Department of Genetics Publications for April 27th – May 31st, 2025

Department of Genetics faculty, postdocs, students and collaborators published 42 papers during April 27th – May 31st 2025.

 

PGV001, a Multi-Peptide Personalized Neoantigen Vaccine Platform: Phase I Study in Patients with Solid and Hematologic Malignancies in the Adjuvant Setting. 

Saxena M, Marron TU, Kodysh J, Finnigan JP Jr, Onkar S, Kaminska A, Tuballes K, Guo R, Sabado RL, Meseck M, O’Donnell TJ, Sebra RP, Parekh S, Galsky MD, Blasquez A, Gimenez G, Bicak M, Cimen Bozkus C, Delbeau-Zagelbaum D, Rodriguez D, Acuna-Villaorduna A, Misiukiewicz KJ, Posner MR, Miles BA, Irie HY, Tiersten A, Doroshow DB, Wolf A, Mandeli J, Brody R, Salazar AM, Gnjatic S, Hammerbacher J, Schadt E, Friedlander P, Rubinsteyn A, Bhardwaj N.

Cancer Discov. 2025 May 2;15(5):930-947. doi: 10.1158/2159-8290.CD-24-0934.

PMID: 40094414 Clinical Trial.

 

Dynamic activation of rAAV transgene expression by a small molecule that recruits endogenous transcriptional machinery. 

Wasserman SR, Muron S, Lee HR, Routh ML, Hepperla AJ, Scoville DM, Huber A, Umana JD, Pereira NE, Foley CA, James LI, Hathaway NA.

Nucleic Acids Res. 2025 Apr 22;53(8):gkaf345. doi: 10.1093/nar/gkaf345.

PMID: 40298110 Free PMC article.

 

Host genetic diversity contributes to disease outcome in Crimean-Congo hemorrhagic fever virus infection. 

Rao D, Lewis M, Meade-White K, Shaia C, Okumura A, Ferris MT, Schäfer A, Baric R, Feldmann H, Hawman DW.

Npj Viruses. 2025 Feb 27;3(1):16. doi: 10.1038/s44298-025-00100-5.

PMID: 40295889 Free PMC article.

 

STAT3-dependent Regulation of CFTR and Ciliogenesis Is Essential for Mucociliary Clearance and Innate Airway Defense in Hyper-IgE Syndrome. 

Sun L, Walls SA, Dang H, Quinney NL, Sears PR, Sadritabrizi T, Hasegawa K, Okuda K, Asakura T, Chang X, Zheng M, Mikami Y, Dizmond FU, Danilova D, Zhou L, Deshmukh A, Cholon DM, Radicioni G, Rogers TD, Kissner WJ, Markovetz MR, Guhr Lee TN, Gutay MI, Esther CR Jr, Chua M, Grubb BR, Ehre C, Kesimer M, Hill DB, Ostrowski LE, Button B, Gentzsch M, Robinson C, Olivier KN, Freeman AF, Randell SH, Vladar E, O’Neal WK, Boucher RC Jr, Chen G.

Am J Respir Crit Care Med. 2025 May 2. Online ahead of print.

PMID: 40315437

 

Chromatin profiling to identify biomarkers in inflammatory bowel diseases. 

Awad A, Alcala AJ, Cowles MW, Sheikh SZ.

Curr Opin Gastroenterol. 2025 Apr 25. doi: 10.1097/MOG.0000000000001104. Online ahead of print.

PMID: 40304726

 

ARTdeConv: adaptive regularized tri-factor non-negative matrix factorization for cell type deconvolution. 

Liu T, Liu C, Li Q, Zheng X, Zou F.

NAR Genom Bioinform. 2025 Apr 26;7(2):lqaf046. doi: 10.1093/nargab/lqaf046. eCollection 2025 Jun.

PMID: 40290316 Free PMC article.

 

Cell-type-specific and inflammatory DNA methylation patterns associated with PTSD. 

