Publications
Core Contributed Publications
As an open-access Core, we do not require investigators to list us as collaborators in order to use our facility, nor do we request authorship on publications. However, we do ask that users acknowledge the facility if data generated by the Core is used in a publication, although this is not mandatory. In some instances, staff have been included as authors when their contributions involved extensive collaboration (bold).
For a complete list of publications supported by Core staff, please visit the following link https://pubmed.ncbi.nlm.nih.gov/collections/65073972/?sort=pubdate
Publications by Year
2025
S. S. Maligireddy, M. D. Mandler, J. C. Lunger, M. Yuen, S. Kulkarni, A. R. Perez, C. M. Fitzsimmons, D. R. Crooks, R. Chari, W. M. Linehan and P. J. Batista. Targeting a pathogenic cryptic exon that drives HLRCC to induce exon skipping.
C. R. Ross, K. Szczepanek, J. Sanford, G. Needle, T. Qiu, L. Pearce, M. P. Lee and K. W. Hunter. Genetic background and oncogenic driver determines the genomic evolution and transcriptomics of mammary tumor metastasis.
C. M. Sayers, M. B. Carter, H. Lei, A. Mendoza, S. Shema, X. Zhang, K. Wilson, L. Chen, C. Klumpp-Thomas, C. J. Thomas, C. M. Heske and J. F. Shern. The Kinase Inhibitor GNF-7 Is Synthetically Lethal in Topoisomerase 1-Deficient Ewing Sarcoma.
K. Mazan-Mamczarz, D. Tsitsipatis, B. G. Childs, A. E. Carr, C. R. Dos Santos, C. Anerillas, B. Romero, J. M. Gregg, C. Henry-Smith, A. N. Okereke, M. Michel, R. Munk, J. L. Martindale, Y. Piao, J. Fan, M. O. Hernandez, N. Kedei, M. L. Viacheslavov, M. M. F. Wong, O. V. Fedorova, M. Batish, S. De, D. J. Baker, M. Gorospe and A. B. Herman. Single-cell and spatial transcriptomics map senescent vascular cells in arterial remodeling during atherosclerosis in mice.
R. Singh, A. Archibald, X. L. Li, R. Kumar, S. Das, E. C. Pehrsson, P. X. Zhao, X. Wen, R. Chari, I. Grammatikakis and A. Lal. Identification of a Novel Intracellular Function of the Secreted Ribonuclease RNASE1 in Inhibiting Gene Expression.
D. J. Wisniewski, D. Voeller, Y. A. Addissie, S. K. Deshmukh, S. Wu, M. B. Lustberg, D. Wangsa, D. Wangsa, K. Heselmeyer-Haddad, G. W. Sledge and S. Lipkowitz. Dual inhibition of EGFR and PI3Kinase signaling in EGFR amplified triple negative breast cancer cells induces apoptosis and reduces tumor growth.
R. Trehan, P. Huang, X. B. Zhu, X. Wang, M. Soliman, D. Strepay, A. Nur, N. Kedei, M. Arhin, S. Ghabra, F. Rodriguez-Matos, M. R. Benmebarek, C. Ma, F. Korangy and T. F. Greten. SPP1 + macrophages cause exhaustion of tumor-specific T cells in liver metastases.
K. A. Nguyen, Z. Liu, J. S. Davies, C. P. McIntosh, L. M. Draper, S. M. Norberg, Z. Rae, S. R. Achar, G. Altan-Bonnet, L. Zhang, X. Wu, T. J. Meyer, M. C. Kelly, N. Taylor, C. S. Hinrichs and K. Ishii. CD22 TCR-engineered T cells exert antileukemia cytotoxicity without causing inflammatory responses.
Y. Ueda, S. Omiya, J. Pinney, M. A. Bylicky and M. J. Aryankalayil. Liver quad culture chip as a model for radiation injury research.
