Qi Chen

Qi Chen, MD, PhD

Academic Information

Departments Primary - Surgery , Adjunct - Human Genetics

Divisions: Urology

Education History

Graduate Training Institute of Zoology, Chinese Academy of Sciences
 PhD
Professional Medical Chongqing Medical University
 MD

Selected Publications

Journal Article

  1. Shi J, Zhang Y, Li Y, Zhang L, Zhang X, Yan M, Chen Q, Zhang Y (2025). Optimized identification and characterization of small RNAs with PANDORA-seq. Nat Protoc. (Read full article)
  2. Zhang X, Shi J, Thakore P, Gonzales AL, Earley S, Chen Q, Zhou T, Feng Earley Y (2025). Mitochondrial Small RNA Alterations Associated with Increased Lysosome Activity in an Alzheimer's Disease Mouse Model Uncovered by PANDORA-seq. Int J Mol Sci, 26(7). (Read full article)
  3. Zhang X, Shi J, Thakore P, Gonzales AL, Earley S, Chen Q, Zhou T, Earley YF (2024). Mitochondrial small RNA alterations associated with increased lysosome activity in an Alzheimer's Disease Mouse Model uncovered by PANDORA-seq. bioRxiv. (Read full article)
  4. Kodali S, Proietti L, Valcarcel G, Lpez-Rubio AV, Pessina P, Eder T, Shi J, Jen A, Lupin-Garcia N, Starner AC, Bartels MD, Cui Y, Sands CM, Planas-Riverola A, Martnez A, Velasco-Hernandez T, Toms-Daza L, Alber B, Manhart G, Mayer IM, Kollmann K, Fatica A, Menendez P, Shishkova E, Rau RE, Javierre BM, Coon J, Chen Q, Van Nostrand EL, Sardina JL, Grebien F, Di Stefano B (2024). RNA sequestration in P-bodies sustains myeloid leukaemia. Nat Cell Biol, 26(10), 1745-1758. (Read full article)
  5. Yuan X, Su Y, Johnson B, Kirchner M, Zhang X, Xu S, Jiang S, Wu J, Shi S, Russo JJ, Chen Q, Zhang S (2024). Mass Spectrometry-Based Direct Sequencing of tRNAs De Novo and Quantitative Mapping of Multiple RNA Modifications. J Am Chem Soc, 146(37), 25600-25613. (Read full article)
  6. Hernandez R, Li X, Shi J, Dave TR, Zhou T, Chen Q, Zhou C (2024). Paternal hypercholesterolemia elicits sex-specific exacerbation of atherosclerosis in offspring. JCI Insight, 9(17). (Read full article)
  7. Wang X, Yu D, Yu J, Hu H, Hang R, Amador Z, Chen Q, Chai J, Chen X (2024). Toll/interleukin-1 receptor (TIR) domain-containing proteins have NAD-RNA decapping activity. Nat Commun, 15(1), 2261. (Read full article)
  8. Xue Y, Gong Y, Li X, Peng F, Ding G, Zhang Z, Shi J, Savul IS, Xu Y, Chen Q, Han L, Mao S, Sun Z (2023). Sex differences in paternal arsenic-induced intergenerational metabolic effects are mediated by estrogen. Cell Biosci, 13(1), 165. (Read full article)
  9. Holmes AD, Chan PP, Chen Q, Ivanov P, Drouard L, Polacek N, Kay MA, Lowe TM (2023). A standardized ontology for naming tRNA-derived RNAs based on molecular origin. Nat Methods, 20(5), 627-628. (Read full article)
  10. Hernandez R, Shi J, Liu J, Li X, Wu J, Zhao L, Zhou T, Chen Q, Zhou C (2023). PANDORA-Seq unveils the hidden small noncoding RNA landscape in atherosclerosis of LDL receptor-deficient mice. J Lipid Res, 64(4), 100352. (Read full article)
  11. Zhu L, Zhou T, Iyyappan R, Ming H, Dvoran M, Wang Y, Chen Q, Roberts RM, Susor A, Jiang Z (2022). High-resolution ribosome profiling reveals translational selectivity for transcripts in bovine preimplantation embryo development. Development, 149(21). (Read full article)
  12. Zhang L, Li Y, Wang J, Hong C, Lu W, Qu Y, Black SM, Chen Q, Zhou T, Jin W, Duan E, Tang H, Zhang Y (2022). RNA Modification Signature of Peripheral Blood as a Potential Diagnostic Marker for Pulmonary Hypertension. Hypertension, 79(3), e67-e69. (Read full article)
