Identification of P3H1 as a Predictive Prognostic Biomarker for Bladder Urothelial Carcinoma Based on the Cancer Genome Atlas Database

References

• Bray F, Ferlay J, Soerjomataram I, et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68(6):394–424. doi:10.3322/caac.21492
   PubMed Web of Science ®Google Scholar
• Slovacek H, Zhuo J, Taylor JM. Approaches to Non-Muscle-Invasive Bladder Cancer. Curr Oncol Rep. 2021;23(9):105. doi:10.1007/s11912-021-01091-1
   PubMed Web of Science ®Google Scholar
• Chen X, Zhang J, Ruan W, et al. Urine DNA methylation assay enables early detection and recurrence monitoring for bladder cancer. J Clin Invest. 2020;130(12):6278–6289. doi:10.1172/JCI139597
   PubMed Web of Science ®Google Scholar
• Nakauma-González JA, Rijnders M, Van Riet J, et al. Comprehensive Molecular Characterization Reveals Genomic and Transcriptomic Subtypes of Metastatic Urothelial Carcinoma. Eur Urol. 2022;81(4):331–336. doi:10.1016/j.eururo.2022.01.026
   PubMed Web of Science ®Google Scholar
• Xie R, Cheng L, Huang M, et al. NAT10 Drives Cisplatin Chemoresistance by Enhancing ac4C-Associated DNA Repair in Bladder Cancer. Cancer Res. 2023;83(10):1666–1683. doi:10.1158/0008-5472.CAN-22-2233
   PubMed Web of Science ®Google Scholar
• Anderson NM, Simon MC. The tumor microenvironment. Current Biol. 2020;30(16):R921–R925. doi:10.1016/j.cub.2020.06.081
   PubMed Web of Science ®Google Scholar
• Theocharis AD, Skandalis SS, Gialeli C, et al. Extracellular matrix structure. Adv Drug Deliv Rev. 2016;97:4–27. doi:10.1016/j.addr.2015.11.001
   PubMed Web of Science ®Google Scholar
• Naba A, Pearce OMT, Del Rosario A, et al. Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics. J Proteome Res. 2017;16(8):3083–3091. doi:10.1021/acs.jproteome.7b00191
   PubMed Web of Science ®Google Scholar
• Kadler KE, Baldock C, Bella J, et al. Collagens at a glance. Journal of Cell Science. 2007;120(12):1955–1958. doi:10.1242/jcs.03453
   PubMed Web of Science ®Google Scholar
• Lou J, Stowers R, Nam S, et al. Stress relaxing hyaluronic acid-collagen hydrogels promote cell spreading, fiber remodeling, and focal adhesion formation in 3D cell culture. Biomaterials. 2018;154:213–222. doi:10.1016/j.biomaterials.2017.11.004
   PubMed Web of Science ®Google Scholar
• Appert-Collin A, Bennasroune A, Jeannesson P, et al. Role of LRP-1 in cancer cell migration in 3-dimensional collagen matrix. Cell Adh Migr. 2017;11(4):316–326. doi:10.1080/19336918.2016.1215788
   PubMed Web of Science ®Google Scholar
• Lamandé SR, Bateman JF. Collagen VI disorders: insights on form and function in the extracellular matrix and beyond. Matrix Biol. 2018;71-72:348–367. doi:10.1016/j.matbio.2017.12.008
   PubMed Web of Science ®Google Scholar
• Vranka JA, Sakai LY, Bächinger HP. Prolyl 3-hydroxylase 1, enzyme characterization and identification of a novel family of enzymes. J Biol Chem. 2004;279(22):23615–23621. doi:10.1074/jbc.M312807200
   PubMed Web of Science ®Google Scholar
• Shah R, Smith P, Purdie C, et al. The prolyl 3-hydroxylases P3H2 and P3H3 are novel targets for epigenetic silencing in breast cancer. Br J Cancer. 2009;100(10):1687–1696. doi:10.1038/sj.bjc.6605042
   PubMed Web of Science ®Google Scholar
• Ding R, Zhao C, Jing Y, et al. Basement membrane-related regulators for prediction of prognoses and responses to diverse therapies in hepatocellular carcinoma. BMC Med Genomics. 2023;16(1):81. doi:10.1186/s12920-023-01504-z
