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Northwestern University Feinberg School of Medicine
Qi Cao Lab

Publications

Learn more about the work we do in the Cao Lab through our recent publications.

  1. Meng Q, Shen J, Ren Y, Liu Q, Wang R, Li Q, Jiang W, Wang Q, Zhang Y, Trinidad JC  et al.  EZH2 directly methylates PARP1 and regulates its activity in cancer.  Sci Adv  2024 Nov 29;10(48):eadl2804. pii:eadl2804
  2. Li Y, Wang TY, Guo Q, Ren Y, Lu X, Cao Q, Yang R  A Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.  bioRxiv  2024 Oct 26;. pii:2024.10.23.619929
  3. Medd MM, Cao Q  Perspectives on CRISPR Genome Editing to Prevent Prion Diseases in High-Risk Individuals.  Biomedicines  2024 Aug 01;12(8). pii:1725
  4. Li Y, Yi Y, Gao X, Wang X, Zhao D, Wang R, Zhang LS, Gao B, Zhang Y, Zhang L  et al.  2'-O-methylation at internal sites on mRNA promotes mRNA stability.  Mol Cell  2024 Jun 20;84(12):2320-2336.e6. doi:10.1016/j.molcel.2024.04.011
  5. Zhang M, Wu K, Zhang W, Lin X, Cao Q, Zhang L, Chen K  The therapeutic potential of targeting the CHD protein family in cancer.  Pharmacol Ther  2024 Apr;256:108610. doi:10.1016/j.pharmthera.2024.108610
  6. Serritella AV, Saenz-Lopez Larrocha P, Dhar P, Liu S, Medd MM, Jia S, Cao Q, Wu JD  The Human Soluble NKG2D Ligand Differentially Impacts Tumorigenicity and Progression in Temporal and Model-Dependent Modes.  Biomedicines  2024 Jan 16;12(1). pii:196
  7. Gao X, Yi Y, Lv J, Li Y, Arulsamy K, Babu SS, Bruno I, Zhang L, Cao Q, Chen K  Low RNA stability signifies strong expression regulatability of tumor suppressors.  Nucleic Acids Res  2023 Nov 27;51(21):11534-11548. doi:10.1093/nar/gkad838
  8. Li Y, Yi Y, Lv J, Gao X, Yu Y, Babu SS, Bruno I, Zhao D, Xia B, Peng W  et al.  Low RNA stability signifies increased post-transcriptional regulation of cell identity genes.  Nucleic Acids Res  2023 Jul 07;51(12):6020-6038. doi:10.1093/nar/gkad300
  9. Lv J, Meng S, Gu Q, Zheng R, Gao X, Kim JD, Chen M, Xia B, Zuo Y, Zhu S  et al.  Publisher Correction: Epigenetic landscape reveals MECOM as an endothelial lineage regulator.  Nat Commun  2023 May 18;14(1):2842. pii:2842
  10. Lv J, Meng S, Gu Q, Zheng R, Gao X, Kim JD, Chen M, Xia B, Zuo Y, Zhu S  et al.  Epigenetic landscape reveals MECOM as an endothelial lineage regulator.  Nat Commun  2023 Apr 25;14(1):2390. pii:2390
  11. Gupta K, Wang G, Zhang S, Gao X, Zheng R, Zhang Y, Meng Q, Zhang L, Cao Q, Chen K  StripeDiff: Model-based algorithm for differential analysis of chromatin stripe.  Sci Adv  2022 Dec 09;8(49):eabk2246. pii:eabk2246
  12. Zhao D, Zhang M, Huang S, Liu Q, Zhu S, Li Y, Jiang W, Kiss DL, Cao Q, Zhang L  et al.  CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells.  Nucleic Acids Res  2022 Nov 28;50(21):12186-12201. doi:10.1093/nar/gkac1090
  13. Yi Y, Li Y, Li C, Wu L, Zhao D, Li F, Fazli L, Wang R, Wang L, Dong X  et al.  Methylation-dependent and -independent roles of EZH2 synergize in CDCA8 activation in prostate cancer.  Oncogene  2022 Mar;41(11):1610-1621. doi:10.1038/s41388-022-02208-x
  14. Lu B, Zou C, Yang M, He Y, He J, Zhang C, Chen S, Yu J, Liu KY, Cao Q  et al.  Pharmacological Inhibition of Core Regulatory Circuitry Liquid-liquid Phase Separation Suppresses Metastasis and Chemoresistance in Osteosarcoma.  Adv Sci (Weinh)  2021 Oct;8(20):e2101895. pii:2101895
