Spatially resolved proteomics surveys the chemo-refractory proteins related to high-grade serous ovarian cancer

Abstract

High-grade serous ovarian carcinoma (HGSC) is a lethal malignancy characterized by high incidence, mortality, and chemoresistance. However, its molecular drivers are unknown. In this study, spatially resolved proteomics was applied to 1144 formalin-fixed paraffin-embedded tissue spots obtained by laser capture microdissection from 10 patients with HGSC and divergent carboplatin-paclitaxel (CP) responses. Specific sampling revealed stroma-driven tumour heterogeneity, identifying 642 tumour-specific and 180 stroma-specific proteins, with 505 CP-responsive therapeutic targets. Most of these protein signatures represented previously unreported associations with chemoresistance in HGSCs. Two clinically significant spatial proteomic maps were generated by introducing tumour (TS) and chemical (CS) scores. TS analysis revealed conserved tissue architecture across CP response groups, whereas CS mapping revealed pretreatment metabolic reprogramming (rather than proliferation) as the defining feature of chemo-resistant tumours, challenging current resistance paradigms. Immunohistochemical validation of HGSC tissue microarrays confirmed the spatial proteomic localization of TFRC and PDLIM3, which are linked to tumour progression, while establishing their novel role as chemotherapy resistance biomarkers through this study, with broader predictive potential observed across additional targets in the discovery cohort. This study developed a spatially resolved proteomic framework to enhance the diagnostic and therapeutic strategies for HGSC.

Keywords

drug resistance / formalin-fixed paraffin-embedded / high-grade serous ovarian carcinoma / laser capture microdissection / spatial proteomics

References

[1] Gaona-Luviano P, Medina-Gaona LA, Magaña-Pérez K. Epidemiology of ovarian cancer. Chin Clin Oncol. 2020; 9: 47.

[2] Bell S, McKeeve C, Roxburgh P, Herrington CS. An overview of the molecular pathology of ovarian carcinomas. Diagnos Histopathol. 2024; 30: 477-486.

[3] Wu P, Gao W, Su M, et al. Adaptive mechanisms of tumor therapy resistance driven by tumor microenvironment. Front Cell Dev Biol. 2021; 9: 641469.

[4] Zhang Q, Ding J, Wang Y, et al. Tumor microenvironment manipulates chemoresistance in ovarian cancer. Oncol Rep. 2022; 47: 1-7.

[5] Yang Y, Yang Y, Yang J, et al. Tumor microenvironment in ovarian cancer: function and therapeutic strategy. Front Cell Dev Biol. 2020; 8: 758.

[6] Holohan C, Van Schaeybroeck S, Longley DB, Johnston PG. Cancer drug resistance: an evolving paradigm. Nat Rev Cancer. 2013; 13: 714-726.

[7] Cancer Genome Atlas Research Network (2011) Integrated genomic analyses of ovarian carcinoma. Nature 474: 609-615.

[8] Fang F, Cardenas H, Huang H, et al. Genomic and epigenomic signatures in ovarian cancer associated with resensitization to platinum drugs. Cancer Res. 2018; 78: 631-644.

[9] Patch A-M, Christie EL, Etemadmoghadam D, et al. Whole-genome characterization of chemoresistant ovarian cancer. Nature. 2015; 521: 489-494.

[10] Muñoz-Galván S, Carnero A. Leveraging genomics, transcriptomics, and epigenomics to understand the biology and chemoresistance of ovarian cancer. Cancers. 2021; 13: 4029.

[11] Fekete JT, Ősz Á, Pete I, et al. Predictive biomarkers of platinum and taxane resistance using the transcriptomic data of 1816 ovarian cancer patients. Gynecol Oncol. 2020; 156: 654-661.

[12] Berkel C, Cacan E. Transcriptomic analysis reveals tumor stage- or grade-dependent expression of miRNAs in serous ovarian cancer. Hum Cell. 2021; 34: 862-877.

[13] Qian J, Olbrecht S, Boeckx B, et al. A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling. Cell Res. 2020; 30: 745-762.

