Title: Detection of Neanderthal Adaptively Introgressed Genetic Variants that Modulate Reporter Gene Expression in Human Immune Cells

to be driver variants of positive selection including an emVar that may contribute to protection against severe COVID-19 response. We endogenously deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2 respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of experimentally identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans.

[1]  C. Greenwood,et al.  A Neanderthal OAS1 isoform protects individuals of European ancestry against COVID-19 susceptibility and severity , 2021, Nature Medicine.

[2]  Kelsey E. Witt,et al.  The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans , 2020, Proceedings of the National Academy of Sciences.

[3]  Evan T. Geller,et al.  Massively parallel discovery of human-specific substitutions that alter enhancer activity , 2020, Proceedings of the National Academy of Sciences.

[4]  P. Maes,et al.  STAT2 signaling restricts viral dissemination but drives severe pneumonia in SARS-CoV-2 infected hamsters , 2020, Nature Communications.

[5]  Hunter B. Fraser,et al.  The cis-regulatory effects of modern human-specific variants , 2020, bioRxiv.

[6]  S. Pääbo,et al.  A genetic variant protective against severe COVID-19 is inherited from Neandertals , 2020, bioRxiv.

[7]  G. Coop,et al.  The timing of human adaptation from Neanderthal introgression , 2020, bioRxiv.

[8]  R. Silverman,et al.  SARS-CoV-2 induces double-stranded RNA-mediated innate immune responses in respiratory epithelial derived cells and cardiomyocytes , 2020, bioRxiv.

[9]  S. Pääbo,et al.  The major genetic risk factor for severe COVID-19 is inherited from Neanderthals , 2020, bioRxiv.

[10]  The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic , 2020, European Journal of Human Genetics.

[11]  The COVID-19 Host Genetics Initiative The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic , 2020, European Journal of Human Genetics.

[12]  Bjarni V. Halldórsson,et al.  The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes , 2020, Nature.

[13]  Phillip A. Richmond,et al.  JASPAR 2020: update of the open-access database of transcription factor binding profiles , 2019, Nucleic Acids Res..

[14]  Christopher D. Brown,et al.  The GTEx Consortium atlas of genetic regulatory effects across human tissues , 2019, Science.

[15]  Bing Ren,et al.  A Compendium of Promoter-Centered Long-Range Chromatin Interactions in the Human Genome , 2019, Nature Genetics.

[16]  Y. Okada,et al.  Biological characterization of expression quantitative trait loci (eQTLs) showing tissue-specific opposite directional effects , 2019, European Journal of Human Genetics.

[17]  G. Rassidakis,et al.  AP-1 Transcription Factors as Regulators of Immune Responses in Cancer , 2019, Cancers.

[18]  S. Pääbo,et al.  Limits of long-term selection against Neandertal introgression , 2019, Proceedings of the National Academy of Sciences.

[19]  O. Andreassen,et al.  A global overview of pleiotropy and genetic architecture in complex traits , 2019, Nature Genetics.

[20]  D. Petrov,et al.  Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans , 2018, Cell.

[21]  Wei Yang,et al.  The Role of Autoimmune Regulator (AIRE) in Peripheral Tolerance , 2018, Journal of immunology research.

[22]  F. A. Kolpakov,et al.  HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis , 2017, Nucleic Acids Res..

[23]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[24]  Michael C. Westaway,et al.  Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans , 2017, Molecular biology and evolution.

[25]  E. Eichler,et al.  A high-coverage Neandertal genome from Vindija Cave in Croatia , 2017, Science.

[26]  N. Huntington,et al.  The life and death of immune cell types: the role of BCL‐2 anti‐apoptotic molecules , 2017, Immunology and cell biology.

[27]  Manolis Kellis,et al.  Chromatin-state discovery and genome annotation with ChromHMM , 2017, Nature Protocols.

[28]  J. Kelso,et al.  The Contribution of Neanderthals to Phenotypic Variation in Modern Humans , 2017, American journal of human genetics.

[29]  J. Kelso,et al.  Functional implications of Neandertal introgression in modern humans , 2017, Genome Biology.

[30]  Rajiv C. McCoy,et al.  Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression , 2017, Cell.

[31]  David C. Wilson,et al.  Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease , 2016, Nature Genetics.

[32]  J. Akey,et al.  Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments , 2016, Current Biology.

[33]  Matthew T. Maurano,et al.  Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells , 2016, Cell.

