Cancer diagnosis using nucleic acid hybridization

• US 5,688,641 A
• Filed: 10/13/1994
• Issued: 11/18/1997
• Est. Priority Date: 02/28/1991
• Status: Expired due to Fees

• Current Assignee: Dana-Farber Cancer Institute
• Original Assignee: Dana-Farber Cancer Institute
• Inventors: Tomasetto, Catherine Laure, Lee, Sam Whan, Zou, Zhiqiang, Sager, Ruth
• Primary Examiner(s): Walsh, Stephen
• Assistant Examiner(s): SPECTOR, LORRAINE
• Application Number:
  US08/322,742
• Time in Patent Office: 1,132 Days
• Field of Search: 436/501, 436/503, 436/811, 435/6, 435/40.5, 530/350, 536/23.5
• US Class Current: 435/6.14
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: C07K 14/47 from mammals
• CPC Class Codes: C07K 14/811 Serine protease (E.C. 3.4.21) inhibitors
• CPC Class Codes: C07K 16/38 against protease inhibitors of peptide structure
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: G01N 33/5011 for testing antineoplastic activity
• CPC Class Codes: G01N 33/57484 involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
• CPC Class Codes: Y10S 436/811 Test for named disease, body condition or organ function

Abstract

A method of determining whether a test cell from a given human tissue type is (a) normal, or (b) cancerous or precancerous, by contacting the mRNA of the test cell with a nucleic acid probe which contains a nucleotide sequence at least 15 nucleotides in length which is complementary to a portion of the coding sequence of a candidate tumor suppressor gene, which gene is one that is expressed at a given control level in normal cells of that tissue type; and determining the approximate amount of hybridization of the probe to the mRNA of the test cell, an amount of hybridization one-third or less that seen with the mRNA of a normal cell of that tissue type being an indication that the test cell is cancerous or precancerous. Alternatively, an antibody specific for the candidate tumor suppressor gene product can be substituted for the nucleic acid probe as a means for determining the level of expression of the gene in the test cell. The invention also includes methods of treating a cancerous cell by increasing the level of expression of a candidate tumor suppression gene in the cell; novel candidate tumor suppressor genes; and their use in diagnosis, prognosis, and therapy.

Claims

1. A method of determining, by in situ hybridization, whether a sample containing a test cell from human breast tissue is (a) normal, or (b) cancerous, said method comprising the steps of:

contacting the mRNA of said test cell in situ with a nucleic acid probe comprising a nucleotide sequence at least 15 nucleotides in length which is complementary to a portion of the coding sequence or a candidate tumor suppressor gene, said gene being one which is normally expressed in normal cells of human breast tissue; and

determining whether said probe hybridizes to said mRNA under high stringency conditions selected to permit hybridization of said probe to normal cells of human breast tissue, wherein the failure to hybridize to said mRNA is an indication that said test cell is cancerous;

provided that said gene encodes connexin 26, connexin 43, preproelafin, CaN19 is protein, or HBp17.

2. The method of claim 1, said method comprising the additional steps of:

contacting the mRNA of said test cell in situ with a second nucleic acid probe comprising a nucleotide sequence at least 15 nucleotides in length which is complementary to a portion of the coding sequence of a second candidate tumor suppressor gene different from said first candidate tumor supprestor gene, said second gene being one which is normally expressed in normal cells of human breast tissue; and

determining whether either of said first and second probes hybridizes to said mRNA under high stringency conditions selected to permit hybridization to normal cells of human breast tissue, wherein failure of either said first probe or said second probe to hybridize with said mRNA is an indication that said test cell is cancerous;

provided that said second gene encodes connexin 26, connexin 43, preproelafin, CaN19 protein, or HBp17.

