Review
Oncology
Zihao Wang, Xingyun Wu, Hai-Ning Chen, Kui Wang
Summary: Metastasis is the major cause of cancer death as cancer cells can colonize in distant organs. Metastases reprogram their metabolic states to adapt to new environments, displaying different metabolic properties compared with primary lesions. Amino acid metabolic reprogramming plays a crucial role in cancer metastasis, providing energy supply and maintaining homeostasis. This review summarizes the role of amino acid metabolism in cancer cell colonization in common metastatic organs and discusses the potential of targeting organ-specific metastasis for cancer treatment.
FRONTIERS IN ONCOLOGY
(2023)
Article
Endocrinology & Metabolism
Jing Zhao, Ke Yao, Hua Yu, Ling Zhang, Yuyan Xu, Lang Chen, Zhen Sun, Yuqing Zhu, Cheng Zhang, Yuli Qian, Shuyan Ji, Hongru Pan, Min Zhang, Jie Chen, Cristina Correia, Taylor Weiskittel, Da-Wei Lin, Yuzheng Zhao, Sriram Chandrasekaran, Xudong Fu, Dan Zhang, Heng-Yu Fan, Wei Xie, Hu Li, Zeping Hu, Jin Zhang
Summary: This study reveals the dynamic metabolic remodelling during early mouse embryo development, with two-cell embryos favoring reductive metabolism and blastocysts showing a more oxidative state. There is a reciprocal relationship between alpha-KG and l-2-HG, with different levels in two-cell embryos and blastocysts. The data demonstrate interconnected metabolic, transcriptional, and epigenetic network remodelling, highlighting key metabolites for epigenetic reprogramming.
Review
Immunology
Kara R. Eichelberger, James E. Cassat
Summary: Successful pathogens such as Staphylococcus aureus and Candida albicans exhibit metabolic flexibility to adapt to various host niches. Co-infection of these two microorganisms alters microbial metabolism, enhances virulence, and leads to the formation of polymicrobial biofilms. The metabolic changes induced during co-infection impact interactions with host immune cells, resulting in greater microbial survival and immune evasion.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Luz Marina Sanchez-Mendoza, Carlos Perez-Sanchez, Sandra Rodriguez-Lopez, Chary Lopez-Pedrera, Miguel Calvo-Rubio, Rafael de Cabo, Maria I. Buron, Jose A. Gonzalez-Reyes, Jose M. Villalba
Summary: The study investigates the effect of sex on metabolic adaptations induced by overexpression of CYB5R3 and the modulation of key markers related to mitochondrial function in skeletal muscle. It was found that CYB5R3 overexpression leads to enhanced mitochondrial biogenesis and function, as well as increased mitochondrial abundance in skeletal muscle. These beneficial actions are predominantly observed in females, with differences in NADH levels and the abundance of cytochrome c and DRP-1. The results also show ultrastructural changes in transgenic females, including an increase in the number and size of mitochondria.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Eduardo Larriba, Ana Belen Sanchez-Garcia, Cristina Martinez-Andujar, Alfonso Albacete, Jose Manuel Perez-Perez
Summary: Plants have remarkable regenerative capacity, with tissue-specific metabolic differences and divergent developmental pathways playing important roles in de novo organ formation. Successful regeneration in plants depends on a specific metabolic switch involving the differential regulation of photosynthesis-related gene expression and gluconeogenesis pathway activation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Johan Gustafsson, Mihail Anton, Fariba Roshanzamir, Rebecka Jornsten, Eduard J. Kerkhoven, Jonathan L. Robinson, Jens Nielsen
Summary: Single-cell RNA sequencing combined with genome-scale metabolic models has the potential to unravel metabolism differences across cell types and cell states. This study develops a method for generating cell-type-specific models and evaluates the impact of RNA-Seq normalization methods on model topology. The approach successfully detects unique metabolic profiles and cancer-associated differences.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biotechnology & Applied Microbiology
Alex M. Mawla, Talitha van der Meulen, Mark O. Huising
Summary: Using ATAC-Seq, the chromatin landscape of mouse alpha, beta, and delta cells were compared, revealing that alpha and delta cells are poised, but repressed, from becoming beta cells. Differential chromatin accessibility also showed preferentially enriched distal-intergenic regions in beta cells compared to alpha or delta cells.
