Department of Genetics /genetics/ Fri, 25 Apr 2025 14:09:54 +0000 en-US hourly 1 Anne Thessen Publishes Exposomics Paper in Science /genetics/anne-thessen-publishes-exposomics-paper-in-science/ Fri, 25 Apr 2025 14:09:54 +0000 /genetics/?p=15106 Dr. Anne Thessen (Associate Professor, Genetics) was a co-author of a recently published Science paper titled “Integrating exosomes in biomedicine”.

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]]> Anne Thessen

Dr. Anne Thessen (Associate Professor, Genetics)

Dr. Anne Thessen (Associate Professor, Genetics) was a co-author of a recently published titled “Integrating exosomes in biomedicine”.

The Perspective article resulted from her participation in the Banbury Conference on Integrating Exposomics into the Biomedical Enterprise held in December 2023. The conference attendees crafted an operational definition of exposomics and proposed the inclusion of this data in biomedical research studies. From the paper “the exposome is posited as an integrated compilation of all physical, chemical, biological, and (psycho) social influences that “impact biology””. The authors proposed that gaps in our understanding of human health and disease can be filled by integrating exposomics.

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]]> Department of Genetics Publications for March 2nd – 29th, 2025 /genetics/department-of-genetics-publications-for-march-2nd-29th-2025/ Sun, 20 Apr 2025 23:53:17 +0000 /genetics/?p=15040 Department of Genetics faculty, postdocs, students and collaborators published 30 papers during March 2nd - 29th 2025.

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]]> Genetics PublicationsDepartment of Genetics faculty, postdocs, students and collaborators published 30 papers during March 2nd – 29th 2025.

 

Mandel HL, Shah SN, Bailey LC, Carton T, Chen Y, Esquenazi-Karonika S, Haendel M, Hornig M, Kaushal R, Oliveira CR, Perlowski AA, Pfaff E, Rao S, Razzaghi H, Seibert E, Thomas GL, Weiner MG, Thorpe LE, Divers J; RECOVER EHR Cohort.

J Med Internet Res. 2025 Mar 5;27:e59217. doi: 10.2196/59217.

ʲѱ:40053748

 

Choi SH, Jurgens SJ, Xiao L, Hill MC, Haggerty CM, Sveinbjörnsson G, Morrill VN, Marston NA, Weng LC, Pirruccello JP, Arnar DO, Gudbjartsson DF, Mantineo H, von Falkenhausen AS, Natale A, Tveit A, Geelhoed B, Roselli C, Van Wagoner DR, Darbar D, Haase D, Soliman EZ, Davogustto GE, Jun G, Calkins H, Anderson JL, Brody JA, Halford JL, Barnard J, Hokanson JE, Smith JD, Bis JC, Young K, Johnson LSB, Risch L, Gula LJ, Kwee LC, Chaffin MD, Kühne M, Preuss M, Gupta N, Nafissi NA, Smith NL, Nilsson PM, van der Harst P, Wells QS, Judy RL, Schnabel RB, Johnson R, Smit RAJ, Gabriel S, Knight S, Furukawa T, Blackwell TW, Nauffal V, Wang X, Min YI, Yoneda ZT, Laksman ZWM, Bezzina CR, Alonso A, Psaty BM, Albert CM, Arking DE, Roden DM, Chasman DI, Rader DJ, Conen D, McManus DD, Fatkin D, Benjamin EJ, Boerwinkle E, Marcus GM, Christophersen IE, Smith JG, Roberts JD, Raffield LM, Shoemaker MB, Cho MH, Cutler MJ, Rienstra M, Chung MK, S Olesen M, Sinner MF, Sotoodehnia N, Kirchhof P, Loos RJF, Nazarian S, Mohanty S, Damrauer SM, Kaab S, Heckbert SR, Redline S, Shah SH, Tanaka T, Ebana Y; Regeneron Genetics Center; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Holm H, Stefansson K, Ruff CT, Sabatine MS, Lunetta KL, Lubitz SA, Ellinor PT.

Nat Genet. 2025 Mar 6. doi: 10.1038/s41588-025-02074-9. Online ahead of print.

ʲѱ:40050430

 

Ghoshal A, Tse EG, Hossain MA, Asressu KH, Merten EM, Sears JD, Howell S, Perveen S, Burdick J, Morales NL, Martinez SA, Law I, Davenport BJ, Morrison TE, Streblow ZJ, Streblow DN, Mordant AL, Webb TS, Cabrera A, Herring LE, Arrowsmith CH, Pearce KH, Moorman NJ, Heise MT, Couñago RM, Brown PJ, Willson TM.

