HOTAIR (HOX transcript antisense RNA) is a HOXC-cluster long intervening non-coding RNA (lincRNA) whose cancer relevance is tightly coupled to how its transcription is wired into hormone, hypoxia, inflammatory, and developmental signaling. HOTAIR is known to associate with cancer cell proliferation, motility, tumor invasion, and metastasis. The present mini-review focuses on the regulatory architecture and mechanistic complexity of HOTAIR transcriptional regulation, with emphasis on three organizing principles. First, we consider the impact of promoter choice between a canonical proximal promoter (P1), which supports the 2.2-2.4 kb transcript, and an alternative upstream promoter/TSS (P2), which contributes to context-dependent transcription initiation. Second, we examine the long-distance enhancer-promoter communication between HOTAIR distal enhancer and P1/P2. Third, we summarize the recent epigenetic and epi-transcriptomic mechanisms involved in HOTAIR transcript initiation and elongation. A combination of these events determines isoform-specific transcription to govern cell-type-, context-, and cancer specific modulation of HOTAIR expression that promotes tumor formation and cancer progression. Finally, the review proposes how large-scale RNA datasets, long-read sequencing, and isoform-specific studies can refine our understanding of this versatile lincRNA's regulation.
RAD51 paralogs (RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3) are evolutionarily conserved essential proteins for cell survival and genome maintenance. RAD51 paralogs were originally identified to play a role in homologous recombination-mediated repair of DNA double-strand breaks (DSBs). However, investigations over the last decade have uncovered new roles of RAD51 paralogs beyond DSB repair in replication stress responses, including replication fork progression, fork stability, and its restart. Recent structural studies have not only uncovered the molecular architecture of previously known RAD51 paralog complexes but also identified novel paralog complex assemblies, providing mechanistic insights into their various genome-maintenance functions. Additionally, a role for RAD51 paralogs in resolving R-loops has been identified, and studies with cancer-associated variants suggest that RAD51 paralogs are potential determinants of cancer susceptibility and therapeutic responses. In the present review, we highlight the recently deciphered structures and novel functions of RAD51 paralog complexes and discuss the clinical and therapeutic implications.
Unlike the cornea and tear fluid, glycosylation within the retina remains remarkably underexplored. This review highlights the diverse roles of glycans in retinal development and vision, with a focus on major glycan classes, including glycosphingolipids (GSLs; glycans attached to lipids), N- and O-linked glycans on proteins, glycosaminoglycans (GAGs) on proteoglycans, O-mannosylated proteoglycans, and intracellular O-GlcNAcylation. Together, these components provide a comprehensive framework for understanding glycan-mediated processes in retinal biology. Current knowledge of the retinal glycosylation nanolandscape, primarily derived from lectin binding and anti-glycan antibody studies, is summarised. The review also examines the roles of altered glycosylation in immune regulation and retinal diseases such as retinitis pigmentosa, age-related macular degeneration and diabetic retinopathy. Finally, key gaps in knowledge and priority areas for future research are discussed. The retina remains understudied with regard to the complex patterns of glycosylation. Alterations of these patterns could represent consequences or be driving pathology, given the well-established roles of glycan patterns in development and homeostasis in other tissues.
G protein-coupled receptors (GPCRs) are membrane proteins that act as signal transducers across cell membranes. Class B1 GPCRs, a subset of 15 receptors activated by peptide hormones, are involved in important physiological processes and diseases, making them a popular target for drug development. GPCRs are dynamic proteins and can adopt a myriad of conformational states, allowing them to bind and activate multiple intracellular signal transducers, including G proteins and β-arrestins, though all class B1 GPCRs primarily couple to the stimulatory G protein (Gs). Cryogenic electron microscopy (cryo-EM) structures of all class B1 GPCRs bound to Gs are available and provide meaningful insights into receptor function. However, there is a dearth of structural information on class B1 GPCRs in inactive and intermediate states or bound to other signal transducers, meaning we are currently only afforded a small vista into the conformational landscape these GPCRs sample. As cryo-EM-based 3D reconstructions are heavily dependent on protein stability and conformational homogeneity, currently available structures are largely limited to only those most stable conformations (i.e. Gs complexes). The present review focuses on technical aspects of obtaining class B1 GPCR structures using cryo-EM and new in silico methods that allow insight into unseen GPCR conformations, revealing more structural details of the conformational landscape.
