The Coronavirus Disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has revealed the virus's ability to induce multi-organ damage, including significant liver injury. The molecular mechanisms of liver dysfunction in COVID-19 patients are explored, focusing on direct viral infection, immune-mediated damage, and the gut–liver axis. SARS-CoV-2 enters liver cells through the Angiotensin-Converting Enzyme 2 (ACE2) and Transmembrane Serine Protease 2 (TMPRSS2) receptors, but alternative pathways, such as CD209/Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin (DC-SIGN) and AXL receptors, can also contribute to viral entry. Additionally, immune responses, particularly the cytokine storm, exacerbate liver inflammation, leading to hepatocyte damage. Pre-existing liver conditions, such as metabolic-associated fatty liver disease (MAFLD), alcohol-related liver disease (ALD), and liver fibrosis, heighten the risk of severe outcomes in COVID-19 patients. Post-COVID-19 liver complications, including fibrosis progression and persistent liver damage, have been reported, with emerging evidence suggesting chronic inflammation, viral persistence, and autoimmune reactions as potential contributors. Furthermore, Drug-Induced Liver Injury (DILI) from COVID-19 treatments remains a concern, highlighting the need for careful management. Consequently, understanding the interplay between SARS-CoV-2 and the liver is critical for improving patient outcomes and developing targeted therapies to mitigate liver-related complications in both acute and Long COVID-19 phases. This article is categorized under:
The immune-oncology-microbiome (IOM) trio highlights the significant role of microbiomes in cancer progression by modulating immune evasion, genomic instability, and inflammation-key hallmarks of cancer. While microbiomes can exert both protective and detrimental effects on tumor development and treatment response, the mechanistic underpinnings-particularly those involving intratumoral microbiomes-remain poorly understood. To elucidate these dynamics, we frame the interplay between cancer, immune cells, and microbiomes through the lens of the Anna Karenina Principle (AKP)-using Leo Tolstoy's aphorism: "All happy families are alike; each unhappy family is unhappy in its own way." In biomedical terms, this translates to: all healthy systems including intratumoral microbiomes are alike, but each dysfunctional system fails in its own way. We hypothesize that either AKP or its inverse (anti-AKP) may govern microbial interactions that influence cancer progression. Analyzing four published cancer tissue microbiome datasets (Nejman 2020, Science), we identified two distinct patterns: AKP-driven increased microbial heterogeneity in lung and ovarian cancers, and anti-AKP-driven decreased heterogeneity in breast and colon cancers. We further propose cancer microbiome therapy (CMT) as an emerging frontier in microbiome-based therapeutics. The CMT may include the following strategies: (i) Restoring a healthy microbiome (including barrier tissue, tumor, blood microbiomes) to enhance immune function through ecosystem engineering; (ii) Developing specific microbial agents (species or their metabolites) to modulate crossroads of cancer immunotherapy; (iii) Engineering microbial agents to suppress cancer-causing microbes (oncomicrobes and complicit) and halt cancer progression; (iv) Reviving historical approaches like Coley's toxin and oncolytic viruses for direct cancer cell targeting. This article is categorized under: Cancer > Genetics/Genomics/Epigenetics Cancer > Computational Models.
The nucleolus, traditionally known for its role in ribosome biogenesis, is now recognized for its broader functions, including cellular stress adaptation and its involvement in various pathological processes, such as ribosomal alterations, viral infections, autoimmune disorders, and age-related diseases. Disruptions in nucleolar function can impair protein synthesis, cellular homeostasis, and immune responses, leading to multisystem disorders and increased susceptibility to neoplasms. This review classifies nucleolus-associated diseases into seven categories: deficiencies in protein synthesis, ribosomal and non-ribosomal alterations, cancer and nucleolar alterations, diseases related to aging and cellular stress, autoimmune diseases, and viral diseases. Understanding the complexity of the nucleolus and its dysfunctions represents a fundamental step toward advancing knowledge of the molecular basis of these pathologies, laying the groundwork for future research addressing its implications in cell biology and the development of human diseases. This article is categorized under: Immune System Diseases > Molecular and Cellular Physiology Neurological Diseases > Molecular and Cellular Physiology.
Molecular research has gradually revealed the biological significance of genetically encoded information and how this information is transmitted and utilized in a cell. The scientific advances of the last few decades have brought about paradigm shifts in the strategies traditionally used to decipher biological information. From unidirectional approaches, we now have multidirectional model-system-based integrated OMICs that aim to describe the pathophysiology of diseases through a combination of genetic, transcriptomic, proteomic, and metabolomic data. Compared to other vertebrate models, zebrafish have a wealth of advantages that make them a powerful tool with a wide range of applications in biomedical research. The high degree of genetic conservation with humans, coupled with the availability of various gene manipulation techniques, has made zebrafish an immensely popular multi-utility genetic toolbox. This review describes the advances in the field of zebrafish-based biomedical research with a focus on its applications in disease modeling, functional omics, toxicology, and pharmacology. This article is categorized under: Cancer > Genetics/Genomics/Epigenetics Infectious Diseases > Molecular and Cellular Physiology Congenital Diseases > Molecular and Cellular Physiology.
Noncanonical proteins, encoded by previously overlooked genomic regions (part of the "dark genome"), are emerging as crucial players in human health and disease, expanding our understanding of the "dark proteome." This review explores their landscape, including proteins derived from long non-coding RNAs, circular RNAs, and alternative open reading frames. Recent advances in ribosome profiling, mass spectrometry, and proteogenomics have unveiled their involvement in critical cellular processes. We examine their roles in cancer, neurological disorders, cardiovascular diseases, and infectious diseases, highlighting their potential as novel biomarkers and therapeutic targets. The review addresses challenges in identifying and characterizing these proteins, particularly recently evolved ones, and discusses implications for drug discovery, including cancer immunotherapy and neoantigen sources. By synthesizing recent findings, we underscore the significance of noncanonical proteins in expanding our understanding of the human genome and proteome, and their promise in developing innovative diagnostic tools and targeted therapies. This overview aims to stimulate further research into this unexplored biological space, potentially revolutionizing approaches to disease treatment and personalized medicine.