Sci Rep. 2025 Mar 1;15(1):7264. doi: 10.1038/s41598-025-91673-x.

ʲѱ:40025188Free PMC article.

 

Bäckman J, Wallert J, Halvorsen M, Roelstraete B, de Schipper E, Strom NI, Eide TO, Höffler KD, Mattheisen M, Hansen B, Kvale G, Hagen K, Haavik J; Nordic OCD and Related Disorders Consortium (NORDiC); Mataix-Cols D, Rück C, Crowley JJ.

Am J Med Genet B Neuropsychiatr Genet. 2025 Mar 7:e33026. doi: 10.1002/ajmg.b.33026. Online ahead of print.

ʲѱ:40052195

 

Gessner KH, Preisser JS, Pfaff E, Wang R, Walters K, Bradford R, Clark M, Ehlers M, Nielsen M.

Anesthesiol Perioper Sci. 2025;3(1):2. doi: 10.1007/s44254-024-00083-1. Epub 2025 Jan 17.

ʲѱ:40051586Free PMC article.

 

Koulouri A, Zannas AS.

J Alzheimers Dis Rep. 2024 Oct 18;8(1):1372-1380. doi: 10.1177/25424823241284227. eCollection 2024.

ʲѱ:40034348Free PMC article.𱹾.

 

Chen Y, Davidson NM, Wan YK, Yao F, Su Y, Gamaarachchi H, Sim A, Patel H, Low HM, Hendra C, Wratten L, Hakkaart C, Sawyer C, Iakovleva V, Lee PL, Xin L, Ng HEV, Loo JM, Ong X, Ng HQA, Wang J, Koh WQC, Poon SYP, Stanojevic D, Tran HD, Lim KHE, Toh SY, Ewels PA, Ng HH, Iyer NG, Thiery A, Chng WJ, Chen L, DasGupta R, Sikic M, Chan YS, Tan BOP, Wan Y, Tam WL, Yu Q, Khor CC, Wüstefeld T, Lezhava A, Pratanwanich PN, Love MI, Goh WSS, Ng SB, Oshlack A; SG-NEx consortium; Göke J.

Nat Methods. 2025 Mar 13. doi: 10.1038/s41592-025-02623-4. Online ahead of print.

ʲѱ:40082608

 

Sun Z, Yi Z, Wei C, Wang W, Ren T, Cravedi P, Tedla F, Ward SC, Azeloglu E, Schrider DR, Li Y, Khan A, Zanoni F, Fu J, Ali S, Liu S, Liang D, Liu T, Li H, Xi C, Vy TH, Mosoyan G, Sun Q, Kumar A, Zhang Z, Farouk S, Campell K, Ochando J, Lee K, Coca S, Xiang J, Connolly P, Gallon L, O’Connell PJ, Colvin R, Menon MC, Nadkarni G, He JC, Kraft M, Jiang X, Zhang X, Kiryluk K, Cherukuri A, Lakkis FG, Zhang W, Chen SH, Heeger PS, Zhang W.

Nat Med. 2025 Mar 10. doi: 10.1038/s41591-025-03568-z. Online ahead of print.

ʲѱ:40065170

 

Parsons VA, Vadlamudi S, Voos KM, Rohy AE, Moxley AH, Cannon ME, Rosen JD, Mills CA, Herring LE, Broadaway KA, Lorenzo DN, Mohlke KL.

Diabetologia. 2025 Mar 10. doi: 10.1007/s00125-025-06391-w. Online ahead of print.

ʲѱ:40064677

 

Felsheim BM, Fernandez-Martinez A, Fan C, Pfefferle AD, Hayward MC, Hoadley KA, Rashid NU, Tolaney SM, Somlo G, Carey LA, Sikov WM, Perou CM.

NPJ Breast Cancer. 2025 Mar 8;11(1):24. doi: 10.1038/s41523-025-00740-z.

ʲѱ:40057511Free PMC article.

 

Liu R, Zhang Z, Won H, Marron JS.

Bioinformatics. 2025 Mar 4;41(3):btaf026. doi: 10.1093/bioinformatics/btaf026.

ʲѱ:40036585Free PMC article.

