Article
Genetics & Heredity
Juan Chen, Ruixian Zhang, Min Xie, Chunyan Luan, Xiaolan Li
Summary: This study identified PLAUR as an important gene in regulating dermatomyositis-associated interstitial lung disease (DM-ILD) through neutrophil-associated immune response. The findings enrich our understanding of the disease and may benefit DM-ILD patients.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Lirong Hu, Abdul Sammad, Congcong Zhang, Luiz F. Brito, Qing Xu, Yachun Wang
Summary: This study evaluated the changes in milk yield, physiological indicators, blood biochemical parameters, and alternative splicing patterns in lactating Holstein cows under heat stress conditions. The results showed that heat stress negatively impacted various biological processes of Holstein cows. Additionally, heat stress increased the occurrence of alternative splicing events, with genes involved in mRNA splicing, immune, and metabolic processes being enriched. Two candidate genes associated with heat stress responses in dairy cows were identified.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Keng Po Lai, Nathan Yi Kan Tam, Yuelong Chen, Chi Tim Leung, Xiao Lin, Chau Fong Tsang, Yin Cheung Kwok, William Ka Fai Tse, Shuk Han Cheng, Ting Fung Chan, Richard Yuen Chong Kong
Summary: Recent studies have shown that hypoxia affects sex differentiation and reproductive function in fish, leading to a male-biased population. The molecular mechanisms through which hypoxia alters fish sex differentiation and sex ratios are still poorly understood. In this study, we conducted sequencing of small RNAs and transcripts in marine medaka embryos exposed to hypoxia, and identified dysregulated miRNAs and mRNAs. Our findings suggest that miRNA-mRNA interactions may play a role in regulating embryonic development and sex determination in response to hypoxic stress.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Genetics & Heredity
Ali Ali, Gary H. H. Thorgaard, Mohamed Salem
Summary: The study achieved a full-length transcriptome assembly of rainbow trout using Iso-Seq, identifying numerous previously unannotated transcripts and isoforms not mapped to the reference genome. Most genes had multiple isoforms, with intron retention and exon skipping being major alternative splicing events. The improved annotation allowed for the identification of characteristic alternative splicing events associated with various phenotypic traits in rainbow trout.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Tara N. Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A. Rosenfeld, Jennifer VanOudenhove, Daryl A. Scott, Elizabeth J. Leslie, Justin Cotney
Summary: Craniofacial disorders are one of the most common congenital defects that arise during early pregnancy. The authors utilized RNA-seq analysis to identify 239 genes that are highly expressed during craniofacial development. Gene co-expression analysis revealed that regulatory hubs containing these genes are associated with known disease causing genes and are less susceptible to mutation in the normal healthy population. By combining transcriptomic and epigenomic data, they identified 539 genes likely to contribute to craniofacial disorders, many of which have not been previously implicated in these disorders.
NATURE COMMUNICATIONS
(2023)
Article
Endocrinology & Metabolism
Erin R. Okawa, Manoj K. Gupta, Sevim Kahraman, Praneeth Goli, Masaji Sakaguchi, Jiang Hu, Kaiti Duan, Brittany Slipp, Jochen K. Lennerz, Rohit N. Kulkarni
Summary: Insulin and insulin-like growth factor-1 receptors are crucial for maintaining pluripotency and normal lineage development of stem cells. Dysregulation in the function and signaling of these receptors leads to upregulation of compensatory pathways to maintain pluripotency, while causing abnormalities in directed differentiation toward the three lineages.
