US20230092981A1 - Methods of predicting susceptibility to infectious disease and related methods of treatment - Google Patents
Methods of predicting susceptibility to infectious disease and related methods of treatment Download PDFInfo
- Publication number
- US20230092981A1 US20230092981A1 US17/875,298 US202217875298A US2023092981A1 US 20230092981 A1 US20230092981 A1 US 20230092981A1 US 202217875298 A US202217875298 A US 202217875298A US 2023092981 A1 US2023092981 A1 US 2023092981A1
- Authority
- US
- United States
- Prior art keywords
- subject
- mutation
- cells
- infection
- chip
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Abandoned
Links
- 238000000034 method Methods 0.000 title claims abstract description 70
- 208000015181 infectious disease Diseases 0.000 title claims abstract description 61
- 238000011282 treatment Methods 0.000 title claims description 34
- 208000035473 Communicable disease Diseases 0.000 title description 5
- 230000035772 mutation Effects 0.000 claims abstract description 135
- 210000004369 blood Anatomy 0.000 claims description 77
- 239000008280 blood Substances 0.000 claims description 77
- 208000025721 COVID-19 Diseases 0.000 claims description 76
- 108010024491 DNA Methyltransferase 3A Proteins 0.000 claims description 55
- 210000004027 cell Anatomy 0.000 claims description 55
- 102100024812 DNA (cytosine-5)-methyltransferase 3A Human genes 0.000 claims description 54
- 101000653374 Homo sapiens Methylcytosine dioxygenase TET2 Proteins 0.000 claims description 48
- 102100030803 Methylcytosine dioxygenase TET2 Human genes 0.000 claims description 48
- 108090000623 proteins and genes Proteins 0.000 claims description 38
- 238000012163 sequencing technique Methods 0.000 claims description 35
- 102100033444 Tyrosine-protein kinase JAK2 Human genes 0.000 claims description 30
- 101000742054 Homo sapiens Protein phosphatase 1D Proteins 0.000 claims description 29
- 101000997832 Homo sapiens Tyrosine-protein kinase JAK2 Proteins 0.000 claims description 29
- 102100038675 Protein phosphatase 1D Human genes 0.000 claims description 28
- 108010078814 Tumor Suppressor Protein p53 Proteins 0.000 claims description 26
- 101000584612 Homo sapiens GTPase KRas Proteins 0.000 claims description 25
- 102100030708 GTPase KRas Human genes 0.000 claims description 24
- 102100031711 Splicing factor 3B subunit 1 Human genes 0.000 claims description 24
- 230000011132 hemopoiesis Effects 0.000 claims description 24
- 101000728236 Homo sapiens Polycomb group protein ASXL1 Proteins 0.000 claims description 23
- 101000587430 Homo sapiens Serine/arginine-rich splicing factor 2 Proteins 0.000 claims description 23
- 101000707567 Homo sapiens Splicing factor 3B subunit 1 Proteins 0.000 claims description 23
- 102100029799 Polycomb group protein ASXL1 Human genes 0.000 claims description 23
- 102100029666 Serine/arginine-rich splicing factor 2 Human genes 0.000 claims description 23
- 229960005486 vaccine Drugs 0.000 claims description 19
- 241001678559 COVID-19 virus Species 0.000 claims description 18
- 241000711573 Coronaviridae Species 0.000 claims description 10
- 208000001528 Coronaviridae Infections Diseases 0.000 claims description 9
- 241000315672 SARS coronavirus Species 0.000 claims description 9
- 206010069754 Acquired gene mutation Diseases 0.000 claims description 8
- 210000003958 hematopoietic stem cell Anatomy 0.000 claims description 8
- 230000037439 somatic mutation Effects 0.000 claims description 8
- 108700024394 Exon Proteins 0.000 claims description 7
- 241000127282 Middle East respiratory syndrome-related coronavirus Species 0.000 claims description 5
- 239000003795 chemical substances by application Substances 0.000 claims description 5
- 229940124977 antiviral medication Drugs 0.000 claims description 4
- 210000001082 somatic cell Anatomy 0.000 claims description 4
- 102000015098 Tumor Suppressor Protein p53 Human genes 0.000 claims 3
- 238000002054 transplantation Methods 0.000 claims 2
- 210000000601 blood cell Anatomy 0.000 abstract description 3
- 239000000523 sample Substances 0.000 description 45
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 31
- 201000010099 disease Diseases 0.000 description 30
- 102100025064 Cellular tumor antigen p53 Human genes 0.000 description 24
- 230000000392 somatic effect Effects 0.000 description 24
- 206010061218 Inflammation Diseases 0.000 description 19
- 102000004889 Interleukin-6 Human genes 0.000 description 19
- 108090001005 Interleukin-6 Proteins 0.000 description 19
- 230000002068 genetic effect Effects 0.000 description 19
- 230000004054 inflammatory process Effects 0.000 description 19
- 108020004707 nucleic acids Proteins 0.000 description 16
- 102000039446 nucleic acids Human genes 0.000 description 16
- 150000007523 nucleic acids Chemical class 0.000 description 16
- 102000004127 Cytokines Human genes 0.000 description 13
- 108090000695 Cytokines Proteins 0.000 description 13
- 210000004602 germ cell Anatomy 0.000 description 13
- 230000002757 inflammatory effect Effects 0.000 description 11
- 208000024172 Cardiovascular disease Diseases 0.000 description 10
- 108020004414 DNA Proteins 0.000 description 9
- 206010028980 Neoplasm Diseases 0.000 description 9
- 208000036142 Viral infection Diseases 0.000 description 9
- 210000000349 chromosome Anatomy 0.000 description 9
- 230000009385 viral infection Effects 0.000 description 9
- 102100040247 Tumor necrosis factor Human genes 0.000 description 8
- 238000004458 analytical method Methods 0.000 description 8
- 108010038501 Interleukin-6 Receptors Proteins 0.000 description 7
- 102000010781 Interleukin-6 Receptors Human genes 0.000 description 7
- 108060008682 Tumor Necrosis Factor Proteins 0.000 description 7
- 239000003814 drug Substances 0.000 description 7
- 230000003394 haemopoietic effect Effects 0.000 description 7
- 230000028993 immune response Effects 0.000 description 7
- 230000000770 proinflammatory effect Effects 0.000 description 7
- 230000011664 signaling Effects 0.000 description 7
- 108010074051 C-Reactive Protein Proteins 0.000 description 6
- 206010050685 Cytokine storm Diseases 0.000 description 6
- 102100026720 Interferon beta Human genes 0.000 description 6
- 102100037850 Interferon gamma Human genes 0.000 description 6
- 108010047761 Interferon-alpha Proteins 0.000 description 6
- 102000006992 Interferon-alpha Human genes 0.000 description 6
- 108090000467 Interferon-beta Proteins 0.000 description 6
- 108010074328 Interferon-gamma Proteins 0.000 description 6
- 102000003810 Interleukin-18 Human genes 0.000 description 6
- 108090000171 Interleukin-18 Proteins 0.000 description 6
- 208000008589 Obesity Diseases 0.000 description 6
- 239000000090 biomarker Substances 0.000 description 6
- 201000011510 cancer Diseases 0.000 description 6
- 206010052015 cytokine release syndrome Diseases 0.000 description 6
- 206010012601 diabetes mellitus Diseases 0.000 description 6
- 229940079593 drug Drugs 0.000 description 6
- 208000010125 myocardial infarction Diseases 0.000 description 6
- 235000020824 obesity Nutrition 0.000 description 6
- 210000000130 stem cell Anatomy 0.000 description 6
- 102100035765 Angiotensin-converting enzyme 2 Human genes 0.000 description 5
- 108090000975 Angiotensin-converting enzyme 2 Proteins 0.000 description 5
- 102100032752 C-reactive protein Human genes 0.000 description 5
- 101001002634 Homo sapiens Interleukin-1 alpha Proteins 0.000 description 5
- 101000599048 Homo sapiens Interleukin-6 receptor subunit alpha Proteins 0.000 description 5
- 101001055222 Homo sapiens Interleukin-8 Proteins 0.000 description 5
- 102100020881 Interleukin-1 alpha Human genes 0.000 description 5
- 108090001007 Interleukin-8 Proteins 0.000 description 5
- 102000004890 Interleukin-8 Human genes 0.000 description 5
- 102100026236 Interleukin-8 Human genes 0.000 description 5
- 241000725643 Respiratory syncytial virus Species 0.000 description 5
- 230000006378 damage Effects 0.000 description 5
- 230000034994 death Effects 0.000 description 5
- 231100000517 death Toxicity 0.000 description 5
- 230000007614 genetic variation Effects 0.000 description 5
- 230000028709 inflammatory response Effects 0.000 description 5
- 238000012544 monitoring process Methods 0.000 description 5
- 230000004044 response Effects 0.000 description 5
- 238000012360 testing method Methods 0.000 description 5
- MZOFCQQQCNRIBI-VMXHOPILSA-N (3s)-4-[[(2s)-1-[[(2s)-1-[[(1s)-1-carboxy-2-hydroxyethyl]amino]-4-methyl-1-oxopentan-2-yl]amino]-5-(diaminomethylideneamino)-1-oxopentan-2-yl]amino]-3-[[2-[[(2s)-2,6-diaminohexanoyl]amino]acetyl]amino]-4-oxobutanoic acid Chemical compound OC[C@@H](C(O)=O)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCN=C(N)N)NC(=O)[C@H](CC(O)=O)NC(=O)CNC(=O)[C@@H](N)CCCCN MZOFCQQQCNRIBI-VMXHOPILSA-N 0.000 description 4
- 206010001052 Acute respiratory distress syndrome Diseases 0.000 description 4
- 206010061765 Chromosomal mutation Diseases 0.000 description 4
- 208000006545 Chronic Obstructive Pulmonary Disease Diseases 0.000 description 4
- 108091092584 GDNA Proteins 0.000 description 4
- 206010019280 Heart failures Diseases 0.000 description 4
- 101001033249 Homo sapiens Interleukin-1 beta Proteins 0.000 description 4
- 102000014150 Interferons Human genes 0.000 description 4
- 108010050904 Interferons Proteins 0.000 description 4
- 102100039065 Interleukin-1 beta Human genes 0.000 description 4
- 108090000174 Interleukin-10 Proteins 0.000 description 4
- 102000003814 Interleukin-10 Human genes 0.000 description 4
- 102100030698 Interleukin-12 subunit alpha Human genes 0.000 description 4
- 102100036701 Interleukin-12 subunit beta Human genes 0.000 description 4
- 102100037792 Interleukin-6 receptor subunit alpha Human genes 0.000 description 4
- 208000019693 Lung disease Diseases 0.000 description 4
- 241000700605 Viruses Species 0.000 description 4
- 230000001154 acute effect Effects 0.000 description 4
- 208000006673 asthma Diseases 0.000 description 4
- 238000002659 cell therapy Methods 0.000 description 4
- 208000026106 cerebrovascular disease Diseases 0.000 description 4
- 230000007812 deficiency Effects 0.000 description 4
- 238000011161 development Methods 0.000 description 4
- 230000018109 developmental process Effects 0.000 description 4
- 230000002526 effect on cardiovascular system Effects 0.000 description 4
- 208000037797 influenza A Diseases 0.000 description 4
- 230000001404 mediated effect Effects 0.000 description 4
- 238000002483 medication Methods 0.000 description 4
- 210000002901 mesenchymal stem cell Anatomy 0.000 description 4
- 238000002493 microarray Methods 0.000 description 4
- 239000003607 modifier Substances 0.000 description 4
- 230000008569 process Effects 0.000 description 4
- 230000002829 reductive effect Effects 0.000 description 4
- 230000004083 survival effect Effects 0.000 description 4
- 238000002560 therapeutic procedure Methods 0.000 description 4
- 108700028369 Alleles Proteins 0.000 description 3
- 208000023275 Autoimmune disease Diseases 0.000 description 3
- 101000999356 Bos taurus Interferon alpha-F Proteins 0.000 description 3
- 101000999355 Bos taurus Interferon alpha-G Proteins 0.000 description 3
- 101000999354 Bos taurus Interferon alpha-H Proteins 0.000 description 3
- 206010061818 Disease progression Diseases 0.000 description 3
- 101001034846 Homo sapiens Interferon-induced transmembrane protein 3 Proteins 0.000 description 3
- 101001010600 Homo sapiens Interleukin-12 subunit alpha Proteins 0.000 description 3
- 101000852992 Homo sapiens Interleukin-12 subunit beta Proteins 0.000 description 3
- 101000611183 Homo sapiens Tumor necrosis factor Proteins 0.000 description 3
- 206010020772 Hypertension Diseases 0.000 description 3
- 101710147309 Interferon epsilon Proteins 0.000 description 3
- 102100026688 Interferon epsilon Human genes 0.000 description 3
- 102100022469 Interferon kappa Human genes 0.000 description 3
- 102100040035 Interferon-induced transmembrane protein 3 Human genes 0.000 description 3
- 102000015696 Interleukins Human genes 0.000 description 3
- 108010063738 Interleukins Proteins 0.000 description 3
- 208000029523 Interstitial Lung disease Diseases 0.000 description 3
- 102100026238 Lymphotoxin-alpha Human genes 0.000 description 3
- 102100026894 Lymphotoxin-beta Human genes 0.000 description 3
- 241000124008 Mammalia Species 0.000 description 3
- 208000013616 Respiratory Distress Syndrome Diseases 0.000 description 3
- 206010038687 Respiratory distress Diseases 0.000 description 3
- 238000009098 adjuvant therapy Methods 0.000 description 3
- 201000000028 adult respiratory distress syndrome Diseases 0.000 description 3
- 230000003110 anti-inflammatory effect Effects 0.000 description 3
- 230000005540 biological transmission Effects 0.000 description 3
- 230000007211 cardiovascular event Effects 0.000 description 3
- 239000000969 carrier Substances 0.000 description 3
- 230000001413 cellular effect Effects 0.000 description 3
- 208000020832 chronic kidney disease Diseases 0.000 description 3
- 238000001514 detection method Methods 0.000 description 3
- 230000005750 disease progression Effects 0.000 description 3
- 230000037433 frameshift Effects 0.000 description 3
- 208000019622 heart disease Diseases 0.000 description 3
- 210000002865 immune cell Anatomy 0.000 description 3
- 206010022000 influenza Diseases 0.000 description 3
- 208000037798 influenza B Diseases 0.000 description 3
- 108010080375 interferon kappa Proteins 0.000 description 3
- 229940047124 interferons Drugs 0.000 description 3
- 210000000265 leukocyte Anatomy 0.000 description 3
- 208000019423 liver disease Diseases 0.000 description 3
- 210000004072 lung Anatomy 0.000 description 3
- OHDXDNUPVVYWOV-UHFFFAOYSA-N n-methyl-1-(2-naphthalen-1-ylsulfanylphenyl)methanamine Chemical compound CNCC1=CC=CC=C1SC1=CC=CC2=CC=CC=C12 OHDXDNUPVVYWOV-UHFFFAOYSA-N 0.000 description 3
- 210000003819 peripheral blood mononuclear cell Anatomy 0.000 description 3
- 230000035935 pregnancy Effects 0.000 description 3
- 208000024891 symptom Diseases 0.000 description 3
- 230000003612 virological effect Effects 0.000 description 3
- 238000007482 whole exome sequencing Methods 0.000 description 3
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 2
- UUUHXMGGBIUAPW-UHFFFAOYSA-N 1-[1-[2-[[5-amino-2-[[1-[5-(diaminomethylideneamino)-2-[[1-[3-(1h-indol-3-yl)-2-[(5-oxopyrrolidine-2-carbonyl)amino]propanoyl]pyrrolidine-2-carbonyl]amino]pentanoyl]pyrrolidine-2-carbonyl]amino]-5-oxopentanoyl]amino]-3-methylpentanoyl]pyrrolidine-2-carbon Chemical compound C1CCC(C(=O)N2C(CCC2)C(O)=O)N1C(=O)C(C(C)CC)NC(=O)C(CCC(N)=O)NC(=O)C1CCCN1C(=O)C(CCCN=C(N)N)NC(=O)C1CCCN1C(=O)C(CC=1C2=CC=CC=C2NC=1)NC(=O)C1CCC(=O)N1 UUUHXMGGBIUAPW-UHFFFAOYSA-N 0.000 description 2
- 102100030988 Angiotensin-converting enzyme Human genes 0.000 description 2
- 206010002653 Anosmia Diseases 0.000 description 2
- 208000031229 Cardiomyopathies Diseases 0.000 description 2
- 206010011086 Coronary artery occlusion Diseases 0.000 description 2
- 206010011224 Cough Diseases 0.000 description 2
- 201000003883 Cystic fibrosis Diseases 0.000 description 2
- 230000005778 DNA damage Effects 0.000 description 2
- 231100000277 DNA damage Toxicity 0.000 description 2
- 201000010374 Down Syndrome Diseases 0.000 description 2
- 206010014561 Emphysema Diseases 0.000 description 2
- 208000002250 Hematologic Neoplasms Diseases 0.000 description 2
- 101000764535 Homo sapiens Lymphotoxin-alpha Proteins 0.000 description 2
- 101000764294 Homo sapiens Lymphotoxin-beta Proteins 0.000 description 2
- 241000725303 Human immunodeficiency virus Species 0.000 description 2
- -1 IFN-λ) Proteins 0.000 description 2
- 108010065805 Interleukin-12 Proteins 0.000 description 2
- 102000013462 Interleukin-12 Human genes 0.000 description 2
- 101001089108 Lotus tetragonolobus Anti-H(O) lectin Proteins 0.000 description 2
- 102000004083 Lymphotoxin-alpha Human genes 0.000 description 2
- 108090000542 Lymphotoxin-alpha Proteins 0.000 description 2
- 208000009525 Myocarditis Diseases 0.000 description 2
- 108091028043 Nucleic acid sequence Proteins 0.000 description 2
- 108090000882 Peptidyl-Dipeptidase A Proteins 0.000 description 2
- 102000029797 Prion Human genes 0.000 description 2
- 108091000054 Prion Proteins 0.000 description 2
- 229940096437 Protein S Drugs 0.000 description 2
- 206010037660 Pyrexia Diseases 0.000 description 2
- 240000004808 Saccharomyces cerevisiae Species 0.000 description 2
- 101710198474 Spike protein Proteins 0.000 description 2
- 208000006011 Stroke Diseases 0.000 description 2
- 230000001594 aberrant effect Effects 0.000 description 2
- 230000002411 adverse Effects 0.000 description 2
- 239000002333 angiotensin II receptor antagonist Substances 0.000 description 2
- 229940125364 angiotensin receptor blocker Drugs 0.000 description 2
- 239000003242 anti bacterial agent Substances 0.000 description 2
- 229940088710 antibiotic agent Drugs 0.000 description 2
- 239000003443 antiviral agent Substances 0.000 description 2
- QVGXLLKOCUKJST-UHFFFAOYSA-N atomic oxygen Chemical compound [O] QVGXLLKOCUKJST-UHFFFAOYSA-N 0.000 description 2
- 230000001580 bacterial effect Effects 0.000 description 2
- 230000008901 benefit Effects 0.000 description 2
- 210000001185 bone marrow Anatomy 0.000 description 2
- 230000000747 cardiac effect Effects 0.000 description 2
- 201000011529 cardiovascular cancer Diseases 0.000 description 2
- 230000008859 change Effects 0.000 description 2
- 230000001684 chronic effect Effects 0.000 description 2
- 208000029078 coronary artery disease Diseases 0.000 description 2
- 230000000875 corresponding effect Effects 0.000 description 2
- 239000003246 corticosteroid Substances 0.000 description 2
- 229960001334 corticosteroids Drugs 0.000 description 2
