MGH Pathology Research

Boyraz B, Sgroi DC, Iafrate AJ, Lerwill MF

Atypical cystic hypersecretory lesions of the breast commonly harbour TP53 alterations.

Histopathology. 2023;83(6):989-993 - PMID: 37771083 - DOI: 10.1111/his.15056

Staedtke V, Topilko P, Le LQ, Grimes K, Largaespada DA, Cagan RL, Steensma MR, Stemmer-Rachamimov A, Blakeley JO, Rhodes SD, Ly I, Romo CG, Lee SY, Serra E

Existing and Developing Preclinical Models for Neurofibromatosis Type 1-Related Cutaneous Neurofibromas.

J Invest Dermatol. 2023;143(8):1378-1387 - PMID: 37330719 - PMCID: PMC11246562 - DOI: 10.1016/j.jid.2023.01.042

Song X, Zhang H, Zhang Y, Goh B, Bao B, Mello SS, Sun X, Zheng W, Gazzaniga FS, Wu M, Qu F, Yin Q, Gilmore MS, Oh SF, Kasper DL

Gut microbial fatty acid isomerization modulates intraepithelial T cells.

Nature. 2023;619(7971):837-843 - PMID: 37380774 - DOI: 10.1038/s41586-023-06265-4

Chen Z, Javed N, Moore M, Wu J, Sun G, Vinyard M, Collins A, Pinello L, Najm FJ, Bernstein BE

Integrative dissection of gene regulatory elements at base resolution.

Cell Genom. 2023;3(6):100318 - PMID: 37388913 - PMCID: PMC10300548 - DOI: 10.1016/j.xgen.2023.100318

Dagogo-Jack I, Manoogian A, Jessop N, Georgantas NZ, Fintelmann FJ, Farahani A, Digumarthy SR, Price MC, Folch EE, Keyes CM, Do A, Peterson JL, Mino-Kenudson M, Pitman M, Rivera M, Nardi V, Dias-Santagata D, Le LP, Iafrate AJ, Heist RS, Ritterhouse LR, Lennerz JK

Integrated Radiology, Pathology, and Pharmacy Program to Accelerate Access to Osimertinib.

JCO Oncol Pract. 2023;19(9):786-792 - PMID: 37437226 - PMCID: PMC10538938 - DOI: 10.1200/OP.23.00031

Wang L, Trasanidis N, Wu T, Dong G, Hu M, Bauer DE, Pinello L

Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics.

Nat Methods. 2023;20(9):1368-1378 - PMID: 37537351 - DOI: 10.1038/s41592-023-01971-3

Garcia-Sayan E, Lee M, Stone JR, Stone DM, Smulevitz B, McPherson DD, Fisher-Hoch SP, McCormick JB, Laing ST

Endothelial Dysfunction and Cardiometabolic Risk Factors in Mexican American Adults: The Cameron County Hispanic Cohort.

Am J Cardiol. 2023;205:75-83 - PMID: 37595411 - DOI: 10.1016/j.amjcard.2023.07.165

Stone JR

The Winding Path Toward Understanding Clinically Isolated Aortitis.

J Am Coll Cardiol. 2023;82(11):1065-1067 - PMID: 37673507 - DOI: 10.1016/j.jacc.2023.07.005

Nair V, Fishbein GA, Padera R, Seidman MA, Castonguay M, Leduc C, Tan CD, Rodriguez ER, Maleszewski JJ, Miller D, Romero M, Lomasney J, d'Amati G, De Gaspari M, Rizzo S, Angelini A, Basso C, Litovsky S, Buja LM, Stone JR, Veinot JP

Consensus Statement on the Processing, Interpretation and Reporting of Temporal Artery Biopsy for Arteritis.

Cardiovasc Pathol. 2023;67:107574 - PMID: 37683739 - DOI: 10.1016/j.carpath.2023.107574

Park JS, Gazzaniga FS, Kasper DL, Sharpe AH

Microbiota-dependent regulation of costimulatory and coinhibitory pathways via innate immune sensors and implications for immunotherapy.