J. Yan, X. Chen, S. Choksi and Z. G. Liu. TGFB signaling induces mitophagy via PLSCR3-mediated cardiolipin externalization in conjunction with a BNIP3L/NIX-, BNIP3-, and FUNDC1-dependent mechanism.
M. R. Benmebarek, C. Oguz, M. Seifert, B. Ruf, Y. Myojin, K. C. Bauer, P. Huang, C. Ma, M. Villamor-Paya, F. Rodriguez-Matos, M. Soliman, R. Trehan, C. Monge, C. Xie, D. E. Kleiner, B. J. Wood, E. B. Levy, A. Budhu, N. Kedei, C. T. Mayer, X. W. Wang, J. Lack, W. Telford, F. Korangy and T. F. Greten. Anti-vascular endothelial growth factor treatment potentiates immune checkpoint blockade through a BAFF- and IL-12-dependent reprogramming of the TME.
C. Stathopoulou, M. Zhao, Q. Jiang, J. Hong, J. Bian, J. Zhang, M. Ho and R. Hassan. Temporal mapping of the anti-tumor effects of nanobody-based MSLN.CAR-T cell therapy in metastatic solid tumors.
C. B. Khandwala, P. Sarkar, H. B. Schmidt, M. Ma, G. V. Pusapati, F. Lamoliatte, M. Kinnebrew, B. B. Patel, D. Tillo, A. M. Lebensohn and R. Rohatgi. Direct ionic stress sensing and mitigation by the transcription factor NFAT5.
R. Sebastian, E. G. Sun, M. Fedkenheuer, H. Fu, S. Jung, B. L. Thakur, C. E. Redon, G. Pegoraro, A. D. Tran, J. M. Gross, S. Mosavarpour, N. A. Kusi, A. Ray, A. Dhall, L. S. Pongor, R. Casellas and M. I. Aladjem. Mechanism for local attenuation of DNA replication at double-strand breaks.
T. McErlain, M. J. Glass, E. C. McCulla, C. A. Madden, L. E. Ziemer, K. E. Overdahl, A. K. Jarmusch, M. J. Kruhlak, A. T. Chesler, H. H. Yang, M. P. Lee, C. M. Branco and M. Murgai. Pericyte-tumor crosstalk facilitates metastatic tumor cell latency through PIEZO1-activated lysophospholipid transfer.
R. R. Xiang, S. A. Lee, C. F. Tyndall, A. R. Bhatia, J. Yin, C. Singler, B. J. Hauk, M. P. Kipp and D. Y. Takeda. CRISPR screening identifies regulators of enhancer-mediated androgen receptor transcription in advanced prostate cancer.
J. R. Hoskins, A. C. Wickramaratne, C. P. Jewell, L. M. Jenkins and S. Wickner. Hsp90, DnaK, and ClpB collaborate in protein reactivation.
E. Edmondson, T. Kimura, E. Hwang, M. Kim, A. Warner, Y. Zhu, L. Zhao, Y. Yu, X. Zhu, M. Hernandez, N. Kedei and S. Y. Cheng. TRalpha1 mutant suppresses KLF9 to cause endometrial metaplasia with ectopic IL-33 expression leading to uterine fibrosis and infertility.
H. Li, T. Furusawa, R. Cavero, Y. Xiao, R. Chari, X. Wu, D. Sun, O. Hartmann, A. Dhall, R. Holewinski, T. Andresson, B. Karim, M. Villamor-Payà, D. Gallardo, C.-P. Day, L. R. Pal, N. U. Nair, E. Ruppin, M. I. Aladjem, Y. Pommier, M. E. Diefenbacher, J. M. Lim, R. L. Levine, T. H. Stracker and U. Weyemi. Metabolic dependency mapping identifies Peroxiredoxin 1 as a driver of resistance to ATM inhibition.
C. R. Ross, K. Szczepanek, J. Sanford, T. Qiu, L. Pearce and K. W. Hunter. Investigating the genomic landscape of mouse models of breast cancer metastasis.
