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John M. Ashton, Ph.D.

John M. Ashton, Ph.D.

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About Me

John M. Ashton, Ph.D., M.B.A., is an associate professor of Biomedical Genetics, assistant director for Shared Resources, and director of the Genomics Shared Resource for the Wilmot Cancer Institute. He also directs the University of Rochester Genomic Research Center, GRC Bioinformatics, and the Fun...
John M. Ashton, Ph.D., M.B.A., is an associate professor of Biomedical Genetics, assistant director for Shared Resources, and director of the Genomics Shared Resource for the Wilmot Cancer Institute. He also directs the University of Rochester Genomic Research Center, GRC Bioinformatics, and the Functional Genomics Center. He is also a member of the Genetics, Epigenetics and Metabolism Research Program at Wilmot. In those roles, Ashton works directly with graduate students, postdoctoral fellows, and principal investigators, offering advice, consultation, and mentorship on experimental design and analyses.

Faculty Appointments

Associate Professor - Department of Biomedical Genetics (SMD)

Credentials

Education

MBA | Simon Business School. Competitive and Organizational Strategy, Computer Information Systems. 2017

PhD | University of Rochester. Genetics. 2011

MS | University of Rochester. Genetics. 2008

BS | Rochester Institute of Technology. Biotechnology. 2003

Research

Ashton’s research expertise and interests are in cancer biology, specifically leukemia stem cell (LSC) biology. His graduate thesis work led to the discovery of novel gene sets and pathways critical for regulating LSC function. He also showed that perturbation of these gene sets through pharmacologi...
Ashton’s research expertise and interests are in cancer biology, specifically leukemia stem cell (LSC) biology. His graduate thesis work led to the discovery of novel gene sets and pathways critical for regulating LSC function. He also showed that perturbation of these gene sets through pharmacological interventions led to impairment of LSC function.

He has also focused on the development and refinement of gene transfer techniques in order to perform genetic manipulation in primary human leukemia patient samples to investigate mechanisms critical to LSC function. Currently, he is adapting single-cell transcriptomic methodologies for use with primary stem and progenitor cell populations to characterize molecular mechanisms underlying malignant stem cell biology.

Publications

Journal Articles

Temporal Single Cell Analysis of Leukemia Microenvironment Identifies Taurine-Taurine Transporter Axis as a Key Regulator of Myeloid Leukemia.

Rodems BJ, Sharma S, Baker CD, Kaszuba CM, Ito T, Liesveld JL, Calvi LM, Becker MW, Jordan CT, Ashton JM, Bajaj J

bioRxiv : the preprint server for biology.. 2024 May 14 Epub 05/14/2024.

Single-Cell Transcriptomic Profiling Identifies Molecular Phenotypes of Newborn Human Lung Cells.

Bhattacharya S, Myers JA, Baker C, Guo M, Danopoulos S, Myers JR, Bandyopadhyay G, Romas ST, Huyck HL, Misra RS, Dutra J, Holden-Wiltse J, McDavid AN, Ashton JM, Al Alam D, Potter SS, Whitsett JA, Xu Y, Pryhuber GS, Mariani TJ

Genes.. 2024 February 2615 (3)Epub 02/26/2024.

Corrigendum: Single cell RNA sequencing analysis of mouse cochlear supporting cell transcriptomes with activated ERBB2 receptor indicates a cell-specific response that promotes CD44 activation.

Piekna-Przybylska D, Na D, Zhang J, Baker C, Ashton JM, White PM

Frontiers in cellular neuroscience.. 2024 18 :1428589. Epub 05/24/2024.

Identifying Bone Marrow Microenvironmental Populations in Myelodysplastic Syndrome and Acute Myeloid Leukemia.

Kaszuba CM, Rodems BJ, Sharma S, Franco EI, Ashton JM, Calvi LM, Bajaj J

Journal of visualized experiments : JoVE.. 2023 November 10 (201)Epub 11/10/2023.

p53 Regulates the Extent of Fibroblast Proliferation and Fibrosis in Left Ventricle Pressure Overload.

