Article
Multidisciplinary Sciences
Yanhe Li, Caihong Zheng, Yingdong Liu, Jincan He, Qiang Zhang, Yalin Zhang, Xiaochen Kou, Yanhong Zhao, Kuisheng Liu, Dandan Bai, Yanping Jia, Xiaoxiao Han, Yifan Sheng, Jiqing Yin, Hong Wang, Shuai Gao, Wenqiang Liu, Shaorong Gao
Summary: Somatic cell nuclear transfer (SCNT) can reprogram differentiated somatic cells into totipotency, but most SCNT blastocysts are arrested at the peri-implantation stage. In this study, a 3D in vitro culture system for SCNT peri-implantation embryos was developed, and it was found that persistent Wnt signals blocked the pluripotency transition of epiblasts, leading to defects in epiblast transformation events and implantation failure. Manipulating Wnt signals improved the cloning efficiency and enhanced the lineage developmental trajectories of SCNT blastocysts during peri-implantation development.
NATIONAL SCIENCE REVIEW
(2023)
Article
Developmental Biology
Luchun Zhang, Meng Yuan, Xingwei Huang, Qianzi Cao, Shaogang Huang, Ruizhen Sun, Lei Lei
Summary: Inhibiting METTL5, an enzyme that methylates 18S rRNA m(6)A, during nuclear transfer can improve the developmental rate and cell number of embryos. Inhibition of METTL5 also decreases repressive histone modification levels and increases activating histone modification and mRNA levels of specific genes.
Article
Cell Biology
Jin Sun, Weisheng Zheng, Wenqiang Liu, Xiaochen Kou, Yanhong Zhao, Zehang Liang, Lu Wang, Zihao Zhang, Jing Xiao, Rui Gao, Shaorong Gao, Cizhong Jiang
Summary: The study derived TSCs from blastocysts using different methods and analyzed the dynamics of transcription and DNA methylation, revealing the crucial role of FGF4 treatment in TSC formation. Specific DNA methylation remodeling processes and transcription factor networks play a key role in TSC pluripotency.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Lihua Cao, Xiaoli Dai, Shihai Huang, Kaiyuan Shen, Deshun Shi, Xiangping Li
Summary: Suv39h1 and Suv39h2 are key regulators of H3K9me3 dynamics, influencing the early development of SCNT embryos. Their inhibition leads to reduced levels of H3K9me3 and altered expression of related enzymes, affecting cell proliferation and developmental competence in porcine embryos. These findings suggest that careful regulation of H3K9me3 and Suv39h1/2 levels is crucial for successful SCNT embryo development.
REPRODUCTION IN DOMESTIC ANIMALS
(2021)
Article
Cell Biology
Dandan Bai, Jin Sun, Chuan Chen, Yanping Jia, Yanhe Li, Kuisheng Liu, Yalin Zhang, Jiqing Yin, Yingdong Liu, Xiaoxiao Han, Jingling Ruan, Xiaochen Kou, Yanhong Zhao, Hong Wang, Zheng Wang, Miaoxin Chen, Xiaoming Teng, Cizhong Jiang, Shaorong Gao, Wenqiang Liu, Hong Wang, Zheng Wang, Miaoxin Chen
Summary: Assisted reproductive technology is widely used for treating human infertility, but in vitro fertilization (IVF) is associated with a low pregnancy rate and various health issues in offspring. This study reveals that IVF manipulation disrupts gene expression in extraembryonic tissues and leads to abnormal H3K4me3 modification, which is a major cause of implantation failure and abnormal placental development in IVF embryos.
Article
Agriculture, Dairy & Animal Science
Muhammad Rosyid Ridlo, Eui Hyun Kim, Anukul Taweechaipaisankul, Byeong Chun Lee, Geon A. Kim
Summary: Successful attenuation of ER stress signaling benefits in vitro embryonal development, with adiponectin treatment enhancing the developmental capacity of porcine embryos by reducing ER stress and apoptosis, improving cleavage rates, blastocyst formation rates, and total cell numbers.
