Researcher Profile

Researcher Profile

James Broach, PhD

James Broach, PhD

Distinguished Professor and Chair, Department of Biochemistry and Molecular Biology
Professor, Department of Otolaryngology - Head and Neck Surgery
Scientific Program:Next-Generation Therapies
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Research Interests

The Dr. James Broach lab has studied a variety of biological processes using the yeast Saccharomyces as a model system.  These studies have focused primarily on the interaction of cells with their environment, exploring the nature of signaling pathways that cells use to perceive their nutritional state - such as the Ras/protein kinase A pathway and the Target of Rapamycin Complex – and the transcriptional and metabolic responses of those cells to changes in nutritional state.  More recently, the lab has focused on the cell’s stress response, using single cell imaging and genome sequencing-based studies of chromatin structure and transcriptional remodeling.  These studies yielded the remarkable finding that genetically identical cells in the same environment mount quite different responses to an applied stress, allowing the population as a whole to hedge its bets regarding the best survival strategy in the face of an uncertain future.


More recently, the lab has expanded its interest to the application of genomic tools to issues of disease onset and treatment. The work is conducted through the Institute for Personalized Medicine, comprising a biorepository, in which biological samples from all consented patients of the Milton S. Hershey Medical Center are stored; a genomics core, in which state of the art genotyping and NextGen sequencing is applied to the biological samples; and a bioinformatics core, in which patient outcome data obtained from electronic medical records are correlated with genomic profiling and sequencing results. The lab works closely with clinicians at the Milton S. Hershey Medical Center to identify patients whose disorder or response to treatment shows a familial pattern of inheritance, as well as cohorts of patients that have phenotypically distinct disease presentations or responses to treatment.  The lab has successfully pursued studies in a variety of diseases, including various cancers, ALS, multiple sclerosis, inflammatory bowel disease, epilepsy and osteoporosis.

  • Yeasts
  • Saccharomyces cerevisiae
  • Genes
  • Proteins
  • Plasmids
  • Growth
  • Mutation
  • Genome
  • DNA
  • Nutrients
  • Chromatin
  • Genetic Recombination

Recent Publications


Costa, ACT, Hornick, J, Antunes, TFS, Santos, AMC, Fernandes, AAR, Broach, JR & Fernandes, PMB 2021, 'Complete genome sequence and analysis of a Saccharomyces cerevisiae strain used for sugarcane spirit production', Brazilian Journal of Microbiology, vol. 52, no. 3, pp. 1087-1095.
Goldrich, DY, Labarge, B, Chartrand, S, Zhang, L, Sadowski, HB, Zhang, Y, Pham, K, Way, H, Lai, CYJ, Pang, AWC, Clifford, B, Hastie, AR, Oldakowski, M, Goldenberg, D & Broach, JR 2021, 'Identification of somatic structural variants in solid tumors by optical genome mapping', Journal of Personalized Medicine, vol. 11, no. 2, 142, pp. 1-21.
Isaacs, AM, Morton, SU, Movassagh, M, Zhang, Q, Hehnly, C, Zhang, L, Morales, DM, Sinnar, SA, Ericson, JE, Mbabazi-Kabachelor, E, Ssenyonga, P, Onen, J, Mulondo, R, Hornig, M, Warf, BC, Broach, JR, Townsend, RR, Limbrick, DD, Paulson, JN & Schiff, SJ 2021, 'Immune activation during Paenibacillus brain infection in African infants with frequent cytomegalovirus co-infection', iScience, vol. 24, no. 4, 102351.
Raca, G, Abdel-Azim, H, Yue, F, Broach, J, Payne, JL, Reeves, ME, Gowda, C, Schramm, J, Desai, D, Dovat, E, Hu, T, Berg, AS, Bhojwani, D, Payne, KJ & Dovat, S 2021, 'Increased Incidence of IKZF1 deletions and IGH-CRLF2 translocations in B-ALL of Hispanic/Latino children—a novel health disparity', Leukemia, vol. 35, no. 8, pp. 2399-2402.
The American Genome Center (TAGC), The FALS Sequencing Consortium, The Genomics England Research Consortium, The International ALS/FTD Genomics Consortium (iAFGC), The International FTD Genetics Consortium (IFGC), The International LBD Genomics Consortium (iLBDGC), The NYGC ALS Consortium, the University of Maryland Brain and Tissue Bank and NIH NeuroBioBank & The PROSPECT Consortium 2021, 'Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis', Neuron, vol. 109, no. 3, pp. 448-460.e4.