Smith AK, Katrinli S, Maihofer AX, Aiello AE, Baker DG, Boks MP, Brick LA, Chen CY, Dalvie S, Fani N, Fortier CB, Gelernter J, Geuze E, Gillespie CF, Hayes JP, Hong S, Kessler RC, King AP, Koen N, Koenen KC, Liberzon I, Linnstaedt SD, McLean SA, Michopoulos V, Milberg WP, Miller MW, Mufford MS, Nugent NR, Orcutt HK, Powers A, Rauch SAM, Ressler KJ, Risbrough VB, Rutten BPF, Smoller JW, Stein DJ, Stein MB, Ursano RJ, Verfaellie MH, Vermetten E, Vinkers CH, Wani AH, WareVinkers EB, Wildman DE, Wolf EJ, Zhao Y, Logue MW, Nievergelt CM, Uddin M, Zannas AS; PGC-PTSD Epigenetics Workgroup; PsychENCODE PTSD Brainomics Project; Traumatic Stress Brain Research Group.

Brain Behav Immun. 2025 Apr 24;128:540-548. doi: 10.1016/j.bbi.2025.04.031. Online ahead of print.

PMID: 40286993

 

Atezolizumab plus personalized neoantigen vaccination in urothelial cancer: a phase 1 trial. 

Saxena M, Anker JF, Kodysh J, O’Donnell T, Kaminska AM, Meseck M, Hapanowicz O, Niglio SA, Salazar AM, Shah HR, Kinoshita Y, Brody R, Rubinsteyn A, Sebra RP, Bhardwaj N, Galsky MD.

Nat Cancer. 2025 May 9. doi: 10.1038/s43018-025-00966-7. Online ahead of print.

PMID: 40346292

 

A Social Web to Stimulate Interdisciplinary Collaborations. 

Sharanowski BJ, Maughan H, Goodey NM, Meyer WK, Li-Byarlay H, Mayes ML, Smith KN.

Integr Comp Biol. 2025 May 9:icaf033. doi: 10.1093/icb/icaf033. Online ahead of print.

PMID: 40343776

 

Prenatal Detection of TGFBR1 Variant Associated With Severe Ventriculomegaly and Loeys-Dietz Syndrome. 

Hodges MB, Harris S, Murphy B, Gilmore KL, Vora NL.

Prenat Diagn. 2025 May 5. doi: 10.1002/pd.6811. Online ahead of print.

PMID: 40325597

 

FPLS-DC: functional partial least squares through distance covariance for imaging genetics. 

Pan W, Shan Y, Li C, Huang S, Li T, Li Y, Zhu H.

Bioinformatics. 2024 Mar 29;40(4):btae173. doi: 10.1093/bioinformatics/btae173.

PMID: 38552322 Free PMC article.

 

Perspectives on the Current and Future State of Artificial Intelligence in Medical Genetics. 

Solomon BD, Cheatham M, de Guimarães TAC, Duong D, Haendel MA, Hsieh TC, Javanmardi B, Johnson B, Krawitz P, Kruszka P, Laurent T, Lee NC, McWalter K, Michaelides M, Mohnike K, Pontikos N, Guillen Sacoto MJ, Shwetar YJ, Ustach VD, Waikel RL, Woof W.

Am J Med Genet A. 2025 May 15:e64118. doi: 10.1002/ajmg.a.64118. Online ahead of print.

PMID: 40375359 Review.

 

Specific Bacterial Taxa and Their Metabolite, DHPS, May Be Linked to Gut Dyshomeostasis in Patients with Alzheimer’s Disease, Parkinson’s Disease, and Amyotrophic Lateral Sclerosis. 

Christopher CJ, Morgan KH, Tolleson CM, Trudell R, Fernandez-Romero R, Rice L, Abiodun BA, Vickery Z, Jones KA, Woodall BM, Nagy C, Mieczkowski PA, Bowen G, Campagna SR, Ellis JC.

Nutrients. 2025 May 6;17(9):1597. doi: 10.3390/nu17091597.

PMID: 40362907 Free PMC article.

 

Genome-wide analyses identify 30 loci associated with obsessive-compulsive disorder. 