- 238000012217 deletion Methods 0.000 description 2
- 230000037430 deletion Effects 0.000 description 2
- 230000001627 detrimental effect Effects 0.000 description 2
- 230000004064 dysfunction Effects 0.000 description 2
- 230000002538 fungal effect Effects 0.000 description 2
- 230000003862 health status Effects 0.000 description 2
- 210000000987 immune system Anatomy 0.000 description 2
- 230000004968 inflammatory condition Effects 0.000 description 2
- 238000001802 infusion Methods 0.000 description 2
- 239000003112 inhibitor Substances 0.000 description 2
- 229940079322 interferon Drugs 0.000 description 2
- 230000010468 interferon response Effects 0.000 description 2
- 229940100601 interleukin-6 Drugs 0.000 description 2
- 229940047122 interleukins Drugs 0.000 description 2
- 238000002955 isolation Methods 0.000 description 2
- 230000000670 limiting effect Effects 0.000 description 2
- 150000002632 lipids Chemical class 0.000 description 2
- 238000005259 measurement Methods 0.000 description 2
- 239000000203 mixture Substances 0.000 description 2
- 230000000926 neurological effect Effects 0.000 description 2
- 210000000056 organ Anatomy 0.000 description 2
- 239000001301 oxygen Substances 0.000 description 2
- 229910052760 oxygen Inorganic materials 0.000 description 2
- 230000003071 parasitic effect Effects 0.000 description 2
- 210000005259 peripheral blood Anatomy 0.000 description 2
- 239000011886 peripheral blood Substances 0.000 description 2
- 230000000144 pharmacologic effect Effects 0.000 description 2
- 238000002616 plasmapheresis Methods 0.000 description 2
- 102000004169 proteins and genes Human genes 0.000 description 2
- 208000002815 pulmonary hypertension Diseases 0.000 description 2
- 238000011160 research Methods 0.000 description 2
- 102200010335 rs2228145 Human genes 0.000 description 2
- 102200087780 rs77375493 Human genes 0.000 description 2
- 238000012216 screening Methods 0.000 description 2
- 210000002966 serum Anatomy 0.000 description 2
- 208000007056 sickle cell anemia Diseases 0.000 description 2
- 230000000391 smoking effect Effects 0.000 description 2
- 239000007787 solid Substances 0.000 description 2
- 208000011117 substance-related disease Diseases 0.000 description 2
- 230000009885 systemic effect Effects 0.000 description 2
- 210000001519 tissue Anatomy 0.000 description 2
- 230000007704 transition Effects 0.000 description 2
- 102000003390 tumor necrosis factor Human genes 0.000 description 2
- 239000013598 vector Substances 0.000 description 2
- GUAHPAJOXVYFON-ZETCQYMHSA-N (8S)-8-amino-7-oxononanoic acid zwitterion Chemical compound C[C@H](N)C(=O)CCCCCC(O)=O GUAHPAJOXVYFON-ZETCQYMHSA-N 0.000 description 1
- 102000040650 (ribonucleotides)n+m Human genes 0.000 description 1
- 108700022172 2019-nCoV Vaccine mRNA-1273 Proteins 0.000 description 1
- 208000010470 Ageusia Diseases 0.000 description 1
- 108091093088 Amplicon Proteins 0.000 description 1
- 208000003017 Aortic Valve Stenosis Diseases 0.000 description 1
- 102100026189 Beta-galactosidase Human genes 0.000 description 1
- 241000283690 Bos taurus Species 0.000 description 1
- 208000020446 Cardiac disease Diseases 0.000 description 1
- 102000019034 Chemokines Human genes 0.000 description 1
- 108010012236 Chemokines Proteins 0.000 description 1
- 108020004705 Codon Proteins 0.000 description 1
- 238000000018 DNA microarray Methods 0.000 description 1
- 206010012289 Dementia Diseases 0.000 description 1
- 101000785401 Drosophila melanogaster Polycomb protein Asx Proteins 0.000 description 1
- 102000004190 Enzymes Human genes 0.000 description 1
- 108090000790 Enzymes Proteins 0.000 description 1
- 241000283073 Equus caballus Species 0.000 description 1
- 206010053172 Fatal outcomes Diseases 0.000 description 1
- 241000282326 Felis catus Species 0.000 description 1
- 208000031886 HIV Infections Diseases 0.000 description 1
- 208000037357 HIV infectious disease Diseases 0.000 description 1
- 208000010496 Heart Arrest Diseases 0.000 description 1
- 208000013875 Heart injury Diseases 0.000 description 1
- 102100031573 Hematopoietic progenitor cell antigen CD34 Human genes 0.000 description 1
- 101000721661 Homo sapiens Cellular tumor antigen p53 Proteins 0.000 description 1
- 101000777663 Homo sapiens Hematopoietic progenitor cell antigen CD34 Proteins 0.000 description 1
- 241000205701 Human adenovirus 26 Species 0.000 description 1
- 206010061598 Immunodeficiency Diseases 0.000 description 1
- 108010034143 Inflammasomes Proteins 0.000 description 1
- 102000000589 Interleukin-1 Human genes 0.000 description 1
- 108010002352 Interleukin-1 Proteins 0.000 description 1
- 101710194995 Interleukin-12 subunit alpha Proteins 0.000 description 1
- 101710187487 Interleukin-12 subunit beta Proteins 0.000 description 1
- 108010002350 Interleukin-2 Proteins 0.000 description 1
- 102000000588 Interleukin-2 Human genes 0.000 description 1
- 108010002586 Interleukin-7 Proteins 0.000 description 1
- 102000000704 Interleukin-7 Human genes 0.000 description 1
- 229940024452 Janssen COVID-19 vaccine Drugs 0.000 description 1
- 108010019437 Janus Kinase 2 Proteins 0.000 description 1
- 206010072206 Janus kinase 2 mutation Diseases 0.000 description 1
- ONIBWKKTOPOVIA-BYPYZUCNSA-N L-Proline Chemical compound OC(=O)[C@@H]1CCCN1 ONIBWKKTOPOVIA-BYPYZUCNSA-N 0.000 description 1
- 108010059881 Lactase Proteins 0.000 description 1
- 206010064912 Malignant transformation Diseases 0.000 description 1
- 108010090054 Membrane Glycoproteins Proteins 0.000 description 1
- 102000012750 Membrane Glycoproteins Human genes 0.000 description 1
- 229940026207 Moderna COVID-19 vaccine Drugs 0.000 description 1
- 241000699666 Mus <mouse, genus> Species 0.000 description 1
- 206010049565 Muscle fatigue Diseases 0.000 description 1
- 108020004485 Nonsense Codon Proteins 0.000 description 1
- 206010053159 Organ failure Diseases 0.000 description 1
- 229940025109 Oxford–AstraZeneca COVID-19 vaccine Drugs 0.000 description 1
- 241000282577 Pan troglodytes Species 0.000 description 1
- 206010033661 Pancytopenia Diseases 0.000 description 1
- 241000009328 Perro Species 0.000 description 1
- 229940026233 Pfizer-BioNTech COVID-19 vaccine Drugs 0.000 description 1
- 241000288906 Primates Species 0.000 description 1
- ONIBWKKTOPOVIA-UHFFFAOYSA-N Proline Natural products OC(=O)C1CCCN1 ONIBWKKTOPOVIA-UHFFFAOYSA-N 0.000 description 1
- 208000010378 Pulmonary Embolism Diseases 0.000 description 1
- 238000011529 RT qPCR Methods 0.000 description 1
- 241000700159 Rattus Species 0.000 description 1
- 208000004756 Respiratory Insufficiency Diseases 0.000 description 1
- 208000037847 SARS-CoV-2-infection Diseases 0.000 description 1
- 101000629318 Severe acute respiratory syndrome coronavirus 2 Spike glycoprotein Proteins 0.000 description 1
- 101710190353 Splicing factor 3B subunit 1 Proteins 0.000 description 1
- 210000001744 T-lymphocyte Anatomy 0.000 description 1
- 206010043395 Thalassaemia sickle cell Diseases 0.000 description 1
- 208000002903 Thalassemia Diseases 0.000 description 1
- 208000007536 Thrombosis Diseases 0.000 description 1
- 206010047249 Venous thrombosis Diseases 0.000 description 1
- 230000005856 abnormality Effects 0.000 description 1
- 230000004913 activation Effects 0.000 description 1
- 230000032683 aging Effects 0.000 description 1
- 150000001413 amino acids Chemical class 0.000 description 1
- 239000003416 antiarrhythmic agent Substances 0.000 description 1
- 239000000427 antigen Substances 0.000 description 1
- 108091007433 antigens Proteins 0.000 description 1
- 102000036639 antigens Human genes 0.000 description 1
- 206010002906 aortic stenosis Diseases 0.000 description 1
- 238000003556 assay Methods 0.000 description 1
- 229940052143 bamlanivimab Drugs 0.000 description 1
- 108010005774 beta-Galactosidase Proteins 0.000 description 1
- 230000033228 biological regulation Effects 0.000 description 1
- 238000004159 blood analysis Methods 0.000 description 1
- 230000036772 blood pressure Effects 0.000 description 1
- 208000027499 body ache Diseases 0.000 description 1
- 230000003293 cardioprotective effect Effects 0.000 description 1
- 229940051183 casirivimab Drugs 0.000 description 1
- 230000030833 cell death Effects 0.000 description 1
- 210000003169 central nervous system Anatomy 0.000 description 1
- 238000002512 chemotherapy Methods 0.000 description 1
- 208000037998 chronic venous disease Diseases 0.000 description 1
- 230000015271 coagulation Effects 0.000 description 1
- 238000005345 coagulation Methods 0.000 description 1
- 238000010835 comparative analysis Methods 0.000 description 1
- 150000001875 compounds Chemical class 0.000 description 1
- 238000002591 computed tomography Methods 0.000 description 1
- 230000001276 controlling effect Effects 0.000 description 1
- 230000002596 correlated effect Effects 0.000 description 1
- 208000024389 cytopenia Diseases 0.000 description 1
- 230000003247 decreasing effect Effects 0.000 description 1
- 230000007123 defense Effects 0.000 description 1
- 230000002950 deficient Effects 0.000 description 1
- 230000001419 dependent effect Effects 0.000 description 1
- 238000009795 derivation Methods 0.000 description 1
- 229960003957 dexamethasone Drugs 0.000 description 1
- UREBDLICKHMUKA-CXSFZGCWSA-N dexamethasone Chemical compound C1CC2=CC(=O)C=C[C@]2(C)[C@]2(F)[C@@H]1[C@@H]1C[C@@H](C)[C@@](C(=O)CO)(O)[C@@]1(C)C[C@@H]2O UREBDLICKHMUKA-CXSFZGCWSA-N 0.000 description 1
- 238000003745 diagnosis Methods 0.000 description 1
- 238000009792 diffusion process Methods 0.000 description 1
- 208000035475 disorder Diseases 0.000 description 1
- 238000002651 drug therapy Methods 0.000 description 1
- 238000013399 early diagnosis Methods 0.000 description 1
- 230000001516 effect on protein Effects 0.000 description 1
- 230000000694 effects Effects 0.000 description 1
- 206010014599 encephalitis Diseases 0.000 description 1
- 230000003511 endothelial effect Effects 0.000 description 1
- 229940088598 enzyme Drugs 0.000 description 1
- 230000006718 epigenetic regulation Effects 0.000 description 1
- 210000003743 erythrocyte Anatomy 0.000 description 1
- 229940051243 etesevimab Drugs 0.000 description 1
- 238000011156 evaluation Methods 0.000 description 1
- 230000007717 exclusion Effects 0.000 description 1
- 238000000605 extraction Methods 0.000 description 1
- 230000020764 fibrinolysis Effects 0.000 description 1
- 239000012530 fluid Substances 0.000 description 1
- 239000007789 gas Substances 0.000 description 1
- 201000005787 hematologic cancer Diseases 0.000 description 1
- 208000024200 hematopoietic and lymphoid system neoplasm Diseases 0.000 description 1
- 230000002439 hemostatic effect Effects 0.000 description 1
- 230000005745 host immune response Effects 0.000 description 1
- 208000033519 human immunodeficiency virus infectious disease Diseases 0.000 description 1
- 238000003384 imaging method Methods 0.000 description 1
- 229940051184 imdevimab Drugs 0.000 description 1
- 230000005934 immune activation Effects 0.000 description 1
- 230000036737 immune function Effects 0.000 description 1
- 230000000899 immune system response Effects 0.000 description 1
- 230000036039 immunity Effects 0.000 description 1
- 230000007365 immunoregulation Effects 0.000 description 1
- 230000001506 immunosuppresive effect Effects 0.000 description 1
- 208000033065 inborn errors of immunity Diseases 0.000 description 1
- 230000002458 infectious effect Effects 0.000 description 1
- 230000003993 interaction Effects 0.000 description 1
- 210000003734 kidney Anatomy 0.000 description 1
- 208000017169 kidney disease Diseases 0.000 description 1
- 238000003771 laboratory diagnosis Methods 0.000 description 1
- 229940116108 lactase Drugs 0.000 description 1
- 231100000516 lung damage Toxicity 0.000 description 1
- 210000004698 lymphocyte Anatomy 0.000 description 1
- 108700021021 mRNA Vaccine Proteins 0.000 description 1
- 229940126582 mRNA vaccine Drugs 0.000 description 1
- 229940038694 mRNA-based vaccine Drugs 0.000 description 1
- 210000002540 macrophage Anatomy 0.000 description 1
- 230000036212 malign transformation Effects 0.000 description 1
- 230000007246 mechanism Effects 0.000 description 1
- 208000030159 metabolic disease Diseases 0.000 description 1
- 238000010208 microarray analysis Methods 0.000 description 1
- 230000000116 mitigating effect Effects 0.000 description 1
- 210000001616 monocyte Anatomy 0.000 description 1
- 229940031346 monovalent vaccine Drugs 0.000 description 1
- 230000008383 multiple organ dysfunction Effects 0.000 description 1
- 210000000440 neutrophil Anatomy 0.000 description 1
- 239000002547 new drug Substances 0.000 description 1
- 230000037434 nonsense mutation Effects 0.000 description 1
- 239000002773 nucleotide Substances 0.000 description 1
- 125000003729 nucleotide group Chemical group 0.000 description 1
- 238000012261 overproduction Methods 0.000 description 1
- 230000008506 pathogenesis Effects 0.000 description 1
- 239000013610 patient sample Substances 0.000 description 1
- 230000007505 plaque formation Effects 0.000 description 1
- 239000013641 positive control Substances 0.000 description 1
- 230000000069 prophylactic effect Effects 0.000 description 1
- 238000011321 prophylaxis Methods 0.000 description 1
- 230000001681 protective effect Effects 0.000 description 1
- 208000005069 pulmonary fibrosis Diseases 0.000 description 1
- 102000005962 receptors Human genes 0.000 description 1
- 108020003175 receptors Proteins 0.000 description 1
- 230000009467 reduction Effects 0.000 description 1
- 239000012925 reference material Substances 0.000 description 1
- 208000037922 refractory disease Diseases 0.000 description 1
- RWWYLEGWBNMMLJ-MEUHYHILSA-N remdesivir Drugs C([C@@H]1[C@H]([C@@H](O)[C@@](C#N)(O1)C=1N2N=CN=C(N)C2=CC=1)O)OP(=O)(N[C@@H](C)C(=O)OCC(CC)CC)OC1=CC=CC=C1 RWWYLEGWBNMMLJ-MEUHYHILSA-N 0.000 description 1
- RWWYLEGWBNMMLJ-YSOARWBDSA-N remdesivir Chemical compound NC1=NC=NN2C1=CC=C2[C@]1([C@@H]([C@@H]([C@H](O1)CO[P@](=O)(OC1=CC=CC=C1)N[C@H](C(=O)OCC(CC)CC)C)O)O)C#N RWWYLEGWBNMMLJ-YSOARWBDSA-N 0.000 description 1
- 230000008439 repair process Effects 0.000 description 1
- 230000010076 replication Effects 0.000 description 1
- 230000000241 respiratory effect Effects 0.000 description 1
- 201000004193 respiratory failure Diseases 0.000 description 1
- 208000023504 respiratory system disease Diseases 0.000 description 1
- 238000012502 risk assessment Methods 0.000 description 1
- 229920002477 rna polymer Polymers 0.000 description 1
- 230000028327 secretion Effects 0.000 description 1
- 238000004062 sedimentation Methods 0.000 description 1
- 238000011451 sequencing strategy Methods 0.000 description 1
- 238000011476 stem cell transplantation Methods 0.000 description 1
- 230000035882 stress Effects 0.000 description 1
- 208000023516 stroke disease Diseases 0.000 description 1
- 230000000153 supplemental effect Effects 0.000 description 1
- 239000004094 surface-active agent Substances 0.000 description 1
- 208000011580 syndromic disease Diseases 0.000 description 1
- 230000008685 targeting Effects 0.000 description 1
- 230000001225 therapeutic effect Effects 0.000 description 1
- 229940113082 thymine Drugs 0.000 description 1
- 229960003989 tocilizumab Drugs 0.000 description 1
- 238000002627 tracheal intubation Methods 0.000 description 1
- 230000002103 transcriptional effect Effects 0.000 description 1
- 238000009423 ventilation Methods 0.000 description 1
- 229940023147 viral vector vaccine Drugs 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/12—Viral antigens
- A61K39/215—Coronaviridae, e.g. avian infectious bronchitis virus
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Definitions
- One of the reasons for its rapid and widespread diffusion is the presence of a large number of asymptomatic or paucisymptomatic patients, who are not recognized as infected and therefore contribute to the spread of the virus.
- Data on the spread of the virus have led scientists to think that the actual number of infected people is much higher than the number of positive tests. For example, in Italy a ratio of 1 positive patient tested for every 10 infected people is considered reasonable, leading to more than 1 million infected people (corresponding to more than 1.7% of the Italian population) in total.
- the present inventions generally concern methods of identifying subjects at risk of developing a severe COVID-19 infection and/or severe complications from COVID-19 infection.
- methods of identifying a subject at risk of developing a severe complication from Coronavirus disease 2019 (COVID-19) infection such methods generally comprising a step of determining whether the subject has clonal hematopoiesis of indeterminate potential (CHIP).
- CHIP indeterminate potential
- the step of determining whether the subject has CHIP comprises sequencing at least part of the genome of one or more cells in a blood sample of the subject to identify a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1, wherein the presence of said mutation indicates that the subject has CHIP and is at risk of developing a severe COVID-19 infection and/or a severe complication from COVID-19 infection.
- the methods disclosed herein further comprise a step of treating a subject identified as having CHIP, or that is otherwise at risk of developing a severe COVID-19 infection or a severe complication from COVID-19 infection.
- treating the subject comprises administering to the subject one or more agents or vaccines to reduce the subject's likelihood of contracting COVD-19 infection.
- methods of treating a subject at risk of developing a severe COVID-19 infection such methods generally comprising a step of determining whether the subject has clonal hematopoiesis of indeterminate potential (CHIP).
