Review
Cell Biology
Ulises Ahumada-Castro, Galdo Bustos, Eduardo Silva-Pavez, Andrea Puebla-Huerta, Alenka Lovy, Cesar Cardenas
Summary: Recent studies have shown that cross-organelle communication plays a significant role in metabolism, with calcium ions playing a crucial role in this process, especially in cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Gunes Parlakgul, Ana Paula Arruda, Song Pang, Erika Cagampan, Nina Min, Ekin Guney, Grace Yankun Lee, Karen Inouye, Harald F. Hess, C. Shan Xu, Gokhan S. Hotamisligil
Summary: This study reveals the complex structural organization of organelles in liver tissue and highlights the significant alterations in obese mice. The functional importance of these structural changes on cellular and systemic metabolism is also demonstrated.
Article
Medicine, General & Internal
Yuanyuan Luo, Shuaishuai Zhou, Tao Xu, Wanling Wu, Pingping Shang, Shuai Wang, Defeng Pan, Dongye Li
Summary: This study investigated the mechanism of SERCA2a-SUMOylation after ischemia/reperfusion injury (I/RI) and found that Senp1 and Senp2 proteins are involved in the regulation. Inhibition of Senp2 expression reversed the decline of SUMOylation and improved cardiac function.
CHINESE MEDICAL JOURNAL
(2023)
Review
Cell Biology
Rossella Venditti, Cathal Wilson, Maria Antonietta De Matteis
Summary: This review focuses on the regulation and physiological roles of membrane contact sites (MCSs) in cells, tissues, and whole organisms. It discusses the dynamic response of MCSs to physiological stimuli, their molecular composition, and how mutations of MCS components related to genetic diseases can provide insights into their physiological relevance.
CURRENT OPINION IN CELL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jinghong Xu, Takuya Hashino, Reiji Tanaka, Koichiro Kawaguchi, Hideki Yoshida, Takao Kataoka
Summary: BCL-RAMBO interacts with GRP75 and mortalin, and mediates apoptosis by activating caspases and cleaving PARP-1.
SCIENTIFIC REPORTS
(2023)
Article
Cell Biology
Ruiyuan Xu, Jianlu Song, Rexiati Ruze, Yuan Chen, Xinpeng Yin, Chengcheng Wang, Yupei Zhao
Summary: This study reveals squalene epoxidase (SQLE) as a novel oncogene that promotes pancreatic cancer (PC) growth by mitigating endoplasmic reticulum stress and activating lipid raft-regulated Src/PI3K/Akt signaling pathway. SQLE facilitates cell proliferation, induces cell cycle progression, and inhibits apoptosis in vitro, while promoting tumor growth in vivo. SQLE inhibitors effectively suppress PC cell proliferation and xenograft tumor growth, highlighting the potential of SQLE as a therapeutic target for PC.
CELL DEATH & DISEASE
(2023)
Article
Multidisciplinary Sciences
Nazmiye Ozkan, Max Koppers, Inge van Soest, Alexandra van Harten, Daphne Jurriens, Nalan Liv, Judith Klumperman, Lukas C. Kapitein, Casper C. Hoogenraad, Ginny G. Farias
Summary: This study demonstrates the role of endoplasmic reticulum (ER) tubules in regulating lysosome localization and function in neurons, by promoting lysosomal fission. These findings suggest that ER - lysosome inter-organelle membrane contact sites play a crucial role in determining lysosomal availability in axons.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Jianhuang Lin, Heng Liu, Takeshi Fukumoto, Joseph Zundell, Qingqing Yan, Chih-Hang Anthony Tang, Shuai Wu, Wei Zhou, Dajiang Guo, Sergey Karakashev, Chih-Chi Andrew Hu, Kavitha Sarma, Andrew Kossenkov, Rugang Zhang
Summary: The arginine methyltransferase CARM1 regulates the IRE1 alpha/XBP1 pathway in the unfolded protein response, affecting the growth of ovarian cancers expressing CARM1. Inhibition of this pathway shows selective sensitivity in CARM1-expressing ovarian cancer cells. Pharmacological inhibition of the IRE1 alpha/XBP1 pathway alone or in combination with immune checkpoint blockade represents a potential therapeutic strategy for CARM1-expressing cancers.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Yaobin Liu, Rukmini Mukherjee, Florian Bonn, Thomas Colby, Ivan Matic, Marius Glogger, Mike Heilemann, Ivan Dikic
Summary: The SidE family of Legionella effectors, particularly SdeA, catalyzes non-canonical phosphoribosyl-linked ubiquitination of host proteins to disrupt Golgi integrity. This disruption prevents Golgi linking proteins GRASP55 and GRASP65 from clustering and forming oligomeric structures on multiple serine residues, impacting the host secretory pathway. The Golgi manipulation strategy by Legionella highlights how the bacterium hijacks the secretory pathway to promote bacterial infection.