[34]  William J. Astle,et al.  Allelic Landscape of Human Blood Cell Trait Variation and Links , 2016 .

[35]  Zachary A. Szpiech,et al.  Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens , 2016, Cell.

[36]  Aaron J. Sams,et al.  Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans , 2016, Genome Biology.

[37]  Fernando Racimo,et al.  Signatures of Archaic Adaptive Introgression in Present-Day Human Populations , 2016, bioRxiv.

[38]  Yun S. Song,et al.  The Simons Genome Diversity Project: 300 genomes from 142 diverse populations , 2016, Nature.

[39]  Jacob C. Ulirsch,et al.  Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits , 2016, Cell.

[40]  Eric S. Lander,et al.  Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay , 2016, Cell.

[41]  D. Reich,et al.  The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans , 2016, Current Biology.

[42]  D. Reich,et al.  The genetic history of Ice Age Europe , 2016, Nature.

[43]  Jonathan Scott Friedlaender,et al.  Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals , 2016, Science.

[44]  Gerard Tromp,et al.  The phenotypic legacy of admixture between modern humans and Neandertals , 2016, Science.

[45]  J. Casanova,et al.  Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes. , 2016, American journal of human genetics.

[46]  A. Andrés,et al.  Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors , 2016, American journal of human genetics.

[47]  J. Michael Cherry,et al.  ENCODE data at the ENCODE portal , 2015, Nucleic Acids Res..

[48]  R. Nielsen,et al.  The Genetic Cost of Neanderthal Introgression , 2015, Genetics.

[49]  G. Coop,et al.  The Strength of Selection against Neanderthal Introgression , 2015, bioRxiv.

[50]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[51]  Melissa Drappier,et al.  Inhibition of the OAS/RNase L pathway by viruses , 2015, Current Opinion in Virology.

[52]  N. Sharma,et al.  The proteome of Hypobaric Induced Hypoxic Lung: Insights from Temporal Proteomic Profiling for Biomarker Discovery , 2015, Scientific Reports.

[53]  Tim Clarke,et al.  High Altitude Medicine and Physiology, 4th edn , 2015 .

[54]  Jun S. Liu,et al.  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.

[55]  P. Elliott,et al.  UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age , 2015, PLoS medicine.

[56]  Joel Hirschhorn,et al.  SNPsnap: a Web-based tool for identification and annotation of matched SNPs , 2015, Bioinform..

[57]  Feng Zhang,et al.  Genome engineering using CRISPR-Cas9 system. , 2015, Methods in molecular biology.

[58]  N. Warner,et al.  A Genome-wide Small Interfering RNA (siRNA) Screen Reveals Nuclear Factor-κB (NF-κB)-independent Regulators of NOD2-induced Interleukin-8 (IL-8) Secretion* , 2014, The Journal of Biological Chemistry.

[59]  Asan,et al.  Altitude adaptation in Tibet caused by introgression of Denisovan-like DNA , 2014, Nature.

[60]  L. Pagani,et al.  The Andean Adaptive Toolkit to Counteract High Altitude Maladaptation: Genome-Wide and Phenotypic Analysis of the Collas , 2014, PloS one.

[61]  R. Nielsen,et al.  On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure , 2014, Molecular biology and evolution.

[62]  M. Butler,et al.  Human cell‐based artificial antigen‐presenting cells for cancer immunotherapy , 2014, Immunological Reviews.

[63]  C. Marosi,et al.  Association of mean platelet volume with risk of venous thromboembolism and mortality in patients with cancer , 2013, Thrombosis and Haemostasis.

[64]  Swapan Mallick,et al.  The genomic landscape of Neanderthal ancestry in present-day humans. , 2016 .

[65]  H. Tsutsui,et al.  GATA-1 regulates the generation and function of basophils , 2013, Proceedings of the National Academy of Sciences.

[66]  C. Dinarello,et al.  Interleukin-18 and IL-18 Binding Protein , 2013, Front. Immunol..

[67]  Chuong B. Do,et al.  A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci , 2013, Nature Genetics.

[68]  M. Peters,et al.  Identification of genetic loci associated with Helicobacter pylori serologic status. , 2013, JAMA.

[69]  A. Clark,et al.  Population genetic tools for dissecting innate immunity in humans , 2013, Nature Reviews Immunology.

[70]  Eugen C. Buehler,et al.  Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis , 2013, Proceedings of the National Academy of Sciences.

