A 12-gene panel in estimating hormone-treatment responses of castration-resistant prostate cancer patients generated using a combined analysis of bulk and single-cell sequencing data

References

• Siegel RL, Miller KD, Fuchs HE, et al. Cancer statistics, 2022. CA Cancer J Clin. 2022;72(1):1–16. doi:10.3322/caac.21708.
   Web of Science ®Google Scholar
• Vellky JE, Ricke WA. Development and prevalence of castration-resistant prostate cancer subtypes. Neoplasia. 2020;22(11):566–575. doi:10.1016/j.neo.2020.09.002.
   PubMed Web of Science ®Google Scholar
• Sharifi N, Gulley JL, Dahut WL. Androgen deprivation therapy for prostate cancer. JAMA. 2005;294(2):238–244. doi:10.1001/jama.294.2.238.
   PubMed Web of Science ®Google Scholar
• Lassi K, Dawson NA. Emerging therapies in castrate-resistant prostate cancer. Curr Opin Oncol. 2009;21(3):260–265. doi:10.1097/CCO.0b013e32832a1868.
   PubMed Web of Science ®Google Scholar
• Dong B, Miao J, Wang Y, et al. Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer. Commun Biol. 2020;3(1):778. doi:10.1038/s42003-020-01476-1.
   PubMed Web of Science ®Google Scholar
• Wang Z, Wang T, Hong D, et al. Single-cell transcriptional regulation and genetic evolution of neuroendocrine prostate cancer. iScience. 2022;25(7):104576. doi:10.1016/j.isci.2022.104576.
   PubMed Web of Science ®Google Scholar
• Cheng Q, Butler W, Zhou Y, et al. Pre-existing castration-resistant prostate cancer – like cells in primary prostate cancer promote resistance to hormonal therapy. Eur Urol. 2022;81(5):446–455. doi:10.1016/j.eururo.2021.12.039.
   PubMed Web of Science ®Google Scholar
• Henry GH, Malewska A, Joseph DB, et al. A cellular anatomy of the normal adult human prostate and prostatic urethra. Cell Rep. 2018;25(12):3530–3542.e5. doi:10.1016/j.celrep.2018.11.086.
   PubMed Web of Science ®Google Scholar
• Chen S, Zhu G, Yang Y, et al. Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to human prostate cancer progression. Nat Cell Biol. 2021;23(1):87–98. doi:10.1038/s41556-020-00613-6.
   PubMed Web of Science ®Google Scholar
• Song H, Weinstein HNW, Allegakoen P, et al. Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states. Nat Commun. 2022;13(1):141. doi:10.1038/s41467-021-27322-4.
   PubMed Web of Science ®Google Scholar
• Hao Y, Hao S, Andersen-Nissen E, et al. Integrated analysis of multimodal single-cell data. Cell. 2021;184(13):3573–3587.e29. doi:10.1016/j.cell.2021.04.048.
   PubMed Web of Science ®Google Scholar
• Mcginnis CS, Murrow LM, Gartner ZJ. DoubletFinder : doublet detection in Single-Cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 2019;8(4):329–337.e4. doi:10.1016/j.cels.2019.03.003.
   PubMed Web of Science ®Google Scholar
• Oughtred R, Stark C, Breitkreutz BJ, et al. The BioGRID interaction database: 2019 update. Nucleic Acids Res. 2019;47(D1):D529–D541. doi:10.1093/nar/gky1079.
   PubMed Web of Science ®Google Scholar
• Ji AL, Rubin AJ, Thrane K, et al. Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma. Cell. 2020;182(2):497–514.e22. doi:10.1016/j.cell.2020.05.039.
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi:10.1186/s13059-014-0550-8.
   PubMed Web of Science ®Google Scholar
• Mou T, Deng W, Gu F, et al. Reproducibility of methods to detect differentially expressed genes from Single-Cell RNA sequencing. Front Genet. 2019;10(January):1331. doi:10.3389/fgene.2019.01331.
   PubMedGoogle Scholar
• Ritchie ME, Phipson B, Wu D, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47–e47. doi:10.1093/nar/gkv007.
   PubMed Web of Science ®Google Scholar
• Harada N, Yasunaga R, Higashimura Y, et al. Glyceraldehyde-3-phosphate dehydrogenase enhances transcriptional activity of androgen receptor in prostate cancer cells. J Biol Chem. 2007;282(31):22651–22661. doi:10.1074/jbc.M610724200.
   PubMed Web of Science ®Google Scholar
• Bonollo F, Thalmann GN, Kruithof-de Julio M, et al. The role of Cancer-Associated fibroblasts in prostate cancer tumorigenesis. Cancers (Basel). 2020;12(7):1887. doi:10.3390/cancers12071887.
