Basic Sciences

Introduction Microbial dysbiosis plays a pivotal role in the pathogenesis of ulcerative colitis (UC) and inflammation-associated colorectal cancer. Among emerging pathobionts, Parasutterella excrementihominis has recently gained attention because of its enrichment in patients with UC, although its direct mechanistic contribution to intestinal inflammation and tumorigenesis has remained uncertain.

Problem Statement The pathways through which specific gut bacteria promote chronic mucosal inflammation and colitis-associated colorectal cancer (CAC) are incompletely understood. In particular, the role of bacterial metabolites in triggering pathogenic neutrophil extracellular trap formation (NETosis) and inflammation-driven carcinogenesis has not been clearly defined.

Summary This study identified P. excrementihominis as a potent microbial driver of experimental colitis and CAC progression. Stool analyses confirmed significant enrichment of the bacterium in patients with UC. In murine dextran sulphate sodium colitis and azoxymethane/DSS CAC models, colonisation with P. excrementihominis markedly aggravated intestinal inflammation, enhanced tumour burden and promoted colonic neutrophil infiltration with excessive NET formation. Mechanistic investigations demonstrated that the bacterium altered host carbohydrate metabolism, resulting in increased production of succinic acid and 6-hydroxyhexanoic acid. These metabolites triggered pathogenic NETosis through activation of succinate receptor-1 and GPR84 signalling pathways in lipopolysaccharide-primed neutrophils. Importantly, this process was dependent on Gasdermin D-mediated NETosis, linking microbial metabolic activity directly to inflammatory tissue injury and tumorigenesis. Neutrophil-specific deletion of gasdermin D significantly attenuated metabolite-induced tumour progression, confirming the central pathogenic role of NETosis. The study provides compelling evidence that microbial metabolites can orchestrate immune-mediated colorectal carcinogenesis through neutrophil activation pathways. These findings position P. excrementihominis and its metabolite–NETosis axis as promising therapeutic targets for UC and CAC, with potential implications for microbiome-directed interventions in inflammation-driven colorectal cancer.

Introduction Psychosocial stressors such as loneliness, chronic stress and social disadvantage are increasingly recognized as major contributors to cardiometabolic disease. Natural killer cell activity plays a central role in immune surveillance, inflammation regulation and cardiovascular health, yet the biological pathways linking chronic stress to NK-cell dysfunction remain incompletely understood.

Problem Statement Although cortisol is a key neuroendocrine mediator of chronic stress through activation of the hypothalamic–pituitary–adrenal axis, its relationship with NK-cell dysfunction in humans—particularly in populations exposed to persistent psychosocial adversity—has not been clearly established. The interaction between loneliness, cortisol signalling and innate immune suppression remains poorly characterized.

Summary This translational study explored the relationship between psychosocial stress, cortisol and NK-cell biology in African American women from under-resourced communities who were at elevated cardiovascular risk. Higher plasma cortisol levels were associated with reduced proportions of proliferative NK-cell subsets, and this relationship was strongly modified by loneliness, suggesting that social isolation amplifies cortisol-mediated immune dysregulation. Individuals with moderate-to-high loneliness demonstrated significant inverse associations between cortisol and NK-cell distribution, whereas this pattern was absent in participants with low loneliness scores. Functional analyses further demonstrated that elevated cortisol correlated with impaired NK-cell degranulation and reduced interferon-γ production, indicating compromised cytotoxic immune activity. Mechanistic experiments showed that cortisol directly suppressed NK-cell function in vitro, reducing degranulation and cytokine production while increasing PD-1 surface expression. Importantly, the study identified FABP4 as a potential mediator of this dysfunction, as inhibition of FABP4 restored PD-1 expression and NK-cell cytolytic activity. Transcriptomic profiling further supported suppression of NK-cell cytotoxic pathways in individuals with high cortisol levels. These findings provide important mechanistic insight into how chronic psychosocial stress and loneliness may impair innate immunity and potentially contribute to heightened cardiovascular and cancer risk. The study also highlights potential therapeutic relevance of targeting PD-1 and FABP4 pathways to reverse stress-associated immune dysfunction. Overall, the work establishes loneliness as a biologically relevant modifier of cortisol-driven NK-cell impairment and reinforces the growing concept that adverse social determinants of health exert direct immunometabolic effects.

