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Clonal hematopoiesis of indeterminate potential (CHIP) occurs when hematopoietic stem cells (HSCs) acquire a mutation, most commonly a null variant in TET2 or DNMT3A, that confers a selective advantage. Blood cancers may result if additional cooperating mutations are acquired. However, CHIP may also cause atherosclerosis and other inflammatory diseases because these mutations alter the function or development of effector immune cells derived from the HSCs. Genome-wide association studies have implicated microglia, the resident myeloid cells in the brain, as key players in the biology of Alzheimer's disease (AD). Here, we asked whether CHIP associated with AD dementia or neuropathologic change, and whether mutant marrow-derived cells could be found in the brains of CHIP carriers. To test for an association, we used data from the Trans-omics for Precision Medicine project (TOPMed) and the Alzheimer's Disease Sequencing Project (ADSP), where whole genome or exome sequencing data as well as AD phenotype data was available on 5,730 persons. TOPMed contained population-based cohorts unselected for AD, while ADSP was a case-control study for AD. We surprisingly discovered that the presence of CHIP was associated with a reduced risk of AD dementia in both projects (fixed-effects meta-analysis odds ratio 0.64, p = 3.0 x 10-5, adjusted for age, sex and APOE genotype) (Figure 1). The protective effect of CHIP was strongest in those with APOE e3 or e4 alleles, but not seen in those with APOE e2 allele. No substantial differences in AD risk were seen based on mutated driver gene. In addition, the presence of CHIP was associated with a reduced burden of amyloid plaques and neurofibrillary tangles in the brains of those without dementia. In sum, our human genetic analyses indicated that CHIP was robustly associated with protection from AD dementia and AD-related neuropathologic changes. A causal link between CHIP and AD would be strengthened by finding the mutated cells infiltrating the brain. However, it is presumed that bone marrow progenitors have minimal contribution to the adult microglial pool. To determine if the mutations seen in the blood of CHIP carriers could also be found in the brain, we obtained 8 occipital cortex samples from autopsy of donors with CHIP, 6 of whom were cognitively normal at the time of death. The 8 CHIP carriers had mutations in DNMT3A, TET2, ASXL1, SF3B1, and GNB1 with the highest frequency in DNMT3A and TET2, which is representative of the relative proportion of these mutations in the general population. We detected the CHIP somatic variants in the microglia enriched (NeuN- c-Maf+) fraction of brain in 7 out of 8 CHIP carriers, with a VAF ranging from 0.02 to 0.28 (representing 4% to 56% of nuclei) (Figure 2), but at low levels or absent in the other fractions of brain. We then performed single-cell ATAC-sequencing on brain samples from 2 CHIP carriers and 1 control to specify the cellular population harboring CHIP mutations. This revealed that hematopoietic cells in the 3 samples formed a single myeloid cluster that had accessible chromatin at the microglia marker genes TMEM119, P2RY12, and SALL1, but not in genes specific to monocytes or dendritic cells. We further determined that the proportion of cells in this cluster bearing the CHIP mutations ranged from ~40-80% in these two samples, indicating widespread replacement of the endogenous microglial pool by mutant cells. We show here that, unexpectedly, the presence of CHIP is associated with protection from AD dementia. CHIP is also associated with lower levels of neuritic plaques and neurofibrillary tangles in those without dementia, indicating a possible modulating effect of CHIP on the underlying pathophysiology of AD. Consistent with this hypothesis, we also detect substantial infiltration of brain by marrow-derived mutant cells which adopt a microglial-like phenotype. We speculate that the mutations associated with CHIP confer circulating precursor cells with an enhanced ability to engraft in the brain, to differentiate into microglia once engrafted, and/or to clonally expand relative to unmutated cells in the brain microenvironment. These non-mutually exclusive possibilities could provide protection from AD by supplementing the phagocytic capacity of the endogenous microglial system during aging. Figure 1 Figure 1. Disclosures Jaiswal: Novartis: Consultancy, Honoraria; Foresite Labs: Consultancy; Genentech: Consultancy, Honoraria; AVRO Bio: Consultancy, Honoraria; Caylo: Current holder of stock options in a privately-held company.

