Center for RNA Biology and Therapeutics Projects

There is a diversity of approaches to research at City of Hope’s Center for RNA Biology and Therapeutics, encompassing multiple disciplines, phases of study and diseases of interest.

Figure legend for Project webpage image: Showcasing the roles of RNA modification regulators



Figure legend for Project webpage image: Showcasing the roles of RNA modification regulators (e.g., TET2 and YTHDF2) in (A) cancer stem cell homing and (B) tumor immune evasion.

 

 

 

Discover Our Labs

We encourage team science and work to connect basic researchers and clinicians. The current list of laboratories affiliated with the Center for RNA Biology and Therapeutics is below. We welcome inquiries from investigators interested in participating.

  • Michael E. Berens, Ph.D. (TGen)
    Development transcriptomics of GBM tissue as a prospective treatment-planning aid to prioritize patient-specific therapies
    Email: [email protected]
  • Supriyo Bhattacharya
    Developing data-driven in-silico methods to understand disease mechanisms involving long noncoding RNAs and RNA modifications. Studying neopeptides derived from the translation of long noncoding RNAs and their impact on cellular biology, including their function as neoantigens in cancer and diabetes.
    Email:  [email protected]
  • Mark Boldin, M.D., Ph.D.
    Control of inflammation and cancer by noncoding RNA
    Email: [email protected]
  • Jianjun Chen, Ph.D. (Director)
    Study of the functions and mechanisms of RNA modifications and ncRNAs in cancer, and development of targeted therapeutics and RNA-based therapeutics for cancer treatment
    Email: [email protected]
  • Zhen Chen, Ph.D.
    The role of noncoding RNAs and endothelial stress response in diabetes complications
    Email: [email protected]
  • Xiaolan Deng, Ph.D. (Associate Director) 
    Development of anticancer therapy targeting RNA/DNA epigenetics and personalized immunotherapy
    Email: [email protected]
  • Sangeeta Dhawan, Ph.D.
    Study of how epigenetic modifications regulate pancreatic beta cell dysfunction in diabetes, through their effects on RNA processing, non-coding RNAs, dsRNA response, and transposable elements under metabolic stress.
    Email: [email protected]
  • John D. Fryer, Ph.D. (TGen)
    Understanding aberrant mRNA splicing to develop novel therapies
    Email: [email protected]
  • Ajay Goel, Ph.D., M.S.
    MicroRNA as a potential signature for pancreatic cancer risk
    Email: [email protected]
  • Zhaohui Gu, Ph.D.
    Integrating functional genomics to define how RNA features, including mRNA expression, circRNA biogenesis, alternative splicing, and alternative polyadenylation, regulate normal B-cell differentiation and drive malignant transformation in B-ALL.
    Email: [email protected]
  • Haiyong Han Ph.D. (Tgen) 
    Developing innovative RNA-based biomarkers and therapeutics for pancreatic cancer
    Email: [email protected]
  • David Horne, Ph.D.
    Developing molecular targeted therapies and mRNA LNPs for various applications in oncology and other conditions.
    Email: [email protected]
  • Robert R. Jenq, M.D.
    Exploring RNA therapies as a strategy to target intestinal microbes and employing RNA therapies as an approach to modulate the immune system in the setting of bone marrow transplantation and T cell therapies.
    Email: [email protected]
  • Kendall Van Keuren-Jensen, Ph.D. (TGen)
    Investigating how RNA and other molecular signals released from the diseased or injured central nervous system are captured in accessible biofluids, and applying advanced transcriptomic and extracellular vesicle–based approaches to elucidate mechanisms of neurological dysfunction and enable minimally invasive diagnostics.
    Email: [email protected]
  • Marcin Kortylewski, Ph.D.
    RNA drugs for precision immunotherapy targeting cancer
    Email: [email protected]
  • Ya-Huei Kuo, Ph.D. 
    Uncovering leukemia-driving RNA regulatory mechanisms and dynamics as the basis for novel therapy design and prediction.
    Email: [email protected]
  • Keehoon Lee, Ph.D. (TGen) 
    Applying advanced laboratory and computer technology to explore the next frontier in our understanding of how the human microbiome relates to human health and disease.
    Email: [email protected]
  • Ling Li, Ph.D. 
    Study of how epigenetic modifications or the interaction of RNA and proteins, particularly those non-histone proteins, affect immune gene expression.
    Email: [email protected]
  • Rose Li, M.D., Ph.D.
    Identification of RNA modification-based biomarkers for cancer early diagnosis, classification, risk stratification and prognosis.
    Email: [email protected]