Article
Biology
Louise van der Weyden, Victoria Harle, Gemma Turner, Victoria Offord, Vivek Iyer, Alastair Droop, Agnieszka Swiatkowska, Roy Rabbie, Andrew D. Campbell, Owen J. Sansom, Mercedes Pardo, Jyoti S. Choudhary, Ingrid Ferreira, Mark Tullett, Mark J. Arends, Anneliese O. Speak, David J. Adams
Summary: The research identified a cell surface protein, LRRN4CL, through CRISPR technology, showing that its upregulated expression is associated with decreased survival in melanoma patients. This study reveals a potential role for LRRN4CL in melanoma and identifies it as a therapeutic target.
COMMUNICATIONS BIOLOGY
(2021)
Article
Medicine, Research & Experimental
Lin Zhang, Ming Fan, Francesco Napolitano, Xin Gao, Ying Xu, Lihua Li
Summary: Analyzing gene expression profiles between metastatic tumor tissues and control tissues revealed organ-specific metastasis genes and pathways. These genes and pathways interact with the molecular characteristics of cancer cells and target organs, influencing the metastasis process. Understanding organ-specific metastasis genes and pathways may identify potential drug targets and aid in the development of targeted treatment strategies.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Genetics & Heredity
Peter Zeller, Jake Yeung, Helena Vinas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, Alexander van Oudenaarden
Summary: Post-translational histone modifications impact chromatin activity and gene expression. Lineage choice in single cells and the underlying chromatin states remain understudied. Using sortChIC, we map active and repressive histone modifications in mouse bone marrow, revealing cell-type-specific dynamic changes. Lineage choice occurs at the progenitor stage, while chromatin dynamics differentiate differentiation trajectories and lineages in hematopoiesis.
Article
Endocrinology & Metabolism
Maria Andrikopoulou, Sunil K. Panigrahi, Giselle D. Jaconia, Cynthia Gyamfi-Bannerman, Richard M. Smiley, Gabrielle Page-Wilson
Summary: The study revealed that during early pregnancy, there are specific adaptations in the central regulation of energy balance, including reduced transport of leptin into the brain and decreased melanocortin tone favoring increased appetitive drive.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2021)
Article
Biology
Ulrike Lischetti, Aizhan Tastanova, Franziska Singer, Linda Grob, Matteo Carrara, Phil F. F. Cheng, Julia M. Martinez M. Gomez, Federica Sella, Veronika Haunerdinger, Christian Beisel, Mitchell P. Levesque
Summary: CITE-seq technology bridges the gap between RNA and protein in single-cell analysis, but its application to solid biopsies is limited. Applying CITE-seq to clinically relevant solid biopsies is an essential step in single-cell translational studies.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biology
Jonathan M. Monk
Summary: This article analyzes the metabolic diversity and speciation of Escherichia through the construction of genome-scale models. The results indicate that strain-specific metabolic capabilities correspond to different species and nutrient niches. This work marks a first step towards a curated reconstruction of pan-Escherichia metabolism.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Weiwei Luo, Junru Wang, Ying Zhou, Meixia Pang, Xiaomu Yu, Jingou Tong
Summary: This study used RNA sequencing and small RNA sequencing technologies to investigate the molecular mechanism of head development in bighead carp at different stages of development. Six key pathways and 114 candidate genes related to head development were identified. Additionally, 19 key miRNAs that play a role in the development of various tissues and mineralization of the head bone system were also discovered.
