lymphokine_RCC

Role of CXCL9/10/11, CXCL13 and XCL1 in recruitment and suppression of cytotoxic T cells in renal cell carcinoma

Terms of use

The pipeline results are included in a publication by Renate Pichler et al. (DOI: 10.3389/fimmu.2023.1095195). The analysis concerns solely publicly available data cited below. To reference and use analysis results, please cite our GitHub repository; the data sources listed below and our publication. In any questions, please contact Renate Pichler or Piotr Tymoszuk.

Data sources

This is a complete R analysis pipeline of 8 publicly available renal whole-transcriptome datasets:

• TCGA KIRC project: clinical information and normalized RNAseq data can be obtained from the GDC Data Portal of the National Cancer Insitute. the data set was first analyzed by Creighton and colleagues ¹. Data extraction was done with the TCGA-Assembler-2 script available from @compgenome365/TCGA-Assembler-2

• CheckMate 010, CheckMate 025 everolimus, CheckMate 025 nivolumab datasets: clinical information and normalized RNAseq data available as Supplementary Tables S1 and S4 accompanying the publication of Braun et al. ²

• RECA-EU project: clinical information and normalized RNAseq data can be downloaded from the ICGC Data Portal

• GSE73731 and GSE167093 datasets: normalized microarray expression data and clinical information ³⁴ can be accessed from Gene Expression Ominibus, e.g. with the GEOquery R package ⁵

• E-MTAB 1980 dataset: normalized microarray expression data and clinical information ⁶ can be obtained from ArrayExpressData

Usage

To make sure to install required development packages prior to runung the pipeline:

devtools::install_github('PiotrTymoszuk/ExDA')
devtools::install_github('PiotrTymoszuk/microViz')
devtools::install_github('PiotrTymoszuk/kmOptimizer')
devtools::install_github('PiotrTymoszuk/coxExtensions')
devtools::install_github('PiotrTymoszuk/trafo')
devtools::install_github('PiotrTymoszuk/gseaTools')
devtools::install_github('PiotrTymoszuk/biggrExtra')
devtools::install_github('PiotrTymoszuk/clustTools')
devtools::install_github('PiotrTymoszuk/soucer')
devtools::install_github('PiotrTymoszuk/somKernels')
devtools::install_github('PiotrTymoszuk/figur')

To launch the entire pipeline, source the exec.R file:

source('exec.R')

Contact

The maintainer of the repository is Piotr Tymoszuk.

Footnotes

1. Creighton CJ, Morgan M, Gunaratne PH, Wheeler DA, Gibbs RA, Robertson G, Chu A, Beroukhim R, Cibulskis K, Signoretti S, et al. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 2013 499:7456 (2013) 499:43–49. doi: 10.1038/nature12222 ↩

2. Braun DA, Hou Y, Bakouny Z, Ficial M, Sant’ Angelo M, Forman J, Ross-Macdonald P, Berger AC, Jegede OA, Elagina L, et al. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nature medicine (2020) 26:909. doi: 10.1038/S41591-020-0839-Y ↩

3. Wei X, Choudhury Y, Lim WK, Anema J, Kahnoski RJ, Lane B, Ludlow J, Takahashi M, Kanayama HO, Belldegrun A, et al. Recognizing the Continuous Nature of Expression Heterogeneity and Clinical Outcomes in Clear Cell Renal Cell Carcinoma. Scientific reports (2017) 7: doi: 10.1038/S41598-017-07191-Y ↩

4. Laskar RS, Li P, Ecsedi S, Abedi-Ardekani B, Durand G, Robinot N, Hubert JN, Janout V, Zaridze D, Mukeria A, et al. Sexual dimorphism in cancer: insights from transcriptional signatures in kidney tissue and renal cell carcinoma. Human molecular genetics (2021) 30:343–355. doi: 10.1093/HMG/DDAB031 ↩

5. Sean D, Meltzer PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics (Oxford, England) (2007) 23:1846–1847. doi: 10.1093/BIOINFORMATICS/BTM254 ↩

6. Sato Y, Yoshizato T, Shiraishi Y, Maekawa S, Okuno Y, Kamura T, Shimamura T, Sato-Otsubo A, Nagae G, Suzuki H, et al. Integrated molecular analysis of clear-cell renal cell carcinoma. Nature Genetics 2013 45:8 (2013) 45:860–867. doi: 10.1038/ng.2699 ↩