Supported by CCR Office of Science and Technology Resources (OSTR)



Congratulations to the following authors for their recent publications featuring data derived from the CCR Genomics Core.


Immune signature of pheochromocytoma and paraganglioma in context of neuroendocrine neoplasms associated with prognosis

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

PubMed Link

Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and is Associated with Worse Outcomes

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.

PubMed Link

A diagnosis of Birt–Hogg–Dubé syndrome in individuals with Smith–Magenis syndrome: Recommendation for cancer screening

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.

PubMed Link


Context-Dependent Function of Long Noncoding RNA PURPL in Transcriptome Regulation during p53 Activation

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.

PubMed Link

Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade

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.

PubMed Link

Single-cell sequencing reveals activation of core transcription factors in PRC2-deficient malignant peripheral nerve sheath tumor

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.

PubMed Link

Anti-GD2 Antibodies Conjugated to IL15 and IL21 Mediate Potent Antitumor Cytotoxicity against Neuroblastoma

Nguyen, R., Zhang, X., Sun, M., Abbas, S., Seibert, C., Kelly, M. C., Shern, J. F., & Thiele, C. J.

PubMed Link

The homeobox transcription factor DUXBL controls exit from totipotency

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.

bioRxiv Link

A Knock-In Mouse Model of Thymoma With the GTF2I L424H Mutation

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.

PubMed Link

OMA1 mediates local and global stress responses against protein misfolding in CHCHD10 mitochondrial myopathy

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.

PubMed Link

Differential VHL Mutation Patterns in Bilateral Clear Cell RCC Distinguishes Between Independent Primary Tumors and Contralateral Metastatic Disease

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.

PubMed Link

Spatial meta-transcriptomics reveal associations of intratumor bacteria burden with lung cancer cells showing a distinct oncogenic signature

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.

PubMed Link

Mcm2 hypomorph leads to acute leukemia or hematopoietic stem cell failure, dependent on genetic context

64. 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.

PubMed Link

Dependence on Bcl6 and Blimp1 drive distinct differentiation of murine memory and follicular helper CD4+ T cells

Ciucci, T., Vacchio, M. S., Chen, T., Nie, J., Chopp, L. B., McGavern, D. B., Kelly, M. C., & Bosselut, R.

PubMed Link

NuRD complex recruitment to Thpok mediates CD4+ T cell lineage differentiation

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.

PubMed Link

The transcription factor LRF promotes integrin β7 expression by and gut homing of CD8αα+ intraepithelial lymphocyte precursors

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.

PubMed Link

Systematic identification of molecular mediators of interspecies sensing in a community of 2 frequently coinfecting bacterial pathogens

Zarrella, T. M., & Khare, A.

PubMed Link

Convergence of SIRT1 and ATR signaling to modulate replication origin dormancy

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.

PubMed Link

ASXL1 and STAG2 are Common Mutations in GATA2 Deficiency Patients with Bone Marrow Disease and Myelodysplastic Syndrome

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

PubMed Link


Screening by deep sequencing reveals mediators of microRNA tailing in C. elegans

Vieux, K. F., Prothro, K. P., Kelley, L. H., Palmer, C., Maine, E. M., Veksler-Lublinsky, I., & McJunkin, K.

PubMed Link

Repeated strand invasion and extensive branch migration are hallmarks of meiotic recombination

Ahuja, J. S., Harvey, C. S., Wheeler, D. L., & Lichten, M

PubMed Link

Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response

Amin R, Shukla A, Zhu JJ, Kim S, Wang P, Tian SZ, Tran AD, Paul D, Cappell SD, Burkett S, Liu H.

PubMed Link

Direct identification of neoantigen-specific TCRs from tumor specimens by high-throughput single-cell sequencing

Lu Y, Zheng Z, Lowery FJ, et al

PubMed Link

EML4-ALK induces cellular senescence in mortal normal human cells and promotes anchorage-independent growth in hTERT-transduced normal human cells

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.

PubMed Link

Dynamics of replication origin over-activation

Fu, H., Redon, C.E., Thakur, B.L. et al.

PubMed Link

Characterization of genetically defined sporadic and hereditary type 1 papillary renal cell carcinoma cell lines

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PubMed Link

Comprehensive characterization of Alu-mediated breakpoints in germline VHL gene deletions and rearrangements in patients from 71 VHL families

Vocke CD, Ricketts CJ, Schmidt LS, Ball MW, Middelton LA, Zbar B, Marston Linehan W.

PubMed Link

CTCF is a Barrier for Totipotent-like Reprogramming

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.

PubMed Link

The ETS Transcription Factor ERF Controls the Exit from the Embryonic Rosette-stage of Pluripotency

Vega-Sendino M, Olbrich T, Tillo D, Tran AD, Domingo CM, Franco M, FitzGerald PC, Kruhlak MJ and Ruiz S.

Direct Link

Mitochondrial DNA alterations underlie an irreversible shift to aerobic glycolysis in fumarate hydratase-deficient renal cancer

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.

PubMed Link

Multifocal Renal Cell Carcinomas With Somatic IDH2 Mutation: Report of a Previously Undescribed Neoplasm

Merino MJ, Ricketts CJ, Moreno V, Yang Y, Fan TWM, Lane AN, Meltzer PS, Vocke CD, Crooks DR, Linehan WM.

PubMed Link

The intrinsic kinase activity of BRD4 spans its BD2-B-BID domains

Jocelyn D. Weissman, Amit K. Singh, Ballachanda N. Devaiah, Peter Schuck, Ross C. LaRue, Dinah S. Singer

PubMed Link


Image-based pooled whole genome CRISPR screening for Parkin and TFEB subcellular localization

41. Gil Kanfer, Shireen A. Sarraf, Yaakov Maman, Heather Baldwin, Kory R. Johnson, Michael E. Ward, Martin Kampmann, Jennifer Lippincott-Schwartz, Richard J. Youle

PubMed Link

Metastatic and recurrent adrenocortical cancer is not defined by its genomic landscape

Fojo, T., Huff, L., Litman, T. et al.

PubMed Link

Somatic Mutations in UBA1 and Severe Adult-Onset Autoinflammatory Disease

39. 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

PubMed Link

Novel renal medullary carcinoma cell lines, UOK353 and UOK360, provide preclinical tools to identify new therapeutic treatments

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

PubMed Link

TRF2-mediated telomere protection is dispensable in pluripotent stem cells

Markiewicz-Potoczny, M., Lobanova, A., Loeb, A.M. et al.

PubMed Link

Clinical and Molecular Characterization of Microphthalmia-Associated Transcription Factor (MITF)-Related Renal Cell Carcinoma

Martin Lang ,Cathy D. Vocke ,Christopher J. Ricketts ,Adam R. Metwalli , Mark W. Ball , Laura S. Schmidt , W. Marston Linehan

PubMed Link

A germline 1;3 translocation disrupting the VHL gene: a novel genetic cause for von Hippel-Lindau

Ricketts CJ, Vocke CD, Lang M, Chen X, Zhao Y, Tran B, Tandon M, Schmidt LS, Ball MW, Linehan WM.

PubMed Link

Repeat expansions confers WRN dependence in microsatellite unstable cancers

Niek van Wietmarschen et al.

PubMed Link

Dissecting transcriptional amplification by MYC

Nie Z, Guo C, Das SK, et al.

PubMed Link

53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination

Callen et al.

PubMed Link