Non-small cell lung cancer proteome subtypes expose targetable oncogenic drivers and immune evasion mechanisms

Proteome-level data of non-small cell lung cancer remains limited. In this study, we have collected 141 cases, and performed histological review, methylation profiling (113), custom panel sequencing (140), microarray expression profiling (118) and mass-spectrometry based proteomics (141). We identified six distinct groups of patients driven by histology, growth pattern, immune cell infiltration, druggable driver mutations, and hypomethylation-associated neoantigen burden. We validated the subtypes in independent proteomics datasets. Proteomics can refine treatment-oriented subtyping of non-small cell lung cancer.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001007918	Targeted sequencing of non-small cell lung cancer samples. BAM files of paired end reads aligned to hg19 using BWA MEM v0.7.1573. This targeted panel covers 370 genes of clinical relevance in non-small cell lung cancer.	Illumina NovaSeq 6000	140

Publications	Citations
Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms. Lehtiö J, Arslan T, Siavelis I, Pan Y, Socciarelli F, Berkovska O, Umer HM, Mermelekas G, Pirmoradian M, Jönsson M, Brunnström H, Brustugun OT, Purohit KP, Cunningham R, Foroughi Asl H, Isaksson S, Arbajian E, Aine M, Karlsson A, Kotevska M, Gram Hansen C, Drageset Haakensen V, Helland Å, Tamborero D, Johansson HJ, Branca RM, Planck M, Staaf J, Orre LM. Nat Cancer 2: 2021 1224-1242	39

Publications

Citations

Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms.
Lehtiö J, Arslan T, Siavelis I, Pan Y, Socciarelli F, Berkovska O, Umer HM, Mermelekas G, Pirmoradian M, Jönsson M, Brunnström H, Brustugun OT, Purohit KP, Cunningham R, Foroughi Asl H, Isaksson S, Arbajian E, Aine M, Karlsson A, Kotevska M, Gram Hansen C, Drageset Haakensen V, Helland Å, Tamborero D, Johansson HJ, Branca RM, Planck M, Staaf J, Orre LM. Nat Cancer 2: 2021 1224-1242