Bacterial metabolism is increasingly recognised as a driver of virulence in pathogens, and this includes the reduction of sulfoxides, which has traditionally been linked to anaerobic energy generation and maintenance of cellular proteins. Sulfoxide reduction is catalysed by two major enzyme groups, the Msr peptide methionine sulfoxide reductases that repair damaged proteins, and several types of mononuclear molybdenum enzymes that either convert small molecular S- and N-oxides or repair damaged proteins. Where these enzymes support virulence, they appear to be regulated by exposure to oxidising stressors such as hypochlorite and are often required for hypochlorite resistance and successful host interactions, either by maintaining the integrity of proteins or repairing damage to nutrient molecules such as amino acids and vitamins. As the virulence-supporting S- and N-oxide reductases retain their original architecture and links to metabolic processes, so that their action often also contributes to cellular redox balancing, energy generation, and access to specific nutrients, all of which support in-host survival.
Inward-rectifying K+ (Kir) channels are ubiquitously present in variety of cells and play an important role in maintaining resting membrane potential and supporting K+ homeostasis. They are an important family of K+ channels that connects cellular metabolism to membrane excitability, and exhibit complex lipid-protein interaction landscape. Dysfunction of Kir channels is, therefore, associated with multi-factorial diseases and are important drug targets. Recent high-resolution structural dynamics and functional studies of several Kir channels have significantly advanced our understanding of the mechanisms of voltage-dependent pore block and channel gating regulation mediated by lipids, and other modulators. In the present minireview, based on recent knowledge derived from prokaryotic and eukaryotic Kir channels, we highlight the binding sites of the channel for various ligands/modulators, and also provide an emerging model focusing on the structural rearrangements associated with the transition of the channel from the closed/deactivated to open/activated conformation during lipid-dependent gating, which should be broadly applicable to all Kir channels.
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II serves as a dynamic platform coordinating transcription and RNA processing. Recent advances in mass spectrometry, structural biology, and sequencing approaches have revealed a far more complex, combinatorial CTD code than previously appreciated. The present review examines the CTD as an integrative signaling hub that translates diverse environmental signals into genomic outputs. We explore the hierarchical transitions between phosphorylation states, highlighting how combinatorial marks rather than isolated modifications shape transcriptional progression and prevent cryptic initiation through cross-talk with the histone code. Special focus is given to the roles of 'enigmatic' marks such as pTyr1 and pThr4, whose functional significance has been complicated by biochemical masking effects and species-specific regulatory nodes. We also discuss emerging evidence that CTD remodeling contributes to stress-responsive transcription, including oxidative stress, heat shock, and DNA damage. Together, these observations support a dynamic model of the CTD in which combinatorial phosphorylation states coordinate transcriptional progression, genome stability, and stress-responsive gene regulation.
Pancreatic cancer, predominantly represented by Pancreatic Ductal Adenocarcinoma (PDAC), is one of the most frequent and deadly types of cancer. In contrast with other types of cancer, for which advances in prevention, early detection, and treatment have contributed to decreasing incidence and mortality, PDAC continues to be rarely diagnosed at early stages of the disease and exhibits a poor prognosis. As a consequence, therapeutic efficacy remains limited, which is reflected in high mortality. Therefore, the development of novel and effective therapeutic strategies against PDAC is urgent. However, a major component limiting therapeutic efficacy is the highly complex PDAC tumor microenvironment (TME), which is composed of cancer-associated fibroblasts, immunosuppressive cells, cancer stem cells, and a dense extracellular matrix, a structural and biochemical scaffold that sustains tumor development and influences several PDAC phenotypes including metabolism, immune infiltration, metastasis, and therapeutic response. The present review focuses on and discusses the key components of the PDAC TME, with particular emphasis on ECM remodeling, stromal components, their impact on tumor progression and therapeutic resistance, and emerging strategies to target these processes.