Zhang, J, Lee, D, Dhiman, V, Jiang, P, Xu, J, McGillivray, P, Yang, H, Liu, J, Meyerson, W, Clarke, D, Gu, M, Li, S, Lou, S, Xu, J, Lochovsky, L, Ung, M, Ma, L, Yu, S, Cao, Q, Harmanci, A, Yan, KK, Sethi, A, Gürsoy, G, Schoenberg, MR, Rozowsky, J, Warrell, J, Emani, P, Yang, YT, Galeev, T, Kong, X, Liu, S, Li, X, Krishnan, J, Feng, Y, Rivera-Mulia, JC, Adrian, J, Broach, JR, Bolt, M, Moran, J, Fitzgerald, D, Dileep, V, Liu, T, Mei, S, Sasaki, T, Trevilla-Garcia, C, Wang, S, Wang, Y, Zang, C, Wang, D, Klein, RJ, Snyder, M, Gilbert, DM, Yip, K, Cheng, C, Yue, F, Liu, XS, White, KP & Gerstein, M 2020, 'An integrative ENCODE resource for cancer genomics', Nature communications, vol. 11, no. 1, 3696.
Jin, SC, Dong, W, Kundishora, AJ, Panchagnula, S, Moreno-De-Luca, A, Furey, CG, Allocco, AA, Walker, RL, Nelson-Williams, C, Smith, H, Dunbar, A, Conine, S, Lu, Q, Zeng, X, Sierant, MC, Knight, JR, Sullivan, W, Duy, PQ, DeSpenza, T, Reeves, BC, Karimy, JK, Marlier, A, Castaldi, C, Tikhonova, IR, Li, B, Peña, HP, Broach, JR, Kabachelor, EM, Ssenyonga, P, Hehnly, C, Ge, L, Keren, B, Timberlake, AT, Goto, J, Mangano, FT, Johnston, JM, Butler, WE, Warf, BC, Smith, ER, Schiff, SJ, Limbrick, DD, Heuer, G, Jackson, EM, Iskandar, BJ, Mane, S, Haider, S, Guclu, B, Bayri, Y, Sahin, Y, Duncan, CC, Apuzzo, MLJ, DiLuna, ML, Hoffman, EJ, Sestan, N, Ment, LR, Alper, SL, Bilguvar, K, Geschwind, DH, Günel, M, Lifton, RP & Kahle, KT 2020, 'Exome sequencing implicates genetic disruption of prenatal neuro-gliogenesis in sporadic congenital hydrocephalus', Nature Medicine, vol. 26, no. 11, pp. 1754-1765.
Russo, M, Newell, JM, Budurlean, L, Houser, KR, Sheldon, K, Kesterson, J, Phaeton, R, Hossler, C, Rosenberg, J, DeGraff, D, Shuman, L, Broach, JR & Warrick, JI 2020, 'Mutational profile of endometrial hyperplasia and risk of progression to endometrioid adenocarcinoma', Cancer, vol. 126, no. 12, pp. 2775-2783.
Paulson, JN, Williams, BL, Hehnly, C, Mishra, N, Sinnar, SA, Zhang, L, Ssentongo, P, Mbabazi-Kabachelor, E, Wijetunge, DSS, Von Bredow, B, Mulondo, R, Kiwanuka, J, Bajunirwe, F, Bazira, J, Bebell, LM, Burgoine, K, Couto-Rodriguez, M, Ericson, JE, Erickson, T, Ferrari, M, Gladstone, M, Guo, C, Haran, M, Hornig, M, Isaacs, AM, Kaaya, BN, Kangere, SM, Kulkarni, AV, Kumbakumba, E, Li, X, Limbrick, DD, Magombe, J, Morton, SU, Mugamba, J, Ng, J, Olupot-Olupot, P, Onen, J, Peterson, MR, Roy, F, Sheldon, K, Townsend, R, Weeks, AD, Whalen, AJ, Quackenbush, J, Ssenyonga, P, Galperin, MY, Almeida, M, Atkins, H, Warf, BC, Lipkin, WI, Broach, JR & Schiff, SJ 2020, 'Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants', Science Translational Medicine, vol. 12, no. 563, eaba0565.


Bann, DV, Jin, Q, Sheldon, KE, Houser, KR, Nguyen, L, Warrick, JI, Baker, MJ, Broach, JR, Gerhard, GS & Goldenberg, D 2019, 'Genetic variants implicate dual oxidase-2 in familial and sporadic nonmedullary thyroid cancer', Cancer Research, vol. 79, no. 21, pp. 5490-5499.
Pool, C, Walter, V, Bann, D, Goldenberg, D, Broach, J, Hennessy, M, Cottrill, E, Washburn, E, Williams, N, Crist, H, Imamura, Y & Warrick, JI 2019, 'Molecular characterization of tumors meeting diagnostic criteria for the non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP)', Virchows Archiv, vol. 474, no. 3, pp. 341-351.
The NYGC ALS Consortium 2019, 'Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia', Cell Reports, vol. 29, no. 5, pp. 1164-1177.e5.
The ITALSGEN Consortium & The International ALS Genomics Consortium 2019, 'Shared polygenic risk and causal inferences in amyotrophic lateral sclerosis', Annals of Neurology, vol. 85, no. 4, pp. 470-481.