- CHIP indeterminate potential
- the step of determining whether the subject has CHIP comprises sequencing at least part of the genome of one or more cells in a blood sample of the subject to identify a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1; wherein the presence of said mutation indicates that the subject has CHIP and is at risk of developing a severe COVID-19 infection; and treating the subject having CHIP to reduce the subject's risk of contracting a severe COVID-19 infection.
- treating the subject comprises administering to the subject one or more agents or vaccines to reduce the subject's likelihood of contracting COVD-19 infection.
- the subject is at risk of requiring hospitalization. In certain embodiments, the subject is under the age of about 30, 40, 50, 60, 70, 80, 90, 100 years old or older. In certain embodiments, the subject has a severe autoimmune disease.
- the subject has a comorbid condition (e.g., a comorbid condition selected from the group consisting of cancer, cerebrovascular disease, chronic kidney disease, chronic obstructive pulmonary disease (COPD), diabetes mellitus, heart conditions, obesity, pregnancy, history of smoking, Down syndrome, human immunodeficiency virus (HIV), neurologic conditions, interstitial lung disease, pulmonary fibrosis, pulmonary hypertension, Sickle cell disease, solid organ or blood stem cell transplantation, substance use disorders, use of corticosteroids or other immunosuppressive medications, cystic fibrosis, thalassemia, asthma, hypertension, immune deficiencies, and liver disease).
- the comorbid condition is selected from the group consisting of cancer, cerebrovascular disease, chronic kidney disease, chronic obstructive pulmonary disease (COPD), diabetes mellitus, heart conditions, obesity, pregnancy, and history of smoking.
- the mutation is a somatic mutation.
- the mutation is a somatic mutation in DNMT3A and/or TET2.
- the methods may comprise sequencing at least part of the genome of one or more cells in a blood sample of a subject in need of treatment; identifying in the blood sample a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1, wherein the presence of said mutation indicates an increased susceptibility to an infection; and treating the subject, for example, by vaccinating the subject and/or reducing the incidence of hematopoietic clones comprising the mutation in the subject's blood.
- the methods may comprise sequencing one or more nucleic acids selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS, and SF3B1 from one or more cells in a blood sample of the subject; detecting the presence of a mutation in the sequenced nucleic acids; and treating the subject by reducing the incidence of hematopoietic clones comprising the mutation (e.g., a mis-sense mutation) in the subject's blood.
- the mutation e.g., a mis-sense mutation
- the infection may be a viral or a non-viral infection.
- the infection is a viral infection and the virus is a coronavirus (e.g., severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)), influenza (e.g., influenza A (e.g., H1N1, H5N1, H1N2, H2N1, H3N1, H3N2, H2N3) or influenza B), or respiratory syncytial virus (RSV).
- the infection is a non-viral infection (e.g., a bacterial, fungal, yeast, parasitic, or prion infection).
- the infection is Coronavirus disease 2019 (COVID-19).
- the infection results in respiratory distress and/or a cytokine storm.
- a coronavirus e.g., severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
- the methods may comprise sequencing at least part of the genome of one or more cells in a blood sample of a subject in need of treatment; identifying in the blood sample a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS, and SF3B1, wherein the presence of said mutation indicates an increased susceptibility to an infection.
- the method further comprises a step of treating the subject, for example, by vaccinating the subject or reducing the incidence of hematopoietic clones comprising the mutation in the subject's blood.
- the method further comprises a step of treating the subject by implementing measures intended to reduce the subject's exposure to the infection and/or likelihood of contracting such infection (e.g., self-isolation, quarantine and/or social distancing).
- the treatment comprises administering one or more agents or vaccines to the subject to reduce the likelihood of contracting the infection and/or developing complications therefrom.
- the methods may comprise sequencing one or more nucleic acids selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1 from one or more cells in a blood sample of the subject; and detecting the presence of a mutation in the sequenced nucleic acids, and wherein the presence of the mutation indicates an increased susceptibility to a coronavirus infection.
- the gene or nucleic acid is selected from the group consisting of TET2, DNMT3A, PPM1D, JAK2, and combinations thereof.
- the mutation is a mis-sense mutation, frame-shift mutation, nonsense mutation, or splice-site disruption.
- the mutation is in DNMT3A in exons 7 to 23.
- the mutation is a mis-sense mutation in DNMT3A selected from the group consisting of G543C, S714C, F732C, Y735C, R736C, R749C, F751C, W753C, and L889C.
- the mutation is a V617F mutation in JAK2.
- the mutation is a disruptive mutation in TET2.
- the mutation is a disruptive mutation in PPM1D.
- the mutation increases inflammation, induces a pro-inflammatory state in the subject, or causes elevations in inflammatory cytokines.
- the cytokines are or comprise interleukins (e.g., IL-6, IL-8, IL-1 ⁇ , IL-1 ⁇ , IL-12, IL-18), interferons (e.g., IFN- ⁇ , IFN- ⁇ , IFN- ⁇ , IFN- ⁇ ), and/or tumor necrosis factors (IFN- ⁇ , IFN- ⁇ , IFN- ⁇ , IFN- ⁇ ).
- interleukins e.g., IL-6, IL-8, IL-1 ⁇ , IL-1 ⁇ , IL-12, IL-18
- interferons e.g., IFN- ⁇ , IFN- ⁇ , IFN- ⁇ , IFN- ⁇
- tumor necrosis factors IFN- ⁇ , IFN- ⁇ , IFN- ⁇
- reducing the incidence of hematopoietic clones comprising the mutation in the subject's blood reduces inflammation or
- the methods described herein further comprise identifying in the blood sample at least one genetic variant selected from the group consisting of: ACE2, CRP, IL1A, IL1B, IL6, IL6R, CXCL8, IL10, IL12A, IL12B, IL18, IFITM3, TNF, LTA, LTB, IFN- ⁇ 1, IFN- ⁇ 2, IFN- ⁇ 4, IFN- ⁇ 5, IFN- ⁇ 6, IFN- ⁇ 7, IFN- ⁇ 8, IFN- ⁇ 10, IFN- ⁇ 13, IFN- ⁇ 14, IFN- ⁇ 16, IFN- ⁇ 17, IFN- ⁇ 21, IFN-beta, IFN-epsilon, IFN-gamma, IFN-kappa, IFN-lambda, and IFN-omega.
- the subject is a human subject, and in some embodiments, is at least 20, 30, 40, 50, 60, 70 years of age or older. In some embodiments, the subject has a comorbid condition (e.g., cardiovascular disease, diabetes, asthma, emphysema, obesity, cancer).
- a comorbid condition e.g., cardiovascular disease, diabetes, asthma, emphysema, obesity, cancer.
- the one or more cells in the blood sample are nucleated cells. In some embodiments, the one or more cells in the blood sample are somatic cells.
- the methods may comprise sequencing DNMT3A nucleic acids from one or more cells in a blood sample of a subject; detecting the presence of a mis-sense mutation in the sequenced DNMT3A nucleic acids; sequencing TET2 nucleic acids from one or more cells in the blood sample of the subject; and detecting the presence of a disruptive mutation in the sequenced TET2 nucleic acids, wherein the presence of a mis-sense mutation in the sequenced DNMT3A nucleic acids and/or the TET2 nucleic acids indicates the subject's increased susceptibility to a coronavirus infection.
- the methods comprise sequencing at least part of the genome of one or more cells in a blood sample of a subject in need of treatment; identifying in the blood sample a somatic sequence mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1; identifying in the blood sample a somatic structural chromosomal mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1; and/or identifying in the blood sample a germline sequence mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1, wherein the presence of one or more somatic sequence mutations, so
- ARDS acute respiratory distress syndrome
- Described herein are methods for detecting and/or treating genetic variations associated with a dysfunctional immune response that results in an increased mortality risk in a subject. Also described herein are methods for identifying and/or treating subjects at risk of, e.g., susceptible to, a dysfunctional immune response associated with genetic variations.
- a blood sample from the subject is sequenced and one or more genetic variations or mutations are identified.
- genetic variations are identified in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1.
- a dysfunctional immune response may include an inflammatory and/or interferon response.
- the one or more genetic variations result in increased mortality risk in a subject having an infection (e.g., COVID-19 infection).
- Described herein are methods for treating infections in a subject comprising sequencing at least part of the genome of one or more cells in a blood sample of a subject in need of treatment; identifying in the blood sample a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1, wherein the presence of said mutation indicates an increased susceptibility to an infection; and treating the subject by reducing the incidence of hematopoietic clones comprising the mutation in the subject's blood.
- an identified mutation in the one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1 is an indicator of clonal hematopoiesis of indeterminate potential (CHIP).
- mutations are somatic sequence mutations, somatic structural chromosomal mutations, and/or germline sequence mutations.
- somatic sequence mutations in one or more genes are identified in a blood sample.
- somatic structural chromosomal mutations are identified in a blood sample.
- germline sequence mutations are identified in a blood sample.
- Sequencing of DNA can be performed on tissues or cells. Sequencing of specific cell types (for example, hematopoietic cells obtained by flow sorting) can identify mutations in specific cell types that provide specific predictive value. Some cell types may provide a greater predictive value than other cell types.
- the one or more cells in a blood sample are nuclear cells, e.g., are somatic cells.
- Sequencing can also be conducted in single cells, using appropriate single-cell sequencing strategies.
- Single-cell analyses can be used to identify high-risk combinations of mutations co-occurring in the same cells. Co-occurrence signifies that the mutations are occurring in the same cell clone and carry a greater risk, and therefore have a greater predictive value, than occurrence of the same mutations in different individual cells.
- At least part of the genome of one or more cells in a blood sample, e.g., of a subject in need of treatment, is sequenced.
- the part of the genome that is sequenced is limited to specific genes, the whole exome, or parts of an exome.
- the sequencing may be whole exome sequencing (WES).
- Sequencing can be carried out according to any suitable technique, many of which are generally known in the art. Many proprietary sequencing systems are available commercially and can be used in the context of the present invention, such as for example from Illumina, USA.
- Single-cell sequencing methods are known in the art, as noted for example by Eberwine et al., Nature Methods 11, 25-27 (2014) doi:10.1038/nmeth.2769 Published online 30 Dec. 2013; and especially single cell sequencing in microfluidic droplets (Nature 510, 363-369 (2014) doi:10.1038/nature13437), the entire contents of which are incorporated herein by reference.
- Sequencing may be performed of specific genes only, specific parts of the genome, or the whole genome.
- specific parts of a gene can be sequenced; for example, in DNMT3A, exons 7 to 23 can be sequenced.
- that part can be the exome.
- the exome is the part of the genome formed by exons, and thus an exon sequencing method sequences the expressed sequences in the genome.
- Exome sequencing requires enrichment of sequencing targets for exome sequences; several techniques can be used, including PCR, molecular inversion probes, hybrid capture of targets, and solution capture of targets. Sequencing of targets can be conducted by any suitable technique.
- a mutation e.g., a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1 is identified in a blood sample (e.g., a blood sample from a subject).
- a blood sample e.g., a blood sample from a subject.
- the presence of a mutation indicates an increased susceptibility to an infection (e.g., a human subject's increased susceptibility to COVID-19 infection and/or the corresponding sequalae).
- a mutation in one or more genes is selected from the group consisting of DNMT3A, TET2, PPM1D, and JAK2.
- a mutation in DNMT3A is identified, e.g., in a blood sample.
- a mutation in TET2 is identified, e.g., in a blood sample.
- a mutation in PPM1D is identified, e.g., in a blood sample.
- a mutation in JAK2 is identified, e.g., in a blood sample.
- DNMT3A is DNA (cytosine-5-1-methyltransferase 3 alpha and is encoded on chromosome 2 (HGMC 2978).
- ASXL1 is additional sex combs like transcriptional regulator 1 and is encoded on chromosome 20 (HGNC 18318).
- TET2 is tet methylcytosine dioxygenase 2 and is encoded on chromosome 4 (HGNC 25941).
- PPM1D is protein phosphatase, Mg2+/Mn2+ dependent, 1D and is encoded on chromosome 17 (HGNC 9277).
- JAK2 is janus kinase 2 and is encoded on chromosome 9 (HGNC 6192).
- TP53 is tumor protein p53 and is encoded on chromosome 17 (HGNC 11998).
- SRSF2 is serine and arginine rich splicing factor 2 and is encoded on chromosome 17 (HGNC 10783).
- KRAS is KRAS proto-oncogene and is encoded on chromosome 12 (HGNC 6407).
- SF3B1 is splicing factor 3b subunit 1 and is encoded on chromosome 2 (HGNC 10768).
- Mutations in genes can be disruptive (e.g., they have an observed or predicted effect on protein function) or non-disruptive.
- a non-disruptive mutation is typically a mis-sense mutation, in which a codon is altered such that it codes for a different amino acid, but the encoded protein is still expressed.
- somatic mutations may be mis-sense mutations or disruptive mutations (e.g., frame-shift, nonsense, or splice-site disruptions).
- Putative somatic mutations include but are not limited to those alleles that comprise at least one of non-silent/disruptive nucleotide changes, indels, mis-sense mutations, frameshifts, stop mutations (addition or deletion), read-through mutations, splice mutations; and a confirmed change not due to a sequencing error or artifact of the testing system.
- mutations in DNMT3A are predominantly mis-sense mutations.
- mutations (e.g., mis-sense mutations) in DNMT3A are localized in exons 7 to 23.
- mutations in DNMT3A are enriched for cysteine-forming mutations.
- a common base-pair change in somatic variants is a cytosine-to-thymine transition.
- a mutation in DNMT3A is a mis-sense mutation selected from the group consisting of G543C, S714C, F732C, Y735C, R736C, R749C, F751C, W753C, and L889C.
- mutations in TET2 and/or PPM1D are disruptive mutations.
- a mutation in JAK2 is a V617F mutation. Additional non-limiting examples of mutations found in DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1 are described in: Genovese, et al., “Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence” N Engl J Med (2014) 371:2477-2487; Jaisawal et al., “Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes” N Engl J Med (2014) 371:2488-2498; Bick, et al.
- a blood sample obtained from a subject may further be sequenced to identify at least one additional genetic variant.
- a blood sample may be sequenced to identify at least one genetic variant for a tumor necrosis factor (e.g., TNF, LTA, and LTB), interferon (e.g., IFN- ⁇ 1, IFN- ⁇ 2, IFN- ⁇ 4, IFN- ⁇ 5, IFN- ⁇ 6, IFN- ⁇ 7, IFN- ⁇ 8, IFN- ⁇ 10, IFN- ⁇ 13, IFN- ⁇ 14, IFN- ⁇ 16, IFN- ⁇ 17, IFN- ⁇ 21, IFN-beta, IFN-epsilon, IFN-gamma, IFN-kappa, IFN-lambda, and IFN-omega), or interleukin (e.g., IL1A, IL1B, IL6, IL6R, CXCL8, IL10, IL12A, IL12B, and IL18).
- TNF tumor necrosis factor
- At least one genetic variant is selected from the group consisting of ACE2, CRP, IL1A, IL1B, IL6, IL6R, CXCL8, IL10, IL12A, IL12B, IL18, IFITM3, TNF, LTA, LTB, IFN- ⁇ 1, IFN- ⁇ 2, IFN- ⁇ 4, IFN- ⁇ 5, IFN- ⁇ 6, IFN- ⁇ 7, IFN- ⁇ 8, IFN- ⁇ 10, IFN- ⁇ 13, IFN- ⁇ 14, IFN- ⁇ 16, IFN- ⁇ 17, IFN- ⁇ 21, IFN-beta, IFN-epsilon, IFN-gamma, IFN-kappa, IFN-lambda, and IFN-omega.
- a mutation in one or more genes may cause an increase in inflammation, induce a pro-inflammatory state in a subject, or cause an elevation in inflammatory cytokines (e.g., interleukins, interferons, and/or tumor necrosis factors).
- inflammatory cytokines include IL-6, IL-8, IL-1 ⁇ , IL-1 ⁇ , IL-12, IL-18, IFN- ⁇ , IFN- ⁇ , IFN- ⁇ , IFN- ⁇ , TNF- ⁇ , TNF- ⁇ , and TNF- ⁇ .
- a subject has or is susceptible to an infection.
- An infection may be a viral infection or a non-viral infection.
- a viral infection may be caused by a coronavirus, influenza, respiratory syncytial virus (RSV), among others.
- a coronavirus is selected from the group consisting of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
- SARS-CoV severe acute respiratory syndrome coronavirus
- MERS-CoV Middle East respiratory syndrome coronavirus
- SARS-CoV-2 severe acute respiratory syndrome coronavirus 2
- an infection is Coronavirus disease 2019 (COVID-19).
- influenza is influenza A or influenza B.
- a non-viral infection is a bacterial, yeast (e.g., fungal), parasitic, or prion infection.
- the viral or non-viral infection results in respiratory distress or complications (e.g., acute respiratory distress syndrome, interstitial pneumonia, other respiratory disease) and/or a cytokine storm.
- Additional symptoms or complications of the infection include lung damage, blood complications (e.g., blood clots, hemostatic derangement), central nervous system complications (e.g., encephalitis), kidney damage, organ failure, acute cardiac injury (e.g., cardiac arrest, coronary artery occlusion, heart failure, myocarditis, cardiomyopathy), and loss of smell or taste.
- blood complications e.g., blood clots, hemostatic derangement
- central nervous system complications e.g., encephalitis
- kidney damage e.g., organ failure
- acute cardiac injury e.g., cardiac arrest, coronary artery occlusion, heart failure, myocarditis, cardiomyopathy
- loss of smell or taste e.g., smell or taste.
- a subject may be treated by reducing the incidence of hematopoietic clones comprising a mutation in one or more genes in the subject's blood.
- Treatment, “treatment,” “treated,” “treating,” etc. refer to providing medical or surgical attention, care, or management to an individual. The individual is usually ill or injured, or at increased risk of becoming ill relative to an average member of the population and in need of such attention, care, or management. Treating can refer to prolonging survival as compared to expected survival if not receiving treatment. Thus, one of skill in the art realizes that a treatment may improve the disease condition, but may not be a complete cure for the disease.
- the term “treatment” includes prophylaxis, and may further include the implementation of measures intended to reduce the subject's likelihood of contracting an infectious disease (e.g., COVID-19).
- the treatment may include medical and/or pharmacologic interventions intended to reduce the subject's likelihood of contracting an infectious disease (e.g., the prophylactic administration of one or more vaccines, convalescent plasma infusion and/or antibodies to the subject).
- the treatment may include non-pharmacologic interventions, such as self-isolation and/or quarantine of a subject identified as being susceptible to developing an infectious disease and/or the associated complications.
- treatment is “effective” if the disease is prevented and/or if progression of a disease is reduced or halted. “Treatment” can also mean prolonging survival as compared to expected survival if not receiving treatment.
- a treatment is not necessarily curative, and in certain aspects may reduce the effect of an infection by a certain percentage over an untreated infection.
- treatment may reduce inflammation or reduce the presence of inflammatory cytokines in a subject suffering from an infection.
- methods of treatment may be personalized medicine procedures, in which the DNA of an individual is analyzed to provide guidance on the appropriate therapy for that specific individual. The methods of the invention may provide guidance as to whether treatment is necessary or most effective, as well as revealing progress of the treatment and guiding the requirement for further treatment of the individual.
- the treatment may comprise the recommendation and/or implementation of measures intended to reduce the subject's likelihood of contracting an infection, and which measures are not isolated to the subject.
- the treatment may comprise vaccinating members of the subject's community (e.g., family, co-workers and/or healthcare providers) in an effort to reduce the transmission of the infection.
- treatment comprises reducing the incidence of the presence of clonal hematopoiesis in the subject's blood.