Strom NI, Gerring ZF, Galimberti M, Yu D, Halvorsen MW, Abdellaoui A, Rodriguez-Fontenla C, Sealock JM, Bigdeli T, Coleman JR, Mahjani B, Thorp JG, Bey K, Burton CL, Luykx JJ, Zai G, Alemany S, Andre C, Askland KD, Bäckman J, Banaj N, Barlassina C, Nissen JB, Bienvenu OJ, Black D, Bloch MH, Børte S, Bosch R, Breen M, Brennan BP, Brentani H, Buxbaum JD, Bybjerg-Grauholm J, Byrne EM, Cabana-Dominguez J, Camarena B, Camarena A, Cappi C, Carracedo A, Casas M, Cavallini MC, Ciullo V, Cook EH, Crosby J, Cullen BA, De Schipper EJ, Delorme R, Djurovic S, Elias JA, Estivill X, Falkenstein MJ, Fundin BT, Garner L, Gironda C, Goes FS, Grados MA, Grove J, Guo W, Haavik J, Hagen K, Harrington K, Havdahl A, Höffler KD, Hounie AG, Hucks D, Hultman C, Janecka M, Jenike E, Karlsson EK, Kelley K, Klawohn J, Krasnow JE, Krebs K, Lange C, Lanzagorta N, Levey D, Lindblad-Toh K, Macciardi F, Maher B, Mathes B, McArthur E, McGregor N, McLaughlin NC, Meier S, Miguel EC, Mulhern M, Nestadt PS, Nurmi EL, O’Connell KS, Osiecki L, Ousdal OT, Palviainen T, Pedersen NL, Piras F, Piras F, Potluri S, Rabionet R, Ramirez A, Rauch S, Reichenberg A, Riddle MA, Ripke S, Rosário MC, Sampaio AS, Schiele MA, Skogholt AH, Sloofman LG, Smit J, Artigas MS, Thomas LF, Tifft E, Vallada H, van Kirk N, Veenstra-VanderWeele J, Vulink NN, Walker CP, Wang Y, Wendland JR, Winsvold BS, Yao Y, Zhou H; Estonian Biobank; 23andMe Inc.; Agrawal A, Alonso P, Berberich G, Bucholz KK, Bulik CM, Cath D, Denys D, Eapen V, Edenberg H, Falkai P, Fernandez TV, Fyer AJ, Gaziano JM, Geller DA, Grabe HJ, Greenberg BD, Hanna GL, Hickie IB, Hougaard DM, Kathmann N, Kennedy J, Lai D, Landén M, Hellard SL, Leboyer M, Lochner C, McCracken JT, Medland SE, Mortensen PB, Neale BM, Nicolini H, Nordentoft M, Pato M, Pato C, Pauls DL, Piacentini J, Pittenger C, Posthuma D, Ramos-Quiroga JA, Rasmussen SA, Richter MA, Rosenberg DR, Ruhrmann S, Samuels JF, Sandin S, Sandor P, Spalletta G, Stein DJ, Stewart SE, Storch EA, Stranger BE, Turiel M, Werge T, Andreassen OA, Børglum AD, Walitza S, Hveem K, Hansen BK, Rück C, Martin NG, Milani L, Mors O, Reichborn-Kjennerud T, Ribasés M, Kvale G, Mataix-Cols D, Domschke K, Grünblatt E, Wagner M, Zwart JA, Breen G, Nestadt G, Kaprio J, Arnold PD, Grice DE, Knowles JA, Ask H, Verweij KJ, Davis LK, Smit DJ, Crowley JJ, Scharf JM, Stein MB, Gelernter J, Mathews CA, Derks EM, Mattheisen M.

Nat Genet. 2025 May 13. doi: 10.1038/s41588-025-02189-z. Online ahead of print.

PMID: 40360802

 

Tourette Syndrome and Chronic Tic Disorders. 

Halvorsen MW.

Psychiatr Clin North Am. 2025 Jun;48(2):281-292. doi: 10.1016/j.psc.2025.01.006. Epub 2025 Mar 4.

PMID: 40348418 Review.

 

Roles and future opportunities for genomic architecture in understanding repeated evolution. 

Kellermeyer R, Alvarez-Ponce D, Arsuaga J, Chain FJJ, Dennis MY, Margres MJ, Meisel RP, Meyer WK, Moon TS, Smith KN, Wolfe TD, Zhou CY, McGaugh S.

Integr Comp Biol. 2025 May 15:icaf040. doi: 10.1093/icb/icaf040. Online ahead of print.

PMID: 40372385

 

Microglia Single-Cell RNA-Seq Enables Robust and Applicable Markers of Biological Aging. 

