Patient samples

For melanoma/lung cohorts, 58 patient samples and data were procured based on availability of tissue and were not collected according to a prespecified power analysis. These samples included 48 melanoma samples and 10 lung cancer samples. Included in these 58 samples were 8 relapse specimens (50 baseline pre–anti–PD-1 therapy), of which 5 were matched to a pre–anti–PD-1 therapy sample. Of these, 3 pairs were successfully RNA sequenced, 5 pairs were successfully scored for LAG-3 IHC, and 4 had sufficient tissue for FCRL6 IHC.

RNA sequencing

Total RNA quality was assessed using the 2200 Tapestation (Agilent). At least 20 ng DNase-treated total RNA, with at least 30% of the RNA fragments with a size >200 nt, was used to generate RNA Access libraries (Illumina) following the manufacturer’s recommendations. Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA Library Quantification Kits (KAPA Biosystems). Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000). Bcl2fastq2 Conversion Software (Illumina) was used to generate demultiplexed Fastq files.

QC for the paired-end raw sequencing reads of all samples was performed using FastQC for the analysis of sequence quality, GC content, the presence of adaptors, overrepresented k-mers, and duplicated reads. Sequencing reads were mapped to human reference genome GRCH38 (release-85, Ensembl) using STAR 2.2.1 with 2-pass mapping (53, 54). QC for read alignment and mapping was evaluated with RSeQC for sequencing saturation, mapped read clipping profile, mapped read distribution, and coverage uniformity. The transcripts per million (TPM) values were calculated using RSEM (56) and used to assess the global quality and reproducibility of the RNA-sequencing data set and exported for downstream data analyses.

