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15. Analysis of Methylome, Transcriptome, and Lipid Metabolites to Understand the Molecular Abnormalities in Polycystic Ovary Syndrome

Author

Zhang,Fei, Ding,Yicen, Zhang,Bohan, He,Mengju, Wang,Zhijiang, Lu,Chunbo, Kang,Yani, Zhang,Fei, Ding,Yicen, Zhang,Bohan, He,Mengju, Wang,Zhijiang, Lu,Chunbo, and Kang,Yani

Abstract

Fei Zhang,1 Yicen Ding,1 Bohan Zhang,1 Mengju He,1 Zhijiang Wang,2 Chunbo Lu,3 Yani Kang1 1School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, People’s Republic of China; 2Department of Pharmaceutical Engineering, Zhejiang Pharmaceutical University, Ningbo, People’s Republic of China; 3Department of Obstetrics and Gynecology, Qiuai Central Health Center, Ningbo, People’s Republic of ChinaCorrespondence: Chunbo Lu, Department of Obstetrics and Gynecology, Qiuai Central Health Center, Ningbo, 315100, People’s Republic of China, Tel +86-13567881644, Email lucbnb@126.com Yani Kang, School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, 200240, People’s Republic of China, Tel +86-13661848623, Email kangyani@sjtu.eduPurpose: This study aimed to identify differentially methylated genes (DMGs) and differentially expressed genes (DEGs) to investigate new biomarkers for the diagnosis and treatment of polycystic ovary syndrome (PCOS).Methods: To explore the potential biomarkers of PCOS diagnosis and treatment, we performed methyl-binding domain sequencing (MBD-seq) and RNA sequencing (RNA-seq) on ovarian granulosa cells (GCs) from PCOS patients and healthy controls. MBD-seq was also performed on the ovarian tissue of constructed prenatally androgenized (PNA) mice. Differential methylation and expression analysis were implemented to identify DMGs and DEGs, respectively. The identified gene was further verified by real-time quantitative PCR (RT-qPCR) and methylation-specific PCR (MSP) in clinical samples. Furthermore, ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) was carried out on PCOS patients and healthy controls to identify differential lipid metabolites.Results: Compared to the control group, 13,526 DMGs related to the promoter region and 2429 DEGs were found. The function analysis of DMGs and DEGs showed that they were mainly enriched in glycerophospholipid, ovarian ste

Published
2023

25. Additional file 2 of CPSF6 links alternative polyadenylation to metabolism adaption in hepatocellular carcinoma progression

Author

Tan, Sheng, Zhang, Ming, Xinglong Shi, Keshuo Ding, Zhao, Qiang, Qianying Guo, Wang, Hao, Zhengsheng Wu, Kang, Yani, Zhu, Tao, Jielin Sun, and Xiaodong Zhao

Subjects
neoplasms, digestive system diseases
Abstract

Additional file 2 Supplementary Table S1. Clinicopathologic correlation of CPSF6 expression in HCCs. The expression level of CPSF6 protein was detected by immunohistochemistry.

Published
2021
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26. An Iron Metabolism-Related SLC22A17 for the Prognostic Value of Gastric Cancer

Author

Wei,Jianming, Gao,Xibo, Qin,Yulan, Liu,Tong, and Kang,Yani

Subjects
OncoTargets and Therapy
Abstract

Jianming Wei,1,* Xibo Gao,2,* Yulan Qin,3 Tong Liu,1 Yani Kang3 1Department of General Surgery, Tianjin Medical University General Hospital, Tianjin 300052, People’s Republic of China; 2Department of Dermatology, Tianjin Children’s Hospital, Tianjin 300074, People’s Republic of China; 3School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China*These authors contributed equally to this workCorrespondence: Yani Kang Tel +86-21-3420-7324Email kangyani@sjtu.edu.cnPurpose: Gastric cancer (GC) is a type of malignant cancer with a poor prognosis. The iron’s metabolism plays an important role in the process of GC. The aim of this study was to evaluate the effectiveness of SLC22A17, associated with iron metabolism, in predicting the prognosis of GC patients.Materials and Methods: We analyzed genes related to iron metabolism of gastric cancer mRNA-seq data from TCGA database. We identified an iron metabolism-related SLC22A17 as an independent prognostic factor using univariate and multivariate Cox regression analysis.Results: Further research showed that SLC22A17 was related with many pathways involved in the process of gastric cancer, and the expression was associated with diverse cancer-infiltrating immune cells. The expression of SLC22A17 was associated with T (Topography).Conclusion: We validated that SLC22A17 associated with iron metabolism could serve as a prognostic biomarker for GC patients.Keywords: gastric cancer, iron metabolism, SLC22A17, prognostic marker

