Publications & Presentations

Clinical Pipeline: Publications and Key International Conference Presentations

Gene Editing & Stem Cell Research

1. Zhou Y, Xie D, Ding C, Wu W, Cao T, Liu Q, Keefe DL, Zhou C, Huang J. Human embryo editing: 10 years of breakthroughs and challenges. Protein & Cell. 2026;pwag030. DOI
2. Cao T, Zhang A, Wu W, Wen J, Mu M, Liu S, Chen Y, Zhang D, Liu H, Deng S, He X, Huang J. Long-term in vivo CRISPR/Cas9 gene editing in liver triggers host immunity and clonal mutations in DNA damage response genes beyond off-target effects. Protein & Cell. 2026;pwag057. DOI
3. Xie D, Wang J, Huang L, Zhao Z, Wang R, Long H, Ni Q, Liu H, Hu M, Huang J. A novel X-linked retinitis pigmentosa beagle dog model for ophthalmic research established rapidly by editing the RPGR gene in zygotes. Experimental Eye Research. 2025;261:110697. DOI
4. Hu S, Chen Y, Zhou Y, Cao T, Liu S, Ding C, Xie D, Liang P, Huang L, Liu H, Huang J. In vivo adenine base editing ameliorates Rho-associated autosomal dominant retinitis pigmentosa. Journal of Genetics and Genomics. 2025;52(7):887-900. DOI
5. Liu Q, Li X, Xu H, Luo Y, Cheng L, Liang J, He Y, Liu H, Fang J, Huang J. Therapeutic gene correction of HBB frameshift CD41-42 (-TCTT) deletion in human hematopoietic stem cells. Advanced Biotechnology. 2025;3(1):2. DOI
6. Luo Y, Zhang JD, Zhao XG, Chen WC, Chen WX, Hou YR, Ren YH, Xiao ZD, Zhang Q, Diao LT, Xie SJ. Simplifying the protocol for low-pollution-risk, efficient mouse myoblast isolation and differentiation. Advanced Biotechnology. 2025;3(1):8. DOI
7. Wang J, Qiu Y, Zhang L, Zhou X, Hu S, Liu Q, Yin S, Su Z, Liu S, Liu H, Wu X, Huang J. Adenine base editor corrected ADPKD point mutations in hiPSCs and kidney organoids. Advanced Biotechnology. 2024;2(2):20. DOI
8. Wang J, Zhang L, Wu G, Wu J, Zhou X, Chen X, Niu Y, Jiao Y, Liu Q, Liang P, Shi G, Wu X, Huang J. Correction of a CADASIL point mutation using adenine base editors in hiPSCs and blood vessel organoids. Journal of Genetics and Genomics. 2024;51(2):197-207. DOI
9. Diao LT, Xie SJ, Xu WY, Zhang HH, Hou YR, Hu YX, Liang XX, Liang JB, Zhang Q, Xiao ZD. CRISPR/Cas13 sgRNA-Mediated RNA-RNA Interaction Mapping in Live Cells with APOBEC RNA Editing. Advanced Science. 2024;11(45):e2409004. DOI
10. Hu S, Chen Y, Xie D, Xu K, Fu Y, Chi W, Liu H, Huang J. Nme2Cas9-mediated therapeutic editing in inhibiting angiogenesis after wet age-related macular degeneration onset. Clinical and Translational Medicine. 2023;13(8):e1383. DOI
11. Liu Q, Chen Y, Hu S, Liu W, Xie D, Yang X, Huang W, Liu S, Chen X, Liu H, Huang J. Screening an Effective Dual-Adeno-Associated Virus Split-Cytosine Base Editor System for C-to-T Conversion In Vivo. Human Gene Therapy. 2023;34(13-14):629-638. DOI
12. Zhi S, Chen Y, Wu G, Wen J, Wu J, Liu Q, Li Y, Kang R, Hu S, Wang J, Liang P, Huang J. Dual-AAV delivering split prime editor system for in vivo genome editing. Molecular Therapy. 2022;30(1):283-294. DOI
