Publications

Ruf, B., Bruhns, M., Babaei, S., Kedei, N., Ma, L., Revsine, M., Benmebarek, M. R., Ma, C., Heinrich, B., Subramanyam, V., Qi, J., Wabitsch, S., Green, B. L., Bauer, K. C., Myojin, Y., Greten, L. T., McCallen, J. D., Huang, P., Trehan, R., Wang, X., … Greten, T. F. Tumor-associated macrophages trigger MAIT cell dysfunction at the HCC invasive margin.

Yazdani K, Seshadri S, Tillo D, Yang M, Sibley CD, Vinson C, Schneekloth. Decoding complexity in biomolecular recognition of DNA i-motifs with microarrays.

Zong D, Koussa NC, Cornwell JA, Pankajam AV, Kruhlak MJ, Wong N, Chari R, Cappell SD, Nussenzweig A. Comprehensive mapping of cell fates in microsatellite unstable cancer cells support dual targe6ng of WRN and ATR.

Schmidt LS, Vocke CD, Ricketts CJ, Blake Z, Choo KK, Nielsen D, Gautam R, Crooks DR, Reynolds KL, Krolus JL, Bashyal M, Karim B, Cowen EW, Malayeri AA, Merino MJ, Srinivasan R, Ball MW, Zbar B, Marston Linehan W. PRDM10 RCC: A Birt-Hogg-Dubé-like Syndrome Associated With Lipoma and Highly Penetrant, Aggressive Renal Tumors Morphologically Resembling Type 2 Papillary Renal Cell Carcinoma

Crooks DR, Cawthon GM, Fitzsimmons CM, Perez M, Ricketts CJ, Vocke CD, Yang Y, Middelton L, Nielsen D, Schmidt LS, Tandon M, Merino MJ, Ball MW, Meier JL, Batista PJ, Linehan WM. Cryptic splice mutation in the fumarate hydratase gene in patients with clinical manifestations of Hereditary Leiomyomatosis and Renal Cell Cancer.

Lang M, Schmidt LS, Wilson KM, Ricketts CJ, Sourbier C, Vocke CD, Wei D, Crooks DR, Yang Y, Gibbs BK, Zhang X, Klumpp-Thomas C, Chen L, Guha R, Ferrer M, McKnight C, Itkin Z, Wangsa D, Wangsa D, James A, Difilippantonio S, Karim B, Morís F, Ried T, Merino MJ, Srinivasan R, Thomas CJ, Linehan WM. High-throughput and targeted drug screens identify pharmacological candidates against MiT-translocation renal cell carcinoma.

West RR, Bauer TR, Tuschong LM, Embree LJ, Calvo KR, Tillo D, Davis J, Holland SM, Hickstein DD. A novel GATA2 distal enhancer mutation results in the MonoMAC syndrome in 2 second cousins.

Chandni B. Khandwala, Parijat Sarkar, H. Broder Schmidt, Mengxiao Ma, Maia Kinnebrew, Ganesh V. Pusapati, Bhaven B. Patel, Desiree Tillo, Andres M. Lebensohn, Rajat Rohatgi. Direct ionic stress sensing and mitigation by the transcription factor NFAT5.

Gasparski AN, Moissoglu K, Pallikkuth S, Meydan S, Guydosh NR, Mili S. mRNA location and translation rate determine protein targeting to dual destinations.

Silva, K. P. T., Sundar, G., & Khare, A. Efflux pump gene amplifications bypass necessity of multiple target mutations for resistance against dual-targeting antibiotic.

Ghosal, S., Vanova, K. H., Uher, O., Das, S., Patel, M., Meuter, L., Huynh, T. T., Jha, A., Talvacchio, S., Knue, M., Prodanov, T., Zeiger, M. A., Nilubol, N., Taieb, D., Crona, J., Shankavaram, U. T., & Pacak, K. Immune signature of pheochromocytoma and paraganglioma in context of neuroendocrine neoplasms associated with prognosis.

