguous nucleotides in length and contains at least one CpG pair. In some cases, it can be at least 18, 20, 25, 30, 50, 80, 100, 150, 200, 250, or 300 contiguous nucleotides in length and contains at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, or 30 CpG pairs. For any one “CpG-containing genomic sequence” at a given location, e.g., within a region of the human DLEC1 genomic sequence (such as the region containing the promoter and exon 1), nucleotide sequence variations may exist from individual to individual and from allele to allele even for the same individual. Furthermore, a “CpG-containing genomic sequence” may encompass a nucleotide sequence transcribed or not transcribed for protein production, and the nucleotide sequence can be a protein-coding sequence, a non protein-coding sequence (such as a transcription promoter), or a combination thereof.
The term “immunoglobulin” or “antibody” (used interchangeably herein) refers to an antigen-binding protein having a basic four-polypeptide chain structure consisting of two heavy and two light chains, said chains being stabilized, for example, by interchain disulfide bonds, which has the ability to specifically bind antigen. Both heavy and light chains are folded into domains.
The term “antibody” also refers to antigen- and epitope-binding fragments of antibodies, e.g., Fab fragments, that can be used in immunological affinity assays. There are a number of well characterized antibody fragments. Thus, for example, pepsin digests an antibody C-terminal to the disulfide linkages in the hinge region to produce F(ab)′2, a dimer of Fab which itself is a light chain joined to VH-CH1 by a disulfide bond. The F(ab)′2 can be reduced under mild conditions to break the disulfide linkage in the hinge region thereby converting the (Fab′)2 dimer into an Fab′ monomer. The Fab′ monomer is essentially a Fab with part of the hinge region (see, e.g., Fundamental Immunology, Paul, ed., Raven Press, N.Y. (1993), for a more detailed description of other antibody fragments). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that fragments can be synthesized de novo either chemically or by utilizing recombinant DNA methodology. Thus, the term antibody also includes antibody fragments either produced by the modification of whole antibodies or synthesized using recombinant DNA methodologies.
The phrase “specifically binds,” when used in the context of describing a binding relationship of a particular molecule to a protein or peptide, refers to a binding reaction that is determinative of the presence of the protein in a heterogeneous population of proteins and other biologics. Thus, under designated binding assay conditions, the specified binding agent (e.g., an antibody) binds to a particular protein at least two times the background and does not substantially bind in a significant amount to other proteins present in the sample. Specific binding of an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein or a protein but not its similar “sister” proteins. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein or in a particular form. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein (see, e.g., Harlow & Lane, Antibodies, A Laboratory Manual (1988) for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity). Typically a specific or selective binding reaction will be at least twice background signal or noise and more typically more than 10 to 100 times background. On the other hand, the term “specifically bind” when used in the context of referring to a polynucleotide sequence forming a double-stranded complex with another polynucleotide sequence describes “polynucleotide hybridization” based on the Watson-Crick base-pairing, as provided in the definition for the term “polynucleotide hybridization method.”
As used in this application, an “increase” or a “decrease” refers to a detectable positive or negative change in quantity from a comparison control, e.g., an established standard control (such as an average expression level of DLEC1 mRNA or DLEC1 protein found in non-cancerous esohpagus tissue). An increase is a positive change that is typically at least 10%, or at least 20%, or 50%, or 100%, and can be as high as at least 2-fold or at least 5-fold or even 10-fold of the control value. Similarly, a decrease is a negative change that is typically at least 10%, or at least 20%, 30%, or 50%, or even as high as at least 80% or 90% of the control value. Other terms indicating quantitative changes or differences from a comparative basis, such as “more,” “less,” “higher,” and “lower,” are used in this application in the same fashion as described above. In contrast, the term “substantially the same” or “substantially lack of change” indicates little to no change in quantity from the standard control value, typically within ±10% of the standard control, or within +5%, 2%, or even less variation from the standard control.
A “polynucleotide hybridization method” as used herein refers to a method for detecting the presence and/or quantity of a pre-determined polynucleotide sequence based on its ability to form Watson-Crick base-pairing, under appropriate hybridization conditions, with a polynucleotide probe of a known sequence. Examples of such hybridization methods include Southern blot, Northern blot, and in situ hybridization.
“Primers” as used herein refer to oligonucleotides that can be used in an amplification method, such as a polymerase chain reaction (PCR), to amplify a nucleotide sequence based on the polynucleotide sequence corresponding to a gene of interest, e.g., the cDNA or genomic sequence for human DLEC1 or a portion thereof. Typically at least one of the PCR primers for amplification of a polynucleotide sequence is sequence-specific for that polynucleotide sequence. The exact length of the primer will depend upon many factors, including temperature, source of the primer, and the method used. For example, for diagnostic and prognostic applications, depending on the complexity of the target sequence, the oligonucleotide primer typically contains at least 10, or 15, or 20, or 25 or more nucleotides, although it may contain fewer nucleotides or more nucleotides. The factors involved in determining the appropriate length of primer are readily known to one of ordinary skill in the art. The primers used in particular embodiments are shown in Table 1 of the disclosure where their specific applications are indicated. In this disclosure the term “primer pair” means a pair of primers that hybridize to opposite strands a target DNA molecule or to regions of the target DNA which flank a nucleotide sequence to be amplified. In this disclosure the term “primer site”, means the area of the target DNA or other nucleic acid to which a primer hybridizes.
A “label,” “detectable label,” or “detectable moiety” is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means. For example, useful labels include 32P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins that can be made detectable, e.g., by incorporating a radioactive component into the peptide or used to detect antibodies specifically reactive with the peptide. Typically a detectable label is attached to a probe or a molecule with defined binding characteristics (e.g., a polypeptide with a known binding specificity or a polynucleotide), so as to allow the presence of the probe (and therefore its binding target) to be readily detectable.
“Standard control” as used herein refers to a predetermined amount or concentration of a polynucleotide sequence or polypeptide, e.g., DLEC1 mRNA or DLEC1 protein, that is present in an established normal disease-free tissue sample, e.g., a normal esophagus epithelial tissue sample. The standard control value is suitable for the use of a method of the present invention, to serve as a basis for comparing the amount of DLEC1 mRNA or DLEC1 protein that is present in a test sample. An established sample serving as a standard control provides an average amount of DLEC mRNA or DLEC1 protein that is typical for a esophagus epithelial tissue sample (e.g., esophagus lining) of an average, healthy human without any esophagus disease especially esophageal cancer as conventionally defined. A standard control value may vary depending on the nature of the sample as well as other factors such as the gender, age, ethnicity of the subjects based on whom such a control value is established.
The term “average,” as used in the context of describing a human who is healthy, free of any esophagus disease (especially esophageal cancer) as conventionally defined, refers to certain characteristics, especially the amount of human DLEC1 mRNA or DLEC1 protein, found in the person'"'"'s esophagus tissue, e.g., epithelial tissue or esophagus lining, that are representative of a randomly selected group of healthy humans who are free of any esophageal diseases (especially esophageal cancer). This selected group should comprise a sufficient number of humans such that the average amount of DLEC1 mRNA or protein in the esophagus epithelium among these individuals reflects, with reasonable accuracy, the corresponding amount of DLEC1 mRNA/protein in the general population of healthy humans. In addition, the selected group of humans generally have a similar age to that of a subject whose esophagus tissue sample is tested for indication of esophageal cancer. Moreover, other factors such as gender, ethnicity, medical history are also considered and preferably closely matching between the profiles of the test subject and the selected group of individuals establishing the “average” value.
The term “amount” as used in this application refers to the quantity of a polynucleotide of interest or a polypeptide of interest, e.g., human DLEC1 mRNA or DLEC1 protein, present in a sample. Such quantity may be expressed in the absolute terms, i.e., the total quantity of the polynucleotide or polypeptide in the sample, or in the relative terms, i.e., the concentration of the polynucleotide or polypeptide in the sample.
The term “treat” or “treating,” as used in this application, describes to an act that leads to the elimination, reduction, alleviation, reversal, or prevention or delay of onset or recurrence of any symptom of a relevant condition. In other words, “treating” a condition encompasses both therapeutic and prophylactic intervention against the condition.
The term “effective amount” as used herein refers to an amount of a given substance that is sufficient in quantity to produce a desired effect. For example, an effective amount of an polynucleotide encoding DLEC1 mRNA is the amount of said polynucleotide to achieve an increased level of DLEC1 protein expression or biological activity, such that the symptoms of esophageal cancer are reduced, reversed, eliminated, prevented, or delayed of the onset in a patient who has been given the polynucleotide for therapeutic purposes. An amount adequate to accomplish this is defined as the “therapeutically effective dose.” The dosing range varies with the nature of the therapeutic agent being administered and other factors such as the route of administration and the severity of a patient'"'"'s condition.
The term “subject” or “subject in need of treatment,” as used herein, includes individuals who seek medical attention due to risk of, or actual suffering from, esophageal cancer especially ESCC. Subjects also include individuals currently undergoing therapy that seek manipulation of the therapeutic regimen. Subjects or individuals in need of treatment include those that demonstrate symptoms of esophageal cancer (especially ESCC) or are at risk of suffering from esophogeal cancer (especially ESCC) or its symptoms. For example, a subject in need of treatment includes individuals with a genetic predisposition or family history for esophageal cancer (especially ESCC), those that have suffered relevant symptoms in the past, those that have been exposed to a triggering substance or event, as well as those suffering from chronic or acute symptoms of the condition. A “subject in need of treatment” may be at any age of life.
“Inhibitors,” “activators,” and “modulators” of DLEC1 protein are used to refer to inhibitory, activating, or modulating molecules, respectively, identified using in vitro and in vivo assays for DLEC1 protein binding or signaling, e.g., ligands, agonists, antagonists, and their homologs and mimetics. The term “modulator” includes inhibitors and activators. Inhibitors are agents that, e.g., partially or totally block carbohydrate binding, decrease, prevent, delay activation, inactivate, desensitize, or down regulate the activity of DLEC1 protein. In some cases, the inhibitor directly or indirectly binds to DLEC1 protein, such as a neutralizing antibody. Inhibitors, as used herein, are synonymous with inactivators and antagonists. Activators are agents that, e.g., stimulate, increase, facilitate, enhance activation, sensitize or up regulate the activity of DLEC1 protein. Modulators include DLEC1 protein ligands or binding partners, including modifications of naturally-occurring ligands and synthetically-designed ligands, antibodies and antibody fragments, antagonists, agonists, small molecules including carbohydrate-containing molecules, siRNAs, RNA aptamers, and the like.