13. Cao T, Liu S, Qiu Y, Gao M, Wu J, Wu G, Liang P, Huang J. Generation of C-to-G transversion in mouse embryos via CG editors. Transgenic Research. 2022;31(4-5):445-455. DOI
14. Zhang X, Li T, Ou J, Huang J, Liang P. Homology-based repair induced by CRISPR-Cas nucleases in mammalian embryo genome editing. Protein & Cell. 2022;13(5):316-335. DOI
15. Wen J, Cao T, Wu J, Chen Y, Zhi S, Huang Y, Zhen P, Wu G, Aagaard L, Zhong J, Liang P, Huang J. Single AAV-mediated CRISPR-Nme2Cas9 efficiently reduces mutant hTTR expression in a transgenic mouse model of transthyretin amyloidosis. Molecular Therapy. 2022;30(1):164-174. DOI
16. Sun H, Zhi S, Wu G, Wu G, Cao T, Hao H, Songyang Z, Liang P, Huang J. Cost-effective generation of A-to-G mutant mice by zygote electroporation of adenine base editor ribonucleoproteins. Journal of Genetics and Genomics. 2020;47(6):337-340. DOI
17. Su X, Chen W, Cai Q, Liang P, Chen Y, Cong P, Huang J. Effective generation of maternal genome point mutated porcine embryos by injection of cytosine base editor into germinal vesicle oocytes. Science China Life Sciences. 2020;63(7):996-1005. DOI
18. Chen Y, Zhi S, Liang P, Zheng Q, Liu M, Zhao Q, Ren J, Cui J, Huang J, Liu Y, Songyang Z. Single AAV-Mediated CRISPR-SaCas9 Inhibits HSV-1 Replication by Editing ICP4 in Trigeminal Ganglion Neurons. Molecular Therapy - Methods & Clinical Development. 2020;18:33-43. DOI
19. Huang Y, Ding C, Liang P, Li D, Tang Y, Meng W, Sun H, Lu H, Chen Y, Chen X, Huang Q, Fang J, Zhou C, Yang S, Huang J. HBB-deficient Macaca fascicularis monkey presents with human β-thalassemia. Protein & Cell. 2019;10(7):538-542. DOI
20. Liang P, Huang J. Off-target challenge for base editor-mediated genome editing. Cell Biology and Toxicology. 2019;35(3):185-187. DOI
21. Liang P, Wen J, Huang J. Off-target effects of cytidine base editor and adenine base editor: What can we do?. Journal of Genetics and Genomics. 2019;46(11):509-512. DOI
22. Su X, Chen W, Cai Q, Liang P, Chen Y, Cong P, Huang J. Production of non-mosaic genome edited porcine embryos by injection of CRISPR/Cas9 into germinal vesicle oocytes. Journal of Genetics and Genomics. 2019;46(7):335-342. DOI
23. Yu J, Lu W, Ge T, Huang R, Chen B, Ye M, Bai Y, Shi G, Songyang Z, Ma W, Huang J. Interaction Between Sympk and Oct4 Promotes Mouse Embryonic Stem Cell Proliferation. Stem Cells. 2019;37(6):743-753. DOI
24. Liang P, Xie X, Zhi S, Sun H, Zhang X, Chen Y, Chen Y, Xiong Y, Ma W, Liu D, Huang J, Songyang Z. Genome-wide profiling of adenine base editor specificity by EndoV-seq. Nature Communications. 2019;10(1):67. DOI
25. Zhang Z, Wan T, Chen Y, Chen Y, Sun H, Cao T, Songyang Z, Tang G, Wu C, Ping Y, Xu F, Huang J. Cationic Polymer‐Mediated CRISPR/Cas9 Plasmid Delivery for Genome Editing. Macromolecular Rapid Communications. 2019;40(5):e1800068. DOI
26. Liang P, Sun H, Zhang X, Xie X, Zhang J, Bai Y, Ouyang X, Zhi S, Xiong Y, Ma W, Liu D, Huang J, Songyang Z. Effective and precise adenine base editing in mouse zygotes. Protein & Cell. 2018;9(9):808-813. DOI