MOLECULAR METABOLISM
(2021)
Article
Biochemistry & Molecular Biology
Siras Hakobyan, Henry Loeffler-Wirth, Arsen Arakelyan, Hans Binder, Manfred Kunz
Summary: Genetic splice variants have been found to play a crucial role in different cancers, but little is known about them in melanoma. Analysis of a genome-wide transcriptomic dataset revealed a multitude of differentially expressed splice genes between benign nevi and primary melanomas, indicating potential involvement of mutations in the splicing machinery.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Arun Kumar Burramsetty, Ken Nishimura, Takumi Kishimoto, Muhammad Hamzah, Akihiro Kuno, Aya Fukuda, Koji Hisatake
Summary: This study identified and characterized proteins associated with the Nanog promoter in mouse embryonic stem cells (mESCs) using unbiased methods. The results revealed the importance of these proteins, including RNA-binding proteins (RBPs), in the maintenance of pluripotency and the reprogramming of somatic cells. The findings highlight the functional relevance of RBPs in ESC differentiation and somatic cell reprogramming.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Virology
Amanda Westergren Jakobsson, Bo Segerman, Ola Wallerman, Sara Bergstrom Lind, Hongxing Zhao, Carl-Johan Rubin, Ulf Pettersson, Goran Akusjarvi
Summary: Utilizing the Nanopore long-read sequencing platform, we revealed the remarkable complexity of the human adenovirus type 2 transcriptome, identifying over 900 alternatively spliced mRNAs, with more than 850 being novel. The virus demonstrates a significant capacity to generate novel exon combinations, with the E3 region showing the highest complexity in late infection.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xue Wang, Changyun Ping, Puwen Tan, Chenguang Sun, Guang Liu, Tao Liu, Shuchun Yang, Yanmin Si, Lijun Zhao, Yongfei Hu, Yuyan Jia, Xiaoshuang Wang, Meili Zhang, Fang Wang, Dong Wang, Jia Yu, Yanni Ma, Yue Huang
Summary: The study reveals the critical role of RNA-binding proteins in pluripotency exit of embryonic stem cells, with hnRNPLL being identified as a key regulator of alternative splicing in ES cells. Its depletion leads to sustained expression of ES cell-preferred isoforms, resulting in differentiation deficiency and developmental defects. This highlights the potential application of targeting RBPs in controlling ES cell fate.
Article
Cell & Tissue Engineering
Yao Yi, Yingying Zeng, Tsz Wing Sam, Kiyofumi Hamashima, Rachel Jun Rou Tan, Tushar Warrier, Jun Xiang Phua, Reshma Taneja, Yih-Cherng Liou, Hu Li, Jian Xu, Yuin-Han Loh
Summary: A sub-population of mESCs, known as 2-cell-like cells, is identified by the expression of MERVL and 2C transcripts. This study reveals that ribosomal proteins (RPs) RPL14, RPL18, and RPL23 are crucial for maintaining mESC identity and regulating the expression of 2C transcripts. Disruption of RPs leads to DUX-dependent activation of 2C transcripts and changes in chromatin structure. Mechanistically, knockdown of RPs enhances the binding of RPL11 to MDM2, preventing P53 protein degradation and activating downstream pathways, including DUX. This study uncovers the important roles of RPs in 2C transcript activation and provides new insights into their functions.
Article
Oncology
Liwei Song, Mengjun Yu, Renjing Jin, Meng Gu, Ziyu Wang, Dailun Hou, Shaofa Xu, Jinghui Wang, Teng Ma
Summary: In this study, we utilized the PacBio Single Molecule, Real-Time (SMRT) Sequencing platform to investigate the transcriptome after DNA-PK inactivation. We identified a large number of new transcripts and gene structures, and validated some of the new transcripts. These findings contribute to our understanding of the role of DNA-PK in transcriptome regulation and RNA metabolism.