Pongor, L. S., Schultz, C. W., Rinaldi, L., Wangsa, D., Redon, C. E., Takahashi, N., Fialkoff, G., Desai, P., Zhang, Y., Burkett, S., Hermoni, N., Vilk, N., Gutin, J., Rona, G., Zhao, Y., Nichols, S., Vilimas, R., Sciuto, L., Graham, C., Caravaca, J. M., … Thomas, A. Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and is Associated with Worse Outcomes.

vocke, C. D., Fleming, L. R., Piskorski, A. M., Amin, A., Phornphutkul, C., de la Monte, S., Vilboux, T., Duncan, F., Pellegrino, J., Braddock, B., Middelton, L. A., Schmidt, L. S., Merino, M. J., Cowen, E. W., Introne, W. J., Linehan, W. M., & Smith, A. C. M. A diagnosis of Birt–Hogg–Dubé syndrome in individuals with Smith–Magenis syndrome: Recommendation for cancer screening.

Hartford, C. C. R., Shrestha, R. L., Pongor, L., Zhao, Y., Chen, X., Fromont, C., Chaudhary, R., Li, X. L., Pasterczyk, K. R., Kumar, R., Muys, B. R., Tsitsipatis, D., Chari, R., Gorospe, M., Aladjem, M. I., Khan, J., Basrai, M. A., Grammatikakis, I., & Lal, A. Context-Dependent Function of Long Noncoding RNA PURPL in Transcriptome Regulation during p53 Activation.

Goldberg, L., Negi, V., Chung, Y. J., Onozawa, M., Zhu, Y. J., Walker, R. L., Pierce, R., Patel, D. P., Krausz, K. W., Gonzalez, F. J., Goodell, M. A., Rodriguez, B., Meltzer, P. S., & Aplan, P. D. Mutant Idh2 Cooperates with a NUP98-HOXD13 Fusion to Induce Early Immature Thymocyte Precursor ALL.

Palmer, D. C., Webber, B. R., Patel, Y., Johnson, M. J., Kariya, C. M., Lahr, W. S., Parkhurst, M. R., Gartner, J. J., Prickett, T. D., Lowery, F. J., Kishton, R. J., Gurusamy, D., Franco, Z., Vodnala, S. K., Diers, M. D., Wolf, N. K., Slipek, N. J., McKenna, D. H., Sumstad, D., Viney, L., … Restifo, N. P. Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade.

Zhang, X., Lou, H. E., Gopalan, V., Liu, Z., Jafarah, H. M., Lei, H., Jones, P., Sayers, C. M., Yohe, M. E., Chittiboina, P., Widemann, B. C., Thiele, C. J., Kelly, M. C., Hannenhalli, S., & Shern, J. F. Single-cell sequencing reveals activation of core transcription factors in PRC2-deficient malignant peripheral nerve sheath tumor.

Nguyen, R., Zhang, X., Sun, M., Abbas, S., Seibert, C., Kelly, M. C., Shern, J. F., & Thiele, C. J. Anti-GD2 Antibodies Conjugated to IL15 and IL21 Mediate Potent Antitumor Cytotoxicity against Neuroblastoma.

Vega-Sendino M, Olbrich T, Stein P, Tillo D, Carey GI, Savy V, Saykali B, Domingo CN, Maity TK, Jenkins LM, Williams CJ, Ruiz S. The homeobox transcription factor DUXBL controls exit from totipotency.

He, Y., Kim, I. K., Bian, J., Polyzos, A., Di Giammartino, D. C., Zhang, Y. W., Luo, J., Hernandez, M. O., Kedei, N., Cam, M., Borczuk, A. C., Lee, T., Han, Y., Conner, E. A., Wong, M., Tillo, D. C., Umemura, S., Chen, V., Ruan, L., White, J. B., … Giaccone, G. A Knock-In Mouse Model of Thymoma With the GTF2I L424H Mutation.

Shammas, M. K., Huang, X., Wu, B. P., Fessler, E., Song, I. Y., Randolph, N. P., Li, Y., Bleck, C. K., Springer, D. A., Fratter, C., Barbosa, I. A., Powers, A. F., Quirós, P. M., Lopez-Otin, C., Jae, L. T., Poulton, J., & Narendra, D. P. OMA1 mediates local and global stress responses against protein misfolding in CHCHD10 mitochondrial myopathy.