Article
Biochemistry & Molecular Biology
Chunqiong Shang, Xuejiao Cao, Tian Tian, Qiandong Hou, Zhuang Wen, Guang Qiao, Xiaopeng Wen
Summary: Flower bud differentiation is essential for the reproductive success of plants. This study used RNA-Seq and nutrient quantification to identify stage-specific genes involved in flower bud differentiation using buds from the Chinese cherry cultivar 'Manaohong'. The sugar metabolism pathways were found to dynamically change during flower bud differentiation. The decrease in the contents of total sugar, soluble sugar, and protein suggests that differentiation is an energy-consuming process. Changes in the contents of D-glucose and sorbitol were consistent with the expression trends of the bglX and SORD genes, respectively, indicating the important role of these substances in the transition from physiological to morphological differentiation. Additionally, the WRKY and SBP gene families, as well as floral meristem identity genes, were significantly differentially expressed during the transition from vegetative to reproductive growth. This study provides evidence of the involvement of sugar metabolism in flower bud differentiation in Chinese cherry and identifies candidate genes for further elucidation of this process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Charles J. David, Yun-Han Huang, Mo Chen, Jie Su, Yilong Zou, Nabeel Bardeesy, Christine A. Iacobuzio-Donahue, Joan Massague
Correction
Cell Biology
Thomas Welte, Ik Sun Kim, Lin Tian, Xia Gao, Hai Wang, June Li, Xue B. Holdman, Jason I. Herschkowitz, Adam Pond, Guorui Xie, Sarah Kurley, Tuan Nguyen, Lan Liao, Lacey E. Dobrolecki, Lan Pang, Qianxing Mo, Dean P. Edwards, Shixia Huang, Li Xin, Jianming Xu, Yi Li, Michael T. Lewis, Tian Wang, Thomas F. Westbrook, Jeffrey M. Rosen, Xiang H. -F. Zhang
NATURE CELL BIOLOGY
(2016)
Article
Cell Biology
Thomas Welte, Ik Sun Kim, Lin Tian, Xia Gao, Hai Wang, June Li, Xue B. Holdman, Jason I. Herschkowitz, Adam Pond, Guorui Xie, Sarah Kurley, Tuan Nguyen, Lan Liao, Lacey E. Dobrolecki, Lan Pang, Qianxing Mo, Dean P. Edwards, Shixia Huang, Li Xin, Jianming Xu, Yi Li, Michael T. Lewis, Tian Wang, Thomas F. Westbrook, Jeffrey M. Rosen, Xiang H. -F. Zhang
NATURE CELL BIOLOGY
(2016)
Article
Multidisciplinary Sciences
Lin Tian, Amit Goldstein, Hai Wang, Hin Ching Lo, Ik Sun Kim, Thomas Welte, Kuanwei Sheng, Lacey E. Dobrolecki, Xiaomei Zhang, Nagireddy P. Utluri, Thuy L. P. Hung, Sendurai A. Mani, Fabio Stossi, Arun Sreekumar, Michael A. Mancini, William K. Decker, Chenghang Zong, Michael T. Lewis, Xiang H. -F. Zhang
Article
Multidisciplinary Sciences
Hai Wang, Lin Tian, Amit Goldstein, Jun Liu, Hin-Ching Lo, Kuanwei Sheng, Thomas Welte, Stephen T. C. Wong, Zbigniew Gugala, Fabio Stossi, Chenghang Zong, Zonghai Li, Michael A. Mancini, Xiang H. -F. Zhang
NATURE COMMUNICATIONS
(2017)
Article
Chemistry, Medicinal
Louis J. Cohen, Sun Han, Yun-Han Huang, Sean F. Brady
ACS INFECTIOUS DISEASES
(2018)
Article
Immunology
Dan Liang, Lin Tian, Ran You, Matthew M. Halpert, Vanaja Konduri, Yunyu C. Baig, Silke Paust, Doyeun Kim, Sunghoon Kim, Fuli Jia, Shixia Huang, Xiang Zhang, Farrah Kheradmand, David B. Corry, Brian E. Gilbert, Jonathan M. Levitt, William K. Decker