FRONTIERS IN ONCOLOGY
(2022)
Article
Genetics & Heredity
Zhengwang Sun, Mengchen Yin, Yi Ding, Zixu Zhu, Yangbai Sun, Kun Li, Wangjun Yan
Summary: This study systematically dissected the transcriptomic profile of Synovial sarcoma from different perspectives through deep total RNA sequencing, revealing upregulated and downregulated genes, differentially alternative spliced genes, known and potentially novel gene fusions, as well as differentially expressed circular RNAs. These findings provide novel insights into the biology and molecular mechanism of Synovial sarcoma.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
Mingyue Li, Miao Bai, Yulun Wu, Shuo Yang, Lihua Zheng, Luguo Sun, Chunlei Yu, Yanxin Huang
Summary: Gastric adenocarcinoma (GAC) is a highly lethal malignant tumor with unclear pathogenesis. This study analyzed the gene expression profiles of GAC tumor tissues and adjacent normal tissues, identifying 465 differentially expressed genes (DEGs). Further analysis revealed enrichment of DEGs in pathways related to extracellular matrix, protein digestion and absorption, and gastric acid secretion. Six key genes associated with poor GAC prognosis were identified, including P4HA3 and MATN3, which have rarely been reported in relation to GAC. Functional analysis demonstrated that upregulation of P4HA3 enhanced the proliferation and migration ability of GAC cells. This study provides new insights for the selection of prognostic markers and therapeutic targets for GAC.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Dan Li, Jihong Yang, Vikas Malik, Yuting Huang, Xin Huang, Hongwei Zhou, Jianlong Wang
Summary: RNA helicase eIF4A3 plays a crucial role in maintaining pluripotency of stem cells by post-transcriptionally controlling the cell cycle, particularly the efficient nuclear export of Ccnb1 mRNA.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Yu-Chan Chang, Chien-Hsiu Li, Ming-Hsien Chan, Chih-Yeu Fang, Zhi-Xuan Zhang, Chi-Long Chen, Michael Hsiao
Summary: RAB3C plays a key role in the progression of colorectal cancer (CRC) and its overexpression is associated with drug resistance. RAB3C-induced dystrophin expression promotes vesicle formation and packaging. The RAB3C-dystrophin axis is positively correlated with PIK3CA genetic alterations in CRC patients, providing potential therapeutic options for CRC treatment.
MOLECULAR ONCOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Chien-Hsiu Li, Ming-Hsien Chan, Yu-Chan Chang, Michael Hsiao
Summary: Gold nanotechnology has revolutionized molecular biology applications, particularly in diagnosing and treating at the molecular and cellular levels. The combination of plasmonic resonance, biochemistry, and optoelectronic engineering has enhanced molecule detection and increased the possibility of analyzing atoms. Gold nanoparticles offer superior analytical properties that can be utilized for drug screening, gene sequencing, and detecting physiological functions.
Article
Oncology
Shin-Yi Chung, Yu-Chan Chang, Dennis Shin-Shian Hsu, Ya-Chi Hung, Meng-Lun Lu, Yi-Ping Hung, Nai-Jung Chiang, Chun-Nan Yeh, Michael Hsiao, John Soong, Yeu Su, Ming-Huang Chen
Summary: CX-5461 can enhance the efficacy of immune checkpoint inhibitors in the treatment of colorectal cancer by altering the tumor microenvironment and activating the interferon signaling pathway. In addition, CX-5461 can inhibit tumor growth by increasing PD-L1 expression and cytotoxic T-cell numbers.
Article
Cell Biology
Yung-Wei Lin, Yu-Ching Wen, Chi-Hao Hsiao, Feng-Ru Lai, Shun-Fa Yang, Yi-Chieh Yang, Kuo-Hao Ho, Feng-Koo Hsieh, Michael Hsiao, Wei-Jiunn Lee, Ming-Hsien Chien
Summary: SPOCK1 is found to be upregulated in ccRCC tissues and is associated with advanced clinical stages and metastasis. Knockdown and overexpression of SPOCK1 in ccRCC cells affect cell clonogenic ability, migration/invasion ability, and tumor growth and invasion in vitro and in vivo. The mechanism involves the activation of the Snail/Slug-MMP-2 axis to promote EMT and cell motility.
