Noncanonical role of NCOR1 as a facilitator of DNA mismatch repair and its deficiency sensitizes cancers to immune checkpoint blockade therapy
DNA was extracted from mouse Hepa1-6 and B16 cell lines using the DNAeasy kit (Qiagen, USA) according to the manufacturer's instructions. Exonic DNA was captured using the Agilent whole exome capture kit (SureSelect Mouse All Exon; Agilent, USA). Captured DNA was sequenced using Novaseq 6000 (Illumina, USA) at Bioguoke Corporation (Beijing, China). The raw data of paired-end 150-bp reads in Fastq format were initially processed using Trim Galore (v.0.6.7) to remove the adaptor sequences and low-quality score bases. Then, paired-end reads were aligned with BWA-mem (v.2.0) to the mm10 mouse reference genome. Single nucleotide variant (SNV) calling from exomes was performed using VarScan (v.2.4.4) (Koboldt et al., 2009) with parameters --p-value 0.05 --min-coverage 10 --min-var-freq 0.15. SNV annotation was performed using ANNOVAR (http://www.openbioinformatics.org/annovar). The mutational burden (number of variants per megabase pairs [Mb]) was calculated considering all variants. Potential neoantigens were calculated from the coding variations, annotated and filtered for gene expression values (expected count > 10) using bulk RNA sequencing (RNA-seq) data from the same sample.