27. Zhan S, Cao S, Du H, Sun Y, Li L, Ding C, Zheng H, Huang J. Parental genetic material and oxygen concentration affect hatch dynamics of mouse embryo in vitro. Reproductive Biology and Endocrinology. 2018;16(1):39. DOI
28. Zhang Z, Sun H, Chen Y, Cao T, Songyang Z, Huang J, Huang Y. Analysis of hpf1 expression and function in early embryonic development of zebrafish. Development Genes and Evolution. 2018;228(2):141-147. DOI

RNA & Oncology Research

1. Hu YX, Diao LT, Hou YR, Lv G, Tao S, Xu WY, Xie SJ, Ren YH, Xiao ZD. Pseudouridine synthase 1 promotes hepatocellular carcinoma through mRNA pseudouridylation to enhance the translation of oncogenic mRNAs. Hepatology. 2024;80(5):1058-1073. DOI
2. Tao S, Hou Y, Diao L, Hu Y, Xu W, Xie S, Xiao Z. Long noncoding RNA study: Genome-wide approaches. Genes & Diseases. 2023;10(6):2491-2510. DOI
3. Tao S, Xie SJ, Diao LT, Lv G, Hou YR, Hu YX, Xu WY, Du B, Xiao ZD. RNA-binding protein CCDC137 activates AKT signaling and promotes hepatocellular carcinoma through a novel non-canonical role of DGCR8 in mRNA localization. Journal of Experimental & Clinical Cancer Research. 2023;42(1):194. DOI
4. Hou YR, Diao LT, Hu YX, Zhang QQ, Lv G, Tao S, Xu WY, Xie SJ, Zhang Q, Xiao ZD. The Conserved LncRNA DIO3OS Restricts Hepatocellular Carcinoma Stemness by Interfering with NONO-Mediated Nuclear Export of ZEB1 mRNA. Advanced Science. 2023;10(23):e2301983. DOI
5. Liu K, Qiu D, Liang X, Huang Y, Wang Y, Jia X, Li K, Zhao J, Du C, Qiu X, Cui J, Xiao Z, Qin Y, Zhang Q. Lipotoxicity-induced STING1 activation stimulates MTORC1 and restricts hepatic lipophagy. Autophagy. 2022;18(4):860-876. DOI
6. Li H, Zhong Y, Cao G, Shi H, Liu Y, Li L, Yin P, Chen J, Xiao Z, Du B. METTL3 promotes cell cycle progression via m(6)A/YTHDF1-dependent regulation of CDC25B translation. International Journal of Biological Sciences. 2022;18(8):3223-3236. DOI
7. Xie SJ, Tao S, Diao LT, Li PL, Chen WC, Zhou ZG, Hu YX, Hou YR, Lei H, Xu WY, Chen WJ, Peng YW, Zhang Q, Xiao ZD. Characterization of Long Non-coding RNAs Modified by m(6)A RNA Methylation in Skeletal Myogenesis. Frontiers in Cell and Developmental Biology. 2021;9:762669. DOI
8. Xie SJ, Lei H, Yang B, Diao LT, Liao JY, He JH, Tao S, Hu YX, Hou YR, Sun YJ, Peng YW, Zhang Q, Xiao ZD. Dynamic m(6)A mRNA Methylation Reveals the Role of METTL3/14-m(6)A-MNK2-ERK Signaling Axis in Skeletal Muscle Differentiation and Regeneration. Frontiers in Cell and Developmental Biology. 2021;9:744171. DOI
9. Liu K, Qiu D, Liang X, Huang Y, Zhao J, Qiu X, Zhang Q, Xiao ZD, Qin Y. Human DUBs' gene expression and regulation in antiviral signaling in response to poly (I:C) treatment. Molecular Immunology. 2021;129:45-52. DOI
10. Xie SJ, Diao LT, Cai N, Zhang LT, Xiang S, Jia CC, Qiu DB, Liu C, Sun YJ, Lei H, Hou YR, Tao S, Hu YX, Xiao ZD, Zhang Q. mascRNA and its parent lncRNA MALAT1 promote proliferation and metastasis of hepatocellular carcinoma cells by activating ERK/MAPK signaling pathway. Cell Death Discovery. 2021;7(1):110. DOI
