G protein-coupled receptor that binds melanocyte-stimulating hormones (alpha- and beta-MSH) and corticotropin/ACTH, which are peptide products of the POMC precursor (PubMed:12646665, PubMed:14764818, PubMed:25163632, PubMed:32327598, PubMed:33858992, PubMed:8392067). Functions as a central component of the leptin-melanocortin pathway, which is essential for maintaining energy homeostasis (PubMed:32327598, PubMed:33858992). Upon activation, couples to G(s) protein, stimulating adenylate cyclase and the cAMP-dependent signaling pathway, which promotes anorexogenic signaling in the hypothalamus and contributes to a negative energy balance (PubMed:12588803, PubMed:14764818, PubMed:25163632, PubMed:33858992). Regulates food intake: activation by agonists suppresses appetite, whereas the antagonist Agouti-related protein/AGRP precludes agonist-induced signaling, thereby stimulating appetite (PubMed:9311920, PubMed:29311635). Modulates the firing activity of neurons in paraventricular nucleus (PVN) of the hypothalamus via alpha-MSH and AGRP regulation of inwardly rectifying potassium channel KCNJ13 closure, independently of G(s) signaling (PubMed:32327598). In the PVN, also interacts with opsin 3/OPN3, which couples to G(i/o) proteins to inhibit MC4R-mediated cAMP signaling, thereby promoting food intake (PubMed:39951488). In intestinal epithelial cells, contributes to inhibition of hepatic glucose production via nesfatin-1/NUCB2, leading to increased cAMP levels and glucagon-like peptide 1 (GLP-1) secretion (PubMed:39562740). Interaction with MGRN1 displaces the G(s) protein, further decreasing MC4R signaling activity (PubMed:19737927). Also activated by gamma-MSH, though with low potency (PubMed:8392067)

A phenome-wide association study of CNVs genotyped from genome sequencing read depth in the UK Biobank.

Abstract: We developed a read-depth-based approach that allows accurate and scalable copy-number genotyping from genome sequencing data, including mosaic, recurrent, and multiallelic copy-number variants (CNVs) that are difficult to genotype using other methods. We genotyped each 5-kb segment throughout the genome in the UK Biobank cohort and performed phenome-wide association studies (PheWASs) using 13,215 traits under three different association models, identifying 501 CNVs associated with 1,537 traits. Of these, almost 75% were not found by comparable single-nucleotide variant (SNV)-based PheWASs. We detected signals with multiallelic CNVs, including a coding repeat within MUC1 (mucin 1, cell-surface associated) associated with stomach/duodenal polyps (p = 7.7 × 10-24), copy number of AMY1 (amylase alpha) genes associated with denture use (p = 2.4 × 10-29), and a multiallelic coding CNV within NEB, encoding muscle sarcomere protein, associated with muscle mass (p = 9.7 × 10-24). We also identified intergenic CNVs with effects on traits known to be regulated by nearby genes. For example, carriers of rare non-coding deletions ∼100 kb upstream of MC4R, coding mutations in which are the most common cause of monogenic obesity, were, on average, ∼14 kg heavier than control subjects. In some cases, non-coding CNVs encompassed regulatory elements of the adjacent candidate gene. Using burden tests, we identified an excess of rare damaging non-coding SNVs within some of these regulatory elements associated with the same traits observed in CNV carriers. Our study provides a detailed map of functional CNVs, including complex loci that are recalcitrant to other methods, providing numerous insights into their effects on human traits.

Genetic variability in the leptin-melanocortin pathway and its role in weight loss.

Abstract: Obesity is a multifactorial disease characterized by an excessive and abnormal accumulation of body fat that results from both genetic and environmental factors. In this review, we revisited the literature on the variability of obesity-associated genes and their impact on the effectiveness of obesity treatment interventions. Individuals harboring variants of these genes were found to have either better or worse outcomes after weight loss therapies. The majority of the genetic variants were identified in genes that play a role in the leptin-melanocortin pathway (LEPR, NPY, POMC, MC4R, GHRL, GHSR, GLP-1R, BDNF), which regulates food intake and energy expenditure. Both these processes are key elements for energy homeostasis, therefore relevant for the success/failure of weight loss strategies. Some genetic alterations were found to modulate the outcomes of different weight loss interventions, while others were only linked to the effectiveness of bariatric surgery, according to the studies here included and available. Herein, we revisited the most relevant molecular data, with a primarily focus on human studies, concerning how the genetic background influences the outcomes of weight loss interventions. Our aim is to gather relevant information on the genetic data related to weight loss strategies that can be compelling to guide clinical decisions, setting realistic expectations, and ultimately improving the long-term health conditions of individuals with obesity.

Melanocortin 3 Receptors Do Not Specifically Localize to Primary Cilia in Cultured Human and Rodent Neurons.