 

Ciavatta DJ, Kain R, Inrueangsri N, Croci S, Karabayas M, Zulcinski M, Morgan AW.

Rheumatology (Oxford). 2025 Mar 1;64(Supplement_1):i109-i111. doi: 10.1093/rheumatology/keae387.

PMID: 40071404𱹾.

 

Bae-Jump VL, Sill MW, Gehrig PA, Merker JD, Corcoran DL, Pfefferle AD, Hayward MC, Walker JL, Hagemann AR, Waggoner SE, O’Cearbhaill RE, McDonald ME, Edelson MI, DiSilvestro PA, McNally AL, Fleury A, Littell RD, Ueland FR, Lankes HA, Aghajanian C.

Gynecol Oncol. 2025 Mar 7;195:66-74. doi: 10.1016/j.ygyno.2025.03.003. Online ahead of print.

ʲѱ:40056832

 

Jain S, Trinidad M, Nguyen TB, Jones K, Neto SD, Ge F, Glagovsky A, Jones C, Moran G, Wang B, Rahimi K, Çalıcı SZ, Cedillo LR, Berardelli S, Özden B, Chen K, Katsonis P, Williams A, Lichtarge O, Rana S, Pradhan S, Srinivasan R, Sajeed R, Joshi D, Faraggi E, Jernigan R, Kloczkowski A, Xu J, Song Z, Özkan S, Padilla N, de la Cruz X, Acuna-Hidalgo R, Grafmüller A, Barrón LTJ, Manfredi M, Savojardo C, Babbi G, Martelli PL, Casadio R, Sun Y, Zhu S, Shen Y, Pucci F, Rooman M, Cia G, Raimondi D, Hermans P, Kwee S, Chen E, Astore C, Kamandula A, Pejaver V, Ramola R, Velyunskiy M, Zeiberg D, Mishra R, Sterling T, Goldstein JL, Lugo-Martinez J, Kazi S, Li S, Long K, Brenner SE, Bakolitsa C, Radivojac P, Suhr D, Suhr T, Clark WT.

Hum Genet. 2025 Mar 8. doi: 10.1007/s00439-025-02731-3. Online ahead of print.

ʲѱ:40055237

 

Jackson ON, Keenan TF, Nelson-Maney NP, Rommel SA, McLellan WA, Pabst DA, Costidis AM, Caron KM, Kernagis DN, Rotstein DS, Thayer VG, Harms CA, Piscitelli-Doshkov MA, Doshkov P, Schweikert LE, Yopak KE, Braun M, Tift MS.

Animals (Basel). 2025 Mar 4;15(5):729. doi: 10.3390/ani15050729.

ʲѱ:40076012Free PMC article.

 

Misumi I, Yue Z, Jiang Z, Karampoori A, Whitmire JK, Cullen JM, Block T, Lemon SM, Du Y, Li Y.

Antiviral Res. 2025 Mar 19:106145. doi: 10.1016/j.antiviral.2025.106145. Online ahead of print.

ʲѱ:40118118

 

Anand JR, Droby GN, Joseph S, Patel U, Zhang X, Klomp JA, Der CJ, Purvis JE, Wolff SC, Bowser JL, Vaziri C.

NAR Cancer. 2025 Mar 20;7(1):zcaf009. doi: 10.1093/narcan/zcaf009. eCollection 2025 Mar.

ʲѱ:40115747Free PMC article.

 

Liu S, Corcoran DL, Garcia-Recio S, Marron JS, Perou CM.

NAR Genom Bioinform. 2025 Mar 19;7(1):lqaf023. doi: 10.1093/nargab/lqaf023. eCollection 2025 Mar.

ʲѱ:40109353Free PMC article.

 

Matentzoglu N, Bello SM, Stefancsik R, Alghamdi SM, Anagnostopoulos AV, Balhoff JP, Balk MA, Bradford YM, Bridges Y, Callahan TJ, Caufield H, Cuzick A, Carmody LC, Caron AR, de Souza V, Engel SR, Fey P, Fisher M, Gehrke S, Grove C, Hansen P, Harris NL, Harris MA, Harris L, Ibrahim A, Jacobsen JOB, Köhler S, McMurry JA, Munoz-Fuentes V, Munoz-Torres MC, Parkinson H, Pendlington ZM, Pilgrim C, Robb SMC, Robinson PN, Seager J, Segerdell E, Smedley D, Sollis E, Toro S, Vasilevsky N, Wood V, Haendel MA, Mungall CJ, McLaughlin JA, Osumi-Sutherland D.