  13. Qu Y, Chen Q, Guo S, Ma C, Lu Y, Shi J, Liu S, Zhou T, Noda T, Qian J, Zhang L, Zhu X, Lei X, Cao Y, Li W, Li W, Plachta N, Matzuk MM, Ikawa M, Duan E, Zhang Y, Wang H (2021). Cooperation-based sperm clusters mediate sperm oviduct entry and fertilization. Protein Cell, 12(10), 810-817. (Read full article)
  14. Liu C, Liu H, Zhang H, Wang L, Li M, Cai F, Wang X, Wang L, Zhang R, Yang S, Liu W, Liang Y, Wang L, Song X, Su S, Gao H, Jiang J, Li J, Luo M, Gao F, Chen Q, Li W, Chen ZJ (2021). Paternal USP26 mutations raise Klinefelter syndrome risk in the offspring of mice and humans. EMBO J, 40(13), e106864. (Read full article)
  15. Shi J, Zhang Y, Tan D, Zhang X, Yan M, Zhang Y, Franklin R, Shahbazi M, Mackinlay K, Liu S, Kuhle B, James ER, Zhang L, Qu Y, Zhai Q, Zhao W, Zhao L, Zhou C, Gu W, Murn J, Guo J, Carrell DT, Wang Y, Chen X, Cairns BR, Yang XL, Schimmel P, Zernicka-Goetz M, Cheloufi S, Zhang Y, Zhou T, Chen Q (2021). PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nat Cell Biol, 23(4), 424-436. (Read full article)
  16. Gu W, Shi J, Liu H, Zhang X, Zhou JJ, Li M, Zhou D, Li R, Lv J, Wen G, Zhu S, Qi T, Li W, Wang X, Wang Z, Zhu H, Zhou C, Knox KS, Wang T, Chen Q, Qian Z, Zhou T (2020). Peripheral blood non-canonical small non-coding RNAs as novel biomarkers in lung cancer. Mol Cancer, 19(1), 159. (Read full article)
  17. Zhang X, Trebak F, Souza LAC, Shi J, Zhou T, Kehoe PG, Chen Q, Feng Earley Y (2020). Small RNA modifications in Alzheimer's disease. Neurobiol Dis, 145, 105058. (Read full article)
  18. Wang J, Xie X, Shi J, He W, Chen Q, Chen L, Gu W, Zhou T (2020). Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma. Genomics Proteomics Bioinformatics, 18(4), 468-480. (Read full article)
  19. Sui Y, Meng Z, Park SH, Lu W, Livelo C, Chen Q, Zhou T, Zhou C (2020). Myeloid-specific deficiency of pregnane X receptor decreases atherosclerosis in LDL receptor-deficient mice. J Lipid Res, 61(5), 696-706. (Read full article)
  20. Huang L, Meng TG, Ma XS, Wang ZB, Qi ST, Chen Q, Zhang QH, Liang QX, Wang ZW, Hu MW, Guo L, Ouyang YC, Hou Y, Zhao Y, Sun QY (2018). Rad9a is involved in chromatin decondensation and post-zygotic embryo development in mice. Cell Death Differ, 26(5), 969-980. (Read full article)
  21. Durnin L, Kwok B, Kukadia P, McAvera R, Corrigan RD, Ward SM, Zhang Y, Chen Q, Koh SD, Sanders KM, Mutafova-Yambolieva VN (2018). An ex vivo bladder model with detrusor smooth muscle removed to analyse biologically active mediators released from the suburothelium. J Physiol, 597(6), 1467-1485. (Read full article)
  22. Wang J, Wang L, Feng G, Wang Y, Li Y, Li X, Liu C, Jiao G, Huang C, Shi J, Zhou T, Chen Q, Liu Z, Li W, Zhou Q (2018). Asymmetric Expression of LincGET Biases Cell Fate in Two-Cell Mouse Embryos. Cell, 175(7), 1887-1901.e18. (Read full article)
  23. Qian J, Zhang Y, Qu Y, Zhang L, Shi J, Zhang X, Liu S, Kim BH, Hwang SJ, Zhou T, Chen Q, Ward SM, Duan E, Zhang Y (2018). Caffeine consumption during early pregnancy impairs oviductal embryo transport, embryonic development and uterine receptivity in mice. Biol Reprod, 99(6), 1266-1275. (Read full article)
  24. Zhou T, Xie X, Li M, Shi J, Zhou JJ, Knox KS, Wang T, Chen Q, Gu W (2018). Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages. RNA, 24(11), 1443-1456. (Read full article)