[14] Xu J, Fang Y, Chen K, et al. Single-cell RNA sequencing reveals the tissue architecture in human high-grade serous ovarian cancer. Clin Cancer Res. 2022; 28: 3590-3602.

[15] Elhanani O, Ben-Uri R, Keren L. Spatial profiling technologies illuminate the tumor microenvironment. Cancer Cell. 2023; 41: 404-420.

[16] Zhang K, Erkan EP, Jamalzadeh S, et al. Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer. Sci Adv. 2022; 8: eabm1831.

[17] Denisenko E, de Kock L, Tan A, et al. Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones. Nat Commun. 2024; 15: 2860.

[18] Qian L, Zhu J, Xue Z, et al. Proteomic landscape of epithelial ovarian cancer. Nat Commun. 2024; 15: 6462.

[19] Labrie M, Kendsersky ND, Ma H, et al. Proteomics advances for precision therapy in ovarian cancer. Expert Rev Proteomics. 2019; 16: 841-850.

[20] Zhang H, Liu T, Zhang Z, et al. Integrated proteogenomic characterization of human high-grade serous ovarian cancer. Cell. 2016; 166: 755-765.

[21] Chowdhury S, Kennedy JJ, Ivey RG, et al. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell. 2023; 186: 3476-3498. e35.

[22] Hunt AL, Bateman NW, Barakat W, et al. Extensive three-dimensional intratumor proteomic heterogeneity revealed by multiregion sampling in high-grade serous ovarian tumor specimens. iScience. 2021; 24: 102757.

[23] Eckert MA, Coscia F, Chryplewicz A, et al. Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts. Nature. 2019; 569: 723-728.

[24] Scalise CB, Kincaid K, Thigpen H, et al. A spatial proteomic study of platinum refractory HGSOC implicates dual AKT and WNT activity linked to an immunosuppressive tumor microenvironment. Gynecol Oncol. 2024; 185: 83-94.

[25] Marczyk M, Fu C, Lau R, et al. The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues. BMC Cancer. 2019; 19: 1189.

[26] Buczak K, Kirkpatrick JM, Truckenmueller F, et al. Spatially resolved analysis of FFPE tissue proteomes by quantitative mass spectrometry. Nat Protoc. 2020; 15: 2956-2979.

[27] Hu B, He R, Pang K, et al. High-resolution spatially resolved proteomics of complex tissues based on microfluidics and transfer learning. Cell. 2025; 188: 734-748. e22.

[28] Chen H, Zhang Y, Zhou H, et al. Routine workflow of spatial proteomics on micro-formalin-fixed paraffin-embedded tissues. Anal Chem. 2023; 95: 16733-16743.

[29] Lu S, Yang W, Liu Y, et al. Diagnostic and prognostic value of CPZ in patients with gastric cancer by integrated analysis. J Gastrointest Surg. 2023; 27: 1253-1255.

[30] McDermott JE, Arshad OA, Petyuk VA, et al. Proteogenomic characterization of ovarian HGSC Implicates mitotic kinases, replication stress in observed chromosomal instability. Cell Rep Med. 2020; 1: 100004.

[31] Bradbury M, Borràs E, Castellví J, et al. BRCA1 mutations in high-grade serous ovarian cancer are associated with proteomic changes in DNA repair, splicing, transcription regulation and signaling. Sci Rep. 2022; 12: 4445.

[32] Hu Y, Pan J, Shah P, et al. Integrated proteomic and glycoproteomic characterization of human high-grade serous ovarian carcinoma. Cell Rep. 2020; 33: 108276.

[33] Ni M, Zhou J, Gong W, et al. Proteomic analysis reveals CAAP1 negatively correlates with platinum resistance in ovarian cancer. J Proteomics. 2023; 277: 104864.

[34] Huang D, Chowdhury S, Wang H, et al. Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory, high-grade serous ovarian cancer. Cell Rep Med. 2021; 2: 100471.

[35] Lombardi R, Sonego M, Pucci B, et al. HSP90 identified by a proteomic approach as druggable target to reverse platinum resistance in ovarian cancer. Mol Oncol. 2021; 15: 1005-1023.