Exp Mol Med. 2023;55(9):1913-1921 - PMID: 37696895 - PMCID: PMC10545783 - DOI: 10.1038/s12276-023-01075-0

Da Silveira Cavalcante L, Lopera Higuita M, González-Rosa JM, Marques B, To S, Pendexter CA, Cronin SEJ, Gopinathan K, de Vries RJ, Ellett F, Uygun K, Langenau DM, Toner M, Tessier SN

Zebrafish as a high throughput model for organ preservation and transplantation research.

FASEB J. 2023;37(10):e23187 - PMID: 37718489 - PMCID: PMC10754348 - DOI: 10.1096/fj.202300076R

Ryu J, Barkal S, Yu T, Jankowiak M, Zhou Y, Francoeur M, Phan QV, Li Z, Tognon M, Brown L, Love MI, Lettre G, Ascher DB, Cassa CA, Sherwood RI, Pinello L

Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification.

medRxiv. 2023;:ePub - PMID: 37732177 - PMCID: PMC10508837 - DOI: 10.1101/2023.09.08.23295253

Krauson AJ, Casimero FVC, Siddiquee Z, Stone JR

Duration of SARS-CoV-2 mRNA vaccine persistence and factors associated with cardiac involvement in recently vaccinated patients.

NPJ Vaccines. 2023;8(1):141 - PMID: 37758751 - PMCID: PMC10533894 - DOI: 10.1038/s41541-023-00742-7

Zeng J, Nguyen MA, Liu P, Ferreira da Silva L, Lin LY, Justus DG, Petri K, Clement K, Porter SN, Verma A, Neri NR, Rosanwo T, Ciuculescu MF, Abriss D, Mintzer E, Maitland SA, Demirci S, Tisdale JF, Williams DA, Zhu LJ, Pruett-Miller SM, Pinello L, Joung JK, Pattanayak V, Manis JP, Armant M, Pellin D, Brendel C, Wolfe SA, Bauer DE

Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells.

bioRxiv. 2023;:ePub - PMID: 37292647 - PMCID: PMC10245949 - DOI: 10.1101/2023.05.27.542323

Blum SM, Zlotoff DA, Smith NP, Kernin IJ, Ramesh S, Zubiri L, Caplin J, Tirard A, Sen P, Song Y, Barth J, Slowikowski K, Nasrallah M, Tantivit J, Manakongtreecheep K, Arnold BY, McGuire J, Pinto CJ, McLoughlin D, Jackson M, Chan P, Lawless A, Sharova T, Nieman LT, Gainor JF, Juric D, Mino-Kenudsen M, Sullivan RJ, Boland GM, Stone JR, Thomas MF, Neilan TG, Reynolds KL, Villani AC

Immune Responses in Checkpoint Myocarditis Across Heart, Blood, and Tumor.

bioRxiv. 2023;:ePub - PMID: 37790460 - PMCID: PMC10542127 - DOI: 10.1101/2023.09.15.557794

Huynh MJ, Gusev A, Palmas F, Vandergrift L, Berker Y, Wu CL, Wu S, Cheng LL, Feldman AS

Characterization of the metabolomic profile of renal cell carcinoma by high resolution magic angle spinning proton magnetic resonance spectroscopy.

Urol Oncol. 2023;41(11):459.e9-459.e16 - PMID: 37863744 - DOI: 10.1016/j.urolonc.2023.09.005

Stone JR, Avants BB, Tustison N, Gill J, Wilde EA, Neumann KD, Gladney LA, Kilgore MO, Bowling F, Wilson CM, Detro JF, Belanger H, Deary K, Linsenbardt H, Ahlers S

Neurological effects of repeated blast exposure in Special Operations personnel.