- treatment or monitoring includes repeating the sequencing of a blood sample of the subject monthly, bi-monthly, or quarterly, and reducing (or monitoring reduction in) the incidence of the presence of clonal hematopoiesis in the subject's blood.
- treatment or monitoring comprises including the subject as a candidate to receive a bone marrow transplant.
- treatment includes administering to the subject a bone marrow transplant.
- treatment includes transfusing the subject with blood in which clonal hematopoiesis is absent.
- a subject is identified as being high risk based on gene sequencing (e.g., performing a CHIP assessment).
- a subject identified as being high risk has an increased risk of contracting an infection and/or of having a serious reaction to an infection.
- high risk subjects are treated by early targeting of inflammation.
- a high risk subject may be treated by administering pro-inflammatory driver inhibitors and/or low-dose hypomethylating drugs.
- high risk subjects may be treated by vaccinating the subject and/or vaccinating members of the subject's community to reduce the transmission of the infection, and thereby reduce the likelihood that the subject will become infected.
- vaccinating the subject and/or vaccinating members of the subject's community to reduce the transmission of the infection comprising the administration of a single vaccine dose or the administration of two vaccine doses.
- One or more vaccine boosters may optionally be administered after administration of the initial vaccine dose(s).
- a vaccine booster may be administered about 6 months, 9 months, 12 months, 15 months, 18 months, 21 months, or 24 months after receiving the initial vaccine dose(s).
- a vaccine booster may be administered yearly.
- the vaccine is an mRNA vaccine or a viral vector vaccine.
- the vaccine is a BNT162b2 vaccine (a lipid nanoparticle-formulated,5 nucleoside-modified RNA (modRNA) encoding the SARS-CoV-2 full-length spike, modified by two proline mutations to lock it in the prefusion conformation).
- the vaccine is a mRNA-1273 vaccine (a lipid nanoparticle-encapsulated mRNA-based vaccine that encodes the prefusion stabilized full-length spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)).
- the vaccine is a Ad26.COV2.
- S Vaccine a monovalent vaccine composed of a recombinant, replication-incompetent human adenovirus type 26 (Ad26) vector that encodes a SARS-CoV-2 spike (S) protein in a stabilized conformation.
- Ad26 human adenovirus type 26
- the vaccine is a ChAdOx1 nCoV-19 vaccine (a replication-deficient chimpanzee adenoviral vector ChAdOx1, containing the SARS-CoV-2 structural surface glycoprotein antigen (spike protein; nCoV-19) gene).
- treating a subject for an infection includes adjuvant treatment.
- adjuvant treatment for preventing sequelae of acute pulmonary disease may include administration of one or more antiviral medications (e.g., remdesivir), anti-inflammatory medications, antibiotics, plasmapheresis, convalescent plasma infusion, monoclonal antibodies (e.g., bamlanivimab, etesevimab, casirivimab, imdevimab, recombinant humanized anti-interleukin-6 receptor monoclonal antibodies (e.g., tocilizumab)), corticosteroids (e.g., dexamethasone), supplemental oxygen, and mesenchymal stem cell/iPS cell therapy.
- antiviral medications e.g., remdesivir
- anti-inflammatory medications antibiotics
- plasmapheresis e.g., convalescent plasma infusion
- monoclonal antibodies e.g., bamlanivimab,
- adjuvant treatment for preventing sequelae of cardiac and/or infectious disease includes administration of one or more antiviral medications, anti-inflammatory medications, antibiotics, plasmapheresis, convalescent plasma, mesenchymal stem cell/iPS cell therapy, blood thinners, anti-arrhythmic drugs, and cardioprotective drugs.
- blood pressure medications may be administered to a subject including angiotensin converting enzyme (ACE) inhibitors and/or angiotensin receptor blockers (ARBs).
- ACE angiotensin converting enzyme
- ARBs angiotensin receptor blockers
- a subject's susceptibility to an infection is predicted using the sequencing and detection methods described herein.
- a subject's susceptibility to an infection may be predicted by sequencing one or more nucleic acids selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1 from one or more cells in a blood sample of the subject; and detecting the presence of a mutation in the sequenced nucleic acids.
- the presence of the mutation indicates an increased susceptibility to a coronavirus (e.g., COVID-19) infection.
- a subject's increased mortality risk e.g., resulting from a dysfunctional immune response, is predicted using the sequencing and detection methods described herein.
- the dysfunctional immune response is an inflammatory or interferon response.
- a subject's susceptibility to an infection is predicted by sequencing DNMT3A and TET2 nucleic acids from one or more cells in a blood sample from the subject and detecting the presence of a mutation (e.g., mis-sense mutations or disruptive mutations) in the sequenced nucleic acids.
- a mutation e.g., mis-sense mutations or disruptive mutations
- the presence of a mutation in the sequenced DNMT3A and/or TET2 nucleic acids may indicate a subject's increased susceptibility to the infection.
- the subject is a mammal, e.g., a primate, e.g., a human.
- a primate e.g., a human.
- patient and “subject” are used interchangeably herein.
- the subject is a mammal.
- the mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but are not limited to these examples.
- the subject is a human.
- the subject may be any age from birth to death, e.g., the subject may be an infant, a toddler, a child, a teenager, a young adult, or an adult.
- the subject may be at least about 1 day old, 1 year old, 5 years old, 10 years old, 20 years old, 30 years old, 40 years old, 50 years old, 60 years old, 70 years old, 80 years old, 90 years old, or 100 years old.
- the subject is under the age of 40, between the ages of 40-60, or over the age of 60.
- the subject may exhibit one or more risk factors including asthma, chronic lung disease, interstitial lung disease, cystic fibrosis, pulmonary hypertension, chronic obstructive pulmonary disease (COPD), diabetes, obesity, being aged 65 years or older, heart condition (e.g., heart failure, coronary artery disease, cardiomyopathies, hypertension, etc.), high blood pressure, chronic kidney disease, immunocompromised (e.g., undergoing therapy for cancer), liver disease, dementia or other neurological condition, down syndrome, HIV infection, pregnancy, sickle cell disease or thalassemia, stroke or cerebrovascular disease, solid organ or blood stem cell transplant, substance use disorder, or history of being a smoker.
- the subject has a comorbid condition selected from the group consisting of cardiovascular disease, lung disease, kidney disease, liver disease, neurological condition, cerebrovascular disease, diabetes, obesity, asthma, emphysema, and cancer.
- a DNA microarray will be used to identify, and report inherited genetic variants (e.g., TET2, DNMT3A, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS, and/or SF3B1) associated with a variety of cardiovascular and metabolic disorders, as well as with certain cancers. These cancers and disorders, if pre-existing, can increase the risk of death related to COVID 19 complications. Also included in this microarray are genetic variants associated with pro- and anti-inflammatory effects. Some of these include ACE2, CRP, IL-6R, IL-1A GC, and IL-10. Furthermore, the microarray may elucidate which inborn errors of immunity can cause life-threatening COVID 19 in previously healthy younger patients.
- inherited genetic variants e.g., TET2, DNMT3A, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS, and/or SF3B1
- these cancers and disorders if
- the microarray may test for various biomarkers present in the blood that are involved in immunity and inflammation, which may impact COVID 19 infection response.
- biomarkers may include hsCRP, IL-6, IL-8, and TNF-alpha.
- CHIP Clonal hematopoiesis of indeterminate potential
- somatic exonic mutations are acquired at a rate of approximately 1.3 per hematopoietic stem cell per decade and are rarely detected in people under age 40 years.
- Clonal hematopoiesis increases with age and is found in approximately 10 percent of people without known hematologic malignancies older than 65 years, in almost 12 percent of those aged 80 to 89 years, and in more than 18 percent of those older than 90 years.
- a screen will also be performed for germline/inherited variants associated with cardiovascular disease, cancer, and inflammation.
- the association between CHIP, inflammation, and leukocyte dysfunction will be examined so the CHIP-related comorbidities in COVID 19 can be more effectively managed clinically.
- the presence of CHIP as a disease modifier might explain why some patients are more responsive or refractory to treatments, or why some patients undergo more slow or rapid disease progression.
- this dynamic measurement may elucidate novel opportunities to develop new drug therapies focusing on the genetic abnormalities of CHIP.
- iPS cells can be programmed to produce virtually any cell type in the human body, such as immune cells and alveolar cells of the lung which produce surfactant (AE2).
- AE2 cells play various roles in alveolar fluid balance, coagulation/fibrinolysis, and host defense. AE2 cells proliferate, differentiate into AE1 cells, and contribute to epithelial repair and immunoregulation.
- iPS cells can be differentiated into mesenchymal stem cells (MSCs) which are known to modulate the pro-inflammatory immune cytokine response which is largely responsible for the cascade of events leading to severe pulmonary disease. Whether these cells can restore healthy lung tissue after a COVID 19 infection will be examined.
- MSCs mesenchymal stem cells
- Blood-derived iPS cells represent a personalized cell resource for individuals to generate AE2 cells and cells of immune function as a therapy option.
- CHIP is a genetic issue unique to the nucleated cells contained within blood. It refers to the unhealthy expansion of the same set of detrimental mutations and damage to an individual's DNA in their nucleated blood cells. CHIP may potentially explain the age-related prevalence of inflammatory conditions. A connection between CHIP mutations and heart diseases is believed to be mediated by inflammation. It has been more recently postulated that CHIP may be associated with broader biological impact which may be explained by the fact that people with CHIP have an aberrant inflammatory system compared with those without CHIP. Specifically, key cytokines such as serum IL-6 and IL-8 have been shown to be elevated in people with CHIP, establishing its relevance to the human systemic inflammatory landscape and its impact on poorer health status, and increased and potentially novel comorbidities.
- somatic exonic mutations are acquired at a rate of approximately 1.3 per hematopoietic stem cell per decade, and are rarely detected in people under age 40 years.
- Clonal hematopoiesis increases with age and is found in approximately 10 percent of people without known hematologic malignancies older than 65 years, in almost 12 percent of those aged 80 to 89 years, and in more than 18 percent of those older than 90 years.
- CHIP-related comorbidities in COVID 19 may be more effectively managed clinically.
- CHIP as a disease modifier may explain why some patients are more responsive or refractory to treatments, or why some patients undergo more slow or rapid disease progression.
- Somatic changes associated with CHIP may be detected and monitored, as well as screening for germline/inherited variants associated with cardiovascular disease, cancer, and inflammation. Blood samples will be evaluated with a target sequence panel specific to genes with somatic (accumulated) and germline (inherited) variants associated with CHIP, including but not limited to TET2 and DNMT3A, both of which have been associated with a dysfunctional response to inflammation and infection.
- microarray-based methods are used to measure somatic structural DNA variation and damage across the genome, additionally associated with CHIP. Genetic test results will be correlated with serologic and clinical data from the subject's medical record.
- Blood samples will be collected from a variety of subjects.
- the blood samples will be assessed to identify samples that are seropositive COVID 19, Influenza A, Influenza B, RSV, SARS-CoV, and MERS-CoV.
- normal control blood samples will also be obtained.
- the blood samples will be assayed for clonal hematopoiesis (CHIP) using an assay that screens for somatic variations in TET2, DNMT3A, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS, and SF3B1.
- CHIP clonal hematopoiesis
- Additional assessments will be performed on the blood samples including evaluating the samples for additional variants in other genes, as well as performing additional blood analysis. Further, clinical data will be collected for the subjects from who the blood samples were taken from.
- samples will be evaluated for one or more variants in ACE2, IFITM3, IL-1A, IL-1B, IL-6, IL-6R, CXCL8, IL-12A, IL-12B, IL-18, TNF- ⁇ , TNF- ⁇ , and TNF- ⁇ .
- the samples will be assessed for additional features such as arterial blood gas, white count with differential (lymphocytes, neutrophils, cytokine levels, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), Lactase, MB-CK enzyme, etc.)
- Clinical data for the subjects from whom the blood samples are obtained will additionally be considered including, but not limited to, the development of any complications related to the diagnosis (MI, myocarditis, pulmonary embolism), vital signs, O 2 sat, O 2 requirements, intubation status, mortality, and cause(s) of death.
- MI myocarditis
- pulmonary embolism vital signs
- O 2 sat erythrocyte sedimentation rate
- intubation status mortality
- cause(s) of death MB-CK enzyme, etc.
- any imaging obtained from the subject will be considered, including chest X rays (CXR) and CT scans.
- CXR chest X rays
- CT scans any co-morbidities and
- CHIP may be utilized as a disease modifier to explain why some COVID 19 patients undergo a faster and more severe disease progression, and why some patients are more responsive/refractory to treatments.
- CHIP may be utilized as a disease modifier in determining which patients are more susceptible to poor cardiac outcomes.
- CHIP may also be utilized to provide guidance on mitigation strategies for population management, e.g., establishing quarantine protocols and identifying groups of individuals to be quarantined, possibly more restrictively than other individuals.
- Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-COV-2) is an enveloped single-stranded, positive-sense ribonucleic acid (ssRNA+) coronavirus which belongs to the family of Coronaviridae (2).
- the infection manifests itself as mild-moderate symptoms, such as coughing, muscle fatigue and fever to severe respiratory failure which requires ICU care and ventilation (3).
- CHIP-driver mutations allele fraction of >10% were protected from cardiovascular events if they also had a simultaneous germline sequence variation in the IL-6 receptor (IL-6R) (24). While most of these outcomes were studied in monocytes and macrophages, CHIP mutations have also been shown to alter the function of other leukocyte populations (25). Thus, the presence of CHIP might dysregulate the entire inflammatory system and therefore may corrupt disease outcome in COVID-19 patients.
- IL-6R IL-6 receptor
- CHIP chronic myocardial infarction
- 27, 29 the hypothesis that CHIP is associated with disease severity in COVID-19 patients was tested.
- Three age groups were evaluated—under 40 years-old, 40-60 years old and those older than 65 years. While CHIP has been reported to be rare in younger people with frequencies of about 1 in 1000 in those younger than 40 and about 0.7% in those under 50, CHIP has been more recently found in higher frequencies in younger individuals with early-onset myocardial infarction and in some advanced autoimmune disease, and hence it was hypothesized that it could be a risk factor in younger populations with severe COVID-19 disease (27, 29).
- Patient samples were collected both through collaboration and under the IRB of the New York Blood Center (NYBC) as well as via a prospective procurement contract through iSpecimen.
- Patients included in the study were confirmed to be PCR positive for SARS-CoV-2 infection and classified as either severe hospitalization or non-hospitalized.
- Severe hospitalized patients were defined as infected and admitted to the hospital for a minimum of seven days, with a priority towards patients admitted to the ICU and requiring oxygen support.
- Non-hospitalized patients were defined as infected and symptomatic (fever, loss of smell, body aches, coughing) or asymptomatic, but not requiring hospitalization.
- Samples were excluded from collection and/or analysis if the patient had previously received blood stem cell transplant or had undergone chemotherapy. Samples procured through NYBC were delivered as cryopreserved PBMCs while samples received from iSpecimen were supplied as frozen whole blood (WB).
- gDNA Genomic DNA
- PBMC peripheral blood mononuclear cell
- WB PerkinElmer Chemagic 360 B5K automated extraction platform.
- Custom DNA target sequencing libraries were constructed using Agilent SureSelect chemistry.
- the resulting libraries were analyzed on the Agilent 4200 TapeStation System and quantified by KAPA qPCR. Samples were sequenced using the Illumina MiSeq platform with an averages sequencing coverage>1000 ⁇ across amplicons. DNA sequence quality was verified and then BAM (Binary Alignment/Map) and VCF (Variant Call Format) files were generated.
- BAM Binary Alignment/Map
- VCF Variariant Call Format
- somatic variants were annotated against GenBank gene models and the ClinVar database. Both somatic and germline coding variants from genes DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SF3B1, SRSF2, and KRAS were extracted from the annotated VCF. Upon analysis CHIP accumulated/somatic variants were defined as having >1.5% variant allele frequency (VAF) and 20 or more variant cells.
- VAF variant allele frequency
- extracted gDNA was normalized and aliquoted to 25 ng/ul in 50 ul total volume. Normalized and aliquoted gDNA samples were run on the Illumina InfiniumTM Global Screening Array (GSA)—24 v2.0 BeadChip in the labs of Diagnomics (San Diego, Calif. USA). The resulting iDAT files were converted to GTC files using the Illumina Array Analysis Platform and a VCF file with genotype information was generated. SNP and indel markers were annotated against GenBank gene models and a table with all the genotyped markers from genes IL6R, CXCL8, IL6, and ACE2 were extracted from the VCF using the BCFtools+split ⁇ vep plugin.
- the cohort of severe disease in the under 40 group included 9 patients. Two patients (22.2%) had CHIP with VAF>1.5%. One of these patients had two CHIP mutations (DNMT3A and SF3B1) both with a VAF>1.5%. A third patient had a somatic mutation in TP53 with a VAF of 0.8% overall resulting in 3 patients (33.3%) having detectable somatic CHIP mutations. The expected CHIP in individuals under the age of 40 is about 0.1%. In addition, a fourth patient in this group had a germline mutation in TP53. Collection of samples from COVID-19 infected but non-hospitalized individuals in this age group is under way.
- the cohort in the 40-60 age group included 36 patients with severe disease and 4 non-hospitalized infected patients.
- 7 additional patients with severe disease had CHIP mutations (3 with DNMT3A, 1 with TET2, 1 with KRAS and 1 with TP53) with a VAF ⁇ 1.5%, overall resulting in 10 patients (27.8%) having detectable somatic CHIP mutations.
- the expected frequency of CHIP in a matched healthy 40-60 group would be approximately 2-3%.
- This cohort includes 43 hospitalized patients with severe disease, 46 non-hospitalized infected patients and a historic control of 106 individuals.
- the median age for each group is 69.5, 68.7, and 82 respectively.
- the frequency of CHIP>1.5% VAF was 14%, 16%, 35% respectively.
- a COVID-19 infected patient with two large clone CHIP mutations also had an IL-6R coding mutation which may have protected this patient from developing severe disease.
- IL-6R coding mutation which may have protected this patient from developing severe disease.
- 5.1% of patients with CHIP and a simultaneous genetic deficiency in IL-6 signaling were non-hospitalized when infected with COVID-19.
- only 1.6% of patients with CHIP and this coding mutation developed severe COVID-19 disease. Therefore, genetically reduced IL-6 signaling may abrogate the risk of developing severe disease among carriers of CHIP.
- the first cohort was composed of patients with solid tumors treated at Memorial Sloan Kettering Cancer Center (MSK) with blood previously sequenced using MSK-IMPACT, a previously validated targeted gene panel capturing all commonly mutated CH-associated genes.
- MSK Memorial Sloan Kettering Cancer Center
- CH was observed in 51% and 30% of patients with severe versus non-severe Covid-19, respectively (adjusted OR: 1.85, 95% CI 1.10-3.12).
- the second cohort included 112 previously healthy individuals without cancer who were hospitalized for Covid-19 between January and April 2020 at four tertiary hospitals in South Korea (KoCH cohort).
- the KoCH cohort was sequenced using a custom targeted NGS panel from Agilent (89 genes) which was designed to include commonly occurring CH genes.
- CHIP may provide an explanation why some younger patients infected with COVID-19 have a clinical course that requires hospitalization. This is consistent with prior studies implicating CHIP in dysfunctional inflammatory responses with elevated cytokines and decreased interferons which is the typical profile of patients with severe disease (REF). Therefore, this would be the presumed mechanism in the younger cohort with severe disease in our study.
