Genes & Human Disease Research Program

The human genome is composed of more than 3 billion nucleotides that essentially functions as a molecular hard drive that stores all the information needed for how the cells in our body function. Of the 3 billion nucleotides, roughly 2% encodes for the different proteins that perform the various cellular functions needed for life. The remaining 98% of the human genome regulates what, when, and how each gene is expressed during the life of a cell. The random inheritance of different variations of the DNA sequences of encoded genes and non-protein coding regulatory regions from a person’s parents provides, in many ways, the characteristics that make each individual unique. Unfortunately, inheritance of genetic variations also increases a person’s risk of developing different human diseases.

The Genes and Human Disease Research Program focuses on identifying and understanding how genetic variations cause human diseases. While our investigators share this focus, each has their own specific interests including determining the function of non-coding RNA, and understanding how the complex 3D organization of the genome, disease-associated non-coding variants, and the epigenome regulate gene expression in health and disease. In addition, our faculty are developing and applying new machine and deep-learning approaches to identify new disease-associated genetic variations and define disease-associated gene networks.

The Genes and Human Disease Research Program works closely with the OMRF CLIA certified Clinical Genomics Center, the OMRF CAP-accredited Biorepository and the OMRF Quantitative Analysis Core. These Cores were established using funding from various grants through the NIH Institutional Development Award (IDeA) program, and continue to be supported by the OMRF. Our investigators benefit from the state-of-the-art sequencing technologies, sample procurement, processing and storage, and data analysis expertise afforded by these Cores.

2024

Bhaskaran S, Piekarz KM, Brown J, Yang B, Ocañas SR, Wren JD, Georgescu C, Bottoms C, Murphy A, Thomason J, Saunders D, Smith N, Towner R, Van Remmen H. The nitrone compound OKN-007 delays motor neuron loss and disease progression in the G93A mouse model of amyotrophic lateral sclerosis. Front Neurosci 18:1505369, 2024 November, PMID: 39633896, PMCID: PMC11614777

Blankenship HE, Carter KA, Pham KD, Cassidy NT, Markiewicz AN, Thellmann MI, Sharpe AL, Freeman WM, Beckstead MJ. VTA dopamine neurons are hyperexcitable in 3xTg-AD mice due to casein kinase 2-dependent SK channel dysfunction. Nat Commun 15:9673, 2024 November, PMID: 39516200, PMCID: PMC11549218

Zhang Y, Liu Y, Qin W, Zheng S, Xiao J, Xia X, Yuan X, Zeng J, Shi Y, Zhang Y, Ma H, Varshney GK, Fei JF, Liu Y. Cytosine base editors with increased PAM and deaminase motif flexibility for gene editing in zebrafish. Nat Commun 15:9526, 2024 November, PMID: 39496611, PMCID: PMC11535530

Barish S, Lin SJ, Maroofian R, Gezdirici A, Alhebby H, Trimouille A, Biderman Waberski M, Mitani T, Huber I, Tveten K, Holla ØL, Busk ØL, Houlden H, Ghayoor Karimiani E, Beiraghi Toosi M, Shervin Badv R, Najarzadeh Torbati P, Eghbal F, Akhondian J, Al Safar A, Alswaid A, Zifarelli G, Bauer P, Marafi D, Fatih JM, Huang K, Petree C, Calame DG, von der Lippe C, Alkuraya FS, Wali S, Lupski JR, Varshney GK, Posey JE, Pehlivan D. Homozygous variants in WDR83OS lead to a neurodevelopmental disorder with hypercholanemia. Am J Hum Genet, 2024 October, PMID: 39471804, PMCID: PMC11568760

Patterson AS, Dugdale J, Koleilat A, Krauss A, Hernandez-Herrera GA, Wallace JG, Petree C, Varshney GK, Schimmenti LA. Vital Dye Uptake of YO-PRO-1 and DASPEI Depends Upon Mechanoelectrical Transduction Function in Zebrafish Hair Cells. J Assoc Res Otolaryngol, 2024 October, PMID: 39433714

Ree R, Lin SJ, Sti Dahl LO, Huang K, Petree C, Varshney GK, Arnesen T. Naa80 is required for actin N-terminal acetylation and normal hearing in zebrafish. Life Sci Alliance 7, 2024 October, PMID: 39384430, PMCID: PMC11465159

