Review
Medicine, General & Internal
Xuejun He, Ningzhi Zhang, Wenye Cao, Yiqiao Xing, Ning Yang
Summary: Advancements in high-throughput sequencing (HTS) technology have provided new insights into the etiology, signaling pathways, and biomarkers of ocular diseases, aiding in improving their diagnosis and research.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Medicine, General & Internal
Haixia Xing, Hongwei Liu, Jie Pan
Summary: This study characterized the saliva microbiota of Candida carriage Sjogren's syndrome patients using high-throughput sequencing. The results showed significant microbial dysbiosis in SS patients, which differed from oral candidiasis and healthy patients.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Physiology
Heather Ikert, Michael D. J. Lynch, Andrew C. Doxey, John P. Giesy, Mark R. Servos, Barbara A. Katzenback, Paul M. Craig
Summary: This study identified altered plasma miRNAs in response to acute stress in rainbow trout, as well as changes in miRNAs in fish epidermal mucus and surrounding water. The expression profiles of miRNAs in mucus and water were different from those in plasma, indicating that the plasma miRNA response was not associated with external samples.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Biology
Elena S. Vashukova, Polina Y. Kozyulina, Roman A. Illarionov, Natalya O. Yurkina, Olga Pachuliia, Mariya G. Butenko, Tatyana B. Postnikova, Lada A. Ivanova, Dina R. Eremeeva, Marina S. Zainulina, Olesya N. Bespalova, Andrey S. Glotov
Summary: The study evaluated the profiles of miRNAs in pregnant women's plasma and serum samples at three time points, revealing a decrease in miRNA reads by one-third during pregnancy. Several miRNAs showed level changes during pregnancy, and differences were observed between plasma and serum samples for 36 miRNAs. The results were validated using qRT-PCR, confirming changes in circulating miRNA profiles during gestation and providing a basis for further research on molecular mechanisms and biomarkers of gestation abnormalities.
Review
Hematology
Jennifer Gebetsberger, Kristina Mott, Aline Bernar, Eva Klopocki, Werner Streif, Harald Schulze
Summary: This article discusses the diagnostic approach and advantages, limitations, and ethical issues of genetic testing for inherited platelet disorders (IPDs). It also provides information on the clinical significance of different variants and their correct reporting.
Article
Plant Sciences
Luis Galipienso, Laura Elvira-Gonzalez, Leonardo Velasco, Jose angel Herrera-Vasquez, Luis Rubio
Summary: High-throughput sequencing from symptomatic tomato and pepper plants collected in Panama resulted in obtaining the complete genomes of southern tomato virus and bell pepper endornavirus, as well as almost-complete genomes of three other BPEV isolates. The study revealed significant genetic diversity among the Panamanian BPEV isolates and no direct correlation between geographic and genetic distances for both STV and BPEV. Evolutionary analysis indicated purifying selection in all encoding regions of both viruses and recombination only in BPEV.
Article
Genetics & Heredity
Eu Jeen Yang, Ye Jee Shim, Heung Sik Kim, Young Tak Lim, Ho Joon Im, Kyung-Nam Koh, Hyery Kim, Jin Kyung Suh, Eun Sil Park, Na Hee Lee, Young Bae Choi, Jeong Ok Hah, Jae Min Lee, Jung Woo Han, Jae Hee Lee, Young-Ho Lee, Hye Lim Jung, Jung-Sook Ha, Chang-Seok Ki
Summary: This study successfully diagnosed 10 patients with Glanzmann thrombasthenia and 1 patient with platelet type bleeding disorder 18 using next-generation sequencing (NGS). Common variants were found in ITGB3 and ITGB2B in Korean patients, as well as novel variants in GT and RASGRP2. The application of NGS proved to be effective for accurately diagnosing heterogeneous inherited platelet function disorders.
Review
Pharmacology & Pharmacy
Charles Hadley S. King, Jonathon Keeney, Nuria Guimera, Souvik Das, Michiel Weber, Brian Fochtman, Mark O. Walderhaug, Sneh Talwar, Janisha A. Patel, Raja Mazumder, Eric F. Donaldson
Summary: This project demonstrates the use of the IEEE 2791-2020 Standard (BioCompute Objects [BCO]) to enable clear communication of NGS analysis results. It replicates a clinical trial and performs two independent analyses to validate the consistency of the results, showcasing how a template BCO enhances confidence in the regulatory submission process.
