Article
Biochemistry & Molecular Biology
Chenge Xin, Chaonan Zhu, Ying Jin, Hui Li
Summary: This study highlights the critical role of the VEGF signaling pathway in the mesendodermal induction of hESCs, along with the important involvement of the MEK-ERK cascade in this process. Furthermore, it suggests potential crosstalk between the VEGF signaling pathway and other known pathways in mesendodermal differentiation. These findings offer new insights and approaches for the study of hESCs.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Cell & Tissue Engineering
Yun-Sheng Yang, Man-Hua Liu, Zhao-Wen Yan, Guo-Qiang Chen, Ying Huang
Summary: In this study, researchers found that FAM122A plays a critical role in mesendodermal specification and cardiac differentiation. Its deficiency results in embryonic lethality, cardiovascular defects, and impaired cardiac functions. Further investigation revealed that Fam122a deficiency affects mesendodermal specification and cardiac differentiation from mouse embryonic stem cells through dysregulation of histone modification and Wnt and Hippo signaling pathways via modulation of PP2A activity. These findings significantly contribute to our understanding of the regulatory network of mesendodermal/cardiac differentiation and propose the potential importance of FAM122A in cardiac regeneration.
Article
Medicine, Research & Experimental
Kilian Sottoriva, Na Yoon Paik, Zachary White, Thilinie Bandara, Lijian Shao, Teruyuki Sano, Kostandin Pajcini
Summary: After hematopoietic stem cell transplantation, long-term impairment of T cell-mediated adaptive immunity is a major clinical obstacle. This study identified a Notch/IL-21 signaling axis in bone marrow common lymphoid progenitor (CLP) cells, which can improve the potential of T cell and fate of human cord blood cells.
Article
Immunology
Spencer T. Chen, Thiago Y. Oliveira, Anna Gazumyan, Melissa Cipolla, Michel C. Nussenzweig
Summary: Germinal centers (GCs) are crucial for the selection of high-affinity antibodies. The study found that B cell receptor (BCR) signaling plays a vital role in GC selection. These findings are fundamental for understanding adaptive immunity and vaccine development.
Article
Cell Biology
Tao Liang, Jianbo Bai, Wei Zhou, Hao Lin, Shixin Ma, Xuechen Zhu, Qinghua Tao, Qiaoran Xi
Summary: This study reveals the transcriptional regulatory function of HMCES in the context of TGF-b family signaling. HMCES contributes to early development by maintaining nodal/activin- or BMP-signaling-regulated transcriptional network. HMCES competitively binds chromatin to limit binding by R-SMAD proteins, thereby repressing their regulatory effects.
Article
Biology
Christine E. Cucinotta, Rachel H. Dell, Keean Ca Braceros, Toshio Tsukiyama
Summary: This study found that there is robust transcription activity within the first few minutes of quiescence exit. The chromatin-remodeling enzyme RSC is already bound to genes induced upon quiescence exit. Depletion of RSC results in severe defects during quiescence exit, including a global decrease in Pol II loading and aberrant transcription initiation.
Article
Optics
Haiwen Wang, Cheng Guo, Weiliang Jin, Alex Y. Song, Shanhui Fan
Summary: Recent research has shown that optical pulses can carry transverse orbital angular momentum (OAM) and introduced a compact device for generating spatiotemporal vortices with arbitrarily oriented OAM. By controlling the structural symmetry of the device, the position and dispersion of the transmission nodal line can be manipulated. This advancement opens up possibilities for pulse shaping and sensing in the spatiotemporal domain.
Article
Oncology
Fen Ma, Seiji Arai, Keshan Wang, Carla Calagua, Amanda R. Yuan, Larysa Poluben, Zhongkai Gu, Joshua W. Russo, David J. Einstein, Huihui Ye, Meng Xiao He, Yu Liu, Eliezer Van Allen, Adam G. Sowalsky, Manoj K. Bhasin, Xin Yuan, Steven P. Balk
Summary: This study reveals the importance of Wnt/beta-catenin signaling in prostate cancer, showing its role in stem cell maintenance and invasion. It identifies new effectors and drivers of this pathway in prostate cancer, such as ROR1 and APC genomic loss. The findings suggest that targeting Wnt/beta-catenin signaling may be a potential therapeutic strategy for prostate cancer.
Editorial Material
Biochemistry & Molecular Biology
Hernan Morales-Navarrete, Patrick Mueller
Summary: A new study combines various techniques to investigate the mechanisms of cell internalization during gastrulation in zebrafish embryos, revealing the important role of coupling signaling and active mechanical forces in triggering the process.
