get_scores_signature_genes: Get the gene signatures for each score of immune response

In olapuentesantana/easierData: easier internal data and exemplary dataset from IMvigor210CoreBiologies package

Description

Obtain the gene signatures for each score of immune response: CYT, TLS, IFNy, Ayers_expIS, Tcell_inflamed, Roh_IS, Davoli_IS, chemokines, IMPRES, MSI and RIR.

Usage

get_scores_signature_genes()

Value

A list with the gene signature of each score of immune response.

References

Rooney, Michael S., Sachet A. Shukla, Catherine J. Wu, Gad Getz, and Nir Hacohen. 2015. “Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity.” Cell 160 (1): 48–61. https://doi.org/10.1016/j.cell.2014.12.033.

Cabrita, Rita, Martin Lauss, Adriana Sanna, Marco Donia, Mathilde Skaarup Larsen, Shamik Mitra, Iva Johansson, et al. 2020. “Tertiary Lymphoid Structures Improve Immunotherapy and Survival in Melanoma.” Nature 577 (7791):561–65. https://doi.org/10.1038/s41586-019-1914-8.

McClanahan, Mark Ayers AND Jared Lunceford AND Michael Nebozhyn AND Erin Murphy AND Andrey Loboda AND David R. Kaufman AND Andrew Albright AND Jonathan D. Cheng AND S. Peter Kang AND Veena Shankaran AND Sarina A. Piha-Paul AND Jennifer Yearley AND Tanguy Y. Seiwert AND Antoni Ribas AND Terrill K. 2017. “IFN-y–Related mRNA Profile Predicts Clinical Response to PD-1 Blockade.” The Journal of Clinical Investigation 127 (8): 2930–40. https://doi.org/10.1172/JCI91190.

Roh, Whijae, Pei-Ling Chen, Alexandre Reuben, Christine N. Spencer, Peter A. Prieto, John P. Miller, Vancheswaran Gopalakrishnan, et al. 2017. “Integrated Molecular Analysis of Tumor Biopsies on Sequential CTLA-4 and PD-1 Blockade Reveals Markers of Response and Resistance.” Science Translational Medicine 9 (379). https://doi.org/10.1126/scitranslmed.aah3560.

Davoli, Teresa, Hajime Uno, Eric C. Wooten, and Stephen J. Elledge. 2017. “Tumor Aneuploidy Correlates with Markers of Immune Evasion and with Reduced Response to Immunotherapy.” Science 355 (6322). https://doi.org/10.1126/science.aaf8399.

Messina, Jane L., David A. Fenstermacher, Steven Eschrich, Xiaotao Qu, Anders E. Berglund, Mark C. Lloyd, Michael J. Schell, Vernon K. Sondak, Jeffrey S. Weber, and James J. Mulé. 2012. “12-Chemokine Gene Signature Identifies Lymph Node-Like Structures in Melanoma: Potential for Patient Selection for Immunotherapy?” Scientific Reports 2 (1): 765. https://doi.org/10.1038/srep00765.

Auslander, Noam, Gao Zhang, Joo Sang Lee, Dennie T. Frederick, Benchun Miao, Tabea Moll, Tian Tian, et al. 2018. “Robust Prediction of Response to Immune Checkpoint Blockade Therapy in Metastatic Melanoma.” Nature Medicine 24(10): 1545–49. https://doi.org/10.1038/s41591-018-0157-9.

Fu, Yelin, Lishuang Qi, Wenbing Guo, Liangliang Jin, Kai Song, Tianyi You, Shuobo Zhang, Yunyan Gu, Wenyuan Zha, and Zheng Guo. 2019. “A Qualitative Transcriptional Signature for Predicting Microsatellite Instability Status of Right-Sided Colon Cancer.” BMC Genomics 20 (1): 769. https://doi.org/10.1186/s12864-019-6129-8.

Jerby-Arnon, Livnat, Parin Shah, Michael S. Cuoco, Christopher Rodman, Mei-Ju Su, Johannes C. Melms, Rachel Leeso, et al. 2018. “A Cancer Cell Program Promotes t Cell Exclusion and Resistance to Checkpoint Blockade.” Cell 175 (4): 984–997.e24. https://doi.org/10.1016/j.cell.2018.09.006.

Óscar Lapuente-Santana, Maisa van Genderen, Peter A. J. Hilbers, Francesca Finotello, and Federica Eduati. 2021. Interpretable Systems Biomarkers Predict Response to Immune-Checkpoint Inhibitors. Patterns, 100293. https://doi.org/10.1016/j.patter.2021.100293.

Examples

if (interactive()) {
    easier_sigs <- get_scores_signature_genes()
}

olapuentesantana/easierData documentation built on Dec. 22, 2021, 4:19 a.m.