Introduction Metabolic dysfunction-associated steatotic liver disease affects nearly one-third of the global population and spans a disease spectrum from steatosis to steatohepatitis, fibrosis and cirrhosis. Despite major advances in clinical hepatology, the molecular mechanisms driving transition from simple steatosis to progressive fibrotic liver injury remain incompletely understood.

Problem Statement Existing in vitro liver disease models—including immortalized hepatocyte systems and induced pluripotent stem cell organoids—often fail to fully reproduce the complex metabolic and fibrotic interactions observed in human MASLD. More physiologically relevant human models are needed to better study disease biology and evaluate antifibrotic therapies.

Summary This translational study developed a human di-lineage hepatic spheroid platform combining primary human hepatocytes and hepatic stellate cells in physiologic proportions to model steatotic liver disease and fibrosis. Exposure to free fatty acids and transforming growth factor-β1 successfully induced hallmark features of MASLD and MASH, including intracellular lipid accumulation, increased collagen deposition, impaired ApoB100 secretion and development of a profibrotic secretory profile characterized by reduced matrix metalloproteinases and increased tissue inhibitors of metalloproteinases. Multiomic integration using transcriptomics and proteomics demonstrated strong concordance between gene and protein expression and identified activation of extracellular matrix remodeling and TGFB signaling alongside suppression of metabolic and cholesterol pathways. Importantly, the molecular signatures observed in the spheroids closely mirrored fibrosis-associated gene expression patterns in human liver tissue from the GepLiver database, supporting translational relevance of the model. Key fibrosis-associated markers such as COL1A1, ACTA2, TGFBI and PLOD2 were strongly upregulated, whereas lipid metabolic regulators including APOA2 and FABP1 were suppressed, reflecting simultaneous fibrotic remodeling and metabolic dysfunction. The spheroids also demonstrated pharmacologic responsiveness to resmetirom and obeticholic acid, both of which reduced lipid accumulation and collagen expression, paralleling observations from clinical studies. Although limited by exclusion of additional liver-resident immune and endothelial cell populations, this simplified human primary-cell platform provides a robust and physiologically relevant experimental system for studying MASLD progression, identifying therapeutic targets and evaluating antifibrotic interventions.

Introduction Alzheimer’s disease (AD) is increasingly recognized as a multifactorial disorder driven by complex interactions among genetic susceptibility, metabolic dysfunction, neuroinflammation and environmental exposures. With currently available pharmacotherapies offering only modest disease modification, attention has shifted toward preventive lifestyle-based interventions targeting multiple biological pathways involved in cognitive decline.

Problem Statement Single-domain interventions such as isolated dietary modification or exercise alone may provide limited protection against neurodegeneration. A major challenge in preventive neurology is defining integrated multimodal strategies capable of simultaneously addressing metabolic, inflammatory, vascular and neurodegenerative mechanisms underlying Alzheimer’s disease progression.

Summary This comprehensive review proposes a multidomain framework for Alzheimer’s prevention integrating physical activity, nutrition, intermittent fasting, sleep optimization and gut microbiome modulation. Exercise emerged as a central neuroprotective intervention, with aerobic and resistance training shown to enhance hippocampal neurogenesis, synaptic plasticity and neuronal resilience through activation of BDNF–TrkB signaling and exercise-induced myokines such as IGF-1 and cathepsin B. Dietary approaches including Mediterranean, MIND and ketogenic diets demonstrated potential to reduce oxidative stress, improve mitochondrial efficiency and attenuate amyloid-related neurotoxicity, particularly in metabolically vulnerable APOE4 carriers. Intermittent fasting was highlighted as an additional metabolic intervention capable of promoting ketone utilization, autophagy activation and angiogenesis while simultaneously reshaping gut microbial composition. The review also underscores the growing importance of the gut–brain axis, where microbial metabolites including short-chain fatty acids and tryptophan derivatives may modulate neuroinflammation and neuronal survival. Sleep quality, particularly preservation of slow-wave sleep architecture, was identified as another key determinant of cognitive health through facilitation of glymphatic clearance of amyloid-β and tau proteins. Importantly, the authors emphasize that these interventions likely exert synergistic rather than isolated effects, supporting a precision lifestyle medicine approach for dementia prevention. The review also identifies major research gaps, including optimal intervention intensity, long-term adherence strategies and individualized protocols for genetically high-risk populations.