Article
Biochemistry & Molecular Biology
Ran Tong, Han Wang, Ying Jin, Hui Li
Summary: This study discovers a crucial role of HESX1 in the commitment of human embryonic stem cells (hESCs) to mesendodermal (ME) cells, which is regulated by OCT4 and NANOG. Knockdown of HESX1 impairs ME commitment of hESCs, while overexpression of HESX1 enhances ME marker expression. Additionally, HESX1 affects ME induction in hESCs by modulating ERK1/2 signaling.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Manar Elkenani, Gunsmaa Nyamsuren, Karl Toischer, Ibrahim M. Adham, Belal A. Mohamed
Summary: PELO deletion disrupts embryonic development between E4.5 and E5.5, affecting the first differentiation process of ESCs. Mutant ESCs cultured under differentiation conditions show enhanced PI3K-PKB/AKT signaling, nuclear accumulation of FOXO1, and upregulation of Oct4 gene.
Article
Immunology
Nele Twisselmann, Julia Pagel, Axel Kunstner, Markus Weckmann, Annika Hartz, Kirsten Glaser, Anne Hilgendorff, Wolfgang Gopel, Hauke Busch, Egbert Herting, Jason B. Weinberg, Christoph Haertel
Summary: Research indicates that preterm infants exhibit dysregulated macrophage activation, which results in sustained lung inflammation potentially due to T cell polarization-induced RORC upregulation and TLR4 surface expression. Experiments with a double-hit model show that exposure to 65% or 3% oxygen, followed by LPS stimulation, leads to exaggerated pro-inflammatory response in preterm macrophages, possibly mediated by downregulation of major transcriptional factors Egr2 and Gfi1.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Lydia M. M. Parkinson, Sarah L. L. Gillen, Laura M. M. Woods, Lewis Chaytor, Daniel Marcos, Fahad R. R. Ali, Jason S. S. Carroll, Anna Philpott
Summary: ASCL1 plays a role in maintaining proliferation and controlling differentiation in neuroblastoma cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Cell Biology
Thulaj Meharwade, Loick Joumier, Maxime Parisotto, Vivian Huynh, Edroaldo Lummertz da Rocha, Mohan Malleshaiah
Summary: Embryonic stem cells can simulate multiple states resembling different stages of early embryogenesis, and bone morphogenetic protein (BMP) signaling can induce the totipotent state. Cross-activated pathways can constrain the role of BMP, but by inhibiting these pathways, we can enhance the proportion of totipotent cells.
Article
Immunology
Judith Wienke, Saskia R. Veldkamp, Eva M. Struijf, Fjodor A. Yousef A. Yengej, M. Marlot van der Wal, Annet van Royen-Kerkhof, Femke van Wijk
Summary: This study found that activated endothelial cells can induce sustained CD69 expression, increased cytokine response, and a phenotypic profile reminiscent of tissue-resident memory T cells (TRM) in T cells. The interaction with activated endothelial cells during transmigration plays an important role in the differentiation and residency of TRM cells.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Nanoscience & Nanotechnology
Jun Zha, Xiangfu Meng, Wentao Fan, Qing You, Nan Xia, Wanmiao Gu, Yan Zhao, Lin Hu, Jin Li, Haiteng Deng, Hui Wang, Nan Yan, Zhikun Wu
Summary: In this study, surface site specific antigalvanic replacement with remaining composition/structure and surface replacement-dependent selectivity in the electrocatalytic reduction of CO2 was achieved for the first time. Density functional theory calculations explained the catalysis selectivity switch induced by replacing Ag with Cu and the facilitation of C2 production by Cu replacement. Furthermore, CO2 electroreduction to C2 on well-defined metal nanoclusters was reported for the first time in this study.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Biochemistry & Molecular Biology
Xiao Han, Yang Yang, Sujuan Liu, Yanmei Niu, Heng Shao, Li Fu
Summary: Skeletal muscle insulin resistance is closely linked to hyperglycemia and metabolic disorders. Regular exercise can enhance insulin sensitivity in skeletal muscle, and this study aimed to explore the underlying mechanisms. The results showed that SESN3 plays a crucial role in amplifying the beneficial effects of exercise on insulin sensitivity in skeletal muscle and systemic glucose levels. The SESN3/mTORC2/AKT pathway mediated the effects of exercise on skeletal muscle insulin sensitivity.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2023)
Article
Chemistry, Physical
Wentao Fan, Ying Yang, Qing You, Jin Li, Haiteng Deng, Nan Yan, Zhikun Wu
Summary: There are unresolved fundamental issues regarding metal nanoclusters, including the transformation from face-centered cubic (fcc) to hexagonal close-packed (hcp) structures and photoexcitation electron transfer. This study successfully achieved the fcc-to-hcp structure transformation and revealed size and shape-dependent photoexcitation electron transfer for metal nanoclusters. A new thermally induced ligand exchange method was developed to synthesize a rod-shaped hcp Au42(SCH2Ph)32 nanocluster, which exhibited specific absorption and dual emission properties. The findings also suggest a possible structure transformation pathway and predict a novel rod-shaped hcp Au58(SR)40 nanocluster with a larger aspect ratio. Additionally, a kernel-based middle-to-both ends sp <- sp photoexcitation electron transfer mechanism was observed in rod-like gold nanoclusters, indicating the potential for tunable and practical applications.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Biochemistry & Molecular Biology