Chucair-Elliott AJ, Pham K, Cleuren ACA, Schafer CM, Griffin CT, Ocanas SR, Freeman WM, Elliott MH. Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds. Exp Eye Res:110101, 2024 September, PMID: 39303842, PMCID: PMC11532013

Pollalis D, Nair GKG, Leung J, Bloemhof CM, Bailey JK, Pennington BO, Kelly KR, Khan AI, Yeh AK, Sundaram KS, Clegg DO, Peng CC, Xu L, Georgescu C, Wren JD, Lee SY. Dynamics of microRNA secreted via extracellular vesicles during the maturation of embryonic stem cell-derived retinal pigment epithelium. J Extracell Biol 3:e70001, 2024 September, PMID: 39281021, PMCID: PMC11393772

Kim H, Ranjit R, Claflin DR, Georgescu C, Wren JD, Brooks SV, Miller BF, Ahn B. Unacylated Ghrelin Protects Against Age-Related Loss of Muscle Mass and Contractile Dysfunction in Skeletal Muscle. Aging Cell:e14323, 2024 September, PMID: 39223708

Banks E, Francis V, Lin SJ, Kharfallah F, Fonov V, Lévesque M, Han C, Kulasekaran G, Tuznik M, Bayati A, Al-Khater R, Alkuraya FS, Argyriou L, Babaei M, Bahlo M, Bakhshoodeh B, Barr E, Bartik L, Bassiony M, Bertrand M, Braun D, Buchert R, Budetta M, Cadieux-Dion M, Calame DG, Cope H, Cushing D, Efthymiou S, Elmaksoud MA, El Said HG, Froukh T, Gill HK, Gleeson JG, Gogoll L, Goh ES, Gowda VK, Haack TB, Hashem MO, Hauser S, Hoffman TL, Hogue JS, Hosokawa A, Houlden H, Huang K, Huynh S, Karimiani EG, Kaulfuß S, Korenke GC, Kritzer A, Lee H, Lupski JR, Marco EJ, McWalter K, Minassian A, Minassian BA, Murphy D, Neira-Fresneda J, Northrup H, Nyaga DM, Oehl-Jaschkowitz B, Osmond M, Person R, Pehlivan D, Petree C, Sadleir LG, Saunders C, Schoels L, Shashi V, Spillmann RC, Srinivasan VM, Torbati PN, Tos T, Undiagnosed Diseases Network, Zaki MS, Zhou D, Zweier C, Trempe JF, Durcan TM, Gan-Or Z, Avoli M, Alves C, Varshney GK, Maroofian R, Rudko DA, McPherson PS. Loss of symmetric cell division of apical neural progenitors drives DENND5A-related developmental and epileptic encephalopathy. Nat Commun 15:7239, 2024 August, PMID: 39174524, PMCID: PMC11341845

Ma H, Stanford D, Freeman WM, Ding XQ. Transcriptomic Analysis Reveals That Excessive Thyroid Hormone Signaling Impairs Phototransduction and Mitochondrial Bioenergetics and Induces Cellular Stress in Mouse Cone Photoreceptors. Int J Mol Sci 25, 2024 July, PMID: 39000540, PMCID: PMC11242393

Qin W, Liang F, Lin SJ, Petree C, Huang K, Zhang Y, Li L, Varshney P, Mourrain P, Liu Y, Varshney GK. ABE-ultramax for high-efficiency biallelic adenine base editing in zebrafish. Nat Commun 15:5613, 2024 July, PMID: 38965236, PMCID: PMC11224239

Cox JEJ, Pham KD, Keck AW, Wright Z, Thomas MA, Freeman WM, Ocañas SR. Flow Cytometry Analysis of Microglial Phenotypes in the Murine Brain During Aging and Disease. Bio Protoc 14:e5018, 2024 June, PMID: 38948260, PMCID: PMC11211077

Kang S, Ko EY, Andrews AE, Shin JE, Nance KJ, Barman PK, Heeger PS, Freeman WM, Benayoun BA, Goodridge HS. Microglia undergo sex-dimorphic transcriptional and metabolic rewiring during aging. J Neuroinflammation 21:150, 2024 June, PMID: 38840206, PMCID: PMC11155174