Article
Multidisciplinary Sciences
Pil-Soo Jeong, Hae-Jun Yang, Se-Been Jeon, Min-Ah Gwon, Min Ju Kim, Hyo-Gu Kang, Sanghoon Lee, Young-Ho Park, Bong-Seok Song, Sun-Uk Kim, Deog-Bon Koo, Bo-Woong Sim
Summary: This study examined the role of luteolin in the maturation of mammalian oocytes. The results showed that supplementation of luteolin during in vitro maturation improved the developmental competence of oocytes. Furthermore, luteolin reduced oxidative stress and mitochondria-mediated apoptosis in oocytes, leading to improved maturation.
Article
Cell Biology
Pil-Soo Jeong, Hae-Jun Yang, Soo-Hyun Park, Min Ah Gwon, Ye Eun Joo, Min Ju Kim, Hyo-Gu Kang, Sanghoon Lee, Young-Ho Park, Bong-Seok Song, Sun-Uk Kim, Deog-Bon Koo, Bo-Woong Sim
Summary: Combining chaetocin and TSA can enhance development and maturation rates of porcine SCNT embryos by improving epigenetic reprogramming. The synergistic effect of the combined treatment is more effective in promoting blastocyst development compared to using chaetocin or TSA alone.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Rina Baba, Satoru Matsuda, Yuuichi Arakawa, Ryuji Yamada, Noriko Suzuki, Tatsuya Ando, Hideyuki Oki, Shigeru Igaki, Masaki Daini, Yasushi Hattori, Shigemitsu Matsumoto, Mitsuhiro Ito, Atsushi Nakatani, Haruhide Kimura
Summary: The inhibition of LSD1 enzyme activity can normalize aberrant gene expression in neurodevelopmental disorders and improve ASD-like behavioral deficits. This suggests that inhibiting LSD1 enzyme activity may be the key to restoring gene expression homeostasis.
Review
Plant Sciences
Muthusamy Ramakrishnan, Mingbing Zhou, Stanislaus Antony Ceasar, Doulathunnisa Jaffar Ali, Theivanayagam Maharajan, Kunnummal Kurungara Vinod, Anket Sharma, Zishan Ahmad, Qiang Wei
Summary: Somatic embryogenesis is a complex process regulated by genetic and epigenetic factors, including DNA and histone modifications, as well as miRNA regulation. These regulations influence the transition of somatic cells and the development of embryos, with the potential for somatic cell regeneration.
PLANT CELL REPORTS
(2023)
Article
Cell & Tissue Engineering
Lingyue Yang, Xiaocui Xu, Ruimin Xu, Chuan Chen, Xiaolei Zhang, Mo Chen, Xiaochen Kou, Yanhong Zhao, Hong Wang, Xiaoyu Liu, Shaorong Gao, Chong Li
Summary: Somatic cell nuclear transfer (SCNT) is a method that reprograms terminally differentiated somatic cells into totipotent embryos, but it has multiple defects. This study used MNase-seq to investigate the distribution of nucleosomes in mouse SCNT embryos and found that the dynamics of nucleosome position in SCNT embryos were delayed compared to fertilized embryos. It was also discovered that the memory of nucleosome occupancy in donor cells was a potential barrier for SCNT-mediated reprogramming.
Article
Endocrinology & Metabolism
Mingru Yin, Weina Yu, Wenzhi Li, Qianqian Zhu, Hui Long, Pengcheng Kong, Qifeng Lyu
Summary: The study found that AOA treatment affects the pre- and post-implantation embryo development in mice, resulting in increased expression of the maternal allele-specific gene Igf2r but significantly lower birth weight in newborn mice. However, no other abnormalities were observed in the offspring born following AOA treatment.
REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY
(2021)
Article
Biology
Xi Dai, Honglian Shao, Nianqin Sun, Baiquan Ci, Jun Wu, Chuanyu Liu, Liang Wu, Yue Yuan, Xiaoyu Wei, Huanming Yang, Longqi Liu, Weizhi Ji, Bing Bai, Zhouchun Shang, Tao Tan
Summary: This study applied scATAC-seq technology to investigate the chromatin status of in vitro cultured cynomolgus monkey embryos. The findings provide insights into the chromatin reorganization and transcriptional regulatory mechanisms during early post-implantation development in primates, including the identification of regulatory factors and lineage specification.