Liu X, Burke RM, Lighthouse JK, Baker CD, Dirkx RA, Kang B, Chakraborty Y, Mickelsen DM, Twardowski J, Mello SS, Ashton JM, Small EM

Circulation research.. 2023 July 21133 (3):271-287. Epub 07/06/2023.

Myelodysplastic syndromes disable human CD271+VCAM1+CD146+ niches supporting normal hematopoietic stem/progenitor cells.

Kawano Y, Kawano H, Ghoneim D, Fountaine TJ, Byun DK, LaMere MW, Mendler JH, Ho T, Salama NA, Myers JR, Hussein SE, Frisch BJ, Ashton JM, Azadniv M, Liesveld JL, Kfoury Y, Scadden DT, Becker MW, Calvi LM

bioRxiv : the preprint server for biology.. 2023 April 28 Epub 04/28/2023.

Preparation of noninfectious scRNAseq samples from SARS-CoV-2-infected epithelial cells.

Osborn RM, Leach J, Zanche M, Ashton JM, Chu C, Thakar J, Dewhurst S, Rosenberger S, Pavelka M, Pryhuber GS, Mariani TJ, Anderson CS

PloS one.. 2023 18 (2):e0281898. Epub 02/24/2023.

Platelet olfactory receptor activation limits platelet reactivity and growth of aortic aneurysms.

Morrell CN, Mix D, Aggarwal A, Bhandari R, Godwin M, Owens Iii AP, Lyden SP, Doyle A, Krauel K, Rondina MT, Mohan A, Lowenstein CJ, Shim S, Stauffer S, Josyula VP, Ture SK, Yule DI, Wagner Iii LE, Ashton JM, Elbadawi A, Cameron SJ

The Journal of clinical investigation.. 2022 May 2132 (9)Epub 1900 01 01.

Identification of a Vitamin-D Receptor Antagonist, MeTC7, which Inhibits the Growth of Xenograft and Transgenic Tumors .

Khazan N, Kim KK, Hansen JN, Singh NA, Moore T, Snyder CWA, Pandita R, Strawderman M, Fujihara M, Takamura Y, Jian Y, Battaglia N, Yano N, Teramoto Y, Arnold LA, Hopson R, Kishor K, Nayak S, Ojha D, Sharon A, Ashton JM, Wang J, Milano MT, Miyamoto H, Linehan DC, Gerber SA, Kawar N, Singh AP, Tabdanov ED, Dokholyan NV, Kakuta H, Jurutka PW, Schor NF, Rowswell-Turner RB, Singh RK, Moore RG

Journal of medicinal chemistry.. 2022 April 2865 (8):6039-6055. Epub 04/11/2022.

Altered TGFB1 regulated pathways promote accelerated tendon healing in the superhealer MRL/MpJ mouse.

Kallenbach JG, Freeberg MAT, Abplanalp D, Alenchery RG, Ajalik RE, Muscat S, Myers JA, Ashton JM, Loiselle A, Buckley MR, van Wijnen AJ, Awad HA

Scientific reports.. 2022 February 2212 (1):3026. Epub 02/22/2022.

Single cell RNA sequencing analysis of mouse cochlear supporting cell transcriptomes with activated ERBB2 receptor indicates a cell-specific response that promotes CD44 activation.

Piekna-Przybylska D, Na D, Zhang J, Baker C, Ashton JM, White PM

Frontiers in cellular neuroscience.. 2022 16 :1096872. Epub 01/06/2023.

Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics.

Misra A, Baker CD, Pritchett EM, Burgos Villar KN, Ashton JM, Small EM

Journal of cardiovascular development and disease.. 2021 December 219 (1)Epub 12/21/2021.

Comparative Analysis of Single-Cell RNA Sequencing Platforms and Methods.