J Neurotrauma. 2023;41(7-8):942-956 - PMID: 37950709 - PMCID: PMC11001960 - DOI: 10.1089/neu.2023.0309

Miller TE, Farran CAE, Couturier CP, Chen Z, D'Antonio JP, Verga J, Villanueva MA, Castro LNG, Tong YE, Saadi TA, Chiocca AN, Fischer DS, Heiland DH, Guerriero JL, Petrecca K, Suva ML, Shalek AK, Bernstein BE

Programs, Origins, and Niches of Immunomodulatory Myeloid Cells in Gliomas.

bioRxiv. 2023;:ePub - PMID: 37961527 - PMCID: PMC10634776 - DOI: 10.1101/2023.10.24.563466

Takahashi M, Chong HB, Zhang S, Lazarov MJ, Harry S, Maynard M, White R, Murrey HE, Hilbert B, Neil JR, Gohar M, Ge M, Zhang J, Durr BR, Kryukov G, Tsou CC, Brooijmans N, Alghali ASO, Rubio K, Vilanueva A, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Assaad J, Makram F, Rachman I, Khandelwal N, Tien PC, Popoola G, Chen N, Vordermark K, Richter M, Patel H, Yang TY, Griesshaber H, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Fisher DE, Maheswaran S, Haber DA, Boland G, Sade-Feldman M, Jenkins R, Hata A, Bardeesy N, Suva ML, Martin B, Liau B, Ott C, Rivera MN, Lawrence MS, Bar-Peled L

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability.

bioRxiv. 2023;:ePub - PMID: 37961514 - PMCID: PMC10634688 - DOI: 10.1101/2023.10.20.563287

Tustison NJ, Yassa MA, Rizvi B, Cook PA, Holbrook AJ, Sathishkumar MT, Tustison MG, Gee JC, Stone JR, Avants BB

ANTsX neuroimaging-derived structural phenotypes of UK Biobank.

Res Sq. 2023;:ePub - PMID: 37961236 - PMCID: PMC10635385 - DOI: 10.21203/rs.3.rs-3459157/v1

Leavitt LA, Nanda P, Stemmer-Rachamimov A, Dunn GP, Jones PS

Spontaneous rupture of an arachnoid cyst in an adult: illustrative case.

J Neurosurg Case Lessons. 2023;5(7):ePub - PMID: 38015025 - PMCID: PMC10550604 - DOI: 10.3171/CASE22420

Broeckling CD, Beger RD, Cheng LL, Cumeras R, Cuthbertson DJ, Dasari S, Davis WC, Dunn WB, Evans AM, Fernández-Ochoa A, Gika H, Goodacre R, Goodman KD, Gouveia GJ, Hsu PC, Kirwan JA, Kodra D, Kuligowski J, Lan RS, Monge ME, Moussa LW, Nair SG, Reisdorph N, Sherrod SD, Ulmer Holland C, Vuckovic D, Yu LR, Zhang B, Theodoridis G, Mosley JD

Current Practices in LC-MS Untargeted Metabolomics: A Scoping Review on the Use of Pooled Quality Control Samples.

Anal Chem. 2023;95(51):18645-18654 - PMID: 38055671 - PMCID: PMC10753522 - DOI: 10.1021/acs.analchem.3c02924

Cardoso BA, Duque M, Gírio A, Fragoso R, Oliveira ML, Allen JR, Martins LR, Correia NC, Silveira AB, Veloso A, Kimura S, Demoen L, Matthijssens F, Jeha S, Cheng C, Pui CH, Grosso AR, Neto JL, De Almeida SF, Van Vlieberghe P, Mullighan CG, Yunes JA, Langenau DM, Pflumio F, Barata JT

CASZ1 upregulates PI3K-AKT-mTOR signaling and promotes T-cell acute lymphoblastic leukemia.