  25. Chen Q, Shi J, Tao Y, Zernicka-Goetz M (2018). Tracing the origin of heterogeneity and symmetry breaking in the early mammalian embryo. Nat Commun, 9(1), 1819. (Read full article)
  26. Zhang Y, Zhang X, Shi J, Tuorto F, Li X, Liu Y, Liebers R, Zhang L, Qu Y, Qian J, Pahima M, Liu Y, Yan M, Cao Z, Lei X, Cao Y, Peng H, Liu S, Wang Y, Zheng H, Woolsey R, Quilici D, Zhai Q, Li L, Zhou T, Yan W, Lyko F, Zhang Y, Zhou Q, Duan E, Chen Q (2018). Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nat Cell Biol, 20(5), 535-540. (Read full article)
  27. Shi J, Ko EA, Sanders KM, Chen Q, Zhou T (2018). SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs. Genomics Proteomics Bioinformatics, 16(2), 144-151. (Read full article)
  28. Qiao J, Zhao H, Zhang Y, Peng H, Chen Q, Zhang H, Zheng X, Jin Y, Ni H, Duan E, Guo Y (2016). GPR39 is region-specifically expressed in mouse oviduct correlating with the Zn(2+) distribution. Theriogenology, 88, 98-105. (Read full article)
  29. Chen Q, Yan M, Cao Z, Li X, Zhang Y, Shi J, Feng GH, Peng H, Zhang X, Zhang Y, Qian J, Duan E, Zhai Q, Zhou Q (2015). Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science, 351(6271), 397-400. (Read full article)
  30. Shi J, Chen Q, Li X, Zheng X, Zhang Y, Qiao J, Tang F, Tao Y, Zhou Q, Duan E (2015). Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq. Development, 142(20), 3468-77. (Read full article)
  31. Deng Z, Lei X, Zhang X, Zhang H, Liu S, Chen Q, Hu H, Wang X, Ning L, Cao Y, Zhao T, Zhou J, Chen T, Duan E (2015). mTOR signaling promotes stem cell activation via counterbalancing BMP-mediated suppression during hair regeneration. J Mol Cell Biol, 7(1), 62-72. (Read full article)
  32. Zhang Y, Chen Q, Zhang H, Wang Q, Li R, Jin Y, Wang H, Ma T, Qiao J, Duan E (2014). Aquaporin-dependent excessive intrauterine fluid accumulation is a major contributor in hyper-estrogen induced aberrant embryo implantation. Cell Res, 25(1), 139-42. (Read full article)
  33. Lei X, Deng Z, Zhang H, Zhao H, Zhou J, Liu S, Chen Q, Ning L, Cao Y, Wang X, Zhang X, Duan E (2014). Rotary suspension culture enhances mesendoderm differentiation of embryonic stem cells through modulation of Wnt/β-catenin pathway. Stem Cell Rev Rep, 10(4), 526-38. (Read full article)
  34. Zhang S, Kong S, Wang B, Cheng X, Chen Y, Wu W, Wang Q, Shi J, Zhang Y, Wang S, Lu J, Lydon JP, DeMayo F, Pear WS, Han H, Lin H, Li L, Wang H, Wang YL, Li B, Chen Q, Duan E, Wang H (2014). Uterine Rbpj is required for embryonic-uterine orientation and decidual remodeling via Notch pathway-independent and -dependent mechanisms. Cell Res, 24(8), 925-42. (Read full article)
  35. Wang H, Wan H, Li X, Liu W, Chen Q, Wang Y, Yang L, Tang H, Zhang X, Duan E, Zhao X, Gao F, Li W (2014). Atg7 is required for acrosome biogenesis during spermatogenesis in mice. Cell Res, 24(7), 852-69. (Read full article)
  36. Zhang Y, Zhang Y, Shi J, Zhang H, Cao Z, Gao X, Ren W, Ning Y, Ning L, Cao Y, Chen Y, Ji W, Chen ZJ, Chen Q, Duan E (2013). Identification and characterization of an ancient class of small RNAs enriched in serum associating with active infection. J Mol Cell Biol, 6(2), 172-4. (Read full article)
  37. Fu Z, Wang B, Wang S, Wu W, Wang Q, Chen Y, Kong S, Lu J, Tang Z, Ran H, Tu Z, He B, Zhang S, Chen Q, Jin W, Duan E, Wang H, Wang YL, Li L, Wang F, Gao S, Wang H (2014). Integral proteomic analysis of blastocysts reveals key molecular machinery governing embryonic diapause and reactivation for implantation in mice. Biol Reprod, 90(3), 52. (Read full article)