Ashton JM, Rehrauer H, Myers J, Myers J, Zanche M, Balys M, Foox J, Mason CE, Steen R, Kuentzel M, Aquino C, Garcia-Reyero N, Chittur SV

Journal of biomolecular techniques : JBT.. 2021 December 1532 (4)Epub 1900 01 01.

Coordination of endothelial cell positioning and fate specification by the epicardium.

Quijada P, Trembley MA, Misra A, Myers JA, Baker CD, Pérez-Hernández M, Myers JR, Dirkx RA, Cohen ED, Delmar M, Ashton JM, Small EM

Nature communications.. 2021 July 612 (1):4155. Epub 07/06/2021.

Prevention of Fibrosis and Pathological Cardiac Remodeling by Salinomycin.

Burke RM, Dirkx RA, Quijada P, Lighthouse JK, Mohan A, O'Brien M, Wojciechowski W, Woeller C, Phipps RP, Alexis JD, Ashton J, Small EM

Circulation research.. 2021 May 28128 (11):1663-1678. Epub 04/07/2021.

Scaffold-mediated CRISPR-Cas9 delivery system for acute myeloid leukemia therapy.

Ho TC, Kim HS, Chen Y, Li Y, LaMere MW, Chen C, Wang H, Gong J, Palumbo CD, Ashton JM, Kim HW, Xu Q, Becker MW, Leong KW

Science advances.. 2021 May 7 (21)Epub 05/19/2021.

Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.

Schroeder GM, Dutta D, Cavender CE, Jenkins JL, Pritchett EM, Baker CD, Ashton JM, Mathews DH, Wedekind JE

Nucleic acids research.. 2020 August 2048 (14):8146-8164. Epub 1900 01 01.

Multisite Evaluation of Next-Generation Methods for Small RNA Quantification.

Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS

Journal of biomolecular techniques : JBT.. 2020 July 31 (2):47-56. Epub 1900 01 01.

A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups.

Mische SM, Fisher NC, Meyn SM, Church KS, Hegstad-Davies RL, Weis-Garcia F, Adams M, Ashton JM, Delventhal KM, Dragon JA, Holmes L, Jagtap P, Kubow KE, Mason CE, Palmblad M, Searle BC, Turck CW, Knudtson KL

Journal of biomolecular techniques : JBT.. 2020 April 31 (1):11-26. Epub 1900 01 01.

Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Patients with Acute Myeloid Leukemia.

Pei S, Pollyea DA, Gustafson A, Stevens BM, Minhajuddin M, Fu R, Riemondy KA, Gillen AE, Sheridan RM, Kim J, Costello JC, Amaya ML, Inguva A, Winters A, Ye H, Krug A, Jones CL, Adane B, Khan N, Ponder J, Schowinsky J, Abbott D, Hammes A, Myers JR, Ashton JM, Nemkov T, D'Alessandro A, Gutman JA, Ramsey HE, Savona MR, Smith CA, Jordan CT

Cancer discovery.. 2020 April 10 (4):536-551. Epub 01/23/2020.

ARID1A, a SWI/SNF subunit, is critical to acinar cell homeostasis and regeneration and is a barrier to transformation and epithelial-mesenchymal transition in the pancreas.

Wang W, Friedland SC, Guo B, O'Dell MR, Alexander WB, Whitney-Miller CL, Agostini-Vulaj D, Huber AR, Myers JR, Ashton JM, Dunne RF, Steiner LA, Hezel AF

Gut.. 2019 July 68 (7):1245-1258. Epub 09/18/2018.

Decellularized Wharton jelly matrix: a biomimetic scaffold for ex vivo hematopoietic stem cell culture.

Li D, Chiu G, Lipe B, Hopkins RA, Lillis J, Ashton JM, Paul S, Aljitawi OS

Blood advances.. 2019 April 93 (7):1011-1026. Epub 1900 01 01.