Published
2020

28. The binding epitope of sintilimab on PD-1 revealed by AbMap

Author

Ma, Mingliang, primary, Qi, Huan, additional, Hu, Chuansheng, additional, Xu, Zhaowei, additional, Wu, Fanlin, additional, Wang, Nan, additional, Lai, Danyun, additional, Li, Yang, additional, Zhang, Hainan, additional, Jiang, Hewei, additional, Meng, Qingfeng, additional, Guo, Shujuan, additional, Kang, Yani, additional, Zhao, Xiaodong, additional, Li, Hua, additional, and Tao, Sheng-ce, additional

Published
2021
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34. CPF impedes cell cycle re‐entry of quiescent lung cancer cells through transcriptional suppression of FACT and c‐MYC

Author

Bi, Ling, primary, Xie, Chanlu, additional, Jiao, Lijing, additional, Jin, Shenyi, additional, Hnit, Su Su Thae, additional, Mu, Yao, additional, Wang, Yilun, additional, Wang, Qian, additional, Ge, Guangbo, additional, Wang, Yaqiao, additional, Zhao, Xiaodong, additional, Shi, Xinglong, additional, Kang, Yani, additional, De Souza, Paul, additional, Liu, Tao, additional, Zhou, Jia, additional, Xu, Ling, additional, and Dong, Qihan, additional

Published
2020
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43. Additional file 6: of Genomic analyses of unique carbohydrate and phytohormone metabolism in the macroalga Gracilariopsis lemaneiformis (Rhodophyta)

Author

Sun, Xue, Wu, Jun, Guangce Wang, Kang, Yani, Ooi, Hong, Tingting Shen, Fangjun Wang, Yang, Rui, Nianjun Xu, and Xiaodong Zhao

Abstract

Figure S1. The phylogenetic relationship of cellulose synthase (CESA) in Gp. lemaneiformis with those of other related species. The tree was constructed based on the maximum likelihood method with 1000 bootstrap replicates using Mega5.10 software. (DOCX 27 kb)

Published
2018
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48. Genome-wide profiling reveals cancer-related genes with switched alternative polyadenylation sites in colorectal cancer

Author

Yang,Xiaochen, Wu,Jun, Xu,Wei, Tan,Sheng, Chen,Changyu, Wang,Xiaoyan, Sun,Jielin, Kang,Yani, Yang,Xiaochen, Wu,Jun, Xu,Wei, Tan,Sheng, Chen,Changyu, Wang,Xiaoyan, Sun,Jielin, and Kang,Yani

Abstract

Xiaochen Yang,1 Jun Wu,1 Wei Xu,1 Sheng Tan,2 Changyu Chen,3 Xiaoyan Wang,4 Jielin Sun,4 Yani Kang1 1School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, 200240, People’s Republic of China; 2The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China; 3Department of General Surgery, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, Anhui, 230031, People’s Republic of China; 4Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, People’s Republic of China Background: Alternative polyadenylation (APA) is an important post-transcriptional regulation in eukaryotic cells. It plays considerable roles in many biological processes and diseases, such as cell differentiation, proliferation and cancer. Colorectal cancer (CRC) is one of the most common malignancies worldwide, which is among the top five in incidence and mortality of all cancers in China. Although there have been some studies on the APA of CRC, the normal and carcinoma samples used for genome-wide profiling were not matched. The purpose of this study was to obtain genes with switched 3'-untranslated region (UTR) that may be associated with intracellular regulation of CRC by analyzing APA patterns of strict control groups from clinical patients. Materials and methods: CRC and matched normal tissues were acquired from surgical specimens from three CRC patients. Their libraries of 3'-terminal fragments of mRNA with poly(A) tails were constructed by 3T-seq technology and sequenced by Illumina Hiseq X Ten. APA patterns of cancer and matched normal tissues were analyzed by bioinformatics analysis, and a representative gene, GPI, was verified by quantitative reverse tran

Published
2018

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