  38. Zhang H, Zhang Y, Zhao H, Zhang Y, Chen Q, Peng H, Lei L, Qiao J, Shi J, Cao Z, Duan E, Jin Y (2013). Hormonal regulation of ovarian bursa fluid in mice and involvement of aquaporins. PLoS One, 8(5), e63823. (Read full article)
  39. Zhang Q, Chen Q, Lu X, Zhou Z, Zhang H, Lin HY, Duan E, Zhu C, Tan Y, Wang H (2013). CUL1 promotes trophoblast cell invasion at the maternal-fetal interface. Cell Death Dis, 4(2), e502. (Read full article)
  40. Wang Q, Lu J, Zhang S, Wang S, Wang W, Wang B, Wang F, Chen Q, Duan E, Leitges M, Kispert A, Wang H (2013). Wnt6 is essential for stromal cell proliferation during decidualization in mice. Biol Reprod, 88(1), 5. (Read full article)
  41. Peng H, Shi J, Zhang Y, Zhang H, Liao S, Li W, Lei L, Han C, Ning L, Cao Y, Zhou Q, Chen Q, Duan E (2012). A novel class of tRNA-derived small RNAs extremely enriched in mature mouse sperm. Cell Res, 22(11), 1609-12. (Read full article)
  42. Chen Q, Peng H, Lei L, Zhang Y, Kuang H, Cao Y, Shi QX, Ma T, Duan E (2010). Aquaporin3 is a sperm water channel essential for postcopulatory sperm osmoadaptation and migration. Cell Res, 21(6), 922-33. (Read full article)
  43. Peng H, Zhang Y, Lei L, Chen Q, Yue J, Tan Y, Duan E (2010). Aquaporin 7 expression in postimplantation mouse uteri: a potential role for glycerol transport in uterine decidualization. Fertil Steril, 95(4), 1514-7.e1-3. (Read full article)
  44. Chen Q, Zhang Y, Peng H, Lei L, Kuang H, Zhang L, Ning L, Cao Y, Duan E (2010). Transient {beta}2-adrenoceptor activation confers pregnancy loss by disrupting embryo spacing at implantation. J Biol Chem, 286(6), 4349-56. (Read full article)
  45. Kuang H, Zhang L, Peng J, Chen Q (2009). Premature ovarian failure, menopause and ovarian cancer, three nodes on the same string: Pten and other potential genes on the go. Med Hypotheses, 73(6), 961-2. (Read full article)
  46. Kuang H, Chen Q, Zhang Y, Zhang L, Peng H, Ning L, Cao Y, Duan E (2009). The cytokine gene CXCL14 restricts human trophoblast cell invasion by suppressing gelatinase activity. Endocrinology, 150(12), 5596-605. (Read full article)
  47. Zhang L, Guo W, Chen Q, Fan X, Zhang Y, Duan E (2009). Adam12 plays a role during uterine decidualization in mice. Cell Tissue Res, 338(3), 413-21. (Read full article)
  48. Kuang H, Chen Q, Fan X, Zhang Y, Zhang L, Peng H, Cao Y, Duan E (2009). CXCL14 inhibits trophoblast outgrowth via a paracrine/autocrine manner during early pregnancy in mice. J Cell Physiol, 221(2), 448-57. (Read full article)
  49. Peng H, Chen Q, Tan Y (2009). Frequent ejaculation associated free radical and lactic acid accumulation cause noninfectious inflammation and muscle dysfunction: a potential mechanism for symptoms in Chronic Prostatitis/Chronic Pelvic Pain Syndrome. Med Hypotheses, 73(3), 372-3. (Read full article)
  50. Zhang Y, Peng S, Kuang H, Chen Q, Liu S, Zhang L, Duan E (2008). Expression and regulation of Dickkopf2 during periimplantation in mice. J Reprod Dev, 55(1), 17-22. (Read full article)
  51. Peng S, Li J, Miao C, Jia L, Hu Z, Zhao P, Li J, Zhang Y, Chen Q, Duan E (2008). Dickkopf-1 secreted by decidual cells promotes trophoblast cell invasion during murine placentation. Reproduction, 135(3), 367-75. (Read full article)