View Our Key Publications

  • Magilnick N, Reyes EY, Wang WL, Vonderfecht SL, Gohda J, Inoue JI, Boldin MP. miR-146a-Traf6 regulatory axis controls autoimmunity and myelopoiesis, but is dispensable for hematopoietic stem cell homeostasis and tumor suppression. Proc Natl Acad Sci USA. 2017 Aug 22;114(34):E7140-E7149. doi: 10.1073/pnas.1706833114. Epub 2017 Aug 7. PMID: 28784800; PMCID: PMC5576818.
  • Huang H, Weng H, Zhou K, Wu T, Zhao BS, Sun M, Chen Z, Deng X, Xiao G, Auer F, Klemm L, Wu H, Zuo Z, Qin X, Dong Y, Zhou Y, Qin H, Tao S, Du J, Liu J, Lu Z, Yin H, Mesquita A, Yuan CL, Hu YC, Sun W, Su R,  Dong L, Shen C, Li C, Qing Y, Jiang X, Wu X, Sun M, Guan JL, Qu LH, Wei M, Müschen  M, Huang G, He C, Yang JH, Chen J. Histone H3 Trimethylation at Lysine 36 Guides m6A RNA Modification Co-transcriptionally. Nature. 2019 Mar 21;567(7748):414-419. PMCID: PMC6438714.
  • Tang X, Miao Y, Luo Y, Sriram K, Qi Z, Lin FM, Gu Y, Lai CH, Hsu CY, Peterson KL, Van Keuren-Jensen K, Fueger PT, Yeo GW, Natarajan R, Zhong S, Chen ZB. Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction. Circulation. 2020 Jul 28;142(4):365-379. doi: 10.1161/CIRCULATIONAHA.119.041231. Epub 2020 May 12. Erratum in: Circulation. 2021 Apr 20;143(16):e871. PMID: 32393053; PMCID: PMC7390348.
  • Shimura T, Kandimalla R, Okugawa Y, Ohi M, Toiyama Y, He C, Goel A. Novel evidence for m6A methylation regulators as prognostic biomarkers and FTO as a potential therapeutic target in gastric cancer. Br J Cancer. 2021 Oct 21. doi: 10.1038/s41416-021-01581-w. Epub ahead of print. PMID: 34675398.
  • Moreira D, Sampath S, Won H, White SV, Su Y-L, Alcantara M, Wang C, Lee P, Maghami E, Massarelli E, Kortylewski M. Myeloid Cell-Targeted STAT3 Inhibition Sensitizes Head and Neck Cancers to Radiotherapy and T cell-Mediated Immunity. J. Clin. Invest., 19, e137001, 2021.
  • Zhang B, Nguyen LXT, Li L, Zhao D, Kumar B, Wu H, Lin A, Pellicano F, Hopcroft L, Su YL, Copland M, Holyoake TL, Kuo CJ, Bhatia R, Snyder DS, Ali H, Stein AS, Brewer C, Wang H, McDonald T, Swiderski P, Troadec E, Chen CC, Dorrance A, Pullarkat V, Yuan YC, Perrotti D, Carlesso N, Forman SJ, Kortylewski M, Kuo YH, Marcucci G. Bone marrow niche trafficking of miR-126 controls the self-renewal of leukemia stem cells in chronic myelogenous leukemia. Nat Med. 2018 May;24(4):450-462. doi: 10.1038/nm.4499. Epub 2018 Mar 5. PMID: 29505034; PMCID: PMC5965294.
  • Idris A, Davis A, Supramaniam A, Acharya D, Kelly G, Tayyar Y, West N, Zhang P, McMillan CLD, Soemardy C, Ray R, O’Meally D, Scott TA, McMillan NAJ, Morris KV. A SARS-CoV-2 targeted siRNA-nanoparticle therapy for COVID-19. Mol Ther. 2021 Jul 7;29(7):2219-2226. doi: 10.1016/j.ymthe.2021.05.004. Epub 2021 May 14. PMID: 33992805
  • Kato M, Wang M, Chen Z,  Deshpande D,  Bhatt K, Jia Y, Oh HJ,  Lanting L, Lai JYC, O’Connor CL,  Wu YF, Hodgin JB, Nelson RG, Bitzer M, Natarajan R. (2016)  An Endoplasmic Reticulum Stress-regulated lncRNA hosting a microRNA megacluster induces Early features of Diabetic Nephropathy. Nature Communications 7: 12864. DOI: 10.1038/ncomms12864.  PMCID: PMC5553130
  • Zhou J, Li H, Xia X, Herrera A, Pollock N, Reebye V, Sodergren MH, Dorman S, Littman BH, Doogan D, Huang K-W, Habib R, Blakey D, Habib NA, Rossi JJ, Anti-inflammatory Activity of MTL-CEBPA, a Small Activating RNA Drug, in LPS-Stimulated Monocytes and Humanized Mice. Molecular Therapy. Volume 27, Issue 5 (2019). Pages 999-1016, ISSN 1525-0016, https://doi.org/10.1016/j.ymthe.2019.02.018.
  • Reebye. V., Saetrom, P., Mintz, P.J., Huang, K.-W., Swiderski, P., Peng, L., Liu, C., Liu, X., Lindkaer-Jensen, S., Zacharoulis, D., Kostomitsopoulos, N., Kasahara, N., Nicholls, J.P., Jiao, L.R., Pai, M., Spalding, D.R., Mizandari, M., Chikovain, T., Emara, M.M., Haoudi, A., Tomalia, D.A., Rossi, J.J. and Habib, N.A. (2014) A Novel RNA oligonucleotide improves liver function and inhibits liver carcinogenesis in vivo. Hepatology  59(1): 216-227. PMCID: PMC4655108
  • Voutila, J., Reebye, V., Roberts, R.C., Protopapa, P., Andrikakou, P., Balkey, D.C., Habib, R., Huber, H., Saetrom, P., Rossi, J.J. and Habib. N. (2017) Development and mechanism of small activating RNA targeting CEBPA, a novel therapeutic in clinical trials for liver cancer. Mol. Ther., 25(12): 2705-2714. PMCID: PMC5768526
  • Zhou, J.H., Lazar, D., Li, H., Xia, X., Satheesan, S., Charlins, P., O’Mealy, D., Akkina, R., Saayman, S., Weinberg, M.S., Rossi, J.J. and Morris, K.V. (2018) Receptor-targeted aptamer-siRNA conjugate-directed transcriptional regulation of HIV-1. Theranostics, 8(6): 1575-1590. PMCID: PMC5858168
  • Reebye, V., Huang, K.-W., Lin, V., Jarvis, S., Cutilas, P., Dorman, S., Ciriello, S., Andrikakou, P., Voutila, J., Saetrom, P., Mintz, P.J., Reccia, I., Rossi, J.J., Huber, H., Habib, R., Kostomitsopoulos, N., Balkey, D.C., Habib, N.A. (2018) Gene activation of CEBPA using saRNA: preclinical studies of the first in human saRNA drub candidate for liver cancer. Oncogene, 37(24): 3216-3228, PMCID: PMC6013054
  • Huang, K.W., Reebye, V., Czysz, K., Ciriello, s., Dorman, s., Reccia, I., Lai, H.S., Peng, L., Kostomitsopoulos, N., Nicolls, J., Habib, R.S., Tomalia, D.A., Saetrom, P., Wilkes, E., Cutillas, P., Rossi, J.J. and Habib, N.A. (2020) Liver Activation of Hepatocellular Nuclear Factor-4α by Small Activating RNA Rescues Dyslipidemia and Improves Metabolic Profile. Mol. Ther. Nucl. Acids. 19(6): 361-370. PMCID: PMC6938799
  • Setten, R.L., Chomchan, P., Epps, E.W., Burnett, J.D. and Rossi, J.J. (2021) CRED9: A differentially expressed elncRNA regulates expressing of transcription factor CEBPA. RNA J. RNA. 2021 Aug; 27(8): 891-906. doi: 10.1261/rna.078752.121  PMCID:  PMC8284328
  • Cui Q, Yin K, Zhang X, Ye P, Chen X, Chao J, Meng H, Wei J, Daniel R, Li L, Qin Y, Sun, G, Zhang M, Klein J, Huynhle M, Wang C, Zhang L, Badie B, Kalkum M, He C, Yi C, Shi Y. 2021. Targeting PUS7 suppresses tRNA pseudouridylation and glioblastoma tumorigenesis. Nature Cancer https://doi.org/10.1038/s43018-021-00238-0.