11. Diao LT, Xie SJ, Lei H, Qiu XS, Huang MC, Tao S, Hou YR, Hu YX, Sun YJ, Zhang Q, Xiao ZD. METTL3 regulates skeletal muscle specific miRNAs at both transcriptional and post-transcriptional levels. Biochemical and Biophysical Research Communications. 2021;552:52-58. DOI
12. Diao LT, Xie SJ, Yu PJ, Sun YJ, Yang F, Tan YY, Tao S, Hou YR, Zheng LL, Xiao ZD, Zhang Q. N(6)-methyladenine demethylase ALKBH1 inhibits the differentiation of skeletal muscle. Experimental Cell Research. 2021;400(2):112492. DOI
13. Liu S, Xie S, Chen H, Li B, Chen Z, Tan Y, Yang J, Zheng L, Xiao Z, Zhang Q, Qu L. The functional analysis of transiently upregulated miR-101 suggests a "braking" regulatory mechanism during myogenesis. Science China Life Sciences. 2021;64(10):1612-1623. DOI
14. Gong LP, Chen JN, Dong M, Xiao ZD, Feng ZY, Pan YH, Zhang Y, Du Y, Zhang JY, Bi YH, Huang JT, Liang J, Shao CK. Epstein-Barr virus-derived circular RNA LMP2A induces stemness in EBV-associated gastric cancer. EMBO Reports. 2020;21(10):e49689. DOI
15. Hong M, Tao S, Zhang L, Diao LT, Huang X, Huang S, Xie SJ, Xiao ZD, Zhang H. RNA sequencing: new technologies and applications in cancer research. Journal of Hematology & Oncology. 2020;13(1):166. DOI
16. Guo M, Xiao ZD, Dai Z, Zhu L, Lei H, Diao LT, Xiong Y. The landscape of long noncoding RNA-involved and tumor-specific fusions across various cancers. Nucleic Acids Research. 2020;48(22):12618-12631. DOI
17. Kim M. Long non-coding RNAs in cancer. Non-coding RNA Research. 2019;4(2):45. DOI
18. Xiao Z, Han L, Lee H, Zhuang L, Zhang Y, Baddour J, Nagrath D, Wood CG, Gu J, Wu X, Liang H, Gan B. Energy stress-induced lncRNA FILNC1 represses c-Myc-mediated energy metabolism and inhibits renal tumor development. Nature Communications. 2017;8(1):783. DOI
19. Dai F, Lee H, Zhang Y, Zhuang L, Yao H, Xi Y, Xiao Z, You MJ, Li W, Su X, Gan B. BAP1 inhibits the ER stress gene regulatory network and modulates metabolic stress response. Proceedings of the National Academy of Sciences. 2017;114(12):3192-3197. DOI
20. Liu X, Xiao Z, Han L, Zhang J, Lee S, Wang W, Lee H, Zhuang L, Chen J, Lin H, Wang J, Liang H, Gan B. LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stress. Nature Cell Biology. 2016;18(4):431-442. DOI
21. Xiao Z, Liu X, Zhuang L, Gan B. NBR2: A former junk gene emerges as a key player in tumor suppression. Molecular & Cellular Oncology. 2016;3(4):e1187322. DOI
22. Lee H, Dai F, Zhuang L, Xiao Z, Kim J, Zhang Y, Ma L, You MJ, Wang Z, Gan B. BAF180 regulates cellular senescence and hematopoietic stem cell homeostasis through p21. Oncotarget. 2016;7(15):19134-19146. DOI
23. Liu X, Xiao Z, Gan B. An lncRNA switch for AMPK activation. Cell Cycle. 2016;15(15):1948-1949. DOI
24. Wang W, Xiao Z, Li X, Aziz KE, Gan B, Johnson RL, Chen J. AMPK modulates Hippo pathway activity to regulate energy homeostasis. Nature Cell Biology. 2015;17(4):490-499. DOI