CELL DEATH AND DIFFERENTIATION
(2021)
Review
Plant Sciences
Vinicius Martins Silva, Fernando Ferrari Putti, Philip J. White, Andre Rodrigues dos Reis
Summary: Phytate, a phosphorus-containing compound, acts as an anti-nutrient in the digestive tract of humans and monogastric animals, while serving as a crucial phosphorus storage form in seeds. Reducing phytic acid content in plants is beneficial for human diet, but excessively low levels may have negative effects. This study explores the genes encoding enzymes involved in phytic acid synthesis and the distribution of phytate accumulation in different plant families.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Jinxuan Li, Qianqian Xiao, Qianqian Tan, Junpeng Chen, Lingyu Sun, Xiao Chen, Ziyu Chu, Hongxia Wu, Zhenzhao Zhang, Hongmei Li, Xiaomin Zhao, Xiao Zhang
Summary: MORN proteins play a crucial role in the cytoskeletal structure of eukaryotes and are essential for the close arrangement of the endoplasmic reticulum and plasma membrane. Through adjacent protein labeling techniques, we identified a network of interactions involving TgMORN2 and endoplasmic reticulum stress-related proteins. The pathogenicity of the KO-TgMORN2 strain was significantly reduced under tunicamycin-induced ER stress. Overall, TgMORN2 functions in ER stress and provides a basis for further research on the function of MORN proteins in Toxoplasma gondii.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Shi-Zheng Jia, Xin-Wen Xu, Zhong-Hao Zhang, Chen Chen, Yu-Bin Chen, Shao-Ling Huang, Qiong Liu, Peter R. Hoffmann, Guo-Li Song
Summary: Selenoprotein K plays a critical role in regulating intracellular calcium flux, degradation pathways, and response to stress in neurons. Knockout of SELENOK in neurons leads to increased apoptosis, activated cascade pathways, and decreased cognitive ability and increased anxiety in older mice.
Review
Cell Biology
Matthieu Moncan, Katarzyna Mnich, Arnaud Blomme, Aitor Almanza, Afshin Samali, Adrienne M. Gorman
Summary: The endoplasmic reticulum is responsible for protein folding, secretion, Ca2+ storage, and lipid synthesis in eukaryotic cells. Disruption to protein folding or Ca2+ homeostasis in the ER leads to what is known as ER stress, triggering the unfolded protein response pathway. Three ER membrane proteins play a crucial role in this process, sensing the accumulation of unfolded/misfolded proteins and activating an integrated transcriptional program.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2021)
Article
Cell Biology
Xin Wen, Bin Su, Mingming Gao, Jiaqi Chen, Donglei Zhou, Hui You, Nannan Li, Shuaikang Chang, Xiaoyun Cheng, Chunhua Qian, Jingyang Gao, Peng Yang, Shen Qu, Le Bu
Summary: Our study reveals that lipocalin 2 (LCN2) plays a protective role in obese individuals, inhibiting cell apoptosis and improving inflammatory state by repressing endoplasmic reticulum stress, thereby alleviating gastric injury associated with obesity.
CELL DEATH & DISEASE
(2021)
Article
Biochemistry & Molecular Biology
Ravi, Ajay Kumar, Shalmoli Bhattacharyya, Jogender Singh
Summary: Thiol antioxidants can modulate cellular physiology and activate the hypoxia response pathway, possibly through the production of hydrogen sulfide.
Article
Biochemistry & Molecular Biology
Caraline Sepich-Poore, Zhong Zheng, Emily Schmitt, Kailong Wen, Zijie Scott Zhang, Xiao-Long Cui, Qing Dai, Allen C. Zhu, Linda Zhang, Arantxa Sanchez Castillo, Haiyan Tan, Junmin Peng, Xiaoxi Zhuang, Chuan He, Sigrid Nachtergaele
Summary: Ribosomal RNAs (rRNAs) carry various chemical modifications, including m6A, which play important roles in mRNA decoding. We identified the METTL5-TRMT112 methyltransferase complex as responsible for the m6A modification on human 18S rRNA. Loss of METTL5 disrupts gene expression and causes developmental defects in humans and mice.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Cell Biology
Jianhui Li, Mark Hochstrasser
Summary: The proteasome is involved in proteolysis and can be degraded through macroautophagy and microautophagy pathways. AMPK-dependent ESCRT-mediated microautophagy regulates proteasome trafficking and degradation in low-glucose conditions. Aberrant proteasomes are more likely to undergo microautophagy, suggesting that the ESCRT system fine-tunes proteasome quality control in response to low-glucose stress.