  • Su R*, Dong L*, Li Y*, Gao M*, Han L*, Wunderlich M, Deng X, Li H, Huang Y, Gao L, Li C, Zhao Z, Robinson S,  Tan B, Qing Y, Qin X, Prince E, Xie J, Qin H, Li W, Shen C, Sun J, Kulkarni P,  Weng H, Huang H, Chen Z, Zhang B, Wu X, Olsen MJ, Müschen M, Marcucci G, Salgia R, Li L, Fathi AT, Li Z, Mulloy JC, Wei M, Horne D, Chen J. Targeting FTO suppresses cancer stem cell maintenance and immune evasion. Cancer Cell. 2020 May 13;S1535-6108(20)30216-6.
  • Yin S, Gambe R, Sun, J, Martinez, AZ, Cartun JZ, Regis, F, Wan Y, Fan, J, Brooks, AN, Herman SE, ten Hacken E, Taylor-Weiner, A, Rassenti L, Ghia EM, Kipps TJ, Obeng EA, Cibulaskis C, Neuberg D, Campagna DR, Fleming MD, Ebert BL, Wiestner A, Leshchiner I, DeCaprio JA, Getz G, Reed R, Carrasco RD, Wu CJ, Wang L. A murine model of chronic lymphocytic leukemia based on B cell-restricted expression of Sf3b1 mutation and Atm deletion. Cancer Cell 2019 35(2):283-296. PMC6372356
  • Wang Z, Pan Z, Adhikari S, Harada BT, Shen L, Yuan W, Abeywardana T, Al-Hadid Q, Stark JM, He C, Lin L, Yang Y. m6 A deposition is regulated by PRMT1-mediated arginine methylation of METTL14 in its disordered C-terminal region. EMBO J. 2021 Mar 1;40(5):e106309. doi: 10.15252/embj.2020106309. Epub 2021 Jan 18. PMID: 33459381; PMCID: PMC7917551.
  • Ma S, Yan J, Barr T, Zhang J, Chen Z, Wang LS, Sun JC, Chen J, Caligiuri MA, Yu J. The RNA m6A reader YTHDF2 controls NK cell antitumor and antiviral immunity. J Exp Med. 2021 Aug 2;218(8):e20210279. doi: 10.1084/jem.20210279. Epub 2021 Jun 23. PMID: 34160549; PMCID: PMC8225680.
  • Zhang B, Nguyen LXT, Li L, Zhao D, Kumar B, Wu H, Lin A, Pellicano F, Hopcroft L, Su YL, Copland M, Holyoake TL, Kuo CJ, Bhatia R, Snyder DS, Ali H, Stein AS, Brewer C, Wang H, McDonald T, Swiderski P, Troadec E, Chen CC, Dorrance A, Pullarkat V, Yuan YC, Perrotti D, Carlesso N, Forman SJ, Kortylewski M, Kuo YH, Marcucci G. (2018) Bone marrow niche trafficking of miR-126 controls the self-renewal of leukemia stem cells in chronic myelogenous leukemia. Nat Med. 24(4):450-462, PMID: 29505034; PMCID: PMC5965294
  • Xiao S, Duan S, Hong Y, Zhang J, Ma S, Caligiuri MA, Yu J. Loss of YTHDF2 enhances Th9 programming and CAR-Th9 cell antitumor efficacy. Nat Immunol. 2025 Sep;26(9):1501-1515. doi: 10.1038/s41590-025-02235-2. Epub 2025 Aug 18. PMID: 40826275; PMCID: PMC12614224.
  • Xiao S, Duan S, Caligiuri MA, Ma S, Yu J. YTHDF2: a key RNA reader and antitumor target. Trends Immunol. 2025 Jun;46(6):485-498. doi: 10.1016/j.it.2025.04.003. Epub 2025 May 20. PMID: 40399203.
  • Xiao S, Ma S, Sun B, Pu W, Duan S, Han J, Hong Y, Zhang J, Peng Y, He C, Yi P, Caligiuri MA, Yu J. The tumor-intrinsic role of the m6A reader YTHDF2 in regulating immune evasion. Sci Immunol. 2024 May 31;9(95):eadl2171. doi: 10.1126/sciimmunol.adl2171. Epub 2024 May 31. PMID: 38820140; PMCID: PMC12068375.
  • Ma S, Sun B, Duan S, Han J, Barr T, Zhang J, Bissonnette MB, Kortylewski M, He C, Chen J, Caligiuri MA, Yu J. YTHDF2 orchestrates tumor-associated macrophage reprogramming and controls antitumor immunity through CD8+ T cells. Nat Immunol. 2023 Feb;24(2):255-266. doi: 10.1038/s41590-022-01398-6. Epub 2023 Jan 19. PMID: 36658237; PMCID: PMC10150872.
  • Wang Z, Pan Z, Adhikari S, Harada BT, Shen L, Yuan W, Abeywardana T, Al-Hadid Q, Stark JM, He C, Lin L, Yang Y. m6 A deposition is regulated by PRMT1-mediated arginine methylation of METTL14 in its disordered C-terminal region. EMBO J. 2021 Mar 1;40(5):e106309. doi: 10.15252/embj.2020106309. Epub 2021 Jan 18. PMID: 33459381; PMCID: PMC7917551.
  • Yuan W, Al-Hadid Q, Wang Z, Shen L, Cho H, Wu X, Yang Y. TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution. Nucleic Acids Res. 2021 Sep 7;49(15):8573-8591. doi: 10.1093/nar/gkab642. PMID: 34329467; PMCID: PMC8421139.
  • Shen L, Ma X, Wang Y, Wang Z, Zhang Y, Pham HQH, Tao X, Cui Y, Wei J, Lin D, Abeywanada T, Hardikar S, Halabelian L, Smith N, Chen T, Barsyte-Lovejoy D, Qiu S, Xing Y, Yang Y. Loss-of-function mutation in PRMT9 causes abnormal synapse development by dysregulation of RNA alternative splicing. Nat Commun. 2024 Apr 1;15(1):2809. doi: 10.1038/s41467-024-47107-9. PMID: 38561334; PMCID: PMC10984984.
  • Zhang Y, Shen L, Ren L, Wei J, Pham HQH, Tao X, Guo J, Wang Z, Shen B, Su R, He C, Yang Y. Arginine methylation-dependent METTL14-SMN interaction regulates RNA m6A homeostasis. EMBO Rep. 2025 Nov;26(22):5483-5500. doi: 10.1038/s44319-025-00590-7. Epub 2025 Oct 6. PMID: 41053315; PMCID: PMC12635257.
  • Saftics A, Purnell B, Beres B, Thompson S, Jiang N, Ghaeli I, Lima C, Armstrong B, Van Keuren-Jensen K, Jovanovic-Talisman T. Single Extracellular VEsicle Nanoscopy-Universal Protocol (SEVEN-UP): Accessible Imaging Platform for Quantitative Characterization of Single Extracellular Vesicles. Anal Chem. 2025 Jan 28;97(3):1654-1664. doi: 10.1021/acs.analchem.4c04614. Epub 2025 Jan 13. PubMed PMID: 39804668; PubMed Central PMCID: PMC11780574.
  • Saftics A, Abuelreich S, Romano E, Ghaeli I, Jiang N, Spanos M, Lennon KM, Singh G, Das S, Van Keuren-Jensen K, Jovanovic-Talisman T. Single Extracellular VEsicle Nanoscopy. J Extracell Vesicles. 2023 Jul;12(7):e12346. doi: 10.1002/jev2.12346. PubMed PMID: 37422692; PubMed Central PMCID: PMC10329735.
  • Oliveira GP Jr, Zigon E, Rogers G, Davodian D, Lu S, Jovanovic-Talisman T, Jones J, Tigges J, Tyagi S, Ghiran IC. Detection of Extracellular Vesicle RNA Using Molecular Beacons. iScience. 2020 Jan 24;23(1):100782. doi: 10.1016/j.isci.2019.100782. Epub 2019 Dec 19. PubMed PMID: 31958756; PubMed Central PMCID: PMC6992906.
  • Li Z#, Weng H#, Su R#, Weng X#, Zuo Z#, Li C, Huang H, Nachtergaele S, Dong L, Hu C, Qin X, Tang L, Wang Y, Hong GM, Huang H, Wang X, Chen P, Gurbuxani S, Arnovitz S, Li Y, Li S, Strong J, Neilly MB, Larson RA, Jiang X, Zhang P, Jin J*, He C*, Chen J*. FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N6-Methyladenosine RNA Demethylase. Cancer Cell. 2017 Jan 9;31(1):127-141. PMCID: PMC5234852.