  15. Ren Y, Wang TY, Anderton LC, Cao Q, Yang R  LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data.  BMC Genomics  2021 Jul 27;22(1):574. pii:574
  16. Wang TY, Liu Q, Ren Y, Alam SK, Wang L, Zhu Z, Hoeppner LH, Dehm SM, Cao Q, Yang R  A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes.  Mol Cell  2021 May 20;81(10):2246-2260.e12. doi:10.1016/j.molcel.2021.03.028
  17. Yang Y, Liu KY, Liu Q, Cao Q  Androgen Receptor-Related Non-coding RNAs in Prostate Cancer.  Front Cell Dev Biol  2021;9:660853. pii:660853
  18. Yi Y, Li Y, Meng Q, Li Q, Li F, Lu B, Shen J, Fazli L, Zhao D, Li C  et al.  A PRC2-independent function for EZH2 in regulating rRNA 2'-O methylation and IRES-dependent translation.  Nat Cell Biol  2021 Apr;23(4):341-354. doi:10.1038/s41556-021-00653-6
  19. Wang G, Xia B, Zhou M, Lv J, Zhao D, Li Y, Bu Y, Wang X, Cooke JP, Cao Q  et al.  MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes.  Genomics Proteomics Bioinformatics  2021 Feb;19(1):140-153. doi:10.1016/j.gpb.2020.10.008
  20. Zhao D, Zhang L, Zhang M, Xia B, Lv J, Gao X, Wang G, Meng Q, Yi Y, Zhu S  et al.  Broad genic repression domains signify enhanced silencing of oncogenes.  Nat Commun  2020 Nov 03;11(1):5560. pii:5560
  21. de Leeuw R, Cao Q, Lam HM  Editorial: Response and Resistance in Castration-Resistant Prostate Cancer.  Front Oncol  2020;10:607298. pii:607298
  22. Li Q, Liu KY, Liu Q, Wang G, Jiang W, Meng Q, Yi Y, Yang Y, Wang R, Zhu S  et al.  Antihistamine Drug Ebastine Inhibits Cancer Growth by Targeting Polycomb Group Protein EZH2.  Mol Cancer Ther  2020 Oct;19(10):2023-2033. doi:10.1158/1535-7163.MCT-20-0250
  23. Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D  et al.  An integrative ENCODE resource for cancer genomics.  Nat Commun  2020 Jul 29;11(1):3696. pii:3696
  24. Xia B, Zhao D, Wang G, Zhang M, Lv J, Tomoiaga AS, Li Y, Wang X, Meng S, Cooke JP  et al.  Machine learning uncovers cell identity regulator by histone code.  Nat Commun  2020 Jun 01;11(1):2696. pii:2696
  25. Wang G, Meng Q, Xia B, Zhang S, Lv J, Zhao D, Li Y, Wang X, Zhang L, Cooke JP  et al.  TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription.  Genome Biol  2020 Apr 02;21(1):84. pii:84
  26. Zhu S, Zhao D, Li C, Li Q, Jiang W, Liu Q, Wang R, Fazli L, Li Y, Zhang L  et al.  BMI1 is directly regulated by androgen receptor to promote castration-resistance in prostate cancer.  Oncogene  2020 Jan;39(1):17-29. doi:10.1038/s41388-019-0966-4
  27. Li F, Yi Y, Miao Y, Long W, Long T, Chen S, Cheng W, Zou C, Zheng Y, Wu X  et al.  N6-Methyladenosine Modulates Nonsense-Mediated mRNA Decay in Human Glioblastoma.  Cancer Res  2019 Nov 15;79(22):5785-5798. doi:10.1158/0008-5472.CAN-18-2868
  28. Liu Q, Wang G, Li Q, Jiang W, Kim JS, Wang R, Zhu S, Wang X, Yan L, Yi Y  et al.  Polycomb group proteins EZH2 and EED directly regulate androgen receptor in advanced prostate cancer.  Int J Cancer  2019 Jul 15;145(2):415-426. doi:10.1002/ijc.32118
  29. Long Z, Li Y, Gan Y, Zhao D, Wang G, Xie N, Lovnicki JM, Fazli L, Cao Q, Chen K  et al.  Roles of the HOXA10 gene during castrate-resistant prostate cancer progression.  Endocr Relat Cancer  2019 Mar 01;26(3):279-292. doi:10.1530/ERC-18-0465