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. Smith A, Denny NDR, Chahrour C, Sharp K, Arachi M, Dopico-Fernandez AM, Elliott N, Harman J, Jackson T, Geng H, Smith O, Bond J, Roberts I, Stam RWW, Crump N, Davies J, Roy A, Milne TA Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients.  View on PubMed
  2. 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.  View on PubMed
  3. Izgutdina A, Rashid T, Temple WC, Patiño-Escobar B, Walunj S, Geng H, Takamatsu H, Gil-Alós D, Kang AS, Ramos E, Chen SY, Johnson H, Nix MA, Naik A, Yuan CM, Wang HW, Aminov S, Sahu S, Larson RC, Carpenter C, Salangsang F, Phojanakong P, Camara Serrano JA, 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. bioRxiv. 2025 May 15.  View on PubMed
  4. Kasap C, Izgutdina A, Patiño-Escobar B, Kang AS, Chilakapati N, Akagi N, Manoj AM, 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 T, Wolf JL, Wong S, Steri V, Shanmugam M, Boise LH, Kortemme T, Parekh S, Stieglitz E, Licht JD, Karlon W, Barwick BG, Wiita A. Targeting high-risk multiple myeloma genotypes with optimized anti-CD70 CAR-T cells. Blood. 2025 May 13.  View on PubMed
  5. 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.  View on PubMed
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. Mlynarczyk C, Teater M, Pae J, Chin CR, Wang L, Arulraj T, Barisic D, Papin A, Hoehn KB, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh HX, Evans CM, Chadburn A, Chen Z, Shen H, Isles HM, Pelzer B, Tsialta I, Doane AS, Geng H, Rehman MH, Melnick J, Morgan W, Nguyen DTT, Elemento O, Kharas MG, Jaffrey SR, Scott DW, Khelashvili G, Meyer-Hermann M, Victora GD, Melnick A. BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science. 2023 01 20; 379(6629):eabj7412.  View on PubMed
  15. Barry M, Wu F, Pati S, Chipman A, Geng H, Kozar R. Lyophilized plasma resuscitation downregulates inflammatory gene expression in a mouse model of sepsis. J Trauma Acute Care Surg. 2022 08 01; 93(2S Suppl 1):S119-S127.  View on PubMed
  16. Tarighat SS, Fei F, Joo EJ, Abdel-Azim H, Yang L, Geng H, Bum-Erdene K, Grice ID, von Itzstein M, Blanchard H, Heisterkamp N. Overcoming Microenvironment-Mediated Chemoprotection through Stromal Galectin-3 Inhibition in Acute Lymphoblastic Leukemia. Int J Mol Sci. 2021 Nov 10; 22(22).  View on PubMed
  17. Geng H, Tsang M, Subbaraj L, Cleveland J, Chen L, Lu M, Sharma J, Vigneron DB, Kurhanewicz J, LaFontaine M, Luks T, Barshop BA, Gangoiti J, Villanueva-Meyer JE, Rubenstein JL. Tumor metabolism and neurocognition in CNS lymphoma. Neuro Oncol. 2021 10 01; 23(10):1668-1679.  View on PubMed
  18. Chan TY, Egbert CM, Maxson JE, Siddiqui A, Larsen LJ, Kohler K, Balasooriya ER, Pennington KL, Tsang TM, Frey M, Soderblom EJ, Geng H, Müschen M, Forostyan TV, Free S, Mercenne G, Banks CJ, Valdoz J, Whatcott CJ, Foulks JM, Bearss DJ, O'Hare T, Huang DCS, Christensen KA, Moody J, Warner SL, Tyner JW, Andersen JL. TNK1 is a ubiquitin-binding and 14-3-3-regulated kinase that can be targeted to block tumor growth. Nat Commun. 2021 09 09; 12(1):5337.  View on PubMed
  19. Drew WL, Miller S, Geng H, Ingebrigtsen D, Suslow LM and Suslow PS. Absence of Influenza and RSV Activity in the San Francisco Bay Area during the COVID-19 Pandemic, 2020-2021. J Adv Virol Res. 2021; 1(1):103.  View on PubMed
  20. Nix MA, Mandal K, Geng H, Paranjape N, Lin YT, Rivera JM, Marcoulis M, White KL, Whitman JD, Bapat SP, Parker KR, Ramirez J, Deucher A, Phojanokong P, Steri V, Fattahi F, Hann BC, Satpathy AT, Manglik A, Stieglitz E, Wiita AP. Surface Proteomics Reveals CD72 as a Target for In Vitro-Evolved Nanobody-Based CAR-T Cells in KMT2A/MLL1-Rearranged B-ALL. Cancer Discov. 2021 08; 11(8):2032-2049.  View on PubMed

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