- CHIP cardiovascular diseases
- CHIP chronic obstructive pulmonary disease
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- Health & Medical Sciences (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Engineering & Computer Science (AREA)
- Genetics & Genomics (AREA)
- Analytical Chemistry (AREA)
- Microbiology (AREA)
- Biochemistry (AREA)
- Biotechnology (AREA)
- Molecular Biology (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- General Health & Medical Sciences (AREA)
- Immunology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- Pathology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
- Farming Of Fish And Shellfish (AREA)
- Investigating Or Analysing Biological Materials (AREA)
Abstract
Disclosed herein are methods for predicting susceptibility to an infection based on the observation of specific mutations in blood cells, as well as methods for treating or reducing susceptibility to an infection in a subject.
Description
- This application is a continuation of U.S. application Ser. No. 17/240,991, filed on Apr. 26, 2021, which claims the benefit of U.S. Provisional Application No. 63/015,104, filed on Apr. 24, 2020. The entire teachings of the above applications are incorporated herein by reference.
- Coronavirus disease 2019 (COVID-19) became a pandemic in early 2020. One of the reasons for its rapid and widespread diffusion is the presence of a large number of asymptomatic or paucisymptomatic patients, who are not recognized as infected and therefore contribute to the spread of the virus. Data on the spread of the virus have led scientists to think that the actual number of infected people is much higher than the number of positive tests. For example, in Italy a ratio of 1 positive patient tested for every 10 infected people is considered reasonable, leading to more than 1 million infected people (corresponding to more than 1.7% of the Italian population) in total.
- Identifying not only individuals at risk of infection, but also those at high risk of morbidity and mortality is one of the most important challenges in reducing the social impact of the disease. In addition, the results provided by cellular, genetic and/or biomarker analyses could guide the development and implementation of desperately needed strategies for the development of new antiviral agents and opportunities for cell therapy.
- The present inventions generally concern methods of identifying subjects at risk of developing a severe COVID-19 infection and/or severe complications from COVID-19 infection. For example, in certain embodiments, disclosed herein are methods of identifying a subject at risk of developing a severe complication from Coronavirus disease 2019 (COVID-19) infection, such methods generally comprising a step of determining whether the subject has clonal hematopoiesis of indeterminate potential (CHIP). In certain aspects, the step of determining whether the subject has CHIP comprises sequencing at least part of the genome of one or more cells in a blood sample of the subject to identify a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1, wherein the presence of said mutation indicates that the subject has CHIP and is at risk of developing a severe COVID-19 infection and/or a severe complication from COVID-19 infection.
- In certain embodiments, the methods disclosed herein further comprise a step of treating a subject identified as having CHIP, or that is otherwise at risk of developing a severe COVID-19 infection or a severe complication from COVID-19 infection. For example, in certain aspects of the methods disclosed herein treating the subject comprises administering to the subject one or more agents or vaccines to reduce the subject's likelihood of contracting COVD-19 infection.
- Also described herein are methods of treating a subject at risk of developing a severe Coronavirus disease 2019 (COVID-19) infection and/or severe complications from COVID-19 infection. For example, in certain embodiments, disclosed herein are methods of treating a subject at risk of developing a severe COVID-19 infection, such methods generally comprising a step of determining whether the subject has clonal hematopoiesis of indeterminate potential (CHIP). In certain aspects the step of determining whether the subject has CHIP comprises sequencing at least part of the genome of one or more cells in a blood sample of the subject to identify a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1; wherein the presence of said mutation indicates that the subject has CHIP and is at risk of developing a severe COVID-19 infection; and treating the subject having CHIP to reduce the subject's risk of contracting a severe COVID-19 infection. For example, in certain aspects of the methods disclosed herein treating the subject comprises administering to the subject one or more agents or vaccines to reduce the subject's likelihood of contracting COVD-19 infection.
- In certain embodiments of the inventions disclosed herein, the subject is at risk of requiring hospitalization. In certain embodiments, the subject is under the age of about 30, 40, 50, 60, 70, 80, 90, 100 years old or older. In certain embodiments, the subject has a severe autoimmune disease. In yet other embodiments, the subject has a comorbid condition (e.g., a comorbid condition selected from the group consisting of cancer, cerebrovascular disease, chronic kidney disease, chronic obstructive pulmonary disease (COPD), diabetes mellitus, heart conditions, obesity, pregnancy, history of smoking, Down syndrome, human immunodeficiency virus (HIV), neurologic conditions, interstitial lung disease, pulmonary fibrosis, pulmonary hypertension, Sickle cell disease, solid organ or blood stem cell transplantation, substance use disorders, use of corticosteroids or other immunosuppressive medications, cystic fibrosis, thalassemia, asthma, hypertension, immune deficiencies, and liver disease). In certain embodiments, the comorbid condition is selected from the group consisting of cancer, cerebrovascular disease, chronic kidney disease, chronic obstructive pulmonary disease (COPD), diabetes mellitus, heart conditions, obesity, pregnancy, and history of smoking.
- In certain aspects, the mutation is a somatic mutation. For example, in certain embodiments of the methods disclosed herein, the mutation is a somatic mutation in DNMT3A and/or TET2.
- Also described herein are methods of treating an infection in a subject. The methods may comprise sequencing at least part of the genome of one or more cells in a blood sample of a subject in need of treatment; identifying in the blood sample a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1, wherein the presence of said mutation indicates an increased susceptibility to an infection; and treating the subject, for example, by vaccinating the subject and/or reducing the incidence of hematopoietic clones comprising the mutation in the subject's blood.
- Also described herein are methods of treating an infection in a subject. The methods may comprise sequencing one or more nucleic acids selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS, and SF3B1 from one or more cells in a blood sample of the subject; detecting the presence of a mutation in the sequenced nucleic acids; and treating the subject by reducing the incidence of hematopoietic clones comprising the mutation (e.g., a mis-sense mutation) in the subject's blood.
- The infection may be a viral or a non-viral infection. In some embodiments, the infection is a viral infection and the virus is a coronavirus (e.g., severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)), influenza (e.g., influenza A (e.g., H1N1, H5N1, H1N2, H2N1, H3N1, H3N2, H2N3) or influenza B), or respiratory syncytial virus (RSV). In some embodiments, the infection is a non-viral infection (e.g., a bacterial, fungal, yeast, parasitic, or prion infection). In certain embodiments, the infection is Coronavirus disease 2019 (COVID-19). In some embodiments, the infection results in respiratory distress and/or a cytokine storm.
- Described herein are methods of treating a coronavirus (e.g., severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)) infection in a subject. The methods may comprise sequencing at least part of the genome of one or more cells in a blood sample of a subject in need of treatment; identifying in the blood sample a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS, and SF3B1, wherein the presence of said mutation indicates an increased susceptibility to an infection. In certain aspects, the method further comprises a step of treating the subject, for example, by vaccinating the subject or reducing the incidence of hematopoietic clones comprising the mutation in the subject's blood. Alternatively, in certain embodiments, the method further comprises a step of treating the subject by implementing measures intended to reduce the subject's exposure to the infection and/or likelihood of contracting such infection (e.g., self-isolation, quarantine and/or social distancing). In certain aspects, the treatment comprises administering one or more agents or vaccines to the subject to reduce the likelihood of contracting the infection and/or developing complications therefrom.
- Also described herein are methods of predicting a subject's susceptibility to a coronavirus infection. The methods may comprise sequencing one or more nucleic acids selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1 from one or more cells in a blood sample of the subject; and detecting the presence of a mutation in the sequenced nucleic acids, and wherein the presence of the mutation indicates an increased susceptibility to a coronavirus infection.
- In some embodiments, the gene or nucleic acid is selected from the group consisting of TET2, DNMT3A, PPM1D, JAK2, and combinations thereof. In some embodiments, the mutation is a mis-sense mutation, frame-shift mutation, nonsense mutation, or splice-site disruption. In some embodiments, the mutation is in DNMT3A in exons 7 to 23. In some embodiments, the mutation is a mis-sense mutation in DNMT3A selected from the group consisting of G543C, S714C, F732C, Y735C, R736C, R749C, F751C, W753C, and L889C. In some embodiments, the mutation is a V617F mutation in JAK2. In some embodiments, the mutation is a disruptive mutation in TET2. In some embodiments, the mutation is a disruptive mutation in PPM1D.
- In some embodiments, the mutation increases inflammation, induces a pro-inflammatory state in the subject, or causes elevations in inflammatory cytokines. In some embodiments, the cytokines are or comprise interleukins (e.g., IL-6, IL-8, IL-1α, IL-1β, IL-12, IL-18), interferons (e.g., IFN-α, IFN-β, IFN-γ, IFN-λ), and/or tumor necrosis factors (IFN-α, IFN-β, IFN-γ, IFN-λ). In some embodiments, reducing the incidence of hematopoietic clones comprising the mutation in the subject's blood reduces inflammation or inflammatory cytokines in the subject.
- In some embodiments, the methods described herein further comprise identifying in the blood sample at least one genetic variant selected from the group consisting of: ACE2, CRP, IL1A, IL1B, IL6, IL6R, CXCL8, IL10, IL12A, IL12B, IL18, IFITM3, TNF, LTA, LTB, IFN-α1, IFN-α2, IFN-α4, IFN-α5, IFN-α6, IFN-α7, IFN-α8, IFN-α10, IFN-α13, IFN-α14, IFN-α16, IFN-α17, IFN-α21, IFN-beta, IFN-epsilon, IFN-gamma, IFN-kappa, IFN-lambda, and IFN-omega.
- In some embodiments, the subject is a human subject, and in some embodiments, is at least 20, 30, 40, 50, 60, 70 years of age or older. In some embodiments, the subject has a comorbid condition (e.g., cardiovascular disease, diabetes, asthma, emphysema, obesity, cancer).
- In some embodiments, the one or more cells in the blood sample are nucleated cells. In some embodiments, the one or more cells in the blood sample are somatic cells.
- Also described herein are methods of predicting a subject's susceptibility to a coronavirus infection. The methods may comprise sequencing DNMT3A nucleic acids from one or more cells in a blood sample of a subject; detecting the presence of a mis-sense mutation in the sequenced DNMT3A nucleic acids; sequencing TET2 nucleic acids from one or more cells in the blood sample of the subject; and detecting the presence of a disruptive mutation in the sequenced TET2 nucleic acids, wherein the presence of a mis-sense mutation in the sequenced DNMT3A nucleic acids and/or the TET2 nucleic acids indicates the subject's increased susceptibility to a coronavirus infection.
- Also described herein are methods of treating an infection in a subject. The methods comprise sequencing at least part of the genome of one or more cells in a blood sample of a subject in need of treatment; identifying in the blood sample a somatic sequence mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1; identifying in the blood sample a somatic structural chromosomal mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1; and/or identifying in the blood sample a germline sequence mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1, wherein the presence of one or more somatic sequence mutations, somatic structural mutations or germline sequence mutations indicates an increased susceptibility to an infection, and treating the subject by reducing the incidence of hematopoietic clones comprising the mutation in the subject's blood.
- The above discussed, and many other features and attendant advantages of the present inventions will become better understood by reference to the following detailed description of the invention.
- For reasons that are not entirely clear, some individuals have dysfunctional immune systems that fail to keep a response to Coronavirus disease 2019 (COVID-19) in check, leading to an uncontrolled immune response. It is generally known that the virus triggers an overproduction of immune cells and their signaling molecules leading to a cytokine storm often associated with a flood of immune cells into the lungs and ultimately resulting in acute respiratory distress syndrome (ARDS).
- Host immune responses to viral infections are generally known to comprise multiple intricate processes that coordinate together to play significant roles in the protection of the host. The understanding of the COVID 19 host interaction will require a comprehensive examination of various cellular, genetic and biomarker factors in a blood sample to elucidate the dynamics of host immune system response, many of which are unclear at this time. Bridging these gaps will pave the way for identifying not only individuals at risk of being infected but those at high risk for morbidity and mortality. In addition, the powerful data provided by cellular/genetic/biomarker analyses could guide strategies for development of novel antiviral agents and opportunities for cell therapy.
- Described herein are methods for detecting and/or treating genetic variations associated with a dysfunctional immune response that results in an increased mortality risk in a subject. Also described herein are methods for identifying and/or treating subjects at risk of, e.g., susceptible to, a dysfunctional immune response associated with genetic variations. In some embodiments, a blood sample from the subject is sequenced and one or more genetic variations or mutations are identified. In some embodiments, genetic variations are identified in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1. A dysfunctional immune response may include an inflammatory and/or interferon response. In some embodiments, the one or more genetic variations result in increased mortality risk in a subject having an infection (e.g., COVID-19 infection).
- Described herein are methods for treating infections in a subject comprising sequencing at least part of the genome of one or more cells in a blood sample of a subject in need of treatment; identifying in the blood sample a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1, wherein the presence of said mutation indicates an increased susceptibility to an infection; and treating the subject by reducing the incidence of hematopoietic clones comprising the mutation in the subject's blood. In some aspects, an identified mutation in the one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1 is an indicator of clonal hematopoiesis of indeterminate potential (CHIP).
- In some aspects, mutations are somatic sequence mutations, somatic structural chromosomal mutations, and/or germline sequence mutations. In some embodiments, somatic sequence mutations in one or more genes are identified in a blood sample. In some embodiments, somatic structural chromosomal mutations are identified in a blood sample. In some embodiments, germline sequence mutations are identified in a blood sample.
- Sequencing of DNA can be performed on tissues or cells. Sequencing of specific cell types (for example, hematopoietic cells obtained by flow sorting) can identify mutations in specific cell types that provide specific predictive value. Some cell types may provide a greater predictive value than other cell types. In some embodiments, the one or more cells in a blood sample are nuclear cells, e.g., are somatic cells.
- Sequencing can also be conducted in single cells, using appropriate single-cell sequencing strategies. Single-cell analyses can be used to identify high-risk combinations of mutations co-occurring in the same cells. Co-occurrence signifies that the mutations are occurring in the same cell clone and carry a greater risk, and therefore have a greater predictive value, than occurrence of the same mutations in different individual cells.
- In some embodiments, at least part of the genome of one or more cells in a blood sample, e.g., of a subject in need of treatment, is sequenced. In some embodiments the part of the genome that is sequenced is limited to specific genes, the whole exome, or parts of an exome. For example, the sequencing may be whole exome sequencing (WES). Sequencing can be carried out according to any suitable technique, many of which are generally known in the art. Many proprietary sequencing systems are available commercially and can be used in the context of the present invention, such as for example from Illumina, USA. Single-cell sequencing methods are known in the art, as noted for example by Eberwine et al., Nature Methods 11, 25-27 (2014) doi:10.1038/nmeth.2769 Published online 30 Dec. 2013; and especially single cell sequencing in microfluidic droplets (Nature 510, 363-369 (2014) doi:10.1038/nature13437), the entire contents of which are incorporated herein by reference.
- Sequencing may be performed of specific genes only, specific parts of the genome, or the whole genome. In some aspects, specific parts of a gene can be sequenced; for example, in DNMT3A, exons 7 to 23 can be sequenced. Where a part of a genome is sequenced, that part can be the exome. The exome is the part of the genome formed by exons, and thus an exon sequencing method sequences the expressed sequences in the genome. There are 180,000 exons in the human genome, which constitute about 1% of the genome, or approximately 30 million base pairs. Exome sequencing requires enrichment of sequencing targets for exome sequences; several techniques can be used, including PCR, molecular inversion probes, hybrid capture of targets, and solution capture of targets. Sequencing of targets can be conducted by any suitable technique.
- Methods of identifying somatic structural chromosomal mutations and germline sequence mutations in blood samples are known to those of skill in the art. Examples of such methods are described in WO 2019/079493 and US 2017/0321284, both of which are incorporated herein by reference.
- In some embodiments, a mutation (e.g., a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1) is identified in a blood sample (e.g., a blood sample from a subject). In certain aspects, the presence of a mutation indicates an increased susceptibility to an infection (e.g., a human subject's increased susceptibility to COVID-19 infection and/or the corresponding sequalae). In some aspects, the presence of a mutation indicates an increased susceptibility to an adverse clinical outcome due to a dysfunctional immune response (e.g., a human subject's increased susceptibility to developing respiratory distress, ARDS and/or cytokine storm). In some embodiments, a mutation in one or more genes is selected from the group consisting of DNMT3A, TET2, PPM1D, and JAK2. In certain embodiments, a mutation in DNMT3A is identified, e.g., in a blood sample. In certain embodiments, a mutation in TET2 is identified, e.g., in a blood sample. In certain embodiments, a mutation in PPM1D is identified, e.g., in a blood sample. In certain embodiments, a mutation in JAK2 is identified, e.g., in a blood sample.
- DNMT3A is DNA (cytosine-5-1-methyltransferase 3 alpha and is encoded on chromosome 2 (HGMC 2978). ASXL1 is additional sex combs like transcriptional regulator 1 and is encoded on chromosome 20 (HGNC 18318). TET2 is tet methylcytosine dioxygenase 2 and is encoded on chromosome 4 (HGNC 25941). PPM1D is protein phosphatase, Mg2+/Mn2+ dependent, 1D and is encoded on chromosome 17 (HGNC 9277). JAK2 is janus kinase 2 and is encoded on chromosome 9 (HGNC 6192). TP53 is tumor protein p53 and is encoded on chromosome 17 (HGNC 11998). SRSF2 is serine and arginine rich splicing factor 2 and is encoded on chromosome 17 (HGNC 10783). KRAS is KRAS proto-oncogene and is encoded on chromosome 12 (HGNC 6407). SF3B1 is splicing factor 3b subunit 1 and is encoded on chromosome 2 (HGNC 10768).
- Mutations in genes can be disruptive (e.g., they have an observed or predicted effect on protein function) or non-disruptive. A non-disruptive mutation is typically a mis-sense mutation, in which a codon is altered such that it codes for a different amino acid, but the encoded protein is still expressed. In some embodiments, somatic mutations may be mis-sense mutations or disruptive mutations (e.g., frame-shift, nonsense, or splice-site disruptions).
- Putative somatic mutations include but are not limited to those alleles that comprise at least one of non-silent/disruptive nucleotide changes, indels, mis-sense mutations, frameshifts, stop mutations (addition or deletion), read-through mutations, splice mutations; and a confirmed change not due to a sequencing error or artifact of the testing system.
- In some embodiments, mutations in DNMT3A are predominantly mis-sense mutations. In some aspects, mutations (e.g., mis-sense mutations) in DNMT3A are localized in exons 7 to 23. In some aspects, mutations in DNMT3A are enriched for cysteine-forming mutations. A common base-pair change in somatic variants is a cytosine-to-thymine transition. In some embodiments, a mutation in DNMT3A is a mis-sense mutation selected from the group consisting of G543C, S714C, F732C, Y735C, R736C, R749C, F751C, W753C, and L889C. In some embodiments, mutations in TET2 and/or PPM1D are disruptive mutations. In some embodiments, a mutation in JAK2 is a V617F mutation. Additional non-limiting examples of mutations found in DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1 are described in: Genovese, et al., “Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence” N Engl J Med (2014) 371:2477-2487; Jaisawal et al., “Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes” N Engl J Med (2014) 371:2488-2498; Bick, et al. “Genetic Interleukin 6 Signaling Deficiency Attenuates Cardiovascular Risk in Clonal Hematopoiesis” Circulation (2020) 141:124-131; Cook et al., “Clonal hematopoiesis and inflammation: Partners in leukemogenesis and comorbidity” Exp Hematol (2020) 83:85-94; Perner et al., “Roles of JAK2 in Aging, Inflammation, Hematopoiesis and Malignant Transformation” Cells (2019) 8(8) 854; Cook et al., “Comorbid and inflammatory characteristics of genetic subtypes of clonal hematopoiesis” Blood Adv. (2019) 3(16): 2482-2486; Uyanik et al., “DNA damage-induced phosphatase Wip1 in regulation of hematopoiesis, immune system and inflammation” Cell Death Discov (2017) 3, 17018; US 2017/0321284; and WO 2019/079493, all incorporated herein by reference.