Article
Cell & Tissue Engineering
Ruimin Xu, Sen Li, Qiu Wu, Chong Li, Manxi Jiang, Lei Guo, Mo Chen, Lingyue Yang, Xin Dong, Hong Wang, Chenfei Wang, Xiaoyu Liu, Xianghong Ou, Shaorong Gao
Summary: The deposition of H3K9me3 in human oocytes and early embryos has been found to be stage-specific, with enhancer-like regions being temporarily established during the 8-cell stage and greater stability during the blastocyst stage. The genes DUX and KRAB-ZNFs have been identified as potential factors involved in the establishment of stage-specific H3K9me3. Furthermore, the presence of bivalent chromatin domains in human blastocysts suggests priming for lineage differentiation.
Article
Cell Biology
Akifumi Ijuin, Hiroe Ueno, Tomonari Hayama, Shunsuke Miyai, Ai Miyakoshi, Haru Hamada, Sumiko Sueyoshi, Shiori Tochihara, Marina Saito, Haruka Hamanoue, Teppei Takeshima, Yasushi Yumura, Etsuko Miyagi, Hiroki Kurahashi, Hideya Sakakibara, Mariko Murase
Summary: This study found that during the process of embryo culture, the number of aneuploid cells significantly decreased and the proportion of healthy embryos significantly increased. Additionally, mitochondrial mutations may lead to decreased mitochondrial function and affect embryonic development. Therefore, analyzing the number of mitochondrial mutations may be a novel method to select better mosaic embryos for transfer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Cell & Tissue Engineering
Ruimin Xu, Sen Li, Qiu Wu, Chong Li, Manxi Jiang, Lei Guo, Mo Chen, Lingyue Yang, Xin Dong, Hong Wang, Chenfei Wang, Xiaoyu Liu, Xianghong Ou, Shaorong Gao
Summary: The deposition of H3K9me3 in human oocytes and early embryos has been found to be stage-specific, with enhancer-like regions being temporarily established during the 8-cell stage and greater stability during the blastocyst stage. The genes DUX and KRAB-ZNFs have been identified as potential factors involved in the establishment of stage-specific H3K9me3. Furthermore, the presence of bivalent chromatin domains in human blastocysts suggests priming for lineage differentiation.
Article
Multidisciplinary Sciences
Wenjie Zheng, Xiaoman Wang, Jinjing Liu, Xin Yu, Lu Li, Heping Wang, Jijun Yu, Xiaoya Pei, Chaoran Li, Zhimian Wang, Menghao Zhang, Xiaofeng Zeng, Fengchun Zhang, Chenfei Wang, Hua Chen, Hou-Zao Chen
Summary: This study provides insights into the immune landscape of Behcet's disease (BD) and highlights the contribution of C1q-high (C1q(hi)) monocytes to BD hyperinflammation. C1q(hi) monocytes demonstrate increased phagocytosis and proinflammatory cytokine secretion, and their presence is clinically relevant. Activated interferon-gamma (IFN-gamma) signaling induces the accumulation of C1q(hi) monocytes, which can be reduced by tofacitinib treatment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Xin Dong, Ke Tang, Yunfan Xu, Hailin Wei, Tong Han, Chenfei Wang
Summary: The study developed a method called SCRIP, which integrates scATAC-seq and a large-scale TR ChIP-seq reference to infer single-cell TR activity and targets. The method showed improved performance in evaluating TR binding activity and exhibited high consistency with TR expressions. Additionally, the method enables the identification of TR target genes and the construction of single-cell gene regulation networks (GRNs).
