James Broach, PhD - Penn State Cancer Institute
Researcher Profile
James Broach, PhD
Distinguished Professor and Interim Chair, Department of Molecular and Precision Medicine
Professor, Department of Otolaryngology - Head and Neck Surgery
Professor, Department of Otolaryngology - Head and Neck Surgery
Scientific Program:Next-Generation Therapies
Recent Publications
2025
Ding, Y, He, B, Bogush, D, Schramm, J, Singh, C, Dovat, K, Randazzo, J, Tukaramrao, D, Hengst, J, Annageldiyev, C, Kudva, A, Desai, D, Sharma, A, Spiegelman, VS, Huang, S, Viet, CT, Dorsam, G, Saulnier Scholler, G, Broach, J, Yue, F & Dovat, S 2025, 'Critical roles of IKAROS and HDAC1 in regulation of heterochromatin and tumor suppression in T-cell acute lymphoblastic leukemia', Leukemia, vol. 39, no. 8, pp. 2010-2020. https://doi.org/10.1038/s41375-025-02651-1
El-Bayoumy, K, Christensen, N, Broach, J, Meyers, C, Stairs, D, Machtay, M, Hu, J, Bitzer, ZT, Schell, TD, Chen, K-M, Sun, Y-W, Desai, D, Walter, V & Zhu, J 2025, 'Current challenges and potential opportunities for interception and prevention of head and neck cancer', Carcinogenesis, vol. 46, no. 2, bgaf025. https://doi.org/10.1093/carcin/bgaf025
Chan, K, Tseng, C, Milarachi, E, Goldrich, D, Schneper, L, Sheldon, K, Aliaga, C, Alam, S, Chatterjee, S, El-Bayoumy, K, Meyers, C, Goldenberg, D & Broach, JR 2025, 'Genome Instability Precedes Viral Integration in Human Papillomavirus–Transformed Tonsillar Keratinocytes', Molecular Cancer Research, vol. 23, no. 2, pp. 119-127. https://doi.org/10.1158/1541-7786.MCR-24-0604
Ericson, JE, Natukwatsa, D, Ssenyonga, P, Onen, J, Mugamba, J, Mulondo, R, Morton, SU, Movassagh, M, Templeton, K, Hehnly, C, Mbabazi-Kabachelor, E, Kulkarni, AV, Warf, BC, Broach, JR, Paulson, JN & Schiff, SJ 2025, 'Poor surgical outcomes following Paenibacillus infant infectious hydrocephalus', Journal of Neurosurgery: Pediatrics, vol. 36, no. 2, pp. 145-156. https://doi.org/10.3171/2025.1.PEDS24254
NYGC ALS Consortium 2025, 'TDP-43 loss induces cryptic polyadenylation in ALS/FTD', Nature Neuroscience, vol. 28, no. 11, pp. 2190-2200. https://doi.org/10.1038/s41593-025-02050-w
2024
Smith, D, Bastug, K, Burgoine, K, Broach, JR, Hammershaimb, EA, Hehnly, C, Morton, SU, Osman, M, Schiff, SJ & Ericson, JE 2025, 'A Systematic Review of Human Paenibacillus Infections and Comparison of Adult and Pediatric Cases', Pediatric Infectious Disease Journal, vol. 44, no. 5, pp. 455-461. https://doi.org/10.1097/INF.0000000000004668
NYGC ALS Consortium 2024, 'A framework for sharing of clinical and genetic data for precision medicine applications', Nature Medicine, vol. 30, no. 12, 134, pp. 3578-3589. https://doi.org/10.1038/s41591-024-03239-5
Costa, ACT, Schneper, L, Russo, M, Fernandes, AAR, Broach, JR & Fernandes, PMB 2024, 'Comparative Transcriptome Analysis of Industrial and Laboratory Saccharomyces cerevisiae Strains after Sequential Stresses', Fermentation, vol. 10, no. 8, 395. https://doi.org/10.3390/fermentation10080395