Review

  1. Yu J, Zhang X, Cai C, Zhou T, Chen Q (2025). Small RNA and Toll-like receptor interactions: origins and disease mechanisms. [Review]. Trends Biochem Sci. (Read full article)
  2. Kuhle B, Chen Q, Schimmel P (2023). tRNA renovatio: Rebirth through fragmentation. [Review]. Mol Cell, 83(22), 3953-3971. (Read full article)
  3. Chen Q, Zhou T (2023). Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. [Review]. J Biol Chem, 299(10), 105225. (Read full article)
  4. Chen Q (2023). Sperm RNA-mediated epigenetic inheritance in mammals: challenges and opportunities. [Review]. Reprod Fertil Dev, 35(2), 118-124. (Read full article)
  5. Shi J, Zhou T, Chen Q (2022). Exploring the expanding universe of small RNAs. [Review]. Nat Cell Biol, 24(4), 415-423. (Read full article)
  6. Chen Q, Zhang X, Shi J, Yan M, Zhou T (2021). Origins and evolving functionalities of tRNA-derived small RNAs. [Review]. Trends Biochem Sci, 46(10), 790-804. (Read full article)
  7. Qian J, Chen Q, Ward SM, Duan E, Zhang Y (2019). Impacts of Caffeine during Pregnancy. [Review]. Trends Endocrinol Metab, 31(3), 218-227. (Read full article)
  8. Zhang Y, Shi J, Rassoulzadegan M, Tuorto F, Chen Q (2019). Sperm RNA code programmes the metabolic health of offspring. [Review]. Nat Rev Endocrinol, 15(8), 489-498. (Read full article)
  9. Zhang Y, Chen Q (2019). The expanding repertoire of hereditary information carriers. [Review]. Development, 146(6). (Read full article)
  10. Shi J, Zhang Y, Zhou T, Chen Q (2018). tsRNAs: The Swiss Army Knife for Translational Regulation. [Review]. Trends Biochem Sci, 44(3), 185-189. (Read full article)
  11. Chen Q, Yan W, Duan E (2016). Epigenetic inheritance of acquired traits through sperm RNAs and sperm RNA modifications. [Review]. Nat Rev Genet, 17(12), 733-743. (Read full article)
  12. Zhang X, Cozen AE, Liu Y, Chen Q, Lowe TM (2016). Small RNA Modifications: Integral to Function and Disease. [Review]. Trends Mol Med, 22(12), 1025-1034. (Read full article)
  13. Chen Q, Zhang Y, Elad D, Jaffa AJ, Cao Y, Ye X, Duan E (2012). Navigating the site for embryo implantation: biomechanical and molecular regulation of intrauterine embryo distribution. [Review]. Mol Aspects Med, 34(5), 1024-42. (Read full article)
  14. Chen Q, Duan EK (2011). Aquaporins in sperm osmoadaptation: an emerging role for volume regulation. [Review]. Acta Pharmacol Sin, 32(6), 721-4. (Read full article)
  15. Chen Q, Zhang Y, Lu J, Wang Q, Wang S, Cao Y, Wang H, Duan E (2009). Embryo-uterine cross-talk during implantation: the role of Wnt signaling. [Review]. Mol Hum Reprod, 15(4), 215-21. (Read full article)

Commentary

  1. Cai C, Chen Q (2024). Father's diet influences son's metabolic health through sperm RNA. Nature, 630(8017), 571-573. (Read full article)
  2. Zhang Y, Shi J, Chen Q (2023). Towards the understanding of "Herbal RNA Code" for traditional medicine. Cell Res, 33(12), 900-901. (Read full article)
  3. Lai LB, Gopalan V, Jansson MD, Chen Q, Zhang X, Wolfram-Schauerte M, Hfer K (2023). Making nucleic acid structures and schematics. Trends Biochem Sci, 48(8), 655-658. (Read full article)
  4. Zhang X, Chen Q (2023). EDC exposure in 3D genome memory in transgenerational obesity. Nat Rev Endocrinol, 19(4), 192-193. (Read full article)
  5. Zhang X, Chen Q (2020). A Twist between ROS and Sperm-Mediated Intergenerational Epigenetic Inheritance. Mol Cell, 78(3), 371-373. (Read full article)
  6. Zhang Y, Chen Q (2020). Human sperm RNA code senses dietary sugar. Nat Rev Endocrinol, 16(4), 200-201. (Read full article)
  7. Liu Y, Chen Q (2018). 150 years of Darwin's theory of intercellular flow of hereditary information. Nat Rev Mol Cell Biol, 19(12), 749-750. (Read full article)
  8. Zhang Y, Shi J, Chen Q (2017). tsRNAs: new players in mammalian retrotransposon control. Cell Res, 27(11), 1307-1308. (Read full article)
  9. Shi J, Zhang X, Liu Y, Chen Q (2017). Epigenetic information in gametes: Gaming from before fertilization: Comment on "Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition" by Qian Wang et al. Phys Life Rev, 20, 146-149. (Read full article)
  10. Shi J, Zhang Y, Chen Q (2016). Molecular carriers of acquired inheritance: absence of evidence is not evidence of absence. Environ Epigenet, 2(2), dvw014. (Read full article)