Department of Genetics Publications for May 12th – June 8th, 2024

Department of Genetics faculty, postdocs, students and collaborators published 23 papers during May 12th – June 8th, 2024.

 

Rigor and reproducibility in human brain organoid research: Where we are and where we need to go. 

Sandoval SO, Cappuccio G, Kruth K, Osenberg S, Khalil SM, Méndez-Albelo NM, Padmanabhan K, Wang D, Niciu MJ, Bhattacharyya A, Stein JL, Sousa AMM, Waxman EA, Buttermore ED, Whye D, Sirois CL; Cross-IDDRC Human Stem Cell Consortium; Williams A, Maletic-Savatic M, Zhao X.

Stem Cell Reports. 2024 May 10:S2213-6711(24)00114-0. doi: 10.1016/j.stemcr.2024.04.008. Online ahead of print.

PMID: 38759644 Review.

 

Implementing Evidence-Based Assertions of Clinical Actionability in the Context of Secondary Findings: Updates from the ClinGen Actionability Working Group. 

Pak CM, Gilmore MJ, Bulkley JE, Chakraborty P, Dagan-Rosenfeld O, Foreman AKM, Gollob MH, Jenkins CL, Katz AE, Lee K, Meeks N, O’Daniel JM, Posey JE, Rego SM, Shah N, Steiner RD, Stergachis AB, Subramanian SL, Trotter T, Wallace K, Williams MS, Goddard KAB, Buchanan AH, Manickam K, Powell B, Ezzell Hunter J; ClinGen Resource.

Genet Med. 2024 May 14:101164. doi: 10.1016/j.gim.2024.101164. Online ahead of print.

PMID: 38757444

 

Pharmacological Analysis of NLRP3 Inflammasome Inhibitor Sodium [(1,2,3,5,6,7-Hexahydro-s-indacen-4-yl)carbamoyl][(1-methyl-1H-pyrazol-4-yl)({[(2S)-oxolan-2-yl]methyl})sulfamoyl]azanide in Cellular and Mouse Models of Inflammation Provides a Translational Framework. 

Doedens JR, Smolak P, Nguyen M, Wescott H, Diamond C, Schooley K, Billinton A, Harrison D, Koller BH, Watt AP, Gabel CA.

ACS Pharmacol Transl Sci. 2024 Apr 18;7(5):1438-1456. doi: 10.1021/acsptsci.4c00061. eCollection 2024 May 10.

PMID: 38751618

 

Whole genome sequencing based analysis of inflammation biomarkers in the Trans-Omics for Precision Medicine (TOPMed) consortium. 

Jiang MZ, Gaynor SM, Li X, Van Buren E, Stilp A, Buth E, Wang FF, Manansala R, Gogarten SM, Li Z, Polfus LM, Salimi S, Bis JC, Pankratz N, Yanek LR, Durda P, Tracy RP, Rich SS, Rotter JI, Mitchell BD, Lewis JP, Psaty BM, Pratte KA, Silverman EK, Kaplan RC, Avery C, North KE, Mathias RA, Faraday N, Lin H, Wang B, Carson AP, Norwood AF, Gibbs RA, Kooperberg C, Lundin J, Peters U, Dupuis J, Hou L, Fornage M, Benjamin EJ, Reiner AP, Bowler RP, Lin X, Auer PL, Raffield LM; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Inflammation Working Group.

Hum Mol Genet. 2024 May 15:ddae050. doi: 10.1093/hmg/ddae050. Online ahead of print.

PMID: 38747556

 

Meningeal lymphatic CGRP signaling governs pain via cerebrospinal fluid efflux and neuroinflammation in migraine models. 

Nelson-Maney NP, Balint L, Beeson AL, Serafin DS, Kistner BM, Douglas ES, Siddiqui AH, Tauro AM, Caron KM.

J Clin Invest. 2024 May 14:e175616. doi: 10.1172/JCI175616. Online ahead of print.

PMID: 38743922

 

The clinical utility of sequencing the entirety of CFTR. 

Sheridan MB, Aksit MA, Pagel K, Hetrick K, Shultz-Lutwyche H, Myers B, Buckingham KJ, Pace RG, Ling H, Pugh E, O’Neal WK, Bamshad MJ, Gibson RL, Knowles MR, Blackman SM, Cutting GR, Raraigh KS.

J Cyst Fibros. 2024 May 10:S1569-1993(24)00062-6. doi: 10.1016/j.jcf.2024.04.018. Online ahead of print.