Genetics. 2025 Mar 17;229(3):iyaf027. doi: 10.1093/genetics/iyaf027.

ʲѱ:40048704Free PMC article.

 

Hysong MR, Shuey MM, Huffman JE, Auer P, Reiner A, Raffield LM.

Blood Adv. 2025 Mar 25;9(6):1452-1462. doi: 10.1182/bloodadvances.2024014399.

ʲѱ:39825822

 

Trotman JB, Abrash EW, Murvin MM, Braceros AK, Li S, Boyson SP, Salcido RT, Cherney RE, Bischoff SR, Kaufmann K, Eberhard QE, Zhang Z, Cowley DO, Calabrese JM.

Mol Cell. 2025 Mar 20;85(6):1117-1133.e14. doi: 10.1016/j.molcel.2025.02.014.

ʲѱ:40118040

 

Wang JR, Alexander TB.

Front Oncol. 2025 Mar 6;15:1578509. doi: 10.3389/fonc.2025.1578509. eCollection 2025.

ʲѱ:40115010Free PMC article. No abstract available.

 

Wu JM, Siddiqui NY, Wiltshire T, Voora D, Schmader K.

Urogynecology (Phila). 2025 Feb 14. doi: 10.1097/SPV.0000000000001668. Online ahead of print.

ʲѱ:40105750

 

Salunke J, Byfield G, Powell SN, Torres DF, Leon-Lozano G, Jackson J, Orphanides AK, Shaw J, Owens T, Berg JS, Branch E, Caro L, Giric S, O’Daniel JM, Powell BC, Ray K, Robinson C, Schilling S, Shaw N, Song E, Waltz M, Roberts MC, Foreman AKM, Foss K, Milko LV.

Public Health Genomics. 2025;28(1):66-84. doi: 10.1159/000543227. Epub 2024 Dec 19.

ʲѱ:40144343

 

Demmer RT, Wu C, Kim JS, Sun Y, Balte P, Cushman M, Boyle R, Tracy RP, Styer LM, Bell TD, Anderson MR, Allen NB, Schreiner PJ, Bowler R, Schwartz DA, Lee JS, Xanthakis V, Rock JM, Bievenue R, Pirzada A, Doyle M, Regan EA, Make BJ, Kanaya AM, Kandula NR, Wenzel SE, Coresh J, Isasi CR, Raffield LM, Elkind MSV, Howard VJ, Ortega VE, Woodruff P, Cole SA, Henderson JM, Mantis NJ, Oelsner EC.

Open Forum Infect Dis. 2025 Mar 20;12(3):ofaf123. doi: 10.1093/ofid/ofaf123. eCollection 2025 Mar.

ʲѱ:40124199Free PMC article.

 

Bridges Y, Souza V, Cortes KG, Haendel M, Harris NL, Korn DR, Marinakis NM, Matentzoglu N, McLaughlin JA, Mungall CJ, Odell A, Osumi-Sutherland D, Robinson PN, Smedley D, Jacobsen JOB.

BMC Bioinformatics. 2025 Mar 22;26(1):87. doi: 10.1186/s12859-025-06105-4.

ʲѱ:40121479Free PMC article.

 

Georgakis MK, Malik R, Bounkari OE, Hasbani NR, Li J, Huffman JE, Shakt G, Tack RWP, Kimball TN, Asare Y, Morrison AC, Tsao NL, Judy R, Mitchell BD, Xu H, Montasser ME, Do R, Kenny EE, Loos RJF, Terry JG, Carr JJ, Bis JC, Psaty BM, Longstreth WT, Young KA, Lutz SM, Cho MH, Broome J, Khan AT, Wang FF, Heard-Costa N, Seshadri S, Vasan RS, Palmer ND, Freedman BI, Bowden DW, Yanek LR, Kral BG, Becker LC, Peyser PA, Bielak LF, Ammous F, Carson AP, Hall ME, Raffield LM, Rich SS, Post WS, Tracy RP, Taylor KD, Guo X, Mahaney MC, Curran JE, Blangero J, Clarke SL, Haessler JW, Hu Y, Assimes TL, Kooperberg C, Bernhagen J, Anderson CD, Damrauer SM, Zand R, Rotter JI, de Vries PS, Dichgans M.