Keener R, Chhetri SB, Connelly CJ, Taub MA, Conomos MP, Weinstock J, Ni B, Strober B, Aslibekyan S, Auer PL, Barwick L, Becker LC, Blangero J, Bleecker ER, Brody JA, Cade BE, Celedon JC, Chang YC, Cupples LA, Custer B, Freedman BI, Gladwin MT, Heckbert SR, Hou L, Irvin MR, Isasi CR, Johnsen JM, Kenny EE, Kooperberg C, Minster RL, Naseri T, Viali S, Nekhai S, Pankratz N, Peyser PA, Taylor KD, Telen MJ, Wu B, Yanek LR, Yang IV, Albert C, Arnett DK, Ashley-Koch AE, Barnes KC, Bis JC, Blackwell TW, Boerwinkle E, Burchard EG, Carson AP, Chen Z, Chen YI, Darbar D, de Andrade M, Ellinor PT, Fornage M, Gelb BD, Gilliland FD, He J, Islam T, Kaab S, Kardia SLR, Kelly S, Konkle BA, Kumar R, Loos RJF, Martinez FD, McGarvey ST, Meyers DA, Mitchell BD, Montgomery CG, North KE, Palmer ND, Peralta JM, Raby BA, Redline S, Rich SS, Roden D, Rotter JI, Ruczinski I, Schwartz D, Sciurba F, Shoemaker MB, Silverman EK, Sinner MF, Smith NL, Smith AV, Tiwari HK, Vasan RS, Weiss ST, Williams LK, Zhang Y, Ziv E, Raffield LM, Reiner AP, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Hematology and Hemostasis Working Group, TOPMed Structural Variation Working Group, Arvanitis M, Greider CW, Mathias RA, Battle A. Validation of human telomere length multi-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as human telomere length regulation genes. Nat Commun 15:4417, 2024 May, PMID: 38789417, PMCID: PMC11126610

Lincoln MR, Connally N, Axisa PP, Gasperi C, Mitrovic M, van Heel D, Wijmenga C, Withoff S, Jonkers IH, Padyukov L, International Multiple Sclerosis Genetics Consortium, Rich SS, Graham RR, Gaffney PM, Langefeld CD, Vyse TJ, Hafler DA, Chun S, Sunyaev SR, Cotsapas C. Genetic mapping across autoimmune diseases reveals shared associations and mechanisms. Nat Genet, 2024 May, PMID: 38741015

Chucair-Elliott AJ, Ocañas SR, Pham K, Machalinski A, Plafker S, Stout MB, Elliott MH, Freeman WM. Age- and sex- divergent translatomic responses of the mouse retinal pigmented epithelium. Neurobiol Aging 140:41-59, 2024 May, PMID: 38723422, PMCID: PMC11173338

Isola JVV, Hense JD, Osorio CAP, Biswas S, Alberola-Ila J, Ocanas SR, Schneider A, Stout MB. Inflammation, immune cells, and cellular senescence in the aging ovary. Reproduction, 2024 May, PMID: 38744316, PMCID: PMC11301429

Brown CA, Wren JD. AutoGDC: A Python Package for DNA Methylation and Transcription Meta-Analyses. bioRxiv, 2024 April, PMID: 38659836, PMCID: PMC11042378

Chen J, Ding Y, Jiang C, Qu R, Wren JD, Georgescu C, Wang X, Reuter DN, Liu B, Giles CB, Mayr CH, Schiller HB, Dai J, Stipp CS, Subramaniyan B, Wang J, Zuo H, Huang C, Fung KM, Rice HC, Sonnenberg A, Wu D, Walters MS, Zhao YY, Kanie T, Hays FA, Papin JF, Wang DW, Zhang XA. CD151 Maintains Endolysosomal Protein Quality to Inhibit Vascular Inflammation. Circ Res, 2024 April, PMID: 38557119, PMCID: PMC11081830