[71]  Patrick G. A. Pedrioli,et al.  The P-body component USP52/PAN2 is a novel regulator of HIF1A mRNA stability , 2013, The Biochemical journal.

[72]  Philip L. F. Johnson,et al.  The complete genome sequence of a Neanderthal from the Altai Mountains , 2013 .

[73]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[74]  Manolis Kellis,et al.  HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants , 2011, Nucleic Acids Res..

[75]  M. Hammer,et al.  A Haplotype at STAT 2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea , 2012 .

[76]  William Stafford Noble,et al.  FIMO: scanning for occurrences of a given motif , 2011, Bioinform..

[77]  H. Virgin,et al.  Autophagy in immunity and inflammation , 2011, Nature.

[78]  C. Piantadosi,et al.  Co-regulation of nuclear respiratory factor-1 by NFκB and CREB links LPS-induced inflammation to mitochondrial biogenesis , 2010, Journal of Cell Science.

[79]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[80]  S. Jane,et al.  The TAL1/SCL Transcription Factor Regulates Cell Cycle Progression and Proliferation in Differentiating Murine Bone Marrow Monocyte Precursors , 2010, Molecular and Cellular Biology.

[81]  Laurent Gil,et al.  Ensembl variation resources , 2010, BMC Genomics.

[82]  N. Hacohen,et al.  A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection , 2009, Cell.

[83]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[84]  Aitor G. Granja,et al.  Viral mechanisms involved in the transcriptional CBP/p300 regulation of inflammatory and immune responses. , 2009, Critical reviews in immunology.

[85]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[86]  A. Clark,et al.  Recent and ongoing selection in the human genome , 2007, Nature Reviews Genetics.

[87]  R. Silverman Viral Encounters with 2′,5′-Oligoadenylate Synthetase and RNase L during the Interferon Antiviral Response , 2007, Journal of Virology.

[88]  Andrew H. Miller,et al.  Cytokine-effects on glucocorticoid receptor function: Relevance to glucocorticoid resistance and the pathophysiology and treatment of major depression , 2007, Brain, Behavior, and Immunity.

[89]  Javier Martín,et al.  Analysis of IRF5 gene functional polymorphisms in rheumatoid arthritis. , 2006, Arthritis & Rheumatism.

[90]  S. Akira,et al.  Pathogen Recognition and Innate Immunity , 2006, Cell.

[91]  R. Jäger,et al.  The AP-2 family of transcription factors , 2005, Genome Biology.

[92]  F. Macian,et al.  NFAT proteins: key regulators of T-cell development and function , 2005, Nature Reviews Immunology.

[93]  Jun O. Liu,et al.  Myocyte Enhancer Factor 2 Mediates Calcium-dependent Transcription of the Interleukin-2 Gene in T Lymphocytes , 2004, Journal of Biological Chemistry.

[94]  N. Chapman,et al.  Association of Mean Platelet Volume With Risk of Stroke Among 3134 Individuals With History of Cerebrovascular Disease , 2004, Stroke.

[95]  I. Verma,et al.  NF-κB regulation in the immune system , 2002, Nature Reviews Immunology.

[96]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[97]  T. Yao [Inflammatory bowel diseases]. , 2002, Nihon Naika Gakkai zasshi. The Journal of the Japanese Society of Internal Medicine.

[98]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[99]  J. Trimarchi,et al.  E2F-6, a member of the E2F family that can behave as a transcriptional repressor. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[100]  Z. Paroush,et al.  Conversion of dorsal from an activator to a repressor by the global corepressor Groucho. , 1997, Genes & development.

[101]  K. Georgopoulos,et al.  The Ikaros gene encodes a family of functionally diverse zinc finger DNA-binding proteins , 1994, Molecular and cellular biology.

[102]  M. Levine,et al.  The dorsal morphogen is a sequence-specific DNA-binding protein that interacts with a long-range repression element in drosophila , 1991, Cell.

[103]  A. Kaftory,et al.  Congenital methemoglobinemia with a deficiency of cytochrome b5. , 1986, The New England journal of medicine.

[104]  P. Strittmatter,et al.  Covalent cross-linking of the active sites of vesicle-bound cytochrome b5 and NADH-cytochrome b5 reductase. , 1984, The Journal of biological chemistry.

[105]  W. Vainchenker,et al.  Myeloid and megakaryocytic properties of K-562 cell lines. , 1983, Cancer research.