Major Histocompatibility Complex Genes as Therapeutic Opportunity for Immune Cold Molecular Cancer Subtypes

Table 1

Characteristics of cancer types included in this study and results of unsupervised clustering of expression probabilities of MHC genes. TCGA cancer type abbreviations are provided in Materials and Methods.

Cancer type	Tumor	Normal adjacent	Molecular subtypes	Molecular subtype source	MHC-low subtypes	% of samples with MHC mutations in molecular subtypes
BLCA	376	17	Ba-Sq; LumNS; LumP; LumU; stroma-rich	[32]	LumNS; LumP; LumU; Stroma-rich	; ; ; ;
BRCA	1090	99	Basal; Her2; LumA; LumB; normal-like	[33]	LumA; LumB	; ; ; ;
COAD	441	33	CMS1; CMS2; CMS3; CMS4	[22]	CMS2; CMS3; CMS4	; ; ;
ESCA	143	5	EAC; ESCC1; ESCC2	[34]	ESCC1	; ;
HNSC	462	40	CIMP; HPV; non-CIMP; NSD1; stem-like	[10]	NSD1; Stem-like	; ; ; ;
LIHC	317	46	iCluster-1; iCluster-2; iCluster-3	[35]	iCluster-1; iCluster-2	; ;
LUAD	474	57	AD-1; AD-2; AD-3; AD-4; AD-5a; AD-5b	[9]	AD-5a; AD-5b	; ; ; ; ;
LUSC	447	46	AD-1; SQ-1; SQ-2a; SQ-2b	[9]	AD-1; SQ-2b	; ; ;
PAAD	146	3	ADEX; immunogenic; progenitor; squamous	[36]	ADEX squamous	; ; ;
PRAD	442	41	S1; S2; S3	[37]	S3	; ;
STAD	334	24	CIN; EBV; GS; MSI	[38]	CIN; GS	; ; ;
THCA	481	49	THCA-1; THCA-2; THCA-3; THCA-4; THCA-5	[39]	THCA-1; THCA-3; THCA-5	; ; ; ;
UCEC	498	32	CN-HIGH; CN-LOW; MSI; POLE	[40]	CN_HIGH	; ; ;