The Hematopoietic Oxidase NOX2 Regulates Self-Renewal of Leukemic Stem Cells.

Adane B, Ye H, Khan N, Pei S, Minhajuddin M, Stevens BM, Jones CL, D'Alessandro A, Reisz JA, Zaberezhnyy V, Gasparetto M, Ho TC, Kelly KK, Myers JR, Ashton JM, Siegenthaler J, Kume T, Campbell EL, Pollyea DA, Becker MW, Jordan CT

Cell reports.. 2019 April 227 (1):238-254.e6. Epub 1900 01 01.

Subversion of Systemic Glucose Metabolism as a Mechanism to Support the Growth of Leukemia Cells.

Ye H, Adane B, Khan N, Alexeev E, Nusbacher N, Minhajuddin M, Stevens BM, Winters AC, Lin X, Ashton JM, Purev E, Xing L, Pollyea DA, Lozupone CA, Serkova NJ, Colgan SP, Jordan CT

Cancer cell.. 2018 October 834 (4):659-673.e6. Epub 09/27/2018.

AMPK/FIS1-Mediated Mitophagy Is Required for Self-Renewal of Human AML Stem Cells.

Pei S, Minhajuddin M, Adane B, Khan N, Stevens BM, Mack SC, Lai S, Rich JN, Inguva A, Shannon KM, Kim H, Tan AC, Myers JR, Ashton JM, Neff T, Pollyea DA, Smith CA, Jordan CT

Cell stem cell.. 2018 July 523 (1):86-100.e6. Epub 06/14/2018.

Targeting the gut microbiome to treat the osteoarthritis of obesity.

Schott EM, Farnsworth CW, Grier A, Lillis JA, Soniwala S, Dadourian GH, Bell RD, Doolittle ML, Villani DA, Awad H, Ketz JP, Kamal F, Ackert-Bicknell C, Ashton JM, Gill SR, Mooney RA, Zuscik MJ

JCI insight.. 2018 April 193 (8)Epub 04/19/2018.

T cell developmental arrest in former premature infants increases risk of respiratory morbidity later in infancy.

Scheible KM, Emo J, Laniewski N, Baran AM, Peterson DR, Holden-Wiltse J, Bandyopadhyay S, Straw AG, Huyck H, Ashton JM, Tripi KS, Arul K, Werner E, Scalise T, Maffett D, Caserta M, Ryan RM, Reynolds AM, Ren CL, Topham DJ, Mariani TJ, Pryhuber GS

JCI insight.. 2018 February 223 (4)Epub 02/22/2018.

Developmental alcohol exposure impairs synaptic plasticity without overtly altering microglial function in mouse visual cortex.

Wong EL, Lutz NM, Hogan VA, Lamantia CE, McMurray HR, Myers JR, Ashton JM, Majewska AK

Brain, behavior, and immunity.. 2018 January 67 :257-278. Epub 09/14/2017.

Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness.

Bhattacharya S, Rosenberg AF, Peterson DR, Grzesik K, Baran AM, Ashton JM, Gill SR, Corbett AM, Holden-Wiltse J, Topham DJ, Walsh EE, Mariani TJ, Falsey AR

Scientific reports.. 2017 July 267 (1):6548. Epub 07/26/2017.

HIV-1 Frameshift RNA-Targeted Triazoles Inhibit Propagation of Replication-Competent and Multi-Drug-Resistant HIV in Human Cells.

Hilimire TA, Chamberlain JM, Anokhina V, Bennett RP, Swart O, Myers JR, Ashton JM, Stewart RA, Featherston AL, Gates K, Helms ED, Smith HC, Dewhurst S, Miller BL

ACS chemical biology.. 2017 June 1612 (6):1674-1682. Epub 05/05/2017.

DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism.

Shen J, Wang C, Li D, Xu T, Myers J, Ashton JM, Wang T, Zuscik MJ, McAlinden A, O'Keefe RJ

JCI insight.. 2017 June 152 (12)Epub 06/15/2017.