- In some embodiments, a blood sample obtained from a subject may further be sequenced to identify at least one additional genetic variant. For example, a blood sample may be sequenced to identify at least one genetic variant for a tumor necrosis factor (e.g., TNF, LTA, and LTB), interferon (e.g., IFN-α1, IFN-α2, IFN-α4, IFN-α5, IFN-α6, IFN-α7, IFN-α8, IFN-α10, IFN-α13, IFN-α14, IFN-α16, IFN-α17, IFN-α21, IFN-beta, IFN-epsilon, IFN-gamma, IFN-kappa, IFN-lambda, and IFN-omega), or interleukin (e.g., IL1A, IL1B, IL6, IL6R, CXCL8, IL10, IL12A, IL12B, and IL18). In some embodiments, at least one genetic variant is selected from the group consisting of ACE2, CRP, IL1A, IL1B, IL6, IL6R, CXCL8, IL10, IL12A, IL12B, IL18, IFITM3, TNF, LTA, LTB, IFN-α1, IFN-α2, IFN-α4, IFN-α5, IFN-α6, IFN-α7, IFN-α8, IFN-α10, IFN-α13, IFN-α14, IFN-α16, IFN-α17, IFN-α21, IFN-beta, IFN-epsilon, IFN-gamma, IFN-kappa, IFN-lambda, and IFN-omega.
- A mutation in one or more genes may cause an increase in inflammation, induce a pro-inflammatory state in a subject, or cause an elevation in inflammatory cytokines (e.g., interleukins, interferons, and/or tumor necrosis factors). Examples of inflammatory cytokines include IL-6, IL-8, IL-1α, IL-1β, IL-12, IL-18, IFN-α, IFN-β, IFN-γ, IFN-λ, TNF-α, TNF-β, and TNF-γ.
- In some embodiments, a subject has or is susceptible to an infection. An infection may be a viral infection or a non-viral infection. For example, a viral infection may be caused by a coronavirus, influenza, respiratory syncytial virus (RSV), among others. In some embodiments, a coronavirus is selected from the group consisting of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In certain embodiments, an infection is Coronavirus disease 2019 (COVID-19). In some embodiments, influenza is influenza A or influenza B. Strains of influenza A include H1N1, H5N1, H1N2, H2N1, H3N1, H3N2, and H2N3. In some embodiments, a non-viral infection is a bacterial, yeast (e.g., fungal), parasitic, or prion infection. In some aspects, the viral or non-viral infection results in respiratory distress or complications (e.g., acute respiratory distress syndrome, interstitial pneumonia, other respiratory disease) and/or a cytokine storm. Additional symptoms or complications of the infection include lung damage, blood complications (e.g., blood clots, hemostatic derangement), central nervous system complications (e.g., encephalitis), kidney damage, organ failure, acute cardiac injury (e.g., cardiac arrest, coronary artery occlusion, heart failure, myocarditis, cardiomyopathy), and loss of smell or taste.
- In some embodiments, a subject may be treated by reducing the incidence of hematopoietic clones comprising a mutation in one or more genes in the subject's blood. “Treat, “treatment,” “treated,” “treating,” etc. refer to providing medical or surgical attention, care, or management to an individual. The individual is usually ill or injured, or at increased risk of becoming ill relative to an average member of the population and in need of such attention, care, or management. Treating can refer to prolonging survival as compared to expected survival if not receiving treatment. Thus, one of skill in the art realizes that a treatment may improve the disease condition, but may not be a complete cure for the disease. As used herein, the term “treatment” includes prophylaxis, and may further include the implementation of measures intended to reduce the subject's likelihood of contracting an infectious disease (e.g., COVID-19). For example, in certain aspects, the treatment may include medical and/or pharmacologic interventions intended to reduce the subject's likelihood of contracting an infectious disease (e.g., the prophylactic administration of one or more vaccines, convalescent plasma infusion and/or antibodies to the subject). In other embodiments, the treatment may include non-pharmacologic interventions, such as self-isolation and/or quarantine of a subject identified as being susceptible to developing an infectious disease and/or the associated complications. Alternatively, treatment is “effective” if the disease is prevented and/or if progression of a disease is reduced or halted. “Treatment” can also mean prolonging survival as compared to expected survival if not receiving treatment.
- A treatment is not necessarily curative, and in certain aspects may reduce the effect of an infection by a certain percentage over an untreated infection. For example, treatment may reduce inflammation or reduce the presence of inflammatory cytokines in a subject suffering from an infection. In some embodiments, methods of treatment may be personalized medicine procedures, in which the DNA of an individual is analyzed to provide guidance on the appropriate therapy for that specific individual. The methods of the invention may provide guidance as to whether treatment is necessary or most effective, as well as revealing progress of the treatment and guiding the requirement for further treatment of the individual.
- It should be noted that in certain aspects, the treatment may comprise the recommendation and/or implementation of measures intended to reduce the subject's likelihood of contracting an infection, and which measures are not isolated to the subject. For example, in certain embodiments, the treatment may comprise vaccinating members of the subject's community (e.g., family, co-workers and/or healthcare providers) in an effort to reduce the transmission of the infection.
- In some embodiments, treatment comprises reducing the incidence of the presence of clonal hematopoiesis in the subject's blood. In other embodiments, treatment or monitoring includes repeating the sequencing of a blood sample of the subject monthly, bi-monthly, or quarterly, and reducing (or monitoring reduction in) the incidence of the presence of clonal hematopoiesis in the subject's blood. In some embodiments, treatment or monitoring comprises including the subject as a candidate to receive a bone marrow transplant. In some embodiments, treatment includes administering to the subject a bone marrow transplant. In some embodiments, treatment includes transfusing the subject with blood in which clonal hematopoiesis is absent.
- In some aspects, a subject is identified as being high risk based on gene sequencing (e.g., performing a CHIP assessment). A subject identified as being high risk has an increased risk of contracting an infection and/or of having a serious reaction to an infection. In some aspects, high risk subjects are treated by early targeting of inflammation. For example, a high risk subject may be treated by administering pro-inflammatory driver inhibitors and/or low-dose hypomethylating drugs. In some embodiments, high risk subjects may be treated by vaccinating the subject and/or vaccinating members of the subject's community to reduce the transmission of the infection, and thereby reduce the likelihood that the subject will become infected.
- In some aspects, vaccinating the subject and/or vaccinating members of the subject's community to reduce the transmission of the infection comprising the administration of a single vaccine dose or the administration of two vaccine doses. One or more vaccine boosters may optionally be administered after administration of the initial vaccine dose(s). For example, a vaccine booster may be administered about 6 months, 9 months, 12 months, 15 months, 18 months, 21 months, or 24 months after receiving the initial vaccine dose(s). In some aspects, a vaccine booster may be administered yearly. In some embodiments, the vaccine is an mRNA vaccine or a viral vector vaccine. In one embodiment, the vaccine is a BNT162b2 vaccine (a lipid nanoparticle-formulated,5 nucleoside-modified RNA (modRNA) encoding the SARS-CoV-2 full-length spike, modified by two proline mutations to lock it in the prefusion conformation). In one embodiment, the vaccine is a mRNA-1273 vaccine (a lipid nanoparticle-encapsulated mRNA-based vaccine that encodes the prefusion stabilized full-length spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)). In one embodiment, the vaccine is a Ad26.COV2.S Vaccine (a monovalent vaccine composed of a recombinant, replication-incompetent human adenovirus type 26 (Ad26) vector that encodes a SARS-CoV-2 spike (S) protein in a stabilized conformation). In one embodiment, the vaccine is a ChAdOx1 nCoV-19 vaccine (a replication-deficient chimpanzee adenoviral vector ChAdOx1, containing the SARS-CoV-2 structural surface glycoprotein antigen (spike protein; nCoV-19) gene).
- In some aspects, treating a subject for an infection includes adjuvant treatment. For example, adjuvant treatment for preventing sequelae of acute pulmonary disease may include administration of one or more antiviral medications (e.g., remdesivir), anti-inflammatory medications, antibiotics, plasmapheresis, convalescent plasma infusion, monoclonal antibodies (e.g., bamlanivimab, etesevimab, casirivimab, imdevimab, recombinant humanized anti-interleukin-6 receptor monoclonal antibodies (e.g., tocilizumab)), corticosteroids (e.g., dexamethasone), supplemental oxygen, and mesenchymal stem cell/iPS cell therapy. In some aspects, adjuvant treatment for preventing sequelae of cardiac and/or infectious disease includes administration of one or more antiviral medications, anti-inflammatory medications, antibiotics, plasmapheresis, convalescent plasma, mesenchymal stem cell/iPS cell therapy, blood thinners, anti-arrhythmic drugs, and cardioprotective drugs. In certain aspects, blood pressure medications may be administered to a subject including angiotensin converting enzyme (ACE) inhibitors and/or angiotensin receptor blockers (ARBs).
- In some embodiments, a subject's susceptibility to an infection is predicted using the sequencing and detection methods described herein. For example, a subject's susceptibility to an infection (e.g., a coronavirus infection) may be predicted by sequencing one or more nucleic acids selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1 from one or more cells in a blood sample of the subject; and detecting the presence of a mutation in the sequenced nucleic acids. In some embodiments, the presence of the mutation indicates an increased susceptibility to a coronavirus (e.g., COVID-19) infection. In some embodiments, a subject's increased mortality risk, e.g., resulting from a dysfunctional immune response, is predicted using the sequencing and detection methods described herein. In some aspects, the dysfunctional immune response is an inflammatory or interferon response.
- In certain embodiments, a subject's susceptibility to an infection (e.g., a coronavirus infection) is predicted by sequencing DNMT3A and TET2 nucleic acids from one or more cells in a blood sample from the subject and detecting the presence of a mutation (e.g., mis-sense mutations or disruptive mutations) in the sequenced nucleic acids. The presence of a mutation in the sequenced DNMT3A and/or TET2 nucleic acids may indicate a subject's increased susceptibility to the infection.
- In certain embodiments, the subject is a mammal, e.g., a primate, e.g., a human. The terms, “patient” and “subject” are used interchangeably herein. Preferably, the subject is a mammal. The mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but are not limited to these examples. In certain embodiments, the subject is a human.
- The subject may be any age from birth to death, e.g., the subject may be an infant, a toddler, a child, a teenager, a young adult, or an adult. The subject may be at least about 1 day old, 1 year old, 5 years old, 10 years old, 20 years old, 30 years old, 40 years old, 50 years old, 60 years old, 70 years old, 80 years old, 90 years old, or 100 years old. In some embodiments, the subject is under the age of 40, between the ages of 40-60, or over the age of 60.
- In other embodiments, the subject may exhibit one or more risk factors including asthma, chronic lung disease, interstitial lung disease, cystic fibrosis, pulmonary hypertension, chronic obstructive pulmonary disease (COPD), diabetes, obesity, being aged 65 years or older, heart condition (e.g., heart failure, coronary artery disease, cardiomyopathies, hypertension, etc.), high blood pressure, chronic kidney disease, immunocompromised (e.g., undergoing therapy for cancer), liver disease, dementia or other neurological condition, down syndrome, HIV infection, pregnancy, sickle cell disease or thalassemia, stroke or cerebrovascular disease, solid organ or blood stem cell transplant, substance use disorder, or history of being a smoker. In some embodiments, the subject has a comorbid condition selected from the group consisting of cardiovascular disease, lung disease, kidney disease, liver disease, neurological condition, cerebrovascular disease, diabetes, obesity, asthma, emphysema, and cancer.
- It is to be understood that the invention is not limited in its application to the details set forth in the description or as exemplified. The invention encompasses other embodiments and is capable of being practiced or carried out in various ways. Also, it is to be understood that the phraseology and terminology employed herein is for the purpose of description and should not be regarded as limiting.
- While certain compounds, compositions and methods of the present invention have been described with specificity in accordance with certain embodiments, the following examples serve only to illustrate the methods and compositions of the invention and are not intended to limit the same.
- The articles “a” and “an” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to include the plural referents. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention also includes embodiments in which more than one, or the entire group members are present in, employed in, or otherwise relevant to a given product or process. Furthermore, it is to be understood that the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, descriptive terms, etc., from one or more of the listed claims is introduced into another claim dependent on the same base claim (or, as relevant, any other claim) unless otherwise indicated or unless it would be evident to one of ordinary skill in the art that a contradiction or inconsistency would arise. Where elements are presented as lists, (e.g., in Markush group or similar format) it is to be understood that each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements, features, etc., certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements, features, etc. For purposes of simplicity those embodiments have not in every case been specifically set forth in so many words herein. It should also be understood that any embodiment or aspect of the invention can be explicitly excluded from the claims, regardless of whether the specific exclusion is recited in the specification. The publications and other reference materials referenced herein to describe the background of the invention and to provide additional detail regarding its practice are hereby incorporated by reference.
- A DNA microarray will be used to identify, and report inherited genetic variants (e.g., TET2, DNMT3A, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS, and/or SF3B1) associated with a variety of cardiovascular and metabolic disorders, as well as with certain cancers. These cancers and disorders, if pre-existing, can increase the risk of death related to COVID 19 complications. Also included in this microarray are genetic variants associated with pro- and anti-inflammatory effects. Some of these include ACE2, CRP, IL-6R, IL-1A GC, and IL-10. Furthermore, the microarray may elucidate which inborn errors of immunity can cause life-threatening COVID 19 in previously healthy younger patients.
- In addition, the microarray may test for various biomarkers present in the blood that are involved in immunity and inflammation, which may impact COVID 19 infection response. These biomarkers may include hsCRP, IL-6, IL-8, and TNF-alpha.
- Clonal hematopoiesis of indeterminate potential (CHIP) is a genetic issue unique to nucleated cells contained within the blood. CHIP refers to the unhealthy expansion of the same set of detrimental mutations and damage to an individual's DNA in their nucleated blood cells. CHIP may potentially explain the age-related prevalence of inflammatory conditions. A connection between CHIP mutations and heart diseases is believed to be mediated by inflammation. It has been more recently postulated that CHIP may be associated with broader biological impact which may be explained by the fact that people with CHIP have an aberrant inflammatory system compared with those without CHIP. Specifically, recent research has demonstrated that structural DNA damage in genes such as TET2 and DNMT3A is associated with a dysfunctional response to inflammation and infection. In addition, key cytokines such as serum IL-6 and IL-8 have been shown to be elevated in people with CHIP, establishing its relevance to the human systemic inflammatory landscape and its impact on poorer health status, and increased and potentially novel comorbidities.
- It is known that somatic exonic mutations are acquired at a rate of approximately 1.3 per hematopoietic stem cell per decade and are rarely detected in people under age 40 years. Clonal hematopoiesis increases with age and is found in approximately 10 percent of people without known hematologic malignancies older than 65 years, in almost 12 percent of those aged 80 to 89 years, and in more than 18 percent of those older than 90 years.
- In addition to detecting and monitoring somatic changes associated with CHIP, a screen will also be performed for germline/inherited variants associated with cardiovascular disease, cancer, and inflammation. The association between CHIP, inflammation, and leukocyte dysfunction will be examined so the CHIP-related comorbidities in COVID 19 can be more effectively managed clinically. For example, the presence of CHIP as a disease modifier might explain why some patients are more responsive or refractory to treatments, or why some patients undergo more slow or rapid disease progression. Furthermore, this dynamic measurement may elucidate novel opportunities to develop new drug therapies focusing on the genetic abnormalities of CHIP.
- Within the PBMCs that are isolated and preserved from the peripheral blood, a variety of potentially therapeutic cell types will be accessed, including small numbers of CD34+ hematopoietic stem cells (HSCs), T-cells and circulating endothelial progenitor cells (EPCs) that allow for the derivation of clinical grade induced pluripotent stem (iPS) cells. Notably iPS cells can be programmed to produce virtually any cell type in the human body, such as immune cells and alveolar cells of the lung which produce surfactant (AE2). AE2 cells play various roles in alveolar fluid balance, coagulation/fibrinolysis, and host defense. AE2 cells proliferate, differentiate into AE1 cells, and contribute to epithelial repair and immunoregulation. In addition, iPS cells can be differentiated into mesenchymal stem cells (MSCs) which are known to modulate the pro-inflammatory immune cytokine response which is largely responsible for the cascade of events leading to severe pulmonary disease. Whether these cells can restore healthy lung tissue after a COVID 19 infection will be examined. Blood-derived iPS cells represent a personalized cell resource for individuals to generate AE2 cells and cells of immune function as a therapy option.
- We will provide genetic evaluation for a better understanding of the genetic history and at risk disease potential, tracking of biomarkers to evaluate progression of disease, measurement of somatic damage and mutations that may contribute to a deranged inflammatory response, and the opportunity to utilize stem cells in potential therapies, potentially including those for COVID 19 or other viral disease.
- CHIP is a genetic issue unique to the nucleated cells contained within blood. It refers to the unhealthy expansion of the same set of detrimental mutations and damage to an individual's DNA in their nucleated blood cells. CHIP may potentially explain the age-related prevalence of inflammatory conditions. A connection between CHIP mutations and heart diseases is believed to be mediated by inflammation. It has been more recently postulated that CHIP may be associated with broader biological impact which may be explained by the fact that people with CHIP have an aberrant inflammatory system compared with those without CHIP. Specifically, key cytokines such as serum IL-6 and IL-8 have been shown to be elevated in people with CHIP, establishing its relevance to the human systemic inflammatory landscape and its impact on poorer health status, and increased and potentially novel comorbidities.
- It is known that somatic exonic mutations are acquired at a rate of approximately 1.3 per hematopoietic stem cell per decade, and are rarely detected in people under age 40 years. Clonal hematopoiesis increases with age and is found in approximately 10 percent of people without known hematologic malignancies older than 65 years, in almost 12 percent of those aged 80 to 89 years, and in more than 18 percent of those older than 90 years.
- Whether an age-related increase in CHIP contributes to the age-related risk of COVID 19 will be assessed. If these phenomena are shown to be linked, the CHIP-related analysis will provide a quantifiable risk assessment. If the complex association between CHIP, inflammation, and leukocyte dysfunction can be unraveled, CHIP-related comorbidities in COVID 19 may be more effectively managed clinically. For example, the presence of CHIP as a disease modifier may explain why some patients are more responsive or refractory to treatments, or why some patients undergo more slow or rapid disease progression.
- By monitoring acquired changes to both sequence and structure of the DNA within the blood it may ultimately provide an additional layer of insight into identifying those at increased risk for infection or COVID 19 complicated mortality. Somatic changes associated with CHIP may be detected and monitored, as well as screening for germline/inherited variants associated with cardiovascular disease, cancer, and inflammation. Blood samples will be evaluated with a target sequence panel specific to genes with somatic (accumulated) and germline (inherited) variants associated with CHIP, including but not limited to TET2 and DNMT3A, both of which have been associated with a dysfunctional response to inflammation and infection. In addition, microarray-based methods are used to measure somatic structural DNA variation and damage across the genome, additionally associated with CHIP. Genetic test results will be correlated with serologic and clinical data from the subject's medical record.
