Table 1.

Major Features from the 8 Panels of Cancer-Immune Gene Expression

	Genes Associated	Subgroup 1	Subgroup 2	Subgroup 3
		UB+ IFN1p- AP-	UB- IFN1s- AP-	UB+ IFN1+ AP+
(De)Ubiquitination	Deubiquitination/E3 ubiquitin ligase	High	Very lowa	High
Type I IFN	Production	Low	Very low	Higha
	Signaling	High	Very low	High
Antigen-presenting machinery	Antigen processing	Low	Low	Low
	MHC class I	Low∗	High	Low
	MHC class II	Low	Low	High
	p-MHC assembly	High	ab. peptidesb	High
	Antigen presentation	Very few p-MHC	MHC-I-bound ab. peptidomeb	p-MHC-II
TGF-β	Signaling	High	Very low	High∗
NK cell activation	NKp30	Low	High	High
	NKp44	Low	Low	Low
	NKp46	Low	Low	High
	NKG2D	Low	Low	High
	NKG2A	Low	Low	High
	CD94	Low	Low	High
DC activation	Maturation	Low	High	High
	Migration to LN	Low	Low	High
TME	Myeloid cell recruitment	Low	High	High
	Angiogenesis	High	Low	Low
T cell activation (Treg included)
neoAg-specific fraction	PD-1	Low	High	High
	CXCR3	Low	High	High
	IFNγ	Very low	Low	Low
Tumor-T cell interaction
T cell responsiveness	IFNGR1	Low	Very low	High
	PD-L1	Low	Very low	High
	CXCL9/10/11	Very low	Low	High

Based on the major features, we temporarily renamed each subgroups as follows: subgroup 1 as subgroup with ubiquitination functioning, type I IFN production defective, antigen presentation defective (abbreviated as UB + IFN1p- AP-); subgroup 2 as subgroup with ubiquitination defective, type I IFN signaling defective, antigen presentation defective (UB- IFN1s- AP-); subgroup 3 as subgroup with ubiquitination functioning, type I IFN functioning, antigen presentation functioning (UB + IFN1+ AP+).

^aHigh, low, or very low indicates relative value within this cohort.

^bAberrant peptides, aberrant peptidome.