DRUG DISCOVERY TODAY
(2022)
Article
Microbiology
Jin Luo, Shuaiyang Zhao, Qiaoyun Ren, Qilin Wang, Zeyu Chen, Jingjing Cui, Yujiao Jing, Peiwen Liu, Ruofeng Yan, Xiaokai Song, Guangyuan Liu, Xiangrui Li
Summary: This study investigated miRNAs in Rhipicephalus microplus ticks in China and found differentially expressed miRNAs at different developmental stages. These differentially expressed miRNAs may be involved in developmental physiology, signal transduction, and cell-extracellular communications. These findings are important for understanding the biology of ticks and improving the understanding of miRNA functioning in the regulation of R. microplus development.
Article
Biochemical Research Methods
Michael Schneider, Asis Shrestha, Agim Ballvora, Jens Leon
Summary: The proposed strategy accurately identifies the allele frequency of populations at low cost. This is particularly important for evolutionary plant breeding of crops with large genomes, such as barley. Whole-genome low coverage re-sequencing at 0.03x coverage per genotype accurately estimates allele frequency when a loci-based haplotyping approach is applied. The implementation of annotated haplotypes capitalizes on the biological background and statistical robustness.
Review
Microbiology
Tara E. Ness, Andrew DiNardo, Maha R. Farhat
Summary: High throughput sequencing (HTS) can detect the presence of Mycobacterium tuberculosis DNA in clinical samples and provide information on drug susceptibility. Multiple studies have laid the groundwork for exploring the clinical application of HTS in tuberculosis diagnosis. This article presents the workflow challenges, strengths, and limitations of different sequencing platforms, as well as the tools used for analysis, to provide a framework for further innovations in the field.
Article
Agriculture, Dairy & Animal Science
Shi Yin, Jingwen Zhou, Liuqing Yang, Yujie Yuan, Xianrong Xiong, Daoliang Lan, Jian Li
Summary: This study investigates the transcriptome dynamics of microRNA (miRNA) in yak corpus luteum (CL) at different developmental stages. The findings reveal key miRNAs and target genes associated with the formation, function, and regression of the CL. The results provide valuable insights into the regulatory mechanisms and gene networks of miRNA in the estrous cycle of yaks.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Claudia Gutierrez-Garcia, Shiek S. S. J. Ahmed, Sathishkumar Ramalingam, Dhivya Selvaraj, Aashish Srivastava, Sujay Paul, Ashutosh Sharma
Summary: This study utilized high-throughput sequencing technology to analyze the miRNA profile of Murraya koenigii and identified miRNAs associated with secondary metabolite biosynthesis. The results showed that these miRNAs targeted key enzymes in the terpenoid backbone and flavonoid biosynthesis pathways. The sequencing results were validated by qPCR. This is the first report of the miRNA profile of Murraya koenigii, providing valuable information for studying the involvement of miRNAs in secondary metabolism.
Article
Biochemistry & Molecular Biology
Ying-Hui Xiong, Xue-Gong Fan, Ya-Yu Chen, Yan Huang, Jun Quan, Pan-Pan Yi, Mei-Fang Xiao, Ze-Bing Huang, Xing-Wang Hu
Summary: This study compared three commonly used EVs isolation kits for isolating EVs from HepG2 cell culture medium. The results showed that the total amount of microRNA isolated from EVs using the EI kit was higher and had a higher quality of high-throughput sequencing data compared to the other two kits.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Peripheral Vascular Disease
Javier Perez-Hernandez, Angela L. Riffo-Campos, Ana Ortega, Olga Martinez-Arroyo, Daniel Perez-Gil, Dolores Olivares, Elena Solaz, Fernando Martinez, Sergio Martinez-Hervas, Felipe J. Chaves, Josep Redon, Raquel Cortes
Summary: This study identified a signature of dysregulated circulating miRNAs associated with albuminuria in hypertension. In particular, miR-26a in exosomes seemed to play a key role in the regulation of TGF-beta, a relevant effector in kidney damage.