- Blood samples will be collected from a variety of subjects. The blood samples will be assessed to identify samples that are seropositive COVID 19, Influenza A, Influenza B, RSV, SARS-CoV, and MERS-CoV. In addition, normal control blood samples will also be obtained. The blood samples will be assayed for clonal hematopoiesis (CHIP) using an assay that screens for somatic variations in TET2, DNMT3A, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS, and SF3B1.
- Additional assessments will be performed on the blood samples including evaluating the samples for additional variants in other genes, as well as performing additional blood analysis. Further, clinical data will be collected for the subjects from who the blood samples were taken from.
- In addition, the samples will be evaluated for one or more variants in ACE2, IFITM3, IL-1A, IL-1B, IL-6, IL-6R, CXCL8, IL-12A, IL-12B, IL-18, TNF-α, TNF-β, and TNF-γ. The samples will be assessed for additional features such as arterial blood gas, white count with differential (lymphocytes, neutrophils, cytokine levels, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), Lactase, MB-CK enzyme, etc.) Clinical data for the subjects from whom the blood samples are obtained will additionally be considered including, but not limited to, the development of any complications related to the diagnosis (MI, myocarditis, pulmonary embolism), vital signs, O2 sat, O2 requirements, intubation status, mortality, and cause(s) of death. Additionally, any imaging obtained from the subject will be considered, including chest X rays (CXR) and CT scans. Finally, any co-morbidities and family history will also be taken into consideration.
- CHIP may be utilized as a disease modifier to explain why some COVID 19 patients undergo a faster and more severe disease progression, and why some patients are more responsive/refractory to treatments. In addition, CHIP may be utilized as a disease modifier in determining which patients are more susceptible to poor cardiac outcomes. CHIP may also be utilized to provide guidance on mitigation strategies for population management, e.g., establishing quarantine protocols and identifying groups of individuals to be quarantined, possibly more restrictively than other individuals.
- The arrival of the newly discovered coronavirus in 2019 has impacted the world gravely, with over 136 million reported cases and over 3 million deaths worldwide. To date, no effective intervention strategies are in place, yet the emergence of mutant strains is dispersing rapidly. In addition, molecular rRT-PCR tests may result in false-negative or false-positive outcomes thereby questioning its status as ‘golden standard’ for laboratory diagnosis of coronavirus disease 2019 (COVID-19) (1). Novel effective diagnostic solutions could be the key to curbing the spread of COVID-19, as early diagnosis is crucial for controlling infectious propagation.
- Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-COV-2) is an enveloped single-stranded, positive-sense ribonucleic acid (ssRNA+) coronavirus which belongs to the family of Coronaviridae (2). The infection manifests itself as mild-moderate symptoms, such as coughing, muscle fatigue and fever to severe respiratory failure which requires ICU care and ventilation (3).
- Important predictors of severe clinical outcomes are advanced age, gender and comorbid conditions including obesity, diabetes, cardiovascular diseases (CVDs) and chronic obstructive pulmonary disease (COPD) (4-7). Furthermore, emerging data indicate that uncontrolled inflammation is associated with disease severity. Indeed, unfettered release of pro-inflammatory cytokines such as IL-6, IL-2, IL-7 and TNF-alpha can cause a so-called cytokine storm, a potential life-threatening phenomenon frequently seen in COVID-19 patients with severe infection (8). In these patients, the hyperactive immune activation may progress to acute respiratory stress syndrome (ARDS) and multiple organ dysfunctions (9). The presence of a cytokine storm may contribute to cardiovascular complications, including unstable plaque formation, coronary artery occlusion, myocardial infarction and, eventually, transition to heart failure (10, 11).
- While it is evident that inflammation and pre-existing comorbidities play a significant role in the pathogenesis of COVID-19, the presence of somatic acquired mutations has now been recognized as possibly another independent determinant for disease outcome (12, 26). These mutations are found in genes involved in epigenetic regulation including DNMT3A, TET2, ASXL1 and JAK2, and result in expansion of genetically identical clones of nucleated peripheral blood stem and progenitor cells. This phenomenon is referred to as clonal hematopoiesis of indeterminate potential (CHIP) and affects a large proportion (>10%) of the older population over the age of 70 (13). Individuals with CHIP are at an increased risk for developing CVDs, including aortic valve stenosis, venous thrombosis, and heart failure (14-16). Growing evidence indicates that the heightened risk might be due to hyper-inflammatory potential in these individuals (17-19). Indeed, a TET2 deletion has been associated with inflammasome activation and subsequent excessive levels of pro-inflammatory cytokines IL-6 and IL-1, whereas DNMT3A mutations have shown increased numbers of chemokines and reduced type-1-interferon secretion compared to non-CHIP carriers (20-23). Remarkably, however, individuals with large DNMT3A or TET2 CHIP-driver mutations (allele fraction of >10%) were protected from cardiovascular events if they also had a simultaneous germline sequence variation in the IL-6 receptor (IL-6R) (24). While most of these outcomes were studied in monocytes and macrophages, CHIP mutations have also been shown to alter the function of other leukocyte populations (25). Thus, the presence of CHIP might dysregulate the entire inflammatory system and therefore may corrupt disease outcome in COVID-19 patients.
- In support of this notion, recent clinical data showed higher CHIP frequencies in patients with severe COVID-19 compared to the control population (26-27). It should be noted, however, that the control group of one study, referenced herein as the Duployez study (26) consisted mostly of individuals with unexplained cytopenia, thereby potentially introducing biases that underestimate the overall risk of CHIP. Furthermore, Shivarov, et al. consolidated data of four large studies on the frequency of CHIP and observed a linear correlation between the presence of CHIP clones and mortality rate in COVID-19-infected patients (12). This suggests that detection of CHIP may be predictive of fatal outcome in patients with COVID-19. However, to date no clinical studies have been identified that have conducted a comparison of CHIP prevalence to mild and severe COVID-19 symptoms.
- In the present study, the hypothesis that CHIP is associated with disease severity in COVID-19 patients was tested. Three age groups were evaluated—under 40 years-old, 40-60 years old and those older than 65 years. While CHIP has been reported to be rare in younger people with frequencies of about 1 in 1000 in those younger than 40 and about 0.7% in those under 50, CHIP has been more recently found in higher frequencies in younger individuals with early-onset myocardial infarction and in some advanced autoimmune disease, and hence it was hypothesized that it could be a risk factor in younger populations with severe COVID-19 disease (27, 29).
- Patients and Samples—Patient samples were collected both through collaboration and under the IRB of the New York Blood Center (NYBC) as well as via a prospective procurement contract through iSpecimen. Patients included in the study were confirmed to be PCR positive for SARS-CoV-2 infection and classified as either severe hospitalization or non-hospitalized. Severe hospitalized patients were defined as infected and admitted to the hospital for a minimum of seven days, with a priority towards patients admitted to the ICU and requiring oxygen support. Non-hospitalized patients were defined as infected and symptomatic (fever, loss of smell, body aches, coughing) or asymptomatic, but not requiring hospitalization. Samples were excluded from collection and/or analysis if the patient had previously received blood stem cell transplant or had undergone chemotherapy. Samples procured through NYBC were delivered as cryopreserved PBMCs while samples received from iSpecimen were supplied as frozen whole blood (WB).
- Molecular Analysis—Genomic DNA (gDNA) was extracted from cryopreserved PBMC and frozen WB samples using the PerkinElmer Chemagic 360 B5K automated extraction platform. For targeted sequencing extracted gDNA was normalized and aliquoted to 25 ng/ul in 25 ul total volume. Custom DNA target sequencing libraries were constructed using Agilent SureSelect chemistry. The resulting libraries were analyzed on the Agilent 4200 TapeStation System and quantified by KAPA qPCR. Samples were sequenced using the Illumina MiSeq platform with an averages sequencing coverage>1000× across amplicons. DNA sequence quality was verified and then BAM (Binary Alignment/Map) and VCF (Variant Call Format) files were generated. Putative somatic variants were annotated against GenBank gene models and the ClinVar database. Both somatic and germline coding variants from genes DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SF3B1, SRSF2, and KRAS were extracted from the annotated VCF. Upon analysis CHIP accumulated/somatic variants were defined as having >1.5% variant allele frequency (VAF) and 20 or more variant cells.
- For microarray analysis, extracted gDNA was normalized and aliquoted to 25 ng/ul in 50 ul total volume. Normalized and aliquoted gDNA samples were run on the Illumina Infinium™ Global Screening Array (GSA)—24 v2.0 BeadChip in the labs of Diagnomics (San Diego, Calif. USA). The resulting iDAT files were converted to GTC files using the Illumina Array Analysis Platform and a VCF file with genotype information was generated. SNP and indel markers were annotated against GenBank gene models and a table with all the genotyped markers from genes IL6R, CXCL8, IL6, and ACE2 were extracted from the VCF using the BCFtools+split−vep plugin.
- The study described herein assessed whether CHIP is associated with disease severity in COVID-19 patients by looking at three age groups of patients—under 40 years-old, 40-60 years old and older than 65 years. The most common somatic mutations identified were DNMT3A and TET2 in all groups, with 54% in those <60, and 71% in those over the age of 65. A summary of the individual groups is provided below.
- The cohort of severe disease in the under 40 group included 9 patients. Two patients (22.2%) had CHIP with VAF>1.5%. One of these patients had two CHIP mutations (DNMT3A and SF3B1) both with a VAF>1.5%. A third patient had a somatic mutation in TP53 with a VAF of 0.8% overall resulting in 3 patients (33.3%) having detectable somatic CHIP mutations. The expected CHIP in individuals under the age of 40 is about 0.1%. In addition, a fourth patient in this group had a germline mutation in TP53. Collection of samples from COVID-19 infected but non-hospitalized individuals in this age group is under way.
- The cohort in the 40-60 age group included 36 patients with severe disease and 4 non-hospitalized infected patients. Three (8.3%) of the 36 patients with severe disease had CHIP with VAF>1.5% with the following mutations: TET2, DNMT3A and KRAS. In addition, 7 additional patients with severe disease had CHIP mutations (3 with DNMT3A, 1 with TET2, 1 with KRAS and 1 with TP53) with a VAF<1.5%, overall resulting in 10 patients (27.8%) having detectable somatic CHIP mutations. The expected frequency of CHIP in a matched healthy 40-60 group would be approximately 2-3%. In addition, 5 patients had germline mutations in CHIP genes (3 with TET2, 1 with PP1MD, 1 with TP53). None of the 4 samples collected in non-hospitalized COVID19 infected patients in this age group demonstrated CHIP with a VAF>1.5%.
- This cohort includes 43 hospitalized patients with severe disease, 46 non-hospitalized infected patients and a historic control of 106 individuals. The median age for each group is 69.5, 68.7, and 82 respectively. The frequency of CHIP>1.5% VAF was 14%, 16%, 35% respectively.
-
TABLE 1 NYBC Study >65 40-60 <40 CHIP > 1.5% CHIP > 1.5% CHIP >1 .5% Severe 6/43 (14%) 3/36 (8.3%) 2/9 (22%) Mild 7/45 (16%) 0/4 (0%) N/A Healthy (33%) (2-3%) (0.1%) Population
Germline Mutations (IL-6R p. Asp358Ala Coding Mutation) - In addition, multiple studies have demonstrated the increased risk of cardiovascular disease in the presence of CHIP (17, 27). However, the risk of incident cardiovascular events such as myocardial infarction, stroke and death is abrogated in those with a simultaneous genetic deficiency of IL-6 signaling (IL-6R p Asp358Ala) (24). It is hypothesized that the increased risk of CVD is mediated by IL-6 signaling. Likewise, the severity of COVID-19 has been associated with a dysfunctional inflammatory response mediated by cytokines, particularly IL-6. In one example, a COVID-19 infected patient with two large clone CHIP mutations (JAK2 mutation with 76% VAF and TET2 mutation with 23% VAF) also had an IL-6R coding mutation which may have protected this patient from developing severe disease. In this study, 5.1% of patients with CHIP and a simultaneous genetic deficiency in IL-6 signaling (by carrying IL6R p.Asp358A1a) were non-hospitalized when infected with COVID-19. On the other hand, only 1.6% of patients with CHIP and this coding mutation developed severe COVID-19 disease. Therefore, genetically reduced IL-6 signaling may abrogate the risk of developing severe disease among carriers of CHIP.
- Additional studies looking at the association of CHIP with COVID-19 have been conducted by other research groups. A first study is identified herein as the French study and described in Duployez, et al., (26), and a second study is identified herein as the MSK study and described in Bolton et al., (28). Both studies assessed the relationship between clonal hematopoiesis and the severity of a COVID-19 infection. The two studies are summarized below.
- 122 patients hospitalized for COVID19. 76% male. 73% ICU.
- A high prevalence of Clonal Hematopoiesis (25%, 38%, 56%, and 82% of patients aged <60 years, 60-70 years, 70-80 years, and >80 years) was reported compared to a retrospective cohort of patients explored within the same pipelines (10%, 21%, 37%, and 44%). 80% of those with CHIP had DNMT3A and/or TET2 mutations. After adjustment for age, the prevalence OR of CH was 3.182 (95% CI: 1.944-5.209, p<0.001) in COVID-19 patients.
-
TABLE 2 French Study summary Age CHIP Positive Control Group <60 25% 10% 60-70 38% 21% 70-80 56% 37% >80 82% 44% - Among 515 individuals with Covid-19 from Memorial Sloan Kettering (MSK) and the Korean Clonal Hematopoiesis (KoCH) consortia, it was found that CH was associated with severe Covid-19 outcomes (OR=1.9, 95%=1.2-2.9, p=0.01).
- The first cohort was composed of patients with solid tumors treated at Memorial Sloan Kettering Cancer Center (MSK) with blood previously sequenced using MSK-IMPACT, a previously validated targeted gene panel capturing all commonly mutated CH-associated genes. In the MSK cohort, CH was observed in 51% and 30% of patients with severe versus non-severe Covid-19, respectively (adjusted OR: 1.85, 95% CI 1.10-3.12).
- The second cohort included 112 previously healthy individuals without cancer who were hospitalized for Covid-19 between January and April 2020 at four tertiary hospitals in South Korea (KoCH cohort). The KoCH cohort was sequenced using a custom targeted NGS panel from Agilent (89 genes) which was designed to include commonly occurring CH genes.
- In the KoCH cohort, CH was observed in 25% and 15.9% of patients with severe versus non-severe Covid-19, respectively (adjusted OR 1.85, 95% CI 0.53-6.43). A comparative analysis of age groups was not performed.
-
TABLE 3 MSK Study summary Severe Severe Non-Severe Control Non- Odds Chip − CHIP + Chip − Severe Chip + Ratio MSK 46 48 223 96 1.85 KoCH 51 17 37 7 1.85 - The frequency of clonal hematopoiesis is rare in healthy individuals under 40 and uncommon in those under 60. The results from the study described herein demonstrate there is a relatively high frequency of CHIP in younger patients infected with COVID-19 who have been hospitalized with severe disease. And when lower VAFs were included in the analysis, this frequency increased further. CHIP may provide an explanation why some younger patients infected with COVID-19 have a clinical course that requires hospitalization. This is consistent with prior studies implicating CHIP in dysfunctional inflammatory responses with elevated cytokines and decreased interferons which is the typical profile of patients with severe disease (REF). Therefore, this would be the presumed mechanism in the younger cohort with severe disease in our study. Furthermore, acute and chronic cardiovascular events are a frequent cause of morbidity and mortality in hospitalized COVID-19 patients and CHIP has been highly associated with cardiovascular diseases such as myocardial infarction and stroke. Not only is CHIP a significant risk factor for myocardial infarction of all ages, but the risk is highest in younger patients who demonstrates early-onset myocardial infarction (27). Mutations in DNMT3A and TET2 were each individually associated with coronary heart disease and in fact, these were the most frequently mutated in the CHIP patients with severe disease who were assessed in the study described herein.
- The data to date does not show a higher frequency of CHIP in individuals >65 years old with severe disease compared to the control groups as was demonstrated in two recent studies (26, 28). It was hypothesized that the presence of other comorbidities in the older patients in the study contribute to a similar degree as CHIP and these comorbidities are less frequent in younger populations.
- Regarding the younger cohort, while there is a paucity of literature studying younger individuals with CHIP, a few recent studies have identified younger patients with severe autoimmune diseases as having CHIP. For example, CHIP was found with a relatively high frequency in patients with RA, but particularly in those with clinically advanced and refractory disease and including some patients in their 30s (BMJ).
- The data provided from this study also demonstrates that genetically reduced IL-6 signaling which has been previously shown to be protective for cardiovascular insults may abrogate the risk of developing severe disease among carriers of CHIP.
-
- 1. Tahamtan, A., and A. Ardebili. 2020. Real-time RT-PCR in COVID-19 detection: issues affecting the results. Expert Rev Mol Diagn 20: 1-2.
- 2. Lotfi, M., M. R. Hamblin, and N. Rezaei. 2020. COVID-19: Transmission, prevention, and potential therapeutic opportunities. Clin Chim Acta 508: 254-266.
- 3. Grant, M. C., L. Geoghegan, M. Arbyn, Z. Mohammed, L. McGuinness, E. L. Clarke, and R. G. Wade. 2020. The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries. Plos One 15: e0234765.
- 4. Lauc, G., and D. Sinclair. 2020. Biomarkers of biological age as predictors of COVID-19 disease severity. Aging Albany Ny 12: 6490-6491.
- 5. Xiao, W.-W., J. Xu, L. Shi, Y.-D. Wang, and H.-Y. Yang. 2020. Is chronic obstructive pulmonary disease an independent predictor for adverse outcomes in coronavirus disease 2019 patients? Eur Rev Med Pharmaco 24: 11421-11427.
- 6. Ou, M., J. Zhu, P. Ji, H. Li, Z. Zhong, B. Li, J. Pang, J. Zhang, and X. Zheng. 2020. Risk factors of severe cases with COVID-19: a meta-analysis. Epidemiol Infect 148: e175.
- 7. Zhang, J., X. Dong, Y. Cao, Y. Yuan, Y. Yang, Y. Yan, C. A. Akdis, and Y. Gao. 2020. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan, China. Allergy 75: 1730-1741.
- 8. Huang, C., Y. Wang, X. Li, L. Ren, J. Zhao, Y. Hu, L. Zhang, G. Fan, J. Xu, X. Gu, Z. Cheng, T. Yu, J. Xia, Y. Wei, W. Wu, X. Xie, W. Yin, H. Li, M. Liu, Y. Xiao, H. Gao, L. Guo, J. Xie, G. Wang, R. Jiang, Z. Gao, Q. Jin, J. Wang, and B. Cao. 2020. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 395: 497-506.
- 9. Zhou, F., T. Yu, R. Du, G. Fan, Y. Liu, Z. Liu, J. Xiang, Y. Wang, B. Song, X. Gu, L. Guan, Y. Wei, H. Li, X. Wu, J. Xu, S. Tu, Y. Zhang, H. Chen, and B. Cao. 2020. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. Lancet 395: 1054-1062.
- 10. Unudurthi, S. D., P. Luthra, R. J. C. Bose, J. McCarthy, and M. I. Kontaridis. 2020. Cardiac inflammation in COVID-19: Lessons from heart failure. Life Sci 260: 118482.
