Long non‐coding RNAs are significantly associated with prognosis and response to therapies in gastric cancer

Shin, Min Kyue; Kim, Jungmin; Kim, Dachan; Lee, Sung Hwan; Shin, Ji‐Hyun; Jeong, Yun Seong; Sohn, Bo Hwa; Kim, Jimin; Kim, Seong Ryong; Ajani, Jaffer A.; Lee, Ju Seog; Cheong, Jae‐Ho

doi:10.1002/ctm2.421

Cited by 2 publications

(2 citation statements)

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“…For discovery and validation of consensus genomic subtypes (CGSs) of GAC, we collected 10 GAC data sets ( N = 2527) and divided the data into 2 groups: a discovery/training set (Korea, Samsung, TCGA, Shanxi, Ruijin, and Singapore1 cohorts, n = 1427) and a validation set (ACRG, Korea National Cancer Center [KNCC], Yonsei Medical Center, and Singapore2 cohorts, n = 1100) (Supplementary Table S 1 ). GAC tumors in the discovery set were stratified according to the 8 genomic subtyping algorithms (Supplementary Table S 2 ) that were independently developed and validated in previous studies [ 6 – 9 , 11 , 17 – 19 ]. Supplementary Figure.…”

Section: Resultsmentioning

confidence: 99%

“…The intrinsic subtype of gastric cancer [ 17 ], Hippo pathway subtypes [ 18 ], TCGA4 subtype [ 6 , 11 ], TCGA risk score [ 11 ], ACRG subtype [ 9 ], Yonsei subtype [ 8 ], mesenchymal subtype [ 7 ], and lncRNA subtypes [ 19 ] and their associated gene signatures were described in earlier studies as listed in Supplementary Table S 2 .…”

Section: Methodsmentioning

confidence: 99%

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Clinically conserved genomic subtypes of gastric adenocarcinoma

Jeong,

Eun,

Lee

et al. 2023

Mol Cancer

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Gastric adenocarcinoma (GAC) is a lethal disease characterized by genomic and clinical heterogeneity. By integrating 8 previously established genomic signatures for GAC subtypes, we identified 6 clinically and molecularly distinct genomic consensus subtypes (CGSs). CGS1 have the poorest prognosis, very high stem cell characteristics, and high IGF1 expression, but low genomic alterations. CGS2 is enriched with canonical epithelial gene expression. CGS3 and CGS4 have high copy number alterations and low immune reactivity. However, CGS3 and CGS4 differ in that CGS3 has high HER2 activation, while CGS4 has high SALL4 and KRAS activation. CGS5 has the high mutation burden and moderately high immune reactivity that are characteristic of microsatellite instable tumors. Most CGS6 tumors are positive for Epstein Barr virus and show extremely high levels of methylation and high immune reactivity. In a systematic analysis of genomic and proteomic data, we estimated the potential response rate of each consensus subtype to standard and experimental treatments such as radiation therapy, targeted therapy, and immunotherapy. Interestingly, CGS3 was significantly associated with a benefit from chemoradiation therapy owing to its high basal level of ferroptosis. In addition, we also identified potential therapeutic targets for each consensus subtype. Thus, the consensus subtypes produced a robust classification and provide for additional characterizations for subtype-based customized interventions.

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