Genome Med. 2025 Mar 21;17(1):27. doi: 10.1186/s13073-025-01456-2.

ʲѱ:40119478Free PMC article.

 

Yan H, Rini CM, Foreman AKM, Berg JS, Henderson GE, Lee K, O’Daniel JM, Roche M, Waltz M.

Per Med. 2025 Apr;22(2):93-101. doi: 10.1080/17410541.2025.2476392. Epub 2025 Mar 18.

ʲѱ:40100039

 

Balint L, Patel S, Serafin DS, Zhang H, Quinn KE, Aghajanian A, Kistner BM, Caron KM.

Arterioscler Thromb Vasc Biol. 2025 Mar 27. doi: 10.1161/ATVBAHA.124.322288. Online ahead of print.

ʲѱ:40143814

 

Geyer J, Opoku KB, Lin J, Ramkissoon L, Mullighan C, Bhakta N, Alexander TB, Wang JR.

Leukemia. 2025 Mar 24. doi: 10.1038/s41375-025-02565-y. Online ahead of print.

ʲѱ:40128561

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]]> Searching for the genetic origins of a debilitating skin disease /genetics/searching-for-the-genetic-origins-of-a-debilitating-skin-disease/ Fri, 11 Apr 2025 13:54:35 +0000 /genetics/?p=14964 Chris Sayed, a dermatologist at the , has spent much of his career focused on what he calls "the worst and most common disease you've never heard of."

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]]> Searching for the genetic origins of a debilitating skin disease
26 March 2025 | Ethan Freedman

dermatologist Chris Sayed used an NC TraCS pilot grant to kickstart his research career.

Christopher Sayed, MDChris Sayed, a dermatologist at the , has spent much of his career focused on what he calls “the worst and most common disease you’ve never heard of.”

Hidradenitis suppurativa or HS is a skin condition that manifests as painful lumps, abscesses, and scarring that can be unbearably uncomfortable. Symptoms generally occur out of the public eye, with lumps growing in places where the skin rubs together like the armpits or inner thighs, so many people walk around without advertising their disease. And for a while, many doctors and scientists assumed that HS only affected a small proportion of the population and dedicated little research toward understanding the disease’s causes or possible treatments.

In recent years, that outlook has changed. Sayed says that many experts now believe millions of Americans likely have HS, potentially affecting up to 1% of the population. Yet the lack of existing research on the disease means scientists still don’t fully understand what causes it in the first place, and dermatologists have few good options to help patients, who suffer in private.

Sayed has long been the go-to dermatologist for HS at , and a few years ago, he started feeling a need to use his growing expertise to uncover some of the secrets surrounding the disease. “All the patients would leave, and it was like ‘Man, I could have done something’,” he says. “It was a missed opportunity every time they walked out the door.”

Dermatologists will tell you all the time that HS is the worst thing we treat. The patients are often miserable, and the dermatologists don’t know how to help.

Sayed

But as a full-time clinician, he didn’t have the time, funding, or resources to undertake a study on the fundamental science of a mysterious illness. So, he turned to the North Carolina Translational and Clinical Sciences (NC TraCS) Institute.

In 2018, Sayed received a  from NC TraCS that allowed him to pursue research on the possible genetic origins of HS. That eventually set the stage for a larger grant from the National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS), a division of the National Institutes of Health (NIH). This past fall, Sayed and his colleagues  another grant from NIAMS, this time totaling $2.3 million, to expand their work—giving them a shot at finally helping those quietly suffering with the condition.

“Dermatologists will tell you all the time that HS is the worst thing we treat,” Sayed says. “The patients are often miserable, and the dermatologists don’t know how to help.”

While dermatologists don’t know exactly what causes the painful lumps to show up in the first place, they know that something inflammatory happens around a hair follicle, starting as a small lump and progressing into a large abscess. As a result, clinicians often prescribe immunomodulating medications to try and calm that inflammation, or antibiotics, which can sometimes help alleviate symptoms.

In 2015, the anti-inflammatory drug adalimumab (Humira) became the first medication approved for moderate to severe HS in the US. It ended up selling well, Sayed says, prompting other drug companies to start trialing other possible therapies. To really tackle the root cause of the disease, however, researchers would first need to understand what causes HS.

Karen MohlkeThrough his practice, Sayed stumbled onto a potential clue: many of his patients said that members of their family also had HS. This observation led him to wonder if there might be genetics at play. If researchers could pinpoint specific genes associated with the disease, they could potentially find out where the symptoms came from, and maybe even discover a path toward developing a cure.