3. The method of claim 1, said method comprising the additional steps of:

contacting the mRNA of said test cell in situ with a second nucleic acid probe comprising a nucleotide sequence at least 15 nucleotides in length which is complementary to a portion of the coding sequence of a second candidate tumor suppressor gene different from said first candidate tumor suppressor gene, said second gene being one which is normally expressed in normal cells of human breast tissue; and

determining whether either of said first and second probes hybridizes to said mRNA under high stringency conditions selected to permit hybridization of both of said probes to normal cells of human breast tissue, wherein failure of either said first probe or said second probe to hybridize with said mRNA is an indication that said test cell is cancerous;

provided that said second gene includes a sequence which hybridizes under stringent conditions to SEQ ID NO;

3 (U1), SEQ ID NO;

4 (U2), SEQ ID NO;

8 (U6), SEQ ID NO;

9 (U7), SEQ ID NO;

10 (U8), SEQ ID NO;

11 (U9), SEQ ID NO;

14 (U9), SEQ ID NO;

SEQ ID NO;

16 (U1), SEQ ID NO;

17 (U1), SEQ ID NO;

18 (U2), or SEQ ID NO;

19 (U2).

4. A method of confirming, by in situ hybridization, a diagnosis that a given fraction of cells in a human breast tissue sample are cancerous, said method comprising the steps of:

contacting the mRNA of said sample in situ with a nucleic acid probe comprising a nucleotide sequence at least nucleotides in length which is complementary to a portion of the coding sequence of a candidate tumor suppressor gene, said gene being one which is expressed in normal cells of human breast tissue at a given control level; and

determining whether the fraction of cells in said sample which, under high stringency hybridization conditions selected to permit hybridization to normal cells of human breast tissue, fail to exhibit detectable hybridization to said probe is approximately equivalent to said given fraction of cells previously diagnosed as being cancerous, said equivalence of fractions being a confirmation of said diagnosis;

provided that said gene encodes connexin 26, connexin 43, preproelafin, CaN19 protein, or HBp17.

5. A method for determining the presence of cancerous cells in the breast tissue of a patient, which method comprises the steps of:

providing a nucleic acid probe comprising a nucleotide sequence at least 15 nucleotides in length which is complementary to a portion of the coding sequence of a candidate tumor suppressor gene, said gene encoding connexin 26, connexin 43, preproelafin, CaN19 protein, or HBp17;

obtaining from a patient a first sample of breast tissue, said first sample potentially comprising cancerous cells;

providing a second sample of breast tissue, substantially all of the cells of said second sample being non-cancerous;

contacting in situ said nucleic acid probe under stringent hybridizing conditions with RNA of each of said first and second tissue samples, said hybridization conditions being selected to permit hybridization of said probe to non-cancerous cells of breast tissue; and

comparing (a) the in situ hybridization of said nucleic acid probe with said first tissue sample, with (b) the in situ hybridization of said nucleic acid probe with said second tissue sample, wherein hybridization with said second tissue sample but not with said first tissue sample indicates the presence of cancerous cells in said first tissue sample.

6. A method of determining, by in situ hybridization, whether a sample containing a test cell from human breast tissue is (a) normal, or (b) cancerous, said method comprising the steps of:

contacting the mRNA of said test cell in situ with a nucleic acid probe comprising a nucleotide sequence at least 15 nucleotides in length which is complementary to a portion of the coding sequence of a candidate tumor suppressor gene, said gene being one which is normally expressed in normal cells of human breast tissue; and

determining whether said probe hybridizes to said mRNA under high stringency conditions selected to permit hybridization to normal cells of human breast tissue, wherein the failure to hybridize to said mRNA is an indication that said test cell is cancerous;

provided that said gene includes a sequence which hybridizes under stringent conditions to SEQ ID NO;

3 (U1), SEQ ID NO;

4 (U2), SEQ ID NO;

8 (U6), SEQ ID NO;

9 (U7), SEQ ID NO;

10 (U8), SEQ ID NO;

11 (U9), SEQ ID NO;

14 (U9), SEQ ID NO;

16 (U1), SEQ ID NO;

17 (U1), SEQ ID NO;

18 (U2), or SEQ ID NO;

19 (U2).

