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Article
Biochemistry & Molecular Biology
Taide Wang et al.
Summary: Amyotrophic lateral sclerosis (ALS) is characterized by selective degeneration of motor neurons in the brain and spinal cord, with recent findings suggesting a role for ferroptosis, an iron-dependent form of regulated cell death, in mediating motor neuron death in ALS. Depletion of the antioxidant enzyme GPX4, a central repressor of ferroptosis, was observed in post-mortem spinal cords of ALS patients and in various ALS mouse models, linking GPX4 depletion and ferroptosis to impaired NRF2 signaling and dysregulation of glutathione synthesis and iron-binding proteins. Overexpression of human GPX4 in ALS mice delayed disease onset, improved locomotor function, and prolonged lifespan, demonstrating the potential for anti-ferroptotic therapeutic strategies for ALS treatment.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Biochemistry & Molecular Biology
Wenqin Luo et al.
Summary: In this study, the ferroptosis-associated patterns of colorectal cancer were characterized through integrative analyses. It was found that ferroptosis is closely related to tumor microenvironment diversity and immune response phenotype, and can serve as potential therapeutic target genes and evaluation indicators for predicting immunotherapy efficacy.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Letter
Oncology
Hengyu Li et al.
Summary: Tumor-associated macrophages (TAMs) promote the activation of hepatic leukemia factor (HLF) in triple-negative breast cancer (TNBC) cells through the secretion of transforming growth factor-beta1 (TGF-beta 1) and subsequently, HLF transactivates gamma-glutamyltransferase 1 (GGT1) to enhance ferroptosis resistance. This process drives TNBC cell proliferation, metastasis, and cisplatin resistance. Additionally, TNBC cells activate the JAK2/STAT3 axis to induce TGF-beta 1 secretion by TAMs, forming a feed-forward circuit. The combination of HLF and GGT1 values can improve the accuracy of TNBC patient prognosis.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yuansheng Zhang et al.
Summary: GEN is an open-access data portal that integrates a vast amount of transcriptomic profiles, including bulk and single-cell RNA sequencing datasets, with abundant gene annotations and online data analysis services. The website also provides opportunities for integrative analysis at both transcriptional and post-transcriptional levels.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Mihaly Varadi et al.
Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Fiona Cunningham et al.
Summary: Ensembl is unique in its flexible infrastructure for access to genomic data and annotation. They have focused on expediting annotation of new assemblies via the Ensembl Rapid Release platform, with the greatest annual number of newly annotated genomes released. They also developed a new method for comparative analyses and annotated non-vertebrate eukaryotes for the first time.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Medical Laboratory Technology
Joseph S. Bednash et al.
Summary: In this study, Syrian golden hamsters infected with SARS-CoV-2 exhibited key features of experimental acute lung injury, supporting their use as a preclinical model for COVID-19 ARDS. The hamsters showed acute infection, viral pneumonia, and systemic illness, but ultimately survived with the clearance of the virus. The model demonstrated histologic evidence of lung injury, increased pulmonary permeability, acute inflammation, and hypoxemia.
TRANSLATIONAL RESEARCH
(2022)
Article
Immunology
Zhiwei Wu et al.
Summary: A 4-FRL signature was identified as a promising biomarker for predicting clinical outcomes and therapeutic responses in colon cancer patients. The signature exhibited a stronger predictive power for survival compared to traditional clinicopathological features. Additionally, the signature was associated with immune landscape, somatic mutation, and drug sensitivity.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, General & Internal
Yu Miao et al.
Summary: This study demonstrated the presence of ferroptosis in osteoarthritis (OA) and identified glutathione peroxidase 4 (GPX4) as a crucial regulator of OA. By downregulating GPX4 expression, the crosstalk between ferroptosis and extracellular matrix degradation pathways influenced the progression of OA.
Article
Oncology
Peng Liao et al.
Summary: T cell-derived interferon gamma (IFN γ) in combination with arachidonic acid (AA) induces immunogenic tumor ferroptosis, serving as a mechanism for CD8(+) T cell-mediated tumor killing. This process involves IFN γ stimulation of ACSL4 and alteration of tumor cell lipid pattern.
Article
Biochemistry & Molecular Biology
Mark A. Greenough et al.
Summary: Presenilin mutations may promote neurodegeneration through derepressing ferroptosis and have implications for the treatment of Alzheimer's disease.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Biochemistry & Molecular Biology
Li Peng et al.
Summary: Extrachromosomal circular DNA (eccDNA) is a type of circular DNA molecule that is separate from chromosomal DNA, and it plays a crucial role in oncogene amplification and tumor progression in various cancers. This study used whole-genome sequencing data and literature curation to identify eccDNA in cancer samples and developed the first integrated database of eccDNA, called eccDNAdb. The database includes a large number of eccDNA and provides gene expression and clinical information, allowing users to explore the biological function and clinical relevance of eccDNA in human cancers.
Review
Biochemistry & Molecular Biology
Zhang-Li Wang et al.
Summary: This review discusses the role of iron dyshomeostasis in Parkinson's disease and the impact of glial cell activation on iron death and neuronal loss. It also explores the effects of iron death on alpha-synuclein aggregation and the potential roles of different types of glial cells in mediating iron death. Additionally, the review examines current clinical trials targeting iron homeostasis in Parkinson's disease.
TRENDS IN MOLECULAR MEDICINE
(2022)
Article
Multidisciplinary Sciences
Samya Van Coillie et al.