   PubMed Web of Science ®Google Scholar
• Zhou P, Liu Z, Hu H, et al. Comprehensive Analysis of Senescence Characteristics Defines a Novel Prognostic Signature to Guide Personalized Treatment for Clear Cell Renal Cell Carcinoma. Front Immunol. 2022;13:901671. doi:10.3389/fimmu.2022.901671
   PubMed Web of Science ®Google Scholar
• Zhang Y, C-Y L, Pan M, et al. Exploration of the Key Proteins of High-Grade Intraepithelial Neoplasia to Adenocarcinoma Sequence Using In-Depth Quantitative Proteomics Analysis. J Oncol. 2021;2021:5538756. doi:10.1155/2021/5538756
   PubMed Web of Science ®Google Scholar
• Huang Z, Wang Q, Wang Y, et al. Upregulated LEPRE1 correlates with poor outcome and its knockdown attenuates cells proliferation, migration and invasion in osteosarcoma. Anticancer Drugs. 2020;31(4):326–332. doi:10.1097/CAD.0000000000000851
   PubMed Web of Science ®Google Scholar
• Thorsson V, Gibbs DL, Brown SD, et al. The Immune Landscape of Cancer. Immunity. 2018;48(4):812–830.e14. doi:10.1016/j.immuni.2018.03.023
   PubMed Web of Science ®Google 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. doi:10.1093/nar/gkv007
   PubMed Web of Science ®Google Scholar
• Kamoun A, De Reyniès A, Allory Y, et al. A Consensus Molecular Classification of Muscle-invasive Bladder Cancer. Eur Urol. 2020;77(4):420–433. doi:10.1016/j.eururo.2019.09.006
   PubMed Web of Science ®Google Scholar
• Sternberger LA, Hardy PH, Cuculis JJ, et al. The unlabeled antibody enzyme method of immunohistochemistry: preparation and properties of soluble antigen-antibody complex (horseradish peroxidase-anti horseradish peroxidase) and its use in identification of spirochetes. J Histochem Cytochem. 1970;18(5):315–333. doi:10.1177/18.5.315
   PubMed Web of Science ®Google Scholar
• Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102
   PubMed Web of Science ®Google Scholar
• Yoshihara K, Shahmoradgoli M, Martínez E, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. #N/A. 2013;4:2612.
   Google Scholar
• Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinf. 2013;14:7. doi:10.1186/1471-2105-14-7
   PubMed Web of Science ®Google Scholar
• Li T, Fan J, Wang B, et al. TIMER: a Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells. Cancer Res. 2017;77(21):e108–e110. doi:10.1158/0008-5472.CAN-17-0307
   PubMed Web of Science ®Google Scholar
• Geeleher P, Cox N, Huang RS. pRRophetic: an R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. PLoS One. 2014;9(9):e107468. doi:10.1371/journal.pone.0107468
   PubMed Web of Science ®Google Scholar
• Mariathasan S, Turley SJ, Nickles D, et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature. 2018;554(7693):544–548. doi:10.1038/nature25501
   PubMed Web of Science ®Google Scholar
• Saginala K, Barsouk A, Aluru JS, et al. Epidemiology of Bladder Cancer. Med sci. 2020;8(1). doi:10.3390/medsci8010015
   Google Scholar
• Kehlet SN, Sanz-Pamplona R, Brix S, et al. Excessive collagen turnover products are released during colorectal cancer progression and elevated in serum from metastatic colorectal cancer patients. Sci Rep. 2016;6:30599. doi:10.1038/srep30599
   PubMed Web of Science ®Google Scholar