Despite the rapid advancement in medical sciences and steady improvement in cancer therapy, cancer remains a significant health concern with grave implications in both developed countries as well as in developing countries. ESCC patients often face a grim prognosis since their disease is most often discovered in more advanced stages due to the lacking of specific symptoms during early development stages. Early detection of cancer such as ESCC is therefore critical for improving patient survival rate. Moreover, it is also of practical importance to predict the likelihood of mortality from cancer among patients who have already received a cancer diagnosis for any time period after the diagnosis.
3p22-21.3 is one of the most frequently deleted chromosome regions in solid tumors including esophageal squamous cell carcinoma (ESCC), even altered at the early premalignant stage. Various genetic studies have been carried out to identify candidate tumor suppressor genes (TSG) at this locus. Deleted in lung and esophageal cancer 1 (DLEC1), located at 3p22-21.3, has been identified frequently methylated in multiple human cancers, which is correlated with tumor poor survival and malignant progression. Thus, DLEC1 methylation could be an important event in tumorigenesis, and serve as a valuable, non-invasive biomarker for human cancers. However, there is no study of investigating DLEC1 methylation in ESCC. This invention provides a method to specifically detect promoter CpG methylation of DLEC1 in ESCC, and its methylation serving as a biomarker for early detection. Methylation-specific PCR (MSP) primers for DLEC1 are tested for not amplifying any not-bisulfited DNA, confirming the detection specificity of DLEC1 methylation in this invention. DLEC1 downregulation/silencing by promoter methylation is detected in ESCC cell lines and primary tumors, but not in immortalized esophageal epithelial cells or normal esophageal tissues. In addition, the present invention provides a method for treating tumor cells by restore DLEC1 gene expression and unmethylation in DLEC1-slienced ESCC cells. The invention also provides a detection method for ESCC and a detection kit useful for such a method.
Practicing this invention utilizes routine techniques in the field of molecular biology. Basic texts disclosing the general methods of use in this invention include Sambrook and Russell, Molecular Cloning, A Laboratory Manual (3rd ed. 2001); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al., eds., 1994)).
For nucleic acids, sizes are given in either kilobases (kb) or base pairs (bp). These are estimates derived from agarose or acrylamide gel electrophoresis, from sequenced nucleic acids, or from published DNA sequences. For proteins, sizes are given in kilodaltons (kDa) or amino acid residue numbers. Protein sizes are estimated from gel electrophoresis, from sequenced proteins, from derived amino acid sequences, or from published protein sequences.
Oligonucleotides that are not commercially available can be chemically synthesized, e.g., according to the solid phase phosphoramidite triester method first described by Beaucage and Caruthers, Tetrahedron Lett. 22:1859-1862 (1981), using an automated synthesizer, as described in Van Devanter et. al., Nucleic Acids Res. 12:6159-6168 (1984). Purification of oligonucleotides is performed using any art-recognized strategy, e.g., native acrylamide gel electrophoresis or anion-exchange high performance liquid chromatography (HPLC) as described in Pearson and Reanier, J. Chrom. 255: 137-149 (1983).
The sequence of interest used in this invention, e.g., the polynucleotide sequence of the human DLEC1 gene, and synthetic oligonucleotides (e.g., primers) can be verified using, e.g., the chain termination method for sequencing double-stranded templates of Wallace et al., Gene 16: 21-26 (1981).
The present invention relates to measuring the amount of DLEC1 mRNA or analyzing the methylation pattern of DLEC1 genomic DNA found in a person'"'"'s esophagus issue, especially esophageal epithelial sample, as a means to detect the presence, to assess the risk of developing, and/or to monitor the progression or treatment efficacy of esophageal squamous cell carcinoma (ESCC). Thus, the first steps of practicing this invention are to obtain a esophageal epithelial tissue sample from a test subject and extract mRNA or DNA from the sample.
A. Acquisition and Preparation of Esophageal Tissue Samples
An esophageal tissue sample is obtained from a person to be tested or monitored for esophagus cancer (e.g., ESCC) using a method of the present invention. Collection of esophageal epithelial tissue sample from an individual is performed in accordance with the standard protocol hospitals or clinics generally follow, such as during an endoscopy. An appropriate amount of esophagus epithelium is collected and may be stored according to standard procedures prior to further preparation.
The analysis of DLEC1 mRNA or DNA found in a patient'"'"'s esophageal epithelial sample according to the present invention may be performed using, e.g., esophagus lining tissue. The methods for preparing tissue samples for nucleic acid extraction are well known among those of skill in the art. For example, a subject'"'"'s esophageal epithelial sample should be first treated to disrupt cellular membrane so as to release nucleic acids contained within the cells.
B. Extraction and Quantitation of RNA
There are numerous methods for extracting mRNA from a biological sample. The general methods of mRNA preparation (e.g., described by Sambrook and Russell, Molecular Cloning: A Laboratory Manual 3d ed., 2001) can be followed; various commercially available reagents or kits, such as Trizol reagent (Invitrogen, Carlsbad, Calif.), Oligotex Direct mRNA Kits (Qiagen, Valencia, Calif.), RNeasy Mini Kits (Qiagen, Hilden, Germany), and PolyATtract® Series 9600™ (Promega, Madison, Wis.), may also be used to obtain mRNA from a biological sample from a test subject. Combinations of more than one of these methods may also be used.
It is essential that all contaminating DNA be eliminated from the RNA preparations. Thus, careful handling of the samples, thorough treatment with DNase, and proper negative controls in the amplification and quantification steps should be used.
1. PCR-Based Quantitative Determination of mRNA Level
Once mRNA is extracted from a sample, the amount of human DLEC1 mRNA may be quantified. The preferred method for determining the mRNA level is an amplification-based method, e.g., by polymerase chain reaction (PCR), especially reverse transcription-polymerase chain reaction (RT-PCR).
Prior to the amplification step, a DNA copy (cDNA) of the human DLEC1 mRNA must be synthesized. This is achieved by reverse transcription, which can be carried out as a separate step, or in a homogeneous reverse transcription-polymerase chain reaction (RT-PCR), a modification of the polymerase chain reaction for amplifying RNA. Methods suitable for PCR amplification of ribonucleic acids are described by Romero and Rotbart in Diagnostic Molecular Biology: Principles and Applications pp. 401-406; Persing et al., eds., Mayo Foundation, Rochester, Minn., 1993; Egger et al., J Clin. Microbiol. 33:1442-1447, 1995; and U.S. Pat. No. 5,075,212.
The general methods of PCR are well known in the art and are thus not described in detail herein. For a review of PCR methods, protocols, and principles in designing primers, see, e.g., Innis, et al., PCR Protocols: A Guide to Methods and Applications, Academic Press, Inc. N.Y., 1990. PCR reagents and protocols are also available from commercial vendors, such as Roche Molecular Systems.
PCR is most usually carried out as an automated process with a thermostable enzyme. In this process, the temperature of the reaction mixture is cycled through a denaturing region, a primer annealing region, and an extension reaction region automatically. Machines specifically adapted for this purpose are commercially available.
Although PCR amplification of the target mRNA is typically used in practicing the present invention. One of skill in the art will recognize, however, that amplification of a mRNA species in a sample may be accomplished by any known method, such as ligase chain reaction (LCR), transcription-mediated amplification, and self-sustained sequence replication or nucleic acid sequence-based amplification (NASBA), each of which provides sufficient amplification. More recently developed branched-DNA technology may also be used to quantitatively determining the amount of mRNA species in a sample. For a review of branched-DNA signal amplification for direct quantitation of nucleic acid sequences in clinical samples, see Nolte, Adv. Clin. Chem. 33:201-235, 1998.
2. Other Quantitative Methods
The DLEC1 mRNA can also be detected using other standard techniques, well known to those of skill in the art. Although the detection step is typically preceded by an amplification step, amplification is not required in the methods of the invention. For instance, the mRNA may be identified by size fractionation (e.g., gel electrophoresis), whether or not proceeded by an amplification step. After running a sample in an agarose or polyacrylamide gel and labeling with ethidium bromide according to well-known techniques (see, e.g., Sambrook and Russell, supra), the presence of a band of the same size as the standard comparison is an indication of the presence of a target mRNA, the amount of which may then be compared to the control based on the intensity of the band. Alternatively, oligonucleotide probes specific to DLEC1 mRNA can be used to detect the presence of such mRNA species and indicate the amount of mRNA in comparison to the standard comparison, based on the intensity of signal imparted by the probe.
Sequence-specific probe hybridization is a well-known method of detecting a particular nucleic acid comprising other species of nucleic acids. Under sufficiently stringent hybridization conditions, the probes hybridize specifically only to substantially complementary sequences. The stringency of the hybridization conditions can be relaxed to tolerate varying amounts of sequence mismatch.
A number of hybridization formats well known in the art, including but not limited to, solution phase, solid phase, or mixed phase hybridization assays. The following articles provide an overview of the various hybridization assay formats: Singer et al., Biotechniques 4:230, 1986; Haase et al., Methods in Virology, pp. 189-226, 1984; Wilkinson, In situ Hybridization, Wilkinson ed., IRL Press, Oxford University Press, Oxford; and Hames and Higgins eds., Nucleic Acid Hybridization: A Practical Approach, IRL Press, 1987.
The hybridization complexes are detected according to well-known techniques. Nucleic acid probes capable of specifically hybridizing to a target nucleic acid, i.e., the mRNA or the amplified DNA, can be labeled by any one of several methods typically used to detect the presence of hybridized nucleic acids. One common method of detection is the use of autoradiography using probes labeled with 3H, 125I, 35S, 14C, or 32P, or the like. The choice of radioactive isotope depends on research preferences due to ease of synthesis, stability, and half lives of the selected isotopes. Other labels include compounds (e.g., biotin and digoxigenin), which bind to antiligands or antibodies labeled with fluorophores, chemiluminescent agents, and enzymes. Alternatively, probes can be conjugated directly with labels such as fluorophores, chemiluminescent agents or enzymes. The choice of label depends on sensitivity required, ease of conjugation with the probe, stability requirements, and available instrumentation.
