Article
Oncology
Rongjia Su, Chengjuan Jin, Lina Zhou, Yannan Cao, Menghua Kuang, Linxia Li, Jiangdong Xiang
Summary: This study identified 7 hub genes associated with immune infiltrates in ovarian cancer using ssGSEA and WGCNA, with LY9 and SLAMF1 recognized as the real hub genes. The study also constructed a lncRNA-miRNA-mRNA ceRNA network related to LY9 and SLAMF1, providing potential targets for immunotherapy in ovarian cancer.
Article
Pathology
Tengyong Wang, Xiaoxuan Chen, Fangqi Jing, Zehua Li, Huaicheng Tan, Yiqiao Luo, Huashan Shi
Summary: The study identified five hub genes associated with the tumorigenesis of non-small cell lung cancer (NSCLC). These genes are related to tumor progression, cell cycle, etc. The expression levels of these genes can distinguish between normal and tumor tissues, and are correlated with patient prognosis and immune infiltration.
PATHOLOGY RESEARCH AND PRACTICE
(2021)
Article
Genetics & Heredity
Linzhuo Fan, Jinhong Hou, Guimin Qin
Summary: Breast cancer is a common malignant tumor in women. This study proposes a computational framework based on stage-specific gene regulatory networks to predict disease genes of breast cancer. Key genes specific to each stage were identified and shown to be significantly associated with breast cancer-related genes.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Xiaoqing Yu, Ling Cen, Y. Ann Chen, Joseph Markowitz, Timothy Shaw, Kenneth Y. Tsai, Jose R. Conejo-Garcia, Xuefeng Wang
Summary: DNA methylation signatures can be used as reliable biomarkers to predict patient prognosis and immune status in tumors. This study introduces the concept of tumor-based expression quantitative trait methylation (eQTM) for the identification of predictive biomarkers. eQTM CpGs and genes represent new and efficient candidate targets for prognosis and immune status monitoring.
Article
Environmental Sciences
Wenbo Jiang, Huanyu Wu, Xinyang Yu, Yu Wang, Wenbo Gu, Wei Wei, Bai Li, XiTao Jiang, Yue Wang, Wanying Hou, Qiuying Dong, Xuemin Yan, Ying Li, Changhao Sun, Tianshu Han
Summary: This study found that participants exposed to third-hand smoke had lower serum melatonin levels, with 820 differentially methylated sites associated with THS and a hub-site located on the CYP1A2 promoter potentially mediating this effect.
ENVIRONMENTAL POLLUTION
(2021)
Article
Cell Biology
Hui Chen, Qin Qin, Zhipeng Xu, Tingting Chen, Xijuan Yao, Bing Xu, Xinchen Sun
Summary: Esophageal carcinoma is characterized by genetic and epigenetic alterations, with DNA methylation being a key factor in its pathogenesis. By analyzing data from TCGA database, specific DNA methylation sites were identified to impact patient prognosis, leading to the classification of patients into seven clusters with distinct characteristics. Further analysis revealed genes and pathways associated with cellular metabolism and autophagy, and the construction of a prognostic prediction model for individualized treatment.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Oncology
Michal Szczyrek, Anna Grenda, Barbara Kuznar-Kaminska, Pawel Krawczyk, Marek Sawicki, Halina Batura-Gabryel, Radoslaw Mlak, Aneta Szudy-Szczyrek, Tomasz Krajka, Andrzej Krajka, Janusz Milanowski
Summary: Methylation status of DICER and DROSHA may serve as potential biomarkers for early detection of lung cancer. Assessing the methylation levels of these genes could help distinguish early-stage NSCLC patients from healthy individuals with certain sensitivity and specificity.
Article
Genetics & Heredity
Xinyang Li, Lu Dong, Huaning Yu, Yan Zhang, Shuo Wang
Summary: The study identified five gene modules related to HCAs exposure in PBMC, with functions in mRNA transcriptional regulation, mitochondrial function, RNA catabolic process, protein targeting, and immune function. Additionally, specific genes MIER1, NDUFA4, MLL3, CD53, and CSF3 were recognized as feature genes in these modules. The expression of these feature genes showed significant differences between PhIP/IQ exposed samples and other samples.
Article
Medicine, General & Internal
Qin Tang, Haojie Zhang, Rong Tang
Summary: Using multiple analysis methods, 2 immune subtypes and 4 hub immune-related genes (IRGs) were identified in ovarian cancer (OV). The study found that patients in the Immunity_H group had longer overall survival and higher stromal and immune scores. Gene set variation analysis revealed a positive relationship between improved immunoreaction and pathways related to classical signaling and immune responses.
Article
Immunology
Chao Li, Tan Yang, Yu Yuan, Rou Wen, Huan Yu
Summary: This study aimed to identify key biomarkers and elucidate immune cell infiltration and related pathways in gastric cancer (GC). The results showed that certain genes were closely associated with GC, and immune cell infiltration was observed in patients with GC. This is of great importance for understanding the development of GC, identifying new immunotherapeutic targets, and disease prevention.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Oncology
Fenglei Yu, Xiaojie Huang, Danting Zhou, Zhenyu Zhao, Fang Wu, Banglun Qian, Qiang Wang, Juan Chen, Qingchun Liang, Yi Jiang, Qi Ding, Qiongzhi He, Jingqun Tang, Xiang Wang, Wenliang Liu, Chen Chen
Summary: This study demonstrated, for the first time, the differences in genetic, epigenetic, and immune profiles between synchronous multiple primary lung cancers (sMPLC) and single primary lung cancer (SPLC). Compared to the similar genetic mutational landscape, the DNA methylation patterns and related immune profiles were significantly different between sMPLC and SPLC, indicating their essential roles in the initiation and development of sMPLC.
CLINICAL EPIGENETICS
(2023)
Article
Cell Biology
Lingling Zu, Jinling He, Ning Zhou, Quanying Tang, Maoli Liang, Song Xu
Summary: This study characterized the transcriptomic landscape of NSCLC cells with organ-specific metastatic potentials and identified miR-660-5p as a key driver associated with NSCLC progression and distant metastasis. A six-gene signature was established to predict NSCLC metastasis, and three genes and two transcription factors from this signature were validated. Aberrant gene signature and miRNA can serve as biomarkers for predicting NSCLC distant metastasis.
CELL DEATH & DISEASE
(2023)
Article
Genetics & Heredity
Liya Huang, Ting Ye, Jingjing Wang, Xiaojing Gu, Ruiting Ma, Lulu Sheng, Binwu Ma
Summary: Pancreatic adenocarcinoma is a leading cause of cancer-related death worldwide. This study employed weighted gene co-expression network analysis to construct a gene interaction network and identified several new genes associated with pancreatic adenocarcinoma. The findings have valuable implications for the diagnosis and treatment of this disease.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Jing Yin Weng, Nicole Salazar
Summary: This study analyzed DNA methylation data from lower-grade glioma and glioblastoma multiforme patients, identifying ten methylation markers associated with glioma grade. These markers, strongly linked to specific molecular alterations, can predict patient survival probabilities.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Chunyang Li, Haopeng Yu, Yajing Sun, Xiaoxi Zeng, Wei Zhang
Summary: This study identified hub genes with diagnostic and therapeutic potential in gastric cancer through weighted gene co-expression network analysis and logistic regression, and successfully validated their discriminative ability in an independent testing set using artificial neural network algorithm.
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.