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ya Han, Yuting Wang, Xin Dong, Dongqing Sun, Zhaoyang Liu, Jiali Yue, Haiyun Wang, Taiwen Li, Chenfei Wang
Summary: TISCH2 is a resource of single-cell RNA-seq data from tumors, providing comprehensive analysis of gene expression in the tumor microenvironment. With added features, users can better utilize the large-scale datasets for analysis and visualization.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xiaoying Shi, Zhiguang Yu, Pengfei Ren, Xin Dong, Xuanxin Ding, Jiaming Song, Jing Zhang, Taiwen Li, Chenfei Wang
Summary: Understanding gene expression patterns across different human cell types is crucial for investigating mechanisms of cell type differentiation and disease occurrence and progression. HUSCH is a large-scale database that integrates high-quality single-cell transcriptomic datasets from different tissues, providing comprehensive visualization and analysis of gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Avinash Sahu, Xiaoman Wang, Phillip Munson, Jan P. G. Klomp, Xiaoqing Wang, Shengqing Stan Gu, Ya Han, Gege Qian, Phillip Nicol, Zexian Zeng, Chenfei Wang, Collin Tokheim, Wubing Zhang, Jingxin Fu, Jin Wang, Nishanth Ulhas Nair, Joost A. P. Rens, Meriem Bourajjaj, Bas Jansen, Inge Leenders, Jaap Lemmers, Mark Musters, Sanne van Zanten, Laura van Zelst, Jenny Worthington, Jun S. Lu, Dejan Juric, Clifford A. Meyer, Arthur Oubrie, X. Shirley Liu, David E. Fisher, Keith T. Flaherty
Summary: Researchers have developed a multiomics computational method called BipotentR to identify cancer cell-specific regulators that modulate both tumor immunity and another oncogenic pathway. They stratified melanoma patients' response to anti-PD-1 therapy based on the tumor activities of these regulators using machine learning and deep neural approaches, enhancing the predictive power of current biomarkers. Their top regulator, ESRRA, activated in immunotherapy-resistant tumors, killed tumors by suppressing energy metabolism and activating two immune mechanisms: cytokine induction and antigen-presentation stimulation.
Article
Oncology
Tong Han, Xujun Wang, Sailing Shi, Wubing Zhang, Jue Wang, Qiu Wu, Ziyi Li, Jingxin Fu, Rongbin Zheng, Jiamin Zhang, Qin Tang, Peng Zhang, Chenfei Wang
Summary: This study performed IFNy sensitivity screens in over 40 cancer cell lines and discovered that activation of double-strand break repair genes could lead to resistance to IFNy in cancer cells. Suppression of single-strand break repair genes increased the reliance on DSB repair genes after IFNy treatment. Inhibition of the DSB repair pathway exhibited a synergistic effect with IFNy treatment both in vitro and in vivo. The relationship between the activation of DSB repair genes and IFNy resistance was further confirmed in clinical tumor profiles. This study provides comprehensive resources and evidence to elucidate a mechanism of IFNy resistance in cancer and has the potential to inform combination therapies to overcome immunotherapy resistance.
CANCER IMMUNOLOGY RESEARCH
(2023)
Article
Cell Biology
Rui Gao, Shiyang Zeng, Dongxu Yang, Xiaocui Li, Wenqiang Liu, Yawei Gao, Dandan Bai, Linfeng Zhang, Chuan Chen, Yunzhe Kang, Beiying Wang, Wei Hong, Mingzhu Wang, Jiqing Yin, Hong Wang, Qiaolin Deng, Shaorong Gao, Yong Zhang, Jiayu Chen
Summary: Histone modifications play critical roles in regulating gene expression during early embryo development. This study provides the first genome-wide profiles of three key histone modifications in human primordial germ cells, revealing the positive correlation between H3K4me3 and gene expression, as well as the important roles of H3K27me3 in regulating specific promoters and X chromosome reactivation. The repressive marks of H3K9me3 and H3K27me3 jointly regulate demethylation-resistant regions in hPGCs.