O. Uher, K. H. Vanova, R. Labitt, K. Petrlakova, J. Ye, H. Wang, M. Masarik, M. Jakubek, J. Zenka, Z. Zhuang and K. Pacak. Neoadjuvant Intratumoral MBT(A) Immunotherapy Prevents Distant Metastases and Recurrence in Murine Models.
J. S. Rosenblum, Y. Cole, D. Dang, P. P. Lookian, H. Alkaissi, M. Patel, A. J. Cappadona, A. Jha, N. Edwards, D. R. Donahue, J. Munasinghe, H. Wang, R. H. Knutsen, A. S. Pappo, R. M. Lechan, B. A. Kozel, J. G. Smirniotopoulos, H. J. Kim, A. Vortmeyer, M. Miettinen, J. D. Heiss, Z. Zhuang and K. Pacak. Head and neck paraganglioma in Pacak-Zhuang syndrome.
2024
K. Y. Lee, E. L. Beatson, M. A. Knechel, E. R. Sommer, G. C. Napoli, E. N. Risdon, A. F. Leon, R. D. Depaz, J. D. Strope, D. K. Price, C. H. Chau and W. D. Figg. Detection of Extracellular Vesicle-Derived RNA as Potential Prostate Cancer Biomarkers: Role of Cancer-type SLCO1B3 and ABCC3.
A. Li, J. C. Hancock, M. Quezado, S. Ahn, N. Briceno, O. Celiku, S. Ranjan, O. Aboud, N. Colwell, S. A. Kim, E. Nduom, S. Kuhn, D. M. Park, E. Vera, K. Aldape, T. S. Armstrong and M. R. Gilbert. TGF-beta and BMP signaling are associated with the transformation of glioblastoma to gliosarcoma and then osteosarcoma.
R. Amin, N.-H. Ha, T. Qiu, R. Holewinski, K. C. Lam, A. Lopès, H. Liu, A. D. Tran, M. P. Lee, S. T. Gamage, T. Andresson, R. S. Goldszmid, J. L. Meier and K. W. Hunter. Loss of NAT10 disrupts enhancer organization via p300 mislocalization and suppresses transcription of genes necessary for metastasis progression.
K. R. Pasterczyk, X. L. Li, R. Singh, M. S. Zibitt, C. C. R. Hartford, L. Pongor, L. M. Jenkins, Y. Hu, P. X. Zhao, B. R. Muys, S. Kumar, N. Roper, M. I. Aladjem, Y. Pommier, I. Grammatikakis and A. Lal. Staufen1 Represses the FOXA1-Regulated Transcriptome by Destabilizing FOXA1 mRNA in Colorectal Cancer Cells.
H. D. Folco, H. Xiao, D. Wheeler, H. Feng, Y. Bai and S. I. S. Grewal. The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity.
W. Y. So, B. Johnson, P. B. Gordon, K. S. Bishop, H. Gong, H. A. Burr, J. R. Staunton, C. Handler, R. Sood, G. Scarcelli and K. Tanner. Macrophage mediated mesoscale brain mechanical homeostasis mechanically imaged via optical tweezers and Brillouin microscopy in vivo.
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. Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma.
S. Sundara Rajan, V. J. Ebegboni, P. Pichling, K. R. Ludwig, T. L. Jones, R. Chari, A. Tran, M. J. Kruhlak, J. Loncarek and N. J. Caplen. Endogenous EWSR1 Exists in Two Visual Modalities That Reflect Its Associations with Nucleic Acids and Concentration at Sites of Active Transcription.
D. Williams, L. M. Glasstetter, T. T. Jong, A. Kapoor, S. Zhu, Y. Zhu, A. Gehrlein, D. J. Vocadlo, R. Jagasia, J. J. Marugan, E. Sidransky, M. J. Henderson and Y. Chen. Development of quantitative high-throughput screening assays to identify, validate, and optimize small-molecule stabilizers of misfolded beta-glucocerebrosidase with therapeutic potential for Gaucher disease and Parkinson’s disease.