Ferreira, RC, Rodrigues, CR, Broach, JR & Briones, MRS 2024, 'Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals', International journal of molecular sciences, vol. 25, no. 7, 3785. https://doi.org/10.3390/ijms25073785
NYGC ALS Consortium 2024, 'Correction to: TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A (Nature, (2022), 603, 7899, (131-137), 10.1038/s41586-022-04436-3)', Nature, vol. 631, no. 8020, pp. E7. https://doi.org/10.1038/s41586-024-07577-9
Budurlean, L, Tukaramrao, DB, Zhang, L, Dovat, S & Broach, J 2024, 'Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection', Journal of Personalized Medicine, vol. 14, no. 3, 291. https://doi.org/10.3390/jpm14030291
The International ALS Genomics Consortium, ITALSGEN Consortium, SLAGEN Consortium, Project MinE ALS Sequencing Consortium & The American Genome Center 2024, 'Mechanism-free repurposing of drugs for C9orf72-related ALS/FTD using large-scale genomic data', Cell Genomics, vol. 4, no. 11, 100679. https://doi.org/10.1016/j.xgen.2024.100679
NYGC ALS Consortium 2024, 'Mitochondrial genome variants associated with amyotrophic lateral sclerosis and their haplogroup distribution', Muscle and Nerve, vol. 70, no. 4, pp. 862-872. https://doi.org/10.1002/mus.28230
The New York Genome Center ALS Sequencing Consortium, Scottish Genomes Partnership, ALS COSMOS Study Group, PLS COSMOS Study Group & GTAC Investigators 2024, 'Rare variant analyses validate known ALS genes in a multi-ethnic population and identifies ANTXR2 as a candidate in PLS', BMC genomics, vol. 25, no. 1, 651. https://doi.org/10.1186/s12864-024-10538-1
2023
PROSPECT Consortium, The American Genome Center, International LBD Genomics Consortium & International ALS/FTD Consortium 2023, 'Genome-wide structural variant analysis identifies risk loci for non-Alzheimer's dementias', Cell Genomics, vol. 3, no. 6, 100316. https://doi.org/10.1016/j.xgen.2023.100316
Salameh, TJ, Roth, K, Schultz, L, Ma, Z, Bonavia, AS, Broach, JR, Hu, B & Howrylak, JA 2023, 'Gut microbiome dynamics and associations with mortality in critically ill patients', Gut Pathogens, vol. 15, no. 1, 66. https://doi.org/10.1186/s13099-023-00567-8
Yu, M, Peterson, MR, Cherukuri, V, Hehnly, C, Mbabazi-Kabachelor, E, Mulondo, R, Nsubuga Kaaya, B, Broach, JR, Schiff, SJ & Monga, V 2023, 'Infection diagnosis in hydrocephalus CT images: a domain enriched attention learning approach', Journal of neural engineering, vol. 20, no. 3, 036033. https://doi.org/10.1088/1741-2552/acd9ee
Ericson, JE, Burgoine, K, Kumbakumba, E, Ochora, M, Hehnly, C, Bajunirwe, F, Bazira, J, Fronterre, C, Hagmann, C, Kulkarni, AV, Kumar, MS, Magombe, J, Mbabazi-Kabachelor, E, Morton, SU, Movassagh, M, Mugamba, J, Mulondo, R, Natukwatsa, D, Kaaya, BN, Olupot-Olupot, P, Onen, J, Sheldon, K, Smith, J, Ssentongo, P, Ssenyonga, P, Warf, B, Wegoye, E, Zhang, L, Kiwanuka, J, Paulson, JN, Broach, JR & Schiff, SJ 2023, 'Neonatal Paenibacilliosis: Paenibacillus Infection as a Novel Cause of Sepsis in Term Neonates With High Risk of Sequelae in Uganda', Clinical Infectious Diseases, vol. 77, no. 5, pp. 768-775. https://doi.org/10.1093/cid/ciad337
