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Congratulations to the following authors for their recent publications featuring data derived from the CCR Genomics Core.
2023
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 LinkExtrachromosomal 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 LinkA 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 Link2022
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 LinkInternal 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 LinkSingle-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 LinkAnti-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 LinkThe 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 LinkOMA1 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 LinkDifferential 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 LinkSpatial 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 LinkMcm2 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 LinkDependence 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 LinkNuRD 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 LinkThe 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 LinkSystematic identification of molecular mediators of interspecies sensing in a community of 2 frequently coinfecting bacterial pathogens
Zarrella, T. M., & Khare, A.
PubMed LinkConvergence 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 LinkASXL1 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 Link2021
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 LinkRepeated strand invasion and extensive branch migration are hallmarks of meiotic recombination
Ahuja, J. S., Harvey, C. S., Wheeler, D. L., & Lichten, M
PubMed LinkNuclear 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 LinkDirect identification of neoantigen-specific TCRs from tumor specimens by high-throughput single-cell sequencing
Lu Y, Zheng Z, Lowery FJ, et al
PubMed LinkEML4-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 LinkCharacterization of genetically defined sporadic and hereditary type 1 papillary renal cell carcinoma cell lines
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PubMed LinkComprehensive 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 LinkCTCF 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 LinkThe 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 LinkMitochondrial 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 LinkMultifocal 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 LinkThe 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 Link2020
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 LinkMetastatic and recurrent adrenocortical cancer is not defined by its genomic landscape
Fojo, T., Huff, L., Litman, T. et al.
PubMed LinkSomatic 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 LinkNovel 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 LinkTRF2-mediated telomere protection is dispensable in pluripotent stem cells
Markiewicz-Potoczny, M., Lobanova, A., Loeb, A.M. et al.
PubMed LinkClinical 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 LinkA 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 Link53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination
Callen et al.
PubMed Link