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Publications

Increasing Area Deprivation Index negatively impacts ovarian cancer survival Hufnagel DH, Khabele D, Yull FE, Hull PC, Schildkraut J, Crispens MA, Beeghly-Fadiel A. Cancer Epidemiol. 2021 Aug 23;74:102013. PMID: 34438316

Induction of apically mistrafficked epiregulin disrupts epithelial polarity via aberrant EGFR signaling Singh B, Bogatcheva G, Krystofiak E, McKinley ET, Hill S, Rose KL, Higginbotham JN, Coffey RJ. J Cell Sci. 2021 Aug 18:jcs.255927. PMID: 34406412

Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy Barone SM, Paul AG, Muehling LM, Lannigan JA, Kwok WW, Turner RB, Woodfolk JA, Irish JM.
Elife. 2021 Aug 5;10:e64653. PMID: 34350827

MuSyC is a consensus framework that unifies multi-drug synergy metrics for combinatorial drug discovery Wooten DJ, Meyer CT, Lubbock ALR, Quaranta V, Lopez CF. Nat Commun. 2021 Jul 29;12(1):4607. PMID: 34326325

Evaluation of Thyroid Nodule Malignant Neoplasms and Obesity Among Children and Young Adults. Carlos Ortega, Jean-Nicole Gallant, Sheau-Chiann Chen, Fei Ye, Huiing Want, Ryan Belcher, Vivian Weiss. Jama Netw Open. 2021 July 1;4 (7):e2116369.

Tissue-specific expression of p73 ad p63 isoforms in human tissues
Clayton Marshall, J Scott Beeler, Brian Lehmann, Paula Gonzalez-Ericsson, Jennifer Pietenpol, et al. Cell Death & Disease Article # 745 (2021)

CMV exposure drives long-term CD57+ CD4 memory T cell inflation following allogeneic stem cell transplant. Yeh AC, Varelias A, Reddy A, et  al.  Blood. 2021 Jun 3:blood.2020009492.

Targeted Deletion of CXCR2 in Myeloid Cells Alters the Tumor Immune Environment to Improve Antitumor Immunity Yang J, Yan C, Vilgelm A, et al. Cancer Immunol Res. 2021 Feb;9 92 0: 200-213.

Thunor: visualization and analysis of high-throughput dose-response datasets. Lubbock ALR, Harris LA, Quaranta V, et al.  Nucleic Acids Res. 2021 Jul 2;49(W1):W633-W640.

Unsupervised logic-based mechanism inference for network-driven biological processes. Prugger M, Einkemmer L, Beik SP, et al.  PLoS Comput Biol. 2021 Jun 2;17(6):e1009035.

Effect of Intravenous Chemotherapy Regimen on Globe Salvage Success Rates for Retinoblastoma Based on Disease Class-A Meta-Analysis
Daniels AB, Patel SN, Milam RW, et al. Cancers (Basel). 2021 May 6;13(9):2216.

Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages. Obradovic A, Chowdhury N, Haake SM, et al. Cell. 2021 May 27;184(11):2988-3005.e16.

Prostate cancer risk variants of the HOXB genetic locus
Dupont WD, Breyer JP, Johnson SH, et al.
Sci Rep. 2021 May 31;11(1):11385.

Inhibition of the PI3K/mTOR Pathway in Breast Cancer to Enhance Response to Immune Checkpoint Inhibitors in Breast Cancer.
Yan C, Yang J, Saleh N, et al. Int J Mol Sci. 2021 May 14;22(10):5207.

The Complex Integration of T-cell Metabolism and Immunotherapy.
Madden MZ, Rathmell JC. Cancer Discovery 2021 July;11(7):1636-1643.

Chemoprevention Against Gastric Cancer  Shah SC, Peek RM Jr. Gastrointest Endosc Clin N Am. 2021 Jul;31(3):519-542.

Novel induction of CD40 expression by tumor cells with RAS/RAF/PI3K pathway inhibition augments response to checkpoint blockade 
Yan C, Saleh N, Yang J, Nebhan C, et al. Mol Cancer. 2021 Jun 6;20 (1):85.

Over-Generalizing About GC (Hypoxia): Pitfalls of Limiting Breadth of Experimental Systems and Analyses in Framing Informatics Conclusions
Boothby MR, Raybuck A, Cho SH, et al. Front Immunol. 2021 May 10;12:664249.

Sunitinib and Axitinib increase secretion and glycolytic activity of small extracellular vesicles in renal cell carcinoma Lim AR, Vincent BG, Weaver AM, et al. Cancer Gene Ther. 2021 Jun 4.

Isocitrate dehydrogenase inhibitor-driven differentiation may resemble secondary graft failure in post-allogeneic haematopoietic cell transplantation relapsed acute myeloid leukaemia. Rasche A, Mason EF, Strickland SA, et al. Haematol. 2021 Jun 7.

Helicobacter pylori: a stealth assassin Wroblewski LE, Peek RM Jr. Trends Cancer. 2021 Jun 9:S2405-8033(21)00108-4.

Molecular determinants for α-tubulin methylation by SETD2
Kearns S, Mason FM, Rathmell WK, et al.  J Biol Chem. 2021 Jun 19;297(1):100898.