Haematologica. 2023;109(6):1713-25 - PMID: 38058200 - PMCID: PMC11141679 - DOI: 10.3324/haematol.2023.282854

Li Z, M Patel Z, Song D, Yan G, Li JJ, Pinello L

Benchmarking computational methods to identify spatially variable genes and peaks.

bioRxiv. 2023;:ePub - PMID: 38076922 - PMCID: PMC10705556 - DOI: 10.1101/2023.12.02.569717

Alborikan S, Althunayyan A, Pandya B, Von Klemperer K, Walker F, Cullen S, Bhan A, Badiani S, Encarnacion D, Monteiro R, Petersen SE, Bhattacharyya S, Lloyd G

Blood biomarkers to detect functional impairment in adult patients with repaired tetralogy of Fallot.

Int J Cardiol Congenit Heart Dis. 2023;14:100483 - PMID: 39712984 - PMCID: PMC11657782 - DOI: 10.1016/j.ijcchd.2023.100483

Xing YH, Dong R, Lee L, Rengarajan S, Riggi N, Boulay G, Rivera MN

DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins.

Nat Biotechnol. 2023;42(1):52-64 - PMID: 37037903 - PMCID: PMC10791585 - DOI: 10.1038/s41587-023-01737-4

Lu DY, Ellegast JM, Ross KN, Malone CF, Lin S, Mabe NW, Dharia NV, Meyer A, Conway A, Su AH, Selich-Anderson J, Taslim C, Byrum AK, Seong BKA, Adane B, Gray NS, Rivera MN, Lessnick SL, Stegmaier K

The ETS transcription factor ETV6 constrains the transcriptional activity of EWS-FLI to promote Ewing sarcoma.

Nat Cell Biol. 2023;25(2):285-297 - PMID: 36658220 - PMCID: PMC9928584 - DOI: 10.1038/s41556-022-01059-8

Wu M, Zheng W, Song X, Bao B, Wang Y, Ramanan D, Yang D, Liu R, Macbeth JC, Do EA, Andrade WA, Yang T, Cho HS, Gazzaniga FS, Ilves M, Coronado D, Thompson C, Hang S, Chiu IM, Moffitt JR, Hsiao A, Mekalanos JJ, Benoist C, Kasper DL

Microbiome induced complement synthesized in the gut protects against enteric infections.

bioRxiv. 2023;:ePub - PMID: 36778396 - PMCID: PMC9915568 - DOI: 10.1101/2023.02.02.523770

Yin Z, Wu L, Zhang Y, Sun Y, Chen JW, Subudhi S, Ho W, Lee GY, Wang A, Gao X, Ren J, Zhu C, Zhang N, Ferraro GB, Muzikansky A, Zhang L, Stemmer-Rachamimov A, Mao J, Plotkin SR, Xu L

Co-Targeting IL-6 and EGFR signaling for the treatment of schwannomatosis and associated pain.

bioRxiv. 2023;:ePub - PMID: 36798353 - PMCID: PMC9934519 - DOI: 10.1101/2023.02.06.527377

Katz G, Hedgire SH, Stone JR, Perez-Espina S, Fernandes A, Perugino CA, Wallace ZS, Stone JH

IgG4-related disease as a variable-vessel vasculitis: A case series of 13 patients with medium-sized coronary artery involvement.

Semin Arthritis Rheum. 2023;60:152184 - PMID: 36848823 - PMCID: PMC10148901 - DOI: 10.1016/j.semarthrit.2023.152184

Kleiner DE, Lisker-Melman M, Wahed AS, Bhan AK, Nalesnik MA, Choi EK, Leonard KK, Ghany MG, Chung RT, Di Bisceglie AM

Immunostaining for Hepatitis B Viral Antigens in Liver: Association with Clinical, Biochemical and Virologic Features of Disease.

J Gastroenterol Hepatol. 2023;38(6):989-998 - PMID: 36890337 - PMCID: PMC10744323 - DOI: 10.1111/jgh.16167

Pavao A, Girinathan B, Peltier J, Altamirano Silva P, Dupuy B, Muti IH, Malloy C, Cheng LL, Bry L

Elucidating dynamic anaerobe metabolism with HRMAS ¹³C NMR and genome-scale modeling.