Komaravolu RK, Mehta-D'souza P, Conner T, Allen M, Lumry J, Batushansky A, Pezant NP, Montgomery CG, Griffin TM. Sex-specific effects of injury and beta-adrenergic activation on metabolic and inflammatory mediators in a murine model of post-traumatic osteoarthritis. Osteoarthritis Cartilage, 2024 March, PMID: 38527663, PMCID: PMC11330734

Winnicki MJ, Brown CA, Porter HL, Giles CB, Wren JD. BioVDB: biological vector database for high-throughput gene expression meta-analysis. Front Artif Intell 7:1366273, 2024 March, PMID: 38525301, PMCID: PMC10957786

Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively Parallel Reporter Assay Confirms Regulatory Potential of hQTLs and Reveals Important Variants in Lupus and Other Autoimmune Diseases. HGG Adv:100279, 2024 February, PMID: 38389303, PMCID: PMC10943488

Xiong Y, Kullberg S, Garman L, Pezant N, Ellinghaus D, Vasila V, Eklund A, Rybicki BA, Iannuzzi MC, Schreiber S, Müller-Quernheim J, Montgomery CG, Grunewald J, Padyukov L, Rivera NV. Corrigendum: Sex differences in the genetics of sarcoidosis across European and African ancestry populations. Front Med (Lausanne) 11:1382584, 2024 February, PMID: 38449888, PMCID: PMC10915398

Banks E, Francis V, Lin SJ, Kharfallah F, Fonov V, Levesque M, Han C, Kulasekaran G, Tuznik M, Bayati A, Al-Khater R, Alkuraya FS, Argyriou L, Babaei M, Bahlo M, Bakhshoodeh B, Barr E, Bartik L, Bassiony M, Bertrand M, Braun D, Buchert R, Budetta M, Cadieux-Dion M, Calame D, Cope H, Cushing D, Efthymiou S, Elmaksoud MA, El Said HG, Froukh T, Gill HK, Gleeson JG, Gogoll L, Goh ES, Gowda VK, Haack TB, Hashem MO, Hauser S, Hoffman TL, Hogue JS, Hosokawa A, Houlden H, Huang K, Huynh S, Karimiani EG, Kaulfuß S, Korenke GC, Kritzer A, Lee H, Lupski JR, Marco EJ, McWalter K, Minassian A, Minassian BA, Murphy D, Neira-Fresneda J, Northrup H, Nyaga D, Oehl-Jaschkowitz B, Osmond M, Person R, Pehlivan D, Petree C, Sadleir LG, Saunders C, Schoels L, Shashi V, Spillman RC, Srinivasan VM, Torbati PN, Tos T, Undiagnosed Diseases Network, Zaki MS, Zhou D, Zweier C, Trempe JF, Durcan TM, Gan-Or Z, Avoli M, Alves C, Varshney GK, Maroofian R, Rudko DA, McPherson PS. Loss of symmetric cell division of apical neural progenitors drives DENND5A-related developmental and epileptic encephalopathy. medRxiv, 2024 January, PMID: 38352438, PMCID: PMC10863025

Isola JVV, Ocañas SR, Hubbart CR, Ko S, Mondal SA, Hense JD, Carter HNC, Schneider A, Kovats S, Alberola-Ila J, Freeman WM, Stout MB. A single-cell atlas of the aging mouse ovary. Nat Aging, 2024 January, PMID: 38200272, PMCID: PMC10798902

2023

Porter HL, Ansere VA, Undi RB, Hoolehan W, Giles CB, Brown CA, Stanford D, Huycke MM, Freeman WM, Wren JD. Methylation Array Signals are Predictive of Chronological Age Without Bisulfite Conversion. bioRxiv, 2023 December, PMID: 38187520, PMCID: PMC10769286

Buryska S, Patel K, Wuertz B, Gaffney PM, Ondrey F. Potential Roles of Activin in Head and Neck Squamous Cell Carcinoma Progression and Mortality. Anticancer Res 43:5299-5310, 2023 December, PMID: 38030164, PMCID: PMC11285815