Adam Frankish, Silvia Carbonell-Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet, Daniel Cerdan-Velez, Fiona Cunningham, Claire Davidson, Sarah Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos Garcia Giron, Jose Manuel Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike Kay, Julien Lagarde, Fergal J. Martin, Laura Martinez Gomez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew Yates, Zahoor Zafrulla, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigo, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek
Summary: GENCODE provides high quality gene and transcript annotation for the human and mouse genomes, supported by experimental data, serving as a reference for genome biology and clinical genomics. The consortium generates data, develops tools and carries out analyses to support the identification and annotation of transcript structures and their function.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Medicine, General & Internal
Yan Li, Hongyan Liu, Shuting Ye, Bumei Zhang, Xiaopei Li, Jiapei Yuan, Yongrui Du, Jianmei Wang, Yang Yang
Summary: Endometriosis is a complex gynecological disorder that affects 6-10% of reproductive-aged women. This study used GWAS summary statistics to examine the causal relationship between coagulation factors and the risk of endometriosis.
Review
Biochemical Research Methods
Xingzhong Zhao, Anyi Yang, Zi-Chao Zhang, Yucheng T. Yang, Xing-Ming Zhao
Summary: Brain imaging genomics is an interdisciplinary field that integrates multimodal medical imaging features and multi-omics data, aiming to bridge the gap between macroscopic brain phenotypes and their molecular characteristics. Recent advances in large-scale imaging and multi-omics datasets have allowed the identification of common genetic variants associated with brain structure and function. Integrative analysis with functional multi-omics data has revealed critical genes, genomic regions, and cell types associated with brain phenotypes. This review highlights the importance of functional genomic datasets in understanding the biological functions of identified genes and cell types, and discusses the challenges and future directions in this field.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Joel Rozowsky, Jiahao Gao, Beatrice Borsari, Yucheng T. Yang, Timur Galeev, Gamze Gursoy, Charles B. Epstein, Kun Xiong, Jinrui Xu, Tianxiao Li, Jason Liu, Keyang Yu, Ana Berthel, Zhanlin Chen, Fabio Navarro, Maxwell S. Sun, James Wright, Justin Chang, Christopher J. F. Cameron, Noam Shoresh, Elizabeth Gaskell, Jorg Drenkow, Jessika Adrian, Sergey Aganezov, Francois Aguet, Gabriela Balderrama-Gutierrez, Samridhi Banskota, Guillermo Barreto Corona, Sora Chee, Surya B. Chhetri, Gabriel Conte Cortez Martins, Cassidy Danyko, Carrie A. Davis, Daniel Farid, Nina P. Farrell, Idan Gabdank, Yoel Gofin, David U. Gorkin, Mengting Gu, Vivian Hecht, Benjamin C. Hitz, Robbyn Issner, Yunzhe Jiang, Melanie Kirsche, Xiangmeng Kong, Bonita R. Lam, Shantao Li, Bian Li, Xiqi Li, Khine Zin Lin, Ruibang Luo, Mark Mackiewicz, Ran Meng, Jill E. Moore, Jonathan Mudge, Nicholas Nelson, Chad Nusbaum, Ioann Popov, Henry E. Pratt, Yunjiang Qiu, Srividya Ramakrishnan, Joe Raymond, Leonidas Salichos, Alexandra Scavelli, Jacob M. Schreiber, Fritz J. Sedlazeck, Lei Hoon See, Rachel M. Sherman, Xu Shi, Minyi Shi, Cricket Alicia Sloan, J. Seth Strattan, Zhen Tan, Forrest Y. Tanaka, Anna Vlasova, Jun Wang, Jonathan Werner, Brian Williams, Min Xu, Chengfei Yan, Lu Yu, Christopher Zaleski, Jing Zhang, Kristin Ardlie, J. Michael Cherry, Eric M. Mendenhall, William S. Noble, Zhiping Weng, Morgan E. Levine, Alexander Dobin, Barbara Wold, Ali Mortazavi, Bing Ren, Jesse Gillis, Richard M. Myers, Michael P. Snyder, Jyoti Choudhary, Aleksandar Milosavljevic, Michael C. Schatz, Bradley E. Bernstein, Roderic Guigo, Thomas R. Gingeras, Mark Gerstein
Summary: Understanding the impact of genetic variants on molecular phenotypes is important in functional genomics. The EN-TEx resource provides 1,635 open-access datasets mapped to diploid genomes, revealing over 1 million allele-specific loci. Deep-learning models can predict allele-specific activity based on local nucleotide-sequence context, emphasizing the importance of transcription-factor-binding motifs sensitive to variants. EN-TEx also shows strong associations between allele-specific and GWAS loci, allowing for the transfer of known eQTLs to difficult-to-profile tissues. Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.