PMID: 38734509

 

Validation of human telomere length multi-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as human telomere length regulation genes. 

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.

Nat Commun. 2024 May 24;15(1):4417. doi: 10.1038/s41467-024-48394-y.

PMID: 38789417

 

Single-cell genomics and regulatory networks for 388 human brains. 

Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X; PsychENCODE Consortium‡; Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M; PsychENCODE Consortium.

Science. 2024 May 24;384(6698):eadi5199. doi: 10.1126/science.adi5199. Epub 2024 May 24.

PMID: 38781369

 

Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. 

Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H; PsychENCODE Consortium†; Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ; PsychENCODE Consortium.

Science. 2024 May 24;384(6698):eadh0829. doi: 10.1126/science.adh0829. Epub 2024 May 24.

PMID: 38781368

 

Histone H1.0 couples cellular mechanical behaviors to chromatin structure. 

Hu S, Chapski DJ, Gehred ND, Kimball TH, Gromova T, Flores A, Rowat AC, Chen J, Packard RRS, Olszewski E, Davis J, Rau CD, McKinsey TA, Rosa-Garrido M, Vondriska TM.

Nat Cardiovasc Res. 2024;3(4):441-459. doi: 10.1038/s44161-024-00460-w. Epub 2024 Apr 10.

PMID: 38765203 Free PMC article.

 

MutLα suppresses error-prone DNA mismatch repair and preferentially protects noncoding DNA from mutations. 

Kadyrova LY, Mieczkowski PA, Kadyrov FA.

J Biol Chem. 2024 May 21:107406. doi: 10.1016/j.jbc.2024.107406. Online ahead of print.

PMID: 38782208

 

Immune features are associated with response to neoadjuvant chemo-immunotherapy for muscle-invasive bladder cancer. 

Beckabir W, Zhou M, Lee JS, Vensko SP, Woodcock MG, Wang HH, Wobker SE, Atassi G, Wilkinson AD, Fowler K, Flick LM, Damrauer JS, Harrison MR, McKinnon KP, Rose TL, Milowsky MI, Serody JS, Kim WY, Vincent BG.

Nat Commun. 2024 May 24;15(1):4448. doi: 10.1038/s41467-024-48480-1.

PMID: 38789460 Clinical Trial.

 

Multi-omics in nasal epithelium reveals three axes of dysregulation for asthma risk in the African Diaspora populations. 

Szczesny B, Boorgula MP, Chavan S, Campbell M, Johnson RK, Kammers K, Thompson EE, Cox MS, Shankar G, Cox C, Morin A, Lorizio W, Daya M, Kelada SNP, Beaty TH, Doumatey AP, Cruz AA, Watson H, Naureckas ET, Giles BL, Arinola GA, Sogaolu O, Falade AG, Hansel NN, Yang IV, Olopade CO, Rotimi CN, Landis RC, Figueiredo CA, Altman MC, Kenny E, Ruczinski I, Liu AH, Ober C, Taub MA, Barnes KC, Mathias RA.

Nat Commun. 2024 May 28;15(1):4546. doi: 10.1038/s41467-024-48507-7.

PMID: 38806494 Free PMC article.

 

Early life exposure to vitamin D deficiency impairs molecular mechanisms that regulate liver cholesterol biosynthesis, energy metabolism, inflammation, and detoxification. 

Knuth MM, Xue J, Elnagheeb M, Gharaibeh RZ, Schoenrock SA, McRitchie S, Brouwer C, Sumner SJ, Tarantino L, Valdar W, Rector RS, Simon JM, Ideraabdullah F.

Front Endocrinol (Lausanne). 2024 May 10;15:1335855. doi: 10.3389/fendo.2024.1335855. eCollection 2024.

PMID: 38800476 Free PMC article.

 

Consideration of disease penetrance in the selection of secondary findings gene-disease pairs: A policy statement of the American College of Medical Genetics and Genomics (ACMG). 

Gordon AS, Lee K, Abul-Husn NS, Amendola LM, Brothers K, Chung WK, Gollob MH, Harrison SM, Hershberger RE, Richards CS, Stewart DR, Martin CL, Miller DT; ACMG Secondary Findings Working Group. Electronic address: documents@acmg.net.

Genet Med. 2024 May 30:101142. doi: 10.1016/j.gim.2024.101142. Online ahead of print.

PMID: 38819344 No abstract available.