Summary: The development of multiorgan dysfunction syndrome (MODS) is the most common cause of death in the intensive care unit (ICU). Catalytic iron is associated with ICU mortality and may induce excessive lipid peroxidation, leading to cellular toxicity and multiorgan dysfunction. Blocking lipid peroxidation with a ferrostatin-analogue can protect mice from injury and death in experimental non-septic MODS.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Jiazheng Zhao et al.
Summary: In this study, we identified CBS, SOCS1 and EGFR as key genes associated with chemoresistance in osteosarcoma. A predictive model was developed and validated to predict the prognosis of patients. These findings have potential research and clinical value.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Brent R. Stockwell
Summary: This review describes the key regulators of ferroptosis and provides an overview of metabolism, ROS biology, and iron biology. Additionally, it highlights the important concepts and unanswered questions in the field of ferroptosis. The future holds promise for further breakthroughs in understanding the mechanisms of ferroptosis and utilizing it for therapeutic purposes.
Article
Multidisciplinary Sciences
Caterina Bartolacci et al.
Summary: Mutant KRAS is associated with poor prognosis in lung cancer and promotes lipid metabolism. This study reveals that fatty acid synthesis is crucial for the viability of mutant KRAS lung cancer cells. Blocking fatty acid synthesis or the Lands cycle promotes ferroptosis, a type of cell death characterized by the accumulation of oxidation-prone phospholipids. Mutant KRAS makes lung cancer cells more reliant on newly synthesized fatty acids.
NATURE COMMUNICATIONS
(2022)
Letter
Biochemistry & Molecular Biology
Yi He et al.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Medicine, Research & Experimental
Ruize Gao et al.
Summary: The study reveals the critical role of YAP/TAZ in suppressing ferroptosis and establishing Sorafenib resistance in hepatocellular carcinoma (HCC). This highlights YAP/TAZ-based rewiring strategies as potential approaches to overcome HCC therapy resistance. The findings provide new insights into improving the efficacy of current therapies in cancer treatment.
EMBO MOLECULAR MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Alex Bateman et al.
Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Clare Pacini et al.
Summary: This study integrates two large CRISPR-Cas9 screens to correct biases, provide greater statistical power, identify additional biomarkers, and improve the detection of common essential genes, enhancing cancer-specific analyses.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Zhimin Tang et al.
Summary: The iron-binding nanoscale Prussian blue analogue CaPB effectively prevents RPE degeneration and subsequent photoreceptor cell degeneration, showing superior therapeutic outcomes in mice upon a single intravitreal injection. The findings suggest that CaPB nanoparticles protect against RPE degradation by inhibiting ferroptotic cell fate, making them promising for future clinical treatment of retinal diseases involving iron-dependent ferroptosis.
Article
Multidisciplinary Sciences
Ali Kishk et al.
Summary: The study uses flux balance analysis to analyze human lung cells infected with SARS-CoV-2, in order to reposition metabolic drugs and drug combinations to inhibit virus replication.
Article
Biochemistry & Molecular Biology
David Sehnal et al.
Summary: Large biomolecular structures are being determined experimentally using established techniques such as crystallography and electron microscopy, with performance requirements for visualization and analysis tools increasing rapidly. The Mol* Viewer is an advanced online web-native 3D visualization tool that allows visualization of complex structures, and is the primary tool used by PDBe and RCSB PDB.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
John Jumper et al.
Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.
Article
Biochemistry & Molecular Biology
Sunghwan Kim et al.
Summary: PubChem, a popular chemical information resource, has made substantial improvements in the past two years by adding data from over 100 new sources, updating its homepage and record pages, introducing new services like the Periodic Table and Pathway pages, and creating a special data collection related to COVID-19 and SARS-CoV-2 in response to the pandemic.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Susan Tweedie et al.
Summary: The HUGO Gene Nomenclature Committee assigns unique symbols and names to human genes, with over 42,000 approved gene symbols in their database. The Vertebrate Gene Nomenclature Committee assigns standardized nomenclature for vertebrate species, expanding to include species like cat, macaque, and pig.
NUCLEIC ACIDS RESEARCH
(2021)
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Biochemistry & Molecular Biology
David P. Nusinow et al.
Article
Biochemistry & Molecular Biology
Lihua Jiang et al.
Article
Mathematical & Computational Biology
Nan Zhou et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2020)
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Multidisciplinary Sciences
Mahmoud Ghandi et al.
Article
Biochemistry & Molecular Biology
David S. Wishart et al.
NUCLEIC ACIDS RESEARCH
(2018)
Article
Orthopedics
K. M. Fisch et al.
OSTEOARTHRITIS AND CARTILAGE
(2018)
Editorial Material
Genetics & Heredity
Barbara E. Stranger et al.
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Biochemical Research Methods
Max Franz et al.
Editorial Material
Medicine, General & Internal
Robert L. Grossman et al.
NEW ENGLAND JOURNAL OF MEDICINE
(2016)
Letter
Biochemical Research Methods
Neville E. Sanjana et al.
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Biotechnology & Applied Microbiology
Michael I. Love et al.
Editorial Material
Genetics & Heredity
John Lonsdale et al.
Letter
Biochemical Research Methods
Jun Li et al.
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Biochemical Research Methods
Mark D. Robinson et al.
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Biochemistry & Molecular Biology
J Moffat et al.
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Multidisciplinary Sciences
A Subramanian et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2005)