Sample Patient_ID Sample_ID TUMOR_TYPE GROUP IMMUNE_THERAPY IMMUNE_RESPONSE HLA_DR
P3437_JMB_001 7 7_pre MEL BASELINE anti-PD1 CR 0.58
P3437_JMB_011 8 8_pre LUNG BASELINE anti-PD1 PR 0.00
P3437_JMB_012 9 9_pre LUNG BASELINE anti-PD1 PD NA
P3437_JMB_014 10 10_pre LUNG BASELINE anti-PD1 PD 0.02
P3437_JMB_015 1 1_pre MEL BASELINE anti-PD1 PR NA
P3437_JMB_016 1 1_post MEL PROGRESSION anti-PD1 RELAPSE NA
P3437_JMB_017 4 4_postB MEL PROGRESSION anti-PD1 RELAPSE 0.43
P3437_JMB_018 4 4_postC MEL PROGRESSION anti-PD1 RELAPSE NA
P3437_JMB_019 3 3_pre MEL BASELINE anti-PD1 MR NA
P3437_JMB_002 11 11_pre MEL BASELINE anti-PD1 PD 0.00
P3437_JMB_020 3 3_post MEL PROGRESSION anti-PD1 RELAPSE NA
P3437_JMB_021 12 12_pre MEL BASELINE anti-PD1 PR 0.00
P3437_JMB_022 13 13_pre MEL BASELINE anti-PD1 PD 0.70
P3437_JMB_023 14 14_pre MEL BASELINE anti-PD1 PR 0.00
P3437_JMB_026 15 15_pre LUNG BASELINE anti-PD1 PD 0.00
P3437_JMB_027 2 2_pre MEL BASELINE anti-PD1 PR NA
P3437_JMB_028 2 2_post MEL PROGRESSION anti-PD1 RELAPSE NA
P3437_JMB_003 16 16_pre MEL BASELINE anti-PD1 CR 0.83
P3437_JMB_004 17 17_pre MEL BASELINE anti-PD1 PD 0.01
P3437_JMB_040 18 18_pre LUNG BASELINE anti-PD1 NA 0.00
P3437_JMB_041 19 19_pre MEL BASELINE anti-PD1 CR 0.00
P3437_JMB_043 20 20_pre LUNG BASELINE anti-PD1 SD 0.60
P3437_JMB_044 21 21_pre MEL BASELINE anti-PD1 PR 0.05
P3437_JMB_045 22 22_pre LUNG BASELINE anti-PD1 PD 0.00
P3437_JMB_046 23 23_pre MEL BASELINE anti-PD1 MR 0.00
P3437_JMB_047 24 24_pre MEL BASELINE anti-PD1 PD 0.25
P3437_JMB_048 25 25_pre MEL BASELINE anti-PD1 PD 0.00
P3437_JMB_049 26 26_pre MEL BASELINE anti-PD1 MR 0.01
P3437_JMB_005 27 27_pre MEL BASELINE anti-PD1 CR 0.63
P3437_JMB_050 28 28_pre MEL BASELINE anti-PD1 CR 0.05
P3437_JMB_051 29 29_pre MEL BASELINE anti-PD1 PD NA
P3437_JMB_053 30 30_pre MEL BASELINE anti-PD1 CR 0.00
P3437_JMB_055 31 31_pre MEL BASELINE anti-PD1 PR 0.00
P3437_JMB_058 32 32_pre MEL BASELINE anti-PD1 PD 0.00
P3437_JMB_006 33 33_pre MEL BASELINE anti-PD1 PR 0.78
P3437_JMB_060 34 34_pre MEL BASELINE anti-PD1 PR 0.02
P3437_JMB_067 4 4_postA MEL PROGRESSION anti-PD1 RELAPSE 0.43
P3437_JMB_069 35 35_pre MEL BASELINE anti-PD1 PD 0.00
P3437_JMB_007 36 36_pre MEL BASELINE anti-PD1 PR 0.10
P3437_JMB_070 37 37_pre MEL BASELINE anti-PD1 MR 0.20
P3437_JMB_071 38 38_pre MEL BASELINE anti-PD1 MR 0.50
P3437_JMB_072 39 39_pre MEL BASELINE anti-PD1 PR 0.00
P3437_JMB_073 40 40_pre MEL BASELINE anti-PD1 CR 0.75
P3437_JMB_074 5 5_post MEL PROGRESSION anti-PD1 RELAPSE 0.00
P3437_JMB_075 41 41_pre MEL BASELINE anti-PD1 PD 0.00
P3437_JMB_077 42 42_pre MEL BASELINE anti-PD1 CR 0.10
P3437_JMB_078 43 43_pre MEL BASELINE anti-PD1 CR 0.25
P3437_JMB_079 44 44_pre MEL BASELINE anti-PD1 PR 0.00
P3437_JMB_008 45 45_pre LUNG BASELINE anti-PD1 PR 0.00
P3437_JMB_083 6 6_post LUNG PROGRESSION anti-PD1 RELAPSE NA
P3437_JMB_084 46 46_pre MEL BASELINE anti-PD1 PD NA
P3437_JMB_085 47 47_pre MEL BASELINE anti-PD1 PD NA
P3437_JMB_088 48 48_pre MEL BASELINE anti-PD1 CR NA
P3437_JMB_009 49 49_pre LUNG BASELINE anti-PD1 SD 0.00
P3437_JMB_090 50 50_pre MEL BASELINE anti-PD1 MR NA
P3437_JMB_093 51 51_pre MEL BASELINE anti-PD1 PD NA
P3437_JMB_095 52 52_pre MEL BASELINE anti-PD1 CR NA
P3437_JMB_096 53 53_pre MEL BASELINE anti-PD1 MR NA

Data are available on reasonable request by sending email to Justin M. Balko or Yaomin Xu.

Reference

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  2. Zlatko Trajanoski; Francesca Finotello; Clemens Mayer; Christina Plattner; Gerhard Laschober; Dietmar Rieder; Hubert Hackl; Anne Krogsdam; Zuzana Loncova; Wilfried Posch; Doris Wilflingseder; Sieghart Sopper; Marieke Ijsselsteijn; Douglas Johnson; Yaomin Xu; Yu Wang; Melinda E. Sanders; Monica V. Estrada; Paula Ericsson-Gonzalez; Pornpimol Charoentong; Justin Balko; Noel de Miranda; Thomas P Brouwer. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Medicine. 2019 May 24;11(1):34. doi: 10.1186/s13073-019-0638-6, PubMed PMID: 31126321; PubMed Central PMCID: PMC6534875.