Stanley N, Dhawka L, Jaikumar S, Huang YC, Zannas AS.

Aging Cell. 2025 May 15:e70095. doi: 10.1111/acel.70095. Online ahead of print.

PMID: 40371813

 

PTSD and epigenetic aging: a longitudinal meta-analysis. 

Zhao X, Katrinli S, McCormick BM, Miller MW, Nugent NR, Wani AH, Zannas AS, Aiello AE, Baker DG, Boks MP, Chen CY, Fortier CB, Gelernter J, Geuze E, Koenen KC, Linnstaedt SD, Luykx JJ, Maihofer AX, McLean SA, Milberg WP, Ratanatharathorn A, Ressler KJ, Risbrough VB, Rutten BPF, Smoller JW, Stein MB, Ursano RJ, Vermetten E, Vinkers CH, Ware EB, Wildman DE, Zhao Y; PGC-PTSD Epigenetics Workgroup; Logue MW, Nievergelt CM, Smith AK, Uddin M, Wolf EJ.

Psychol Med. 2025 May 14;55:e142. doi: 10.1017/S0033291725000558.

PMID: 40366073

 

Early life phthalate exposure impacts gray matter and white matter volume in infants and young children. 

Werder EJ, Lu K, Liu CW, Thistle JE, Rager JE, Li G, Wu Z, Li T, Wang L, Sandler DP, Gilmore JH, Piven J, Zhu H, Lin W, Engel SM.

Environ Res. 2025 May 10:121826. doi: 10.1016/j.envres.2025.121826. Online ahead of print.

PMID: 40355063

 

Cell Type-Level Epigenetics at the Frontier of Atherosclerosis Research. 

Zannas AS.

Circulation. 2025 May 13;151(19):1409-1411. doi: 10.1161/CIRCULATIONAHA.125.074275. Epub 2025 May 12.

PMID: 40354452 No abstract available.

 

Unlocking the Potential of Wear Time of a Wearable Device to Enhance Postpartum Depression Screening and Detection: Cross-Sectional Study. 

Hurwitz E, Meltzer-Brody S, Butzin-Dozier Z, Patel RC, Elhadad N, Haendel MA.

JMIR Form Res. 2025 May 23;9:e67585. doi: 10.2196/67585.

PMID: 40409746

 

Chikungunya virus-specific CD4⁺ T cells are associated with chronic chikungunya viral arthritic disease in humans. 

Agarwal R, Chang J, Côrtes FH, Ha C, Villalpando J, Castillo IN, Gálvez RI, Grifoni A, Sette A, Romero-Vivas CM, Heise MT, Premkumar L, Falconar AK, Weiskopf D.

Cell Rep Med. 2025 May 20;6(5):102134. doi: 10.1016/j.xcrm.2025.102134.

PMID: 40398392

 

Epigenome-wide DNA methylation association study of CHIP provides insight into perturbed gene regulation. 

Kirmani S, Huan T, Van Amburg JC, Joehanes R, Uddin MM, Nguyen NQH, Yu B, Brody JA, Fornage M, Bressler J, Sotoodehnia N, Ong DA, Puddu F, Floyd JS, Ballantyne CM, Psaty BM, Raffield LM, Natarajan P, Conneely KN, Weinstock JS, Carson AP, Lange LA, Ferrier K, Heard-Costa NL, Murabito J, Bick AG, Levy D.

Nat Commun. 2025 May 20;16(1):4678. doi: 10.1038/s41467-025-59333-w.

PMID: 40393957 Free PMC article.

 

Broadly active intranasal influenza vaccine with a nanocomplex particulate adjuvant targeting mast cells and toll-like receptor 9. 

Ontiveros-Padilla L, Hendy DA, Pena ES, Williamson GL, Murphy CT, Lukesh NR, Ashcraft KA, Abraham MA, Landon CD, Staats HF, Abraham SN, Carlock M, Ross TM, Petrovsky N, Heise MT, Bachelder EM, Ainslie KM.

J Control Release. 2025 May 18:113855. doi: 10.1016/j.jconrel.2025.113855. Online ahead of print.