The probes and primers necessary for practicing the present invention can be synthesized and labeled using well known techniques. Oligonucleotides used as probes and primers may be chemically synthesized according to the solid phase phosphoramidite triester method first described by Beaucage and Caruthers, Tetrahedron Letts., 22:1859-1862, 1981, using an automated synthesizer, as described in Needham-VanDevanter et al., Nucleic Acids Res. 12:6159-6168, 1984. Purification of oligonucleotides is by either native acrylamide gel electrophoresis or by anion-exchange HPLC as described in Pearson and Regnier, J. Chrom., 255:137-149, 1983.
C. Detection of Methylation in DLEC1 Genomic Sequence
Methylation status of a segment of DLEC1 genomic sequence containing one or more CpG (cytosine-guanine dinucleotide) pairs is investigated to provide indication as to whether a test subject is suffering from esophageal cancer (especially ESCC), whether the subject is at risk of developing esophageal cancer (especially ESCC), or whether the subject'"'"'s esophageal cancer (especially ESCC) is worsening or improving.
Typically a segment of the DLEC1 genomic sequence that includes the 5′ untranslated region (such as the promoter region) and includes one or more CpG nucleotide pairs is analyzed for methylation pattern. For example, SEQ ID NO:5 or 6 or a portion thereof can be used to determine how many of the CpG pairs within the sequence are methylated and how many are not methylated. The sequence being analyzed should be long enough to contain at least 1 CpG dinucleotide pair and detection of methylation at this CpG site is typically adequate indication of the presence of ESCC cells. The length of the sequence being analyzed is usually at least 15 or 20 contiguous nucleotides, and may be longer with at least 25, 30, 50, 100, 200, 300, 400, or more contiguous nucleotides. At least one, typically 2 or more, often 3, 4, 5, 6, 7, 8, 9, or more, CpG nucleotide pairs are present within the sequence. In the cases of multiple (2 or more) CpG sites are analyzed for methylation status, when at least 50% of the CpG pairs within the analyzed genomic sequence are shown to be methylated, subject being tested is deemed to have esophageal cancer (especially ESCC) or have an elevated risk of developing esophageal cancer (especially ESCC). For example, SEQ ID NO:5, a segment of DLEC1 genomic sequence, and the 107 bp segment of SEQ ID NO:6 are such CpG-containing genomic sequences useful for the analysis. Some or majority of the CpG pairs in this region are found to be methylated in established ESCC cell lines and samples taken from ESCC, whereas non-cancerous esophagus epithelial cells showed very few, if any at all, methylated CpG sites. For the purpose of determining the methylation pattern of a DLEC1 genomic sequence, bisulfite treatment followed by DNA sequencing is particularly useful, since bisulfite converts an unmethylated cytosine (C) to a uracil (U) while leaving methylated cytosines unchanged, allowing immediate identification through a DNA sequencing process. Optionally, an amplification process such as PCR is included after the bisulfite conversion and before the DNA sequencing.
1. DNA Extraction and Treatment
Methods for extracting DNA from a biological sample are well known and routinely practiced in the art of molecular biology, see, e.g., Sambrook and Russell, supra. RNA contamination should be eliminated to avoid interference with DNA analysis. The DNA is then treated with a reagent capable of modifying DNA in a methylation differential manner, i.e., different and distinguishable chemical structures will result from a methylated cytosine (C) residue and an unmethylated C residue following the treatment. Typically, such a reagent reacts with the unmethylated C residue(s) in a DNA molecule and converts each unmethylated C residue to a uracil (U) residue, whereas the methylated C residues remain unchanged. This unmethylated C→U conversion allows detection and comparison of methylation status based on changes in the primary sequence of the nucleic acid. An exemplary reagent suitable for this purpose is bisulfite, such as sodium bisulfite. Methods for using bisulfite for chemical modification of DNA are well known in the art (see, e.g., Herman et al., Proc. Natl. Acad. Sci. USA 93:9821-9826, 1996).
As a skilled artisan will recognize, any other reagents that are unnamed here but have the same property of chemically (or through any other mechanism) modifying methylated and unmethylated DNA differentially can be used for practicing the present invention. For instance, methylation-specific modification of DNA may also be accomplished by methylation-sensitive restriction enzymes, some of which typically cleave an unmethylated DNA fragment but not a methylated DNA fragment, while others (e.g., methylation-dependent endonuclease McrBC) cleave DNA containing methylated cytosines but not unmethylated DNA. In addition, a combination of chemical modification and restriction enzyme treatment, e.g., combined bisulfite restriction analysis (COBRA) (Xiong et al. 1997 Nucleic Acids Res. 25(12): 2532-2534), is useful for practicing the present invention. Other available methods for detecting DNA methylation include, for example, methylation-sensitive restriction endonucleases (MSREs) assay by either Southern blot or PCR analysis, methylation specific or methylation sensitive-PCR (MS-PCR), methylation-sensitive single nucleotide primer extension (Ms-SnuPE), high resolution melting (HRM) analysis, bisulifte sequencing, pyrosequencing, methylation-specific single-strand conformation analysis (MS-SSCA), methylation-specific denaturing gradient gel electrophoresis (MS-DGGE), methylation-specific melting curve analysis (MS-MCA), methylation-specific denaturing high-performance liquid chromatography (MS-DHPLC), methylation-specific microarray (MSO). These assays can be either PCR analysis, quantitative analysis with fluorescence labelling or Southern blot analysis. Exemplary methylation sensitive DNA cleaving reagent such as restriction enzymes include AatII, AciI, AclI, AgeI, AscI, Asp718, AvaI, BbrP1, BceAI, BmgBI, BsaAI, BsaHI, BsiEI, BsiWI, BsmBI, BspDI, BsrFI, BssHII, BstBI, BstUI, ClaI, EagI, EagI-HF™, FauI, FseI, FspI, HaeII, HgaI, HhaI, HinP1I, HpaII, Hpy99I, HpyCH4IV, KasI, MluI, NarI, NgoMIV, NotI, NotI-HF™, NruI, Nt.BsmAI, PaeR7I, PspXI, PvuI, RsrII, SacII, SalI, SalI-HF™, SfoI, SgrAI, SmaI, SnaBI or TspMI.
2. Optional Amplification and Sequence Analysis
Following the modification of DNA in a methylation-differential manner, the treated DNA is then subjected to sequence-based analysis, such that the methylation status of the DLEC1 genomic sequence may be determined. An amplification reaction is optional prior to the sequence analysis after methylation specific modification. A variety of polynucleotide amplification methods are well established and frequently used in research. For instance, the general methods of polymerase chain reaction (PCR) for polynucleotide sequence amplification are well known in the art and are thus not described in detail herein. For a review of PCR methods, protocols, and principles in designing primers, see, e.g., Innis, et al., PCR Protocols: A Guide to Methods and Applications, Academic Press, Inc. N.Y., 1990. PCR reagents and protocols are also available from commercial vendors, such as Roche Molecular Systems.
Although PCR amplification is typically used in practicing the present invention, one of skill in the art will recognize that amplification of the relevant genomic sequence may be accomplished by any known method, such as the ligase chain reaction (LCR), transcription-mediated amplification, and self-sustained sequence replication or nucleic acid sequence-based amplification (NASBA), each of which provides sufficient amplification.
Techniques for polynucleotide sequence determination are also well established and widely practiced in the relevant research field. For instance, the basic principles and general techniques for polynucleotide sequencing are described in various research reports and treatises on molecular biology and recombinant genetics, such as Wallace et al., supra; Sambrook and Russell, supra, and Ausubel et al., supra. DNA sequencing methods routinely practiced in research laboratories, either manual or automated, can be used for practicing the present invention. Additional means suitable for detecting changes (e.g., C→U) in a polynucleotide sequence for practicing the methods of the present invention include but are not limited to mass spectrometry, primer extension, polynucleotide hybridization, real-time PCR, melting curve analysis, high resolution melting analysis, heteroduplex analysis, pyrosequencing, and electrophoresis.
A. Obtaining Samples
The first step of practicing the present invention is to obtain a sample of esophageal epithelium from a subject being tested, assessed, or monitored for ESCC, the risk of developing ESCC, or the severity/progression of the condition. Samples of the same type should be taken from both a control group (normal individuals not suffering from any esophagus disorder especially neoplasia) and a test group (subjects being tested for possible esophagus cancer, for example). Standard procedures routinely employed in hospitals or clinics are typically followed for this purpose, as stated in the previous section.
For the purpose of detecting the presence of esophageal cancer (e.g., ESCC) or assessing the risk of developing esophageal cancer (e.g., ESCC) in test subjects, individual patients'"'"' esophagus epitheliam samples may be taken and the level of human DLEC1 protein may be measured and then compared to a standard control. If a decrease in the level of human DLEC1 protein is observed when compared to the control level, the test subject is deemed to have ESCC or have an elevated risk of developing the condition. For the purpose of monitoring disease progression or assessing therapeutic effectiveness in ESCC patients, individual patient'"'"'s esophageal epithelial samples may be taken at different time points, such that the level of human DLEC1 protein can be measured to provide information indicating the state of disease. For instance, when a patient'"'"'s DLEC1 protein level shows a general trend of increase over time, the patient is deemed to be improving in the severity of esophageal cancer or the therapy the patient has been receiving is deemed effective. A lack of change in a patient'"'"'s DLEC1 protein level or a continuing trend of decrease on other hand would indicate a worsening of the condition and ineffectiveness of the therapy given to the patient. Generally, a lower DLEC1 protein level seen in a patient indicates a more severe form of the ESCC the patient is suffering from and a worse prognosis of the disease, as manifested in shorter life expectancy, higher rate of metastasis, resistance to therapy etc. Among ESCC patients, one who has a lower level of DLEC1 protein expression in the esophageal cancer sample than that found in a second ESCC patient has a higher likelihood of mortality compared to the second patient for any defined time period, such as 1-5 years post-diagnosis.
B. Preparing Samples for DLEC1 Protein Detection
The esophagus tissue sample from a subject is suitable for the present invention and can be obtained by well-known methods and as described in the previous section. In certain applications of this invention, esophagus lining or epithelial tissue may be the preferred sample type.
