Systems and compositions for diagnosing pathogenic fungal infection and methods of using the same

Patent metadata

Field	Value
Publication number	US-11112409-B2
Application number	US-201716077690-A
Country	US
Kind code	B2
Filing date	Feb 10, 2017
Priority date	Feb 12, 2016
Publication date	Sep 7, 2021
Grant date	Sep 7, 2021

Abstract

The present disclosure relates generally to detection of contamination of a sample or diagnosis of subject based upon detection or quantification of amino acid sequences in a sample, specifically to the identification and use of molecular biomarkers for Candida albicans biofilm infections.

First claim

The invention claimed is:

1. A method of diagnosing a subject with a pathogenic fungal infection from the genus Candida , comprising:
a) exposing a sample from the subject to at least one substrate of at least one secreted aspartyl protease (Sap), wherein the at least one substrate comprises at least one enzymatic cleavage site recognizable by the at least one Sap, and wherein the at least one Sap comprises at least about 90% sequence homology to SEQ ID NO: 5 or SEQ ID NO: 6;
b) detecting the presence, absence and/or quantity of enzymatic cleavage of the substrate by the at least one Sap in the sample; and
c) correlating the presence, absence and/or quantity of enzymatic cleavage of the substrate by the at least one Sap to a probability or likelihood that the subject has the pathogenic fungal infection relative to a measurement of a control sample taken from a subject known to have or not to have the pathogenic fungal infection,
wherein the at least one substrate of SEQ ID NO: 5 comprises a peptide with 85% sequence homology to SEQ ID NO: 31 and wherein the at least one substrate of SEQ ID NO: 6 comprises a peptide with 85% sequence homology to SEQ ID NO: 32.

2. The method of claim 1 , wherein the at least one substrate of the at least one Sap is attached to a fluorogenic probe.

3. The method of claim 1 , wherein the at least one Sap comprises the amino acid sequence of SEQ ID NO: 5 or SEQ ID NO: 6.

4. The method of claim 1 , wherein the pathogenic infection comprises a planktonic or biofilm form of any of the species selected from the group consisting of Candida albicans, Candida dubliniensis, Candida tropicalis, Candida parapsilosis, Meyerozyma/Candida guilhermondii , and Candida glabrata.

5. The method of claim 1 , wherein the presence, absence and/or quantity of enzymatic cleavage of the substrate by the at least one Sap in the sample is detected by one or a combination of: fluorescence, optical imaging, field microscopy, quantum dots, chromatography, and/or mass spectrometry.

6. The method of claim 1 , wherein the sample is a human tissue sample comprising a tissue from a brushing, biopsy, or surgical resection of the subject.

7. The method of claim 1 , wherein the at least one substrate of SEQ ID NO: 5 comprises the amino acid sequence of SEQ ID NO: 31 and wherein the at least one substrate of SEQ ID NO: 6 comprises the amino acid sequence of SEQ ID NO: 32.

8. The method of claim 1 , wherein the presence, absence and/or quantity of enzymatic cleavage of the substrate by the at least one Sap in the sample is detected by using a bright field microscope and/or fluorescence microscopy.

9. The method of claim 1 , wherein the correlating step c) further comprises diagnosing the subject with the pathogenic fungal infection from the genus Candida , and the method further comprises a step of administering to the subject a therapeutically effective amount of treatment for the pathogenic fungal infection.

10. The method of claim 1 , further comprising calculating one or more normalized scores based upon the presence, absence and/or quantity of enzymatic cleavage of the substrate by the at least one Sap and correlating the one or more normalized scores to the probability or likelihood that the subject has the pathogenic fungal infection relative to an amount of Sap calculated from the control sample, such that if the one or more normalized scores are greater than the amount of Sap calculated from a planktonic control sample or equal to a positive biofilm control, the correlating step further comprises diagnosing the subject with the pathogenic fungal infection from the genus Candida.