 

Relationships of depression and antidepressant use with epigenetic age acceleration and all-cause mortality among postmenopausal women. 

Beydoun MA, Beydoun HA, Ashe J, Georgescu MF, Horvath S, Lu A, Zannas AS, Shadyab AH, Jung SY, Wassertheil-Smoller S, Casanova R, Zonderman AB, Brunner RL.

Aging (Albany NY). 2024 May 27;16. doi: 10.18632/aging.205868. Online ahead of print.

PMID: 38809417

 

Heterochromatic 3D genome organization is directed by HP1a- and H3K9-dependent and independent mechanisms. 

Stutzman AV, Hill CA, Armstrong RL, Gohil R, Duronio RJ, Dowen JM, McKay DJ.

Mol Cell. 2024 May 18:S1097-2765(24)00395-2. doi: 10.1016/j.molcel.2024.05.002. Online ahead of print.

PMID: 38795706

 

Sex-Dependent Differences in Mouse Placental Gene Expression following a Maternal High-Fat Diet. 

Grace MR, Vora NL, Smeester L, Dotters-Katz SK, Fry RC, Bae-Jump V, Boggess K.

Am J Perinatol. 2024 May;41(S 01):e1273-e1280. doi: 10.1055/a-2008-8286. Epub 2023 Jan 6.

PMID: 36608700

 

Epigenetic and proteomic signatures associate with clonal hematopoiesis expansion rate. 

Mack TM, Raddatz MA, Pershad Y, Nachun DC, Taylor KD, Guo X, Shuldiner AR, O’Connell JR, Kenny EE, Loos RJF, Redline S, Cade BE, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Cho MH, DeMeo DL, Levy D, Johnson AD, Mathias RA, Yanek LR, Heckbert SR, Smith NL, Wiggins KL, Raffield LM, Carson AP, Rotter JI, Rich SS, Manichaikul AW, Gu CC, Chen YI, Lee WJ, Shoemaker MB, Roden DM, Kooperberg C, Auer PL, Desai P, Blackwell TW, Smith AV, Reiner AP, Jaiswal S, Weinstock JS, Bick AG.

Nat Aging. 2024 Jun 4. doi: 10.1038/s43587-024-00647-7. Online ahead of print.

PMID: 38834882

 

Smoking-informed methylation and expression QTLs in human brain and colocalization with smoking-associated genetic loci. 

Carnes MU, Quach BC, Zhou L, Han S, Tao R, Mandal M, Deep-Soboslay A, Marks JA, Page GP, Maher BS, Jaffe AE, Won H, Bierut LJ, Hyde TM, Kleinman JE, Johnson EO, Hancock DB.

Neuropsychopharmacology. 2024 Jun 4. doi: 10.1038/s41386-024-01885-4. Online ahead of print.

PMID: 38830989

 

Sarbecovirus disease susceptibility is conserved across viral and host models. 

Leist SR, Schäfer A, Risemberg EL, Bell TA, Hock P, Zweigart MR, Linnertz CL, Miller DR, Shaw GD, de Villena FPM, Ferris MT, Valdar W, Baric RS.

Virus Res. 2024 May 30:199399. doi: 10.1016/j.virusres.2024.199399. Online ahead of print.

PMID: 38823688

 

The VEGF-Hypoxia Signature Is Upregulated in Basal-like Breast Tumors from Women of African Ancestry and Associated with Poor Outcomes in Breast Cancer. 

Han YJ, Liu S, Hardeman A, Rajagopal PS, Mueller J, Khramtsova G, Sanni A, Ajani M, Clayton W, Hurley IW, Yoshimatsu TF, Zheng Y, Parker J, Perou CM, Olopade OI.

Clin Cancer Res. 2024 Jun 3;30(11):2609-2618. doi: 10.1158/1078-0432.CCR-23-1526.

PMID: 38564595

 

Obsessive-compulsive disorder among individuals of Hispanic and Latin American ancestry: Cultural considerations for assessment and psychotherapy. 

Morris OJ, Wiese AD, Pinciotti CM, Pacheco R, Mallen MCM, Schweissing EJ, Soileau KJ; Latin American Trans-ancestry INitiative for OCD genomics (LATINO); Brazilian Obsessive-Compulsive Spectrum Work Group (GTTOC); Crowley JJ, Storch EA.

Bull Menninger Clin. 2024 Spring;88(2):148-170. doi: 10.1521/bumc.2024.88.2.148.

PMID: 38836850