- 11. Magadum, A., and R. Kishore. 2020. Cardiovascular Manifestations of COVID-19 Infection. Cells 9: 2508.
- 12. Shivarov, V., and M. Ivanova. 2020. Clonal haematopoiesis and COVID-19: A possible deadly liaison. Int J Immunogenet 47: 329-331.
- 13. Jaiswal, S., P. Fontanillas, J. Flannick, A. Manning, P. V. Grauman, B. G. Mar, R. C. Lindsley, C. H. Mermel, N. Burtt, A. Chavez, J. M. Higgins, V. Moltchanov, F. C. Kuo, M. J. Kluk, B. Henderson, L. Kinnunen, H. A. Koistinen, C. Ladenvall, G. Getz, A. Correa, B. F. Banahan, S. Gabriel, S. Kathiresan, H. M. Stringham, M. I. McCarthy, M. Boehnke, J. Tuomilehto, C. Haiman, L. Groop, G. Atzmon, J. G. Wilson, D. Neuberg, D. Altshuler, and B. L. Ebert. 2014. Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes. New Engl J Medicine 371: 2488-2498.
- 14. Mas-Peiro, S., J. Hoffmann, S. Fichtlscherer, L. Dorsheimer, M. A. Rieger, S. Dimmeler, M. Vasa-Nicotera, and A. M. Zeiher. 2019. Clonal haematopoiesis in patients with degenerative aortic valve stenosis undergoing transcatheter aortic valve implantation. Eur Heart J 41: 933-939.
- 15. Sano, S., Y. Wang, Y. Yura, M. Sano, K. Oshima, Y. Yang, Y. Katanasaka, K.-D. Min, S. Matsuura, K. Ravid, G. Mohi, and K. Walsh. 2019. JAK2 V617F-Mediated Clonal Hematopoiesis Accelerates Pathological Remodeling in Murine Heart Failure. Jacc Basic Transl Sci 4: 684-697.
- 16. Bazeley, P., R. Morales, and W. H. W. Tang. 2020. Evidence of Clonal Hematopoiesis and Risk of Heart Failure. Curr Hear Fail Reports 17: 271-276.
- 17. Jaiswal, S., and P. Libby. 2020. Clonal haematopoiesis: connecting ageing and inflammation in cardiovascular disease. Nat Rev Cardiol 17: 137-144.
- 18. Yura, Y., S. Sano, and K. Walsh. 2020. Clonal Hematopoiesis: A New Step Linking Inflammation to Heart Failure. Jacc Basic Transl Sci 5: 196-207.
- 19. Abplanalp, W. T., S. Cremer, D. John, J. Hoffmann, B. Schuhmacher, M. Merten, M. A. Rieger, M. Vasa-Nicotera, A. M. Zeiher, and S. Dimmeler. 2021. Clonal Hematopoiesis-Driver DNMT3A Mutations Alter Immune Cells in Heart Failure. Circ Res 128: 216-228.
- 20. Fuster, J. J., S. MacLauchlan, M. A. Zuriaga, M. N. Polackal, A. C. Ostriker, R. Chakraborty, C.-L. Wu, S. Sano, S. Muralidharan, C. Rius, J. Vuong, S. Jacob, V. Muralidhar, A. A. B. Robertson, M. A. Cooper, V. Andrés, K. K. Hirschi, K. A. Martin, and K. Walsh. 2017. Clonal hematopoiesis associated with TET2 deficiency accelerates atherosclerosis development in mice. Science 355: 842-847.
- 21. Sano, S., K. Oshima, Y. Wang, S. MacLauchlan, Y. Katanasaka, M. Sano, M. A. Zuriaga, M. Yoshiyama, D. Goukassian, M. A. Cooper, J. J. Fuster, and K. Walsh. 2018. Tet2-Mediated Clonal Hematopoiesis Accelerates Heart Failure Through a Mechanism Involving the IL-1β/NLRP3 Inflammasome. J Am Coll Cardiol 71: 875-886.
- 22. Wang, Y., S. Sano, Y. Yura, Z. Ke, M. Sano, K. Oshima, H. Ogawa, K. Horitani, K.-D. Min, E. Miura-Yura, A. Kour, M. A. Evans, M. A. Zuriaga, K. K. Hirschi, J. J. Fuster, E. M. Pietras, and K. Walsh. 2020. Tet2-mediated clonal hematopoiesis in non-conditioned mice accelerates age-associated cardiac dysfunction. Jci Insight 2020 Mar. 26; 5(6).
- 23. Rauch, P. J., A. J. Silver, J. Gopakumar, M. McConkey, E. Sinha, M. Fefer, E. Shvartz, G. Sukhova, P. Libby, B. L. Ebert, and S. Jaiswal. 2018. Loss-of-Function Mutations in Dnmt3a and Tet2 Lead to Accelerated Atherosclerosis and Convergent Macrophage Phenotypes in Mice. Blood 132: 745-745.
- 24. Bick, A. G., J. P. Pirruccello, G. K. Griffin, N. Gupta, S. Gabriel, D. Saleheen, P. Libby, S. Kathiresan, and P. Natarajan. 2019. Genetic IL-6 Signaling Deficiency Attenuates Cardiovascular Risk in Clonal Hematopoiesis. Circulation 141: 124-131.
- 25. Cook, E. K., M. Luo, and M. J. Rauh. 2020. Clonal hematopoiesis and inflammation: partners in leukemogenesis and comorbidity. Exp Hematol 83: 85-94.
- 26. Duployez, N., J. Demonchy, C. Berthon, J. Goutay, M. Caplan, A.-S. Moreau, A. Bignon, A. Marceau-Renaut, D. Garrigue, I. Raczkiewicz, S. Geffroy, M. Bucci, K. Alidjinou, J. Demaret, M. Labalette, T. Brousseau, A. Dupont, A. Rauch, J. Poissy, S. Susen, C. Preudhomme, and B. Quesnel. 2020. Clinico-Biological Features and Clonal Hematopoiesis in Patients with Severe COVID-19. Cancers (2020) 12(7): 1992.
- 27. S. Jaiswal, P. Natarajan, A. J. Silver, C. J. Gibson, A. G. Bick, E. Shvartz, M. McConkey, N. Gupta, S. Gabriel, D. Ardissino, U. Baber, R. Mehran, V. Fuster, J. Danesh, P. Frossard, D. Saleheen, O. Melander, G. K. Sukhova, D. Neuberg, P. Libby, S. Kathiresan, and B. L. Ebert. Clonal Hematopoiesis and Risk of Atherosclerotic Cardiovascular Disease N Engl J Med 2017; 377:111-121.
- 28. Bolton, K., Youngil Koh, Michael B. Foote, Hogune Im, et al. Clonal hematopoiesis is associated with risk of severe Covid-19. medRxiv 2020. 11.25.20233163.
- 29. Savola, P., Lundgren, S., Keränen, M. A. I. et al. Clonal hematopoiesis in patients with rheumatoid arthritis. Blood Cancer Journal 8, 69 (2018).
- 30. Tariq F, Alobaidi B, Xavier M on behalf of Human Dendritic Cell Lab, Newcastle University, United Kingdom, et al HU0026 CLONAL HAEMATOPOIESIS ASSOCIATED SOMATIC MUTATIONS IN RHEUMATOID ARTHRITIS Annals of the Rheumatic Diseases 2020; 79:226.
- 31. Tyrrell, D. J., Goldstein, D. R. Ageing and atherosclerosis: vascular intrinsic and extrinsic factors and potential role of IL-6. Nat Rev Cardiol 18, 58-68 (2021).
- 32. Pedersen K M, Çcolak Y, Ellervik C, et al. Loss-of-function polymorphism in IL6R reduces risk of JAK2V617F somatic mutation and myeloproliferative neoplasm: A Mendelian randomization study. Eclinicalmedicine. 2020 April; 21:100280.
Claims (21)
1. A method of treating a subject at risk of developing a severe complication from Coronavirus disease 2019 (COVID-19) infection, the method comprising
determining whether the subject has clonal hematopoiesis of indeterminate potential (CHIP), wherein the step of determining whether the subject has CHIP comprises sequencing at least part of the genome of one or more cells in a blood sample of the subject to identify a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1, wherein the presence of said mutation indicates that the subject is at risk of developing a severe complication from COVID-19 infection; and
treating the subject identified as being at risk of developing a severe complication from COVID-19, wherein treating the subject comprises administering to the subject a treatment selected from the group consisting of an antiviral medication, monoclonal antibodies, and combinations thereof to reduce the subject's likelihood of contracting a severe complication from COVD-19 infection.
2. The method of claim 1 , wherein treating the subject further comprises administering to the subject one or more agents or vaccines to reduce the subject's likelihood of contracting COVD-19 infection.
3. The method of claim 1 , wherein the subject is under the age of 40.
4. The method of claim 1 , wherein the one or more cells in the blood sample are nucleated cells.
5. The method of claim 1 , wherein the one or more cells in the blood sample are somatic cells.
6. The method of claim 1 , wherein the mutation is a somatic mutation in DNMT3A and/or TET2.
7. The method of claim 1 , wherein the mutation is in DNMT3A in exons 7 to 23.
8. The method of claim 1 , wherein the mutation is a mis-sense mutation in DNMT3A selected from the group consisting of G543C, S714C, F732C, Y735C, R736C, R749C, F751C, W753C, and L889C.
9. A method of treating a subject at risk of developing a severe coronavirus infection comprising determining whether the subject has clonal hematopoiesis of indeterminate potential (CHIP), wherein the step of determining whether the subject has CHIP comprises sequencing at least part of the genome of one or more cells in a blood sample of the subject to identify a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1, wherein the presence of said mutation indicates that the subject has CHIP and is at risk of developing a severe coronavirus infection; and
treating the subject having CHIP by administering a treatment selected from the group consisting of an antiviral medication, monoclonal antibodies, and combinations thereof, to reduce the subject's risk of developing a severe coronavirus infection.
10. The method of claim 9 , wherein the coronavirus is selected from the group consisting of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
11. The method of claim 9 , wherein the coronavirus comprises severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or COVID-19.
12. The method of claim 11 , wherein treating the subject further comprises administering to the subject one or more agents or vaccines to reduce the subject's likelihood of contracting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or COVID-19 infection.
13. The method of claim 9 , wherein the subject is under the age of 40.
14. The method of claim 9 , wherein the one or more cells in the blood sample are nucleated cells.
15. The method of claim 9 , wherein the one or more cells in the blood sample are somatic cells.
16. The method of claim 9 , wherein the mutation is a somatic mutation in DNMT3A and/or TET2.
17. The method of claim 9 , wherein the mutation is in DNMT3A in exons 7 to 23.
18. The method of claim 9 , wherein the mutation is a mis-sense mutation in DNMT3A selected from the group consisting of G543C, S714C, F732C, Y735C, R736C, R749C, F751C, W753C, and L889C.
19. (canceled)
20. (canceled)
21. A method of selecting hematopoietic cells for transplantation, the method comprising the steps of:
(a) obtaining a sample comprising hematopoietic cells from a human subject;
(b) sequencing at least part of the genome of one or more cells in the sample to identify a mutation in one or more genes selected from the group consisting of DNMT3A, TET2, ASXL1, PPM1D, JAK2, TP53, SRSF2, KRAS and SF3B1; and
(c) collecting the remaining hematopoietic cells in the sample for transplantation.
Priority Applications (1)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US17/875,298 US20230092981A1 (en) | 2020-04-24 | 2022-07-27 | Methods of predicting susceptibility to infectious disease and related methods of treatment |
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US202063015104P | 2020-04-24 | 2020-04-24 | |
US17/240,991 US11408026B2 (en) | 2020-04-24 | 2021-04-26 | Methods of predicting susceptibility to infectious disease and related methods of treatment |
US17/875,298 US20230092981A1 (en) | 2020-04-24 | 2022-07-27 | Methods of predicting susceptibility to infectious disease and related methods of treatment |
Related Parent Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
US17/240,991 Continuation US11408026B2 (en) | 2020-04-24 | 2021-04-26 | Methods of predicting susceptibility to infectious disease and related methods of treatment |
Publications (1)
Publication Number | Publication Date |
---|---|
US20230092981A1 true US20230092981A1 (en) | 2023-03-23 |
Family
ID=78221948
Family Applications (2)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
US17/240,991 Active US11408026B2 (en) | 2020-04-24 | 2021-04-26 | Methods of predicting susceptibility to infectious disease and related methods of treatment |
US17/875,298 Abandoned US20230092981A1 (en) | 2020-04-24 | 2022-07-27 | Methods of predicting susceptibility to infectious disease and related methods of treatment |
Family Applications Before (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
US17/240,991 Active US11408026B2 (en) | 2020-04-24 | 2021-04-26 | Methods of predicting susceptibility to infectious disease and related methods of treatment |
Country Status (7)
Country | Link |
---|---|
US (2) | US11408026B2 (en) |
EP (1) | EP4139476A1 (en) |
JP (1) | JP2023523017A (en) |
AU (1) | AU2021258334A1 (en) |
CA (1) | CA3180801A1 (en) |
MX (1) | MX2022013180A (en) |
WO (1) | WO2021217152A1 (en) |
Families Citing this family (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN118475833A (en) * | 2021-12-31 | 2024-08-09 | 深圳迈瑞生物医疗电子股份有限公司 | Blood cell analyzer, method and use of infection marker parameters |
Family Cites Families (6)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP3224381B1 (en) | 2014-11-25 | 2019-09-04 | The Brigham and Women's Hospital, Inc. | Method of identifying a person having a predisposition to or afflicted with a cardiometabolic disease |
WO2016085876A1 (en) | 2014-11-25 | 2016-06-02 | The Broad Institute Inc. | Clonal haematopoiesis |
EP3426804A4 (en) * | 2016-03-11 | 2020-03-25 | The Brigham and Women's Hospital, Inc. | Compositions and methods for treating chemotherapy resistant cancer |
US10041044B2 (en) | 2016-07-29 | 2018-08-07 | Trustees Of Boston University | Age-associated clonal hematopoiesis accelerates cardio-metabolic disease development |
US20200392533A1 (en) * | 2017-04-11 | 2020-12-17 | President And Fellows Of Harvard College | In vivo gene editing of blood progenitors |
CA3079190A1 (en) | 2017-10-17 | 2019-04-25 | President And Fellows Of Harvard College | Methods and systems for detection of somatic structural variants |
-
2021
- 2021-04-26 CA CA3180801A patent/CA3180801A1/en active Pending
- 2021-04-26 US US17/240,991 patent/US11408026B2/en active Active
- 2021-04-26 AU AU2021258334A patent/AU2021258334A1/en active Pending
- 2021-04-26 WO PCT/US2021/029249 patent/WO2021217152A1/en unknown
- 2021-04-26 EP EP21792707.8A patent/EP4139476A1/en not_active Withdrawn
- 2021-04-26 MX MX2022013180A patent/MX2022013180A/en unknown
- 2021-04-26 JP JP2022564551A patent/JP2023523017A/en active Pending
-
2022
- 2022-07-27 US US17/875,298 patent/US20230092981A1/en not_active Abandoned
Non-Patent Citations (2)
Title |
---|
Kruse R.L. Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China. F1000Res. 2020 Jan 31;9:72. * |
Yasuda et al. Leukemic evolution of donor-derived cells harboring IDH2 and DNMT3A mutations after allogeneic stem cell transplantation. Leukemia 28, 426–428 (2014). * |
Also Published As
Publication number | Publication date |
---|---|
EP4139476A1 (en) | 2023-03-01 |
AU2021258334A1 (en) | 2022-11-24 |
JP2023523017A (en) | 2023-06-01 |
CA3180801A1 (en) | 2021-10-28 |
US11408026B2 (en) | 2022-08-09 |
WO2021217152A1 (en) | 2021-10-28 |
US20210332422A1 (en) | 2021-10-28 |
MX2022013180A (en) | 2023-03-23 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
Alphonse et al. | Inositol-triphosphate 3-kinase C mediates inflammasome activation and treatment response in Kawasaki disease | |
Cole et al. | M1-like monocytes are a major immunological determinant of severity in previously healthy adults with life-threatening influenza | |
Belsher et al. | Fatal multiorgan failure due to yellow fever vaccine-associated viscerotropic disease | |
Sharma et al. | Elevation of interleukin‐18 in chronic hepatitis C: implications for hepatitis C virus pathogenesis | |
Livanos et al. | Gastrointestinal involvement attenuates COVID-19 severity and mortality | |
Matuozzo et al. | Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19 | |
Won et al. | Increased interleukin 18-dependent immune responses are associated with myopericarditis after COVID-19 mRNA vaccination | |
Yan et al. | Longitudinal peripheral blood transcriptional analysis reveals molecular signatures of disease progression in COVID-19 patients | |
US20190284531A1 (en) | Detection of t cell exhaustion or lack of t cell costimulation and uses thereof | |
Huang et al. | Interferon-gamma genetic polymorphism and expression in Kawasaki disease | |
Fragoso et al. | The interleukin 6-572 G> C (rs1800796) polymorphism is associated with the risk of developing acute coronary syndrome | |
Lohse et al. | Predictive factors of mortality in patients treated with tocilizumab for acute respiratory distress syndrome related to coronavirus disease 2019 (COVID-19) | |
Ong et al. | Temporal dynamics of the host molecular responses underlying severe COVID-19 progression and disease resolution | |
US11408026B2 (en) | Methods of predicting susceptibility to infectious disease and related methods of treatment | |
Liu et al. | Single-cell analysis reveals macrophage-driven T cell dysfunction in severe COVID-19 patients | |
Rantala et al. | Association of IL-6 and IL-6R gene polymorphisms with susceptibility to respiratory tract infections in young Finnish men | |
Chua et al. | Cross-talk between the airway epithelium and activated immune cells defines severity in COVID-19 | |
Chen et al. | Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery | |
Perez et al. | Single nuclei profiling identifies cell specific markers of skeletal muscle aging, sarcopenia and senescence | |
Kumar et al. | Pharmaco-immunomodulatory interventions for averting cytokine storm-linked disease severity in SARS-CoV-2 infection | |
Chen et al. | COVID‑19 in China: From epidemiology to treatment | |
Gaughan et al. | GB0139, an inhaled small molecule inhibitor of galectin-3, in COVID-19 pneumonitis: a randomised, controlled, open-label, phase 2a experimental medicine trial of safety, pharmacokinetics, and potential therapeutic value | |
Sheikhi et al. | Association of IL-10 gene in protection against COVID-19 disease | |
Yang et al. | Immunocompetent mouse models revealed that S100A4+ monocytes/macrophages facilitate long-term Zika virus infection in the testes | |
Zhao et al. | Longitudinal single-cell immune profiling revealed distinct innate immune response in asymptomatic COVID-19 patients |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
STPP | Information on status: patent application and granting procedure in general |
Free format text: DOCKETED NEW CASE - READY FOR EXAMINATION |
|
AS | Assignment |
Owner name: MORSE BARNES-BROWN PENDLETON PC, MASSACHUSETTS Free format text: LIEN;ASSIGNOR:LIFEVAULT BIO, INC. D/B/A GOODCELL;REEL/FRAME:063695/0491 Effective date: 20230517 |
|
STPP | Information on status: patent application and granting procedure in general |
Free format text: NON FINAL ACTION MAILED |
|
STCB | Information on status: application discontinuation |
Free format text: ABANDONED -- FAILURE TO RESPOND TO AN OFFICE ACTION |