Comprehensive analysis of the collagen family members as prognostic markers in clear cell renal cell carcinoma

Guo, Lingyu; An, Tian; Huang, Zhixin; Wan, Ziyan; Chong, Tie

doi:10.21037/tcr-22-398

Cited by 3 publications

(2 citation statements)

References 40 publications

(40 reference statements)

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“…Recently, we have shown that, for most cancers, survival prediction can be improved by incorporating clinical and transcriptomic data [20]. Additionally, there is an increasing interest in how ECM-related genes could be used to assess the survival of ccRCC patients [21][22][23][24]. To the best of our knowledge, COL7A1 expression in ccRCC was not investigated as an independent prognostic biomarker in this disease, and this is the first ccRCC study using five independent public datasets.…”

Section: Introductionmentioning

confidence: 99%

COL7A1 Expression Improves Prognosis Prediction for Patients with Clear Cell Renal Cell Carcinoma Atop of Stage

Koca

Séraudie

Jardillier

et al. 2023

Cancers

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Clear-cell renal cell carcinoma (ccRCC) accounts for 75% of kidney cancers. Due to the high recurrence rate and treatment options that come with high costs and potential side effects, a correct prognosis of patient survival is essential for the successful and effective treatment of patients. Novel biomarkers could play an important role in the assessment of the overall survival of patients. COL7A1 encodes for collagen type VII, a constituent of the basal membrane. COL7A1 is associated with survival in many cancers; however, the prognostic value of COL7A1 expression as a standalone biomarker in ccRCC has not been investigated. With five publicly available independent cohorts, we used Kaplan–Meier curves and the Cox proportional hazards model to investigate the prognostic value of COL7A1, as well as gene set enrichment analysis to investigate genes co-expressed with COL7A1. COL7A1 expression stratifies patients in terms of aggressiveness, where the 5-year survival probability of each of the four groups was 72.4%, 59.1%, 34.15%, and 8.6% in order of increasing expression. Additionally, COL7A1 expression was successfully used to further divide patients of each stage and histological grade into groups of high and low risk. Similar results were obtained in independent cohorts. In vitro knockdown of COL7A1 expression significantly affected ccRCC cells’ ability to migrate, leading to the hypothesis that COL7A1 may have a role in cancer aggressiveness. To conclude, we identified COL7A1 as a new prognosis marker that can stratify ccRCC patients.

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Section: Introductionmentioning

confidence: 99%

COL7A1 Expression Improves Prognosis Prediction for Patients with Clear Cell Renal Cell Carcinoma Atop of Stage

Koca

Séraudie

Jardillier

et al. 2023

Cancers

View full text Add to dashboard Cite

show abstract

“…Recently, we have shown that, for most cancers, survival prediction can be improved by incorporating clinical and transcriptomic data [17]. Additionally, there is an increasing interest in how ECM-related genes could be used to assess the survival of ccRCC patients [18][19][20][21]. To the best of our knowledge, COL7A1 expression in ccRCC was not investigated as an independent prognostic biomarker in this disease.…”

Section: Introductionmentioning

confidence: 99%

COL7A1 expression improves prognosis prediction for patients with clear cell renal cell carcinoma atop of stage

Koca

Séraudie

Jardiller

et al. 2023

Preprint

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Clear cell renal cell carcinoma (ccRCC) accounts for 75% of kidney cancers. Due to the high recurrence rate, and treatment options that come with high costs and potential side effects correct prognosis of patient survival is essential for the successful and effective treatment of patients. Novel biomarkers could play an important role in the assessment of the overall survival of patients. COL7A1 encodes for collagen type VII, a constituent of the basal membrane. COL7A1 is associated with survival in many cancers; however, the prognostic value of COL7A1 expression as a standalone biomarker in ccRCC has not been investigated. We used Kaplan-Meier curves and Cox proportional hazards model to investigate the prognostic value of COL7A1, as well as Gene Set Enrichment Analysis to investigate genes that are co-expressed with COL7A1. COL7A1 expression was used to stratify patients into four groups of expression, where the 5-year survival probability of each group was 72.4%, 59.1%, 34.15%, and 8.6% in order of increasing expression. Additionally, COL7A1 expression was successfully used to further divide patients of each stage and histological grade into groups of high and low risk. Similar results were obtained in independent cohorts. In-vitro knockdown of COL7A1 expression significantly impacted ccRCC cells' ability to migrate and proliferate. To conclude, we identified COL7A1 as a new prognosis marker that can stratify ccRCC patients.

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Unbiased discovery of cancer pathways and therapeutics using Pathway Ensemble Tool and Benchmark

Wang,

Pattnaik,

Sahoo

et al. 2024

Nat Commun

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Correctly identifying perturbed biological pathways is a critical step in uncovering basic disease mechanisms and developing much-needed therapeutic strategies. However, whether current tools are optimal for unbiased discovery of relevant pathways remains unclear. Here, we create "Benchmark" to critically evaluate existing tools and find that most function sub-optimally. We thus develop the "Pathway Ensemble Tool" (PET), which outperforms existing methods. Deploying PET, we identify prognostic pathways across 12 cancer types. PET-identified prognostic pathways offer additional insights, with genes within these pathways serving as reliable biomarkers for clinical outcomes. Additionally, normalizing these pathways using drug repurposing strategies represents therapeutic opportunities. For example, the top predicted repurposed drug for bladder cancer, a CDK2/9 inhibitor, represses cell growth in vitro and in vivo. We anticipate that using Benchmark and PET for unbiased pathway discovery will offer additional insights into disease mechanisms across a spectrum of diseases, enabling biomarker discovery and therapeutic strategies.The pathogenesis of complex diseases is often underpinned by dysregulation of several cellular pathways. This is well exemplified by neoplastic diseases, where abnormalities in multiple pathways contribute to cancerous transformation or in which cancer-disposing events perturb multiple cellular pathways. Despite notable successes in some cancers, limited therapeutic gains have been made by identification and targeting of single contributory genes. Precisely pinpointing key dysregulated celluar pathways in cancer and ranking

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Comprehensive analysis of the collagen family members as prognostic markers in clear cell renal cell carcinoma

Cited by 3 publications

References 40 publications

COL7A1 Expression Improves Prognosis Prediction for Patients with Clear Cell Renal Cell Carcinoma Atop of Stage

COL7A1 Expression Improves Prognosis Prediction for Patients with Clear Cell Renal Cell Carcinoma Atop of Stage

COL7A1 expression improves prognosis prediction for patients with clear cell renal cell carcinoma atop of stage

Unbiased discovery of cancer pathways and therapeutics using Pathway Ensemble Tool and Benchmark

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