Casanova NG, Camp SM, Gonzalez-Garay ML, Batai K, Garman L, Montgomery CG, Ellis N, Kittles R, Bime C, Hsu AP, Holland S, Lussier YA, Karnes J, Sweiss N, Maier LA, Koth L, Moller DR, Kaminski N, Garcia JGN. Examination of eQTL Polymorphisms Associated with Increased Risk of Progressive Complicated Sarcoidosis in European and African Descent Subjects. Eur J Respir Med 5:359-371, 2023 December, PMID: 38390497, PMCID: PMC10883688

Kelly JA, Tessneer KL, Gaffney PM. Taming the HLA for single-cell genomics. Nat Genet, 2023 November, PMID: 38036786

Lin SJ, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Med 15:102, 2023 November, PMID: 38031187, PMCID: PMC10688095

Blankenship HE, Carter KA, Cassidy NT, Markiewicz AN, Thellmann MI, Sharpe AL, Freeman WM, Beckstead MJ. VTA dopamine neurons are hyperexcitable in 3xTg-AD mice due to casein kinase 2-dependent SK channel dysfunction. bioRxiv, 2023 November, PMID: 38014232, PMCID: PMC10680865

Dezfulian MH, Kula T, Pranzatelli T, Kamitaki N, Meng Q, Khatri B, Perez P, Xu Q, Chang A, Kohlgruber AC, Leng Y, Jupudi AA, Joachims ML, Chiorini JA, Lessard CJ, Darise Farris A, Muthuswamy SK, Warner BM, Elledge SJ. TScan-II: A genome-scale platform for the de novo identification of CD4( ) T cell epitopes. Cell, 2023 November, PMID: 38016469, PMCID: PMC10841602

Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Hoolehan W, Kulpa AM, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. Epigenetics Chromatin 16:45, 2023 November, PMID: 37953264, PMCID: PMC10642035

Kaiyrzhanov R, Rad A, Lin SJ, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain, 2023 November, PMID: 37951597, PMCID: PMC10994533

Kellogg CM, Pham K, Ko S, Cox JEJ, Machalinski AH, Stout MB, Sharpe AL, Beckstead MJ, Chucair-Elliott AJ, Ocañas SR, Freeman WM. Specificity and efficiency of tamoxifen-mediated Cre induction is equivalent regardless of age. iScience 26:108413, 2023 November, PMID: 38058312, PMCID: PMC10696116

Wiley MM, Khatri B, Joachims ML, Tessneer KL, Stolarczyk AM, Rasmussen A, Anaya JM, Aqrawi LA, Bae SC, Baecklund E, Björk A, Brun JG, Bucher SM, Dand N, Eloranta ML, Engelke F, Forsblad-d'Elia H, Fugmann C, Glenn SB, Gong C, Gottenberg JE, Hammenfors D, Imgenberg-Kreuz J, Jensen JL, Johnsen SJA, Jonsson MV, Kelly JA, Khanam S, Kim K, Kvarnström M, Mandl T, Martín J, Morris DL, Nocturne G, Norheim KB, Olsson P, Palm Ø, Pers JO, Rhodus NL, Sjöwall C, Skarstein K, Taylor KE, Tombleson P, Thorlacius GE, Venuturupalli S, Vital EM, Wallace DJ, Grundahl KM, Radfar L, Brennan MT, James JA, Scofield RH, Gaffney PM, Criswell LA, Jonsson R, Appel S, Eriksson P, Bowman SJ, Omdal R, Rönnblom L, Warner BM, Rischmueller M, Witte T, Farris AD, Mariette X, Shiboski CH, Sjögren’s International Collaborative Clinical Alliance (SICCA), Wahren-Herlenius M, Alarcón-Riquelme ME, PRECISESADS Clinical Consortium, Ng WF, UK Primary Sjögren’s Syndrome Registry, Sivils KL, Guthridge JM, Adrianto I, Vyse TJ, Tsao BP, Nordmark G, Lessard CJ. Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland. bioRxiv, 2023 October, PMID: 39071447, PMCID: PMC11275775

Jiang K, Fu Y, Kelly JA, Gaffney PM, Holmes LC, Jarvis JN. Comparison of the three-dimensional chromatin structures of adolescent and adult peripheral blood B cells: implications for the study of pediatric autoimmune diseases. bioRxiv, 2023 September, PMID: 37745336, PMCID: PMC10515843