The plant cell cycle is a highly coordinated and regulated process that integrates endogenous and environmental signals to control cell division, meristem maintenance, and cell fate specification for growth and development. Temperature is a critical environmental signal that regulates the cell cycle to manifest developmental plasticity in Arabidopsis roots and shoots. Arabidopsis plants exhibit either adaptive growth responses or arrested growth, depending on the temperature regime. The temperature-mediated growth dynamics in Arabidopsis involve altered cell-cycle regulation. While plant developmental and physiological responses to temperature have been extensively studied, the integration of temperature signalling cues with cell-cycle dynamics to regulate growth adaptation remains poorly understood. The present review not only compiles existing information on temperature-mediated regulation of cell-cycle dynamics but also provides a perspective on multidisciplinary approaches to investigate cell-cycle dynamics at spatiotemporal resolution in Arabidopsis adaptive growth responses.
Systemic lupus erythematosus develops when autoreactive B cells escape tolerance and enter differentiation pathways that sustain pathogenic autoantibody responses. A defining feature of lupus is the evolving autoantibody repertoire, in which initially focused autoreactivity broadens over time through recruitment of additional self-reactive B cell clones as well as continued mutation and selection of B cells engaged in the response. Here, we review insights from the 564Igi lupus model, in which a defined autoreactive B cell clone creates an autoimmune environment that permits a previously tolerant polyclonal wild-type (WT) B cell repertoire to enter the response. Studies using mixed bone marrow chimera and adoptive transfer approaches show that WT-derived B cells can be recruited into established autoreactive niches, participate in germinal center and extrafollicular pathways, and contribute to epitope-spread autoantibody responses. We discuss how studies in the present model have reframed epitope spreading as a dynamic process of self-reactive B cell evolution, in which otherwise restrained B cells are incorporated into an ongoing autoimmune response and shaped by the niches that support their activation, differentiation, persistence, and diversification.
Despite influenza vaccines being widely available, influenza still causes significant morbidity and mortality annually. Vaccines typically induce humoral-mediated protection against rapidly mutating surface glycoproteins, necessitating that they be updated and administered each year. In contrast, CD8+ T cells, which can control and clear viral infections, can recognise more conserved viral epitopes. Therefore, there is considerable interest in understanding CD8+ T cell responses to influenza virus for the development of future vaccines and therapeutics. Although Alphainfluenzavirus influenzae (FLUAV) and Betainfluenzavirus influenzae (FLUBV) co-circulate in humans and both contribute to seasonal epidemics, there is limited data regarding CD8+ T cell responses to FLUBV. This knowledge gap spans both immunological and molecular insights. In the present review, we summarise the current knowledge of FLUBV-derived CD8+ T cell epitopes at both cellular and molecular levels, in comparison with FLUAV. Collectively, this highlights the limited data available on FLUBV, despite its significant role in human influenza infections.
Myoferlin, a type 2 transmembrane protein in the ferlin family, is traditionally known for its role in membrane fusion during muscle development and repair. Recent research identifies myoferlin as a potential biomarker and a critical driver of cancer progression, particularly in breast cancer and pancreatic ductal adenocarcinoma. While its lack of specificity limits its use as a biomarker, its multifaceted role in cellular membrane dynamics makes it a promising therapeutic target. In cancer cells, myoferlin regulates the recycling and stability of receptor tyrosine kinases, thereby promoting invasion and metastasis. Beyond the plasma membrane, it maintains mitochondrial homeostasis by interacting with the machinery for mitochondrial fusion and calcium exchange at the endoplasmic reticulum-mitochondria interface. Depletion of myoferlin disrupts these processes, leading to mitochondrial fragmentation, reduced ATP production, and iron-dependent cell death. Furthermore, myoferlin influences the tumour microenvironment by regulating pancreatic cancer-associated fibroblasts. It interacts with SEC24 to facilitate the coat protein complex II-mediated transport of the transforming growth factor-beta 1 receptor, driving the desmoplastic reaction and matrix protein deposition. The 'one punch-two hits' strategy-simultaneously targeting the metabolic and signalling pathways of both malignant cells and the stroma-offers a novel therapeutic perspective. The development of small molecules targeting myoferlin's C2 domains confirms its potential to reduce tumour growth and metastatic dissemination.