**Cover Story of this issue of Cancer Cell

***Highlighted (Research Watch) by Cancer Discovery (2017 Feb;7(2):OF9)

  • Su R#, Dong L#, Li C#, Nachtergaele S, Wunderlich M, Qing Y, Deng X, Wang Y, Weng X, Hu C, Yu M, Skibbe J, Dai Q, Zou D, Wu T, Yu K, Weng H, Huang H, Ferchen K, Qin X, Zhang B, Qi J, Sasaki AT, Plas D, Bradner JE, Wei M, Marcucci G, Jiang X, Mulloy J, Jin J*, He C*, Chen J*. R-2HG exhibits anti-tumor activity by targeting FTO/m6A/MYC/CEBPA signaling. Cell. 2018 Jan 11;172(1-2):90-105. PMCID: PMC5766423.

**Highlighted (Research Watch) by Cancer Discovery (2018 Feb;8(2):137)

  • Weng H, Huang H, Wu H, Qin X, Zhao BS, Dong L, Shi H, Skibbe J, Shen C, Hu C, Sheng Y, Wang Y, Wunderlich M, Zhang B, Dore L, Su R, Deng X, Ferchen K, Li C, Sun M, Lu Z, Jiang X, Marcucci G, Mulloy J, Yang J, Qian Z*, Wei M*, He C*, Chen J*. METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and Promotes Leukemogenesis via mRNA m6A Modification. Cell Stem Cell. 2018 Feb 1;22(2):191-205. PMCID: PMC5860916.

**Highlighted by Cell Stem Cell with a Preview article (2018; 22:139–141); ***Best of Cell Stem Cell 2018 collection (one of the seven best articles published by Cell Stem Cell in 2018)

  • Huang H, Weng H, Sun W, Qin X, Shi H, Wu H, Zhao BS, Mesquita A, Liu C, Yuan CL, Hu YC, Hüttelmaier S, Skibbe J, Su R, Deng X, Dong L, Sun M, Li C, Nachtergaele S, Wang Y, Hu C, Ferchen K, Greis KD, Jiang X, Wei M, Qu L, Guan JL, He C*, Yang J*, Chen J*. Recognition of RNA N6-methyadenosine by IGF2BP proteins Enhances mRNA Stability and Translation. Nature Cell Biology. 2018 Mar;20(3):285-295. PMCID: PMC5826585.