Isola JVV, Ocañas SR, Hubbart CR, Ko S, Mondal SA, Hense JD, Carter HNC, Schneider A, Kovats S, Alberola-Ila J, Freeman WM, Stout MB. A single-cell atlas of the aging murine ovary. bioRxiv, 2023 September, PMID: 37162983, PMCID: PMC10168416

Levin AM, She R, Chen Y, Adrianto I, Datta I, Loveless IM, Garman L, Montgomery CG, Li J, Iannuzzi MC, Rybicki BA. Identification of Environmental Exposures Associated with Risk of Sarcoidosis in African Americans. Ann Am Thorac Soc 20:1274-1282, 2023 September, PMID: 37209419, PMCID: PMC10502890

Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively Parallel Reporter Assay Confirms Regulatory Potential of hQTLs and Reveals Important Variants in Lupus and Other Autoimmune Diseases. bioRxiv, 2023 August, PMID: 37645944, PMCID: PMC10462090

Ocañas SR, Pham KD, Cox JEJ, Keck AW, Ko S, Ampadu FA, Porter HL, Ansere VA, Kulpa A, Kellogg CM, Machalinski AH, Thomas MA, Wright Z, Chucair-Elliott AJ, Freeman WM. Microglial senescence contributes to female-biased neuroinflammation in the aging mouse hippocampus: implications for Alzheimer's disease. J Neuroinflammation 20:188, 2023 August, PMID: 37587511, PMCID: PMC10433617

Ansere VA, Bubak MP, Miller BF, Freeman WM. Heterochronic Plasma Transfer: Experimental Design, Considerations, and Technical Challenges. Rejuvenation Res, 2023 August, PMID: 37551981, PMCID: PMC10611967

Accogli A, Lin SJ, Severino M, Kim SH, Huang K, Rocca C, Landsverk M, Zaki M, Al-Maawali A, Srinivasan VM, Al-Thihli K, Schaefer GB, Davis M, Tonduti D, Doneda C, Marten LM, Mühlhausen C, Gomez M, Lamantea E, Mena R, Nizon M, Procaccio V, Begtrup A, Telegrafi A, Cui H, Schulz HL, Mohr J, Biskup S, Loos MA, Aráoz HV, Salpietro V, Keppen LD, Chitre M, Petree C, Raymond L, Vogt J, Swayer LB, Basinger AA, Pedersen SV, Pearson TS, Grange DK, Lingapp L, McDunnah P, Horvath R, Cogne B, Isidor B, Hahn A, Gripp K, Jafarnejad SM, Ostergaard E, Prada CE, Ghezzi D, Gowda VK, Taylor RW, Sonenberg N, Houlden H, Sissler M, Varshney GK, Maroofian R. Clinical, neuroradiological and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genet Med:100938, 2023 July, PMID: 37454282, PMCID: PMC11157694

Liao SY, Jacobson S, Hamzeh NY, Culver DA, Barkes BQ, Mroz M, Macphail K, Pacheco K, Patel DC, Wasfi YS, Koth LL, Langefeld CD, Leach SM, White E, Montgomery C, Maier LA, Fingerlin TE, GRADs Investigators. Genome-wide association study identifies multiple HLA loci for sarcoidosis susceptibility. Hum Mol Genet, 2023 July, PMID: 37399103, PMCID: PMC10407706

Kellogg CM, Pham K, Machalinski AH, Porter HL, Blankenship HE, Tooley KB, Stout MB, Rice HC, Sharpe AL, Beckstead MJ, Chucair-Elliott AJ, Ocañas SR, Freeman WM. Microglial MHC-I induction with aging and Alzheimer's is conserved in mouse models and humans. Geroscience, 2023 July, PMID: 37393197, PMCID: PMC10643718

Corbin JM, Georgescu C, Wang L, Wren JD, Bieniasz M, Xu C, Asch AS, Ruiz Echevarría MJ. An unbiased seed-based RNAi selection screen identifies small RNAs that inhibit androgen signaling and prostate cancer cell growth. Mol Ther Nucleic Acids 33:257-272, 2023 June, PMID: 37554515, PMCID: PMC10404560