PMID: 40393528

 

Species-Dependent Metabolism of a Covalent nsP2 Protease Inhibitor with In Vivo Antialphaviral Activity. 

Hossain MA, Mayo AK, Ghoshal A, Taft-Benz S, Anderson E, Morales NL, Pressey KD, Vargason A, Brouwer KLR, Moorman NJ, Heise MT, Willson TM.

J Med Chem. 2025 May 22;68(10):10473-10485. doi: 10.1021/acs.jmedchem.5c00825. Epub 2025 May 12.

PMID: 40351160

 

AHR activated placental adrenomedullin: A plausible factor in smoke-induced preeclampsia protection. 

Marbrey MW, Kistner B, Douglas ES, Caron KM.

Placenta. 2025 May 15;167:175-180. doi: 10.1016/j.placenta.2025.05.013. Online ahead of print.

PMID: 40408837

 

Snrnp25 is a candidate for the peri-implantation lethal phenotype of the Hba deletions. 

Velásquez-Escobar AM, Hillhouse AE, Magnuson T, Threadgill DW.

Mamm Genome. 2025 May 21. doi: 10.1007/s00335-025-10133-z. Online ahead of print.

PMID: 40399475

 

Cell cycle-regulated transcriptional pausing of Drosophila replication-dependent histone genes. 

Kemp JP Jr, Geisler MS, Hoover M, Cho CY, O’Farrell PH, Marzluff WF, Duronio RJ.

Mol Biol Cell. 2025 May 21:mbcE25050212. doi: 10.1091/mbc.E25-05-0212. Online ahead of print.

PMID: 40397569

 

Alzheimer’s disease knowledge graph enhances knowledge discovery and disease prediction. 

Yang Y, Yu K, Gao S, Yu S, Xiong D, Qin C, Chen H, Tang J, Tang N, Zhu H.

Comput Biol Med. 2025 Jun;192(Pt A):110285. doi: 10.1016/j.compbiomed.2025.110285. Epub 2025 Apr 29.

PMID: 40306017

 

High-dimensional biomarker identification for interpretable disease prediction via machine learning models. 

Dai Y, Wu D, Carroll I, Zou F, Zou B.

Bioinformatics. 2025 May 6;41(5):btaf266. doi: 10.1093/bioinformatics/btaf266.

PMID: 40286292 Free PMC article.

 

Clinical, genetic, and sociodemographic predictors of symptom severity after internet-delivered cognitive behavioural therapy for depression and anxiety. 

Kravchenko O, Bäckman J, Mataix-Cols D, Crowley JJ, Halvorsen M, Sullivan PF, Wallert J, Rück C.

BMC Psychiatry. 2025 May 30;25(1):555. doi: 10.1186/s12888-025-07012-x.

PMID: 40448103

 

Noncanonical Poly(A) Polymerase TENT4 Drives Expression of Subgenomic Hepatitis A Virus RNAs in Infected Cells. 

Li Y, Gupta A, Papas BN, Aponte-Diaz D, Harris JM, Misumi I, Whitmire JK, Cameron CE, Morgan M, Lemon SM.

Viruses. 2025 May 2;17(5):665. doi: 10.3390/v17050665.

PMID: 40431677 Free PMC article.

 

B7-H3 and CSPG4 co-targeting as Pan-CAR-T cell treatment of triple-negative breast cancer. 

Stucchi S, Borea R, Garcia-Recio S, Zingarelli M, Rädler PD, Camerini E, Marnata Pellegry C, O’Connor S, Earp HS, Carey LA, Perou CM, Savoldo B, Dotti G.

J Immunother Cancer. 2025 May 26;13(5):e011533. doi: 10.1136/jitc-2025-011533.

PMID: 40425233 Free PMC article.

 

Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 

Green WD, Gomez A, Plotkin AL, Pratt BM, Merritt EF, Mullins GN, Kren NP, Modliszewski JL, Zhabotynsky V, Woodcock MG, Green JM, Cannon G, Pipkin ME, Dotti G, Thaxton JE, Pylayeva-Gupta Y, Baldwin AS, Morris JP 4th, Stanley N, Milner JJ.

Immunity. 2025 May 22:S1074-7613(25)00193-1. doi: 10.1016/j.immuni.2025.04.030. Online ahead of print.