 

Colon epithelial cell TGFβ signaling modulates the expression of tight junction proteins and barrier function in mice Paula Marincola Smith, Yash A Choksi, et.al. Am J Physiol Gastrointest Liver Physiol. 2021 Jun 1;320(6):G936-G957.

Measurement of Metabolites from Migrating Cells. Demond Williams, Barbara Fingleton. Methods Mol Biol. 2021;2294:143-150.

Targeting Histone Modifications in Bone and Lung Metastatic Cancers Edwards Courtney, Johnson RW. Curr Osteoporos Rep. 2021 Mar 15. 

First-in-human PET imaging and estimated radiation dosimetry of L-[5- 11 C]-glutamine in patients with metastatic colorectal cancer Cohen, A, et al. J Nucl Med. 2021 Apr 30.

EphA2 Is a Clinically Relevant Target for Breast Cancer Bone Metastatic Disease Vaught D, et al. JBMR Plus. 2021 Mar 9;5(4).

Development and Evaluation of a Method to Correct Misinterpretation of Clinical Trial Results With Long-term Survival Chih Yuan Hsu, Emily Pei Ying Lin, Yu Shyr. JAMA Oncol. 2021 Apr 15.

Ex Vivo High Salt Activated Tumor-Primed CD4+T Lymphocytes Exert a Potent Anti-Cancer Response Tiriveedhi V, et al. Cancers (Basel). 2021 Apr 2;13 (7):1690.

Changes in peripheral and local tumor immunity after neoadjuvant chemotherapy reshape clinical outcomes in patients with breast cancer. Margaret L. Axelrod, Mellissa Nixon, Paula I. Gonzalez-Ericsson, Riley E. Bergman, et al. Clin Cancer Res. 

Cell-programmed nutrient partitioning in the tumor microenvironment
Reinfeld, B, Madden M, Wolf M, et al. Nature. 2021 May;593(7858):282-288

Metabolic modulation by CDK4/6 inhibitor promotes chemokine-mediated recruitment of T cells into mammary tumors  Uzhachenko R, Bharti V, et al. Cell Rep. 2021 Apr 6; 35(1):1089444.

The Complex Integration of T-cell Metabolism and Immunotherapy

Madden MZ, Rathmell JC. Cancer Discov. 2021 Apr1.

Obesity, Immunity, and Cancer Rathmell JC. N Engl J Med. 2021 Mar 25;384(12):1160-1162.

Genome-wide CRISPR screen identifies noncanonical NF-κB signaling as a regulator of density-dependent proliferation 
Maria Fomicheva, Ian Macara. eLife 2020 Nov 13;9.

Incorporating Both Genetic and Tobacco Smoking Data to Identify High-Risk Smokers for Lung Cancer Screening
Guochong Jia, Wanqing Wen, Pierre Massion, Xiao-Ou Shu, Wei Zheng. Carcinogenesis, bgab018

Circulating Myeloid Regulatory Cells: Promising Biomarkers in B-Cell Lymphomas. 
Juliette Ferrant, Faustine Lhomme, Simone Le Gallou, Jonathan Irish, et al. Front Immunol. 2021 Feb 2;11:623993

The delta isoform of PI3K predominates in chronic myelomonocytic leukemia and can be targeted effectively with umbralisib and ruxolitinib
Matthew Villaume, M Pia Arrate, Haley Ramsey, et al. Exp Hematol. 2021 Feb 19;S0301-472X(21)00089

Triple-Negative Breast Cancer: Breast Tumors With an Identity Crisis
Sara Nunnery, Ingrid Mayer and Justin Balko. Cancer J. 2021 Jan-Feb 01;27(1):2-7

LncRNAs: Promising new targets in pulmonary fibrosis
Zhang S, Chen H, Yue D, Blackwell TS, Lv C, Song.J Gene Med. 2021 Feb 3:e3318.

Paradigm-Shifting Research in Gastroenterology, Hepatology, and Nutrition: A Top 20 List of Articles Published in 2020
Corley DA, Peek RM Jr, Simpson BA. Gastroenterology. 2021 Jan 14:S0016-5085(21)00087-1

Definition of a small core transcriptional circuit regulated by AML1-ETO
Stengel K, Ellis J, Spielman C, et al. Molecular Cell, Vol 81, issue 3, Feb 2021, pages 530-545

Pushing the boundaries with collision collaboration: the marriage of ideas
Rathmell JC, Rathmell WK. J Clin Invest. 2021 Jan 19;131(2):e145964

Inertial-based Fluidic Platform for Rapid Isolation of Blood-borne Pathogens
Batcho EC, Miller S, Cover TL, McClain MS, Marasco C, Bell CS, Giorgio TD. Mil Med. 2021 Jan 25;186(Suppl 1):129-136.

Disruption of the integrin-linked kinase (ILK) pseudokinase domain affects kidney development in mice
Bulus N, Brown KL, Mernaugh G, Böttcher A, Dong X, Sanders CR, Pozzi A, Fässler R, Zent R. J Biol Chem. 2021 Feb 1:100361.