JOURNAL OF CELL SCIENCE
(2022)
Article
Neurosciences
Erik C. B. Johnson, E. Kathleen Carter, Eric B. Dammer, Duc M. Duong, Ekaterina S. Gerasimov, Yue Liu, Jiaqi Liu, Ranjita Betarbet, Lingyan Ping, Luming Yin, Geidy E. Serrano, Thomas G. Beach, Junmin Peng, Philip L. De Jager, Vahram Haroutunian, Bin Zhang, Chris Gaiteri, David A. Bennett, Marla Gearing, Thomas S. Wingo, Aliza P. Wingo, James J. Lah, Allan I. Levey, Nicholas T. Seyfried
Summary: This study analyzed the proteomes of over 1,000 brain tissues and identified new protein co-expression modules associated with Alzheimer's disease. These modules were highly conserved across cohorts and brain regions and revealed a proteopathic nature of the disease. The study also found disease-associated modules unique to the proteome, which could serve as potential therapeutic targets and biomarkers for Alzheimer's disease.
NATURE NEUROSCIENCE
(2022)
Article
Microbiology
Guangxin Sun, Mengwen Zhang, Hongli Chen, Mark Hochstrasser
Summary: Wolbachia is a bacterium that can affect the reproduction of arthropod hosts through cytoplasmic incompatibility (CI). Researchers have found that the expression of the CinB gene alone in fruit fly males can cause a decrease in embryo viability, but this sterility can be rescued when the females express the corresponding CinA gene. These findings have important implications for understanding the impact of bacteria and insect control.
Article
Multidisciplinary Sciences
Ling Li, Mingming Niu, Alyssa Erickson, Jie Luo, Kincaid Rowbotham, Kai Guo, He Huang, Yuxin Li, Yi Jiang, Junguk Hur, Chunyu Liu, Junmin Peng, Xusheng Wang
Summary: The integration of genomics and proteomics data (proteogenomics) shows promise in advancing our understanding of human disease. This study presents a pipeline called SMAP for verifying sample identity and ensuring data integrity in proteogenomics research. SMAP infers sample-specific protein-coding variants from mass spectrometry data and aligns proteomic samples with genomic samples using discriminant scores. The results demonstrate that SMAP is an effective tool for sample verification in large-scale MS-based proteogenomics studies.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Xiaojun Sun, Huan Sun, Xian Han, Ping-Chung Chen, Yun Jiao, Zhiping Wu, Xue Zhang, Zhen Wang, Mingming Niu, Kaiwen Yu, Danting Liu, Kaushik Kumar Dey, Ariana Mancieri, Yingxue Fu, Ji-Hoon Cho, Yuxin Li, Suresh Poudel, Tess C. Branon, Alice Y. Ting, Junmin Peng
Summary: Proteome profiling is a powerful tool in biological and biomedical studies. In this study, a proximity labeling strategy using TurboID was presented for single-cell-type proteomics of mouse brain. This approach allows labeling of specific cell-type proteomes without the need for cell isolation and includes steps for protein purification and quantitative analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Seong Su Kang, Lanxia Meng, Xingyu Zhang, Zhiping Wu, Ariana Mancieri, Boer Xie, Xia Liu, David Weinshenker, Junmin Peng, Zhentao Zhang, Keqiang Ye
Summary: DOPEGAL, a metabolite of norepinephrine, covalently modifies tau and accelerates its aggregation and propagation, leading to cognitive deficits in Alzheimer's disease. The selective vulnerability of noradrenergic locus ceruleus (LC) neurons in AD may be explained by oxidation of norepinephrine via monoamine oxidase A (MAO-A) into DOPEGAL, which modifies tau and facilitates its aggregation, toxicity, and propagation.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Monicah N. Bwayi, Efren Garcia-Maldonado, Sergio C. Chai, Boer Xie, Shirish Chodankar, Andrew D. Huber, Jing Wu, Kavya Annu, William C. Wright, Hyeong-Min Lee, Jayaraman Seetharaman, Jingheng Wang, Cameron D. Buchman, Junmin Peng, Taosheng Chen
