Research Summary

My research is focused on functional genomics and epigenomics of lymphoma and leukemia, based on computational and statistical modeling and analysis of large-scale data derived from high-throughput microarray (gene expression, DNA methylation, ChIP-Chip, arrayCGH and SNP arrays) and next generation sequencing technologies (RNA-seq, Whole Exome-Seq, ChIP-seq and DNA methylation eRRBS-seq). Applying bioinformatics approaches, we are interested in identifying and evaluating 1) genetic and epigenetic abnormalities in the lymphomagenesis and leukemogenesis, 2) new biomarkers for prognosis and disease classification, and 3) novel therapeutic targets to develop precision medicine for different forms of lymphoma and leukemia. We have profiled 1000+ lymphoma and leukemia patient samples from LLMPP, COG, ECOG and other international consortiums and curated thousands of lymphoma and leukemia patient samples from public GEO, TCGA and TARGET datasets with different array and NGS platforms. Using these data, we have developed an integrative genomic and epigenomic metadata platform to study the master regulators and regulatory networks of hematopoietic malignancies. I have ongoing Intra- and Inter-Programmatic collaborations with numerous Cancer Center Members and Associate Members, including Markus Muschen, Neil Shah, James Rubenstein, Scott Kogan and Mignon Loh.

Education

University of Science & Technology of China, BS, 1999, School of the Gifted Young (Biophysics)
University of Nebraska at Omaha, MS, 2004, Computer Science
University of Nebraska Medical Center, PhD, 2008, Bioinformatics
Weill Cornell Medical College, Postdoc, 2008-2011, Computational Biology

Honors & Awards

  • 2004
    Best Poster Award, IEEE Computer Society Bioinformatics Conference (CSB'04), Stanford Univerisity, CA
  • 2005
    Kerrigan Research Minigrants Award, University of Nebraska at Omaha, Omaha, NE
  • 2007
    Best Poster Award, 2007 Nebraska Research and Innovation Conference, Omaha, NE
  • 2007
    Bukey Fellowship, University of Nebraska Medical Center, Omaha, NE
  • 2008
    Blanche Widaman Fellowship, University of Nebraska Medical Center, Omaha, NE
  • 2008
    Harris Award in Cancer Research, University of Nebraska Medical Center, Omaha, NE

