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. 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
  2. Jun Ma, Michael P Randall, Ming Lu, Lingjing Chen, Huimin Geng, Aishwarya Kumar, Saloni Malla, Mark Noviski, Ryan Rountree, James L. Rubenstein. BTK Degradation As a Novel Therapeutic Strategy in Relapsed CNS Lymphoma: Proof of Concept Studies in Intracranial Patient-Derived, Rodent Models. Blood. 2024 Nov 5; 144(Supplement 1):2988-2988.  View on PubMed
  3. Bonell Patiño-Escobar, Lucy Perez-Lugo, Huimin Geng, Fernando Salangsang, Paul Phojanakong, Juan Antonio Camara Serrano, Veronica Steri, Oscar A Aguilar, Arun P Wiita. CD48: Friend or Foe in NK-Cell Immunosurveillance of Multiple Myeloma?. Blood. 2024 Nov 5; 144(Supplement 1):4646-4646.  View on PubMed
  4. Alastair L Smith, Nicholas Denny, Catherine M Chahrour, Natalina Elliott, Thomas Jackson, Joe Harman, Huimin Geng, Irene Roberts, Nicholas Crump, James Oliver Davies, Anindita Roy, Thomas A Milne. Differential Gene Expression in KMT2A::AFF1 Leukemia Is Driven By Enhancer Heterogeneity. Blood. 2024 Nov 5; 144(Supplement 1):201-201.  View on PubMed
  5. Clarissa Garcia, Kaylyn Lyons, Tian Liu, Ilaria Iacobucci, Amanda Novak, Amy Argabright, Alexis Donnelly, Julian Grandvallet Contreras, Huimin Geng, Sabrina Smith, Xin Zhou, Markus Müschen, John Edgar Dick, Julie R Haines, Angelo D'Alessandro, Charles G. Mullighan, Tzu Phang, M. Eric Kohler, Matthew Witkowski. Inhibiting Free Fatty Acid Transport to Improve CAR-T Cell Therapy of Relapsed B-Cell Acute Lymphoblastic Leukemia. Blood. 2024 Nov 5; 144(Supplement 1):1446-1446.  View on PubMed
  6. Venkata Sesha Sai Abhinav Ayyadevara, Gerald Wertheim, John Chukinas, Joseph Loftus, Sung June Lee, Anil Kumar, Srividya Swaminathan, Rahul S Bhansali, Wayne Childers, Huimin Geng, Thomas A Milne, Xianxin Hua, Kathrin M. Bernt, Thierry Besson, Junwei Shi, John D. Crispino, Martin P Carroll, Sarah K. Tasian, Christian Hurtz. KMT2A -Rearranged ALL Requires DYRK1A for Regulation of ERK Signaling and Cell Proliferation. Blood. 2024 Nov 5; 144(Supplement 1):1455-1455.  View on PubMed
  7. Ruifeng Sun, Jaewoong Lee, Dewan Artadji, Mark E Robinson, Kohei Kume, Zhangliang Cheng, Kadriye Nehir Cosgun, Lai N Chan, Etienne Leveille, Ning Ma, Huimin Geng, Elisabeth Paietta, Nagarajan Vaidehi, Markus Müschen. PKCd-Mediated Phosphorylation of CD25 Initiates Feedback Control of Oncogenic Tyrosine Kinases in Acute Lymphoblastic Leukemia. Blood. 2024 Nov 5; 144(Supplement 1):632-632.  View on PubMed
  8. Venkata Sesha Sai Abhinav Ayyadevara, Ashley Paik, Ria Perencsik, Monika Toma, Tomasz Skorski, Rozbeh Jafari, Gerald Wertheim, Huimin Geng, Christian Hurtz. Targeting the SWI/SNF Chromatin Remodeling Complex Subunit SMARCA4 in ALL. Blood. 2024 Nov 5; 144(Supplement 1):4216-4216.  View on PubMed
  9. Michael P Randall, Huimin Geng, Lingjing Chen, Aishwarya Ballapuram, Chitoh Yung, Ming Lu, Gregory Chin, Michael Mish, Jamie Bates, James L. Rubenstein. Toll-like Receptor 7/8 Pathway Is a Therapeutic Target in Primary CNS Lymphoma. Blood. 2024 Nov 5; 144(Supplement 1):978-978.  View on PubMed