C. Determining the Level of Human DLEC1 Protein
A protein of any particular identity, such as DLEC1 protein, can be detected using a variety of immunological assays. In some embodiments, a sandwich assay can be performed by capturing the polypeptide from a test sample with an antibody having specific binding affinity for the polypeptide. The polypeptide then can be detected with a labeled antibody having specific binding affinity for it. Such immunological assays can be carried out using microfluidic devices such as microarray protein chips. A protein of interest (e.g., human DLEC1 protein) can also be detected by gel electrophoresis (such as 2-dimensional gel electrophoresis) and western blot analysis using specific antibodies. Alternatively, standard immunohistochemical techniques can be used to detect a given protein (e.g., human DLEC1 protein), using the appropriate antibodies. Both monoclonal and polyclonal antibodies (including antibody fragment with desired binding specificity) can be used for specific detection of the polypeptide. Such antibodies and their binding fragments with specific binding affinity to a particular protein (e.g., human DLEC1 protein) can be generated by known techniques.
Other methods may also be employed for measuring the level of DLEC1 protein in practicing the present invention. For instance, a variety of methods have been developed based on the mass spectrometry technology to rapidly and accurately quantify target proteins even in a large number of samples. These methods involve highly sophisticated equipment such as the triple quadrupole (triple Q) instrument using the multiple reaction monitoring (MRM) technique, matrix assisted laser desorption/ionization time-of-flight tandem mass spectrometer (MALDI TOF/TOF), an ion trap instrument using selective ion monitoring SIM) mode, and the electrospray ionization (ESI) based QTOP mass spectrometer. See, e.g., Pan et al., J Proteome Res. 2009 February; 8(2):787-797.
In order to establish a standard control for practicing the method of this invention, a group of healthy persons free of any esophagus disease (especially any form of tumor such as esophageal cancer) as conventionally defined is first selected. These individuals are within the appropriate parameters, if applicable, for the purpose of screening for and/or monitoring esophageal cancer (especially ESCC) using the methods of the present invention. Optionally, the individuals are of same gender, similar age, or similar ethnic background.
The healthy status of the selected individuals is confirmed by well established, routinely employed methods including but not limited to general physical examination of the individuals and general review of their medical history.
Furthermore, the selected group of healthy individuals must be of a reasonable size, such that the average amount/concentration of human DLEC1 mRNA or DLEC1 protein in the esophagus epithelial tissue sample obtained from the group can be reasonably regarded as representative of the normal or average level among the general population of healthy people. Preferably, the selected group comprises at least 10 human subjects.
Once an average value for the DLEC1 mRNA or protein is established based on the individual values found in each subject of the selected healthy control group, this average or median or representative value or profile is considered a standard control. A standard deviation is also determined during the same process. In some cases, separate standard controls may be established for separately defined groups having distinct characteristics such as age, gender, or ethnic background.
By illustrating the correlation of suppressed expression of DLEC1 protein and cancers such as ESCC, the present invention further provides a means for treating patients suffering from the cancer or at heightened risk of developing the cancer at a later time: by way of increasing DLEC1 protein expression or biological activity. As used herein, treatment of ESCC encompasses reducing, reversing, lessening, or eliminating one or more of the symptoms of esophageal cancer (especially ESCC), as well as preventing or delaying the onset of one or more of the relevant symptoms. Additionally, since certain risk factors for ESCC (smoking, drinking, drinking very hot drinks, chewing betel nuts, etc.) are well-known, preventive measures can be prescribed to patients at risk of developing ESCC such as reducing or eliminating alcohol and tobacco consumption and adopting a healthy diet. For individuals who have been deemed to have an increased risk of developing ESCC by the method of this invention and who are then diagnosed as actually having already developed ESCC (e.g., by conventional diagnostic methods such as X-ray and/or CT scan of the chest area in addition to pathological assessment), various treatment strategies are available for treating ESCC in these patients including but not limited to, surgery, chemotherapy, radiotherapy, immunotherapy, photodynamic therapy, or any combination thereof.
A. Increasing DLEC1 Expression or Activity
1. Nucleic Acids Encoding DLEC1 Proteins
Enhancement of DLEC1 gene expression can be achieved through the use of nucleic acids encoding a functional DLEC1 protein. Such nucleic acids can be single-stranded nucleic acids (such as mRNA) or double-stranded nucleic acids (such as DNA) that can translate into an active form of DLEC1 protein under favorable conditions.
In one embodiment, the DLEC1-encoding nucleic acid is provided in the form of an expression cassette, typically recombinantly produced, having a promoter operably linked to the polynucleotide sequence encoding the DLEC1 protein. In some cases, the promoter is a universal promoter that directs gene expression in all or most tissue types; in other cases, the promoter is one that directs gene expression specifically in epithelial cells, especially in esophagus epithelium. Administration of such nucleic acids can increase the DLEC1 protein expression in the target tissue, e.g., esophagus epithelium. Since the human DLEC1 gene sequence is known as Genbank Accession No. NM_007335.3 and provided herein as SEQ ID NO:2, and its cDNA sequence is provided herein as SEQ ID NO:3, one can derive a suitable DLEC1-encoding nucleic acid from the sequence, species homologs, and variants of these sequencesone can derive a suitable DLEC1-encoding nucleic acid from the sequence, species homologs, and variants of these sequences.
2. DLEC1 Proteins
By directly administering an effective amount of an active DLEC1 protein to a patient suffering from ESCC and exhibiting suppressed DLEC1 protein expression or activity, the disease may also be effectively treated. For example, this can be achieved by administering a recombinantly produced DLEC1 protein possessing its biological activity to the patient suffering from esophageal cancer (e.g., ESCC). Formulations and methods for delivering a protein- or polypeptide-based therapeutic agent are well known in the art.
3. Activators of DLEC1 Protein
Increased DLEC1 protein activity can be achieved with an agent that is capable of activating the expression of DLEC1 protein or enhancing the activity of DLEC1 protein. For example, a demethylating agent (e.g., 5-Aza) may be able to activate DLEC1 gene expression by removing the suppression of DLEC1 gene expression caused by methylation of the promoter region of this gene. Other activating agents may include transcriptional activators specific for the DLEC1 promoter and/or enhancer. Such activating agents can be screened for and identified using the DLEC1 expression assays described in the examples herein.
Agonists of the DLEC1 protein, such as an activating antibody, are another kind of activators of the DLEC1 protein. Such activators act by enhancing the biological activity of the DLEC1 protein, typically (but not necessarily) by direct binding with the DLEC1 protein and/or its interacting proteins. Preliminary screening for such agonists may start with a binding assay for identifying molecules that physically interact with DLEC1 protein.
B. Pharmaceutical Compositions
Compounds of the present invention are useful in the manufacture of a pharmaceutical composition or a medicament. A pharmaceutical composition or medicament can be administered to a subject for the treatment of esophageal cancer, especially ESCC.
Compounds used in the present invention, e.g., a DLEC1 protein, a nucleic acid encoding DLEC1 protein, or an activator of DLEC1 gene expression, are useful in the manufacture of a pharmaceutical composition or a medicament comprising an effective amount thereof in conjunction or mixture with excipients or carriers suitable for application.
An exemplary pharmaceutical composition for enhancing DLEC1 expression comprises (i) an express cassette comprising a polynucleotide sequence encoding a human DLEC1 protein as described herein, and (ii) a pharmaceutically acceptable excipient or carrier. The terms pharmaceutically-acceptable and physiologically-acceptable are used synonymously herein. The expression cassette may be provided in a therapeutically effective dose for use in a method for treatment as described herein.
A DLEC1 protein or a nucleic acid encoding a DLEC1 protein can be administered via liposomes, which serve to target the conjugates to a particular tissue, as well as increase the half-life of the composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations the inhibitor to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to, e.g., a receptor prevalent among the targeted cells (e.g., esophageal epithelial cells), or with other therapeutic or immunogenic compositions. Thus, liposomes filled with a desired inhibitor of the invention can be directed to the site of treatment, where the liposomes then deliver the selected inhibitor compositions. Liposomes for use in the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka et al. (1980) Ann. Rev. Biophys. Bioeng. 9: 467, U.S. Pat. Nos. 4,235,871, 4,501,728 and 4,837,028.
Pharmaceutical compositions or medicaments for use in the present invention can be formulated by standard techniques using one or more physiologically acceptable carriers or excipients. Suitable pharmaceutical carriers are described herein and in “Remington'"'"'s Pharmaceutical Sciences” by E. W. Martin. Compounds and agents of the present invention and their physiologically acceptable salts and solvates can be formulated for administration by any suitable route, including via inhalation, topically, nasally, orally, parenterally, or rectally.
Typical formulations for topical administration include creams, ointments, sprays, lotions, and patches. The pharmaceutical composition can, however, be formulated for any type of administration, e.g., intradermal, subdermal, intravenous, intramuscular, intranasal, intracerebral, intratracheal, intraarterial, intraperitoneal, intravesical, intrapleural, intracoronary or intratumoral injection, with a syringe or other devices. Formulation for administration by inhalation (e.g., aerosol), or for oral, rectal, or vaginal administration is also contemplated.
2. Routes of Administration
Suitable formulations for topical application, e.g., to the skin and eyes, are preferably aqueous solutions, ointments, creams or gels well-known in the art. Such may contain solubilizers, stabilizers, tonicity enhancing agents, buffers and preservatives.
Suitable formulations for transdermal application include an effective amount of a compound or agent of the present invention with carrier. Preferred carriers include absorbable pharmacologically acceptable solvents to assist passage through the skin of the host. For example, transdermal devices are in the form of a bandage comprising a backing member, a reservoir containing the compound optionally with carriers, optionally a rate controlling barrier to deliver the compound to the skin of the host at a controlled and predetermined rate over a prolonged period of time, and means to secure the device to the skin. Matrix transdermal formulations may also be used.
