Review
Cell Biology
Chenlu Li, Tiantian Qian, Ruyue He, Chun Wan, Yinghui Liu, Haijia Yu
Summary: Endoplasmic reticulum (ER) forms direct membrane contact sites with the plasma membrane (PM) in eukaryotic cells, playing crucial roles in lipid homeostasis, ion dynamics, and cell signaling through protein-protein or protein-lipid interactions. Distinct tethering factors dynamically regulate the architecture of ER-PM junctions in response to signals, and the physiological roles of these contact sites rely on various regulators acting in diverse cellular processes. This review focuses on proteins at ER-PM contact sites, highlighting recent progress in their mechanisms and physiological roles.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Xinjian Wang, Chengyu Fan, Yanfen Liu, Yan Zou
Summary: The endoplasmic reticulum (ER) and microtubule (MT) network are interconnected and crucial for ER maintenance, MT stability, and various biological processes. ER shaping proteins regulate ER morphology and dynamics, establishing the physical contact structure between ER and MT. Motor proteins and adaptor-linking proteins facilitate bidirectional communication between the two structures. This review summarizes the current understanding of ER-MT interconnection and highlights its importance in maintaining neuronal functions and pathogenesis of neurodegenerative diseases such as Hereditary Spastic Paraplegia (HSP).
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Bowen Wang, Zhiheng Zhao, Michael Xiong, Rui Yan, Ke Xu
Summary: The endoplasmic reticulum (ER) is a versatile organelle with distinct forms of tubules, regulated by Rtn4 and Climp63, that together form a ribbon-like structure of well-defined width.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Vaishali Kumar, Shuvadeep Maity
Summary: Recent studies have highlighted the significance of inter organelle connections in maintaining cellular homeostasis, particularly the specialized physical connection between the endoplasmic reticulum (ER) and mitochondria at the mitochondria-associated ER membrane (MAM). While IRE1alpha and PERK are well-known for their canonical role as ER stress sensors, their potential non-canonical functions at the MAM beyond ER stress signaling have become a focus of current research.
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
Multidisciplinary Sciences
Yun Xiang, Rui Lyu, Junjie Hu
Summary: Membrane curvature is generated by constructing a curved oligomeric scaffold formed by endoplasmic reticulum tubule-forming proteins. The mechanism of curvature generation remains elusive.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Sascha Waidmann, Chloe Beziat, Jonathan Ferreira Da Silva Santos, Elena Feraru, Mugurel I. Feraru, Lin Sun, Seinab Noura, Yohann Boutte, Juergen Kleine-Vehn
Summary: This study reveals a mechanism that integrates multiple external cues into auxin-dependent growth programs in Arabidopsis thaliana. This mechanism involves the regulation of PIN-LIKES (PILS) protein abundance and turnover, which affects nuclear auxin signaling and growth rates, contributing to stress-induced growth adaptation in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Cell Biology
Sonia Sonda, Diana Pendin, Andrea Daga
Summary: The endoplasmic reticulum (ER) is essential for cell function, with its unique membrane architecture playing a critical role. Mutations in ER-shaping proteins have been linked to the neurodegenerative disease hereditary spastic paraplegia (HSP). While some biochemical activities of ER-related HSP proteins have been elucidated, the exact pathological mechanism remains to be determined through further investigation.
Article
Cell Biology
Daniel Crosby, Melissa R. Mikolaj, Sarah B. Nyenhuis, Samantha Bryce, Jenny E. Hinshaw, Tina H. Lee
Summary: ER network formation depends on membrane fusion by the atlastin (ATL) GTPase. Successful reconstitution of fusion activity by the human ATLs has been achieved. The major splice isoforms of ATL1 and ATL2 are found to be autoinhibited to different degrees. Autoinhibition can be relieved by charge reversal of residues in the inhibitory domain, leading to activation of fusion activity. Neurons express an ATL2 splice isoform with full fusion activity due to sequence differences in the inhibitory domain. These findings highlight the importance of autoinhibition and alternate splicing in regulating atlastin-mediated ER fusion.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Cell Biology
Junichi Inaba, Bo Min Kim, Yan Zhao, Andrew M. Jansen, Wei Wei
Summary: Phytoplasma infection disrupts ER homeostasis in tomato plants, leading to abnormal accumulation of ER-resident proteins, disrupted ER network structures, and formation of protein aggregates in the phloem. The ER stress and unfolded protein response (UPR) induced by Phytoplasma infection likely contribute to the host plant's defense mechanisms. Activation of UPR and induction of ER stress decrease phytoplasma titer, while suppression of the ER-resident protein BiP increases phytoplasma titer. Understanding the interactions between phytoplasmas and plant hosts at the subcellular level provides valuable insights for controlling phytoplasma diseases.