To start looking into this, Sayed first recruited some of his colleagues to help.Karen MohlkeԻ, two geneticists, both have extensive experience with genome-wide association studies—when researchers compare the DNA of many people to find variations associated with certain traits or diseases. “I walked in completely unknown to them and said: Here’s a condition you’ve never heard of before, I see a ton of patients, they suffer terribly,” Sayed recalls. “If I can collect some samples, would you be interested in helping with the experiments and analysis?” He also had critical support from his research associate, Sharon Edmiston, a PhD student in genetics and molecular biology, who coordinates the lab effort.

Yun LiThen he turned to NC TraCS, which awarded him a $50,000 pilot grant. That money went toward things like supplies for DNA sample collection—but most of all, the progress he made with the TraCS pilot award allowed him to show external funders that he was prepared to take on this ambitious investigation.

“Being able to prove that we were organized and able to do that work required having those early funds,” Sayed says.

Soon enough, Sayed, Mohlke, and Li got their first grant from NIAMS to start searching for the genetic origins of HS. Their genome-wide association study, which included more than 700 HS patients at ,  two genes, SOX9 and KLF5, that had variations associated with the disease. Both genes are important to epidermal health, Sayed says. SOX9 plays a key role in the function of hair follicles and KLF5 tends to be expressed at high levels in people with Crohn’s disease, another inflammatory condition.

Sharon EdmistonThis discovery was a breakthrough in HS research. But even though the team now suspected that something was happening with SOX9 and KLF5 in HS patients, they still didn’t know what, exactly, was happening. Their latest grant from NIAMS, awarded last fall, is going to try and answer that question. In addition to expanding their genetic analysis of HS patients, the team is going to study how these variations affect biological processes—for example, by causing the cells to produce too much, or too little, of a certain protein. That information could shed a lot of light on what causes the follicular inflammation.

In recent years, the research community has finally started to take HS seriously. Sayed was on the leading edge of this push, and the team’s initial grant in 2019 was the first time NIH had awarded any money toward HS research. Since then, millions more in funding have been devoted to the effort.

Through this process, Sayed has also expanded the scope of his own career. Now, he works as both a patient-focused clinician and a researcher investigating the origins of his patients’ disease. And he knows just how much this work means to people.

“HS is this miserable thing that has been terribly underserved by society and the healthcare system over time,” Sayed says. “And there’s a huge opportunity to raise awareness, understand it better, and find better treatments.”

This article originally appeared in the TRACS news .

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]]> Dr. Yun Li and Team Publish New Model (endoPRS) in AJHG /genetics/dr-yun-li-and-team-publish-new-model-endoprs-in-ajhg/ Tue, 08 Apr 2025 18:27:43 +0000 /genetics/?p=14957 Yun Li, PhD (Professor, Genetics) together with first author Elena Kharitonova (PhD Student, Biostatistics) have published a new paper in the American Journal of Human Genetics (AJHG) titled “EndoPRS: Incorporating endophenotype information to improve polygenic risk scores for clinical endpoints – a study in asthma”.

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]]> Yun Li and Elena Kharitonova

Yun Li, PhD (Professor, Genetics) and Elena Kharitonova (PhD Student, Biostatistics)

Yun Li, PhD (Professor, Genetics) together with first author Elena Kharitonova (PhD Student, Biostatistics) have published a in the American Journal of Human Genetics (AJHG) titled “EndoPRS: Incorporating endophenotype information to improve polygenic risk scores for clinical endpoints – a study in asthma”.

Yun Li Collaborators

Quan Sun, Frank Ockerman, Brian Chen, Micah Hysong, Bjoernar Tuftin, Laura Raffield, & Samir Kelada

This paper introduces endoPRS, “a weighted lasso model that incorporates information from relevant endophenotypes to improve disease risk prediction without making assumptions about the genetic architecture underlying the endophenotype-disease relationship.”  The team applied the endoPRS model to predict the risk of childhood-onset asthma in UK Biobank and All of Us data sets by leveraging a paired genome-wide association study of eosinophil count, a relevant endophenotype, and found that endoPRS significantly improves prediction and transferability compared to many existing PRS methods.