For oral administration, a pharmaceutical composition or a medicament can take the form of, for example, a tablet or a capsule prepared by conventional means with a pharmaceutically acceptable excipient. Preferred are tablets and gelatin capsules comprising the active ingredient, i.e., a DLEC1 protein or a nucleic acid encoding a DLEC1 protein, together with (a) diluents or fillers, e.g., lactose, dextrose, sucrose, mannitol, sorbitol, cellulose (e.g., ethyl cellulose, microcrystalline cellulose), glycine, pectin, polyacrylates and/or calcium hydrogen phosphate, calcium sulfate, (b) lubricants, e.g., silica, talcum, stearic acid, its magnesium or calcium salt, metallic stearates, colloidal silicon dioxide, hydrogenated vegetable oil, corn starch, sodium benzoate, sodium acetate and/or polyethyleneglycol; for tablets also (c) binders, e.g., magnesium aluminum silicate, starch paste, gelatin, tragacanth, methylcellulose, sodium carboxymethylcellulose, polyvinylpyrrolidone and/or hydroxypropyl methylcellulose; if desired (d) disintegrants, e.g., starches (e.g., potato starch or sodium starch), glycolate, agar, alginic acid or its sodium salt, or effervescent mixtures; (e) wetting agents, e.g., sodium lauryl sulphate, and/or (f) absorbents, colorants, flavors and sweeteners.
Tablets may be either film coated or enteric coated according to methods known in the art. Liquid preparations for oral administration can take the form of, for example, solutions, syrups, or suspensions, or they can be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations can be prepared by conventional means with pharmaceutically acceptable additives, for example, suspending agents, for example, sorbitol syrup, cellulose derivatives, or hydrogenated edible fats; emulsifying agents, for example, lecithin or acacia; non-aqueous vehicles, for example, almond oil, oily esters, ethyl alcohol, or fractionated vegetable oils; and preservatives, for example, methyl or propyl-p-hydroxybenzoates or sorbic acid. The preparations can also contain buffer salts, flavoring, coloring, and/or sweetening agents as appropriate. If desired, preparations for oral administration can be suitably formulated to give controlled release of the active compound.
Compounds and agents of the present invention can be formulated for parenteral administration by injection, for example by bolus injection or continuous infusion. Formulations for injection can be presented in unit dosage form, for example, in ampoules or in multi-dose containers, with an added preservative. Injectable compositions are preferably aqueous isotonic solutions or suspensions, and suppositories are preferably prepared from fatty emulsions or suspensions. The compositions may be sterilized and/or contain adjuvants, such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure and/or buffers. Alternatively, the active ingredient can be in powder form for constitution with a suitable vehicle, for example, sterile pyrogen-free water, before use. In addition, they may also contain other therapeutically valuable substances. The compositions are prepared according to conventional mixing, granulating or coating methods, respectively, and contain about 0.1 to 75%, preferably about 1 to 50%, of the active ingredient.
For administration by inhalation, the active ingredient, e.g., a DLEC1 protein or a nucleic acid encoding a DLEC1 protein, may be conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, for example, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide, or other suitable gas. In the case of a pressurized aerosol, the dosage unit can be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, for example, gelatin for use in an inhaler or insufflator can be formulated containing a powder mix of the compound and a suitable powder base, for example, lactose or starch.
The inhibitors can also be formulated in rectal compositions, for example, suppositories or retention enemas, for example, containing conventional suppository bases, for example, cocoa butter or other glycerides.
Furthermore, the active ingredient can be formulated as a depot preparation. Such long-acting formulations can be administered by implantation (for example, subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the active ingredient can be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
A pharmaceutical composition or medicament of the present invention comprises (i) an effective amount of a compound as described herein that increases the level or activity of DLEC1 protein, and (ii) another therapeutic agent. When used with a compound of the present invention, such therapeutic agent may be used individually, sequentially, or in combination with one or more other such therapeutic agents (e.g., a first therapeutic agent, a second therapeutic agent, and a compound of the present invention). Administration may be by the same or different route of administration or together in the same pharmaceutical formulation.
Pharmaceutical compositions or medicaments can be administered to a subject at a therapeutically effective dose to prevent, treat, or control esophageal cancer (especially ESCC) as described herein. The pharmaceutical composition or medicament is administered to a subject in an amount sufficient to elicit an effective therapeutic response in the subject.
The dosage of active agents administered is dependent on the subject'"'"'s body weight, age, individual condition, surface area or volume of the area to be treated and on the form of administration. The size of the dose also will be determined by the existence, nature, and extent of any adverse effects that accompany the administration of a particular compound in a particular subject. For example, each type of DLEC1 protein or nucleic acid encoding a DLEC1 protein will likely have a unique dosage. A unit dosage for oral administration to a mammal of about 50 to 70 kg may contain between about 5 and 500 mg of the active ingredient. Typically, a dosage of the active compounds of the present invention, is a dosage that is sufficient to achieve the desired effect. Optimal dosing schedules can be calculated from measurements of agent accumulation in the body of a subject. In general, dosage may be given once or more daily, weekly, or monthly. Persons of ordinary skill in the art can easily determine optimum dosages, dosing methodologies and repetition rates.
To achieve the desired therapeutic effect, compounds or agents may be administered for multiple days at the therapeutically effective daily dose. Thus, therapeutically effective administration of compounds to treat a pertinent condition or disease described herein in a subject requires periodic (e.g., daily) administration that continues for a period ranging from three days to two weeks or longer. Typically, agents will be administered for at least three consecutive days, often for at least five consecutive days, more often for at least ten, and sometimes for 20, 30, 40 or more consecutive days. While consecutive daily doses are a preferred route to achieve a therapeutically effective dose, a therapeutically beneficial effect can be achieved even if the agents are not administered daily, so long as the administration is repeated frequently enough to maintain a therapeutically effective concentration of the agents in the subject. For example, one can administer the agents every other day, every third day, or, if higher dose ranges are employed and tolerated by the subject, once a week.
Optimum dosages, toxicity, and therapeutic efficacy of such compounds or agents may vary depending on the relative potency of individual compounds or agents and can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, for example, by determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and can be expressed as the ratio, LD50/ED50. Agents that exhibit large therapeutic indices are preferred. While agents that exhibit toxic side effects can be used, care should be taken to design a delivery system that targets such agents to the site of affected tissue to minimize potential damage to normal cells and, thereby, reduce side effects.
The data obtained from, for example, cell culture assays and animal studies can be used to formulate a dosage range for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage can vary within this range depending upon the dosage form employed and the route of administration. For any agents used in the methods of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (the concentration of the agent that achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma can be measured, for example, by high performance liquid chromatography (HPLC). In general, the dose equivalent of agents is from about 1 ng/kg to 100 mg/kg for a typical subject.
Exemplary dosages for DLEC1 protein or a nucleic acid encoding a DLEC1 protein described herein are provided. Dosage for a DLEC1-encoding nucleic acid, such as an expression cassette, can be between 0.1-0.5 mg/eye, with intravitreous administration (e.g., 5-30 mg/kg). Small organic compounds activators can be administered orally at between 5-1000 mg, or by intravenous infusion at between 10-500 mg/ml. Monoclonal antibody activators can be administered by intravenous injection or infusion at 50-500 mg/ml (over 120 minutes); 1-500 mg/kg (over 60 minutes); or 1-100 mg/kg (bolus) five times weekly. DLEC1 Protein or peptide activators can be administered subcutaneously at 10-500 mg; 0.1-500 mg/kg intravenously twice daily, or about 50 mg once weekly, or 25 mg twice weekly.
Pharmaceutical compositions of the present invention can be administered alone or in combination with at least one additional therapeutic compound. Exemplary advantageous therapeutic compounds include systemic and topical anti-inflammatories, pain relievers, anti-histamines, anesthetic compounds, and the like. The additional therapeutic compound can be administered at the same time as, or even in the same composition with, main active ingredient (e.g., a DLEC1 protein or a nucleic acid encoding the protein). The additional therapeutic compound can also be administered separately, in a separate composition, or a different dosage form from the main active ingredient. Some doses of the main ingredient, such as a DLEC1 protein or a nucleic acid encoding a DLEC1 protein, can be administered at the same time as the additional therapeutic compound, while others are administered separately, depending on the particular symptoms and characteristics of the individual.
The dosage of a pharmaceutical composition of the invention can be adjusted throughout treatment, depending on severity of symptoms, frequency of recurrence, and physiological response to the therapeutic regimen. Those of skill in the art commonly engage in such adjustments in therapeutic regimen.
The invention provides compositions and kits for practicing the methods described herein to assess the level of DLEC1 mRNA or DLEC1 protein in a subject, which can be used for various purposes such as detecting or diagnosing the presence of esophageal cancer (especially ESCC), determining the risk of developing esophageal cancer (especially ESCC), and monitoring the progression of esophageal cancer (especially ESCC) in a patient, including assessing the likelihood of mortality from esophageal cancer (especially ESCC).
Kits for carrying out assays for determining DLEC1 mRNA level typically include at least one oligonucleotide useful for specific hybridization with at least one segment of the DLEC1 coding sequence or its complementary sequence. Optionally, this oligonucleotide is labeled with a detectable moiety. In some cases, the kits may include at least two oligonucleotide primers that can be used in the amplification of at least one segment of DLEC1 DNA or mRNA by PCR, particularly by RT-PCR.
Kits for carrying out assays for determining DLEC1 protein level typically include at least one antibody useful for specific binding to the DLEC1 protein amino acid sequence. Optionally, this antibody is labeled with a detectable moiety. The antibody can be either a monoclonal antibody or a polyclonal antibody. In some cases, the kits may include at least two different antibodies, one for specific binding to the DLEC1 protein (i.e., the primary antibody) and the other for detection of the primary antibody (i.e., the secondary antibody), which is often attached to a detectable moiety.
Typically, the kits also include an appropriate standard control. The standard controls indicate the average value of DLEC1 protein or mRNA in the esophagus epithelium of healthy subjects not suffering from esophageal cancer. In some cases such standard control may be provided in the form of a set value. In addition, the kits of this invention may provide instruction manuals to guide users in analyzing test samples and assessing the presence, risk, or state of esophageal cancer (especially ESCC) in a test subject.