Summary: The interactions between nuclear receptors can fundamentally change our understanding of their biology. In this study, the molecular basis of crosstalk between the pregnane X receptor (PXR) and constitutive androstane receptor (CAR) is revealed, demonstrating the formation of a novel heterodimer and mutual inhibition. These findings not only change the perceived functional relationship between PXR and CAR, but also provide new perspectives for elucidating their role and designing approaches to regulate them.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Neurosciences
David Labib, Zhen Wang, Priya Prakash, Matthew Zimmer, Matthew D. Smith, Paul W. Frazel, Lilianne Barbar, Maria L. Sapar, Peter A. Calabresi, Junmin Peng, Shane A. Liddelow, Valentina Fossati
Summary: The study investigated the surface marker profile and proteome of reactive astrocytes induced by proinflammatory factors and proposed several potential markers for this reactive sub-state. Colocalization of these markers with specific cells in post-mortem samples from Alzheimer's disease patients was observed. Proteomic analysis also identified proteins and pathways linked to potential engagement with peripheral immune cells.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Huan Sun, Ka Yang, Xue Zhang, Yingxue Fu, Jay Yarbro, Zhiping Wu, Ping-Chung Chen, Taosheng Chen, Junmin Peng
Summary: Chemoproteomics is a crucial platform for studying the mode of action of compounds. This study presents a pooling strategy to enhance throughput and applies it to a drug library. The findings demonstrate that pooling chemoproteomics screening is an efficient method for dissecting the molecular targets of compound libraries.
Article
Biochemical Research Methods
Huan Sun, Suresh Poudel, David Vanderwall, Dong Geun Lee, Yuxin Li, Junmin Peng
Summary: Tandem mass tag (TMT) mass spectrometry is a popular labeling strategy for protein profiling. In this study, a 29-plex TMT method was developed and validated using pooled samples, demonstrating its ability to correct for noise and restore expected ratio values.
Article
Cell Biology
Shivendra Singh, Ahmed Abu-Zaid, Hongjian Jin, Jie Fang, Qiong Wu, Tingting Wang, Helin Feng, Waise Quarni, Ying Shao, Lily Maxham, Alireza Abdolvahabi, Mi-Kyung Yun, Sivaraja Vaithiyalingam, Haiyan Tan, John Bowling, Victoria Honnell, Brandon Young, Yian Guo, Richa Bajpai, Shondra M. Pruett-Miller, Gerard C. Grosveld, Mark Hatley, Beisi Xu, Yiping Fan, Gang Wu, Eleanor Y. Chen, Taosheng Chen, Peter W. Lewis, Zoran Rankovic, Yimei Li, Andrew J. Murphy, John Easton, Junmin Peng, Xiang Chen, Ruoning Wang, Stephen W. White, Andrew M. Davidoff, Jun Yang
Summary: This study identifies KDM4B as a therapeutic vulnerability for PAX3-FOXO1(+) RMS. Inhibition of KDM4B delays tumor growth and suppresses the expression of core oncogenic transcription factors, causing epigenetic alterations of PAX3-FOXO1-governed superenhancers.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Chemistry, Medicinal
Andrew D. Huber, Yongtao Li, Wenwei Lin, Annalise N. Galbraith, Ashutosh Mishra, Shaina N. Porter, Jing Wu, Rebecca R. Florke Gee, Wei Zhuang, Shondra M. Pruett-Miller, Junmin Peng, Taosheng Chen
Summary: This study describes the discovery of a molecule, SJPYT-195, which can reduce the protein level of PXR by acting as a molecular glue degrader of GSPT1, a translation termination factor. The findings provide insights into the chemical determinants of drug-induced GSPT1 degradation and also present assays and cell models for the discovery of PXR degraders.
ACS MEDICINAL CHEMISTRY LETTERS
(2022)
Article
Biochemical Research Methods
Suresh Poudel, David Vanderwall, Zuo-Fei Yuan, Zhiping Wu, Junmin Peng, Yuxin Li
Summary: A computational pipeline JUMPptm was presented to extract PTMs from unenriched whole proteome. The deep brain proteome of Alzheimer's disease (AD) was analyzed using JUMPptm, revealing dysregulated PTM peptides during AD progression and establishing a valuable pan-PTM profile for AD research.
Meeting Abstract
Biochemistry & Molecular Biology
Junmin Peng
JOURNAL OF NEUROCHEMISTRY
(2022)