Claudin-2 inhibits renal clear cell carcinoma progression by inhibiting YAP-activation
Balawant Kumar, Rizwan Ahmad, Giovanna Giannico, Roy Zent, et al. J Exp Clin Cancer Res. 2021 Feb 23;40(1):77.

NCCN Guidelines Insights:Non-Small Cell Lung Cancer, Version 2.2021 
David ettinger, Douglas Wood, Dara Aisner, et al.J. Natl Compr Canc Netw. 2021 Mar 2;19(3):254-266.

Scientific Rigor in the Age of COVID-19 Shyr Y, Berry LD, Hsu CY. JAMA Oncol. 2021 Feb 1;7(2):171-172.

A Call to Action: Dismantling Racial Injustices in Preclinical Research and Clinical Care of Black Patients Living with Small Cell Lung Cancer 
Thomas PL, Madubata CJ, Aldrich MC, Lee MM, Owonikoko TK, Minna JD, Rudin CM, Sage J, Lovly CM.  Cancer Discov. 2020 Dec 14.

Tuft Cells Inhibit Pancreatic Tumorigenesis in Mice by Producing Prostaglandin D2
DelGiornoKE, ChungCY, VavinskayaV, et al. Gastroenterology. 2020 Jul 24 .

HMCES Maintains Replication Fork Progression and Prevents Double-Strand Breaks in Response to APOBEC Deamination and Abasic Site Formation Mehta PM, Lovejoy A , Zhao Runxiang , Heintzman Darren , Cortez David. Cell Reports. 2020.

Targeting NPM1 in irradiated cells inhibits NPM1 binding to RAD51, RAD51 foci formation and radiosensitizes NSCLC 
Traver G, Sekhar KR, Crooks PA, Keeney DS, Freeman ML. Cancer Lett. 2020 Dec 21;500:220-227

Multimodal Multiplexed Immunoimaging with Nanostars to Detect Multiple Immunomarkers and Monitor Response to Immunotherapies Ou YC, Wen X, Johnson CA, Shae D, Ayala OD, Webb JA, Lin EC, DeLapp RC, Boyd KL, Richmond A, Mahadevan-Jansen A, Rafat M, Wilson JT, Balko JM, Tantawy MN, Vilgelm AE, Bardhan R. ACS Nano. 2020 Jan 28;14(1):651-663

Selective glutamine metabolism inhibition in tumor cells improves anti-tumor T lymphocyte activity in triple-negative breast cancer. Edwards DN, Ngwa VM, Raybuck AL, Wang S, Hwang Y, Kim LC, Cho SH, Paik Y, Wang Q, Zhang S, Manning HC, Rathmell JC, Cook RS, Boothby MR, Chen J. J Clin Invest. 2020 Dec 15:140100.

Glioblastoma Distance From the Subventricular Neural Stem Cell Niche Does Not Correlate With Survival 
Mistry AM, Mummareddy N, Salwi S, Davis LT, Ihrie RA. Front Oncol. 2020 Dec 11;10:564889

RNF43: A Biomarker With Potential Ramifications for Therapeutic Intervention in Gastric Cancer 
Noto JM, Peek RM Jr. Cell Mol Gastroenterol Hepatol. 2020 Dec 18:S2352-345X(20)301983

Baseline characteristics and outcomes of COVID-19 patients admitted to a Respiratory Intensive Care Unit (RICU) in Southern ItalyDi Lecce V, Carpagnano GE, Pierucci P, Quaranta VN, Barratta F, Zito A, Buonamico E, Resta O. Multidiscip Respir Med. 2020 Nov 6;15(1):704.

TBX4 Transcription Factor Is a Positive Feedback Regulator of Itself and Phospho-SMAD1/5
Cai Y, Yan L, Kielt MJ, Cogan JD, Hedges LK, Nunley B, West J, Austin ED, Hamid R. Am J Respir Cell Mol Biol. 2021 Jan;64(1):140-143.

Summary from the Kidney Cancer Association’s Inaugural Think Thank: Coalition for a Cure
Rini B, Abel EJ, Albiges L, Bex A, Brugarolas J, Bukowski RM, Coleman JA, Drake CG, Figlin RA, Futreal A, Hammers H, Powles T, Rathmell WK, Ricketts CJ, Turajlic S, Wood CG, Leibovich BC.  Clin Genitourin Cancer. 2020 Nov 14:S1558-7673(20)30234-2.

AMPKα1 in B Cells Dampens Primary Antibody Responses yet Promotes Mitochondrial Homeostasis and Persistence of B Cell Memory Shawna McLetchie Brookens, Sung Hoon Cho, Paulo Basso and Mark Boothby. 

Colonic epithelial-derived Selenoprotein P is the source for antioxidant-mediated protection in colitis-associated cancer 
Short, SP, Pilat Jennifer M, et al. Gastroenterology.
 2020 Dec 31;S0016-5085(20)35623.

The design and analysis of non-randomized studies: a case study of off-label use of hydroxychloroquine in the COVID-19 pandemic Shyr D, Shyr Y. Expert Opin Investig Drugs. 2020 Dec 29:1-7.