**Featured by Nature Cell Biology with a News & Views article (2018; 20:230–232)

  • Huang H, Weng H, Zhou K, Wu T, Zhao BS, Sun M, Chen Z, Deng X, Xiao G, Auer F, Klemm L, Wu H, Zuo Z, Qin X, Dong Y, Zhou Y, Qin H, Tao S, Du J, Liu J, Lu Z, Yin H, Mesquita A, Yuan CL, Hu YC, Sun W, Su R,  Dong L, Shen C, Li C, Qing Y, Jiang X, Wu X, Sun M, Guan JL, Qu LH, Wei M, Müschen  M, Huang G*, He C*, Yang JH*, Chen J*. Histone H3 Trimethylation at Lysine 36 Guides m6A RNA Modification Co-transcriptionally. Nature. 2019 Mar 21;567(7748):414-419. PMCID: PMC6438714.

**Featured by Nature Reviews Genetics (2019 May; 20(5):254-255), Nature Chemical Biology (2019 May; 15(5):427), and Cancer Research (2019 May, 79: 2445-2446).

  • Huang H, Weng H, Chen J*. m6A Modification in Coding and Non-coding RNAs: Roles and Therapeutic Implications in Cancer. Cancer Cell. 2020 Mar 16;37(3):270-288. PMCID: PMC7141420.
  • Shen C, Sheng Y, Zhu A, Robinson S, Jiang X, Dong L, Chen H, Su R, Yin Z, Li W, Deng X, Chen Y, Hu YC, Weng H, Huang H, Prince E, Cogle CR, Sun M, Zhang B, Chen CW, Marcucci G, He C*, Qian Z*, Chen J*. RNA demethylase ALKBH5 selectively promotes tumorigenesis and cancer stem cell self-renewal in acute myeloid leukemia. Cell Stem Cell. 2020 Jul 2;27(1):64-80. PMCID: PMC7335338.  **Highlighted by Cell Stem Cell with a Preview article (2020 Jul 2;27(1):3-5).
  • Su R, Dong L, Li Y, Gao M, Han L, Wunderlich M, Deng X, Li H, Huang Y, Gao L, Li C, Zhao Z, Robison S, Tan B, Qing Y, Qin X, Prince E, Xie J, Qin H, Li W, Shen C, Sun J, Prakash K, Weng H, Huang H, Chen Z, Zhang B, Wu X, Olsen MJ, Muschen M, Marcucci G, Ravi S, Li, L, Fathi AT, Li Z, Mulloy JC, Wei M, Horne D, Chen J*. Targeting FTO suppresses cancer stem cell maintenance and immune evasion. Cancer Cell. 2020 Jul 13;38(1):79-96. PMCID: PMC7363590. **Highlighted by Molecule Cell with a Spotlight article (2020 Jun 18;78(6):996-998); ***Highlighted by Nature Reviews Drug Discovery (2020 Aug;19(8):510).
  • Su R*, Dong L, Gao M, Li Y, He PC, Liu W, Wei J, Gao L, Han L, Deng X, Zhao Z, Prince E, Tan B, Qing Y, Qin X, Shen C, Zhou K, Chen Z, Xue J, Li W, Qin H, Wu X, Sun M, Nam Y, Chen CW, Horne D, Rosen ST, He C*, Chen J*. METTL16 exerts an m6A-independent function to facilitate translation and tumorigenesis. Nature Cell Biology. 2022 Feb;24(2):205-216. PMCID: PMC9070413.
  • Hu L*,#, Liu S#, Peng Y#, Ge R#, Su R#, Senevirathne C, Harada BT, Dai Q, Wei J, Zhang L, Hao Z, Luo L, Wang H, Wang Y, Luo M, Chen M*, Chen J*, He C*. m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome. Nature Biotechnology. 2022 Aug;40(8):1210-1219. PMCID: PMC9378555. **Featured by Nature Cell Biology (2022 Apr;24(4):403).
  • Deng S, Zhang J, Su J, Zuo Z, Zeng L, Liu K, Zheng Y, Huang X, Bai R, Zhuang L, Ye Y, Li M, Pan L, Deng J, Wu G, Li R, Zhang S, Wu C, Lin D*, Chen J*, Zheng J*. RNA m6A regulates transcription via DNA demethylation and chromatin accessibility. Nature Genetics. 2022 Sep;54(9):1427-1437. PMCID: Pending. ** Featured by Nature Genetics (2022 Sep;54(9):1261-1262).
  • Weng H*, Huang F, Yu Z, Chen Z, Prince E, Kang Y, Zhou K, Wei L, Hu J, Fu C, Aziz T, Li H, Li J, Yang Y, Han L, Zhang S, Ma Y, Sun M, Wu H, Zhang Z, Wunderlich M, Robinson S, Braas D, Hoeve JT, Zhang B, Marcucci G, Mulloy JC, Zhou K, Tao HF, Deng X, Horne D, Wei M*, Huang H*, Chen J*. The m6A Reader IGF2BP2 Regulates Glutamine Metabolism and Represents a Therapeutic Target in Acute Myeloid Leukemia. Cancer Cell. 2022 Dec 12;40(12):1566-1582.e10. PMCID: PMC9772162.
  • Han L, Dong L, Leung K, Zhao Z, Li Y, Gao L, Chen Z, Xue J, Qing Y, Li W, Pokhare SP, Gao M, Chen M, Shen C, Tan B, Small A, Wang K, Zhang Z, Qin X, Yang L, Zhang B, Marcucci G, Chen CW, Wei M*, Su R*, Chen J*, Deng X*. METTL16 drives leukemogenesis and leukemia stem cell self-renewal by reprogramming BCAA metabolism. Cell Stem Cell. 2023 Jan 5;30(1):52-68.e13. PMCID: PMC9838187. ** Featured by Cell Stem Cell. 2023 Jan 5;30(1):3-4.