Article
Biochemical Research Methods
Hailin Wei, Tong Han, Taiwen Li, Qiu Wu, Chenfei Wang
Summary: Single-cell CRISPR screens have been widely used to investigate gene regulatory circuits in diverse biological systems. SCREE is a comprehensive and flexible pipeline for the analysis of various types of single-cell CRISPR screens data.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Weina Zhang, Mingzhu Wang, Zhiwei Song, Qianzheng Fu, Jiayu Chen, Weitao Zhang, Shuai Gao, Xiaoxiang Sun, Guang Yang, Qiang Zhang, Jiaqing Yang, Huanyin Tang, Haiyan Wang, Xiaochen Kou, Hong Wang, Zhiyong Mao, Xiaojun Xu, Shaorong Gao, Ying Jiang
Summary: In this study, it was found that farrerol directly targets the deubiquitinase UCHL3 to regulate homologous recombination (HR) repair. Farrerol enhances the deubiquitinase activity of UCHL3, leading to improved HR repair. This research highlights the importance of farrerol and UCHL3 in promoting somatic cell nuclear transfer (SCNT) efficiency.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Yi Zhang, Guanjue Xiang, Alva Yijia Jiang, Allen Lynch, Zexian Zeng, Chenfei Wang, Wubing Zhang, Jingyu Fan, Jiajinlong Kang, Shengqing Stan Gu, Changxin Wan, Boning Zhang, X. Shirley Liu, Myles Brown, Clifford A. Meyer
Summary: MetaTiME is a method that compares gene expression of single cells in the tumor microenvironment across different tumors and annotates cell types and states using transportable labels and metacomponents. It integrates multiple single-cell sequencing datasets to reveal common cell types and states in the tumor microenvironment. MetaTiME learns meta-components that encode independent components of gene expression and provides a tool to annotate cell states and gene regulators for tumor immunity and cancer immunotherapy.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Junjie Hu, Lele Zhang, Haoran Xia, Yilv Yan, Xinsheng Zhu, Fenghuan Sun, Liangdong Sun, Shuangyi Li, Dianke Li, Jin Wang, Ya Han, Jing Zhang, Dongliang Bian, Huansha Yu, Yan Chen, Pengyu Fan, Qiang Ma, Gening Jiang, Chenfei Wang, Peng Zhang
Summary: This study analyzed the transcriptomes of single cells from non-small cell lung cancer patients before and after neoadjuvant PD-1 blockade combined with chemotherapy. The transcriptomes of cancer cells after treatment were associated with therapy response. Patients with major pathologic response exhibited activated antigen presentation pathways, while patients with non-major pathologic response showed overexpression of estrogen metabolism enzymes and elevated serum estradiol. The study also revealed the expansion and activation of cytotoxic T cells and NK cells after therapy, along with the reduction of immunosuppressive Tregs. The findings provide novel biomarkers for predicting therapy response and potential strategies to overcome immunotherapy resistance.
Article
Biochemistry & Molecular Biology
Guangxu Cao, Jiali Yue, Yetian Ruan, Ya Han, Yong Zhi, Jianqiao Lu, Min Liu, Xinxin Xu, Jin Wang, Quan Gu, Xuejun Wen, Jinli Gao, Qingfeng Zhang, Jiuhong Kang, Chenfei Wang, Fang Li
Summary: This study conducted single-cell RNA and TCR sequencing of cervical cancer tumors and adjacent normal tissues to map the immune landscape. The study revealed tumor-specific germinal center B cells associated with improved clinical outcomes and established a joint model of tumor and stromal cells to predict patients' prognosis. These findings provide information for future combinational immunotherapy.
Article
Biology
Lu Han, Bin Song, Peilin Zhang, Zhi Zhong, Yongxiang Zhang, Xiaochen Bo, Hongyang Wang, Yong Zhang, Xiuliang Cui, Wenxia Zhou
Summary: Cellular transitions play a crucial role in translational medicine research. This study introduces a computational framework, PC3T, which enriches small molecules that induce desired cellular transitions. The framework was able to predict the reprogramming of fibroblasts into hepatic progenitor-like cells and provide a valuable resource for cell state transition research.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Pengfei Ren, Xiaoying Shi, Zhiguang Yu, Xin Dong, Xuanxin Ding, Jin Wang, Liangdong Sun, Yilv Yan, Junjie Hu, Peng Zhang, Qianming Chen, Jing Zhang, Taiwen Li, Chenfei Wang
Summary: SELINA is a comprehensive and automatic cell-type annotation framework based on a pre-curated reference atlas. It employs a multiple-adversarial domain adaptation network to remove batch effects and enhances the annotation of less frequent cell types through synthetic minority oversampling and autoencoder fitting. SELINA creates a comprehensive and uniform reference atlas with 1.7 million cells covering 230 distinct human cell types, and accurately annotates cells within diverse human tissues.
CELL REPORTS METHODS
(2023)