Background: Advanced age, medical co-morbidities and a pro-inflammatory immunologic profile are associated with severe COVID-19. Acquired somatic mutations in hematopoietic stem cells (clonal hematopoiesis or CH) are common in elderly individuals. Previous studies have shown CH is associated with alterations in immunologic repertoire and function. Here, we investigate whether CH predisposes to severe COVID-19 or other infections. Methods: We performed a retrospective cohort study of 39,291 adult cancer patients with non-hematologic malignancies who had their tumor and blood sequenced using a panel of 468 known cancer driver genes. We identified individuals who tested positive for SARS-CoV-2 between March 8, 2020 and June 9, 2020. We determined the association between CH and severe COVID-19 (hypoxic event, hospitalization or death) using multivariable logistic regression models. We used an established aggregation schema for ICD-CM codes to identify distinct infection subtypes. The relationship between CH and risk of incident infections was determined using multivariable Cox regression. Results: In the study cohort, 436 patients were positive for SARS-CoV-2 and 165 developed severe COVID-19. COVID-19 patients with CH were more likely to develop severe disease compared to non-severe (OR=1.8; 95% CI: 1.1-2.9; p=0.01). CH was also more common among patients with severe COVID-19 compared to COVID-19 negative individuals (OR=1.6, 95% CI: 1.2-2.4, p=0.01). In 62,891 person-years of follow-up, 4,059 individuals developed an infection. CH was associated with risk of sepsis (HR=1.13; 95% CI 1.01-1.25, p=0.04) and bacterial enteritis (HR=1.8, 95% CI 1.1-2.8, p=0.01). Conclusions: CH is associated with severe COVID-19 and an increased risk of other infections in cancer patients. Disclosures Bolton: GRAIL: Research Funding. Jee:MDSeq Inc.: Patents & Royalties. Papaemmanuil:Celgene: Consultancy, Honoraria, Research Funding; Prime Oncology: Consultancy, Honoraria; Illumina: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; MSKCC: Patents & Royalties; Kyowa Hakko Kirin: Consultancy, Honoraria; Isabl: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees. Berger:Illumina: Research Funding; Grail: Research Funding; Roche: Consultancy. Levine:Prelude Therapeutics: Research Funding; Qiagen: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Loxo: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Imago: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; C4 Therapeutics: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Isoplexis: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Honoraria, Research Funding; Roche: Consultancy, Honoraria, Research Funding; Lilly: Consultancy, Honoraria; Janssen: Consultancy; Astellas: Consultancy; Morphosys: Consultancy; Novartis: Consultancy; Amgen: Honoraria; Gilead: Honoraria. Zehir:Illumina: Honoraria; Memorial Sloan Kettering Cancer Center: Current Employment.

Background: Experimental disruption of both gene copies (“knockout”) in model organisms has proven useful to understand gene function. Identification of “human knockouts” (i.e., individuals in which null mutations disrupt both copies of a given gene) should therefore provide valuable insights to a gene function that could be of direct relevance to humans. Objective and Methods: We leverage naturally-occurring null mutations and consanguinity in the human population in order to: 1) identify humans knocked out for genes; and 2) characterize the phenotypic consequences of complete gene disruption. We performed whole-exome sequencing in 7,078 individuals living in Pakistan, a region of the world with high levels of consanguinity, and tested whether knockouts differed from wild-type participants across a range of >200 cardiometabolic traits. Results: Median length of genome-wide homozygosity among Pakistani participants was 6-7 times higher than participants of European (CEU, TSI), East Asian (CHB, JPT, CHD) and African ancestries (YRI, MKK), respectively. In Pakistanis, we were able to enumerate 47,656 mutations predicted to be null (nonsense, frameshift, or canonical splice-site); variants were further filtered based on MAF, transcript position, splice sites, and conservation to identify 36,850 “high-confidence” null mutations across 12,131 autosomal genes. Across all participants, 961 distinct genes were completely disrupted by homozygous null mutations. 1,306 participants (18.4%) had at least one gene knocked out. In a phenotypic screen, homozygosity for null mutations at APOC3 was associated with absent plasma apolipoprotein C-III levels; at PLAG27 , with absent enzymatic activity of lipoprotein-associated phospholipase A2 in the blood; at CYP2F1 , with higher plasma interleukin-8 concentrations; and at either A3GALT2 or NRG4 , with markedly reduced plasma insulin C-peptide concentrations. After physiologic challenge with oral fat, APOC3 knockouts, when compared to wild-type family members, displayed marked blunting of the usual post-prandial rise in plasma triglycerides. Conclusion: These observations provide a roadmap to understand the consequences of complete disruption of a large fraction of genes in the human genome.