PMID: 40425012

 

The Eating Disorders Genetics Initiative 2 (EDGI2): study protocol. 

Berthold N, MacDermod CM, Thornton LM, Parker R, Morales SAC, Hog L, Kennedy HL, Guintivano J, Sullivan PF, Crowley JJ, Johnson JS, Birgegård A, Fundín BT, Frans E, Xu J, Ngāti Pūkenga MP, Miller AL, Aguilar MV, Barakat S, Abdulkadir M, White JP, Larsen JT, Trujillo E, Winterman B, Zhang R, Lawson R, Wonderlich S, Wonderlich J, Schaefer LM, Mehler PS, Oakes J, Foster M, Gaudiani J, Vacuán ETC, Compte EJ, Petersen LV, Yilmaz Z, Micali N, Jordan J, Kennedy MA, Maguire S, Huckins LM, Lu Y, Dinkler L, Martin NG, Bulik CM.

BMC Psychiatry. 2025 May 26;25(1):532. doi: 10.1186/s12888-025-06777-5.

PMID: 40419993 Free PMC article.

 

The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization. 

Mullen KR, Tammen I, Matentzoglu NA, Mather M, Balhoff JP, Esdaile E, Leroy G, Park CA, Rando HM, Saklou NT, Webb TL, Vasilevsky NA, Mungall CJ, Haendel MA, Nicholas FW, Toro S.

J Vet Intern Med. 2025 Jul-Aug;39(4):e70133. doi: 10.1111/jvim.70133.

PMID: 40413720 Free PMC article.

 

Spt6-Spn1 interaction is required for RNA polymerase II association and precise nucleosome positioning along transcribed genes. 

Chen B, Dronamraju R, Smith-Kinnaman WR, Peck Justice SA, Hepperla AJ, MacAlpine HK, Simon JM, Mosley AL, MacAlpine DM, Strahl BD.

J Biol Chem. 2025 May;301(5):108436. doi: 10.1016/j.jbc.2025.108436. Epub 2025 Mar 22.

PMID: 40127868 Free PMC article.

 

Geriatric ocular trauma and mortality: A retrospective cohort study. 

Pham VQ, Miller HM, Fernandez EO, de Marchi D, Budi E, Zhu H, Fleischman D.

PLoS One. 2025 May 28;20(5):e0324821. doi: 10.1371/journal.pone.0324821. eCollection 2025.

PMID: 40434983 Free PMC article.

 

Mechanistic Insights and Future Directions for Enfortumab Vedotin in Urothelial Carcinoma: Highlights from the 10th Annual Leo & Anne Albert Institute for Bladder Cancer Care and Research Symposium. 

Fahey CC, Clark-Garvey S, Porten S, Kamat AM, Flaig TW, Taylor JA, Kim WY, Milowsky MI.

Curr Oncol. 2025 May 14;32(5):278. doi: 10.3390/curroncol32050278.

PMID: 40422537 Free PMC article. Review.

 

SLC35A2 loss-of-function variants affect glycomic signatures, neuronal fate and network dynamics. 

Lai D, Sosicka P, Williams DJ, Bowyer ME, Ressler AK, Kohrt SE, Muron SJ, Crino PB, Freeze HH, Boland MJ, Heinzen EL.

Brain. 2025 May 26:awaf198. doi: 10.1093/brain/awaf198. Online ahead of print.

PMID: 40418734

 

Integrating Knowledge: The Power of Ontologies in Psychiatric Research and Clinical Informatics. 

McInnis MG, Coleman B, Hurwitz E, Robinson PN, Williams AE, Haendel MA, McMurry JA.

Biol Psychiatry. 2025 May 23:S0006-3223(25)01213-2. doi: 10.1016/j.biopsych.2025.05.014. Online ahead of print.

PMID: 40414449 Review.

 

CATI: A medical context-enhanced framework for diagnosis code assignment in the UK Biobank study. 

Shen Y, Wang J, Wang Z, Shi Z, Chen H, Wang Z, Jiang Y, Wang X, Cheng C, Wang X, Zhu H, Ye J.

Artif Intell Med. 2025 Aug;166:103136. doi: 10.1016/j.artmed.2025.103136. Epub 2025 May 2.

PMID: 40344999