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]]> Dr. Yun Li and Collaborators Publish Review in AJHG /genetics/dr-yun-li-and-collaborators-publish-review-in-ajhg/ Fri, 04 Apr 2025 18:45:28 +0000 /genetics/?p=14945 Yun Li, PhD (Professor, Genetics and Biostatistics) is a co-corresponding author together with Quan Sun (Biostatistics doctoral candidate) on a new review paper published in the American Journal of Human Genetics, titled “Opportunities and challenges of local ancestry in genetic association analysis”.

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]]> Yun Li and Quan Sun

Yun Li, PhD (Professor, Genetics and Biostatistics) and Quan Sun (Biostatistics doctoral candidate)

Yun Li, PhD (Professor, Genetics and Biostatistics) is a co-corresponding author together with Quan Sun (Biostatistics doctoral candidate) on a published in the American Journal of Human Genetics, titled “Opportunities and challenges of local ancestry in genetic association analysis”.

Mohlke Raffield Horimoto

Drs. Andrea Horimoto, Dr. Laura Raffield, and Dr. Karen Mohlke

Additional authors from the Department of Genetics include Drs. Andrea Horimoto, Dr. Laura Raffield, and Dr. Karen Mohlke. The review summarizes methods for local ancestry inference and illustrates how local ancestry can be utilized in various analyses, including admixture mapping, association testing, and polygenic risk score construction. In addition, current challenges in research involving local ancestry, both in terms of the inference itself and its role in genetic association studies are discussed. Finally, future study directions and methodology development opportunities to help more effectively incorporate local ancestry in genetic analyses are proposed.

 

 

 

 

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]]> Dr. Virginia Miller Named AAAS Fellow /genetics/dr-virginia-miller-named-aaas-fellow/ Tue, 01 Apr 2025 15:14:35 +0000 /genetics/?p=14937 Virginia Miller, PhD (Professor, Genetics and Microbiology & Immunology, Retired) has been named a 2024 Fellow of the American Association for the Advancement of Science, one of the most distinguished honors in the scientific community.

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]]> Miller Virginia

Virginia Miller, PhD (Professor, Genetics and Microbiology & Immunology, Retired)

Virginia Miller, PhD (Professor, Genetics and Microbiology & Immunology, Retired) has been named a 2024 Fellow of the American Association for the Advancement of Science, one of the most distinguished honors in the scientific community.

During her 16 years at , Dr. Miller pursued studies on the molecular genetic analysis and gene regulation of bacterial pathogen virulence. Her laboratory made important contributions to our understanding of gene regulation in Yersinia pestis and Klebsiella pneumoniae.  Congratulations to Dr. Miller!

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]]> Laura Raffield Awarded New Subcontract from UTSW Medical Center /genetics/laura-raffield-awarded-new-subcontract-from-utsw-medical-center/ Thu, 20 Mar 2025 15:49:54 +0000 /genetics/?p=14884 Dr. Laura Raffield (Assistant Professor, Genetics) has received a new subcontract from University of Texas Southwestern Medical Center.

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]]> Laura Raffield

Laura Raffield, PhD (Assistant Professor, Genetics)

Dr. Laura Raffield (Assistant Professor, Genetics) has received a new subcontract from University of Texas Southwestern Medical Center (from a parent R01) to perform proteomic profiling to identify mechanisms of susceptibility and resilience to cardiac dysfunction, using proteomic and genomic data from the Jackson Heart Study.

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]]> Hyejung Won Awarded New Seed Grant from the ALS Association /genetics/hyejung-won-awarded-new-seed-grant-from-the-als-association/ Thu, 20 Mar 2025 15:47:20 +0000 /genetics/?p=14882 Dr. Hyejung Won (Associate Professor, Genetics) was awarded a seed grant from the Amyotrophic Lateral Sclerosis Association for her project titled “Deciphering higher-order chromatin mechanisms for C9orf72-mediated ALS”.

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Hyejung Won, PhD, Associate Professor of Genetics

Dr. Hyejung Won (Associate Professor, Genetics) was awarded a seed grant from the Amyotrophic Lateral Sclerosis Association for her project titled “Deciphering higher-order chromatin mechanisms for C9orf72-mediated ALS”.