7. The method of claim 6, said method comprising the additional steps of:

contacting the mRNA of said test cell in situ with a second nucleic acid probe comprising a nucleotide sequence at least 15 nucleotides in length which is complementary to a portion of the coding sequence of a second candidate tumor suppressor gone different from said first candidate tumor suppressor gene, said second gene being one which is normally expressed in normal cells of human breast tissue; and

determining whether either of said first and second probes hybridizes to said mRNA under high stringency conditions selected to permit hybridization of both of said probes to normal cells of human breast tissue, wherein failure of either said first probe or said second probe to hybridize with said mRNA is an indication that said test cell is cancerous;

provided that said second gene includes a sequence which hybridizes under stringent conditions to SEQ ID NO;

3 (U1), SEQ ID NO;

4 (U2), SEQ ID NO;

8 (U6), SEQ ID NO;

9 (U7), SEQ ID NO;

10 (U8), SEQ ID NO;

11 (U9), SEQ ID NO;

14 (U9), SEQ ID NO;

16 (U1), SEQ ID NO;

17 (U1), SEQ ID NO;

18 (U2), or SEQ ID NO;

19 (U2).

8. The method of claim 6, said method comprising the additional steps of:

contacting the mRNA of said test cell in situ with a second nucleic acid probe comprising a nucleotide sequence at least 15 nucleotides in length which is complementary to a portion of the coding sequence of a second candidate tumor suppressor gene different from said first candidate tumor suppressor gene, said second gene being one which is normally expressed in normal cells of human breast tissue; and

determining whether either of said first and second probes hybridizes to said ERNA under high stringency conditions selected to permit hybridization of both of said probes to normal cells of human breast tissue, wherein failure of either said first probe or said second probe to hybridize with said mRNA is an indication that said test cell is cancerous;

provided that said second gene encodes connexin 26, connexin 43, preproelafin, CaN19 protein, or HBp17.

9. A method of confirming, by in situ hybridization, a diagnosis that a given fraction of cells in a human breast tissue sample are cancerous, said method comprising the steps of:

contacting the mRNA of said sample in situ with a nucleic acid probe comprising a nucleotide sequence at least 15 nucleotides in length which is complementary to a portion of the coding sequence of a candidate tumor suppressor gene, said gene being one which is expressed in normal cells of human breast tissue at a given control level; and

determining whether the fraction of cells in said sample which, under high stringency hybridization conditions selected to permit hybridization to normal cells of human breast tissue, fail to exhibit detectable hybridization to said probe is approximately equivalent to said given fraction of cells previously diagnosed as being cancerous, said equivalence of fractions being a confirmation of said diagnosis;

provided that said gene comprises a sequence which hybridizes under stringent conditions to SEQ ID NO;

3 (U1), SEQ ID NO;

4 (U2), SEQ ID Nor 8 (U6), SEQ ID NO;

9 (U7), SEQ ID NO;

10 (U8), SEQ ID NO;

11 (U9), SEQ ID NO;

14 (U9), SEQ ID NO;

16 (U1), SEQ ID NO;

17 (U1), SEQ ID NO;

18 (U2), or SEQ ID NO;

19 (U2).

10. A method for determining the presence of cancerous cells in the breast tissue of a patient, which method comprises the steps of:

providing a nucleic acid probe comprising a nucleotide sequence at least 15 nucleotides in length which is complementary to a portion of the coding sequence of a candidate tumor suppressor gene, said gene comprising a sequence which hybridizes under stringent conditions to SEQ ID NO;

3 (U1), SEQ ID NO;

4 (U2), SEQ ID NO;

8 (U6), SEQ ID NO;

9 (U7), SEQ ID NO;

10 (U8), SEQ ID NO;

11 (U9), SEQ ID NO;

14 (U9), SEQ ID NO;

16 (U1), SEQ ID NO;

17 (U1), SEQ ID NO;

18 (U2), or SEQ ID NO;

19 (U2);

obtaining from a patient a first sample of breast tissue, said first sample potentially comprising cancerous cells;

providing a second sample of breast tissue, substantially all of the cells of said second sample being non-cancerous;

contacting in situ said nucleic acid probe under stringent hybridizing conditions with RNA of each of said first and second tissue samples, said hybridization conditions being selected to permit hybridization of said probe to non-cancerous cells of breast tissue; and

comparing (a) the in situ hybridization of said nucleic acid probe with said first tissue sample, with (b) the in situ hybridization of said nucleic acid probe with said second tissue sample, wherein hybridization with said second tissue sample but not with said first tissue sample indicates the presence of cancerous cells in said first tissue sample.