  • Chen Z, Zhou K, Xue J, Small A, Xiao G, Nguyen LXT, Zhang Z, Prince E, Weng H, Huang H, Li W, Zhao Z, Qing Y, Shen C, Tan B, Su R, Qin H, Li Y, Han L, Gu Z, Ngo VN, He X, Chao J, Leung K, Wang K, Dong L, Qin X, Cai Z, Sheng Y, Chen Y, Wu X, Zhang B, ShiY, Marcucci G, Qian Z, Xu M, Müschen M, Chen J*, Deng X*. Phosphorylation stabilized TET1 promotes B-cell acute lymphoblastic leukemia development independent of its catalytic activity. Science Translational Medicine. 2023 Mar 29;15(689):eabq8513. doi: 10.1126/scitranslmed.abq8513. Epub 2023 Mar 29. PMCID: PMC1116396.
  • Zhao Z, Qing Y, Dong L, Han L, Wu D, Li Y, Li W, Xue J, Zhou K, Sun M, Tan B, Chen Z, Shen C, Gao L, Small A, Wang K, Leung K, Zhang Z, Qin X, Deng X, Xia Q*, Su R*, Chen J*. QKI shuttles internal m7G-modified transcripts into stress granules and modulates messenger RNA metabolism. Cell. 2023 Jul 20;186(15):3208-3226.e27. PMCID: PMC10527483.  ** Featured by Nature Reviews Molecular Cell Biology (2023 Aug;24(8):522. doi: 10.1038/s41580-023-00635-6.).
  • Deng X*, Qing Y, David Horne, Huang H*, Chen J*. The roles and implications of m6A RNA methylation in cancer. Nature Reviews Clinical Oncology. 2023 Aug;20(8):507-526. PMCID: PMC12466201.
  • Li Y#, Xue M#, Deng X#, Dong L#, Nguyen LXT, Ren L, Han L, Li C, Xue J, Zhao Z, Li W, Qing Y, Shen C, Tan B, Chen Z, Leung K, Wang K, Swaminathan S, Li L, Chen Y, Wunderlich M, Mulloy JC, Li X, Chen H, Zhang B, Horne D, Rosen ST, Marcucci G, Xu M, Li Z, Wei M, Tian J*, Shen B*, Su R*, Chen J*. TET2-mediated mRNA demethylation regulates leukemia stem cell homing and self-renewal. Cell Stem Cell. 2023 Aug 3;30(8):1072-1090.e10. PMCID: PMC11166201.
  • Dou X, Xiao Y, Shen C, Wang K, Liu C, Yu X, Liu J, Dai Q, Ge R, Gao B, Chen M*, Chen J*, He C*. RBFOX2 recognizes N6-methyladenosine to suppress transcription and block myeloid differentiation. Nature Cell Biology. 2023 Sep;25(9):1359-1368. PMCID: PMC10495261
  • Chen M, Shen C, Chen Y, Chen Z, Zhou K, Chen Y, Li W, Zeng C, Qing Y, Wu D, Xu C, Tang T, Che Y, Qin X, Xu Z, Wang K, Leung K, Sau L, Deng X*, Hu J*, Wu Y*, Chen J*. Metformin synergizes with Gilteritinib in treating FLT3-mutated leukemia via targeting PLK1 signaling. Cell Reports Medicine. 2024 Jul 16;5(7):101645. PMID: 39019012 PMCID: PMC11293342
  • Chen Z*, Zeng C, Yang L, Che Y, Chen M, Sau L, Wang B, Zhou K, Chen Y, Qing Y, Shen C, Zhang T, Wunderlich M, Wu D, Li W, Wang K, Leung K, Sun M, Tang T, He X, Zhang L, Swaminathan S, Mulloy JC, Müschen M, Huang H, Weng H, Xiao G, Xiao G, Deng X*, Chen J*. YTHDF2 promotes ATP synthesis and immune evasion in B cell malignancies.  Cell. PMCID: PMC12394000.
  • Shen C*, Che Y, Zhou K, Wang K, Li W, Xue D, Wu T, Yang L, Chen M, Sheng Y, Zhang C, Robinson S, Chen H, Sau L, Chen Z, Wunderlich M, Han L, Tang T, Qing Y, Wu D, Sun M, Leung K, Dąbrowska K, Pirrotte P, Hu YC, Ghoda LY, Zhang B, Mulloy JC, Wei M, Marcucci G, He C*, Deng X*, Chen J*. ALKBH1 drives tumorigenesis and drug resistance via tRNA decoding reprogramming and codon-biased translation. Cancer Discovery. 2025 Aug 4:10.1158/2159-8290.CD-24-1043. doi: 10.1158/2159-8290.CD-24-1043. Online ahead of print. PMCID: PMC12377461.
  • Deng X*, Wu D, Zhao Y, Wu H*, Chen J*. Epitranscriptomic Control of Cancer Hallmarks: Functions, Mechanisms, and Therapeutics of RNA Modifications. Cancer Cell. 2026. In Press.
  • Chen Z, Satake E, Pezzolesi MG, Md Dom ZI, Stucki D, Kobayashi H, Syreeni A, Johnson AT, Wu X, Dahlström EH, King JB, Groop PH, Rich SS, Sandholm N, Krolewski AS, Natarajan R. Integrated analysis of blood DNA methylation, genetic variants, circulating proteins, microRNAs, and kidney failure in type 1 diabetes. Sci Transl Med. 2024 May 22;16(748):eadj3385. doi: 10.1126/scitranslmed.adj3385. Epub 2024 May 22. PMID: 38776390; PMCID: PMC11806497.
  • Kato M, Abdollahi M, Omori K, Malek V, Lanting L, Kandeel F, Rawson J, Tsark W, Zhang L, Wang M, Tunduguru R, Natarajan R. Lowering an ER stress-regulated long noncoding RNA protects mice from diabetes and isolated pancreatic islets from cell death. Mol Ther Nucleic Acids. 2024 Jun 15;35(3):102252. doi: 10.1016/j.omtn.2024.102252. PMID: 39071954; PMCID: PMC11278341.
  • Reddy MA, Amaram V, Das S, Tanwar VS, Ganguly R, Wang M, Lanting L, Zhang L, Abdollahi M, Chen Z, Wu X, Devaraj S, Natarajan R. lncRNA DRAIR is downregulated in diabetic monocytes and modulates the inflammatory phenotype via epigenetic mechanisms. JCI Insight. 2021 Jun 8;6(11):e143289. doi: 10.1172/jci.insight.143289. PMID: 33945509; PMCID: PMC8262346.