Levy, B, Baughn, LB, Akkari, Y, Chartrand, S, LaBarge, B, Claxton, D, Lennon, PA, Cujar, C, Kolhe, R, Kroeger, K, Pitel, B, Sahajpal, N, Sathanoori, M, Vlad, G, Zhang, L, Fang, M, Kanagal-Shamanna, R & Broach, JR 2023, 'Optical genome mapping in acute myeloid leukemia: a multicenter evaluation', Blood Advances, vol. 7, no. 7, pp. 1297-1307. https://doi.org/10.1182/bloodadvances.2022007583
Morton, SU, Hehnly, C, Burgoine, K, Ssentongo, P, Ericson, JE, Kumar, MS, Hagmann, C, Fronterre, C, Smith, J, Movassagh, M, Streck, N, Bebell, LM, Bazira, J, Kumbakumba, E, Bajunirwe, F, Mulondo, R, Mbabazi-Kabachelor, E, Nsubuga, BK, Natukwatsa, D, Nalule, E, Magombe, J, Erickson, T, Ngonzi, J, Ochora, M, Olupot-Olupot, P, Onen, J, Ssenyonga, P, Mugamba, J, Warf, BC, Kulkarni, AV, Lane, J, Whalen, AJ, Zhang, L, Sheldon, K, Meier, FA, Kiwanuka, J, Broach, JR, Paulson, JN & Schiff, SJ 2023, 'Paenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda: an observational case-control study', The Lancet Microbe, vol. 4, no. 8, pp. e601-e611. https://doi.org/10.1016/S2666-5247(23)00106-4
Costa, ACT, Russo, M, Fernandes, AAR, Broach, JR & Fernandes, PMB 2023, 'Transcriptional Response of Multi-Stress-Tolerant Saccharomyces cerevisiae to Sequential Stresses', Fermentation, vol. 9, no. 2, 195. https://doi.org/10.3390/fermentation9020195
2022
NYGC ALS Consortium 2022, 'Cell environment shapes TDP-43 function with implications in neuronal and muscle disease', Communications Biology, vol. 5, no. 1, 314. https://doi.org/10.1038/s42003-022-03253-8
Hehnly, C, Ssentongo, P, Bebell, LM, Burgoine, K, Bazira, J, Fronterre, C, Kumbakumba, E, Mulondo, R, Mbabazi-Kabachelor, E, Morton, SU, Ngonzi, J, Ochora, M, Olupot-Olupot, P, Mugamba, J, Onen, J, Roberts, DJ, Sheldon, K, Sinnar, SA, Smith, J, Ssenyonga, P, Kiwanuka, J, Paulson, JN, Meier, FA, Ericson, JE, Broach, JR & Schiff, SJ 2022, 'Cytomegalovirus infections in infants in Uganda: Newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus', International Journal of Infectious Diseases, vol. 118, pp. 24-33. https://doi.org/10.1016/j.ijid.2022.02.005
Kumar, MS, Slud, EV, Hehnly, C, Zhang, L, Broach, J, Irizarry, RA, Schiff, SJ & Paulson, JN 2022, 'Differential richness inference for 16S rRNA marker gene surveys', Genome biology, vol. 23, no. 1, 166. https://doi.org/10.1186/s13059-022-02722-x
Labarge, B, Hennessy, M, Zhang, L, Goldrich, D, Chartrand, S, Purnell, C, Wright, S, Goldenberg, D & Broach, JR 2022, 'Human Papillomavirus Integration Strictly Correlates with Global Genome Instability in Head and Neck Cancer', Molecular Cancer Research, vol. 20, no. 9, pp. 1420-1428. https://doi.org/10.1158/1541-7786.MCR-21-0831
Shi, A, Fan, F & Broach, JR 2022, 'Microbial adaptive evolution', Journal of Industrial Microbiology and Biotechnology, vol. 49, no. 2, kuab076. https://doi.org/10.1093/jimb/kuab076