Targeted therapy for a subset of acute myeloid leukemias that lack expression of aldehyde dehydrogenase 1A1.

Gasparetto M, Pei S, Minhajuddin M, Khan N, Pollyea DA, Myers JR, Ashton JM, Becker MW, Vasiliou V, Humphries KR, Jordan CT, Smith CA

Haematologica.. 2017 June 102 (6):1054-1065. Epub 03/09/2017.

Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G/S phase transition.

Elbarbary RA, Miyoshi K, Myers JR, Du P, Ashton JM, Tian B, Maquat LE

Science.. 2017 May 26356 (6340):859-862. Epub 1900 01 01.

Index case of acute myeloid leukemia in a family harboring a novel germ line mutation.

Ram J, Flamm G, Balys M, Sivagnanalingam U, Rothberg PG, Iqbal A, Myers JR, Corbett A, Ashton JM, Mendler JH

Blood advances.. 2017 March 141 (8):500-503. Epub 03/14/2017.

Rational design of a parthenolide-based drug regimen that selectively eradicates acute myelogenous leukemia stem cells.

Pei S, Minhajuddin M, D'Alessandro A, Nemkov T, Stevens BM, Adane B, Khan N, Hagen FK, Yadav VK, De S, Ashton JM, Hansen KC, Gutman JA, Pollyea DA, Crooks PA, Smith C, Jordan CT

The Journal of biological chemistry.. 2016 November 25291 (48):25280. Epub 1900 01 01.

Rational Design of a Parthenolide-based Drug Regimen That Selectively Eradicates Acute Myelogenous Leukemia Stem Cells.

Pei S, Minhajuddin M, D'Alessandro A, Nemkov T, Stevens BM, Adane B, Khan N, Hagen FK, Yadav VK, De S, Ashton JM, Hansen KC, Gutman JA, Pollyea DA, Crooks PA, Smith C, Jordan CT

The Journal of biological chemistry.. 2016 October 14291 (42):21984-22000. Epub 08/29/2016.

Evolution of acute myelogenous leukemia stem cell properties after treatment and progression.

Ho TC, LaMere M, Stevens BM, Ashton JM, Myers JR, O'Dwyer KM, Liesveld JL, Mendler JH, Guzman M, Morrissette JD, Zhao J, Wang ES, Wetzler M, Jordan CT, Becker MW

Blood.. 2016 September 29128 (13):1671-8. Epub 07/15/2016.

Leukemic Stem Cells Evade Chemotherapy by Metabolic Adaptation to an Adipose Tissue Niche.

Ye H, Adane B, Khan N, Sullivan T, Minhajuddin M, Gasparetto M, Stevens B, Pei S, Balys M, Ashton JM, Klemm DJ, Woolthuis CM, Stranahan AW, Park CY, Jordan CT

Cell stem cell.. 2016 July 719 (1):23-37. Epub 06/30/2016.

Residual Disease in a Novel Xenograft Model of RUNX1-Mutated, Cytogenetically Normal Acute Myeloid Leukemia.

Sivagnanalingam U, Balys M, Eberhardt A, Wang N, Myers JR, Ashton JM, Becker MW, Calvi LM, Mendler JH

PloS one.. 2015 10 (7):e0132375. Epub 07/15/2015.

miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy.

Baras AS, Mitchell CJ, Myers JR, Gupta S, Weng LC, Ashton JM, Cornish TC, Pandey A, Halushka MK

PloS one.. 2015 10 (11):e0143066. Epub 11/16/2015.

Targeting aberrant glutathione metabolism to eradicate human acute myelogenous leukemia cells.

Pei S, Minhajuddin M, Callahan KP, Balys M, Ashton JM, Neering SJ, Lagadinou ED, Corbett C, Ye H, Liesveld JL, O'Dwyer KM, Li Z, Shi L, Greninger P, Settleman J, Benes C, Hagen FK, Munger J, Crooks PA, Becker MW, Jordan CT

The Journal of biological chemistry.. 2013 November 22288 (47):33542-33558. Epub 10/02/2013.