   PubMed Web of Science ®Google Scholar
• Kim S, Thaper D, Bidnur S, et al. PEG10 is associated with treatment-induced neuroendocrine prostate cancer. J Mol Endocrinol. 2019;63(1):39–49. doi:10.1530/JME-18-0226.
   PubMed Web of Science ®Google Scholar
• Akamatsu S, Wyatt AW, Lin D, et al. The placental gene PEG10 promotes progression of neuroendocrine prostate cancer. Cell Rep. 2015;12(6):922–936. doi:10.1016/j.celrep.2015.07.012.
   PubMed Web of Science ®Google Scholar
• Visakorpi T, Hyytinen E, Koivisto P, et al. In vivo amplification of the androgen receptor gene and progression of human prostate cancer. Nat Genet. 1995;9(4):401–406. doi:10.1038/ng0495-401.
   PubMed Web of Science ®Google Scholar
• Chen CD, Welsbie DS, Tran C, et al. Molecular determinants of resistance to antiandrogen therapy. Nat Med. 2004;10(1):33–39. doi:10.1038/nm972.
   PubMed Web of Science ®Google Scholar
• Beltran H, Prandi D, Mosquera JM, et al. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med. 2016;22(3):298–305. doi:10.1038/nm.4045.
   PubMed Web of Science ®Google Scholar
• Labrecque MP, Coleman IM, Brown LG, et al. Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer. J Clin Invest. 2019;129(10):4492–4505. doi:10.1172/JCI128212.
   PubMed Web of Science ®Google Scholar
• Bluemn EG, Coleman IM, Lucas JM, et al. Androgen receptor Pathway-Independent prostate cancer is sustained through FGF signaling. Cancer Cell. 2017;32(4):474–489.e6. doi:10.1016/j.ccell.2017.09.003.
   PubMed Web of Science ®Google Scholar
• Terry S, Maillé P, Baaddi H, et al. Cross modulation between the androgen receptor axis and protocadherin-PC in mediating neuroendocrine transdifferentiation and therapeutic resistance of prostate cancer. Neoplasia. 2013;15(7):761–772. doi:10.1593/neo.122070.
   PubMed Web of Science ®Google Scholar
• Davies A, Nouruzi S, Ganguli D, et al. An androgen receptor switch underlies lineage infidelity in treatment-resistant prostate cancer. Nat Cell Biol. 2021;23(9):1023–1034. doi:10.1038/s41556-021-00743-5.
   PubMed Web of Science ®Google Scholar
• Su R, Chen L, Jiang Z, et al. Comprehensive analysis of androgen receptor status in prostate cancer with neuroendocrine differentiation. Front Oncol. 2022;12(August):955166. doi:10.3389/fonc.2022.955166.
   PubMedGoogle Scholar
• Zhou H, Zheng T, Wang T, et al. CCDC74A/B are K-fiber crosslinkers required for chromosomal alignment. BMC Biol. 2019;17(1):73. doi:10.1186/s12915-019-0694-9.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Liu L, Zhou M, et al. PPIB-regulated alternative splicing of cell cycle genes contributes to the regulation of cell proliferation. Am J Transl Res. 2022;14(9):6163–6174.
   PubMed Web of Science ®Google Scholar
• Eder T, Weber A, Neuwirt H, et al. Cancer-Associated fibroblasts modify the response of prostate cancer cells to androgen and anti-Androgens in Three-Dimensional spheroid culture. Int J Mol Sci. 2016;17(9):1458. doi:10.3390/ijms17091458.
   PubMed Web of Science ®Google Scholar
• Kato M, Placencio-Hickok VR, Madhav A, et al. Heterogeneous cancer-associated fibroblast population potentiates neuroendocrine differentiation and castrate resistance in a CD105-dependent manner. Oncogene. 2019;38(5):716–730. doi:10.1038/s41388-018-0461-3.
   PubMed Web of Science ®Google Scholar
• Kesch C, Yirga L, Dendl K, et al. High fibroblast-activation-protein expression in castration-resistant prostate cancer supports the use of FAPI-molecular theranostics. Eur J Nucl Med Mol Imaging. 2021;49(1):385–389. doi:10.1007/s00259-021-05423-y.
   PubMed Web of Science ®Google Scholar
• Cao Z, Kyprianou N. Mechanisms navigating the TGF-β pathway in prostate cancer. Asian J Urol. 2015;2(1):11–18. doi:10.1016/j.ajur.2015.04.011.
   PubMedGoogle Scholar