Predictive biomarkers of immunotherapy response with pharmacological applications in solid tumors.

"table 1 summary of cancer datasets with immune-checkpoint inhibitor therapy included in the study dataset id reference sample n patient n tumor type drug sample acquisition outcome method for measuring gene expression gse78220 ncbi geo and cri iatlas28 27 melanoma pembrolizumab pre-treatment os and response by recist rna-seq (illumina hiseq 2000) gse91061 cri iatlas98 56 melanoma nivolumab pre-treatment or on-treatment os and response by recist rna-seq (illumina genome analyzer) gse93157 ncbi geo 5 65 head and neck squamous cell carcinoma nivolumab pre-treatment pfs and response by recist nanostring ncounter pancancer immune profiling panel 22 non-squamous non-small cell lung cancer nivolumab or pembrolizumab pre-treatment pfs and response by recist 25 skin cutaneous melanoma nivolumab or pembrolizumab pre-treatment pfs and response by recist 13 squamous non-small cell lung cancer nivolumab or pembrolizumab pre-treatment pfs and response by recist gse115821 ncbi geo 37 11 melanoma anti-pd-1 and/ or anti-ctla-4 pre-treatment or on-treatment response rna-seq (illumina hiseq 2000 and illumina nextseq 500) gse121810 ncbi geo and cri iatlas28 28 glioblastoma pembrolizumab pre-treatment or on-treatment pfi os response by recist rna-seq (illumina hiseq 3000) gse136961 ncbi geo 21 21 non-small-cell lung cancer anti-pd-1 pre-treatment pfs os rna-seq (ion torrent s5 xl) gse140901 ncbi geo 22 22 hepatocellular carcinoma nivolumab and/ or ipilimumab pre-treatment pfs os response by recist nanostring ncounter pancancer immune profiling panel gse165252 ncbi geo and provided by the author upon request 66 40 esophageal adenocarcinoma atezolizumab pre-treatment or on-treatment pfs os and response rna-seq (illumina hiseq 4000) gse165278 ncbi geo and github 21 21 melanoma ipilimumab pre-treatment or on-treatment os rna-seq (illumina hiseq 2500) gse165745 ncbi geo 24 24 melanoma pembrolizumab or nivolumab pre-treatment response nanostring ncounter vantage 3d human wnt pathways panel gse176307 ncbi geo 84 84 bladder/ ureter/ pelvis cancer pembrolizumab/ nivolumab or atezolizumab/ durvalumab pre-treatment pfs and response by recist rna-seq (ion torrent s5 xl) gse183924 ncbi geo 37 37 esophageal and gastroesophageal junction adenocarcinoma durvalumab pre-treatment rfs rna-seq (illumina novaseq 6000) cristescu 2018 cristescu et al science (2018) and litchfield et al cell (2021) 17 226 bladder cancer pembrolizumab pre-treatment response nanostring ncounter 12 tripla negative breast cancer pembrolizumab pre-treatment response 2 er + her2- breast cancer pembrolizumab pre-treatment response 105 head and neck squamous cell carcinoma pembrolizumab pre-treatment response 86 melanoma pembrolizumab pre-treatment response 4 small cell lung cancer pembrolizumab pre-treatment response gide 2019 cri iatlas88 72 melanoma pembrolizumab and/ or nivolumab and/ or ipilimumab pre-treatment pfi os response by recist rna-seq (illumina hiseq 2500) kim 2018 ena and kim et al nat med (2018) 45 45 gastric cancer pembrolizumab pre-treatment response by recist rna-seq (illumina nextseq 550) liu 2019 liu et al nat med (2019) 121 121 melanoma nivolumab or pembrolizumab pre-treatment pfs os response by recist rna-seq (illumina hiseq 2000 v3 hiseq 2500) mariathasan 2018 cri iatlas348 348 urothelial cancer atezolizumab pre-treatment os and response by recist rna-seq (illumina truseq rna access) miao 2018 miao et al science (2018) 33 33 renal cell carcinoma nivolumab and/ or ipilimumab or atezolizumab pre-treatment pfs os and response by recist rna-seq (illumina hiseq 2000 v3 hiseq 2500) vanallen 2015 cri iatlas and van allen et al science (2015) 42 42 melanoma ipilimumab pre-treatment pfs os and response by recist rna-seq (illumina hiseq 2500) different technological and clinical approaches were utilized in the involved studies such as rna-sequencing (rna-seq) with illumina [ ] or ion torrent platforms [ ] and nanostring ncounter [ ]. table 1 summary