Article
Biochemical Research Methods
Shanshan Li, Zhifeng Luo, Shuhui Meng, Xiaofen Qiu, Fengping Zheng, Weier Dai, Xinzhou Zhang, Weiguo Sui, Qiang Yan, Donge Tang, Yong Dai
Summary: The study investigated proteomic and phosphoproteomic alterations in renal biopsy tissues of membranous nephropathy patients, revealing differential phosphorylation levels of multiple phosphoproteins associated with cellular processes and biological regulation, with most located in the nucleus. The complex protein-protein interaction network and potential signaling pathways identified provide insight into the pathogenic mechanisms of membranous nephropathy.
PROTEOMICS CLINICAL APPLICATIONS
(2022)
Article
Endocrinology & Metabolism
Chunhong Li, Yueying Xiang, Yanyan Zhang, Donge Tang, Yan Chen, Wen Xue, Xiaobin Wang, Jiejing Chen, Yong Dai
Summary: This study characterized mtDNA polymorphisms in patients with T2D and identified 10 mtDNA variants associated with the disease. The findings contribute to the understanding of the role of mtDNA in the pathophysiology of T2D and suggest potential molecular biomarkers for early diagnosis of T2D.
INTERNATIONAL JOURNAL OF DIABETES IN DEVELOPING COUNTRIES
(2022)
Article
Oncology
Junping Liu, Wei Zhang, Wanxia Cai, Yumei Chen, Xiaozhong Cai, Donge Tang, Min Tang, Yong Dai
Summary: In this study, the researchers found that GOLT1B, a golgi vesicle transporter protein, was significantly up-regulated in breast cancer tissues and may serve as a potential prognostic gene for breast cancer. They also uncovered the role of GOLT1B in regulating the immune microenvironment and its impact on the development and treatment outcome of breast cancer.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Wei Zhang, Minmin Wu, Xucan Gao, Chiyu Ma, Huixuan Xu, Liewen Lin, Jingquan He, Wanxia Cai, Yafang Zhong, Donge Tang, Min Tang, Yong Dai
Summary: This study characterized significant molecular changes in the nucleus of CRC patients and identified potentially core nuclear genes within the network, as well as probable upstream regulators. These findings provide insight into the pathogenic molecular alterations in the nucleus of CRC patients and offer a functional context for future drug development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Medicine, General & Internal
Hongwei Wu, Donge Tang, Manhua Yun, Haiping Liu, Shaoxing Huang, Chen Yun, Berthold Hocher, Xinzhou Zhang, Fanna Liu, Lianghong Yin, Yong Dai
Summary: The metabolic characteristics of fatty acids and tryptophan in the intestinal system are disturbed in IgAN patients, leading to active immune-inflammatory reactions.
FRONTIERS IN MEDICINE
(2022)
Article
Oncology
Wenbiao Chen, Donge Tang, Junqi Lin, Xiaoming Huang, Shaoming Lin, Guanle Shen, Yong Dai
Summary: This study investigated the biological function of circSHKBP1 in NSCLC and found that it enhanced proliferation, migration, invasion, and stemness of NSCLC cells. The study also identified the miR-1294/PKM2 axis as the mechanism by which circSHKBP1 regulates NSCLC progression. These findings suggest that circSHKBP1 may serve as a potential prognostic biomarker and therapeutic target for NSCLC.
MOLECULAR THERAPY-ONCOLYTICS
(2022)
Review
Immunology
Yixi Li, Donge Tang, Lianghong Yin, Yong Dai
Summary: Lupus nephritis (LN) is a complex autoimmune disease, and recent research has shown the potential of regulatory T (Treg) cell therapy in treating autoimmune diseases. However, there is limited understanding of Treg cell therapy for LN patients. This review aims to summarize new insights into Treg-targeting techniques in LN patients.
AUTOIMMUNITY REVIEWS
(2022)
Article
Rheumatology
Huixuan Xu, Haiyan Yu, Fengping Zheng, Cantong Zhang, Wanxia Cai, Xinzhou Zhang, Donge Tang, Yong Dai
Summary: This study provides a new perspective for understanding the pathophysiology of chronic hepatitis B (CHB) by analyzing the gene regulatory network in CHB patients using single-cell ATAC sequencing. The specific cell types associated with CHB were found to be located in B-0 and T-3. The regulatory network of the hepatitis B signal pathway composed of genes linked to the differentially expressed peaks of these two CHB disease-specific cell types was drawn.