Selected Publications

  1. Kohei Kume, Zhangliang Cheng, Yanzhi Feng, Ka-Won Kang, Takeshi Ito, Jian-Xin Lin, Liang Xu, Gang Xiao, Mark E. Robinson, Kadriye Nehir Cosgun, Huimin Geng, Chengyu Liang, Arndt Borkhardt, Hongbo Chi, Roberto Chiarle, Thomas G. Graeber, Katsuhiko Funai, Warren J. Leonard, Markus Müschen. Hyperactivation of oncogenic STAT5-signaling as strategy for tyrosine kinase-driven leukemia. Nat Cell Biol. 2026; In Press. View on PubMed
  2. Kumar A, Hamane K, Duault C, Lima-Junior JR, Jung DH, Qin H, Salcido S, Huang M, Guo X, Taghi Khani A, Sanchez Ortiz A, Ghoda L, Marcucci G, Lacayo NJ, Sakamoto KM, Hurtz C, Carroll M, Tasian SK, Geng H, Ji L, Armenian S, Izraeli S, Wu X, Maecker HT, Swaminathan S. Tumor-induced dendritic cell deregulation perturbs T cell proliferation and predicts clinical outcome in acute lymphoblastic leukemia. Cell Rep Med. 2026 Jul 28; 102945. View on PubMed
  3. Trivedi A, Miyazawa B, Fields AT, Matthews M, Vivona L, Keane C, Potter D, Geng H, Zhang H, Taenaka H, Kwek SS, Herrera-Rodriguez K, Nunez-Garcia B, de Menezes EM, Barry M, Nair A, Kuhn B, Norris PJ, Fong L, Fitzpatrick MM, Schreiber M, Kornblith LZ, Pati S. Lyophilized platelet derived extracellular vesicles promote hemostasis and attenuate intracranial hemorrhage following traumatic brain injury. J Transl Med. 2026 Jul 20. View on PubMed
  4. Garcia C, Lyons KU, Contreras JG, Liu T, Donnelly AJ, Novak AJ, Argabright A, Anderson C, Grier A, Smith S, Michlin J, Olusoji J, Mikeska RG, Zhou X, Geng H, Rahkola JT, Patel HN, Jacot JG, Müschen M, D'Alessandro A, Dick JE, Iacobucci I, Mullighan CG, Reisz JA, Phang T, Eric Kohler M, Witkowski MT. FATP2-mediated lipid metabolism enhances chimeric antigen receptor T-cell therapy resistance in B-cell acute lymphoblastic leukemia. Leukemia. 2026 Jun 30. View on PubMed
  5. Ayyadevara VSSA, Perencsik R, Patil S, Gaur S, Paik A, Toma M, Wertheim G, Geng H, Skorski T, Swaminathan S, Hurtz C. Selective sensitivity of Ph-like B-cell acute lymphoblastic leukemia to BRG1 inhibition identifies a therapeutic vulnerability. Leukemia. 2026 Jun 30. View on PubMed
  6. Trivedi A, Miyazawa B, Zhang H, Qiu L, Potter D, Edwards A, Vivona L, Lin M, Keane C, Geng H, Cleary SJ, Nair A, Fitzpatrick M, Looney MR, Pati S. A dried platelet-derived biologic for blood-brain barrier repair and hemorrhage control after TBI in mice. Blood. 2026 06 25; 147(26):3231-3247. View on PubMed
  7. Lee J, Sun R, Kume K, Robinson ME, Cheng Z, Cosgun KN, Ma N, Hurtz C, Geng H, Luger SM, Litzow MR, Paietta E, Chen J, Vaidehi N, Müschen M. Dynamic feedback control of oncogenic tyrosine kinase signaling in acute leukemia. Sci Signal. 2026 Feb 10; 19(924):eadw5054. View on PubMed
  8. Wang X, DeFilippis RA, Geng H, Shah NP, Li HY. An unprecedented potent inhibitor of MV4-11 cells: investigations into the mechanism of action beyond FLT3 inhibition. Bioorg Chem. 2026 Jun 05; 173:109601. View on PubMed
  9. Izgutdina A, Rashid T, Temple WC, Aminov S, Patiño-Escobar B, Walunj S, Geng H, Takamatsu H, Gil-Alós D, Kang AS, Ramos E, Chen SY, Johnson H, Nix MA, Naik A, Li M, Yuan CM, Wang HW, Sahu S, Larson RC, Carpenter C, Salangsang F, Phojanakong P, Serrano JAC, Tariq I, Zakraoui O, Steri V, Valeri A, Martinez-Lopez J, Maus MV, Parekh S, Verma A, Shah NN, Wiita AP. Affinity-matured CD72-targeting nanobody CAR T cells enhance elimination of antigen-low B-cell malignancies. J Immunother Cancer. 2025 Dec 30; 13(12). View on PubMed
  10. Smith AL, Denny N, Chahrour C, Sharp K, Arachi M, Dopico-Fernandez AM, Elliott N, Harman JR, Jackson T, Geng H, Smith O, Bond J, Roberts I, Stam RW, Crump NT, Davies JOJ, Roy A, Milne TA. Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients. Blood. 2025 Oct 23; 146(17):2073-2087. View on PubMed