In a further aspect, the present invention can also be embodied in a device or a system comprising one or more such devices, which is capable of carrying out all or some of the method steps described herein. For instance, in some cases, the device or system performs the following steps upon receiving an esophagus tissue sample, e.g., an esophagus epithelial tissue sample taken from a subject being tested for detecting esophageal cancer (especially ESCC), assessing the risk of developing esophageal cancer (especially ESCC), or monitored for progression of the condition: (a) determining in sample the amount or concentration of DLEC1 mRNA, DLEC1 protein; (b) comparing the amount or concentration with a standard control value; and (c) providing an output indicating whether esophageal cancer (especially ESCC) is present in the subject or whether the subject is at risk of developing esophageal cancer (especially ESCC), or whether there is a change, i.e., worsening or improvement, in the subject'"'"'s esophageal cancer (especially ESCC) condition. In other cases, the device or system of the invention performs the task of steps (b) and (c), after step (a) has been performed and the amount or concentration from (a) has been entered into the device. Preferably, the device or system is partially or fully automated.
The following examples are provided by way of illustration only and not by way of limitation. Those of skill in the art will readily recognize a variety of non-critical parameters that could be changed or modified to yield essentially the same or similar results.
Oncogenic STAT3 signaling activation and 3p22-21.3 locus alteration are common in multiple tumors, especially carcinomas of the nasopharynx, esophagus and lung. Whether these two events are linked remains unclear. CpG methylome analysis has identified a 3p22.2 gene, DLEC1, as a methylated target in esophageal squamous cell (ESCC), nasopharyngeal (NPC) and lung carcinomas. Its epigenetic abnormalities and functions were then further characterized.
CpG methylomes were established by methylated DNA immunoprecipitation. Promoter methylation was analyzed by methylation-specific PCR and bisulfite genomic sequencing. DLEC1 expression and clinical significance were analyzed using TCGA database. DLEC1 functions were analyzed by transfections followed by various cell biology assays. Protein-protein interaction was assessed by docking, Western blot and immunoprecipitation analyses.
The present inventors defined the DLEC1 promoter within a CpG island and p53-regulated. DLEC1 was frequently downregulated in ESCC, lung and NPC cell lines and primary tumors, but was readily expressed in normal tissues and immortalized normal epithelial cells, with mutations rarely detected. DLEC1 methylation was frequently detected in ESCC tumors and correlated with lymph node metastasis, tumor recurrence and progression, with DLEC1 as most frequently methylated among the established 3p22.2 tumor suppressors (RASSF1A, PLCD1 and ZMYND10/BLU).
DLEC1 inhibits carcinoma cell growth through inducing cell cycle arrest and apoptosis, and also suppresses cell metastasis by reversing epithelial-mesenchymal transition (EMT) and cell stemness. Moreover, DLEC1 represses oncogenic signaling including JAK/STAT3, MAPK/ERK, Wnt/β-catenin and AKT pathways in multiple carcinoma types. Particularly, DLEC1 inhibits IL-6-induced STAT3 phosphorylation in a dose-dependent manner. DLEC1 contains three YXXQ motifs and forms a protein complex with STAT3 via protein docking, which blocks STAT3-JAK2 interaction and STAT3 phosphorylation. IL-6 stimulation enhances the binding of DLEC1 with STAT3, which diminishes their interaction with JAK2 and further leads to decreased STAT3 phosphorylation. The YXXQ motifs of DLEC1 are crucial for its inhibition of STAT3 phosphorylation, and disruption of these motifs restores STAT3 phosphorylation through abolishing DLEC1 binding to STAT3.
This study demonstrates, for the first time, predominant epigenetic silencing of DLEC1 in ESCC, and a novel mechanistic link of epigenetic DLEC1 disruption with oncogenic STAT3 signaling in multiple carcinomas.
Chromosomal locus 3p22-21.3 frequently has abnormalities like loss of heterozygosity (LOH) in multiple cancers [1-6], including esophageal squamous cell (ESCC), lung and nasopharyngeal (NPC) carcinomas. Thus, as a typical tumor suppressor gene (TSG) locus, allele loss at 3p21.3 has been shown to be the early premalignant change detected in lung and breast cancers [1, 4]. Multiple genetic and epigenetic studies have been performed to determine the related TSGs at this locus, such as RASSF1A , ZMYND10 [8-10] and PLCD1 . Another candidate 3p22 TSG, deleted in lung and esophageal cancer 1 (DLEC1), was firstly identified in esophageal and lung cancers through sequencing 3p21.3 genomic DNA cosmid clones and expression analysis . However, although DLEC1 downregulation and rare mutations were initially detected in some carcinoma cell lines and primary tissues, its promoter methylation was not detected in any ESCC or lung cancer cell lines or tumor samples , raising questions about its role as a bona fide 3p22-21.3 TSG. After its first identification, DLEC1 promoter methylation and downregulation have been reported in multiple cancers by several groups [13-22], but still not in ESCC yet. DLEC1 methylation/downregulation has been shown to be significantly related to disease progression and poor prognosis of some cancers including lung, ovarian and breast [18-21]; thus, it is a potential biomarker for tumor diagnosis.
The DLEC1 protein has 1,755 amino acids encoded by a polynucleotide sequence of 5,268 nucleotides, with no homology to any known proteins or domains reported so far. Previous studies showed that DLEC1 is a growth suppressor with anti-tumorigenic abilities in vivo . However, the molecular mechanism underlying its tumor suppression still remains unknown.
STAT3 is commonly activated in human malignancies as an oncogenic signaling hallmark, involved in the regulation of cell proliferation, apoptosis, cancer stemness and immune checkpoint [23, 24]. Persistent STAT3 activation is associated with tumor progression of ESCC, NPC and lung cancers [25-27]; thus it is a feasible therapeutic target. STAT3 activation is stimulated by cytokines and growth factors (e.g., IL-6, IFNs, EGF), featured by tyrosine phosphorylation at residue Y705 together with Ser727 phosphorylation, and further functions as a transcription factor to activate target gene transcription . The YXXQ motif is well known as a consensus motif for STAT3 recruitment, which acts as a docking site selectively binding STATs . In addition, STAT3 could also be inactivated by negative regulators, including suppressors of cytokine signaling (SOCS), protein tyrosine phosphatases (PTPs) and protein inhibitors. Although the critical role of oncogenic STAT3 activation in tumorigenesis has been well defined, the mechanisms regulating STAT3 activation are diverse and worthy of further exploration.
An integrative epigenomic and genomic study of ESCC was conducted through genome-wide CpG methylation (methylome) and high-resolution array comparative genomic hybridization (aCGH) analyses, and identified DLEC1 as a methylated target in ESCC, as well as lung cancer and NPC. Its expression and methylation in cell lines and primary tumors of ESCC, lung cancer and NPC, was further examined and its tumor suppressive functions in carcinoma cells was systematically assessed. The underlying mechanism of JAK/STAT3 signaling regulation by DLEC1 in carcinoma cells was also investigated.
Enriched methylated signal in the DLEC1 promoter was detected in ESCC, but not in immortalized esophageal epithelial cells (
Meanwhile, an array CGH study of ESCC  also detected hemizygous 3p22 deletion in 5/10 cell lines where DLEC1 is located (
The DLEC1 Promoter is a CpG Island and p53-Regulated
As promoter CpG methylation directly mediates transcription repression, the DLEC1 promoter was further analyzed. A 756 bp region spanning its promoter and exon 1 as a typical CpG island (CGI) was found (
As five putative p53-binding sites were found in DLEC1 promoter (+18 to −1021) (webstie: tfbind.hgc.jp/), the effect of p53 on DLEC1 promoter activity was then examined. Results showed that p53 upregulated DLEC1 promoter activity, and the region (+18 to −295) might be the core p53 regulatory region (
DLEC1 expression and methylation were further examined in a panel of ESCC and other carcinoma cell lines. DLEC1 was readily detected in normal esophageal, respiratory and digestive tissues including esophagus, larynx, trachea, lung, stomach and colon (
To determine whether an epigenetic mechanism directly mediates DLEC1 silencing, DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (Aza) and histone deacetylase inhibitor Trichostatin A (TSA) were used. After the treatment, DLEC1 expression was increased in cell lines of ESCC, lung and NPC with silenced DLEC1, and even more dramatically increased with Aza+TSA treatment, accompanied by increased unmethylated alleles and decreased methylated alleles as detected by both MSP and BGS (
Frequent DLEC1 Methylation in Primary Carcinomas with Clinical Correlation
DLEC1 expression and methylation were then analyzed in primary ESCC and other carcinomas. First, online GENT database analysis showed significant reduction of DLEC1 RNA in esophageal, lung, and head and neck cancer tissues compared with corresponding normal tissues (
There was a significant correlation between DLEC1 methylation with ESCC tumor size and lymph node metastasis, but not with age, gender, stage, grade, or differentiation in the cohort (Table 2). Further analysis of TCGA datasets showed that esophageal and lung cancer patients with low methylation or high expression of DLEC1 had longer survival (
DLEC1 methylation status was also compared with other well-known TSGs at the 3p21-22 locus (PLCD1, RASSFIA, ZMYND10) in ESCC cell lines and primary tumors. DLEC1 (23/35, 66%) appears to have the highest rate of promoter methylation in these tumors compared to PLDC1 (14%), RASSFIA (20%) and ZMYND10 (35%) (Table 5). DLEC1 methylation was also detected in 74% (37/50) of NPC tumors but no (0/3) normal nasopharyngeal tissues, as well as in 57% (35/61) of lung carcinomas (
As alternative splicings of DLEC1 have been reported previously in tumor and normal tissues , the aberrant splicing of DLEC1 was also examined in carcinoma and normal cell lines in addition to normal tissues. Amplicons generated by primers (listed in Table 6) on exon 5 and 9 had 2 major bands, one wild-type (WT) and one novel aberrant splicing (T1), in most tumor cell lines and normal tissues (
It was found that all four DLEC1 splice variants are expressed in examined tissues and cell lines with varied expression levels. The expression levels of these splice variants were also higher in most normal tissues than that observed in tumor cell lines (
