John Cunningham

Research Summary
My research focuses on the biology and therapy of hemoglobinopathies, the molecular mechanisms underpinning hematopoiesis and the development of the leukemia stem cell, and the transcriptional mechanisms operative during the development of vertebrate organisms. Research projects include characterization of the key factors modulating developmental erythropoiesis, identification of gene regulatory networks in the neural crest and in neuroblastoma, and the development of allogenic stem cell transplant approaches to sickle cell disease. We collaborate with colleagues in developmental biology, informatics, and cancer biology to ensure that we bring a comprehensive perspective to the fundamental question we seek to solve.
Erythropoiesis, Hemoglobinopathies, Hematopoiesis, Neural Crest, Sickle Cell Disease, Gene Regulatory Networks, Transcription Factors, Stem Cell Transplantation
  • University College Dublin, Ireland, MB BCh BAO Medicine 06/1982
  • St Laurences Hospital, Dublin, Ireland, Residency 06/1985
  • Royal College of Physicians , United Kingdom, Membership (MRCP) Medicine 06/1986
  • Mater Misericordiae Hospital, Dublin, Ireland, Hematology Fellowship 06/1987
  • Kings College London, United Kingdom, MSc Biochemistry 06/90
  • Royal Free Hospital School of Medicine , London, United Kingdom, Wellcome Fellowship, Hematology 06/1991
  • Clinical Hematology Branch, National Heart Lung and Blood Institute , National Institutes of Health, Bethesda, MD , Hematology 09/1993
Biosciences Graduate Program Association
Awards & Honors
  • 1988 - 1991 Wellcome Fellowship Wellcome Trust
  • 1991 - 1993 Fogarty Fellowship National Institutes of Health
  • 2015 - 2017 Pritzker Professor University of Chicago
  • 2017 - 2019 Bucksbaum Senior Fellow Bucksbaum Institute, University of Chicago
  • 2017 - 2019 George M. Eisenberg Professor University of Chicago
  1. Fan Y, Artz AS, van Besien K, Stock W, Larson RA, Odenike O, Godley LA, Kline J, Cunningham JM, LaBelle JL, Bishop MR, Liu H. Outcomes following second allogeneic stem cell transplant for disease relapse after T cell depleted transplant correlate with remission status and remission duration after the first transplant. Exp Hematol Oncol. 2019; 8:1. View in: PubMed

  2. Wang Z, Cunningham JM, Yang XH. CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs. Bioinformatics. 2018 09 01; 34(17):i664-i670. View in: PubMed

  3. Pinto N, Volchenboum SL, Skol AD, Rhodes L, Doan A, Fein-Levy C, Lipton JM, Cunningham JM, Onel K. Establishing a translational genomics infrastructure in pediatric cancer: the GREAT KIDS experience. Per Med. 2015 Jun; 12(3):221-229. View in: PubMed

  4. Nassin ML, Nicolaou E, Gurbuxani S, Cohn SL, Cunningham JM, LaBelle JL. Immune Reconstitution Following Autologous Stem Cell Transplantation in Patients with High-Risk Neuroblastoma at the Time of Immunotherapy. Biol Blood Marrow Transplant. 2018 03; 24(3):452-459. View in: PubMed

  5. Yang XH, Tang F, Shin J, Cunningham JM. Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma. BMC Syst Biol. 2017 Oct 03; 11(Suppl 5):92. View in: PubMed

  6. Lapping-Carr G, Khalyfa A, Rangel S, Darlington W, Beyer EC, Peddinti R, Cunningham JM, Gozal D. Exosomes contribute to endothelial integrity and acute chest syndrome risk: Preliminary findings. Pediatr Pulmonol. 2017 Nov; 52(11):1478-1485. View in: PubMed

  7. Yang XH, Tang F, Shin J, Cunningham JM. A c-Myc-regulated stem cell-like signature in high-risk neuroblastoma: A systematic discovery (Target neuroblastoma ESC-like signature). Sci Rep. 2017 03 03; 7(1):41. View in: PubMed

  8. Wang B, Cunningham JM, Yang XH. Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data. Bioinformatics. 2015 Sep 15; 31(18):3043-5. View in: PubMed

  9. Yang XH, Li M, Wang B, Zhu W, Desgardin A, Onel K, de Jong J, Chen J, Chen L, Cunningham JM. Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia. BMC Bioinformatics. 2015 Mar 24; 16:97. View in: PubMed

  10. Yang X, Ai X, Cunningham JM. Computational prognostic indicators for breast cancer. Cancer Manag Res. 2014; 6:301-12. View in: PubMed

  11. Mandal S, Baron BW, Mischeaux M, James K, Roig J, Landers J, Volchenboum SL, Cunningham JM, Reardon B, Musa G, Richa EM. Collection of peripheral blood stem cells from a 7 month-old girl weighing 7 kg with the use of combined heparin and citrate anticoagulation. J Clin Apher. 2013 Aug; 28(4):309-10. View in: PubMed

