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Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.

ABSTRACT: Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.

SUBMITTER: Li Y

PROVIDER: S-EPMC9839644 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.

Li Yize Y Lih Tung-Shing M TM Dhanasekaran Saravana M SM Mannan Rahul R Chen Lijun L Cieslik Marcin M Wu Yige Y Lu Rita Jiu-Hsien RJ Clark David J DJ Kołodziejczak Iga I Hong Runyu R Chen Siqi S Zhao Yanyan Y Chugh Seema S Caravan Wagma W Naser Al Deen Nataly N Hosseini Noshad N Newton Chelsea J CJ Krug Karsten K Xu Yuanwei Y Cho Kyung-Cho KC Hu Yingwei Y Zhang Yuping Y Kumar-Sinha Chandan C Ma Weiping W Calinawan Anna A Wyczalkowski Matthew A MA Wendl Michael C MC Wang Yuefan Y Guo Shenghao S Zhang Cissy C Le Anne A Dagar Aniket A Hopkins Alex A Cho Hanbyul H Leprevost Felipe da Veiga FDV Jing Xiaojun X Teo Guo Ci GC Liu Wenke W Reimers Melissa A MA Pachynski Russell R Lazar Alexander J AJ Chinnaiyan Arul M AM Van Tine Brian A BA Zhang Bing B Rodland Karin D KD Getz Gad G Mani D R DR Wang Pei P Chen Feng F Hostetter Galen G Thiagarajan Mathangi M Linehan W Marston WM Fenyö David D Jewell Scott D SD Omenn Gilbert S GS Mehra Rohit R Wiznerowicz Maciej M Robles Ana I AI Mesri Mehdi M Hiltke Tara T An Eunkyung E Rodriguez Henry H Chan Daniel W DW Ricketts Christopher J CJ Nesvizhskii Alexey I AI Zhang Hui H Ding Li L

Cancer cell 20221222 1

Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, w ...[more]

PMID: 36563681

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Project description:BackgroundIntratumor molecular heterogeneity has been reported for primary clear cell renal cell carcinoma (ccRCC) tumors; however, heterogeneity in metastatic ccRCC tumors has not been explored.ObjectiveTo evaluate intra- and intertumor molecular heterogeneity in resected metastatic ccRCC tumors.Design, setting, and participantsWe identified 111 patients who had tissue available from their primary tumor and at least one metastasis. ClearCode34 genes were analyzed for all tumors.Outcome measurements and statistical analysisPrimary and metastatic tumors were classified as clear cell type A (ccA) or B (ccB) subtypes. Logistic and Cox regression were used to evaluate associations with pathologic features and survival.Results and limitationsIntratumor heterogeneity of ccA/ccB subtypes was observed in 22% (95% confidence interval [CI] 3-60%) of metastatic tumors. Subtype differed across longitudinal metastatic tumors from the same patient in 23% (95% CI 10-42%) of patients and across patient-matched primary and metastatic tumors in 43% (95% CI 32-55%) of patients. Association of subtype with survival was validated in primary ccRCC tumors. The ccA/ccB subtype in metastatic tumors was significantly associated with metastatic tumor location, metastatic tumor grade, and presence of tumor necrosis. A limitation of this study is that we only analyzed patients who had both a nephrectomy and metastasectomy.ConclusionsApproximately one quarter of metastatic tumors displayed intratumor heterogeneity; a similar rate of heterogeneity was observed across longitudinal metastatic tumors. Thus, for biomarker studies it is likely adequate to analyze a single sample per metastatic tumor provided that pathologic review is incorporated into the study design. Subtypes across patient-matched primary and metastatic tumors differed 43% of the time, suggesting that the primary tumor is not a good surrogate for the metastatic tumor.Patient summaryPrimary and secondary/metastatic cancers of the kidney differed in nearly one half of ccRCC patients. The pattern of this relationship may affect tumor growth and the most suitable treatment.