A. R. Foley, V. Bolduc, F. Guirguis, S. Donkervoort, Y. Hu, R. Orbach, R. M. McCarty, A. Sarathy, G. Norato, B. B. Cummings, M. Lek, A. Sarkozy, R. J. Butterfield, J. Kirschner, A. Nascimento, D. N. Benito, S. Quijano-Roy, T. Stojkovic, L. Merlini, G. Comi, M. Ryan, D. McDonald, P. Munot, G. Yoon, E. Leung, E. Finanger, M. E. Leach, J. Collins, C. Tian, P. Mohassel, S. B. Neuhaus, D. Saade, B. T. Cocanougher, M. L. Chu, M. Scavina, C. Grosmann, R. Richardson, B. D. Kossak, S. M. Gospe, Jr., V. Bhise, G. Taurina, B. Lace, M. Troncoso, M. Shohat, A. Shalata, S. H. S. Chan, M. Jokela, J. Palmio, G. Haliloglu, C. Jou, C. Gartioux, H. Solomon-Degefa, C. D. Freiburg, A. Schiavinato, H. Zhou, S. Aguti, Y. Nevo, I. Nishino, C. Jimenez-Mallebrera, S. R. Lamande, V. Allamand, F. Gualandi, A. Ferlini, D. G. MacArthur, S. D. Wilton, R. Wagener, E. Bertini, F. Muntoni and C. G. Bonnemann. The recurrent deep intronic pseudoexon-inducing variant COL6A1 c.930+189C>T results in a consistently severe phenotype of COL6-related dystrophy: Towards clinical trial readiness for splice-modulating therapy.
Y. T. Shirai, N. Hoshi, J. M. Ward, H. Liu, R. E. Cachau, M. P. Lee and S. Kimura. Establishment and Characterization of Amitrole-Induced Mouse Thyroid Adenomatous Nodule-Derived Cell Lines.
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. The homeobox transcription factor DUXBL controls exit from totipotency.
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. The Methyltransferases METTL7A and METTL7B Confer Resistance to Thiol-Based Histone Deacetylase Inhibitors.
E. M. Rosenberg, Jr., X. Jian, O. Soubias, R. A. Jackson, E. Gladu, E. Andersen, L. Esser, A. J. Sodt, D. Xia, R. A. Byrd and P. A. Randazzo. Point mutations in Arf1 reveal cooperative effects of the N-terminal extension and myristate for GTPase-activating protein catalytic activity.
J. Zhan, A. Zeher, R. Huang, W. K. Tang, L. M. Jenkins and D. Xia. Conformations of Bcs1L undergoing ATP hydrolysis suggest a concerted translocation mechanism for folded iron-sulfur protein substrate.
V. Balachandra, R. L. Shrestha, C. M. Hammond, S. Lin, I. A. Hendriks, S. C. Sethi, L. Chen, S. Sevilla, N. J. Caplen, R. Chari, T. S. Karpova, K. McKinnon, M. A. Todd, V. Koparde, K. C. Cheng, M. L. Nielsen, A. Groth and M. A. Basrai. DNAJC9 prevents CENP-A mislocalization and chromosomal instability by maintaining the fidelity of histone supply chains.
C. E. Grant, A. L. Flis, L. Toulabi, A. Zingone, E. Rossi, K. Aploks, H. Sheppard and B. M. Ryan. DRD1 suppresses cell proliferation and reduces EGFR activation and PD-L1 expression in NSCLC.
A. V. Mylvara, A. L. Gibson, T. Gu, C. D. Davidson, A. A. Incao, K. Melnyk, D. Pierre-Jacques, S. M. Cologna, C. P. Venditti, F. D. Porter and W. J. Pavan. Optimization of systemic AAV9 gene therapy in Niemann-Pick disease type C1 mice.