25. Diao L, Xiao Z, Leng X, Li B, Li J, Luo Y, Li S, Yu C, Zhou H, Qu L. Conservation and divergence of transcriptional coregulations between box C/D snoRNA and ribosomal protein genes in Ascomycota. RNA. 2014;20(9):1376-1385. DOI
26. Xiao Z, Diao L, Yang J, Xu H, Huang M, Deng Y, Zhou H, Qu L. Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. Nucleic Acids Research. 2013;41(1):e5. DOI
27. Zhou A, Diao L, Xu H, Xiao Z, Li J, Zhou H, Qu L. β-Catenin/LEF1 transactivates the microRNA-371-373 cluster that modulates the Wnt/β-catenin-signaling pathway. Oncogene. 2012;31(24):2968-2978. DOI
28. Xu H, He J, Xiao Z, Zhang Q, Chen Y, Zhou H, Qu L. Liver-Enriched Transcription Factors Regulate MicroRNA-122 That Targets CUTL1 During Liver Development. Hepatology. 2010;52(4):1431-1442. DOI
29. Liu N, Xiao Z, Yu C, Shao P, Liang Y, Guan D, Yang J, Chen C, Qu L, Zhou H. SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights. BMC Genomics. 2009;10(1):515. DOI
30. Shao P, Zhou H, Xiao Z, He J, Huang M, Chen Y, Qu L. Identification of novel chicken microRNAs and analysis of their genomic organization. Gene. 2008;418(1-2):34-40. DOI
31. He H, Zhou H, Xiao Z, Zeng X, Chen J, Zheng T, Qu L. Identification of three novel noncoding RNAs from Drosophila melanogaster. Chinese Science Bulletin. 2006;51(22):2737-2742. DOI

Genomics Research

1. Shang H, Xu S, Zhang Y, Liang J, Li P, Zeng L, Gu Y, Li H, Wei W, Lu Z, Chen Z, Gong R, Zhang X, Xu H, Wang L. A Multicenter Retrospective Study of HbH in China Including 1421 Patients Over a 12-Year Timespan. eJHaem. 2025;6(4):e70087. DOI
2. Li J, Jing R, Wei H, Wang M, Xiaowei Q, Liu H, Jian L, Ou J, Jiang W, Tian F, Sheng Y, Li H, Xu H, Zhang R, Guan A, Liu K, Jiang H, Ren Y, He J, Huang W, Liao N, Cai X, Ming J, Ling R, Xu Y, Hu C, Zhang J, Guo B, Ouyang L, Shuai P, Liu Z, Zhong L, Zeng Z, Zhang T, Xuan Z, Tan X, Liang J, Pan Q, Chen L, Zhang F, Fan L, Zhang Y, Yang X, BoLi J, Chen C, Jiang J. Germline mutations in 40 cancer susceptibility genes among Chinese patients with high hereditary risk breast cancer. International Journal of Cancer. 2019;144(2):281-289. DOI
3. Zhao P, Liang J, Deng Z, Wang M, Qin J, Chen C, Hu X. Association of Gene Mutations with Response to Arsenic-Containing Compound Qinghuang Powder (复方青黄散) in Patients with Myelodysplastic Syndromes. Chinese Journal of Integrative Medicine. 2019;25(6):409-415. DOI
4. Yin X, Du Y, Zhang H, Wang Z, Wang J, Fu X, Cui Y, Chen C, Liang J, Xuan Z, Zhang X. Identification of a de novo fetal variant in osteogenesis imperfecta by targeted sequencing-based noninvasive prenatal testing. Journal of Human Genetics. 2018;63(11):1129-1137. DOI
5. Wei H, Wang M, Ou J, Jiang W, Tian F, Sheng Y, Li H, Xu H, Zhang R, Guan A, Wang C, Jiang H, Ren Y, He J, Liu J, Huang W, Liao N, Cai X, Ming J, Ling R, Xu Y, Hu C, Zhang J, Guo B, Ouyang L, Shuai P, Liu Z, Zhong L, Jing R, Zeng Z, Zhang M, Zhang T, Xuan Z, Tan X, Liang J, Pan Q, Chen L, Zhang F, Fan L, Zhang Y. Multicenter cross‑sectional screening of the BRCA gene for Chinese high hereditary risk breast cancer populations. Oncology Letters. 2018;15(6):9420-9428. DOI