FRONTIERS IN IMMUNOLOGY
(2018)
Article
Oncology
Yun-Han Huang, Jing Hu, Fei Chen, Nicolas Lecomte, Harihar Basnet, Charles J. David, Matthew D. Witkin, Peter J. Allen, Steven D. Leach, Travis J. Hollmann, Christine A. Iacobuzio-Donahue, Joan Massague
Article
Multidisciplinary Sciences
Jie Su, Sophie M. Morgani, Charles J. David, Qiong Wang, Ekrem Emrah Er, Yun-Han Huang, Harihar Basnet, Yilong Zou, Weiping Shu, Rajesh K. Soni, Ronald C. Hendrickson, Anna-Katerina Hadjantonakis, Joan Massague
Article
Biochemistry & Molecular Biology
Guowei Gu, Lin Tian, Sarah K. Herzog, Yassine Rechoum, Luca Gelsomino, Meng Gao, Lili Du, Jin-Ah Kim, Derek Dustin, Hin Ching Lo, Amanda R. Beyer, David G. Edwards, Thomas Gonzalez, Anna Tsimelzon, Helen J. Huang, Natalie M. Fernandez, Sandra L. Grimm, Susan G. Hilsenbeck, Dan Liu, Jun Xu, Alyssa Alaniz, Shunqiang Li, Gordon B. Mills, Filip Janku, Ralf Kittler, Xiang H. -F. Zhang, Cristian Coarfa, Charles E. Foulds, W. Fraser Symmans, Sebastiano Ando, Suzanne A. W. Fuqua
Summary: Mutations in the estrogen receptor alpha gene (ESR1) are common in ER-positive metastatic breast cancer, leading to clinical resistance to aromatase inhibitors. Cells with the ESR1 Y537S mutation exhibit enhanced migration and invasion potential, and can become the predominant population in distant metastases. Androgen receptor (AR) levels are increased in mutant models, and AR agonists may play a role in inhibiting estrogen-regulated gene expression and distant metastasis in vivo.
Correction
Biochemistry & Molecular Biology
Guowei Gu, Lin Tian, Sarah K. Herzog, Yassine Rechoum, Luca Gelsomino, Meng Gao, Lili Du, Jin-Ah Kim, Derek Dustin, Hin Ching Lo, Amanda R. Beyer, David G. Edwards, Thomas Gonzalez, Anna Tsimelzon, Helen J. Huang, Natalie M. Fernandez, Sandra L. Grimm, Susan G. Hilsenbeck, Dan Liu, Jun Xu, Alyssa Alaniz, Shunqiang Li, Gordon B. Mills, Filip Janku, Ralf Kittler, Xiang H. -F. Zhang, Cristian Coarfa, Charles E. Foulds, W. Fraser Symmans, Sebastiano Ando, Suzanne A. W. Fuqua
Article
Oncology
Yan-Xing Chen, Zi-Xian Wang, Ying Jin, Qi Zhao, Ze-Xia Liu, Zhi-Xiang Zuo, Huai-Qiang Ju, Chengxu Cui, Jun Yao, Yanqiao Zhang, Mengxia Li, Jifeng Feng, Lin Tian, Xiao-Jun Xia, Hui Feng, Sheng Yao, Feng-Hua Wang, Yu-Hong Li, Feng Wang, Rui-Hua Xu
Summary: Although chemotherapy plus PD-1 blockade has become the standard first-line therapy for advanced esophageal squamous cell carcinoma (ESCC), reliable biomarkers for this regimen are lacking. Through whole-exome sequencing, the study identifies immunogenic features and oncogenic alterations associated with chemo+anti-PD-1 efficacy, and establishes an esophageal cancer genome-based immuno-oncology classification. The classification scheme guides individualized treatment strategies and informs biomarker research for chemo+anti-PD-1 treatment in patients with advanced ESCC.
Article
Oncology
Karuna Ganesh, Harihar Basnet, Yasemin Kaygusuz, Ashley M. Laughney, Lan He, Roshan Sharma, Kevin P. O'Rourke, Vincent P. Reuter, Yun-Han Huang, Mesruh Turkekul, Ekrem Emrah Er, Ignas Masilionis, Katia Manova-Todorova, Martin R. Weiser, Leonard B. Saltz, Julio Garcia-Aguilar, Richard Koche, Scott W. Lowe, Dana Pe'er, Jinru Shia, Joan Massague