  • Das S, Zhang E, Senapati P, Amaram V, Reddy MA, Stapleton K, Leung A, Lanting L, Wang M, Chen Z, Kato M, Oh HJ, Guo Q, Zhang X, Zhang B, Zhang H, Zhao Q, Wang W, Wu Y, Natarajan R. A Novel Angiotensin II-Induced Long Noncoding RNA Giver Regulates Oxidative Stress, Inflammation, and Proliferation in Vascular Smooth Muscle Cells. Circ Res. 2018 Dec 7;123(12):1298-1312. doi: 10.1161/CIRCRESAHA.118.313207. doi: 10.1161/RES.0000000000000310. PMID: 30566058; PMCID: PMC6309807.
  • Kato M, Wang M, Chen Z, Bhatt K, Oh HJ, Lanting L, Deshpande S, Jia Y, Lai JY, O'Connor CL, Wu Y, Hodgin JB, Nelson RG, Bitzer M, Natarajan R. An endoplasmic reticulum stress-regulated lncRNA hosting a microRNA megacluster induces early features of diabetic nephropathy. Nat Commun. 2016 Sep 30;7:12864. doi: 10.1038/ncomms12864. PMID: 27686049; PMCID: PMC5553130.
  • Kato M, Putta S, Wang M, Yuan H, Lanting L, Nair I, Gunn A, Nakagawa Y, Shimano H, Todorov I, Rossi JJ, Natarajan R. TGF-beta activates Akt kinase through a microRNA-dependent amplifying circuit targeting PTEN. Nat Cell Biol. 2009 Jul;11(7):881-9. doi: 10.1038/ncb1897. Epub 2009 Jun 21. PMID: 19543271; PMCID: PMC2744130.
  • Kato M, Zhang J, Wang M, Lanting L, Yuan H, Rossi JJ, Natarajan R. MicroRNA-192 in diabetic kidney glomeruli and its function in TGF-beta-induced collagen expression via inhibition of E-box repressors. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3432-7. doi: 10.1073/pnas.0611192104. Epub 2007 Feb 20. PMID: 17360662; PMCID: PMC1805579.
  • DeFranciscis V, Amabile G, Kortylewski M. Clinical applications of oligonucleotides for cancer therapy. Mol Ther. 2025 Jun 4;33(6):2705-2718. doi: 10.1016/j.ymthe.2025.02.045. Epub 2025 Mar 5. PMID: 40045578; PMCID: PMC12172192.
  • Hung CY, Kang EY, Jacek K, Yu C, Zhang X, Zhu Y, Aftabizadeh M, Wong RA, Badie B, Świderski P, Kamińska B, Alizadeh D, Heimberger AB, Brown CE, Kortylewski M. Multimodal glioma immunotherapy combining TLR9-targeted STAT3 antisense oligodeoxynucleotides with PD1 immune checkpoint blockade. Neuro Oncol. 2025 Oct 14;27(9):2296-2312. doi: 10.1093/neuonc/noaf099. PMID: 40214214; PMCID: PMC12526143.
  • Yu C, Kang EY, Wang D, Liang Y, Swiderski P, Feng Y, Li H, Synold T, Forman S, Kwak L, Kortylewski M. Cell-selective telomere damage by thiopurine-based oligonucleotide for diffuse large B cell lymphoma immunotherapy. Mol Ther. 2025 Oct 1;33(10):5028-5043. doi: 10.1016/j.ymthe.2025.07.029. Epub 2025 Jul 23. PMID: 40708199; PMCID: PMC12380039.
  • Alcantara MB, Tang WS, Wang D, Kaniowski D, Kang E, Dizman N, Chehrazi-Raffle A, Meza L, Zengin Z, Hall J, Hsu J, Egelston C, Moreira D, Horsager A, Pal SK, Kortylewski M. Targeting STAT3 in tumor-associated antigen-presenting cells as a strategy for kidney and bladder cancer immunotherapy. Front Immunol. 2024 Jan 8;14:1274781. doi: 10.3389/fimmu.2023.1274781. PMID: 38259453; PMCID: PMC10800835
  • Krishnan P, Branco RCS, Weaver SA, Chang G, Lee CC, Syed F*, Evans-Molina C*. miR-146a-5p mediates inflammation-induced β cell mitochondrial dysfunction and apoptosis. J Biol Chem. 2024 Sep 27:107827. doi: 10.1016/j.jbc.2024.107827. Epub ahead of print. PMID: 39342996
  • Wu W, Syed F, Simpson E, Lee CC, Liu J, Chang G, Dong C, Seitz C, Eizirik DL, Mirmira RG, Liu Y, Evans-Molina C. The Impact of Pro-Inflammatory Cytokines on Alternative Splicing Patterns in Human Islets. Diabetes. 2021 Oct 21:db200847. doi: 10.2337/db20-0847.
  • Kidwell A, Yadav SPS, Maier B, Zollman A, Ni K, Halim A, Janosevic D, Myslinski J, Syed F, Zeng L, Waffo AB, Banno K, Xuei X, Doud EH, Dagher PC, Hato T. Translation Rescue by Targeting Ppp1r15a through Its Upstream Open Reading Frame in Sepsis-Induced Acute Kidney Injury in a Murine Model. J Am Soc Nephrol. 2022 Oct 25:10.1681/ASN.2022060644. doi: 10.1681/ASN.2022060644.
  • Hato T, Maier B, Syed F, Myslinski J, Zollman A, Plotkin Z, Eadon MT, Dagher PC. Bacterial sepsis triggers an antiviral response that causes translation shutdown. J Clin Invest. 2019;129(1):296-309.
