Additional file 1 of Inhibitory immune checkpoints PDCD-1 and LAG-3 hypermethylation may reduce the risk of colorectal cancer
Creators: name: Zhang, Yuanyuan
name: zhang, Lei
name: Sun, Hongru
name: Liu, Ying
name: Xu, Jing
name: Huang, Hao
name: Fu, Jinming
name: Zhang, Ding
name: Tian, Tian
name: Zhao, Yashuang
name: Wang, Guiyu
Publisher: name: figshare
Year: 2021
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 1: Fig. S1. Quantitative Methylation Specific PCR (QMSP) for the detection of PDCD-1 methylation in standard samples. (A) Amplification curves of PDCD-1 gene methylation standards. (B) Melting curves of serial dilutions of methylated DNA from the PDCD-1 gene. (C) Standard curve used in the QMSP assay of PDCD-1 gene. Fig S2. Quantitative Methylation Specific PCR (QMSP) for the detection of LAG-3 methylation in standard samples. (A) Amplification curves of LAG-3 gene methylation standards. (B) Melting curves of serial dilutions of methylated DNA from the LAG-3 gene. (C) Standard curve used in the QMSP assay of LAG-3 gene. Fig. S3. Quantitative Methylation Specific PCR (QMSP) for the detection of ACTB methylation in standard samples. (A) Amplification curves of ACTB gene methylation standards. (B) Melting curves of serial dilutions of methylated DNA from the ACTB gene. (C) Standard curve used in the QMSP assay of ACTB gene. Fig S4. Quantitative Methylation Specific PCR (QMSP) for the detection of PDCD-1 methylation in PBL samples. (A) Amplification curves used in the PDCD-1 QMSP assay. (B) Melting curves of PBL samples from the PDCD-1 gene. Fig S5. Quantitative Methylation Specific PCR (QMSP) for the detection of LAG-3 methylation in PBL samples. (A) Amplification curves used in the LAG-3 QMSP assay. (B) Melting curves of PBL samples from the LAG-3 gene. Fig S6. Quantitative Methylation Specific PCR (QMSP) for the detection of ACTB methylation in PBL samples. (A) Amplification curves used in the ACTB QMSP assay. (B) Melting curves of PBL samples from the ACTB gene. Fig S7. Gene expression and DNA methylation levels of PDCD-1, LAG-3 in TCGA database. (A) Expression of PDCD-1 gene. (B) Expression of LAG-3 gene. (C) Methylation level of PDCD-1 gene. (D) Methylation level of LAG-3 gene. Fig S8. ROC curves of PDCD-1, LAG-3 in the case-control study. (A) cg06291111. (B) cg10191002 (C) PDCD-1 gene (D) LAG-3 gene. Table S1. Primer sequence, amplicon size and reaction conditions. Table S2. Distribution of the basic characteristics of CRC patients and controls in in GEO dataset. Table S3. Distribution of the environmental factors of the CRC patients and controls. Table S4. Association between CRC risk and PDCD-1, LAG-3 methylation levels in PBL calculated by using the average of coefficients and slopes of all standard curves. Table S5. Association between the methylation levels of PDCD-1, LAG-3 and CRC risk stratified by age in GEO dataset. Table S6. Association between the methylation levels of PDCD-1, LAG-3 and CRC risk stratified by different environmental factors in case-control study. Table S7.. Effects of combination and interaction between environmental factors and methylation of PDCD-1 on the risk of CRC. Table S8. Effects of combination and interaction between environmental factors and methylation of LAG-3 on the risk of CRC.