Genomics of NSCLC patients both affirm PD-L1 expression and predict their clinical responses to anti-PD-1 immunotherapy

Brogden, Kim A.; Parashar, Deepak; Hallier, Andrea R.; Braun, Terry; Qian, Fang; Rizvi, Naiyer A.; Bossler, Aaron D.; Milhem, Mohammed M.; Chan, Timothy A.; Abbasi, Taher; Vali, Shireen

doi:10.1186/s12885-018-4134-y

Table 1 Discovery (n = 13) and Validation (n = 16) datasets of patients with non-small cell lung cancer containing PD-1 clinical response and patient-specific simulation models containing PD-1 predicted response, predicted PD-L1 expression, immunosuppressive biomarker expression, and predicted dendritic cell (DC) infiltration index

From: Genomics of NSCLC patients both affirm PD-L1 expression and predict their clinical responses to anti-PD-1 immunotherapy

DISCOVERY DATASET
				Immunosuppressive Biomarkers
Study ID	PD-1 Clinical Response	PD-1 Predicted response	Score	PDL1	TGFB1	IDO1	IL6	VEGFA	TDO2	PGE2	IL10	LGALS9	FASLG	CD47	CTLA4	PDCD1LG2	GM3	GD2	DC Index
VCMG7N	NON-RESPONDER	NON-RESPONDER	MATCH	25.73	4.14	5.27	14.79	11.31	0.98	4.67	14.50	0.20	−5.99	3.20	10.76	1.36	25.57	25.57	17.85
L11LVL	NON-RESPONDER	NON-RESPONDER	MATCH	18.95	−1.08	−2.33	7.89	14.14	1.38	−7.60	8.51	−0.03	−2.32	3.74	6.15	1.51	14.48	14.48	14.73
UC2LIA	NON-RESPONDER	NON-RESPONDER	MATCH	78.62	44.67	5.44	131.81	48.07	3.35	16.14	41.95	2.68	−2.61	6.30	12.10	2.82	25.52	25.52	40.42
X0152B	NON-RESPONDER	NON-RESPONDER	MATCH	21.87	9.51	0.84	16.17	15.78	0.23	38.50	13.54	−0.43	−7.37	7.44	12.07	1.40	−0.01	−0.01	26.80
QIA43T	NON-RESPONDER	NON-RESPONDER	MATCH	41.42	57.12	−3.64	55.10	40.89	4.06	12.60	36.51	1.78	1.26	1.09	6.57	4.83	21.57	21.57	42.21
J0T9TJ	NON-RESPONDER	NON-RESPONDER	MATCH	44.40	26.90	−2.55	20.21	17.96	1.44	20.71	12.71	5.92	− 0.96	2.03	2.24	14.55	14.55	2.56	16.71
3DJF3O	NON-RESPONDER	NON-RESPONDER	MATCH	21.81	7.76	4.19	21.26	9.45	0.78	1.97	11.54	1.58	−8.74	3.34	1.97	1.72	18.63	18.63	18.29
MG6XF2	NON-RESPONDER	NON-RESPONDER	MATCH	11.08	7.54	1.97	81.93	25.47	−0.98	4.74	9.51	1.11	−1.15	2.01	17.50	0.86	5.92	5.92	5.31
C9TGAJ	RESPONDER	RESPONDER	MATCH	43.42	23.05	4.64	37.16	31.76	2.75	9.86	25.25	5.24	−11.30	6.60	11.83	4.15	40.30	40.30	37.91
RDD2UW	RESPONDER	RESPONDER	MATCH	54.86	49.36	10.35	47.04	22.34	1.97	19.41	22.51	14.47	− 0.25	3.40	2.96	4.87	29.93	29.93	32.66
L8MTGU	RESPONDER	RESPONDER	MATCH	34.59	18.21	6.31	38.22	16.49	1.36	2.37	17.06	3.48	− 8.50	4.08	7.70	2.37	26.69	26.69	23.76
2FCOH7	RESPONDER	NON-RESPONDER	MISMATCH	31.78	35.02	−7.84	28.65	63.79	4.39	−32.22	23.15	8.79	−5.90	6.16	48.00	8.42	41.16	41.16	26.35