The tumor-specific promoter methylation of DLEC1 indicates its critical role in multiple carcinoma pathogenesis. Its tumor suppressor functions were thus further evaluated in ESCC and other carcinomas. As confirmed by Western blot, the ectopic expression level of DLEC1 was similar to its physiological expression level in normal tissues and immortalized esophageal epithelial cells (
To explore the mechanism of its growth inhibition, the effects of DLEC1 expression on carcinoma cell apoptosis and cell cycle distribution were next examined. Cell cycle analysis by propidium iodide incorporation showed that DLEC1-expressing KYSE150, H1299 and HONE1 cells obviously had increased G2-M phase cells and decreased S phase cells, indicating that DLEC1 expression induces G2-M arrest in multiple carcinoma cells (
The effects of DLEC1 on carcinoma cell migration and invasion were further assessed. Ectopic expression of DLEC1 dramatically suppressed the migration and invasion of ESCC, lung and NPC carcinoma cells in transwell assays (
It was then investigated whether DLEC1 regulates epithelial mesenchymal transition (EMT) in carcinoma cells. DLEC1-expressing cells adopted an epithelial morphology, concomitant with gain of epithelial marker E-cadherin and loss of mesenchymal marker vimentin (
The subcellular localization of DLEC1 in KYSE410 (endogenous) and H1299 (ectopically expressed) cells was examined using the DLEC1 antibody. Immunostaining showed that DLEC1 is mainly located in the cytoplasm of examined cells (
To gain more insight into the mechanisms underlying tumor suppression by DLEC1, luciferase reporter assay was used to examine its effects on oncogenic signaling pathways in carcinoma cells. Results showed that ectopic expression of DLEC1 markedly repressed the reporter activities of NF-κB, AP-1, STATs-bs, TopFlash, SRE and PAI-1 elements-regulated promoters in either carcinoma cells (ESCC, lung, NPC) or immortalized normal epithelial cells (NP69) (
The regulation of STAT3 signaling by DLEC1 was further investigated in more detail. Carcinoma cells were co-transfected with DLEC1- and STAT3C (a constitutive active form of STAT3)-expression plasmids. Exogenously expressed DLEC1 greatly suppressed the p-STAT3 levels at both Tyr705 and Ser727 sites in STAT3C-transfected carcinoma cells, with no changes in STAT3 total protein levels (
Moreover, DLEC1 was even able to suppress IL-6 treatment-enhanced STAT3 phosphorylation levels in carcinoma cells, without affecting STAT3 total protein level (
DLEC1 Binds to STAT3, which Interferes with its Interaction with JAK2
To investigate the mechanism of STAT3 phosphorylation suppression by DLEC1, the structure basis for possible interaction between DLEC1 and STAT3 was analyzed. RCSB Protein Data Bank (PDB) was used to search for structures and folds related to DLEC1 and STAT3 (
As JAK2 directly phosphorylates STAT3 at Tyr705, the possible interactions of DLEC1 with STAT3 and JAK2 were next examined by reciprocal co-immunoprecipitation (co-IP) experiments with Flag or DLEC1, STAT3 and JAK2 antibodies in carcinoma (KYSE150, H1299) and immortalized cells (HEK293T). Results showed a strong interaction between endogenous DLEC1 and STAT3/p-STAT3 (Tyr705) in HEK293T cells by immunoprecipitation, accompanied by relatively weaker co-precipitation of JAK2. Endogenous JAK2 could also precipitate with both DLEC1 and STAT3/p-STAT3 (Tyr705) (
In agreement with the above computational docking analysis, further protein structure analysis showed that DLEC1 contains three STAT3-specific docking sites—YXXQ motifs (
The effect of YXXQ motifs on DLEC1-STAT3 interaction was further examined by co-IP assay. Results showed that the interaction of DLEC1-YXXQ mutant with STAT3/p-STAT3 (Y705) was greatly decreased (
This study, for the first time, identifies DLEC1 as a methylated 3p22 tumor suppressor gene (TSG) for esophageal squamous cell carcinoma (ESCC). With its early genetic alterations, the 3p22-21.3 locus is well known for being critical in multiple carcinomas and lymphomas. Several candidate TSGs reside in this locus, including RASSF1A, ZMYND10 [8, 10], FUS1 , RBSP3 , NPRL2  and PLCD1 [11, 36]. These TSGs were identified through either genetic approaches (LOH, array-CGH, large-scale chromosomal region cloning and gene mapping, genome sequencing), or functional analysis using monochromosome transfer. Nowadays, epigenetic identification of tumor-specific promoter CpG methylation becomes a new efficient way for TSG discovery . The inventors'"'"' group has previously identified DLEC1 methylation and silencing in gastric , colon , hepatocellular , renal  and prostate  cancers, as well as non-Hodgkin and Hodgkin lymphomas . DLEC1 methylation has also been frequently detected in other carcinomas including nasopharyngeal , lung [18, 19, 22], breast  and ovarian .
However, so far there has been no in-depth mechanism study on the molecular basis of its tumor suppression in human cancers yet, although DLEC1 has been shown to possess growth suppressive abilities in multiple carcinoma types (ovarian , nasopharyngeal , esophageal , gastric , colon , hepatocellular  and renal ). DLEC1 also inhibits NPC cell tumorigenic potential in vivo . Some preliminary mechanisms on its tumor suppression have been proposed. For example, DLEC1 contains 27 potential casein kinase II (CK2) phosphorylation sites, which deregulates cell proliferation, migration and signaling . A bipartite nuclear localization signal (NLS) spanning aa 245-262 is present in DLEC1, but no transcription factor function has been detected . DLEC1 also induces cell cycle arrest in tumor cells . It was previously also shown that in prostate cancer, DLEC1 inhibited NF-κB transcription activity, upregulated p53-binding activity and induced cell apoptosis .
Here, this study has comprehensively analyzed the cancer-related signaling possibly regulated by DLEC1. DLEC1 was found to suppress multiple oncogenic signaling pathways, including JAK/STAT3, MAPK/ERK, AKT, Wnt/β-catenin and TGF-β signaling. Constitutive activation of JAK/STAT3 signaling contributes to multiple tumor initiation and progression, which is maintained by a few positive or negative regulators. The YXXQ motif is crucial for STAT3 activation in response to multiple signaling receptors through phosphorylation at its Tyr 705 and Ser727 sites. Studies have shown that chaperone proteins are involved in the regulation of STAT signaling [38, 39]. For example, acylglycerol kinase potentiates JAK2/STAT3 signaling in ESCC ; Epstein-Barr virus (EBV)-encoded proteins constitutively activated STAT3 in NPC [41, 42]; and, EGFR mutation mediates STAT3 activation via IL-6 production in lung cancer . However, far fewer negative regulators of STAT3 signaling have been reported in ESCC, NPC and lung cancer so far, unlike other carcinomas. The inventors discovered the structural basis for direct regulation of STAT3 by DLEC1, including three YXXQ motifs, resembling phosphatase and chaperone proteins, suggesting its possible binding to STAT3 and regulation of its dephosphorylation. Their experimental data further demonstrated that DLEC1 negatively regulates STAT3 activation through docking and binding to STAT3 and further inhibiting its phosphorylation (
The present inventors discovered that promoter CpG methylation of DLEC1 directly mediates its silencing/downregulation in multiple carcinomas, with histone acetylation also playing some role in DLEC1 regulation. Epigenetic silencing has been found to be the predominant cause of DLEC1 inactivation, as only rare mutations of DLEC1 have been detected in multiple carcinoma tissues from TCGA cohorts even with large sample sizes, suggesting a dominant role of epigenetic disruption of DLEC1 in carcinoma pathogenesis. In this study, four alternative splicings of DLEC1 were also found; however, further investigations of these variants are needed, including their functional significance, relative proportion to other longer functional transcripts, as well as possible connection between the splicing and CpG methylation of the DLEC1 gene body.
Compared with other known methylated 3p22-21.3 TSGs, DLEC1 has relatively higher methylation frequency in ESCC, further supporting its critical role in ESCC pathogenesis. The previous failure of detecting DLEC1 methylation first in Japanese ESCC tumors may be due to a technical issue , or less likely ethnic difference since the ESCC samples in this study are of Chinese origin. As DLEC1 methylation is tumor-specific in ESCC and detectable even in immortalized normal esophageal epithelial cells, it might serve as a non-invasive epigenetic biomarker for the early detection of ESCC. It was also found that DLEC1 methylation is correlated with ESCC recurrence and progression, suggesting its potential even as a marker for prognosis prediction in carcinoma patients. In parallel, DLEC1 methylation has been shown to be of good biomarker value in other malignancies, including non-small cell lung [18, 19], gastric , hepatocellular , renal  and oral carcinomas , as well as pre-invasive lesions of breast cancer . Moreover, DLEC1 methylation has been detected in plasma samples from lung cancer patients, and sera of Hodgkin lymphoma patients .
In summary, this study demonstrates the first evidence of predominant, tumor-specific, DLEC1 methylation in ESCC with its biomarker value. As a critical 3p22 TSG regulated by p53, DLEC1 inhibits the growth and metastasis of multiple carcinoma cells through binding to STAT3 and inhibiting its phosphorylation, and also suppressing other oncogenic signaling pathways. The YXXQ motifs of DLEC1 are crucial for STAT3 phosphorylation. The identification of DLEC1 as a negative regulator of STAT3 signaling reveals a mechanistic link between 3p22 alteration and oncogenic STAT3 signaling activation in multiple carcinoma pathogeneses.
A panel of ESCC, NPC and lung carcinoma cell lines was used. Immortalized normal esophageal epithelial (NE1, NE3, Het-1A), normal nasopharyngeal epithelial (NP69) and HEK293T cell lines were used. Cell lines were maintained in RPMI or DMEM medium (Gibco BRL, Rockville, Md.) with 10% fetal bovine serum. Human normal adult tissue RNA samples were obtained commercially (Stratagene, La Jolla, Calif., or Millipore Chemicon, Billerica, Mass.). Primary carcinoma tissues of Chinese ESCC, NPC and lung, some with matched normal samples, have been descried before [46-49]. Cell lines were treated with 5 μM of 5-Aza-2′-deoxycytidine (Aza) (Sigma, St. Louis, Mo.) for 3 days, or even followed with ˜16 h additional TSA (final concentration 10 mM) treatment as described [46, 47].
Methylated DNA immunoprecipitation (MeDIP) coupled with promoter microarray hybridization (MeDIP-chip) was performed as previously [50, 51]. Briefly, methylated DNA of ESCC (HKESC1, KYSE410) and NPC cell lines (HK1), as well as immortalized esophageal and nasopharyngeal epithelial cells (NE083, NP69) were immunoprecipited by monoclonal antibody against 5-methylcytidine (33D3, Diagenode, Seraing, Belgium), and then hybridized to NimbleGen™ HG18 Meth (385K CGI plus) promoter arrays (Array Star, Inc., MD). Bioinformatics analysis of methylome data was performed as previously described [50, 51].
