README.md

gene-lists

Gene lists related to cancer immunotherapy

Cancer-testis antigens

Last updated: September 10th, 2024

Sources:

• CTpedia
• Human Protein Atlas

Methodology:

• Intersection of genes in CTpedia which have at least one tissue antibody staining in HPA, keeping only expression in testis and placenta.

Class I MHC antigen presentation

Last updated: July 21st, 2018

Sources:

• Frequent HLA class I alterations in human prostate cancer: molecular mechanisms and clinical relevance:
  • LMP2/7
  • peptide transporters TAP1/2
  • chaperones calreticulin, calnexin, ERP57, and tapasin
  • IFR-1 and NLRC5
• Expression of Antigen Processing and Presenting Molecules in Brain Metastasis of Breast Cancer
  • "β2-microgloblin, transporter associated with antigen processing (TAP) 1, TAP2 and calnexin are down-regulated in brain lesions compared with unpaired breast lesions"
• NLRC5/MHC class I transactivator is a target for immune evasion in cancer
• TAPBPR: a new player in the MHC class I presentation pathway

Interferon-gamma response

Last updated: July 21st, 2018

Sources:

• Interferon Receptor Signaling Pathways Regulating PD-L1 and PD-L2 Expression
  • "JAK1/JAK2-STAT1/STAT2/STAT3-IRF1 axis primarily regulates PD-L1 expression, with IRF1 binding to its promoter"
  • "PD-L2 responded equally to interferon beta and gamma and is regulated through both IRF1 and STAT3, which bind to the PD-L2 promoter"
  • "the suppressor of cytokine signaling protein family (SOCS; mostly SOCS1 and SOCS3) are involved in negative feedback regulation of cytokines that signal mainly through JAK2 binding, thereby modulating the activity of both STAT1 and STAT3"
• Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma
  • "resistance-associated loss-of-function mutations in the genes encoding interferon-receptor–associated Janus kinase 1 (JAK1) or Janus kinase 2 (JAK2), concurrent with deletion of the wild-type allele"
• SOCS, inflammation, and cancer
  • "Abnormal expression of SOCS1 and SOCS3 in cancer cells has been reported in human carcinoma associated with dysregulation of signals from cytokine receptors"

Recurrently mutated cancer genes

Last updated: July 21st, 2018

Cancer genes and recurrent mutations extract from Comprehensive Characterization of Cancer Driver Genes and Mutations.

Genes extracted from Table S1 into cancer-driver-genes.csv. Mutations extracted from Table S4 into cancer-driver-variants.csv.

Both datasets were annotated with Ensembl IDs using Ensembl release 92.