Histones are critical for the packaging of nuclear DNA and chromatin assembly, which is facilitated by the high abundance of lysine and arginine residues within these proteins. These residues are the site of post-translational modifications, which regulate cellular processes involving DNA, such as transcription, replication, and repair. Histones are also present in the extracellular environment, following their passive release by dying cells or active release by immune cells as extracellular traps. In the extracellular environment, histones are potent antimicrobial agents and play a role in limiting the spread of infection. However, there is strong evidence that extracellular histones are also involved in propagating disease, owing to their damaging reactions with host cells. Histones are cytotoxic and pro-inflammatory and drive coagulation, which has been associated with organ failure and death in both acute and chronic inflammatory diseases. The present review describes the reactivity of histones in the extracellular environment, with a particular focus on how these reactions are influenced by post-translational modifications relevant to physiological and pathological conditions.
Biosensors enable the in situ measurement of metabolites in living systems over time and space. Fully genetically encoded metabolite biosensors (fGEMBs) use fluorescent proteins (FPs) linked to ligand binding domains (LBDs) to transduce the ligand binding event to a measurable change in the fluorescence behavior of the FP. Because these sensors are genetically encoded, they can be expressed in cells using standard protein expression approaches, and the fluorescence changes are quantified using fluorimetry, fluorescence microscopy, and/or flow cytometry. While there are general sensor design principles to follow, an fGEMB must be engineered for each metabolite based on a particular LBD. This development process can be slow, but there are strategies emerging to increase testing throughput and improve structure-guided design. While genetically-encoded FPs remain popular, there are now numerous chemigenetic and nucleic acid-based metabolite sensors (cGEMBs) that incorporate small molecule fluorophores. De novo design of LBDs is rapidly advancing as well, and the field may soon exhibit a shift away from relying on nature's catalog of LBDs. Despite the engineering challenges, the metabolite biosensor field has expanded significantly in recent years to meet the demand for new and better-performing sensors that visualize metabolites within their cellular environments.
Adipose tissue is a key regulator of metabolic homeostasis; however, its dysfunction can lead to complications, including the development of metabolic disease. While mature adipocytes play an important role in this relationship, their size and buoyancy have made characterizing them difficult at the single cell level. Development of single-nuclear RNA sequencing and spatial transcriptomics have allowed for the study of mature adipocytes at unprecedented resolution and have enabled the identification of previously unappreciated subpopulations of adipocytes, some of which are associated with specific adipose depots or metabolic conditions. Here, we review the recent publications in the field and attempt to synthesize the populations identified by individual studies into classes based on their predicted functionality. We also discuss critical gaps in our current understanding of adipocyte subpopulations, including the current dearth of functional characterization of these populations.
Bottom-up membrane reconstitution has become a powerful framework to investigate the physical principles governing membrane organization and function in highly controlled environments. Among the broad range of available model systems, supported lipid bilayers (SLBs) and giant unilamellar vesicles (GUVs) have emerged as particularly versatile platforms compatible with live optical imaging. In the present mini-review, we summarize recent advances in the preparation and application of these micron-scale membrane systems. We discuss how SLBs and GUVs have enabled major insights into membrane-associated protein assembly, membrane curvature sensing and remodeling, permeability, and cytoskeletal organization. We further highlight emerging developments, including suspended membranes, membrane-coacervate interactions, and the use of GUVs as chassis for bottom-up synthetic biology. Finally, we discuss future perspectives for the field, particularly the growing effort in interfacing synthetic membrane systems and living cells, with potential applications in biomedicine.
Early in mammalian development, one of the two X chromosomes in female embryos is largely silenced through X-chromosome inactivation (XCI). Although essential for dosage compensation, XCI is incomplete, with ∼5%-20% of X-linked genes escaping silencing. Escape from XCI represents an important source of sex-biased gene expression and has been increasingly linked to sex differences in development and disease susceptibility. Yet, how a subset of X-linked genes bypass XCI remains poorly understood. Here, we discuss the studies that have revealed the prevalence and variability of XCI escape across genes, tissues, and individuals in both humans and mice. We then summarize current insights into the molecular features and regulatory mechanisms associated with XCI escape, highlighting key questions that remain to be addressed to understand how X-linked gene dosage is regulated and how it contributes to sex-biased biology.