Article
Multidisciplinary Sciences
Asako Goto, Shota Sakai, Aya Mizuike, Toshiyuki Yamaji, Kentaro Hanada
Summary: Casein kinase 1 gamma (CK1G) plays a role in regulating cellular functions and has been found to inactivate the ceramide transport protein (CERT) through phosphorylation. In this study, it was discovered that loss of the C-terminal region of CK1G3 led to hyperactivation of the kinase and redistribution within the cell. These findings suggest that CK1Gs are regulated through compartmentalization to access specific intracellular organelles.
Article
Multidisciplinary Sciences
Jonas C. Alvim, Robert M. Bolt, Jing An, Yasuko Kamisugi, Andrew Cuming, Fernanda A. L. Silva-Alvim, Juan O. Concha, Luis L. P. da Silva, Meiyi Hu, Dominique Hirsz, Jurgen Denecke
Summary: In contrast to the current model based on fast recycling of the K/HDEL receptor (ERD2) between the ER and the Golgi apparatus, the authors show evidence that ERD2 is specifically retained in the Golgi apparatus and evades joining its ligands en route to the ER.
NATURE COMMUNICATIONS
(2023)
Review
Endocrinology & Metabolism
Ming Yang, Chongbin Liu, Na Jiang, Yan Liu, Shilu Luo, Chenrui Li, Hao Zhao, Yachun Han, Wei Chen, Li Li, Li Xiao, Lin Sun
Summary: The endoplasmic reticulum (ER) is an active organelle involved in various physiological processes. Recent studies have shown that dysfunction of the ER plays a role in the progression of kidney disease, particularly diabetic nephropathy (DN). This review discusses the function of the ER, the regulation of homeostasis through the unfolded protein response (UPR) and ER-phagy, as well as the impact of abnormal ER homeostasis in renal cells in DN. Additionally, potential therapeutic targets for DN related to maintaining ER homeostasis are also explored.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yonis Bare, Tamas Matusek, Sophie Vriz, Maika S. Deffieu, Pascal P. Therond, Raphael Gaudin
Summary: This study demonstrates that newly-synthesised Sonic Hedgehog (SHH) is trafficked through the classical biosynthetic secretory pathway using TMED10 as a cargo receptor, and Rab6 vesicles for Golgi-to-cell surface trafficking. Depletion of TMED10 delays SHH loading onto ER exit sites (ERES) and impairs SHH release. Additionally, the homologue of TMED10, Baiser, is found to participate in Hedgehog (Hh) secretion and signalling in Drosophila wing imaginal disc model. Therefore, TMED10 plays a crucial role in SHH secretion and its interaction with other proteins affects embryonic development.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Anna Kowalczuk, Krzysztof Marycz, Justyna Kornicka, Sylwia Groborz, Justyna Meissner, Malwina Mularczyk
Summary: In this study, the protective effects of THCV isolated from Cannabis sativa L. against ER stress in adipose-derived mesenchymal stem cells were evaluated. It was found that THCV can prevent subcellular alterations, restore cell functions upon ER stress, and decrease the expression of genes involved in the UPR pathway. These findings suggest that THCV has potential as a therapeutic compound for metabolic diseases associated with ER stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Wooyoung Eric Jang, Ji Hwan Park, Gaeun Park, Geul Bang, Chan Hyun Na, Jin Young Kim, Kwang-Youl Kim, Kwang Pyo Kim, Chan Young Shin, Joon-Yong An, Yong-Seok Lee, Min-Sik Kim
Summary: This study revealed the Cntnap2-dependent molecular networks in ASD through multi-omics analysis. The findings showed that ASD cellular processes were mainly linked to excitatory neurons and exhibited mitochondrial dysfunction, axonal impairment, and synaptic activity.