P90A0O	RESPONDER	RESPONDER	MATCH	34.09	19.79	5.98	35.86	15.08	1.67	2.38	17.45	6.00	−7.27	4.36	3.32	2.64	29.91	29.91	28.49
		Total score	92.31
VALIDATION DATASET
				Immunosuppressive Biomarkers
Study ID	Clinical Response	Predicted response	Score	PDL1	TGFB1	IDO1	IL6	VEGFA	TDO2	PGE2	IL10	LGALS9	FASLG	CD47	CTLA4	PDCD1LG2	GM3	GD2	DC Index
195P5D	NON-RESPONDER	NON-RESPONDER	MATCH	27.60	15.20	0.97	26.76	12.90	1.33	9.08	16.51	3.54	− 8.83	5.99	1.66	45.78	25.94	25.94	26.60
ZNT6MQ	NON-RESPONDER	NON-RESPONDER	MATCH	76.54	31.90	−0.45	101.96	36.03	5.64	23.13	40.46	3.63	− 0.76	9.05	2.29	10.64	41.99	41.99	48.94
ZX7V33	NON-RESPONDER	NON-RESPONDER	MATCH	33.70	5.06	5.19	19.67	6.96	0.71	−0.39	9.31	2.49	−7.64	3.26	1.76	1.45	14.28	14.28	16.00
F3FK2W	NON-RESPONDER	RESPONDER	MISMATCH	63.86	17.70	3.87	25.27	15.83	−3.05	5.47	19.72	−4.96	− 4.56	8.16	7.10	2.98	24.03	24.03	34.14
6QFSVV	NON-RESPONDER	RESPONDER	MISMATCH	43.31	44.18	5.31	42.83	19.40	1.86	14.62	18.65	12.46	− 0.10	1.88	2.10	3.29	26.70	26.70	25.50
IPUAS9	NON-RESPONDER	NON-RESPONDER	MATCH	28.49	10.25	5.43	25.29	10.86	2.11	4.85	11.77	2.65	−1.00	3.44	7.14	1.51	13.54	13.54	15.01
GI7AGZ	NON-RESPONDER	RESPONDER	MISMATCH	142.53	96.10	8.52	114.25	69.40	4.12	39.61	49.30	25.56	0.38	5.44	12.89	12.02	67.05	67.05	64.92
CZH5YD	NON-RESPONDER	NON-RESPONDER	MATCH	76.21	17.60	8.11	96.00	30.61	3.17	7.75	28.32	9.96	−2.31	5.56	7.63	32.48	32.48	3.75	26.89
67K46M	NON-RESPONDER	NON-RESPONDER	MATCH	−8.33	3.34	−1.51	8.23	2.40	−0.63	2.74	2.07	−0.55	− 6.25	175.23	−0.45	0.83	3.79	3.79	4.20
3HDJMG	NON-RESPONDER	NON-RESPONDER	MATCH	4.42	4.70	1.12	17.12	9.89	1.35	0.08	10.07	0.06	−1.35	4.61	7.45	0.17	14.17	14.17	14.40
26YMUF	RESPONDER	RESPONDER	MATCH	29.26	9.43	5.84	24.75	10.64	2.47	5.95	13.47	2.17	−1.63	6.50	7.43	0.67	25.92	25.92	23.23
MJXYP6	RESPONDER	RESPONDER	MATCH	137.90	43.67	190.94	91.44	102.75	16.56	49.41	79.19	6.75	2.07	7.67	144.61	4.60	4.13	4.13	73.86
M9GYO4	RESPONDER	RESPONDER	MATCH	185.53	12.45	5.87	53.86	33.00	4.15	11.69	25.87	2.67	−3.16	9.09	21.21	2.04	36.09	36.09	31.90
L6ADEL	RESPONDER	RESPONDER	MATCH	37.43	14.64	4.80	31.24	18.91	1.69	−1.21	20.73	3.77	−13.77	6.07	5.03	4.41	40.54	40.54	34.94
DFZLO2	RESPONDER	RESPONDER	MATCH	60.53	122.62	−0.26	51.22	57.41	3.61	229.90	62.31	8.86	−6.31	11.09	16.77	38.08	38.08	8.48	79.85
SA97V5	RESPONDER	RESPONDER	MATCH	67.03	12.87	15.30	56.46	21.85	−0.43	20.30	20.85	1.21	−1.90	5.28	10.32	2.79	20.96	20.96	23.81
		Total score	81.25

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