Fast Diagnosis and Personalized Treatment for Acne

• US 20150086581A1
• Filed: 03/15/2013
• Published: 03/26/2015
• Est. Priority Date: 03/17/2012
• Status: Abandoned Application

• Current Assignee: Regents of the University of California (University of California)
• Original Assignee: Regents of the University of California (University of California)
• Inventors: Li, Huiying, Tomida, Shuta
• Application Number:
  US14/385,576
• Publication Number:
  US 20150086581A1
• Time in Patent Office: Days
• US Class Current: 424/190.1
• CPC Class Codes: A61K 35/741 Probiotics probiotic yeast, e.g. saccharomyces A61K36/06
• CPC Class Codes: A61K 35/76 Viruses; Subviral particles; Bacteriophages
• CPC Class Codes: A61K 39/0208 Specific bacteria not otherwise provided for
• CPC Class Codes: A61K 39/05 Actinobacteria, e.g. Actinomyces, Streptomyces, Nocardia, Bifidobacterium, Gardnerella, Corynebacterium; Propionibacterium Mycobacterium A61K39/04
• CPC Class Codes: A61P 17/10 Anti-acne agents
• CPC Class Codes: C12N 2795/00032 Use of virus as therapeutic agent, other than vaccine, e.g. as cytolytic agent
• CPC Class Codes: C12N 7/00 Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof preparing medicinal viral antigen or antibody compositions, e.g. virus vaccines, A61K39/00
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 1/701 Specific hybridization probes
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

Methods of diagnosing and treating patients afflicted with acne, including diagnosing one as having acne if the individual possesses RT4, RT5, RT7, RT8, RT9, or RT10. Methods for treating acne include administering an effective amount of a drug specifically targeting RT4, RT5, RT7, RT8, RT9, or RT10, such as small molecules, antisense molecules, siRNAs, biologics, antibodies, phages, vaccines, or combination thereof.

Claims

2. (canceled)

3. A method for diagnosing different types of acne comprising:

obtaining a skin sample from a subject;

isolating bacterial DNA from said sample;

amplifying bacterial DNA in said sample;

and

typing the subject'"'"'s DNA based on one or more of the five major microbiome types of P. acnes strains,

wherein said subject is diagnosed as having acne if said subject is typed to microbiome IV or V.

1. The method of claim 3, wherein:

amplifying bacterial DNA comprises amplifying 16S ribosomal DNA in said sample;

typing the subject'"'"'s DNA comprises sequencing said amplified DNA products and determining whether the DNA sequences correspond to

one or more of the ten major ribotypes (RTs) of P. acnes strains, RT1-RT10 (SEQ ID NOs 1-10).

4. The method of claim 3, wherein:

amplifying bacterial DNA comprises using one or more primer sets to amplify said DNA; and

typing the subject'"'"'s DNA comprises analyzing said amplified DNA for the presence of a sequence having at least 95% homology with at least one of SEQ ID NOs 29-32 and 82-434.

5. The method according to claim 4, wherein said amplified DNA is analyzed for the presence of a sequence having at least 99% homology with at least one of SEQ ID NOs 29-32 and 82-434.

7. The method of claim 3, wherein:

amplifying bacterial DNA comprises using one or more primer sets to amplify said DNA; and

typing the subject'"'"'s DNA comprises using one or more probes to detect said amplified DNA, and analyzing said probe signals for the presence of Locus 1 (at least one sequence having at least 95% homology to at least one of SEQ ID NOs 29 and 82-97), Locus 2 (at least one sequence having at least 95% homology to at least one of SEQ ID NOs 30 and 98-186), Locus 3 (at least one sequence having at least 95% homology to at least one of SEQ ID NOs 31 and 187-423), and/or Locus 4 (at least one sequence having at least 95% homology to at least one of SEQ ID NOs 32 and 424-434).

8. The method according to claim 7, wherein said signals are analyzed for the presence of Locus 1, Locus 2, Locus 3, and/or Locus 4 based upon at least 99% homology.

10. The method according to claim 4, wherein a primer of said primer sets is selected from SEQ ID NOs 11, 2, 17, and 18 (for Locus 1), SEQ ID NOs 13, 14, 20, and 21 (for Locus 2), SEQ ID NOs 15, 16, 23, and 24 (for Locus 3), and SEQ ID NOs 26 and 27 (for Locus 4).

11. The method according to claim 7, wherein a primer of said primer sets is selected from SEQ ID NOs 11, 12, 17, and 18 (for Locus 1), SEQ ID NOs 13, 14, 20, and 21 (for Locus 2), SEQ ID NOs 15, 16, 23, and 24 (for Locus 3), and SEQ ID NOs 26 and 27 (for Locus 4) and wherein said probes are SEQ ID NO:

19 (for Locus

     1), SEQ ID NO;

22 (for Locus

     2), SEQ ID NO;

25 (for Locus

     3), and SEQ ID NO;

28 (for Locus

     4).

6. (canceled)

9. (canceled)

12. A vaccine for the prevention and/or treatment of acne caused by P. acnes comprising a heat inactivated P. acnes strain, an attenuated protein of said strain, or combination thereof, wherein said strain is an RT4 strain, an RT5 strain, an RT7 strain, an RT8 strain, an RT9 strain, or an RT10 strain.

13. The vaccine of claim 12, wherein the vaccine is specific to a subject based on 16S rDNA sequence analysis of the strains of P. acnes affecting said subject.

14. The vaccine according to claim 12, wherein said heat inactivated P. acnes strain, attenuated protein, or combination thereof is specific for at least one of unique genomic loci, regions, or sequences identified for the strains of P. acnes.

15. The vaccine according to claim 12, wherein said heat inactivated P. acnes strain, attenuated protein, or combination thereof is specific for at least one of Locus 1 (SEQ ID NOs 29 and 82-97), Locus 2 (SEQ ID NOs 30 and 98-186), Locus 3 (31 and 187-423), and Locus 4 (32 and 424-434).

16. (canceled)

18-29. -29. (canceled)

30. A composition comprising at least one strain of P. acnes that is associated with healthy or normal skin.

17. A method for treating acne comprising:

administering an effective amount of the composition of claim 30.

31. The composition according to claim 30, wherein said strain is an RT6 strain.

32. The composition according to claim 30, wherein said strain has at least 95% homology to SEQ ID NO:

51, SEQ ID NO;

52, SEQ ID NO;

53, or SEQ ID NO;

54.

33-35. -35. (canceled)

36. A method for the personalized treatment of acne comprising determining the strain(s) of acne affecting a subject and administering to said subject an effective amount of at least one phage specifically directed to said strain(s).

37. The method according to claim 36, wherein said subject is treated with phage directed against an RT4 strain, an RT5 strain, an RT7 strain, and RT8 strain, an RT9 strain, and/or an RT10 strain.

38. A method of claim 36, wherein said phage is selected from:

PHL113M01 (SEQ ID NO;

36), PHL111 M01 (SEQ ID NO;

33), PHL082M00 (SEQ ID NO;

47), PHL060L00 (SEQ ID NO;

34), PHL067M10 (SEQ ID NO;

42), PHL071N05 (SEQ ID NO;

41), PHL112N00 (SEQ ID NO;

35), PHL037M02 (SEQ ID NO;

40), PHL085N00 (SEQ ID NO;

46), PHL115M02 (SEQ ID NO;

43), PHL085M01 (SEQ ID NO;

44), PHL114L00 (SEQ ID NO;

37), PHL010M04 (SEQ ID NO;

38), and PHL066M04 (SEQ ID NO;

39).

39-46. -46. (canceled)