Nat Chem Biol. 2023;19(5):556-564 - PMID: 36894723 - PMCID: PMC10154198 - DOI: 10.1038/s41589-023-01275-9

Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT

Genetic Predisposition to Neuroblastoma Results from a Regulatory Polymorphism that Promotes the Adrenergic Cell State.

bioRxiv. 2023;:ePub - PMID: 36909587 - PMCID: PMC10002714 - DOI: 10.1101/2023.02.28.530457

Vandergrift LA, Wang N, Zhu M, Li B, Chen S, Habbel P, Nowak J, Mason R, Grant A, Wang Y, Malloy C, Cheng LL

¹³ C NMR Quantification of Polyamine Syntheses in Rat Prostate.

NMR Biomed. 2023;36(8):e4931 - PMID: 36939957 - DOI: 10.1002/nbm.4931

Sreekanth V, Jan M, Zhao KT, Lim D, Davis JR, McConkey M, Kovalcik V, Barkal S, Law BK, Fife J, Tian R, Vinyard ME, Becerra B, Kampmann ME, Sherwood RI, Pinello L, Liu DR, Ebert BL, Choudhary A

A molecular glue approach to control the half-life of CRISPR-based technologies.

bioRxiv. 2023;:ePub - PMID: 36945568 - PMCID: PMC10028966 - DOI: 10.1101/2023.03.12.531757

Sanalkumar R, Dong R, Lee L, Xing YH, Iyer S, Letovanec I, La Rosa S, Finzi G, Musolino E, Papait R, Chebib I, Nielsen GP, Renella R, Cote GM, Choy E, Aryee M, Stegmaier K, Stamenkovic I, Rivera MN, Riggi N

Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity.

Sci Adv. 2023;9(13):eabo3789 - PMID: 37000878 - PMCID: PMC10718307 - DOI: 10.1126/sciadv.abo3789

Pirruccello JP, Rämö JT, Choi SH, Chaffin MD, Kany S, Nekoui M, Chou EL, Jurgens SJ, Friedman SF, Juric D, Stone JR, Batra P, Ng K, Philippakis AA, Lindsay ME, Ellinor PT

The Genetic Determinants of Aortic Distention.

J Am Coll Cardiol. 2023;81(14):1320-1335 - PMID: 37019578 - PMCID: PMC11246604 - DOI: 10.1016/j.jacc.2023.01.044

Bathen TF, Cheng LL

Special issue on ex vivo NMR spectroscopy.

NMR Biomed. 2023;36(4):e4893 - PMID: 36624039 - DOI: 10.1002/nbm.4893

Neumann KD, Seshadri V, Thompson XD, Broshek DK, Druzgal J, Massey JC, Newman B, Reyes J, Simpson SR, McCauley KS, Patrie J, Stone JR, Kundu BK, Resch JE

Microglial activation persists beyond clinical recovery following sport concussion in collegiate athletes.

Front Neurol. 2023;14:1127708 - PMID: 37034078 - PMCID: PMC10080132 - DOI: 10.3389/fneur.2023.1127708

Bommakanti K, Seist R, Kukutla P, Cetinbas M, Batts S, Sadreyev RI, Stemmer-Rachamimov A, Brenner GJ, Stankovic KM

Comparative Transcriptomic Analysis of Archival Human Vestibular Schwannoma Tissue from Patients with and without Tinnitus.

J Clin Med. 2023;12(7):ePub - PMID: 37048724 - PMCID: PMC10095534 - DOI: 10.3390/jcm12072642

Jung DJ, Gebremedhin L, Goh B, Yoo JS, Gazzaniga F, Kasper DL, Oh SF

Kinetic and mechanistic diversity of intestinal immune homeostasis characterized by rapid removal of gut bacteria.

Gut Microbes. 2023;15(1):2201154 - PMID: 37069732 - PMCID: PMC10116915 - DOI: 10.1080/19490976.2023.2201154

Tognon M, Giugno R, Pinello L

A survey on algorithms to characterize transcription factor binding sites.

