Publications

2024

Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma

Fitzsimmons, C. M., Mandler, M. D., Lunger, J. C., Chan, D., Maligireddy, S. S., Schmiechen, A. C., Gamage, S. T., Link, C., Jenkins, L. M., Chan, K., Andresson, T., Crooks, D. R., Meier, J. L., Linehan, W. M., & Batista, P. J.

Microenvironment shapes small-cell lung cancer neuroendocrine states and presents therapeutic opportunities.

Desai P, Takahashi N, Kumar R, Nichols S, Malin J, Hunt A, Schultz C, Cao Y, Tillo D, Nousome D, Chauhan L, Sciuto L, Jordan K, Rajapakse V, Tandon M, Lissa D, Zhang Y, Kumar S, Pongor L, Singh A, Schroder B, Sharma AK, Chang T, Vilimas R, Pinkiert D, Graham C, Butcher D, Warner A, Sebastian R, Mahon M, Baker K, Cheng J, Berger A, Lake R, Abel M, Krishnamurthy M, Chrisafis G, Fitzgerald P, Nirula M, Goyal S, Atkinson D, Bateman NW, Abulez T, Nair G, Apolo A, Guha U, Karim B, El Meskini R, Ohler ZW, Jolly MK, Schaffer A, Ruppin E, Kleiner D, Miettinen M, Brown GT, Hewitt S, Conrads T, Thomas A.Cell Rep Med. 2024 Jun 18;5(6):101610. doi: 10.1016/j.xcrm.2024.101610.

The modification landscape of Pseudomonas aeruginosa tRNAs

Mandler, M. D., Maligireddy, S. S., Guiblet, W. M., Fitzsimmons, C. M., McDonald, K. S., Warrell, D. L., & Batista, P. J.

The Methyltransferases METTL7A and METTL7B Confer Resistance to Thiol-Based Histone Deacetylase Inhibitors

Robey, R. W., Fitzsimmons, C. M., Guiblet, W. M., Frye, W. J. E., González Dalmasy, J. M., Wang, L., Russell, D. A., Huff, L. M., Perciaccante, A. J., Ali-Rahmani, F., Lipsey, C. C., Wade, H. M., Mitchell, A. V., Maligireddy, S. S., Terrero, D., Butcher, D., Edmondson, E. F., Jenkins, L. M., Nikitina, T., Zhurkin, V. B., … Batista, P. J.

Targeting SWI/SNF ATPases reduces neuroblastoma cell plasticity

Xu, M., Hong, J. J., Zhang, X., Sun, M., Liu, X., Kang, J., Stack, H., Fang, W., Lei, H., Lacoste, X., Okada, R., Jung, R., Nguyen, R., Shern, J. F., Thiele, C. J., & Liu, Z.

Structure and repair of replication-coupled DNA breaks

Pavani R, Tripathi V, Vrtis KB, Zong D, Chari R, Callen E, Pankajam AV, Zhen G, Matos-Rodrigues G, Yang J, Wu S, Reginato G, Wu W, Cejka P, Walter JC, Nussenzweig A.

Enhanced ac4C detection in RNA via chemical reduction and cDNA synthesis with modified dNTPs

Relier S, Schiffers S, Beiki H, Oberdoerffer S.

The homeobox transcription factor DUXBL controls exit from totipotency

Vega-Sendino, M., Lüttmann, F. F., Olbrich, T., Chen, Y., Kuenne, C., Stein, P., Tillo, D., Carey, G. I., Zhong, J., Savy, V., Radonova, L., Lu, T., Saykali, B., Kim, K. P., Domingo, C. N., Schüler, L., Günther, S., Bentsen, M., Bosnakovski, D., Schöler, H., … Ruiz, S.

2023

Tumor-associated macrophages trigger MAIT cell dysfunction at the HCC invasive margin

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.

Decoding complexity in biomolecular recognition of DNA i-motifs with microarrays.

Yazdani K, Seshadri S, Tillo D, Yang M, Sibley CD, Vinson C, Schneekloth JS Jr.Nucleic Acids Res. 2023 Dec 11;51(22):12020-12030. doi: 10.1093/nar/gkad981.PMID: 37962331

Comprehensive mapping of cell fates in microsatellite unstable cancer cells support dual targe6ng of WRN and ATR

Zong D, Koussa NC, Cornwell JA, Pankajam AV, Kruhlak MJ, Wong N, Chari R, Cappell SD, Nussenzweig A.