Article
Biochemical Research Methods
Kai-Li Chang, Jia-Hong Chen, Tzu-Chieh Lin, Jun-Yi Leu, Cheng-Fu Kao, Jin Yung Wong, Huai-Kuang Tsai
Summary: This study uses the deep learning model "DeepCircle" to analyze the characteristics and predictability of short extrachromosomal circular DNAs (eccDNAs) in the genome. It finds that although eccDNAs do not show apparent specificity in genomic locations, they exhibit similarity in sequence features across different datasets, indicating a certain level of predictability for eccDNAs.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Oncology
Yu-Chan Chang, Ming-Hsien Chan, Yi-Fang Yang, Chien-Hsiu Li, Michael Hsiao
Summary: The glucose transporter family (GLUT) consists of fourteen members and is responsible for glucose homeostasis and transport. Different GLUTs have unique kinetics and distribution, playing important roles in human physiology. GLUT4 mediates insulin-dependent glucose uptake and dysfunction of GLUT4 is associated with insulin resistance, chronic diseases, inflammation, and cancer.
Article
Biochemistry & Molecular Biology
Kenly Wuputra, Chia-Chen Ku, Jia-Bin Pan, Chung-Jung Liu, Kohsuke Kato, Ying-Chu Lin, Yi-Chang Liu, Chang-Shen Lin, Michael Hsiao, Ming-Hong Tai, Inn-Wen Chong, Huang-Ming Hu, Chao-Hung Kuo, Deng-Chyang Wu, Kazunari K. Yokoyama
Summary: By preparing three-dimensional organoids of human stomach cancers and studying the correlation between the tumorigenicity and cytotoxicity of Helicobacter pylori (H. pylori), we found that hepatoma-derived growth factor (HDGF) and tumor necrosis factor (TNFa) had effects on the growth and invasion activity of H. pylori-infected gastric cancer organoids. HDGF controlled the growth of organoids in a species-specific manner, while TNFa decreased cell viability in H. pylori-infected organoids. Additionally, HDGF controlled the invasion activity of H. pylori-infected organoids in a species-dependent manner, whereas TNFa decreased invasion activities of most organoids.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Chien-Hsiu Li, Chih-Yeu Fang, Ming-Hsien Chan, Chi-Long Chen, Yu-Chan Chang, Michael Hsiao
Summary: Based on large cohort survival analyses, this study found that FSTL3 is associated with a significantly worse prognosis in colorectal cancer (CRC) at the RNA and protein levels. Further analysis also showed that FSTL3 expression levels in the cytosol are significantly associated with poor overall and disease-free survival. Molecular simulation analysis revealed that FSTL3 participates in multiple cell motility signalling pathways to control CRC metastasis via the TGF-beta 1/TWIST1 axis.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2023)
Article
Cell Biology
Yu-Ching Wen, Van Thi Ngoc Tram, Wei-Hao Chen, Chien-Hsiu Li, Hsiu-Lien Yeh, Phan Vu Thuy Dung, Kuo-Ching Jiang, Han-Ru Li, Jiaoti Huang, Michael Hsiao, Wei-Yu Chen, Yen-Nien Liu
Summary: Current treatment options for prostate cancer focus on targeting androgen receptor (AR) signaling, but inhibiting AR may promote the development of neuroendocrine prostate cancer (NEPC). Understanding the regulatory mechanisms of AR is crucial for the clinical management of NEPC. This study revealed the tumor-suppressive role of AR and identified its downregulation of CHRM4 expression. CHRM4 overexpression drives neuroendocrine differentiation in prostate cancer cells and is associated with immunosuppressive cytokine responses in the tumor microenvironment (TME). Targeting CHRM4 and evaluating IFNA17 secretion as a prognostic biomarker could be potential therapeutic strategies for NEPC.
CELL DEATH & DISEASE
(2023)
Article
Materials Science, Multidisciplinary
Aishwarya Satpathy, Wen-Tse Huang, Ming-Hsien Chan, Ting-Yi Su, Mikolaj Kaminski, Natalia Majewska, Sebastian Mahlik, Grzegorz Leniec, Slawomir M. Kaczmarek, Michael Hsiao, Ru-Shi Liu
Summary: In the biomedical field, fluorescence imaging in the NIR-II region is growing rapidly due to its advantages of reduced autofluorescence and low photon scattering. This work integrates the ZnGa2O4 spinel oxide system into mesoporous silica and utilizes energy transfer from Cr3+ to Ni2+ to achieve high emission intensity in the NIR-II region. By establishing emission in the NIR-II and NIR-I regions, it enables improved clarity and increased penetration depth for bioimaging purposes.