In Vivo RNAi screening identifies a leukemia-specific dependence on integrin beta 3 signaling.

Miller PG, Al-Shahrour F, Hartwell KA, Chu LP, Järås M, Puram RV, Puissant A, Callahan KP, Ashton J, McConkey ME, Poveromo LP, Cowley GS, Kharas MG, Labelle M, Shterental S, Fujisaki J, Silberstein L, Alexe G, Al-Hajj MA, Shelton CA, Armstrong SA, Root DE, Scadden DT, Hynes RO, Mukherjee S, Stegmaier K, Jordan CT, Ebert BL

Cancer cell.. 2013 July 824 (1):45-58. Epub 06/13/2013.

BCL-2 inhibition targets oxidative phosphorylation and selectively eradicates quiescent human leukemia stem cells.

Lagadinou ED, Sach A, Callahan K, Rossi RM, Neering SJ, Minhajuddin M, Ashton JM, Pei S, Grose V, O'Dwyer KM, Liesveld JL, Brookes PS, Becker MW, Jordan CT

Cell stem cell.. 2013 March 712 (3):329-41. Epub 01/17/2013.

p75NTR: an enhancer of fenretinide toxicity in neuroblastoma.

Ganeshan V, Ashton J, Schor NF

Cancer chemotherapy and pharmacology.. 2013 March 71 (3):777-87. Epub 01/13/2013.

Gene sets identified with oncogene cooperativity analysis regulate in vivo growth and survival of leukemia stem cells.

Ashton JM, Balys M, Neering SJ, Hassane DC, Cowley G, Root DE, Miller PG, Ebert BL, McMurray HR, Land H, Jordan CT

Cell stem cell.. 2012 September 711 (3):359-72. Epub 08/02/2012.

Noncanonical NF-?B signaling regulates hematopoietic stem cell self-renewal and microenvironment interactions.

Zhao C, Xiu Y, Ashton J, Xing L, Morita Y, Jordan CT, Boyce BF

Stem cells.. 2012 April 30 (4):709-18. Epub 1900 01 01.

Functional inhibition of osteoblastic cells in an in vivo mouse model of myeloid leukemia.

Frisch BJ, Ashton JM, Xing L, Becker MW, Jordan CT, Calvi LM

Blood.. 2012 January 12119 (2):540-50. Epub 09/28/2011.

Metabolic regulation of APOBEC-1 complementation factor trafficking in mouse models of obesity and its positive correlation with the expression of ApoB protein in hepatocytes.

Galloway CA, Ashton J, Sparks JD, Mooney RA, Smith HC

Biochimica et biophysica acta.. 2010 November 1802 (11):976-85. Epub 06/09/2010.

Leukemia stem cells in a genetically defined murine model of blast-crisis CML.

Neering SJ, Bushnell T, Sozer S, Ashton J, Rossi RM, Wang PY, Bell DR, Heinrich D, Bottaro A, Jordan CT

Blood.. 2007 October 1110 (7):2578-85. Epub 06/29/2007.

Proteomic profiling and identification of immunodominant spore antigens of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis.

Delvecchio VG, Connolly JP, Alefantis TG, Walz A, Quan MA, Patra G, Ashton JM, Whittington JT, Chafin RD, Liang X, Grewal P, Khan AS, Mujer CV

Applied and environmental microbiology.. 2006 September 72 (9):6355-63. Epub 1900 01 01.

A rapid and sensitive magnetic bead-based immunoassay for the detection of staphylococcal enterotoxin B for high-through put screening.

Alefantis T, Grewal P, Ashton J, Khan AS, Valdes JJ, Del Vecchio VG

Molecular and cellular probes.. 2004 December 18 (6):379-82. Epub 1900 01 01.