Vocke, C. D., Ricketts, C. J., Metwalli, A. R., Pinto, P. A., Gautam, R., Raffeld, M., Merino, M. J., Ball, M. W., & Linehan, W. M. Differential VHL Mutation Patterns in Bilateral Clear Cell RCC Distinguishes Between Independent Primary Tumors and Contralateral Metastatic Disease.

Wong-Rolle, A., Dong, Q., Zhu, Y., Divakar, P., Hor, J. L., Kedei, N., Wong, M., Tillo, D., Conner, E. A., Rajan, A., Schrump, D. S., Jin, C., Germain, R. N., & Zhao, C. Spatial meta-transcriptomics reveal associations of intratumor bacteria burden with lung cancer cells showing a distinct oncogenic signature.

Matsukawa, T., Yin, M., Baslan, T., Chung, Y. J., Cao, D., Bertoli, R., Zhu, Y. J., Walker, R. L., Freeland, A., Knudsen, E., Lowe, S. W., Meltzer, P. S., & Aplan, P. D. Mcm2 hypomorph leads to acute leukemia or hematopoietic stem cell failure, dependent on genetic context.

Ciucci, T., Vacchio, M. S., Chen, T., Nie, J., Chopp, L. B., McGavern, D. B., Kelly, M. C., & Bosselut, R. Dependence on Bcl6 and Blimp1 drive distinct differentiation of murine memory and follicular helper CD4+ T cells.

Gao, Y., Zamisch, M., Vacchio, M., Chopp, L., Ciucci, T., Paine, E. L., Lyons, G. C., Nie, J., Xiao, Q., Zvezdova, E., Love, P. E., Vinson, C. R., Jenkins, L. M., & Bosselut, R. NuRD complex recruitment to Thpok mediates CD4+ T cell lineage differentiation.

Nie, J., Carpenter, A. C., Chopp, L. B., Chen, T., Balmaceno-Criss, M., Ciucci, T., Xiao, Q., Kelly, M. C., McGavern, D. B., Belkaid, Y., & Bosselut, R. The transcription factor LRF promotes integrin β7 expression by and gut homing of CD8αα+ intraepithelial lymphocyte precursors.

Zarrella, T. M., & Khare, A. Systematic identification of molecular mediators of interspecies sensing in a community of 2 frequently coinfecting bacterial pathogens.

Thakur, B. L., Baris, A. M., Fu, H., Redon, C. E., Pongor, L. S., Mosavarpour, S., Gross, J. M., Jang, S. M., Sebastian, R., Utani, K., Jenkins, L. M., Indig, F. E., & Aladjem, M. I. Convergence of SIRT1 and ATR signaling to modulate replication origin dormancy.

Robert R West, Katherine R Calvo, Lisa J Embree, Weixin Wang, Laura M Tuschong, Thomas R Bauer, Desiree Tillo, Justin Lack, Stephenie Droll, Amy P. Hsu, Steven M Holland, Dennis D Hickstein. ASXL1 and STAG2 are Common Mutations in GATA2 Deficiency Patients with Bone Marrow Disease and Myelodysplastic Syndrome.

Vieux, K. F., Prothro, K. P., Kelley, L. H., Palmer, C., Maine, E. M., Veksler-Lublinsky, I., & McJunkin, K. Screening by deep sequencing reveals mediators of microRNA tailing in C. elegans.

Ray S, Tillo D, Assad N, Ufot A, Porollo A, Durell SR, Vinson C. Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182.

Liu X, Weikum ER, Tillo D, Vinson C, Ortlund EA. Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element.

Ray S, Tillo D, Durell SR, Khund-Sayeed S, Vinson C. REL Domain of NFATc2 Binding to Five Types of DNA Using Protein Binding Microarrays.