ADVANCED OPTICAL MATERIALS
(2023)
Article
Crystallography
Kayalvizhi Samuvel Muthiah, Senthilkumar Thirumurugan, Yu-Chien Lin, Rajalakshmi Sakthivel, Udesh Dhawan, An-Ni Wang, Michael Hsiao, Ren-Jei Chung
Summary: Ce3NbO7/g-C3N4 nanocomposites exhibit synergistic enhancement of cancer treatment by generating cytotoxic reactive oxygen species (ROS) and inducing photothermal therapy (PTT) in the tumor microenvironment.
Article
Biochemistry & Molecular Biology
Yu-Chen Chen, Chia-Ying Chen, Tai-Wei Chiang, Ming-Hsien Chan, Michael Hsiao, Huei-Mien Ke, Isheng Jason Tsai, Trees-Juen Chuang
Summary: The study developed a bioinformatics pipeline, NCLscan-hybrid, to detect trans-spliced RNAs (ts-RNAs) and distinguish them from circular RNAs (circRNAs). The pipeline integrates short and long RNA-seq reads, minimizing false positives and proposing out-of-circle and rolling-circle long reads.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jhih-Kai Pan, Wen-Der Lin, Yao-Lung Kuo, Yu-Chia Chen, Zhu-Jun Loh, Forn-Chia Lin, Hui-Chuan Cheng, Michael Hsiao, Pei-Jung Lu
Summary: Through proteomic analysis, high expression of ICAM2 was found in leptomeningeal metastatic TNBC cells, promoting spinal cord colonization and causing poor survival outcomes. Two-way demonstration showed that high levels of ICAM2 promoted BCB adhesion, migration, and stemness abilities, determining the specificity of LM in vivo. The study suggests that targeting ICAM2 is a potential therapeutic strategy for LM in TNBC.
Article
Chemistry, Multidisciplinary
Loan Thi Ngo, Wen-Tse Huang, Ming-Hsien Chan, Ting-Yi Su, Chien-Hsiu Li, Michael Hsiao, Ru-Shi Liu
Summary: This study investigates the neurotoxicity of all-inorganic lead halide perovskite quantum dots (PeQDs) using Caenorhabditis elegans as a model organism. The results show that PeQDs accumulate mainly in the alimentary system and head region, causing a decrease in locomotor behaviors, pharyngeal pumping, brood decline, short lifespan, and abnormal issues in reproduction. Excessive reactive oxygen species formation is also observed. The neurotoxicity of PeQDs is explained by gene expression. This study provides an insight into the neurotoxicity of PeQDs and inspires the development of nontoxic PeQDs.
Article
Multidisciplinary Sciences
Chi-Ling Chiang, Yifan Ma, Ya-Chin Hou, Junjie Pan, Sin-Yu Chen, Ming-Hsien Chien, Zhi-Xuan Zhang, Wei-Hsiang Hsu, Xinyu Wang, Jingjing Zhang, Hong Li, Lili Sun, Shannon Fallen, Inyoul Lee, Xing-Yu Chen, Yeh-Shiu Chu, Chi Zhang, Tai-Shan Cheng, Wen Jiang, Betty Y. S. Kim, Eduardo Reategui, Robert Lee, Yuan Yuan, Hsiao-Chun Liu, Kai Wang, Michael Hsiao, Chi-Ying F. Huang, Yan-Shen Shan, Andrew S. Lee, L. James Lee
Summary: This study reports a dual targeted extracellular vesicle (dtEV) that can effectively suppress large PDAC tumors. The dtEV carries high loads of therapeutic RNA and is delivered to target cells through electroporation. When used in combination with the chemotherapy drug Gemcitabine, the dtEVs can inhibit tumor growth and prolong animal survival.
NATURE COMMUNICATIONS
(2023)