Briones, MRS, Snyder, AM, Ferreira, RC, Neely, EB, Connor, JR & Broach, JR 2018, 'A possible role for platelet-activating factor receptor in amyotrophic lateral sclerosis treatment', Frontiers in Neurology, vol. 9, no. FEB, 39.
Mockus, TE, Shwetank, Lauver, MD, Ren, HM, Netherby, CS, Salameh, T, Kawasawa, YI, Yue, F, Broach, JR & Lukacher, AE 2018, 'CD4 T cells control development and maintenance of brain-resident CD8 T cells during polyomavirus infection', PLoS pathogens, vol. 14, no. 10, e1007365.
Borges, BJP, Arantes, OMN, Fernandes, AAR, Broach, JR & Fernandes, PMB 2018, 'Genetically modified labeling policies: Moving forward or backward?', Frontiers in Bioengineering and Biotechnology, vol. 6, no. NOV, 181.
ITALSGEN Consortium, Genomic Translation for ALS Care (GTAC) Consortium, ALS Sequencing Consortium, NYGC ALS Consortium, Answer ALS Foundation, Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium, SLAGEN Consortium, French ALS Consortium & Project MinE ALS Sequencing Consortium 2018, 'Genome-wide Analyses Identify KIF5A as a Novel ALS Gene', Neuron, vol. 97, no. 6, pp. 1268-1283.e6.
Dixon, JR, Xu, J, Dileep, V, Zhan, Y, Song, F, Le, VT, Yardımcı, GG, Chakraborty, A, Bann, DV, Wang, Y, Clark, R, Zhang, L, Yang, H, Liu, T, Iyyanki, S, An, L, Pool, C, Sasaki, T, Rivera-Mulia, JC, Ozadam, H, Lajoie, BR, Kaul, R, Buckley, M, Lee, K, Diegel, M, Pezic, D, Ernst, C, Hadjur, S, Odom, DT, Stamatoyannopoulos, JA, Broach, JR, Hardison, RC, Ay, F, Noble, WS, Dekker, J, Gilbert, DM & Yue, F 2018, 'Integrative detection and analysis of structural variation in cancer genomes', Nature Genetics, vol. 50, no. 10, pp. 1388-1398.
Bharatula, V & Broach, JR 2018, The nutrient stress response in yeast. in Stress Response Mechanisms in Fungi: Theoretical and Practical Aspects. Springer International Publishing, pp. 131-159.
The New York Genome Center ALS Consortium 2018, 'Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism', eLife, vol. 7, e37754.


Goldenberg, D, Russo, M, Houser, K, Crist, H, Derr, JB, Walter, V, Warrick, JI, Sheldon, KE, Broach, J & Bann, DV 2017, 'Altered molecular profile in thyroid cancers from patients affected by the Three Mile Island nuclear accident', Laryngoscope, vol. 127, pp. S1-S9.
Russo, M, Broach, J, Sheldon, K, Houser, KR, Liu, DJ, Kesterson, J, Phaeton, R, Hossler, C, Hempel, N, Baker, M, Newell, JM, Zaino, R & Warrick, JI 2017, 'Clonal evolution in paired endometrial intraepithelial neoplasia/atypical hyperplasia and endometrioid adenocarcinoma', Human Pathology, vol. 67, pp. 69-77.
Geronimo, A, Sheldon, KE, Broach, JR, Simmons, Z & Schiff, SJ 2017, 'Expansion of C9ORF72 in amyotrophic lateral sclerosis correlates with brain-computer interface performance', Scientific reports, vol. 7, no. 1, 8875.
Coble, JL, Yue, F, Salameh, TJ, Harris, LR, Deiling, S, Ruggiero, FM, Eshelman, MA, Yochum, GS, Koltun, WA, Gerhard, GS & Broach, JR 2017, 'Identification of a rare LAMB4 variant associated with familial diverticulitis through exome sequencing', Human molecular genetics, vol. 26, no. 16, ddx204, pp. 3212-3220.
Chereji, RV, Bharatula, V, Elfving, N, Blomberg, J, Larsson, M, Morozov, AV, Broach, JR & Björklund, S 2017, 'Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly', Nucleic acids research, vol. 45, no. 15, pp. 8806-8821.
Kurischko, C & Broach, JR 2017, 'Phosphorylation and nuclear transit modulate the balance between normal function and terminal aggregation of the yeast RNA-binding protein Ssd1', Molecular biology of the cell, vol. 28, no. 22, pp. 3057-3069.
Gerhard, GS, Bann, DV, Broach, J & Goldenberg, D 2017, 'Pitfalls of exome sequencing: A case study of the attribution of HABP2 rs7080536 in familial non-medullary thyroid cancer', npj Genomic Medicine, vol. 2, no. 1, 8.

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