M. L. Beshiri, B. J. Capaldo, R. Lake, A. T. Ku, D. Burner, C. M. Tice, C. Tran, J. Kostas, A. N. Alilin, J. Yin, S. Agarwal, S. A. Morris, F. H. Karzai, T. L. Lotan, W. L. Dahut, A. G. Sowalsky and K. Kelly. Stem cell dynamics and cellular heterogeneity across lineage subtypes of castrate-resistant prostate cancer.
Relier S, Schiffers S, Beiki H, Oberdoerffer S. Enhanced ac4C detection in RNA via chemical reduction and cDNA synthesis with modified dNTPs.
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. Microenvironment shapes small-cell lung cancer neuroendocrine states and presents therapeutic opportunities.
K. Moissoglu, T. Wang, A. N. Gasparski, M. Stueland, E. L. Paine, L. Jenkins and S. Mili. A KIF1C-CNBP motor-adaptor complex for trafficking mRNAs to cell protrusions.
D. Mukherjee, R. A. Lawal, C. D. Fitzhugh, C. S. Hourigan and L. W. Dillon. TP53 mutation screening for patients at risk of myeloid malignancy.
A. M. Martini, S. A. Alexander and A. Khare. Mutations in the Staphylococcus aureus Global Regulator CodY Confer Tolerance to an Interspecies Redox-Active Antimicrobial.
B. T. Donovan, B. Wang, G. R. Garcia, S. M. Mount and D. R. Larson. Real-Time Visualization of Spliceosome Assembly Reveals Basic Principles of Splice Site Selection.
S. M. Hammoudeh, Y. Ng, B. R. Wei, T. D. Madsen, M. P. Yadav, R. M. Simpson, R. Weigert and P. A. Randazzo. Tongue orthotopic xenografts to study fusion-negative rhabdomyosarcoma invasion and metastasis in live animals.
Mandler, M. D., Maligireddy, S. S., Guiblet, W. M., Fitzsimmons, C. M., McDonald, K. S., Warrell, D. L., & Batista, P. J. The modification landscape of Pseudomonas aeruginosa tRNAs.
R. M. Bertoli, Y. J. Chung, M. J. Difilippantonio, A. Wokasch, M. R. B. Marasco, H. Klimaszewski, S. Gammell, Y. J. Zhu, R. L. Walker, D. Cao, A. Khanna, M. J. Walter, J. H. Doroshow, P. S. Meltzer and P. D. Aplan. The DNA Methyltransferase Inhibitor 5-Aza-4′-thio-2′-Deoxycytidine Induces C>G Transversions and Acute Lymphoid Leukemia Development.
M. Mizunuma, C. E. Redon, L. K. Saha, A. D. Tran, A. Dhall, R. Sebastian, D. Taniyama, M. J. Kruhlak, W. C. Reinhold, N. Takebe and Y. Pommier. Acetalax (Oxyphenisatin Acetate, NSC 59687) and Bisacodyl Cause Oncosis in Triple-Negative Breast Cancer Cell Lines by Poisoning the Ion Exchange Membrane Protein TRPM4.
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. Structure and repair of replication-coupled DNA breaks.
Q. Yao, L. Zhu, Z. Shi, S. Banerjee and C. Chen. Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression.
J. Lyu, X. Xu and C. Chen. A convenient single-cell newly synthesized transcriptome assay reveals gene expression dynamics during early-stage T-cell activation.
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. Targeting SWI/SNF ATPases reduces neuroblastoma cell plasticity.
D. L. Warrell, T. M. Zarrella, C. Machalek and A. Khare. Interspecies surfactants serve as public goods enabling surface motility in Pseudomonas aeruginosa.
O. Uher, K. Hadrava Vanova, K. Petrlakova, R. Labitt, R. Lencova, A. Frejlachova, J. Ye, H. Wang, M. Masarik, J. Zenka, Z. Zhuang and K. Pacak. Role of B cells in intratumoral MBTA immunotherapy of murine pheochromocytoma model.