  12. LaBelle JL, Cunningham JM. Stem cell transplant as an immunomodulatory tool for children with hematologic malignancies. Am Soc Clin Oncol Educ Book. 2013. View in: PubMed

  13. Yang X, Vasudevan P, Parekh V, Penev A, Cunningham JM. Bridging cancer biology with the clinic: relative expression of a GRHL2-mediated gene-set pair predicts breast cancer metastasis. PLoS One. 2013; 8(2):e56195. View in: PubMed

  14. Khalyfa A, Carreras A, Hakim F, Cunningham JM, Wang Y, Gozal D. Effects of late gestational high-fat diet on body weight, metabolic regulation and adipokine expression in offspring. Int J Obes (Lond). 2013 Nov; 37(11):1481-9. View in: PubMed

  15. McNerney ME, Brown CD, Wang X, Bartom ET, Karmakar S, Bandlamudi C, Yu S, Ko J, Sandall BP, Stricker T, Anastasi J, Grossman RL, Cunningham JM, Le Beau MM, White KP. CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia. Blood. 2013 Feb 07; 121(6):975-83. View in: PubMed

  16. Hart LS, Cunningham JT, Datta T, Dey S, Tameire F, Lehman SL, Qiu B, Zhang H, Cerniglia G, Bi M, Li Y, Gao Y, Liu H, Li C, Maity A, Thomas-Tikhonenko A, Perl AE, Koong A, Fuchs SY, Diehl JA, Mills IG, Ruggero D, Koumenis C. ER stress-mediated autophagy promotes Myc-dependent transformation and tumor growth. J Clin Invest. 2012 Dec; 122(12):4621-34. View in: PubMed

  17. Sundaresan NR, Vasudevan P, Zhong L, Kim G, Samant S, Parekh V, Pillai VB, Ravindra PV, Gupta M, Jeevanandam V, Cunningham JM, Deng CX, Lombard DB, Mostoslavsky R, Gupta MP. The sirtuin SIRT6 blocks IGF-Akt signaling and development of cardiac hypertrophy by targeting c-Jun. Nat Med. 2012 Nov; 18(11):1643-50. View in: PubMed

  18. Desgardin AD, Abramova T, Rosanwo TO, Kartha S, Shim EH, Jane SM, Cunningham JM. Regulation of delta-aminolevulinic acid dehydratase by krüppel-like factor 1. PLoS One. 2012; 7(10):e46482. View in: PubMed

  19. Widau RC, Zheng Y, Sung CY, Zelivianskaia A, Roach LE, Bachmeyer KM, Abramova T, Desgardin A, Rosner A, Cunningham JM, Skapek SX. p19Arf represses platelet-derived growth factor receptor ß by transcriptional and posttranscriptional mechanisms. Mol Cell Biol. 2012 Nov; 32(21):4270-82. View in: PubMed

  20. Liu H, Rich ES, Godley L, Odenike O, Joseph L, Marino S, Kline J, Nguyen V, Cunningham J, Larson RA, del Cerro P, Schroeder L, Pape L, Stock W, Wickrema A, Artz AS, van Besien K. Reduced-intensity conditioning with combined haploidentical and cord blood transplantation results in rapid engraftment, low GVHD, and durable remissions. Blood. 2011 Dec 08; 118(24):6438-45. View in: PubMed

  21. Sundaresan NR, Pillai VB, Wolfgeher D, Samant S, Vasudevan P, Parekh V, Raghuraman H, Cunningham JM, Gupta M, Gupta MP. The deacetylase SIRT1 promotes membrane localization and activation of Akt and PDK1 during tumorigenesis and cardiac hypertrophy. Sci Signal. 2011 Jul 19; 4(182):ra46. View in: PubMed

  22. Godley LA, Cunningham J, Dolan ME, Huang RS, Gurbuxani S, McNerney ME, Larson RA, Leong H, Lussier Y, Onel K, Odenike O, Stock W, White KP, Le Beau MM. An integrated genomic approach to the assessment and treatment of acute myeloid leukemia. Semin Oncol. 2011 Apr; 38(2):215-24. View in: PubMed

  23. Zheng Y, Zhao YD, Gibbons M, Abramova T, Chu PY, Ash JD, Cunningham JM, Skapek SX. Tgfbeta signaling directly induces Arf promoter remodeling by a mechanism involving Smads 2/3 and p38 MAPK. J Biol Chem. 2010 Nov 12; 285(46):35654-64. View in: PubMed

  24. Zhao Q, Rank G, Tan YT, Li H, Moritz RL, Simpson RJ, Cerruti L, Curtis DJ, Patel DJ, Allis CD, Cunningham JM, Jane SM. PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat Struct Mol Biol. 2009 Mar; 16(3):304-311. View in: PubMed

  25. Cunningham JM, Buxton OM, Weiss RE. Circadian variation in Cushing's disease and pseudo-Cushing states by analysis of F and ACTH pulsatility. J Endocrinol Invest. 2002 Oct; 25(9):791-9. View in: PubMed