Stine, JG, Schreibman, IR, Faust, AJ, Dahmus, J, Stern, B, Soriano, C, Rivas, G, Hummer, B, Kimball, SR, Geyer, NR, Chinchilli, VM, Loomba, R, Schmitz, K, Sciamanna, C, Strine, C, Wentzel, R, Marlin, S, Sica, C, Vesek, J, Eyster, E, Sinoway, L, Bentz, K, Handley, N, Hershey Fell, B, Mottilla, S, Christ, C, George, S, Novchich, T, Beyer, M, Clarke, K, Myers, T, Glading-Steinruck, M, Krok, K, Ma, T, Riley, T, Thompson, E, Tressler, H, Broach, J, Doan, T, Patrick, S, Reed, S, Hamilton, C, Slavoski, K & Tregea, D 2022, 'NASHFit: A randomized controlled trial of an exercise training program to reduce clotting risk in patients with NASH', Hepatology, vol. 76, no. 1, pp. 172-185. https://doi.org/10.1002/hep.32274
NYGC ALS Consortium 2022, 'NOS1AP is a novel molecular target and critical factor in TDP-43 pathology', Brain Communications, vol. 4, no. 5. https://doi.org/10.1093/braincomms/fcac242
Budurlean, L, Baker, M & Broach, J 2022, 'Rare MYC-N11S germline mutation indicative of inherited breast cancer in a multigeneration family', BMJ case reports, vol. 15, no. 11, e251336. https://doi.org/10.1136/bcr-2022-251336
Wasserfall, C, Dyer, AM, Speake, C, Andersen, DK, Baab, KT, Bellin, MD, Broach, JR, Campbell-Thompson, M, Chinchilli, VM, Lee, PJ, Park, WG, Pratley, RE, Saloman, JL, Sims, EK, Tang, G, Yadav, D, Yazici, C & Conwell, DL 2022, 'Standard Operating Procedures for Biospecimen Collection, Processing, and Storage: From the Type 1 Diabetes in Acute Pancreatitis Consortium', Pancreas, vol. 51, no. 6, pp. 593-597. https://doi.org/10.1097/MPA.0000000000002077
Xu, J, Song, F, Lyu, H, Kobayashi, M, Zhang, B, Zhao, Z, Hou, Y, Wang, X, Luan, Y, Jia, B, Stasiak, L, Wong, JHY, Wang, Q, Jin, Q, Jin, Q, Fu, Y, Yang, H, Hardison, RC, Dovat, S, Platanias, LC, Diao, Y, Yang, Y, Yamada, T, Viny, AD, Levine, RL, Claxton, D, Broach, JR, Zheng, H & Yue, F 2022, 'Subtype-specific 3D genome alteration in acute myeloid leukaemia', Nature, vol. 611, no. 7935, pp. 387-398. https://doi.org/10.1038/s41586-022-05365-x
NYGC ALS Consortium 2022, 'TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A', Nature, vol. 603, no. 7899, pp. 131-137. https://doi.org/10.1038/s41586-022-04436-3
Type 1 Diabetes in Acute Pancreatitis Consortium (T1DAPC) 2022, 'Type 1 Diabetes in Acute Pancreatitis Consortium: From Concept to Reality', Pancreas, vol. 51, no. 6, pp. 563-567. https://doi.org/10.1097/MPA.0000000000002073
Hehnly, C, Shi, A, Ssentongo, P, Zhang, L, Isaacs, A, Morton, SU, Streck, N, Erdmann-Gilmore, P, Tolstoy, I, Reid Townsend, R, Limbrick, DD, Paulson, JN, Ericson, JE, Galperin, MY, Schiff, SJ & Broach, JR 2022, 'Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus', mBio, vol. 13, no. 6. https://doi.org/10.1128/mbio.02688-22
Movassagh, M, Morton, SU, Hehnly, C, Smith, J, Doan, TT, Irizarry, R, Broach, JR, Schiff, SJ, Bailey, JA & Paulson, JN 2022, 'mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis', BMC genomics, vol. 23, no. 1, 439. https://doi.org/10.1186/s12864-022-08558-w