Kaczanowska, S., Beury, D. W., Gopalan, V., Tycko, A. K., Qin, H., Clements, M. E., Drake, J., Nwanze, C., Murgai, M., Rae, Z., Ju, W., Alexander, K. A., Kline, J., Contreras, C. F., Wessel, K. M., Patel, S., Hannenhalli, S., Kelly, M. C., & Kaplan, R. N. Genetically engineered myeloid cells rebalance the core immune suppression program in metastasis.

Cristin D Davidson, Alana L Gibson, Tansy Gu, Laura L Baxter, Benjamin E Deverman, Keith Beadle, Arturo A Incao, Jorge L Rodriguez-Gil, Hideji Fujiwara, Xuntian Jiang, Randy J Chandler, Daniel S Ory, Viviana Gradinaru, Charles P Venditti, William J Pavan. Improved systemic AAV gene therapy with a neurotrophic capsid in Niemann-Pick disease type C1 mice.

Ahuja, J. S., Harvey, C. S., Wheeler, D. L., & Lichten, M. Repeated strand invasion and extensive branch migration are hallmarks of meiotic recombination.

Amin R, Shukla A, Zhu JJ, Kim S, Wang P, Tian SZ, Tran AD, Paul D, Cappell SD, Burkett S, Liu H. Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response.

Lu Y, Zheng Z, Lowery FJ, et al. Direct identification of neoantigen-specific TCRs from tumor specimens by high-throughput single-cell sequencing.

Miyanaga A, Matsumoto M, Beck JA, Horikawa I, Oike T, Okayama H, Tanaka H, Burkett SS, Robles AI, Khan M, Lissa D, Seike M, Gemma A, Mano H, Harris CC. EML4-ALK induces cellular senescence in mortal normal human cells and promotes anchorage-independent growth in hTERT-transduced normal human cells.

Fu, H., Redon, C.E., Thakur, B.L. et al. Dynamics of replication origin over-activation.

Youfeng Yang, Christopher J Ricketts, Cathy D Vocke, J Keith Killian, Hesed M Padilla-Nash, Martin Lang, Darmood Wei, Young H Lee, Darawalee Wangsa, Carole Sourbier, Paul S Meltzer, Thomas Ried, Maria J Merino, Adam R Metwalli, Mark W Ball, Ramaprasad Srinivasan, W Marston Linehan. Characterization of genetically defined sporadic and hereditary type 1 papillary renal cell carcinoma cell lines.

Vocke CD, Ricketts CJ, Schmidt LS, Ball MW, Middelton LA, Zbar B, Marston Linehan W. Comprehensive characterization of Alu-mediated breakpoints in germline VHL gene deletions and rearrangements in patients from 71 VHL families.

Olbrich T, Vega-Sendino M, Tillo D, Wu W, Zolnerowich N, Tran AD, Domingo CN, Franco M, Markiewicz-Potoczny M, Pegoraro G, FitzGerald PC, Kruhlak MJ, Lazzerini-Denchi E, Nora EP, Nussenzweig A, Ruiz S. CTCF is a Barrier for Totipotent-like Reprogramming.

Vega-Sendino M, Olbrich T, Tillo D, Tran AD, Domingo CM, Franco M, FitzGerald PC, Kruhlak MJ and Ruiz S. The ETS Transcription Factor ERF Controls the Exit from the Embryonic Rosette-stage of Pluripotency.

Crooks DR, Maio N, Lang M, Ricketts CJ, Vocke CD, Gurram S, Turan S, Kim YY, Cawthon GM, Sohelian F, De Val N, Pfeiffer RM, Jailwala P, Tandon M, Tran B, Fan TW, Lane AN, Ried T, Wangsa D, Malayeri AA, Merino MJ, Yang Y, Meier JL, Ball MW, Rouault TA, Srinivasan R, Linehan WM. Mitochondrial DNA alterations underlie an irreversible shift to aerobic glycolysis in fumarate hydratase-deficient renal cancer.

Merino MJ, Ricketts CJ, Moreno V, Yang Y, Fan TWM, Lane AN, Meltzer PS, Vocke CD, Crooks DR, Linehan WM. Multifocal Renal Cell Carcinomas With Somatic IDH2 Mutation: Report of a Previously Undescribed Neoplasm.