MOLECULAR PSYCHIATRY
(2023)
Article
Materials Science, Multidisciplinary
R. Raman, Akhilesh Pandey, Sandeep Dalal, Subodh Tyagi, Shiv Kumar
Summary: Polarized Raman spectroscopy is used to determine and validate the crystallographic orientations of Zinc blend crystals. Two crystals of GaAs and ZnTe oriented along (112) are used in the study. Different angles of in-plane rotation and polarization are achieved by fixing the excitation laser polarization and rotating the sample. Raman spectroscopy is used to study crystallographic plane identification by measuring the Raman scattered intensity and fitting it with a transformation matrix relation.
APPLIED PHYSICS A-MATERIALS SCIENCE & PROCESSING
(2023)
Article
Biochemical Research Methods
Nicholas A. Shortreed, Anjali J. Panicker, Kiran K. Mangalaparthi, Jun Zhong, Akhilesh Pandey, Leigh G. Griffiths
Summary: This study optimized a shotgun immunoproteomics approach to improve the quantitative and reproducible identification of antigens, with the potential to facilitate novel antigen identification studies and innovations in various fields.
JOURNAL OF PROTEOMICS
(2023)
Article
Biochemical Research Methods
Ganesh P. Pujari, Kiran K. Mangalaparthi, Benjamin J. Madden, Firdous A. Bhat, M. Cristine Charlesworth, Amy J. French, Gunveen Sachdeva, Eugenio Daviso, Ulrich Thomann, Patrick McCarthy, Sameer Vasantgadkar, Debadeep Bhattacharyya, Akhilesh Pandey
Summary: Lasercapture microdissection (LCM) is essential for proteomic analysis of specific regions from FFPE tissue samples. Automation of sample preparation workflows is still under development. This study presents a simplified and rapid workflow using adaptive focused acoustics (AFA) technology for high-throughput FFPE-based proteomics.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Correction
Neurosciences
Wenhui Qiao, Yixing Chen, Jun Zhong, Benjamin J. Madden, Cristine M. Charlesworth, Yuka A. Martens, Chia-Chen Liu, Joshua Knight, Tadafumi C. Ikezu, Kurti Aishe, Yiyang Zhu, Axel Meneses, Cassandra L. Rosenberg, Lindsey A. Kuchenbecker, Lucy K. Vanmaele, Fuyao Li, Kai Chen, Francis Shue, Maxwell V. Dacquel, John Fryer, Akhilesh Pandey, Na Zhao, Guojun Bu
MOLECULAR NEURODEGENERATION
(2023)
Article
Biochemistry & Molecular Biology
Mithila Sawant, Audrey Wilson, Dhivya Sridaran, Kiran Mahajan, Christopher J. O'Conor, Ian S. Hagemann, Jingqin Luo, Cody Weimholt, Tiandao Li, Juan Carlos Roa, Akhilesh Pandey, Xinyan Wu, Nupam P. Mahajan
Summary: Hormone receptor-positive, HER2-negative advanced breast cancers, which are sensitive to CDK4/6 inhibitors, often develop resistance. However, a study found that the non-receptor tyrosine kinase ACK1 is activated in breast cancer subtypes independent of hormone receptor status. Inhibition of ACK1 resulted in the suppression of cell cycle genes, leading to G2/M arrest and regression of palbociclib-resistant breast tumor growth. ACK1 inhibition also impaired the metastasis of breast cancer cells to the lung.
Article
Clinical Neurology
Neeharika Sriram, Vikram V. Holla, Riyanka Kumari, Nitish Kamble, Jitender Saini, Rohan Mahale, Manjunath Netravathi, Hansashree Padmanabha, Vykuntaraju K. Gowda, Rajani Battu, Akhilesh Pandey, Ravi Yadav, Babylakshmi Muthusamy, Pramod Kumar Pal
Summary: This study aimed to investigate the clinical, radiological, and genetic features of PKAN. The study found that most patients had symptoms before the age of 10, with difficulty walking and dystonia being the most common symptoms. MRI showed hypo intensity signals in the brain. Genetic testing revealed mutations in the PANK2 gene, with 10 novel variants identified.
PARKINSONISM & RELATED DISORDERS
(2023)
Article
Biochemical Research Methods
Hung M. M. Vu, Hazara Begum Mohammad, Thy N. C. Nguyen, Jun Hyung Lee, Yeji Do, Ji-Youn Sung, Seung Hyeun Lee, Min-Sik Kim
Summary: In this study, potential biomarkers for small cell lung cancer (SCLC) were identified through quantitative proteomic analysis of bronchoalveolar lavage fluid (BALF). BALF is an emerging source of biomarkers for lung cancer. CNDP2 and RNPEP were found to be potential markers for SCLC subtypes, and CNDP2 was positively correlated with drug responses. These biomarkers could contribute to the diagnosis and treatment of SCLC.