Article
Oncology
Jiapei Yuan, Yang Tong, Xiaochuan Liu, Mulin Jun Li, Qiang Zhang, Yang Yang
Summary: The researchers built a versatile data portal, eaQTLdb, to explore the effects of genetic variants on enhancer activity in different cancer types. They systematically identified genetic variants, known as eaQTLs, that influence enhancer activity and linked them to cancer hallmarks and patients' overall survival. They also identified eaQTLs associated with the infiltration abundance of different immune cell types and examined their colocalization with diseases/traits GWAS signals.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Biochemical Research Methods
Xueying Wang, Chengting Luo, Lina Xu, Yusong Wang, Lv Jun Guo, Yupei Jiao, Haiteng Deng, Xiaohui Liu
Summary: Isotope tracing assisted metabolic analysis is a useful tool to understand metabolic regulation. This study presents a strategy called pseudo-targeted profiling of isotopic metabolomics (PtPIM) to expand the analysis of isotope labeled metabolites. The PtPIM method successfully broadened metabolite coverage in isotope tracing analysis and revealed the effects of rotenone on mitochondrial function.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Biochemistry & Molecular Biology
Zhiwen Zhu, Dongdong Li, Zeran Jia, Wenhao Zhang, Yuling Chen, Ruixue Zhao, Yan-Ping Zhang, Wen-Hong Zhang, Haiteng Deng, Yinqing Li, Wei Li, Shouhong Guang, Guangshuo Ou
Summary: Eukaryotic organisms adapt to environmental fluctuations by altering their epigenomic landscapes and transcriptional programs. Histone H2Bs are globally degraded in Caenorhabditis elegans during starvation, and the mechanisms underlying this degradation involve ubiquitin and ubiquitin-related enzymes. The retention of aberrant nucleosomal H2Bs leads to abnormal gene expression and impacts animal viability. Furthermore, the ubiquitin-proteasome system regulates chromosomal histone turnover in human cells.
Article
Multidisciplinary Sciences
Qian Gong, Yunjing Wang, Linfang He, Fan Huang, Danfeng Zhang, Yan Wang, Xiang Wei, Meng Han, Haiteng Deng, Lan Luo, Feng Cui, Yiguo Hong, Yule Liu
Summary: This study reveals the mechanism of airborne defense (AD) against aphids and viruses. The volatile compound MeSA is perceived by neighboring plants and converted into salicylic acid, which activates a signaling cascade to induce plant anti-aphid immunity and reduce virus transmission. Aphid-transmitted viruses encode proteins that suppress AD, making plants less repellent to aphids and more suitable for aphid survival, infestation, and viral transmission.
Article
Biochemical Research Methods
Shaoke Lou, Mingjun Yang, Tianxiao Li, Weihao Zhao, Hannah Cevasco, Yucheng T. Yang, Mark Gerstein
Summary: By using the statistical modeling approach MLCrosstalk, the researchers identified linkages between SARS-CoV-2, human genes, miRNAs, and microbes. They found certain human genes and microbial species that are linked to SARS-CoV-2. The findings offer potential insights for developing new treatments for COVID-19.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Huaijin Zhang, Yuling Chen, Xiaohui Liu, Haiteng Deng
Summary: This study found that mitochondrial dysfunction, rotenone treatment, elevated Ca2+ levels, and activation of the JNK-STAT3 pathway all contribute to increased resistance of glioblastoma to TMZ. Inhibiting JNK or STAT3 can increase sensitivity to TMZ. Co-administration of TMZ with a JNK or STAT3 inhibitor holds promise as an effective treatment for glioblastoma.