Introduction Adoptive cellular immunotherapies have transformed cancer treatment, but current strategies generally require ex vivo cell engineering, manufacturing complexity and individualized processing. The ability to selectively reprogram cytotoxic effector CD8 T cells directly in vivo represents a major next frontier in immunotherapy and RNA-based medicine.

Problem Statement Existing lipid nanoparticle (LNP) platforms lack precise targeting specificity for cytotoxic effector T-cell subsets, limiting their ability to selectively manipulate immune responses in vivo. Developing efficient, transient and clinically scalable approaches for targeted CD8 T-cell reprogramming remains a critical unmet challenge in immunotherapy.

Summary This study introduces a highly innovative ligand-directed mRNA-LNP platform capable of selectively targeting CX3CR1-positive cytotoxic effector CD8 T cells in vivo using fractalkine (CX3CL1)-conjugated nanoparticles. By exploiting the natural interaction between fractalkine and the CX3CR1 receptor expressed on effector T cells, the investigators achieved remarkably efficient and selective mRNA delivery in both murine models and nonhuman primates. In mice, fractalkine-conjugated mRNA-LNPs targeted up to 95% of circulating and splenic effector CD8 T cells, enabling successful transient cellular reprogramming. Delivery of IL-2–encoding mRNA induced robust exogenous IL-2 secretion, while CD62L-encoding mRNA restored lymphoid homing receptor expression on differentiated effector cells. Importantly, the platform demonstrated impressive translational potential in rhesus macaques, where nearly all peripheral effector CD8 T cells were successfully targeted and reprogrammed to express human CD62L, including trafficking into lymphoid tissues. The work establishes proof-of-concept that endogenous immune cells can be rapidly modified in vivo without ex vivo manipulation or viral engineering. The transient nature of mRNA expression may also offer important safety advantages compared with permanent genetic modification approaches. Beyond oncology, this platform may have broad applications in infectious disease, vaccine development, autoimmunity and immune modulation. Overall, the study represents a major advance in targeted RNA therapeutics and demonstrates the feasibility of highly selective in vivo immune-cell engineering using receptor ligand–guided mRNA nanoparticle technology.

Introduction Intestinal fibrosis is a major complication of Crohn’s disease, frequently leading to strictures, bowel obstruction and surgery. While fibroblast activation is central to fibrogenesis, the metabolic pathways driving intestinal fibrosis remain poorly understood. Emerging evidence suggests that metabolic reprogramming and non-coding RNAs critically regulate fibrotic responses across multiple organs.

Problem Statement There are currently no effective antifibrotic therapies for Crohn’s disease. The molecular mechanisms linking fibroblast metabolism, extracellular matrix production and intestinal fibrogenesis remain incompletely defined. Identifying metabolic regulators and upstream non-coding RNA pathways could uncover novel biomarkers and therapeutic targets for fibrostenotic Crohn’s disease.

Summary This elegant translational study identifies pentose phosphate pathway (PPP) activation as a metabolic hallmark of fibroblasts in Crohn’s disease–associated intestinal fibrosis. Through integrated metabolomics, single-cell RNA sequencing and spatial transcriptomics, the investigators demonstrated marked upregulation of PPP activity within fibrotic intestinal fibroblasts, particularly involving the xylulokinase (XYLB)-xylulose-5-phosphate (Xu5P) axis. Xu5P promoted extracellular matrix synthesis by epigenetically enhancing collagen gene transcription through increased H3K27 acetylation and reduced H3K27 trimethylation at collagen loci. Mechanistically, the circular RNA circPLCE1 emerged as a critical antifibrotic regulator. CircPLCE1 expression was significantly reduced in strictured Crohn’s disease tissue and inversely correlated with fibrosis severity, bowel wall thickness and magnetic resonance fibrosis markers. Functional studies showed that circPLCE1 directly binds XYLB and competitively suppresses its enzymatic activity. Loss of circPLCE1 restored XYLB function, increased Xu5P accumulation, amplified PPP and glycolytic flux, enhanced NADPH production and accelerated fibrogenesis both in vitro and in vivo. Fibroblast-specific circPLCE1 knockdown aggravated intestinal fibrosis in murine models, whereas circPLCE1 restoration attenuated fibrotic injury. Importantly, inhibition of XYLB reversed the profibrotic metabolic phenotype induced by circPLCE1 loss, confirming XYLB as the critical downstream effector. These findings establish a novel circPLCE1/XYLB/Xu5P metabolic regulatory axis driving intestinal fibrosis in Crohn’s disease and provide compelling mechanistic support for targeting fibroblast metabolism as a future antifibrotic strategy

Introduction Regulatory T cells (Tregs) are central mediators of immune tolerance and immune homeostasis. In cancer, however, these same suppressive functions are frequently exploited by tumors to evade antitumor immunity, making Tregs an increasingly important therapeutic target in modern immuno-oncology.