T. B. Updegrove, T. Delerue, V. Anantharaman, H. Cho, C. Chan, T. Nipper, H. Choo-Wosoba, L. M. Jenkins, L. Zhang, Y. Su, H. Shroff, J. Chen, C. A. Bewley, L. Aravind and K. S. Ramamurthi. Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity.
L. Miao, L. Collado, S. Barkdull, Y. Saito, J.-H. Jo, J. Han, S. Dell’Orso, M. C. Kelly, S. Conlan, H. H. Kong and I. Brownell. Estimating and correcting index hopping misassignments in single-cell RNA-seq data.
T. Delerue, T. B. Updegrove, S. Chareyre, V. Anantharaman, M. C. Gilmore, L. M. Jenkins, D. L. Popham, F. Cava, L. Aravind and K. S. Ramamurthi. Bacterial spore surface nanoenvironment requires a AAA+ ATPase to promote MurG function.
C. D. Vocke, C. J. Ricketts, S. Pack, M. Raffeld, S. Hewitt, A. P. Lebensohn, L. O’Brien, R. Gautam, K. Reynolds, L. S. Schmidt, K. Choo, A. Kenigsberg, S. Gurram, E. Y. Chew, N. Nilubol, P. Chittaboina, M. J. Merino, M. W. Ball and W. M. Linehan. A novel pathogenic germline chromosome 3 inversion in von Hippel-Lindau disease.
U. Lee, L. Szabova, V. J. Collins, M. Gordon, K. Johnson, D. Householder, S. Jorgensen, L. Lu, L. Bassel, F. Elloumi, C. J. Peer, A. E. Nelson, S. Varriano, S. Varma, R. D. Roberts, Z. W. Ohler, W. D. Figg, S. K. Sharan, Y. Pommier and C. M. Heske. Treatment with novel topoisomerase inhibitors in Ewing sarcoma models reveals heterogeneity of tumor response.
G. J. Starrett, B. C. Baikie, B. K. Stoff, H. E. Grossniklaus, I. Van Buren, E. G. Berry, R. A. Novoa, K. E. Rieger, K. Y. Sarin, C. F. Lynch, M. C. Royer, M. L. Piaskowski, I. Brownell, E. Y. Chu, R. Godse, S. C. Chen, K. J. Yu, A. M. Goldstein, E. A. Engels and M. R. Sargen. Multiomics Profiling Distinguishes Sebaceous Carcinoma from Benign Sebaceous Neoplasms and Provides Insight into the Genetic Evolution of Sebaceous Carcinogenesis.
K. E. Hebron, O. L. Perkins, A. Kim, X. Jian, S. A. Girald-Berlingeri, H. Lei, J. F. Shern, E. A. Conner, P. A. Randazzo and M. E. Yohe. ASAP1 and ARF1 regulate myogenic differentiation in rhabdomyosarcoma by modulating TAZ activity.
S. Li, K. Fatema, S. Nidharshan, A. Singh, P. S. Rajagopal, D. Notani, D. Y. Takeda and S. Hannenhalli. Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry.
J. Sipola, A. D. Munzur, E. M. Kwan, C. C. Y. Seo, B. J. Hauk, K. Parekh, Y. J. R. Liao, C. Q. Bernales, G. Donnellan, I. Bloise, E. Fung, S. W. S. Ng, G. Wang, G. Vandekerkhove, M. Nykter, M. Annala, C. Maurice-Dror, K. N. Chi, C. Herberts, A. W. Wyatt and D. Y. Takeda. Plasma cell-free DNA chromatin immunoprecipitation profiling depicts phenotypic and clinical heterogeneity in advanced prostate cancer.
Z. Duan, D. Li, N. Li, S. Lin, H. Ren, J. Hong, C. S. Hinrichs and M. Ho. CAR-T cells based on a TCR mimic nanobody targeting HPV16 E6 exhibit antitumor activity against cervical cancer.
2023
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.
2022
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.
2021
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.
2020
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.