• Willumsen N, Bager CL, Leeming DJ, et al. Serum biomarkers reflecting specific tumor tissue remodeling processes are valuable diagnostic tools for lung cancer. Cancer Medicine. 2014;3(5):1136–1145. doi:10.1002/cam4.303
   PubMed Web of Science ®Google Scholar
• Bager CL, Willumsen N, Leeming DJ, et al. Collagen degradation products measured in serum can separate ovarian and breast cancer patients from healthy controls: a preliminary study. Cancer Biomark. 2015;15(6):783–788. doi:10.3233/CBM-150520
   PubMed Web of Science ®Google Scholar
• Rakoff-Nahoum S, Medzhitov R. Toll-like receptors and cancer. Nat Rev Cancer. 2009;9(1):57–63. doi:10.1038/nrc2541
   PubMed Web of Science ®Google Scholar
• Mo Q, Nikolos F, Chen F, et al. Prognostic Power of a Tumor Differentiation Gene Signature for Bladder Urothelial Carcinomas. J National Cancer Institute. 2018;110(5):448–459. doi:10.1093/jnci/djx243
   PubMedGoogle Scholar
• Hoogenkamp HR, Pot MW, Hafmans TG, et al. Scaffolds for whole organ tissue engineering: construction and in vitro evaluation of a seamless, spherical and hollow collagen bladder construct with appendices. Acta Biomater. 2016;43:112–121. doi:10.1016/j.actbio.2016.07.022
   PubMed Web of Science ®Google Scholar
• Chang L-C, Chiang S-K, Chen S-E, et al. Targeting 2-oxoglutarate dehydrogenase for cancer treatment. Am J Cancer Res. 2022;12(4):1436–1455.
   PubMed Web of Science ®Google Scholar
• Läubli H, Borsig L. Altered Cell Adhesion and Glycosylation Promote Cancer Immune Suppression and Metastasis. Front Immunol. 2019;10:2120. doi:10.3389/fimmu.2019.02120
   PubMed Web of Science ®Google Scholar
• Bala MM, Bala KA. Severe cases of osteogenesis imperfecta type VIII due to a homozygous mutation in P3H1 (LEPRE1) and review of the literature. Adv Clin Exp Med. 2021;30(12):1233–1238. doi:10.17219/acem/141367
   PubMed Web of Science ®Google Scholar
• Zhang Q, Liu S, Wang H, et al. ETV4 Mediated Tumor-Associated Neutrophil Infiltration Facilitates Lymphangiogenesis and Lymphatic Metastasis of Bladder Cancer. Adv. Sci. 2023;10(11):e2205613. doi:10.1002/advs.202205613
   Web of Science ®Google Scholar
• Chen Y, Song Y, Du W, et al. Tumor-associated macrophages: an accomplice in solid tumor progression. J Biomed Sci. 2019;26(1):78. doi:10.1186/s12929-019-0568-z
   PubMed Web of Science ®Google Scholar
• Qiu S, Deng L, Liao X, et al. Tumor-associated macrophages promote bladder tumor growth through PI3K/AKT signal induced by collagen. Cancer Sci. 2019;110(7):2110–2118. doi:10.1111/cas.14078
   PubMed Web of Science ®Google Scholar
• Honda K, Yanai H, Negishi H, et al. IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature. 2005;434(7034):772–777. doi:10.1038/nature03464
   PubMed Web of Science ®Google Scholar
• Shortman K, Naik SH. Steady-state and inflammatory dendritic-cell development. Nat Rev Immunol. 2007;7(1):19–30. doi:10.1038/nri1996
   PubMed Web of Science ®Google Scholar
• Huang M, Dong W, Xie R, et al. HSF1 facilitates the multistep process of lymphatic metastasis in bladder cancer via a novel PRMT5-WDR5-dependent transcriptional program. Cancer Communications. 2022;42(5):447–470. doi:10.1002/cac2.12284
   Web of Science ®Google Scholar
• Souza-Fonseca GF, Rossi GR, Dagley LF, et al. TGF-β and CIS inhibition overcomes NK cell suppression to restore anti-tumor immunity. Cancer Immunol Res. 2022;10(9):1047–1054. doi:10.1158/2326-6066.CIR-21-1052
   PubMed Web of Science ®Google Scholar