IP Library › Granted Patent US 12,234,513
Granted Patent B2
US 12,234,513 · App. 18/645,942 · Granted Feb 25, 2025

Methods for assessing risk of developing a viral disease using a genetic test

Inventors: Eli Hatchwell (Winchester, GB); Peggy S. Eis (Fitchburg, WI); Edward B. Smith, III (New York, NY); Yassine Taoufik (Paris, FR)
Assignees: PML Screening, LLC; The Université Paris-Saclay; The Assistance Publique—Hôpitaux de Paris (APHP); The Institut National de la Santé et de la Recherche Medicale (INSERM)
C12Q1/6883C12Q2600/106C12Q2600/156
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Quick Facts
Patent No.
US 12,234,513
App. No.
18/645,942
Granted
Feb 25, 2025
Kind
B2
Abstract

This document provides methods and materials related to treating a disease. For example, this document provides methods for treating a subject's disease based on identifying the risk of progressive multifocal leukoencephalopathy PML using a genetic test.

Claims (61)

1. A method of treating a condition in a subject in need of immunosuppressive therapy, comprising: administering a therapeutically effective amount of an immunosuppressive agent to the subject, wherein the immunosuppressive agent has a potential to induce progressive multifocal leukoencephalopathy (PML) due to a John Cunningham virus (JCV) infection, wherein:

(i) when the subject has been identified as not having one or more genetic variations that disrupt or modulate a C8B gene, a FCN2 gene, or a LY9 gene, the administering is based on the subject having been identified as not having the one or more genetic variations; and

(ii) when the subject has been identified as having one or more genetic variations that disrupt or modulate a C8B gene, a FCN2 gene, or a LY9 gene, the potential of the immunosuppressive agent to induce PML is known to be higher when administered to a subject having the one or more genetic variations compared to the potential of the immunosuppressive agent to induce PML when administered to a subject not having the one or more genetic variations; and

wherein the immunosuppressive agent comprises cladribine.

2. The method of claim 1 , wherein the subject has been identified as having the one or more genetic variations that disrupt or modulate a C8B gene, a FCN2 gene, or a LY9 gene.

3. The method of claim 2 , wherein the method comprises obtaining a baseline magnetic resonance image (MRI) of a subject prior to the administering.

4. The method of claim 2 , wherein the method comprises monitoring the subject for development PML due to an infection of the brain by JCV after the administering, wherein the monitoring comprises:

(i) obtaining a magnetic resonance image (MRI) of the subject after the administering;

(ii) comparing an MRI of the subject that was obtained after the administering to a baseline MRI of the subject that was obtained prior to the administering; or

(iii) an increased PML monitoring regimen of the subject compared to a PML monitoring regimen of a subject that has been identified as not having one or more genetic variations that disrupt or modulate a C8B gene, a FCN2 gene, or a LY9 gene.

5. The method of claim 1 , wherein the subject has been identified as not having the one or more genetic variations that disrupt or modulate a C8B gene, a FCN2 gene, or a LY9 gene.

6. The method of claim 5 , wherein the subject has been identified as not having one or more genetic variations that disrupt or modulate a STXBP2 gene.

7. The method of claim 5 , wherein the subject has been identified as not having a chr1:57409459 C>A genetic variation, the chromosome position defined with respect to UCSC hg19.

8. The method of claim 5 , wherein the subject has been identified as not having a chr9:137779251 G>A genetic variation, the chromosome position defined with respect to UCSC hg19.

9. The method of claim 5 , wherein the subject has been identified as not having a chr1:160769595 AG>A genetic variation, the chromosome position defined with respect to UCSC hg19.

10. The method of claim 6 , wherein the subject has been identified as not having a chr19:7712287 G>C genetic variation, the chromosome position defined with respect to UCSC hg19.

11. The method of claim 5 , wherein the subject has been identified as

(i) not having a genetic variation that disrupts or modulates a C8B gene,

(ii) not having a genetic variation that disrupts or modulates a FCN2 gene, and

(iii) not having a genetic variation that disrupts or modulates a LY9 gene.

12. The method of claim 6 , wherein the subject has been identified as

(i) not having a genetic variation that disrupts or modulates a C8B gene,

(ii) not having a genetic variation that disrupts or modulates a FCN2 gene,

(iii) not having a genetic variation that disrupts or modulates a LY9 gene, and

(iv) not having a genetic variation that disrupts or modulates an STXBP2 gene.

13. The method of claim 11 , wherein the subject has been identified as

(i) not having a chr1:57409459 C>A genetic variation,

(ii) not having a chr9:137779251 G>A genetic variation, and

(iii) not having a chr1:160769595 AG>A genetic variation,

wherein the chromosome positions are defined with respect to UCSC hg19.

14. The method of claim 12 , wherein the subject has been identified as

(i) not having a chr1:57409459 C>A genetic variation,

(ii) not having a chr9:137779251 G>A genetic variation,

(iii) not having a chr1:160769595 AG>A genetic variation, and

(iv) not having a chr19:7712287 G>C genetic variation,

wherein the chromosome positions are defined with respect to UCSC hg19.