As the spread of antimicrobial resistance outpaces antibiotic discovery and marketing, there is a critical need to revisit approved compounds with untapped potential. Metal-based complexes (metallo-antimicrobials) represent ideal candidates for such efforts due to their pleiotropic effects, which, unlike antibiotics with single protein targets, may have lower resistance potential. With its well-characterised safety profile, nitroxoline, an 8-hydroxyquinoline derivative, is a prominent compound of this kind. Here, we review recent advances in our understanding of nitroxoline's multimodal mode of action, focusing on its disruption of metal homeostasis at the intracellular and extracellular level. We further explore its clinical utility, including its low propensity for resistance development, and its potential for both combinatorial therapy and as an anti-biofilm agent. Although beyond the scope of the present review, we refer to nitroxoline's antifungal effects whenever they represent a relevant comparison with its antibacterial activity. We highlight current knowledge gaps in nitroxoline's mechanism and in vivo activity that should be bridged to accelerate its repurposing, particularly in the treatment of multidrug-resistant and biofilm-associated infections. Several recent reviews have examined nitroxoline from chemical, clinical, and repurposing perspectives [1, 2, 3, 4]. The present work complements these by providing a mechanistic synthesis of nitroxoline's effects in bacteria, linking its multimodal mode of action to the knowledge gaps that should be addressed before clinical repurposing can proceed.
Breast cancer is associated with a highly fibrotic tumour microenvironment, where cancer-associated fibroblasts (CAFs) secrete excessive amounts of extracellular matrix (ECM). Fibrosis and collagen deposition correlate with poor patient survival, indicating that the ECM plays a role in promoting tumorigenesis. The ECM is constantly remodelled through extracellular and intracellular degradation pathways. While protease-dependent extracellular ECM degradation has been well studied, the intracellular degradation pathway is less understood. Here, I will describe the evidence supporting a role for ECM internalisation and lysosomal degradation in promoting breast cancer progression. Both cancer cells and CAFs are reported to uptake ECM components via different ECM receptors. These include TEM8 in fibroblasts, Endo180 in both cancer cells and CAFs, and α2β1 integrin in cancer cells. Importantly, this process has been associated with metabolic reprogramming under nutrient deprivation conditions representative of the breast cancer TME, cancer cell growth in vitro and in vivo, and cancer cell migration and invasion. Therefore, regulators of ECM endocytosis and lysosomal delivery might represent novel potential targets to prevent tumour growth and metastasis in ECM-rich breast cancers.
Amyotrophic lateral sclerosis (ALS) is the most common form of adult-onset motor neuron disease, characterised by the degeneration of upper and lower motor neurons. The cytoplasmic aggregation of TDP-43 (TAR DNA-binding protein 43), an RNA-binding protein, is considered a hallmark of ALS pathology, found in nearly all postmortem cases of ALS. TDP-43 is normally primarily nuclear, where it has a widespread role in gene regulation. Mutations, extrinsic stressors, and alterations in RNA homeostasis in ALS lead to nuclear depletion of TDP-43 and the formation of cytosolic TDP-43 aggregates. This causes multiple downstream effects on neuronal function and degeneration as well as gene expression. TDP-43 is a promising target as a biomarker, as it is found to be elevated in the biofluids of ALS patients, and its cytoplasmic aggregation can also be observed in peripheral tissues; however, methodological variability and technical limitations currently preclude the establishment of TDP-43 as a standalone biomarker. There are also promising therapeutic strategies in development targeting TDP-43 pathology, but a critical challenge that remains is achieving a balance between eliminating toxic aggregates and preserving the essential functions of TDP-43. In summary, with further research, considering TDP-43 pathology in ALS gives hope for finding future novel diagnostics and therapeutics for ALS.