Jocelyn D. Weissman, Amit K. Singh, Ballachanda N. Devaiah, Peter Schuck, Ross C. LaRue, Dinah S. Singer. The intrinsic kinase activity of BRD4 spans its BD2-B-BID domains.

Zhe Sun, Alexander V Yakhnin, Peter C FitzGerald, Carl E Mclntosh, Mikhail Kashlev. Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria.

Gil Kanfer, Shireen A. Sarraf, Yaakov Maman, Heather Baldwin, Kory R. Johnson, Michael E. Ward, Martin Kampmann, Jennifer Lippincott-Schwartz, Richard J. Youle. Image-based pooled whole genome CRISPR screening for Parkin and TFEB subcellular localization.

Ray S, Tillo D, Ufot A, Assad N, Durell S, Vinson C. bZIP Dimers CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun Prefer to Bind to Some Double-Stranded DNA Sequences Containing 5-Formylcytosine and 5-Carboxylcytosine.

Wu G, Tillo D, Ray S, Chang TC, Schneekloth JS Jr, Vinson C, Yang D. Custom G4 Microarrays Reveal Selective G-Quadruplex Recognition of Small Molecule BMVC: A Large-Scale Assessment of Ligand Binding Selectivity.

Ray S, Tillo D, Boer RE, Assad N, Barshai M, Wu G, Orenstein Y, Yang D, Schneekloth JS Jr, Vinson C. Custom DNA Microarrays Reveal Diverse Binding Preferences of Proteins and Small Molecules to Thousands of G-Quadruplexes.

Fojo, T., Huff, L., Litman, T. et al. Metastatic and recurrent adrenocortical cancer is not defined by its genomic landscape.

Beck, David & Ferrada, Marcela & Sikora, KA & Ombrello, AK & Collins, JC & Pei, W & Balanda, N & Ross, DL & Cardona, D & Wu, Z & Patel, B & Manthiram, K & Groarke, EM & Gutierrez-Rodrigues, Fernanda & Hoffmann, P & Rosenzweig, S & Nakabo, Shuichiro & Dillon, LW & Hourigan, CS & Grayson, Peter. Somatic Mutations in UBA1 and Severe Adult-Onset Autoinflammatory Disease.

Wei D, Yang Y, Ricketts CJ, Vocke CD, Ball MW, Sourbier C, Wangsa D, Wangsa D, Guha R, Zhang X, Wilson K, Chen L, Meltzer PS, Ried T, Thomas CJ, Merino MJ, Linehan WM. Novel renal medullary carcinoma cell lines, UOK353 and UOK360, provide preclinical tools to identify new therapeutic treatments.

Markiewicz-Potoczny, M., Lobanova, A., Loeb, A.M. et al. TRF2-mediated telomere protection is dispensable in pluripotent stem cells.

Martin Lang ,Cathy D. Vocke ,Christopher J. Ricketts ,Adam R. Metwalli , Mark W. Ball , Laura S. Schmidt , W. Marston Linehan. Clinical and Molecular Characterization of Microphthalmia-Associated Transcription Factor (MITF)-Related Renal Cell Carcinoma.

Ricketts CJ, Vocke CD, Lang M, Chen X, Zhao Y, Tran B, Tandon M, Schmidt LS, Ball MW, Linehan WM. A germline 1;3 translocation disrupting the VHL gene: a novel genetic cause for von Hippel-Lindau.

Niek van Wietmarschen et al. Repeat expansions confers WRN dependence in microsatellite unstable cancers.

Nie Z, Guo C, Das SK, et al. Dissecting transcriptional amplification by MYC.

Callen et al. 53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination.

Alexander V Yakhnin, Peter C FitzGerald, Carl McIntosh, Helen Yakhnin, Maria Kireeva, Joshua Turek-Herman, Zachary F Mandell, Mikhail Kashlev, Paul Babitzke. NusG controls transcription pausing and RNA polymerase translocation throughout the Bacillus subtilis genome.