Garman L, Pezant N, Dawkins BA, Rasmussen A, Levin AM, Rybicki BA, Iannuzzi MC, Bagavant H, Deshmukh US, Montgomery CG. Inclusivity in Research Matters: Variants in PVT1 Specific to People of African Descent Are Associated with Pulmonary Fibrosis. Am J Respir Crit Care Med, 2023 June, PMID: 37348127, PMCID: PMC10870883

Rasmussen A, Dawkins BA, Li C, Pezant N, Levin AM, Rybicki BA, Iannuzzi MC, Montgomery CG. Multiple Correspondence Analysis and HLA-Associations of Organ Involvement in a Large Cohort of African-American and European-American Patients with Sarcoidosis. Lung, 2023 June, PMID: 37322162, PMCID: PMC10284928

Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. bioRxiv, 2023 June, PMID: 37333391, PMCID: PMC10274634

Kellogg CM, Pham K, Machalinski AH, Porter HL, Blankenship HE, Tooley K, Stout MB, Rice HC, Sharpe AL, Beckstead MJ, Chucair-Elliott AJ, Ocañas SR, Freeman WM. Microglial MHC-I induction with aging and Alzheimer's is conserved in mouse models and humans. bioRxiv, 2023 June, PMID: 36945372, PMCID: PMC10028873

Ocañas SR, Pham KD, Cox JEJ, Keck AW, Ko S, Ampadu FA, Porter HL, Ansere VA, Kulpa A, Kellogg CM, Machalinski AH, Chucair-Elliott AJ, Freeman WM. Microglial senescence contributes to female-biased neuroinflammation in the aging mouse hippocampus: implications for Alzheimer's disease. bioRxiv, 2023 June, PMID: 36945656, PMCID: PMC10028852

Mohammed S, Thadathil N, Ohene-Marfo P, Tran AL, Van Der Veldt M, Georgescu C, Oh S, Nicklas EH, Wang D, Haritha NH, Luo W, Janknecht R, Miller BF, Wren JD, Freeman WM, Deepa SS. Absence of either Ripk3 or Mlkl reduces incidence of hepatocellular carcinoma independent of liver fibrosis. Mol Cancer Res, 2023 May, PMID: 37204757, PMCID: PMC10472095

Min J, Yang S, Cai Y, Vanderwall DR, Wu Z, Li S, Liu S, Liu B, Wang J, Ding Y, Chen J, Jiang C, Wren JD, Csiszar A, Ungvari Z, Greco C, Kanie T, Peng J, Zhang XA. Tetraspanin Tspan8 restrains interferon signaling to stabilize intestinal epithelium by directing endocytosis of interferon receptor. Cell Mol Life Sci 80:154, 2023 May, PMID: 37204469, PMCID: PMC10484302

Xiong Y, Kullberg S, Garman L, Pezant N, Ellinghaus D, Vasila V, Eklund A, Rybicki BA, Iannuzzi MC, Schreiber S, Müller-Quernheim J, Montgomery CG, Grunewald J, Padyukov L, Rivera NV. Sex differences in the genetics of sarcoidosis across European and African ancestry populations. Front Med (Lausanne) 10:1132799, 2023 May, PMID: 37250650, PMCID: PMC10213734

Longobardi S, Lopez-Davis C, Khatri B, Georgescu C, Pritchett-Frazee C, Lawrence C, Rasmussen A, Radfar L, Scofield RH, Baer AN, Robinson SA, Darrah E, Axtell RC, Pardo G, Wren JD, Koelsch KA, Guthridge JM, James JA, Lessard CJ, Farris AD. Autoantibodies identify primary Sjögren's syndrome in patients lacking serum IgG specific for Ro/SS-A and La/SS-B. Ann Rheum Dis, 2023 May, PMID: 37147113, PMCID: PMC10546962

Subramaniyan B, Gurung S, Bodas M, Moore AR, Larabee JL, Reuter D, Georgescu C, Wren JD, Myers DA, Papin JF, Walters MS. The Isolation and In Vitro Differentiation of Primary Fetal Baboon Tracheal Epithelial Cells for the Study of SARS-CoV-2 Host-Virus Interactions. Viruses 15, 2023 March, PMID: 37112842, PMCID: PMC10146425