PROTEOMICS CLINICAL APPLICATIONS
(2023)
Review
Biology
Siheun Lee, Hung M. M. Vu, Jung-Hyun Lee, Heejin Lim, Min-Sik Kim
Summary: Cell-to-cell variation in a population of the same cell type is influenced by stochastic gene and protein expression as well as environmental factors. Understanding this cellular heterogeneity is crucial for studying fundamental biology and complex diseases, and it requires advanced technologies for single-cell molecular profiling. Recent advances in mass spectrometry (MS)-based methods have greatly contributed to this field by enabling the analysis of proteins and metabolites at the single-cell level. This review provides an overview of the latest developments in MS-based single-cell analysis and their applications in biology and medicine.
Article
Biochemical Research Methods
Dong-Gi Mun, Neha S. Joshi, Rohit Budhraja, Gunveen S. Sachdeva, Taewook Kang, Firdous A. Bhat, Husheng Ding, Benjamin J. Madden, Jun Zhong, Akhilesh Pandey
Summary: This study compared the performance of an automated platform, AccelerOme, with manual sample processing. The results demonstrated that the automated platform performs at a level similar to a manual process performed by an expert for TMT-based proteomics. It has the potential to replace manual pipelines and be applied to large-scale TMT-based studies, providing robust results and high sample throughput.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Neurosciences
Paul W. Frazel, David Labib, Theodore Fisher, Ran Brosh, Nicolette Pirianian, Anne Marchildon, Jef D. Boeke, Valentina Fossati, Shane A. Liddelow
Summary: Researchers used single-cell/single-nucleus RNA sequencing to analyze the differentiation of macroglia in the brain and spinal cord. They identified candidate genes involved in glial cell fate specification and observed heterogeneous expression of astrocyte surface markers during differentiation. The researchers also optimized a mouse astrocyte differentiation protocol and explored potential genomic regulatory sites mediating glial differentiation using multi-omic analysis.
NATURE NEUROSCIENCE
(2023)
Article
Public, Environmental & Occupational Health
Varsha Nair, Sneha D. Mallya, Akhilesh Kumar Pandey, Prashant Kumar Singh, Amit Yadav, Muralidhar M. Kulkarni
Summary: The objective of this study was to identify the factors associated with quit attempts among tobacco users in India. The study found significant differences in quit attempt rates across different states, suggesting the need for tailored tobacco control policies for specific groups to increase the utilization of cessation services.
CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH
(2023)
Article
Biotechnology & Applied Microbiology
Neha Joshi, Firdous Bhat, Anikha Bellad, Gajanan Sathe, Anu Jain, Sandip Chavan, Ravi Sirdeshmukh, Akhilesh Pandey
Summary: For precision in clinical oncology practice, the detection of tumor-derived peptides and proteins in urine can provide a noninvasive alternative for diagnosis or screening. In this study, comparative quantitative proteomic profiling of urine samples from gastric cancer patients and healthy controls identified differentially expressed proteins, including known and novel candidates related to gastric cancer progression. Targeted proteomics validation confirmed the abundance changes of selected proteins. Overall, this study provides molecular candidates for biomarker development in gastric cancer and supports the potential of urinary proteomics for noninvasive diagnostics and personalized/precision medicine.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jae Hun Jung, Da-Qing Yang, Hongming Song, Xiangyu Wang, Xinyan Wu, Kwang Pyo Kim, Akhilesh Pandey, Seul Kee Byeon
Summary: Lipids play important roles in health and disease, including cancer. Mutations in the PIK3CA gene, which codes for the PI3K catalytic subunit p110α, are frequently found in cancer cells. We used untargeted lipidomics to analyze changes in lipid profiles in breast cancer cells with these mutations. Our results reveal a potential link between altered lipid profile and carcinogenesis caused by PIK3CA mutations.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Genetics & Heredity
Guojon Olafsson, Max A. B. Haase, Jef D. Boeke
Summary: This study demonstrates that the differences in protein composition from different species may lead to complementation failure during mitosis.
G3-GENES GENOMES GENETICS
(2023)