15. The method of claim 1 , wherein the condition is multiple sclerosis or a relapsing form of multiple sclerosis.

16. The method of claim 10 , wherein the condition is multiple sclerosis or a relapsing form of multiple sclerosis.

17. The method of claim 5 , wherein the subject has been identified as not having one or more other genetic variations that disrupt or modulate a corresponding gene according to Tables 1, 3, 6-10, 28A, 29, 31, 34-36, 40, 47 and 48.

18. The method of claim 14 , wherein the subject has been further identified as not having one or more other genetic variations selected from the group consisting of: chr16:67694078 G>T, chr21:45708270 T>C, chr21:45713696 G>A, chr5:77334964 T>C, chr5:77437092 G>C, chr1:155317682 C>T, chr1:155449630 T>G, chr1:155450331 C>T, chr3:11402163 G>A, chr11:108123551 C>T, chr11:108138003 T>C, chr11:108143456 C>G, chr11:108186610 G>A, chr11:108186631 A>G, chr11:108198384 C>G, chr8:11407690 C>T, chr5:40959622 C>T, chr1:57373778 G>A, chr1:57378149 G>T, chr1:57383295 G>A, chr1:57422511 C>T, chr5:39311336 A>T, chr7:2959240 C>T, chr7:2962933 C>T, chr7:2983958 T>C, chr19:49843566 G>A, chr1:196918605 A>G, chr1:196871610 A>T, chr1:196973890 G>A, chr8:61769428 A>G, chr8:61777922 C>G, chr11:72145307 C>G, chr10:14977469 C>A, chr10:14977469 C>T, chr3:58191230 G>T, chr2:230579019 G>A, chr9:304628 G>A, chr9:312134 G>A, chr9:399233 A>G, chr9:446401 A>G, chr12:12673965 G>A, chr18:43456296 C>T, chr18:43496539 G>A, chr18:43529551 C>T, chr18:43531186 C>T, chr4:126237697 A>C, chr4:126238305 C>A, chr4:126239241 G>A, chr4:126239623 G>A, chr4:126240377 G>T, chr4:126240390 A>G, chr4:126240968 A>T, chr4:126241248 C>G, chr4:126328170 C>T, chr4:126336758 G>A, chr4:126336851 G>A, chr4:126372003 A>G, chr4:126372975 A>C, chr4:126373570 C>T, chr4:126389832 G>A, chr4:126408663 A>G, chr4:126411179 C>T, chr4:126411493 C>T, chr4:126412106 C>G, chr4:126412154 G>A, chr4:126412634 C>G, chr1:27699670 AG>A, chr3:128204761 C>T, chr3:128205808 C>T, chr1:92946625 G>C, chr2:163136505 C>G, chr2:163139085 A>T, chr22:23915583 T>C, chr22:23915745 G>A, chr8:42176189 G>A, chr12:44166753 A>G, chr12:44167821 A>T, chr12:49421042 C>T, chr12:49421811 C>A, chr12:49433083 G>A, chr12:49433533 G>C, chr12:49440564 C>T, chr19:48643270 C>T, chr13:108861092 G>T, chr1:235897907 C>T, chr22:35806756 G>A, chr6:30673359 T>G, chr6:30675830 T>A, chr1:12064892 G>A, chr3:37061893 T>C, chr2:15519924 C>T, chr1:183532364 T>A, chr4:103522068 A>G, chr4:103522150 G>A, chr4:103528328 C>T, chr11:119045378 C>T, chr16:50733536 T>C, chr16:50745021 C>T, chr16:50753867 G>T, chr6:3015818 G>A, chr6:51484077 G>C, chr6:51798908 C>T, chr19:44153248 T>C, chr16:81902826 C>T, chr16:81904539 C>T, chr16:81946278 A>G, chr16:81960772 C>A, chr3:171321023 C>T, chr3:171379953 C>T, chr3:171431726 C>G, chr3:171455697 G>C, chr3:171455739 A>G, chr10:72358167 G>A, chr3:53213691 G>C, chr3:53221390 T>C, chr8:48690299 A>G, chr8:48773526 T>C, chr8:48798507 T>C, chr8:48826575 C>G, chr6:31595795 C>T, chr6:31603045 A>G, chr12:56385915 GGGA>G, chr11:36595321 C>T, chr11:36596528 G>C, chr11:36596863 C>T, chr2:109382448 C>T, chr20:62309621 T>C, chr14:94847262 T>A, chr18:61570402 G>A, chr6:144508353 G>A, chr19:7705818 C>T, chr11:67818269 G>A, chr21:45815307 T>C, chr21:45844780 C>T, chr2:47273468 A>G, chr2:47277182 T>C, chr11:9608330 G>A, chr2:98351032 C>G, chr2:98351066 C>T, chr16:67694044 C>T, chr21:45708278 G>A, chr22:36661354 C>T, chr1:57333311 C>A, chr8:61732632 A>G, chr6:52101833 C>T, chr4:151520216 G>A, chr4:151793903 T>C, chr16:81939089 T>C, chr16:81942028 C>G, chr16:81942175 A>G, chr2:109384800 C>T, chr6:144508563 G>A, chr19:4817852 G>A, chr5:138856923 C>T, and chr2:98351081 C>T,

wherein the chromosome positions are defined with respect to UCSC hg19.