of cancer datasets with immune-checkpoint inhibitor therapy included in the study dataset id reference sample n patient n tumor type drug sample acquisition outcome method for measuring gene expression gse78220 ncbi geo and cri iatlas28 27 melanoma pembrolizumab pre-treatment os and response by recist rna-seq (illumina hiseq 2000) gse91061 cri iatlas98 56 melanoma nivolumab pre-treatment or on-treatment os and response by recist rna-seq (illumina genome analyzer) gse93157 ncbi geo 5 65 head and neck squamous cell carcinoma nivolumab pre-treatment pfs and response by recist nanostring ncounter pancancer immune profiling panel 22 non-squamous non-small cell lung cancer nivolumab or pembrolizumab pre-treatment pfs and response by recist 25 skin cutaneous melanoma nivolumab or pembrolizumab pre-treatment pfs and response by recist 13 squamous non-small cell lung cancer nivolumab or pembrolizumab pre-treatment pfs and response by recist gse115821 ncbi geo 37 11 melanoma anti-pd-1 and/ or anti-ctla-4 pre-treatment or on-treatment response rna-seq (illumina hiseq 2000 and illumina nextseq 500) gse121810 ncbi geo and cri iatlas28 28 glioblastoma pembrolizumab pre-treatment or on-treatment pfi os response by recist rna-seq (illumina hiseq 3000) gse136961 ncbi geo 21 21 non-small-cell lung cancer anti-pd-1 pre-treatment pfs os rna-seq (ion torrent s5 xl) gse140901 ncbi geo 22 22 hepatocellular carcinoma nivolumab and/ or ipilimumab pre-treatment pfs os response by recist nanostring ncounter pancancer immune profiling panel gse165252 ncbi geo and provided by the author upon request 66 40 esophageal adenocarcinoma atezolizumab pre-treatment or on-treatment pfs os and response rna-seq (illumina hiseq 4000) gse165278 ncbi geo and github 21 21 melanoma ipilimumab pre-treatment or on-treatment os rna-seq (illumina hiseq 2500) gse165745 ncbi geo 24 24 melanoma pembrolizumab or nivolumab pre-treatment response nanostring ncounter vantage 3d human wnt pathways panel gse176307 ncbi geo 84 84 bladder/ ureter/ pelvis cancer pembrolizumab/ nivolumab or atezolizumab/ durvalumab pre-treatment pfs and response by recist rna-seq (ion torrent s5 xl) gse183924 ncbi geo 37 37 esophageal and gastroesophageal junction adenocarcinoma durvalumab pre-treatment rfs rna-seq (illumina novaseq 6000) cristescu 2018 cristescu et al science (2018) and litchfield et al cell (2021) 17 226 bladder cancer pembrolizumab pre-treatment response nanostring ncounter 12 tripla negative breast cancer pembrolizumab pre-treatment response 2 er + her2- breast cancer pembrolizumab pre-treatment response 105 head and neck squamous cell carcinoma pembrolizumab pre-treatment response 86 melanoma pembrolizumab pre-treatment response 4 small cell lung cancer pembrolizumab pre-treatment response gide 2019 cri iatlas88 72 melanoma pembrolizumab and/ or nivolumab and/ or ipilimumab pre-treatment pfi os response by recist rna-seq (illumina hiseq 2500) kim 2018 ena and kim et al nat med (2018) 45 45 gastric cancer pembrolizumab pre-treatment response by recist rna-seq (illumina nextseq 550) liu 2019 liu et al nat med (2019) 121 121 melanoma nivolumab or pembrolizumab pre-treatment pfs os response by recist rna-seq (illumina hiseq 2000 v3 hiseq 2500) mariathasan 2018 cri iatlas348 348 urothelial cancer atezolizumab pre-treatment os and response by recist rna-seq (illumina truseq rna access) miao 2018 miao et al science (2018) 33 33 renal cell carcinoma nivolumab and/ or ipilimumab or atezolizumab pre-treatment pfs os and response by recist rna-seq (illumina hiseq 2000 v3 hiseq 2500) vanallen 2015 cri iatlas and van allen et al science (2015) 42 42 melanoma ipilimumab pre-treatment pfs os and response by recist rna-seq (illumina hiseq 2500) different technological and clinical approaches were utilized in the involved studies such as rna-sequencing (rna-seq) with illumina [ ] or ion torrent platforms [ ] and nanostring ncounter [ ]."

"Competing interests The authors declare no competing interests."

"Funding Open access funding provided by Semmelweis University."