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

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.

Cryptic splice mutation in the fumarate hydratase gene in patients with clinical manifestations of Hereditary Leiomyomatosis and Renal Cell Cancer

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.

High-throughput and targeted drug screens identify pharmacological candidates against MiT-translocation renal cell carcinoma

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.

A novel GATA2 distal enhancer mutation results in the MonoMAC syndrome in 2 second cousins

West RR, Bauer TR, Tuschong LM, Embree LJ, Calvo KR, Tillo D, Davis J, Holland SM, Hickstein DD.

Direct ionic stress sensing and mitigation by the transcription factor NFAT5

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.

mRNA location and translation rate determine protein targeting to dual destinations

Gasparski AN, Moissoglu K, Pallikkuth S, Meydan S, Guydosh NR, Mili S

Efflux pump gene amplifications bypass necessity of multiple target mutations for resistance against dual-targeting antibiotic.

Silva, K. P. T., Sundar, G., & Khare, A.

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

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.

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.

2022

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.

Mutant Idh2 Cooperates with a NUP98-HOXD13 Fusion to Induce Early Immature Thymocyte Precursor ALL

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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

2021

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.

Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182.

Ray S, Tillo D, Assad N, Ufot A, Porollo A, Durell SR, Vinson C.ACS Omega. 2021 Dec 28;7(1):129-139. doi: 10.1021/acsomega.1c04148. eCollection 2022 Jan 11.PMID: 35036684

Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element.

Liu X, Weikum ER, Tillo D, Vinson C, Ortlund EA.Nucleic Acids Res. 2021 Sep 7;49(15):8923-8933. doi: 10.1093/nar/gkab605.PMID: 34289059

REL Domain of NFATc2 Binding to Five Types of DNA Using Protein Binding Microarrays

Ray S, Tillo D, Durell SR, Khund-Sayeed S, Vinson C.ACS Omega. 2021 Feb 2;6(6):4147-4154. doi: 10.1021/acsomega.0c04069. eCollection 2021 Feb 16.PMID: 33644537

Genetically engineered myeloid cells rebalance the core immune suppression program in metastasis.

9. 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.

Improved systemic AAV gene therapy with a neurotrophic capsid in Niemann-Pick disease type C1 mice

25. 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.

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

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

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.

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

Lu Y, Zheng Z, Lowery FJ, et al

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.

Dynamics of replication origin over-activation

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

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

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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.

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.

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.

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.

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.

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

2020

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

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

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.

Ray S, Tillo D, Ufot A, Assad N, Durell S, Vinson C.Biochemistry. 2020 Sep 29;59(38):3529-3540. doi: 10.1021/acs.biochem.0c00475. Epub 2020 Sep 20.PMID: 32902247

Custom G4 Microarrays Reveal Selective G-Quadruplex Recognition of Small Molecule BMVC: A Large-Scale Assessment of Ligand Binding Selectivity.

Wu G, Tillo D, Ray S, Chang TC, Schneekloth JS Jr, Vinson C, Yang D.Molecules. 2020 Jul 30;25(15):3465. doi: 10.3390/molecules25153465.PMID: 32751510

Custom DNA Microarrays Reveal Diverse Binding Preferences of Proteins and Small Molecules to Thousands of G-Quadruplexes.

Ray S, Tillo D, Boer RE, Assad N, Barshai M, Wu G, Orenstein Y, Yang D, Schneekloth JS Jr, Vinson C.ACS Chem Biol. 2020 Apr 17;15(4):925-935. doi: 10.1021/acschembio.9b00934. Epub 2020 Apr 7.PMID: 32216326

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

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

Somatic Mutations in UBA1 and Severe Adult-Onset Autoinflammatory Disease

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

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

TRF2-mediated telomere protection is dispensable in pluripotent stem cells

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

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

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.

Repeat expansions confers WRN dependence in microsatellite unstable cancers

Niek van Wietmarschen et al.

Dissecting transcriptional amplification by MYC

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

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

Callen et al.