Extended Data Table 1. Commonly differentially regulated genes and GSEA pathways in mLama4⁺ TILs during checkpoint blockade therapy.

a, 25 differentially expressed genes (p<0.05) that are commonly up-regulated (red) or down-regulated (blue) in mLama4-specific CD8⁺ TILs from mice treated with all checkpoint blockade mAbs versus TILs from control mAb treated mice. Genes underlined and in bold are those involved in CD8⁺ T effector cells in acute verses chronic infection. b, GSEA pathway analysis showing selected pathways (and their p values) altered in mLama4-specific CD8⁺ TILs during different checkpoint blockade treatments.

a
Commonly Altered Genes in Checkpoint Blockade Treated Groups
Gene	anti-PD-1		anti-CTLA-4		anti-PD-1 + anti-CTLA-4
	Fold Change	p value	Fold Change	p value	Fold Change	p value
Abcf1	1.8498	0.0009	1.6563	0.0010	1.6133	0.0091
Arhgap11a	2.2469	0.0085	2.5201	0.0003	2.1815	0.0004
Brca1	3.0675	0.0050	4.1248	0.0004	3.6843	0.0003
Cep128	2.2903	0.0020	2.6134	<10−4	2.1577	0.0079
Clspn	2.6332	0.0003	2.0996	0.0002	2.5427	<10−4
Golga4	2.1608	0.0046	1.6866	0.0089	2.1701	0.0003
Kif20b	2.6334	0.0003	2.6786	<10−4	2.2927	0.0001
Lef1	2.0932	0.0033	2.0713	0.0019	2.1006	0.0012
Lmnb1	2.6944	<10−4	2.6335	0.0002	2.1587	0.0002
Nusap1	2.3610	0.0011	2.2774	<10−4	1.8717	0.0036
Pbdc1	2.2750	0.0002	1.8901	0.0038	1.7994	0.0086
Ripk1	2.7563	0.0003	2.3822	0.0022	2.9873	0.0002
Sclt1	2.8084	0.0013	2.4172	0.0035	2.4687	0.0044
Smc1a	1.6027	0.0070	1.5141	0.0043	1.5802	0.0033
Smc2	2.4076	0.0005	2.3176	<10−4	1.7604	0.0013
Smc3	2.1347	0.0008	1.7558	0.0001	1.7829	0.0030
5330439K02Rik	7.0531	0.0040	7.7751	0.0060	8.5834	0.0079
Atp2b2	5.4570	0.0021	7.6665	0.0008	37.4543	<10−4
Dnajb1	1.9973	0.0061	2.0345	0.0007	3.1415	<10−4
Ephx1	2.8845	0.0059	3.3558	0.0006	6.8748	0.0001
Errfi1	1.8630	0.0054	2.0856	0.0018	2.7131	0.0006
Ifitm1	2.8256	0.0002	2.1070	0.0002	2.4488	0.0001
Klhdc8a	6.9301	0.0044	8.7394	0.0036	9.7055	0.0048
Tctn2	8.3409	0.0012	13.5967	0.0004	14.7772	0.0007
Xcl1	2.8113	0.0001	2.9306	<10−4	2.2410	<10−4

b
	p value
GSEA Pathway	anti-PD-1	anti-CTLA-4	anti-PD-1 + anti-CTLA-4
REACTOME_IL_2_SIGNALING	0.0353	0.2631	0.0562
REACTOME_GLYCOLYSIS	0.0487	0.8937	0.0586
BIOCARTA_TNFR1_PATHWAY	0.0395	0.3855	0.0564
REACTOME_INTERFERON_SIGNALING	0.0350	0.5374	0.0311
ST_TYPE_I_INTERFERON_PATHWAY	0.0173	0.0519	0.0063
KEGG_OXIDATIVE_PHOSPHORYLATION	<10−4	0.3731	<10−4
REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT	<10−4	0.9532	<10−4
REACTOME_GLUCOSE_METABOLISM	0.0115	0.9055	0.0114
KEGG_PENTOSE_PHOSPHATE_PATHWAY	0.0167	0.6182	0.0278
REACTOME_CELL_CYCLE_CHECKPOINTS	0.0534	<10−4	0.0730
SA_G2_AND_M_PHASES	0.1285	0.0023	0.1081
KEGG_JAK_STAT_SIGNALING_PATHWAY	0.1608	<10−4	0.1568
REACTOME_SYNTHESIS_OF_DNA	0.0619	<10−4	0.0563
PID_E2F_PATHWAY	0.0813	<10−4	0.0670
KEGG_CELL_CYCLE	0.0530	<10−4	0.0454
REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS	0.0619	0.0066	0.0461
PID_NFAT_TFPATHWAY	0.0693	0.0054	0.0486
PID_GMCSF_PATHWAY	0.0875	0.0678	0.0467
BIOCARTA_CXCR4_PATHWAY	0.0525	0.9422	0.0462
GOLDRATH_NAIVE_VS_EFF_CD8_TCELL_UP	<10−4	<10−4	0.0052
GSE10239_KLRG1INT_VS_KLRG1HIGH_EFF_CD8_TCELL_DN	<10−4	<10−4	<10−4
KEGG_MAPK_SIGNALING_PATHWAY	<10−4	<10−4	<10−4
KEGG_CHEMOKINE_SIGNALING_PATHWAY	<10−4	<10−4	<10−4
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION	0.0054	<10−4	<10−4