CLINICAL RHEUMATOLOGY
(2022)
Article
Immunology
Yafang Zhong, Wei Zhang, Xiaoping Hong, Zhipeng Zeng, Yumei Chen, Shengyou Liao, Wanxia Cai, Yong Xu, Gang Wang, Dongzhou Liu, Donge Tang, Yong Dai
Summary: Our study identified ABCB1, IFI27, and PLSCR1 as potential diagnostic genes for Chinese SLE patients and uncovered their most relevant immune cells. The findings in this paper provide possible biomarkers for diagnosing Chinese SLE patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Haiyan Yu, Donge Tang, Hongwei Wu, Chunhong Li, Yongping Lu, Fang He, Xiaogang Zhang, Yane Yang, Wei Shi, Wenlong Hu, Zhipeng Zeng, Weier Dai, Minglin Ou, Yong Dai
Summary: This study used integrated single-cell RNA sequencing and single-cell transposase-accessible chromatin sequencing analyses to investigate cellular heterogeneity and transcriptional regulatory networks during human spine development. The findings revealed that fibroblasts with stem cell characteristics can differentiate into chondrocytes and neurons may originate from neuroendocrine cells. The interaction between macrophages and neurons involving NRP2_SEMA3C and CD74_APP is crucial for spinal cord development.
Article
Multidisciplinary Sciences
Wencong Song, Chunhong Li, Jie Qiu, Jiyou Dong, Dongzhou Liu, Yong Dai
Summary: This study examined the expression profiles of exosomal miRNAs and proteins in the plasma of SLE patients and healthy subjects and discussed the underlying signaling network of circulating exosomes. The study identified differentially expressed exosomal miRNAs and proteins in SLE patients and healthy controls, as well as consensus molecules and signaling pathways. These findings indicate the potential application of exosomes in the clinical treatment and diagnosis of SLE disease.
Article
Rheumatology
Fengping Zheng, Lishan Tan, Fan Zhang, Sanmu Li, Zhiwei Lai, Huixuan Xu, Zuying Xiong, Yong Dai
Summary: This study investigated the role of circRNA in systemic lupus erythematosus (SLE) by analyzing its expression in plasma and peripheral blood mononuclear cells (PBMCs). Differentially expressed circRNAs were identified and their potential diagnostic and pathogenic roles in SLE were explored through network analysis.
CLINICAL RHEUMATOLOGY
(2023)
Article
Gastroenterology & Hepatology
Wenjun Pu, Xi Wang, Xiaoni Zhong, Dong Zhao, Zhipeng Zeng, Wanxia Cai, Yafang Zhong, Jianrong Huang, Donge Tang, Yong Dai
Summary: This study analyzed and compared the spatial distribution of metabolites in healthy control and hepatitis B cirrhosis tissue samples using LC-MS/MS and mass spectrometry imaging system. The results showed that hepatitis B cirrhosis induced region-specific autophagy and dysregulation of unsaturated fatty acids, amino acids, and phosphatidylcholines metabolism. The mass spectrometry imaging system provided additional metabolites' spatial information, which can promote biomarker screening technology and support the exploration of novel mechanisms in liver cirrhosis.
HEPATOLOGY COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Yan Yang, Chiyu Ma, Shishi Li, Wanxia Cai, Weier Dai, Xinzhou Zhang, Lianghong Yin, Donge Tang, Fanna Liu, Yong Dai
Summary: By analyzing the microbiota and serum metabolites in urine samples from patients with diabetic kidney disease (DKD), it was found that DKD patients had a different urinary microbiota compared to the healthy controls, with the most abundant microbiota being Proteobacteria and Acidobacteria. Short-chain fatty acids and protein-bound uremic toxins were shown to be specific to DKD. Furthermore, the study revealed that the metabolism of arginine and proline may play a major role in the regulation of DKD.
Article
Biochemistry & Molecular Biology
Yingwei Zhang, Zeyu Zhang, Chundi Li, Donge Tang, Yong Dai
Summary: This study demonstrated that Empagliflozin treatment can significantly improve the metabolites involved in fatty acid oxidation pathway in the heart of db/db diabetic mice, suggesting its potential therapeutic intervention for diabetic cardiomyopathy.