19. The method of claim 14 , wherein the subject has been further identified as not having any of the following other genetic variations: chr16:67694044 C>T, chr21:45708278 G>A, chr22>36661354 C>T, chr1:57333311 C>A, chr8:61732632 A>G, chr6:52101833 C>T, chr4:151520216 G>A, chr4:151793903 T>C, chr16:81939089 T>C, chr16:81942028 C>G, chr16:81942175 A>G, chr2>109384800 C>T, chr6:144508563 G>A, chr19:4817852 G>A, or chr5:138856923 C>T, wherein the chromosome positions are defined with respect to UCSC hg19.

20. The method of claim 1 , wherein the subject has been tested with a genetic assay for a presence of the one or more genetic variations.

21. The method of claim 1 , wherein the method further comprises testing the subject for the presence of the one or more genetic variations prior to the administering.

22. The method of claim 1 , wherein the subject has been identified as not having the one or more genetic variations based on results of a genetic assay.

23. A method comprising:

(a) monitoring a subject with a condition for development of progressive multifocal leukoencephalopathy (PML) due to an infection of the brain by John Cunningham virus (JCV), wherein the subject has been treated with an immunosuppressive agent that has a potential to induce PML due to a JCV infection; or

(b) obtaining a baseline magnetic resonance image (MRI) of a subject with a condition, wherein the subject is in need of an immunosuppressive agent that has a potential to induce PML due to a JCV infection;

wherein the subject has been identified as having one or more genetic variations that disrupt or modulate a C8B gene, a FCN2 gene, or a LY9 gene, and wherein the immunosuppressive agent comprises cladribine.

24. The method of claim 23 , wherein the subject has been treated with the immunosuppressive agent and the monitoring comprises:

(i) obtaining a magnetic resonance image (MRI) of a subject; or

(ii) an increased PML monitoring regimen of the subject compared to a PML monitoring regimen of a subject that has been identified as not having one or more genetic variations that disrupt or modulate a C8B gene, a FCN2 gene, or a LY9 gene.

25. The method of claim 24 , wherein the monitoring comprises obtaining a magnetic resonance image (MRI) of a subject and the method further comprises comparing the MRI to a baseline MRI of the subject that was obtained prior to the subject having been treated with the immunosuppressive agent.

26. The method of claim 23 , wherein the subject is in need of the immunosuppressive agent and wherein:

(i) the subject is known or scheduled to receive the immunosuppressive agent;

(ii) the method further comprises administering the immunosuppressive agent to the subject; and/or

(iii) the method further comprises obtaining an MRI of the subject after the subject has been treated with the immunosuppressive agent, and comparing the MRI to the baseline MRI.

27. A method comprising performing an assay on a polynucleic acid sample from a subject with a condition to determine whether one or more genetic variations are present, wherein the subject is in need of an immunosuppressive therapy comprising an immunosuppressive agent that has a potential to induce progressive multifocal leukoencephalopathy (PML) due to a John Cunningham virus (JCV) infection; wherein the one or more genetic variations disrupt or modulate a C8B gene, a FCN2 gene, or a LY9 gene; and wherein the immunosuppressive agent comprises cladribine.

28. The method of claim 27 , wherein the method further comprises administering the immunosuppressive agent to the subject.

29. The method of claim 27 , wherein the method further comprises identifying the subject as not having the one or more genetic variations based on results of the assay, or identifying the subject as having the one or more genetic variations based on results of the assay.

30. The method of claim 27 , wherein the method further comprises sending results of the assay to a doctor or healthcare provider.

Assignments (2)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Dec 5, 2024
From: TAOUFIK, YASSINE
To: UNIVERSITE PARIS-SACLAY; THE ASSISTANCE PUBLIQUE-HOPITAUX DE PARIS (APHP); THE INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE (INSERM)
Reel/Frame 069523/0631 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Nov 19, 2024
From: HATCHWELL, ELI; EIS, PEGGY S.; SMITH, EDWARD B., III
To: PML SCREENING, LLC
Reel/Frame 069314/0803 →
Continuity (6)
Division 17161171 · Jan 28, 2021
Division 16602348 · Aug 15, 2019
Continuation PCTUS2019045721 · Aug 8, 2019
Provisional Application 62716072 · Aug 8, 2018
Provisional Application 62716183 · Aug 8, 2018
Related Publication 20240287611A1 · Aug 29, 2024
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