11. A method of diagnosing a subject with a pathogenic fungal infection from the genus Candida , the method comprising:
a) exposing a sample from the subject to at least one substrate of at least one secreted aspartyl protease (Sap), wherein the at least one substrate comprises at least one enzymatic cleavage site recognizable by the at least one Sap, and wherein the at least one Sap comprises at least about 90% sequence homology to SEQ ID NO: 5 or SEQ ID NO: 6;
b) detecting the presence, absence and/or quantity of enzymatic cleavage of the substrate by the at least one Sap in the sample;
c) calculating one or more normalized scores corresponding to the amount of enzymatic cleavage of the substrate detected in step (b);
d) correlating the one or more normalized scores to a probability or likelihood that the subject has the pathogenic fungal infection relative to a measurement of an amount of Sap calculated from a control sample taken from a subject known to have or not to have the pathogenic fungal infection, such that if the one or more normalized scores are greater than the amount of Sap calculated from a planktonic control sample or equal to a positive biofilm control, the correlating step further comprises diagnosing the subject with the pathogenic fungal infection from the genus Candida ; and wherein the at least one substrate comprises a peptide of about 8 amino acids in length and at least about 85% sequence homology to SEQ ID NO: 22 or SEQ ID NO: 23.

12. The method of claim 11 , wherein the at least one substrate of the at least one Sap comprises the amino acid sequence of SEQ ID NO: 22 or SEQ ID NO: 23.

13. The method of claim 11 , wherein the at least one substrate of the at least one Sap is attached to a fluorogenic probe.

14. The method of claim 11 , wherein the at least one Sap comprises the amino acid sequence of SEQ ID NO: 5 or SEQ ID NO: 6.

15. The method of claim 11 , wherein the pathogenic infection comprises a planktonic or biofilm form of any of the species selected from the group consisting of Candida albicans, Candida dubliniensis, Candida tropicalis, Candida parapsilosis, Meyerozyma/Candida guilliermondii , and Candida glabrata.

16. The method of claim 11 , wherein the presence, absence and/or quantity of enzymatic cleavage of the substrate by the at least one Sap in the sample is detected by one or a combination of: fluorescence, optical imaging, field microscopy, fluorescence microscopy, quantum dots, chromatography, and/or mass spectrometry.

17. A method of diagnosing a subject with a pathogenic fungal infection from the genus Candida , comprising:
a) exposing a sample from the subject to at least one substrate of at least one secreted aspartyl protease (Sap), wherein the at least one substrate comprises at least one enzymatic cleavage site recognizable by the at least one Sap, and wherein the at least one Sap comprises at least about 90% sequence homology to SEQ ID NO: 5 or SEQ ID NO: 6;
b) detecting the presence, absence and/or quantity of enzymatic cleavage of the substrate by the at least one Sap in the sample; and
c) correlating the presence, absence and/or quantity of enzymatic cleavage of the substrate by the at least one Sap to a probability or likelihood that the subject has the pathogenic fungal infection relative to a measurement of a control sample taken from a subject known to have or not to have the pathogenic fungal infection, wherein the at least one substrate comprises a peptide of about 8 amino acids in length and comprises the amino acid sequence comprising about 85% sequence homology to SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 31, or SEQ ID NO: 32.

18. The method of claim 17 , wherein the at least one substrate of the at least one Sap is attached to a fluorogenic probe.

19. The method of claim 17 , wherein the at least one substrate comprises the amino acid sequence of SEQ I

Assignees

• Univ California

Inventors

• Nobile Clarissa
• Winter Michael
• Craik Charles
• Johnson Alexander
• O'Donoghue Anthony

Classifications

• G01N2333/8142

  Aspartate protease (E.C. 3.4.23) inhibitors, e.g. HIV protease inhibitors · CPC title

• G01N2333/40

  from Candida · CPC title

• C12N9/60

  from yeast · CPC title

• G01N2333/96

  from yeast · CPC title

• C07K14/40

  from Candida · CPC title