[36] Yu K-H, Levine DA, Zhang H, et al. Predicting ovarian cancer patients’ clinical response to platinum-based chemotherapy by their tumor proteomic signatures. J Proteome Res. 2016; 15: 2455-2465.

[37] Qian L, Zhu J, Xue Z, et al. Resistance prediction in high-grade serous ovarian carcinoma with neoadjuvant chemotherapy using data-independent acquisition proteomics and an ovary-specific spectral library. Mol Oncol. 2023; 17: 1567-1580.

[38] Yang C, Li J, Guo Y, et al. Role of TFRC as a novel prognostic biomarker and in immunotherapy for pancreatic carcinoma. Front Mol Biosci. 2022; 9: 756895.

[39] Yang F, Zhou Y, Zhang Y, et al. PDLIM3 regulates migration and invasion of head and neck squamous cell carcinoma via YAP-mediated epithelial-mesenchymal transition. Int J Mol Sci. 2025; 26: 3147.

[40] Horai Y, Mizukawa M, Nishina H, et al. Quantification of histopathological findings using a novel image analysis platform. J Toxicol Pathol. 2019; 32: 319-327.

[41] Sazonova EV, Kopeina GS, Imyanitov EN, Zhivotovsky B. Platinum drugs and taxanes: can we overcome resistance?. Cell Death Discov. 2021; 7: 1-10.

[42] Fundytus A, Sengar M, Lombe D, et al. Access to cancer medicines deemed essential by oncologists in 82 countries: an international, cross-sectional survey. The Lancet Oncology. 2021; 22: 1367-1377.

[43] Yan Z, Duan C, Li X, et al. circ-TFRC downregulation suppresses ovarian cancer progression via miR-615-3p/IGF2 axis regulation. Cancer Cell Int. 2024; 24: 152.

[44] Huang Y, Huang J, Huang Y, et al. TFRC promotes epithelial ovarian cancer cell proliferation and metastasis via up-regulation of AXIN2 expression. Am J Cancer Res. 2020; 10: 131-147.

[45] Zhang J, Yang Y, Li X, et al. PDLIM3 supports hedgehog signaling in medulloblastoma by facilitating cilia formation. Cell Death Differ. 2023; 30: 1198-1210.

[46] Nie Z, Chen M, Gao Y, et al. Ferroptosis and tumor drug resistance: current status and major challenges. Front Pharmacol. 2022; 13: 879317.

[47] Yan H, Zou T, Tuo Q, et al. Ferroptosis: mechanisms and links with diseases. Sig Transduct Target Ther. 2021; 6: 1-16.

[48] Zhang C, Liu X, Jin S, et al. Ferroptosis in cancer therapy: a novel approach to reversing drug resistance. Molecular Cancer. 2022; 21: 47.

[49] Jiang X, Xu Z, Jiang S, et al. PDZ and LIM domain-encoding genes: their role in cancer development. Cancers. 2023; 15: 5042.

[50] Zhao L, Yu C, Zhou S, et al. Epigenetic repression of PDZ-LIM domain-containing protein 2 promotes ovarian cancer via NOS2-derived nitric oxide signaling. Oncotarget. 2016; 7: 1408-1420.

[51] Jia Y, Shi H, Cao Y, et al. PDZ and LIM domain protein 4 suppresses the growth and invasion of ovarian cancer cells via inactivation of STAT3 signaling. Life Sci. 2019; 233: 116715.

[52] Weiss CAM, Brown LA, Miranda L, et al (2025) Single cell spatial proteomics maps human liver zonation patterns and their vulnerability to fibrosis. 2025.04.13.648568

[53] Nordmann TM, Anderton H, Hasegawa A, et al. Spatial proteomics identifies JAKi as treatment for a lethal skin disease. Nature. 2024; 635: 1001-1009.

[54] Korsunsky I, Millard N, Fan J, et al. Fast, sensitive and accurate integration of single-cell data with harmony. Nat Methods. 2019; 16: 1289-1296.

[55] Newman AM, Steen CB, Liu CL, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol. 2019; 37: 773-782.

[56] Wu T, Hu E, Xu S, et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (Camb). 2021; 2: 100141.

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2025 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.