  11. Kasap C, Izgutdina A, Patiño-Escobar B, Kang AS, Chilakapati N, Akagi N, Manoj A, Johnson H, Rashid T, Werner J, Barpanda A, Geng H, Lin YT, Rampersaud S, Gil-Alós D, Sobh A, Dupéré-Richer D, Aleman A, Wicaksono G, Kelii KMK, Dalal R, Ramos E, Vijayanarayanan A, Lakhani K, Salangsang F, Phojanakong P, Camara Serrano JA, Zakraoui O, Tariq I, Chari A, Chung A, Kumar AD, Martin TG, Wolf J, Wong SW, Steri V, Shanmugam M, Boise LH, Kortemme T, Parekh S, Stieglitz E, Licht JD, Karlon WJ, Barwick BG, Wiita AP. Targeting high-risk multiple myeloma genotypes with optimized anti-CD70 CAR T cells. Blood. 2025 Aug 14; 146(7):819-833. View on PubMed
  12. Xavier S, Nguyen V, Khairnar V, Phan A, Yang L, Nelson MS, Shukla RP, Wang J, Li A, Geng H, Lee J, Sadras T, Pham LV, Weisenburger DD, Chan WC, Lang KS, Shouse GP, Danilov AV, Song JY, Parekh S, Müschen M, Ngo VN. CEACAM1 as a mediator of B-cell receptor signaling in mantle cell lymphoma. Nat Commun. 2025 May 29; 16(1):4967. View on PubMed
  13. Ayyadevara VSSA, Wertheim G, Gaur S, Chukinas JA, Loftus JP, Lee SJ, Kumar A, Swaminathan S, Bhansali RS, Childers W, Geng H, Milne TA, Hua X, Bernt KM, Besson T, Shi J, Crispino JD, Carroll M, Tasian SK, Hurtz C. DYRK1A inhibition results in MYC and ERK activation rendering KMT2A-R acute lymphoblastic leukemia cells sensitive to BCL2 inhibition. Leukemia. 2025 05; 39(5):1078-1089. View on PubMed
  14. Geng H, Mo S, Chen L, Ballapuram A, Tsang M, Lu M, Rauschecker AM, Wen KW, Devine WP, Solomon DA, Rubenstein JL. Identification of genomic biomarkers of disease progression and survival in primary CNS lymphoma. Blood Adv. 2025 Mar 11; 9(5):1117-1131. View on PubMed
  15. Choudhry P, Kasap C, Patiño-Escobar B, Gugliemini O, Geng H, Sarin V, Kang A, Kishishita A, Rampersaud S, Sarah L, Lin YT, Paranjape N, Ramkumar P, Patton JC, Marcoulis M, Wang D, Phojanakong P, Steri V, Hann B, Barwick BG, Kampmann M, Wiita AP. Functional multiomics reveals genetic and pharmacologic regulation of surface CD38 in multiple myeloma. Blood Neoplasia. 2024 Sep; 1(3):100025. View on PubMed
  16. Ganapathi KA, Nicolae A, Egan C, Geng H, Xi L, Pack SD, McFadden JR, Raffeld M, Jaffe ES, Pittaluga S. Peripheral T-cell lymphomas expressing CD30 and CD15 expand the spectrum of anaplastic large cell lymphoma, ALK-negative. Br J Haematol. 2024 May; 204(5):1862-1871. View on PubMed
  17. Wadhwa A, Wang S, Patiño-Escobar B, Bidkar AP, Bobba KN, Chan E, Meher N, Bidlingmaier S, Su Y, Dhrona S, Geng H, Sarin V, VanBrocklin HF, Wilson DM, He J, Zhang L, Steri V, Wong SW, Martin TG, Seo Y, Liu B, Wiita AP, Flavell RR. CD46-Targeted Theranostics for PET and 225Ac-Radiopharmaceutical Therapy of Multiple Myeloma. Clin Cancer Res. 2024 03 01; 30(5):1009-1021. View on PubMed
  18. Shaz BH, Schäfer R, Fontaine MJ, Norris PJ, McKenna DH, Jin P, Reems JA, Stroncek D, Tanashi M, Marks D, Geng H, Pati S, for Biomedical Excellence for Safer Transfusion (BEST). Local manufacturing processes contribute to variability in human mesenchymal stromal cell expansion while growth media supplements contribute to variability in gene expression and cell function: a Biomedical Excellence for Safer Transfusion (BEST) collaborative study. Cytotherapy. 2024 06; 26(6):531-539. View on PubMed
  19. Crump NT, Smith AL, Godfrey L, Dopico-Fernandez AM, Denny N, Harman JR, Hamley JC, Jackson NE, Chahrour C, Riva S, Rice S, Kim J, Basrur V, Fermin D, Elenitoba-Johnson K, Roeder RG, Allis CD, Roberts I, Roy A, Geng H, Davies JOJ, Milne TA. MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia. Nat Commun. 2023 08 25; 14(1):5208. View on PubMed
  20. Feng X, Sun R, Lee M, Chen X, Guo S, Geng H, Müschen M, Choi J, Pereira JP. Cell circuits between leukemic cells and mesenchymal stem cells block lymphopoiesis by activating lymphotoxin beta receptor signaling. Elife. 2023 03 13; 12. View on PubMed

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