  • Wang H, He X, Zhang L, Dong H, Huang F, Xian J, Li M, Chen W, Lu X, Pathak KV, Huang W, Li Z, Zhang L, Nguyen LXT, Yang L, Feng L, Gordon DJ, Zhang J, Pirrotte P, Chen CW, Salhotra A, Kuo YH, Horne D, Marcucci G, Sykes DB, Tiziani S, Jin H, Wang X, Li L. Disruption of dNTP homeostasis by ribonucleotide reductase hyperactivation overcomes AML differentiation blockade. Blood. 2022 Jun 30;139(26):3752-3770. doi: 10.1182/blood.2021015108. PMID: 35439288; PMCID: PMC9247363.
  • Dong, H., He, X., Zhang, L. et al. Targeting PRMT9-mediated arginine methylation suppresses cancer stem cell maintenance and elicits cGAS-mediated anticancer immunity. Nat Cancer 5, 601–624 (2024). https://doi.org/10.1038/s43018-024-00736-x
  • [dataset]  (2025). Inhibition of ADSS2-mediated de novo AMP biosynthesis resensitizes acute myeloid leukemia to BH3 mimetics, geo, V1.
  • Rodnoi P, Rajkumar M, Moin ASM, Georgia SK, Butler AE, Dhawan S. Neuropeptide Y expression marks partially differentiated β cells in mice and humans. JCI Insight. 2017 Jun 15;2(12). doi: 10.1172/jci.insight.94005. eCollection 2017 Jun 15. PubMed PMID: 28614797; PubMed Central PMCID: PMC5470892.
  • Parveen N, Wang JK, Bhattacharya S, Cuala J, Rajkumar MS, Butler AE, Wu X, Shih HP, Georgia SK, Dhawan S. DNA Methylation-Dependent Restriction of Tyrosine Hydroxylase Contributes to Pancreatic β-Cell Heterogeneity. Diabetes. 2023 May 1;72(5):575-589. doi: 10.2337/db22-0506. PubMed PMID: 36607262; PubMed Central PMCID: PMC10130487.
  • Varghese SS, Dhawan S. Senescence: a double-edged sword in beta-cell health and failure? Front Endocrinol (Lausanne). 2023; 14:1196460. doi: 10.3389/fendo.2023.1196460. eCollection 2023. PubMed PMID: 37229454; PubMed Central PMCID: PMC10203573.
  • Varghese SS, Hernandez-De La Pe.a AG, Dhawan S. Safeguarding genomic integrity in beta-cells: implications for beta-cell differentiation, growth, and dysfunction. Biochem Soc Trans. 2024 Oct 30;52(5):2133-2144. doi: 10.1042/BST20231519. Review. PubMed PMID: 39364746; PubMed Central PMCID: PMC11555696.
  • Varghese SS, Hernandez-De La Pe.a AG, Pandey A, Anchondo L, Wu X, Bhattacharya S, Dhawan S. Developmental control of DNA damage responses in α- and β-cells shapes the selective beta-cell susceptibility in diabetes. bioRxiv. 2025 Nov 12; doi: 10.1101/2025.11.10.687707. PubMed PMID: 41292712; PubMed Central PMCID: PMC12642488.
  • Yifei Miao, Nassim E Ajami, Tse-Shun Huang, Feng-Mao Lin, Chih-Hong Lou, Yun-Ting Wang, Shuai Li, Jian Kang, Hannah Munkacsi, Mano R Maurya, Shakti Gupta, Shu Chien, Shankar Subramaniam, Zhen Chen. Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function. Nat Commun. 2018. DOI: 10.1038/s41467-017-02113-y     
  • Xiaofang Tang, Yifei Miao, Yingjun Luo, Kiran Sriram, Zhijie Qi, Feng-Mao Lin, Yusu Gu, Chih-Hung Lai, Chien-Yi Hsu, Kirk L Peterson, Kendall Van Keuren-Jensen, Patrick T Fueger, Gene W Yeo, Rama Natarajan, Sheng Zhong, Zhen Bouman Chen. Suppression of endothelial AGO1 promotes adipose tissue browning and improves metabolic dysfunction. Circulation. 2020. DOI: 10.1161/CIRCULATIONAHA.119.041231
  • Xiaofang Tang, Yingjun Luo, Dongqiang Yuan, Riccardo Calandrelli, Naseeb Kaur Malhi, Kiran Sriram, Yifei Miao, Chih-Hong Lou, Walter Tsark, Alonso Tapia, Aleysha T Chen, Guangyu Zhang, Daniel Roeth, Markus Kalkum, Zhao V Wang, Shu Chien, Rama Natarajan, John P Cooke, Sheng Zhong, Zhen Bouman Chen. Long non-coding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models. J Clin Invest. 2023. DOI: 10.1172/JCI161759
  • Kiran Sriram, Zhijie Qi, Dongqiang Yuan, Naseeb Kaur Malhi, Xuejing Liu, Riccardo Calandrelli, Yingjun Luo, Alonso Tapia, Shengyan Jin, Ji Shi, Martha Salas Ruirui Dang, Brian Armstrong, Saul J. Priceman, Ping Wang, Jiayu Liao, Rama Natarajan, Sheng Zhong, Zhen Bouman Chen. Regulation of nuclear transcription by mitochondrial RNA. Elife. 2024. DOI: 10.7554/eLife.86204
  • Naseeb Kaur Malhi, Yingjun Luo, Xiaofang Tang, Rahuljeet Singh Chadha, Alonso Tapia, Xuejing Liu, Muxi Chen, Dongqiang Yuan, Meirigeng Qi, Lu Wei, John P Cooke, Rama Natarajan, Kevin W Southerland, Zhen Bouman Chen. Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response. Accepted in principle, Sci Trans Med 2026