The project is based on the findings that one of the leading causes of amyotrophic lateral sclerosis (ALS) is GGGGCC (G4C2) short tandem repeats (STRs) in the intron of C9orf72. While the genetic cause is clear, progress towards developing disease-altering therapies in C9orf72-mediated ALS (C9-ALS) has been slow due to the incomplete mechanistic understanding of the disease. Three broad mechanisms have been proposed for C9-ALS: (1) downregulation of C9orf72, (2) transcribed STRs form RNA foci that sequester RNA binding proteins (RBPs), and (3) translated dipeptide repeats (DPRs) form toxic protein aggregates. Recently, another mechanism was proposed that STRs may cause disease by altering three-dimensional (3D) chromatin structure. To investigate the impact of C9orf72 G4C2 STRs (C9-STRs) on 3D chromatin structure, Dr. Won acquired genome-wide chromosome conformation maps of neurons and glia sorted from the cortex of C9-ALS. Notably, Dr. Won’s lab found ectopic loop formation in C9-ALS neurons, but not in glia. Based on this finding, they are proposing a new mechanism by which C9-STRs contribute to the ALS pathophysiology: transcribed STRs interact with DNA and induce ectopic loop formation, which can lead to widespread transcriptional dysregulation observed in C9-ALS brains. Because ectopic loops in C9-ALS can arise from the compensatory mechanism in postmortem brain samples, they propose to recapitulate these findings in isogenic induced pluripotent stem cell (iPSC) lines with and without C9-STRs. After differentiating isogenic iPSCs into neurons, they will generate genome-wide chromosome conformation maps to identify C9-STR-mediated changes in chromatin looping and leverage Capture Hybridization Analysis of RNA Targets (CHART) to identify DNA targets that interact with C9-STR RNA. The successful completion of this proposal will begin to elucidate the role of STRs in regulating 3D chromatin structure and pathophysiology of neurodegenerative diseases.

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]]> Chuck Perou Awarded New DoD Grant /genetics/chuck-perou-awarded-new-dod-grant/ Thu, 20 Mar 2025 15:42:13 +0000 /genetics/?p=14880 Dr. Chuck Perou (Distinguished Professor, Genetics and Pathology and Laboratory Medicine) received a new grant from the Department of Defense for his project titled “The Breast Cancer Cellular Atlas”.

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Dr. Chuck Perou (Distinguished Professor, Genetics and Pathology and Laboratory Medicine)

Dr. Chuck Perou (Distinguished Professor, Genetics and Pathology and Laboratory Medicine) received a new grant from the Department of Defense for his project titled “The Breast Cancer Cellular Atlas”.

This project is focused on generating a series of novel biobanks of early and metastatic breast cancers. These include hundreds of treatment-naive surgical samples, which are increasingly uncommon as more patients receiving neoadjuvant therapy. To address the temporal dimension of breast cancer evolution,  the Perou lab has assembled 2 longitudinal cohorts sampled throughout neoadjuvant therapy with standard of care chemo- or endocrine therapies. They have established a biobank from 500 patients with metastatic breast cancer who have donated paired tissue specimens of localized and metastatic disease. They have also assembled a biobank of multiple metastatic lesions each from 50 donors who died of breast cancer. Finally, the lab established 74 patient-derived xenograft models from these specimens, which provides a renewable resource of patient-matched models. These molecular data will be complemented by the collection of detailed epidemiological, treatment, survival and histopathology data.

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]]> Alexander Rubinsteyn Receives New Grant from Jaime Leandro Foundation /genetics/alexander-rubinsteyn-receives-new-grant-from-jaime-leandro-foundation/ Thu, 20 Mar 2025 15:39:27 +0000 /genetics/?p=14878 Dr. Alex Rubinsteyn (Associate Professor, Genetics) was awarded a new grant from the Jaime Leandro Foundation for his project titled “Optimization of personalized cancer immunotherapeutic approaches”.

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]]> Alex Rubinsteyn, PhD

Dr. Alex Rubinsteyn (Associate Professor, Genetics)

Dr. Alex Rubinsteyn (Associate Professor, Genetics) was awarded a new grant from the Jaime Leandro Foundation for his project titled “Optimization of personalized cancer immunotherapeutic approaches”.

The project is focused on three aims: 1) Computational biology (LENS, TCRSift, EXACTO, and MHCFlurry development and packaging; 2) Experimental biology (optimization of flow cytometry panels for advanced immune monitoring, assay for assessing antigen specific T cell function, and method optimization to discover antigen specific CD8+ T cells; 3) Discovery science (focused on optimal vaccine formulation and timing of neoantigen vaccination and TCR-T therapy.

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