Problem Statement Although depletion or functional inhibition of Tregs can enhance antitumor immune responses, indiscriminate disruption of Treg biology risks severe immune-related toxicities and systemic autoimmunity. The challenge is therefore to selectively target intratumoral Tregs while preserving peripheral immune tolerance.

Summary This comprehensive review examines the evolving role of Treg-directed therapies in cancer immunotherapy and highlights both the therapeutic promise and biologic complexity of this strategy. Intratumoral Tregs suppress cytotoxic antitumor responses through multiple mechanisms, including IL-10 and TGF-β secretion, IL-2 consumption, metabolic competition, and inhibitory receptor signaling via CTLA-4, TIGIT and related checkpoints. High Treg infiltration is generally associated with poor clinical outcomes across many solid tumors, although prognostic implications vary by tumor type and immune contexture. Advances in single-cell and spatial profiling have demonstrated that tumor-associated Tregs possess distinct transcriptional, metabolic and spatial programs compared with peripheral Tregs, including enrichment of FOXP3+Helios+CCR8+ phenotypes that may serve as biomarkers and therapeutic targets. Current therapeutic approaches fall into three principal categories: direct depletion strategies using antibodies against CD25, CCR4 or CCR8; functional inhibition through checkpoint blockade targeting CTLA-4 or TIGIT; and disruption of metabolic pathways supporting Treg fitness, including PI3K and adenosine signaling. Novel IL-2 variants designed to preferentially modulate effector immune cells while limiting Treg expansion are also under active investigation. Despite encouraging preclinical activity, clinical translation has been complicated by narrow therapeutic windows and high-grade immune toxicities resulting from systemic immune dysregulation. Emerging strategies therefore focus on selectively impairing intratumoral Tregs while sparing systemic immune control, often through combinatorial approaches with PD-1 or PD-L1 blockade. The review emphasizes that deeper understanding of Treg heterogeneity, tissue-specific biology and metabolic dependencies will be essential for developing safer and more effective next-generation cancer immunotherapies.

Introduction Metformin remains the cornerstone first-line therapy for type 2 diabetes mellitus, yet its dominant therapeutic mechanism has remained controversial for decades. While traditional models emphasized hepatic gluconeogenesis suppression, emerging evidence increasingly points toward the intestine as a central therapeutic site of action.

Problem Statement The concentrations required for direct mitochondrial complex I inhibition are generally achieved in the intestine rather than the liver during standard metformin dosing, raising uncertainty regarding the true biologic target responsible for metformin-induced glucose lowering, enhanced intestinal glucose uptake and postprandial glycaemic control.

Summary This landmark study demonstrates that metformin exerts its principal glucose-lowering effects through selective inhibition of mitochondrial complex I within intestinal epithelial cells. Using human metabolomic datasets and genetically engineered mice expressing metformin-resistant yeast NDI1 specifically in intestinal epithelium, the investigators established that intestinal complex I inhibition is essential for multiple hallmark clinical effects of metformin. Mechanistically, metformin transformed the intestine into a high-capacity glucose disposal organ by increasing intestinal glucose uptake, accelerating glycolysis and promoting conversion of glucose into lactate and lactoyl-phenylalanine. Metformin also suppressed citrulline synthesis, a mitochondrial-dependent metabolic process unique to small intestinal epithelium, providing a clinically measurable biomarker of intestinal mitochondrial inhibition. Importantly, resistance to intestinal complex I inhibition markedly attenuated metformin-induced improvements in glucose tolerance, postprandial glycaemia and pyruvate tolerance in both lean and obese mice. The study further demonstrated that metformin’s efficacy depends on repeated acute bolus exposure rather than cumulative chronic metabolic remodeling, supporting the clinical importance of mealtime dosing. Beyond metformin, phenformin and berberine were shown to share the same intestine-specific mitochondrial complex I–dependent mechanism, suggesting a broader therapeutic paradigm centered on gut-restricted mitochondrial modulation. These findings substantially redefine metformin pharmacology by shifting the primary mechanistic focus from hepatic gluconeogenesis toward intestinal mitochondrial bioenergetics and glucose disposal. The work also opens new avenues for development of gut-selective mitochondrial therapeutics aimed at optimizing glycaemic control while minimizing systemic toxicity.