Illumina 27K DNA methylation microarray was conducted previously . DLEC1 methylation status was analyzed accordingly.
MSP and BGS were conducted according to previous reports [46, 47]. MSP and BGS primers are listed in Table 6. MSP was conducted for 40 cycles at the annealing temperatures of 60° C. for M and 58° C. for U. Amplified products from BGS primer set were cloned into pCR4-Topo vector (Invitrogen, Carlsbad, Calif.), with 6-8 colonies randomly chosen and sequenced.
Four pairs of primers (Table 6) were used to generate 4 DLEC1 fragments based on published DLEC1 sequence (GenBank accession number AB020522). Reverse transcription was carried out using normal testis RNA as template (BD Biosciences, Palo Alto, Calif.). The 4 product fragments were ligated to generate pcDNA3.1 (+)-Flag-DLEC1 and pCMV-Flag-DLEC i-V5 expression plasmids. The mutation for three YXXQ motifs of DLEC1 (DLEC1-3Y, YXXQ-GGGG (“GGGG” disclosed as SEQ ID NO: 7)) was introduced by PCR into pCMV-Flag-DLEC1-V5 vector, with sequence confirmed. STAT3C expression plasmid was a gift from Prof. Honglin Chen (University of Hong Kong) . Cells were transfected with lipofectamine 3000 (Invitrogen, Carlsbad, Calif.), and the cells were cultured in RPMI 1640 supplemented with 10% FBS and selected in 400 μg/mL of G418 for 20-30 days to establish some stable cell pools, with confirmed DLEC1 expression.
Colony formation assay was conducted as previously described . All experiments were performed in triplicate wells 3 times. To monitor cell proliferation, 1000 cells were plated in a 96-well plate and incubated at 37° C. in selective media for 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT) assay.
Flow cytometry analysis of cell cycle and apoptosis was described previously . Cells were stained with propidium iodide (PI) and Annexin V-FITC (BD Biosciences, Bedford, Mass.), and sorted by Accuri C6 (BD Biosciences, Bedford, Mass.) according to the manufacturer'"'"'s protocol.
Transwell migration and invasion assays were performed as previously described [32, 40]. The numbers of migrated or invaded cells were observed and counted using a light microscope. Five fields were randomly chosen and the numbers of penetrated cells were counted.
Antibodies used were: cleaved caspase-3 (#9661), cleaved poly (ADP-ribose) polymerase (#9541), AKT-total (#4691), phospho-AKT(Ser473) (#4060), JAK2 (#9945S), phospho-SAPK/JNK (Thr183/Tyr185) (#6251S), STAT3 (#9139S), phospho-STAT3 (Tyr705) (9145S) and phospho-STAT3 (Ser 727), E-cadherin (#4065) (9134) (Cell Signaling, Beverly, Mass.); Flag M2 (F3165), Vimentin (V6630), DLEC1 (HPA019077) and β-actin (AC-74) (Sigma-Aldrich, St. Louis, Mo.); anti-mouse Ig G-HRP (P0161), anti-rabbit Ig G-HRP (P0448) (Dako, Glostrup, Denmark); Twist (sc-15393; Santa Cruz, Calif., USA); a-tubulin (Lab Vision Corporation, Fremont, Calif.); V5-Tag (MCA1360; AbD Serotec, Raleigh, N.C.).
Human IL-6 (PF01229) (Peprotech, Rocky Hill, N.J.) was used. Western blot and IP experiments were performed according to previous protocols [48, 49].
To find possible interaction in 3D structure between DLEC1 and STAT3, RCSB Protein Data Bank online tool (website: rcsb.org/pdb/home/home.do) was firstly used to predict 3D structures of DLEC1 and STAT3. Protein-protein docking was conducted using the Z-DOCK server (website: zdock.umassmed.edu/), which provides 5 top models regarding possible interaction between two proteins.
All statistical analyses were conducted with R-3.3.0 (website: r-project.org). Statistical significance was defined asp value <0.05. Basic statistical tests and generation of boxplots and scatterplots were performed by using built-in functions including the base distribution of R. Survival analyses and the generation of related plots were performed by using the survival package v2.41-3 (website: cran.r-proj ect.org/web/packages/survival/index.html). Kaplan-Meier method was used to estimate the overall survival of patients; log-rank test was used to compare survival distributions of groups of patients with different levels of DNA methylation or gene expression.
For expression data, log 2 transformed and normalized values were used. For methylation data, the β-value, a measure of DNA methylation level ranging from 0 to 1 for completely unmethylated to completely methylated, was used. The correlation of DNA methylation with gene expression or continuous numerical clinical features was investigated by calculating Spearman'"'"'s rank correlation coefficients and two-tailed p values using the ‘cor.test’ function in R. For two groups (mutant or wild-type) of DNA methylation, gene expression or clinical data, Wilcoxon rank sum test was applied to calculate two-tailed p values using the ‘wilcox.test’ function in R. For data with more than two groups, Kruskal-Wallis rank sum test was applied to calculate the P values using the ‘kruskal.test’ function in R.
Whole-genome arrays (1-Mb resolution) and aCGH was performed and analyzed as previously . Hybridized slides were scanned and analyzed with the GenePixPro 4.0 image analysis software.
RNA was reverse-transcribed using MuLV reverse transcriptase (GeneAmp RNA PCR kit, Applied Biosystems). RT-PCR was performed as described previously using GAPDH as a control . Primers used were listed in Table 6.
Multiplex differential genomic DNA-PCR was performed using primer pair DLEC1A/C for 35 cycles (annealing temperature 58° C.) with AmpliTaq Gold, using 0.1 ug of DNA per 12.5 ul PCR reaction . GAPDH and DLEC1 were employed to detect DLEC1 deletion in a region spanning exon 1 and intron 1.
Different regions of the DLEC1 promoter were cloned by PCR from normal human placenta DNA (sigma-Aldrich, USA). PCR was carried out with a high-fidelity Platinum PfX DNA polymerase (Life Technologies, USA) with 10% DMSO. The sequences and orientations of the cloned fragments were confirmed by sequencing. The longest and shorter fragments were amplified from primer pairs DLEC1F1-R and DLEC1F2-R respectively (Table 6). Restriction enzyme Bst XI was employed to digest the longest fragment to produce an intermediate one. These fragments were then linked to pGL2-Enhancer Vector (Promega) to generate p(−295)DLEC1EN, p(−685)DLEC1EN and p(−1021)DLEC1EN. Promoter activities of these fragments were assessed by transient transfection in CNE1 and CNE2 cell lines using Transfast (Promega).
DLEC1y1, DLEC1y2, DLEC1N and DLEC1G (Table 6) were used to generate different splicing fragments. Desired PCR products were purified using QIAex II (Qiagen). Purified PCR amplicons were sequenced and aligned with DLEC1 mRNA sequence using the “bl2seq” program (website: ncbi.nlm.nih.gov/blast).
ChIP assay was performed as described previously. Primers used were listed in Table 6. Antibody to acetylated histone H4 (Upstate Biotechnology) was used to precipitate cross-linked chromatin. ACTIN was employed as a control for normalization of each PCR product.
Clinical, mRNA expression and genome-wide DNA methylation data of 185 esophageal cancer, 585 lung adenocarcinoma and 504 lung squamous cell carcinoma patients was obtained from public databases of The Cancer Genome Atlas (TCGA). Raw datasets were downloaded from TCGA Data Portal (http://gdac.broadinstitute.org/) and analyzed. “Level 3” methylation data (Illumina Infinium Human DNA Methylation 450 platform) was retrieved from Johns Hopkins University and University of Southern California. mRNAseq expression data (level 3, normalized gene expression data, Illumina HiSeq 2000 platform) was retrieved from University of North Carolina or Canada'"'"'s Michael Smith Genome Sciences Centre. Genomic mutation data (Illumina Genome Analyzer platform) was retrieved from Washington University School of Medicine Proteomics (for esophageal cancer) and Broad Institute of MIT and Harvard (for lung cancer) and analyzed.
Cell motility was assessed using a scratch wound-healing assay. Cells transient transfected with DLEC1 were cultured in 6-well plates until confluent. A single scratch was produced in the cell layer using a sterile tip. After incubation for 24 and 48 hours, cells were photographed under a phase contrast microscope. The experiments were performed in triplicates.
Cells grown on coverslips were stained by indirect immunofluorescence as described previously [11, 49]. Briefly, cells were incubated with primary antibodies against DLEC1, E-cadherin, or Vimentin and then incubated with Alexa Fluor 594-conjugated secondary antibody against mouse IgG (A11062) (Invitrogen Molecular Probes, Carlsbad, Calif.), or FITC-conjugated secondary antibody against rabbit IgG (F0205) (DAKO, Denmark). To analyze the effects of DLEC1 on actin stress fiber formation, cells were serum starved for 24 h before incubation in medium-containing 5% fetal bovine serum. After 1 h, cells were fixed and stained by Rhodamine-labeled phalloidin (Invitrogen Molecular Probes). Cells were then counterstained with DAPI and imaged with an Olympus BX51 microscope (Olympus Corporation, Tokyo, Japan).
The promoter activities were determined by luciferase reporter assays. Luciferase reporters of several key signaling pathways, including NF-κB-luc, AP-1-luc, SRE-luc, STATs-bs-luc, TopFlash-luc, and PAI-luc were used to examine signaling pathway regulated by DLEC1. Cells were transiently co-transfected with DLEC1 expression vector and phRL-TK (the luciferase reporters). DLEC1-promoter luciferase reporters were co-transfected with expression vector encoding wild-type p53. After 48 h, cells were lysed and luciferase activities were measured using Dual-Luciferase® Reporter Assay System (Promega, Madison, Wis.). To normalize transfection efficiency, phRL-TK luciferase activities were measured as an internal control. At least three independent experiments were performed, with each repeated in triplicates.
All patents, patent applications, and other publications, including GenBank Accession Numbers, cited in this application are incorporated by reference in the entirety for all purposes.
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