6. Xie Y, Luo X, Li Y, Chen L, Ma W, Huang J, Cui J, Zhao Y, Xue Y, Zuo Z, Ren J. DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning. Genomics, Proteomics & Bioinformatics. 2018;16(4):294-306. DOI
7. Qi H, Xuan Z, Du Y, Cai L, Zhang H, Wen X, Kong X, Yang K, Mi Y, Fu X, Cao S, Wang J, Chen C, Liang J. High resolution global chromosomal aberrations from spontaneous miscarriages revealed by low coverage whole genome sequencing. European Journal of Obstetrics & Gynecology and Reproductive Biology. 2018;224:21-28. DOI
8. Borensztein M, Syx L, Ancelin K, Diabangouaya P, Picard C, Liu T, Liang J, Vassilev I, Galupa R, Servant N, Barillot E, Surani A, Chen C, Heard E. Xist-dependent imprinted X inactivation and the early developmental consequences of its failure. Nature Structural & Molecular Biology. 2017;24(3):226-233. DOI
9. Wang B, Liu Y, Hou G, Wang L, Lv N, Xu Y, Xu Y, Wang X, Xuan Z, Jing Y, Li H, Jin X, Deng A, Wang L, Gao X, Dou L, Liang J, Chen C, Li Y, Yu L. Mutational spectrum and risk stratification of intermediate-risk acute myeloid leukemia patients based on next-generation sequencing. Oncotarget. 2016;7(22):32065-32078. DOI
10. Zhang H, Zhao Y, Song J, Zhu Q, Yang H, Zheng M, Xuan Z, Wei Y, Chen Y, Yuan P, Yu Y, Li D, Liang J, Fan L, Chen C, Qiao J. Statistical Approach to Decreasing the Error Rate of Noninvasive Prenatal Aneuploid Detection caused by Maternal Copy Number Variation. Scientific Reports. 2015;5(1):16106. DOI
11. Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Claydon VE, Hainsworth R, Gamboa JL, Zibenigus M, Zenebe G, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biology. 2014;15(2):R36. DOI
12. DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Asian Genetic Epidemiology Network Type 2 Diabetes (AGEN-T2D) Consortium, South Asian Type 2 Diabetes (SAT2D) Consortium, et al. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nature Genetics. 2014;46(3):234-244. DOI
13. Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Whole-Genome Sequencing Uncovers the Genetic Basis of Chronic Mountain Sickness in Andean Highlanders. The American Journal of Human Genetics. 2013;93(3):452-462. DOI
14. Kelly MA, Rees SD, Hydrie MZI, Shera AS, Bellary S, O’Hare JP, Kumar S, Taheri S, Basit A, Barnett AH, DIAGRAM Consortium, SAT2D Consortium, et al. Circadian Gene Variants and Susceptibility to Type 2 Diabetes: A Pilot Study. PLoS ONE. 2012;7(4):e32670. DOI
15. Kooner JS, Saleheen D, Sim X, Sehmi J, Zhang W, Frossard P, et al. Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci. Nature Genetics. 2011;43(10):984-989. DOI
16. Liu N, Enkemann SA, Liang P, Hersmus R, Zanazzi C, Huang J, Wu C, Chen Z, Looijenga LHJ, Keefe DL, Liu L. Genome-wide Gene Expression Profiling Reveals Aberrant MAPK and Wnt Signaling Pathways Associated with Early Parthenogenesis. Journal of Molecular Cell Biology. 2010;2(6):333-344. DOI