Table 2.

Summary of 22 transcriptomic predictive biomarkers included in this study for ICB response prediction.

Biomarker Category	Biomarker	Definition	Correlation to ICB Response	Data Type	Tumor Type	Reference
Immune-checkpoint molecule	PD-1	PD-1 mRNA expression	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[35,36]
Immune-checkpoint molecule	PD-L1	PD-L1 mRNA expression	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[8,37]
Immune-checkpoint molecule	PD-L2	PD-L2 mRNA expression	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[36,38]
Immune-checkpoint molecule	CTLA-4	CTLA-4 mRNA expression	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[8]
Immune-checkpoint molecule	IMPRES (immuno-predictive score)	A predictor of ICB response in melanoma which encompasses 15 pairwise transcriptomics relations between immune checkpoint genes.	Positive	RNA-seq/NanoString nCounter/MicroArray	Melanoma	[13]
Tumor-infiltrating lymphocyte (TIL)	CIBERSORT.CD8	Fraction of tumor- infiltrating CD8 + T cells	Positive	RNA-seq/MicroArray	Multiple Cancer Types	[17]
Tumor-infiltrating lymphocyte (TIL)	gene.CD8	The mean expression of CD8A and CD8B genes/the CD8 gene expression	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[17]
Tumor-infiltrating lymphocyte (TIL)	TIS (T Cell Infiltration Score)	T cell infiltration score about nine T cell subsets	Positive	RNA-seq/MicroArray	Multiple Cancer Types	[16]
Effector molecule	CYT (immune cytolytic activity)	Immune cytolytic activity	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[39]
Effector molecule	IFN-gamma	IFN-γ 10-gene expression	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[15]
Effector molecule	Expanded immune signature	IFN-γ 28-gene expression	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[15]
Effector molecule	T cell-inflamed GEP(gene expression profiles)	IFN-γ–responsive genes expression	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[15]
Antigen associated	CRMA (anti-CTLA-4 resistance associated MAGE-A)	MAGE-A genes expression	Negative	RNA-seq/NanoString nCounter/MicroArray	Melanoma	[40]
Antigen presentation	APM (Antigen Presenting Machinery)	Seven antigen presenting machinery (APM) genes expression	Positive	RNA-seq/MicroArray	Multiple Cancer Types	[16]
Immune resistance	Pan_F_TBRS (pan-fibroblast TGF-β response signature)	Pan-fibroblast TGF-β response signature	Negative	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[10]
Immune resistance	EMT (epithelial–mesenchymal transition)	Epithelial–mesenchymal transition (EMT)-related gene expression	Negative	RNA-seq/NanoString nCounter/MicroArray	Melanoma, UC	[18,41]
Immune resistance	C-ECM-up (cancer-associated extracellular matrix genes upregulated)	Cancer-associated ECM upregulated genes enrichment score	Negative	RNA-seq/MicroArray	Multiple Cancer Types	[30]
Immune resistance	IRP (ImmuneResistanceProgram)	Resistance program that is associated with T cell exclusion and immune evasion	Negative	RNA-seq/MicroArray	Melanoma	[42]
Immune resistance	IPRES (Innate Anti-PD-1 RESistance)	Innate anti-PD-1 resistance gene signature	Negative	RNA-seq/MicroArray	Multiple Cancer Types	[18]
Comprehensive	TIDE (Tumor Immune Dysfunction And Exclusion)	A computational method to model two primary mechanisms of tumor immune evasion	Negative	RNA-seq/NanoString nCounter/MicroArray	Melanoma, NSCLC	[11]
Comprehensive	IPS (Immunophenoscore)	A scoring scheme for the quantification termed immunophenoscore.	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[12]
Comprehensive	IS (Immune Signature)	Bayesian probability of the immune signature	Positive	RNA-seq/NanoString nCounter/MicroArray	Multiple Cancer Types	[43]