Project description:Renal cell carcinoma (RCC) is one of the leading causes of cancer-related death worldwide. Tumour metastasis and heterogeneity lead to poor survival outcomes and drug resistance in patients with metastatic RCC (mRCC). In this study, we aimed to assess intratumoural heterogeneity (ITH) in mRCC cells by performing a combined analysis of bulk data and single-cell RNA-sequencing data, and develop novel biomarkers for prognosis prediction on the basis of the potential molecular mechanisms underlying tumorigenesis. Eligible single-cell cohorts related to mRCC were acquired using the Gene Expression Omnibus (GEO) dataset to identify potential mRCC subpopulations. We then performed gene set variation analysis to understand the differential function in primary RCC and mRCC samples. Subsequently, we applied weighted correlation network analysis to identify coexpressing gene modules that were related to the external trait of metastasis. Protein-protein interactions were used to screen hub subpopulation-difference (sub-dif) markers (ACTG1, IL6, CASP3, ACTB and RAP1B) that might be involved in the regulation of RCC metastasis and progression. Cox regression analysis revealed that ACTG1 was a protective factor (HR < 1), whereas the other four genes (IL6, CASP3, ACTB and RAP1B) were risk factors (HR > 1). Kaplan-Meier survival analysis suggested the potential prognostic value of these sub-dif markers. The expression of sub-dif markers in mRCC was further evaluated in clinical samples by immunohistochemistry (IHC). Additionally, the genetic features of sub-dif marker expression patterns, such as genetic variation profiles, correlations with tumour-infiltrating lymphocytes (TILs), and targeted signalling pathway activities, were assessed in bulk RNA-seq datasets. In conclusion, we established novel subpopulation markers as key prognostic factors affecting EMT-related signalling pathway activation in mRCC, which could facilitate the implementation of a treatment for mRCC patients.

Project description:Bilateral renal clear cell carcinoma (BRCC) is a rare type of renal cell carcinoma (RCC) that accounts for only 1-5% of RCC cases and has a poor clinical prognosis. The origin, tumor microenvironment, cellular molecular features, and intra-tumoral heterogeneity of BRCC are still unclear. We downloaded BRCC single-cell transcriptome sequencing data from the gene expression omnibus database biochip GSE171306, containing 3,575 cells from left-sided clear cell renal cell carcinoma (ccRCC) and 3,568 cells from right-sided ccRCC, and used a series of R packages for data quality control (QC) and subsequent analysis of BRCC single-cell transcriptome data, including the use of the R packages Seurat and scCancer for cell QC, identification of major cell types, and cell annotation; R package scran for calculation of cell cycle scores; R package infercnv for malignancy scoring of tumor cells; R package ReactomeGSA for functional enrichment analysis; R package Monocle 2 for the analysis of cell differentiation trajectories; and R package CellphoneDB for the analysis of intercellular interactions. In this study, by analyzing the high-quality single-cell transcriptome data of BRCC, we identified 18 cell types and found that left- and right-sided ccRCC were approximately the same in terms of cell type and the number of each cell but differed significantly in terms of tumor cell malignancy score, tumor microenvironment, and cell stemness score. In the cell differentiation trajectory analysis of BRCC, we found that endothelial cells and macrophages play an extremely important role in its tumor progression. Further cell communication analysis was performed, and we found that it may signal through ligand-receptors, such as vascular endothelial growth factor-vascular endothelial growth factor receptor1 (VEGF-VEGFR1), MIF-(CD74-CXCR4), and growth arrest-specific protein 6-AXL, to influence the development of BRCC. The analysis of single-cell transcriptomic data of human BRCC suggests that left- and right-sided ccRCC may be of the same tumor origin, but the left-sided ccRCC is more malignant and has a better immune response.

Project description:Clear cell renal cell carcinoma (ccRCC) is the most common form of renal cancer. Due to inactivation of the von Hippel-Lindau tumour suppressor, the hypoxia-inducible transcription factors (HIFs) are constitutively activated in these tumours, resulting in a pseudo-hypoxic phenotype. The HIFs induce the expression of genes involved in angiogenesis and cell survival, but they also reset the cellular metabolism to protect cells from oxygen and nutrient deprivation. ccRCC tumours are highly vascularized and the cytoplasm of the cancer cells is filled with lipid droplets and glycogen, resulting in the histologically distinctive pale (clear) cytoplasm. Intratumoural heterogeneity may occur, and in some tumours, areas with granular, eosinophilic cytoplasm are found. Little is known regarding these traits and how they relate to the coexistent clear cell component, yet eosinophilic ccRCC is associated with higher grade and clinically more aggressive tumours. In this study, we have for the first time performed RNA sequencing comparing histologically verified clear cell and eosinophilic areas from ccRCC tissue, aiming to analyse the characteristics of these cell types. Findings from RNA sequencing were confirmed by immunohistochemical staining of biphasic ccRCC. We found that the eosinophilic phenotype displayed a higher proliferative drive and lower differentiation, and we confirmed a correlation to tumours of higher stage. We further identified mutations of the tumour suppressor p53 (TP53) exclusively in the eosinophilic ccRCC component, where mTORC1 activity was also elevated. Also, eosinophilic areas were less vascularized, yet harboured more abundant infiltrating immune cells. The cytoplasm of clear cell ccRCC cells was filled with lipids but had very low mitochondrial content, while the reverse was found in eosinophilic tissue. We herein suggest possible transcriptional mechanisms behind these phenomena. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

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Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.

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Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.

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