Brief Bioinform. 2023;24(3):ePub - PMID: 37099664 - PMCID: PMC10422928 - DOI: 10.1093/bib/bbad156

Park JS, Gazzaniga FS, Wu M, Luthens AK, Gillis J, Zheng W, LaFleur MW, Johnson SB, Morad G, Park EM, Zhou Y, Watowich SS, Wargo JA, Freeman GJ, Kasper DL, Sharpe AH

Targeting PD-L2-RGMb overcomes microbiome-related immunotherapy resistance.

Nature. 2023;617(7960):377-385 - PMID: 37138075 - PMCID: PMC10219577 - DOI: 10.1038/s41586-023-06026-3

Brett JO, Dubash TD, Johnson GN, Niemierko A, Mariotti V, Kim LSL, Xi J, Pandey A, Dunne S, Nasrazadani A, Lloyd MR, Kambadakone A, Spring LM, Micalizzi DS, Onozato ML, Che D, Nayar U, Brufsky A, Kalinsky K, Ma CX, O'Shaughnessy J, Han HS, Iafrate AJ, Ryan LY, Juric D, Moy B, Ellisen LW, Maheswaran S, Wagle N, Haber DA, Bardia A, Wander SA

A Gene Panel Associated With Abemaciclib Utility in ESR1-Mutated Breast Cancer After Prior Cyclin-Dependent Kinase 4/6-Inhibitor Progression.

JCO Precis Oncol. 2023;7:e2200532 - PMID: 37141550 - PMCID: PMC10530719 - DOI: 10.1200/PO.22.00532

Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT

Genetic predisposition to neuroblastoma results from a regulatory polymorphism that promotes the adrenergic cell state.

J Clin Invest. 2023;133(10):ePub - PMID: 37183825 - PMCID: PMC10178836 - DOI: 10.1172/JCI166919

Jordan JT, Orr CC, Thalheimer RD, Cambillo JV, Beauchamp RL, Shaikh G, Muzikansky A, Stemmer-Rachamimov A, Giovannini M, Kalamarides M, Barker FG, Ramesh V, Plotkin SR

Prospective phase II trial of the dual mTORC1/2 inhibitor vistusertib for progressive or symptomatic meningiomas in persons with neurofibromatosis 2.

Neurooncol Adv. 2023;5(1):vdad041 - PMID: 37215956 - PMCID: PMC10195194 - DOI: 10.1093/noajnl/vdad041

Rubio K, Romero-Olmedo AJ, Sarvari P, Swaminathan G, Ranvir VP, Rogel-Ayala DG, Cordero J, Gunther S, Mehta A, Bassaly B, Braubach P, Wygrecka M, Gattenlahner S, Tresch A, Braun T, Dobreva G, Rivera MN, Singh I, Graumann J, Barreto G

Non-canonical integrin signaling activates EGFR and RAS-MAPK-ERK signaling in small cell lung cancer.

Theranostics. 2023;13(8):2384-2407 - PMID: 37215577 - PMCID: PMC10196829 - DOI: 10.7150/thno.79493

Chen H, Ryu J, Vinyard ME, Lerer A, Pinello L

SIMBA: single-cell embedding along with features.

Nat Methods. 2023;21(6):1003-1013 - PMID: 37248389 - PMCID: PMC11166568 - DOI: 10.1038/s41592-023-01899-8

Park JS, Gazzaniga FS, Wu M, Luthens AK, Gillis J, Zheng W, LaFleur MW, Johnson SB, Morad G, Park EM, Zhou Y, Watowich SS, Wargo JA, Freeman GJ, Kasper DL, Sharpe AH

Publisher Correction: Targeting PD-L2-RGMb overcomes microbiome-related immunotherapy resistance.

Nature. 2023;618(7966):E27 - PMID: 37264079 - PMCID: PMC12025598 - DOI: 10.1038/s41586-023-06237-8