Introduction Post-translational modifications are fundamental regulators of gene expression, chromatin organization and cellular behavior. Dopaminylation, a recently identified modification involving covalent attachment of dopamine to glutamine residues on proteins, has emerged as a novel signaling mechanism, although its biologic functions and substrate landscape remain poorly understood.

Problem Statement The absence of robust methods to comprehensively identify dopaminylated proteins has limited understanding of how dopamine-mediated protein modification influences transcriptional regulation and cancer biology. Whether dopaminylation participates directly in epigenetic control mechanisms and tumor growth regulation has remained largely unknown.

Summary This study introduces a chemoproteomic platform capable of systematically identifying dopaminylated proteins and substantially expands the known dopaminylation landscape. Using an alkyne-functionalized dopamine probe, the investigators identified more than a thousand putative dopaminylated proteins and characterized histone H4 dopaminylation at glutamine 27 as a previously unrecognized epigenetic modification. Functional analyses demonstrated that H4Q27 dopaminylation acts as a transcriptional repressor in neuroblastoma cells by inhibiting binding of the transcription factor CEBPD at the CCND1 promoter, leading to cyclin D1 suppression and reduced cellular proliferation. These findings establish a direct mechanistic link between dopamine-associated protein modification and chromatin-mediated control of tumor growth. Importantly, the work extends the biologic significance of dopamine beyond neurotransmission and suggests that dopaminylation may represent a broader regulatory system influencing transcriptional programs, cell-cycle progression and oncogenesis. The large-scale substrate dataset generated in this study also provides a major resource for future exploration of dopamine-mediated signaling across multiple physiologic and disease contexts. Overall, this research identifies dopaminylation as an emerging epigenetic mechanism with potential implications for cancer biology and future therapeutic targeting.

Introduction The discovery of synthetic lethality between BRCA1/BRCA2 deficiency and PARP inhibition fundamentally transformed cancer therapeutics and became one of the defining advances in modern precision oncology. By selectively targeting DNA repair vulnerabilities in tumor cells, PARP inhibitors established a new paradigm in which inherited or acquired genomic defects could guide highly personalized cancer treatment.

Problem Statement Before the development of PARP inhibitors, targeted cancer therapies largely focused on directly inhibiting activated oncogenic drivers. However, many tumor suppressor gene alterations, including BRCA1 and BRCA2 loss, were considered therapeutically “undruggable.” A major challenge was determining whether vulnerabilities created by defective DNA repair pathways could be exploited therapeutically without excessive toxicity to normal tissues.

Summary This perspective reviews the scientific and clinical evolution of PARP inhibitor synthetic lethality over the past two decades and highlights its transformative impact on oncology. The original observation that PARP inhibition selectively kills BRCA-deficient cells established the first successful therapeutic strategy directly linked to a germline biomarker and fundamentally changed treatment approaches in breast, ovarian, prostate and pancreatic cancers. Beyond improving survival, PARP inhibitors also demonstrated that targeting DNA repair dependency could achieve meaningful efficacy with comparatively favorable tolerability. Importantly, the clinical success of PARP inhibitors extended the role of BRCA testing from hereditary cancer risk assessment to routine therapeutic decision-making, embedding germline genetics into mainstream oncology practice. The article also emphasizes the broader biologic significance of synthetic lethality, showing how functional redundancies within tumor cells create exploitable therapeutic dependencies. This concept has since driven extensive efforts to identify additional synthetic lethal interactions across cancer biology. At the same time, the review acknowledges ongoing challenges, including resistance mechanisms, incomplete biomarker precision and variability in response beyond canonical BRCA-mutated tumors. Overall, the PARP inhibitor story represents a landmark example of translational medicine in which fundamental biologic discovery directly reshaped cancer care and established synthetic lethality as a central framework for future targeted therapy development.