Stout MB, Vaughan KL, Isola JVV, Mann SN, Wellman B, Hoffman JM, Porter HL, Freeman WM, Mattison JA. Assessing tolerability and physiological responses to 17α-estradiol administration in male rhesus macaques. Geroscience, 2023 March, PMID: 36897526, PMCID: PMC10651821

Jackson A, Lin SJ, Jones EA, Chandler KE, Orr D, Moss C, Haider Z, Ryan G, Holden S, Harrison M, Burrows N, Jones WD, Loveless M, Petree C, Stewart H, Low K, Donnelly D, Lovell S, Drosou K, Genomics England Research Consortium, Solve-RD consortium, Varshney GK, Banka S. Clinical, genetic, epidemiologic, evolutionary, and functional delineation of TSPEAR-related autosomal recessive ectodermal dysplasia 14. HGG Adv 4:100186, 2023 March, PMID: 37009414, PMCID: PMC10064225

Felten R, Ye T, Schleiss C, Schwikowski B, Sibilia J, Monneaux F, Dumortier H, Jonsson R, Lessard C, Ng F, Takeuchi T, Mariette X, Gottenberg JE. Identification of new candidate drugs for primary Sjögren's syndrome using a drug repurposing transcriptomic approach. Rheumatology (Oxford), 2023 March, PMID: 36869684, PMCID: PMC10629788

Chioma OS, Mallott E, Shah-Gandhi B, Wiggins Z, Langford M, Lancaster AW, Gelbard A, Wu H, Johnson JE, Lancaster L, Wilfong EM, Crofford LJ, Montgomery CG, Van Kaer L, Bordenstein S, Newcomb DC, Drake WP. Low Gut Microbial Diversity Augments Estrogen-Driven Pulmonary Fibrosis in Female-Predominant Interstitial Lung Disease. Cells 12, 2023 February, PMID: 36899902, PMCID: PMC10000459

Ocañas SR, Isola JVV, Saccon TD, Pham KD, Chucair-Elliott AJ, Schneider A, Freeman WM, Stout MB. Cell-Specific Paired Interrogation of the Mouse Ovarian Epigenome and Transcriptome. J Vis Exp, 2023 February, PMID: 36912526, PMCID: PMC10165884

Ocañas SR, Ansere VA, Kellogg CM, Isola JVV, Chucair-Elliott AJ, Freeman WM. Chromosomal and gonadal factors regulate microglial sex effects in the aging brain. Brain Res Bull, 2023 February, PMID: 36804773, PMCID: PMC10810555

Ding Y, Chen J, Li S, Wren JD, Bajpai AK, Wang J, Tanaka T, Rice HC, Hays FA, Lu L, Zhang XA. EWI2 and its relatives in Tetraspanin-enriched membrane domains regulate malignancy. Oncogene, 2023 February, PMID: 36788350

Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJF, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. Res Sq, 2023 February, PMID: 36778386, PMCID: PMC9915771

Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJF, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. bioRxiv, 2023 January, PMID: 36747810, PMCID: PMC9900832

Hopiavuori BR, Masser DR, Wilkerson JL, Brush RS, Mandal NA, Anderson RE, Freeman WM. Isolation of Neuronal Synaptic Membranes by Sucrose Gradient Centrifugation. Methods Mol Biol 2625:7-15, 2023 January, PMID: 36653629

Shen Y, Khatri B, Rananaware S, Li D, Ostrov DA, Jain PK, Lessard CJ, Nguyen CQ. Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population. PLoS One 18:e0276700, 2023 January, PMID: 36649279, PMCID: PMC9844918

Isola JVV, Ko S, Ocañas SR, Stout MB. Role of Estrogen Receptor α in Aging and Chronic Disease. Adv Geriatr Med Res 5, 2023 January, PMID: 37425648, PMCID: PMC10327608

Bagavant H, Araszkiewicz AM, Rasmussen A, Pezant N, Montgomery C, Scofield RH, Farris D, Lessard CJ, Deshmukh US. Anti-vimentin antibodies are associated with higher severity of Sjögren's disease. Clin Immunol 247:109243, 2023 January, PMID: 36702181, PMCID: PMC10037908