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Supplementary Table S3. Clinicopathologic features of patients with gastric cancer according to the expression status of TMEFF2.

Supplementary Table S5. Mutation summary in patients.

Supplementary Table S1. The extent of inflammation in pre-cancerous lesions of Renji dataset.

Purpose: The role and clinical implication of the transmembrane protein with EGF and two follistatin motifs 2 (TMEFF2) in gastric cancer is poorly understood.Experimental Design: Gene expression profile analyses were performed and Gene Set Enrichment Analysis (GSEA) was used to explore its gene signatures. AGS and MKN45 cells were transfected with TMEFF2 or control plasmids and analyzed for gene expression patterns, proliferation, and apoptosis. TMEFF2 expression was knocked down with shRNAs, and the effects on genome stability were assessed. Interactions between TMEFF2 and SHP-1 were determined by mass spectrometry and immunoprecipitation assays.Results: Integrated analysis revealed that TMEFF2 expression was significantly decreased in gastric cancer cases and its expression was negatively correlated with the poor pathologic stage, large tumor size, and poor prognosis. GSEA in The Cancer Genome Atlas (TCGA) and Jilin datasets revealed that cell proliferation, apoptosis, and DNA damage–related genes were enriched in TMEFF2 lower expression patients. Gain of TMEFF2 function decreased cell proliferation by increasing of apoptosis and blocking of cell cycle in gastric cancer cells. The protein tyrosine phosphatase SHP-1 was identified as a binding partner of TMEEF2 and mediator of TMEFF2 function. TMEFF2 expression positively correlated with SHP-1, and a favorable prognosis was more likely in patients with gastric cancer with higher levels of both TMEFF2 and SHP-1.Conclusion: TMEFF2 acts as a tumor suppressor in gastric cancer through direct interaction with SHP-1 and can be a potential biomarker of carcinogenesis. Clin Cancer Res; 20(17); 4689–704. ©2014 AACR.

Supplementary Table S2. Sequence of primers for real-time PCR.

Supplementary Figure S1. Identification of TMEFF2 as a key regulator in gastric cancer progression and the expression of TMEFF2 decreased in gastric carcinogenesis. Supplementary Figure S2. Gene Set Enrichment Analysis (GSEA) in TMEFF2-higher/lower expression patients. Supplementary Figure S3. The mRNA levels of the top-score tumorigenesis genes were measured in gastric cells after transfection of TMEFF2 overexpression plasmid or siRNA Supplementary Figure S4. Functional impact of TMEFF2 Supplementary Figure S5. Cell proliferation assays were performed in MKN45 cells after overexpression of SHP-1WT/ΔSH2D1/ΔSH2D2/ΔPTPD or these constructs combined with TMEFF2. n = 3, non-parametric Mann-Whitney test. Supplementary Figure S6. Correlation of TMEFF2 and SHP-1 expression in human GC.

Supplementary Table S4. Proteins identified by mass spectrometry from the TMEFF2 co-immunoprecipitate sample.

Supplementary Table S2. LncRNAs associated with CNVs.

Supplementary Figures S1-S4. Binding of transcription factors to upregulated lncRNAs (S1); P53 mutant R248W transactivated GAPLINC through specifically binding to its promoter (S2); Knockdown of GAPLINC by two different siRNAs respectively inhibited gastric cancer cell proliferation (S3); CD44 could rescue the invasion inhibition effect of GAPLINC knockdown (S4).

Supplementary Methods. Description of additional methods and procedures used in the study.

Supplementary Table S4. Univariable and multivariable Cox regression analysis of survival prediction.

Supplementary Table S1. Deregulated lncRNAs in gastric cancer.

Supplementary Table S3. LncRNAs associated with mutant p53 and Stat1.

Supplementary Table S5. Growth of human gastric cancer xenograft in nude mice injected by GAPLINC stable knockdown clone and control clone.