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Proteomic Analysis in Renca Cells with Smarcd1 Overexpression or Knockdown Compared to Controls

ABSTRACT: In this study, we performed a proteomic analysis on Renca cells to investigate the impact of SMARCD1 overexpression and knockdown. This dataset provides a comprehensive view of protein-level changes and helps to validate the role of SMARCD1 in ccRCC.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Kidney Cancer

SUBMITTER: Vic Un

LAB HEAD: Waikeong Un

PROVIDER: PXD068898 | Pride | 2026-07-09

REPOSITORIES: Pride

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	db.peptides.csv	Csv
	db.proteins.csv	Csv
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Proteomic Analysis in MAFF-knockdown 786-O and Caki-1 Cells

Project description:This project comprises a comparative proteomic analysis of MAFF-knockdown and control 786-O and Caki-1 human renal cancer cell lines. The data aims to identify protein targets and signaling pathways regulated by MAFF in ccRCC, providing critical insights into the mechanism by which MAFF influences tumor biology and progression.

2026-07-09 | PXD068979 | Pride

SMARCD1 Affinity Purification-mass Spectrometry (AP-MS) in HEK-293 Cells

Project description:This study reports the identification of the FLAG-tagged SMARCD1 protein interactome in HEK-293 cells using Affinity Purification-Mass Spectrometry (AP-MS). The data provides a comprehensive list of proteins that physically associate with SMARCD1, thereby contributing to the understanding of its molecular functions and regulatory complexes.

2026-07-09 | PXD068854 | Pride

Overexpression of Parkin in clear cell renal cell carcinoma decreases tumor aggressiveness by regulating CKS2 levels

Project description:Here we analyzed ccRCC 786-O cells with overexpressed Parkin in contrast to wild type and control cells. While differences between 786-O wild type and control cells were rather moderate, quite some differences were found between 786-O wild type/control cells and cells overexpressed with Parkin.

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Single-Cell Transcriptomics Reveal Distinct Biological and Immunometabolic Landscapes in Renal Medullary Carcinoma Compared to Clear Cell Renal Cell Carcinoma

Project description:Renal medullary carcinoma (RMC) is a rare, highly aggressive kidney malignancy primarily affecting young individuals of African descent with sickle cell trait. The currently available targeted therapies and immunotherapies approved for clear cell renal cell carcinoma (ccRCC) are ineffective against RMC, highlighting the urgent need for novel treatment approaches specifically tailored to the distinct biological and immune hallmarks of RMC. Here, we performed single-cell RNA-sequencing (scRNA-seq) of tumor samples from five patients with RMC and five patients with ccRCC to define their immunometabolic and transcriptomic landscapes. Differential expression analysis identified ENPP3 and CA9 as distinct cell surface markers upregulated in ccRCC, whereas MUC16, TROP2, and EPCAM were upregulated in RMC tumors cells. RMC displayed a more immunosuppressive tumor microenvironment (TME), with lower infiltration of T and NK cells but an enrichment of immunosuppressive SPP1+ macrophages, contrasting with the more immune-rich TME in ccRCC. Ligand-receptor interaction analyses revealed stronger VEGF-VEGFR signaling in ccRCC and enhanced APP-CD74 signaling in RMC. Nephron anatomy mapping indicated that RMC originates in the loop of Henle, whereas ccRCC arises from proximal tubule cells. We uncovered distinct metabolic reprogramming, with RMC demonstrating higher oxidative phosphorylation (OXPHOS) and lower glycolysis compared to ccRCC. These findings were validated in vitro with RMC cell lines showing elevated oxygen consumption and diminished extracellular acidification compared with ccRCC cell lines. Overall, this study underscores the distinct origins, gene expression patterns, and immunometabolic features of RMC versus ccRCC, offering insights for future tailored therapeutic strategies against RMC.

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YAP conveys an invasive phenotype to clear cell renal cell carcinoma cell lines via endothelin-2

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Urinary Extracellular Vesicles RNA Profile in Clear Cell Renal Cell Carcinoma as Biomarker

Project description:Background: Renal cell carcinoma (RCC) accounts for about 2% of all cancers. Renal biopsy is the gold standard among the diagnostic tools, but it is invasive and not suitable for all patients. Therefore, new reliable and non-invasive biomarkers for ccRCC detection are required. Secretion of extracellular vesicles (EVs), containing RNA molecules that can be transferred between cells, seems to be a general characteristic of malignant transformation. Consistently, cancer-derived EVs are enriched in the blood, urine and various malignant effusions of cancer patients. Therefore, urinary samples can be a non-invasive approach for discovering diagnostic biomarkers. Methods: We enrolled 33 clear-cell RCC (ccRCC) patients and 22 healthy subjects (HS), age and sex-matched, for urine collection and extracellular vesicles isolation by differential centrifugation. Transcriptional profiles of urinary EVs from 12 patients with ccRCC and 11 HS were generated using the Illumina HumanHT-12 v4 BeadChip oligonucleotide arrays. Microarray analysis led to the identification of RNA that were then validated using RT-qPCR. Results: We showed for the first time that urinary exosomal shuttle RNA (esRNA) was significantly different in ccRCC patients compared to HS and we identified three EVs esRNA involved in the tumor biology that are potentially suitable as non-invasive biomarkers. GSTA1, CEBPA and PCBD1 RNA levels decreased in urinary EVs of patients compared to HS. After 1 month post-operation, the levels of RNA increased to reach the normal level. Conclusions: This study suggests, for the first time, the potential use of the RNA content of urinary EVs to provide a non-invasive first step to diagnose the ccRCC. Total RNA obtained from urinary extracellular vesicles isolated from ccRCC patients and healthy subjects.

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Expression data from 786-O renal cell cancer cells treated with pentamidine

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