  10. Priya Choudhry, Corynn Kasap, Bonell Patiño-Escobar, Olivia Gugliemini, Huimin Geng, Vishesh Sarin, Amrik Kang, Audrey Kishishita, Sham Rampersaud, Letitia Sarah, Yu-Hsiu T. Lin, Neha Paranjape, Poornima Ramkumar, Jonathan C. Patton, Makeba Marcoulis, Donghui Wang, Paul Phojanakong, Veronica Steri, Byron Hann, Benjamin G. Barwick, Martin Kampmann, Arun P. Wiita. Functional multi-omics reveals genetic and pharmacologic regulation of surface CD38 in multiple myeloma. . 2024 Jun 1; 100025.  View on PubMed
  11. 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
  12. 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
  13. Kasap C, Izgutdina A, Patiño-Escobar B, Kang A, Chilakapati N, Akagi N, Johnson H, Rashid T, Werner J, Barpanda A, Geng H, Lin YT, Rampersaud S, Gil-Alós D, Sobh A, Dupéré-Richer D, Wicaksono G, Kawehi Kelii KM, Dalal R, Ramos E, Vijayanarayanan A, Salangsang F, Phojanakong P, Serrano JAC, Zakraoui O, Tariq I, Steri V, Shanmugam M, Boise LH, Kortemme T, Stieglitz E, Licht JD, Karlon WJ, Barwick BG, Wiita AP. Targeting high-risk multiple myeloma genotypes with optimized anti-CD70 CAR-T cells. bioRxiv. 2024 Feb 28.  View on PubMed
  14. 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
  15. 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
  16. J. Ma, M. Lu, L. Chen, H. Geng, A. Kumar, M. Noviski, R. Rountree, C. Guiducci, J. Rubenstein. BTK Degradation as a Novel Therapeutic Strategy in Relapsed CNS Lymphoma: Proof of Concept Studies in Intracranial Preclinical including Patient-Derived Models. Hematological Oncology. 2023 Jun 9; 41(S2):546-547.  View on PubMed
  17. S. Mo, H. Geng, A. Ballapuram, L. Chen, M. Lu, W. P. Devine, K. W. Wen, D. Solomon, J. Rubenstein. IDENTIFICATION OF GENOMIC BIOMARKERS OF DISEASE PROGRESSION AND SURVIVAL IN NEWLY-DIAGNOSED PRIMARY CNS LYMPHOMA. Hematological Oncology. 2023 Jun 9; 41(S2):40-41.  View on PubMed
  18. B. Shaz, R. Schäfer, M. Fontaine, P. Norris, D. McKenna, B. Miyazawa, P. Jin, J. Reems, D. Stroncek, M. Takanashi, D.C. Marks, H. Geng, S. Pati. 41 Mesenchymal Stem/Stromal Cells: LOCAL MANUFACTURING PROCESSES CONTRIBUTE TO VARIABILITY IN HUMAN MESENCHYMAL STROMAL CELL (MSC) EXPANSION WHILE GROWTH MEDIA SUPPLEMENTS CONTRIBUTE TO VARIABILITY IN GENE EXPRESSION AND CELL FUNCTION. THE BEST COLLABORATIVE STUDY. Cytotherapy. 2023 May 1; 25(6):s29-s30.  View on PubMed
  19. Ogana HA, Hurwitz S, Hsieh CL, Geng H, Müschen M, Bhojwani D, Wolf MA, Larocque J, Lieber MR, Kim YM. Artemis inhibition as a therapeutic strategy for acute lymphoblastic leukemia. Front Cell Dev Biol. 2023; 11:1134121.  View on PubMed
  20. Lee J, Robinson ME, Sun R, Kume K, Ma N, Cosgun KN, Chan LN, Leveille E, Geng H, Vykunta VS, Shy BR, Marson A, Katz S, Chen J, Paietta E, Meffre E, Vaidehi N, Müschen M. Dynamic phosphatase-recruitment controls B-cell selection and oncogenic signaling. bioRxiv. 2023 Mar 15.  View on PubMed

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