The complete genome of a novel virus, provisionally named areca palm velarivirus 1 (APV1), was identified in areca palm exhibiting leaf yellowing symptoms in Hainan province, China. The genome of APV1 consists of 16,080 nucleotides and possesses 11 open reading frames (ORFs), sharing 56.4% nucleotide sequence identity with little cherry virus 1 (NC_001836.1). The genome organization of APV1 is highly similar to that of members of the genus Velarivirus (family Closteroviridae). Phylogenetic analysis placed APV1 together with members of the genus Velarivirus.
Gastric cancer is the fifth most common malignancy and the third leading cause of cancer-related mortality worldwide. Immunotherapy offers promising new treatment options for gastric cancer patients; however, it is only effective in a limited fraction of patients. In this study, we evaluated the composition of 22 tumor-infiltrating lymphocytes (TILs) in TCGA Stomach Adenocarcinoma (STAD) using deconvolution-based method by analyzing the publicly available bulk tumor RNA-seq data. The patients were classified into high-TIL and low-TIL subtypes based on their immune cell profiles and prognosis outputs. The differentially expressed genes (DEGs) between the two subtypes were identified, and GO/KEGG analysis showed that broad immune genes, such as PD-L1 and PD-1, were highly expressed in the high-TIL subtype. A comprehensive protein–protein interaction (PPI) network centered on DEGs was built, and 16 hub genes of the network were further identified. Based on the hub genes, an elastic model with 11 gene signatures (NKG7, GZMB, IL2RB, CCL5, CD8A, IDO1, MYH1, GNLY, CXCL11, GBP5 and PRF1) was developed to predict the high-TIL subtype. In summary, our findings showed that the compositions of TILs within the tumor immune microenvironment of stomach cancer patients are highly heterogeneous, and the profiles of TILs have the potential to be predictive markers of patients’ responses and overall survival outcomes.
Gastric cancer is a leading cause of cancerassociated deaths worldwide and is considered to be an age-related disease. In younger patients, gastric cancer is biologically more aggressive, and prognosis is worse compared with that in elderly patients. In the present case report, the whole genome and transcriptome was sequenced in a 26-year-old patient with gastric cancer who presented with gastric cancer-related symptoms and was admitted to the First Affiliated Anhui Medical Hospital (Hefei, China) in December 2016. In total, 9 germline and 4 somatic mutations were identified in the patient, and there were more deleterious sites in the germline mutated genes. Genes with somatic mutations, such as MUC2, MUC4, SLC8A2, and with structural variations, including CCND3, FGFR2 and FGFR3, were found to be differentially expressed. Cancer-associated pathways, such as the 'calcium signaling pathway', 'cGMP-PKG signaling pathway' and 'transcriptional mis-regulation' were also enriched at both the genomic and transcriptomic levels. The genes found to have germline (SFRP4), somatic (MUC2, MUC4, SLC8A2) mutations, or structural variations (CCND3, FGFR2 and FGFR3) were differentially expressed in the patient and could be promising precision therapy targets.
A 40-year old female patient from the Chinese Han population presented colorectal cancer (CRC) related symptoms including abdominal discomfort, tenesmus and severe back pain, and was admitted to the First Affiliated Anhui Medical University in October, 2008. The size of her tumor was 3 cm × 3 cm, and the carcinoma had invaded the serosa layer, covering 3/4 of the intestine tube. She was diagnosed with stage III CRC after examination. The patient presented a good prognosis with over 8-year survival after curative surgery and adjuvant therapy with Oxaliplatin and Huaier granules, a traditional Chinese medicine. Using the whole-genome sequencing (WGS) data, we profiled the germline and somatic mutations and obtained an all-inclusive data of the genomic alterations. The genomic alterations were compared with those of stage III CRC patients in The Cancer Genome Atlas Network (TCGA). Mutations in APC, TP53, KRAS, SMAD4, FBXW7 and PIK3CA defined as drivers in TCGA patients were not recorded in our study. However, mutations in MUC4, MUC16, ARID1B, BAZ1A, BRCA2, CTNND1 and NCOA2 rarely reported in TCGA patients were predominant in our patient. Additionally, we observed loss of heterozygosity (LOH) in POLE, RET, BMPR1A, NCOA4 and 30 other genes in contrast to deletion and amplification events recorded in TCGA patients. Overall, we produced a genomic mutation profile of a long-term surviving CRC patient and identified recurrent and rare mutations that could provide a valuable resource for further study into the alterations that characterize advanced CRC which may be useful to design clinical therapy for personalized medicine.
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