Abstract: The melanocortin-3 receptor (MC3R) and the melanocortin-4 receptor (MC4R), both expressed in hypothalamic nuclei, are key downstream effectors of leptin signaling and play important roles in energy homeostasis. While pathogenic variants in the MC4R gene represent the most common cause of monogenic obesity, the clinical significance of MC3R variants is less clear. MC4R localizes to the primary cilium, a sensory organelle present on nearly all human cells. To better understand the pathophysiological mechanisms of MC3R variants, we investigated whether MC3R localizes to the primary cilium and assessed the impact of rare MC3R variants identified in individuals with obesity on ciliary expression. Using human RPE cells, human NGN2-induced iNeurons, and primary mouse hypothalamic neurons, we found that, in contrast to MC4R, neither wild type MC3R nor rare MC3R variants localized specifically to the primary cilium in vitro in any cell type, including hypothalamic neurons. These findings suggest that MC3R and MC4R may utilize distinct signaling pathways or that additional factors, such as accessory proteins, are required for MC3R targeting to primary cilia in vivo. Further studies are needed to clarify the role of MC3R variants in monogenic obesity and their broader implications for human disease.

Cellular signatures of melanocortin pathway genes across the locus coeruleus.

Abstract: Obesity and Alzheimer’s disease (AD) are epidemiologically associated. The locus coeruleus (LC)—the brain’s primary and most significant source of norepinephrine—is one of the earliest sites of neurodegeneration in AD. The LC participates in feeding behavior through connections with the hypothalamus. The cellular composition of the LC has been characterized at single-cell resolution. However, the constituent cellular signatures of genes related to energy homeostasis—such as the melanocortin pathway genes—in the LC are unclear. We performed single-nucleus RNA sequencing and spatial transcriptomics (Visium) in the human LC, and HiPlex RNAscope in the LC of mice. The melanocortin pathway gene MRAP2 was expressed in the majority of DBH neurons across the LC. Mrap2 was also co-expressed with AD-associated genes such as App, Psen1, Psen2, and Sorl1. More than 20% of Dbh neurons in the LC were positive for Mrap2, App, Psen1, and Psen2. Mrap2 is expressed in the central nervous system and modulates the trafficking and signaling of all five G-protein coupled receptors (GPCRs) of the melanocortin receptor family: Mc1r, Mc2r, Mc3r, Mc4r, and Mc5r. In mice, among the melanocortin receptors, Mc5r showed the highest co-expression with Mrap2, accounting for 17.9% of Mrap2-positive cells, followed by Mc2r with 10.9% of Mrap2-positive cells. Mc1r, Mc3r, and Mc4r showed very limited co-expression with Mrap2. Our study reveals that many Mrap2-positive cells do not express any melanocortin receptor genes, warranting future studies into metabolically relevant GPCRs downstream of MRAP2 in the LC. In summary, our study characterizes melanocortin molecular substrates in the human and mouse LC and highlights MRAP2 as a potential link between pathways of energy homeostasis and neurodegeneration. The online version contains supplementary material available at 10.1186/s40478-026-02287-x.

Maternal Nutrition and Hypothalamic Programming of Offspring Metabolic Health.

Abstract: The hypothalamus plays a central role in regulating metabolism by integrating hormonal and nutrient-derived signals to maintain energy homeostasis across the life span. Maternal nutritional status during critical windows of development is a major environmental factor that can permanently alter this regulation. Both maternal overnutrition and undernutrition have been shown to disturb circulating leptin, insulin, and glucagon-like peptide-1 (GLP-1), and to disrupt the normal development of hypothalamic nuclei implicated in energy balance. Experimental and clinical studies indicate that these insults miswire proopiomelanocortin (POMC) and neuropeptide Y/agouti-related peptide (NPY/AgRP) pathways, alter leptin and insulin receptor signaling, trigger neuroinflammation, glial and vascular changes, and are accompanied by enduring epigenetic alterations, including DNA methylation and chromatin remodeling at genes such as Pomc, Npy, Mc4r, Lepr, and Insr. Together, these adaptations establish new set points for appetite, energy expenditure, and glucose regulation, thereby increasing the lifelong risk of obesity and type 2 diabetes in the offspring. In this narrative review, we synthesize evidence from animal models and human studies linking maternal nutrition to hypothalamic programming via leptin, insulin, and GLP-1. We also highlight major gaps, including limited data on GLP-1 in maternal undernutrition, the specific role of individual micronutrients, and the timing and reversibility of hypothalamic programming, to inform future mechanistic, translational, and preventive research.


Key player in the regulation of energy balance and body weight control. Once released into the circulation, has central and peripheral effects by binding LEPR, found in many tissues, which results in the activation of several major signaling pathways (PubMed:15899045, PubMed:17344214, PubMed:19688109). In the hypothalamus, acts as an appetite-regulating factor that induces a decrease in food intake and an increase in energy consumption by inducing anorexinogenic factors and suppressing orexigenic neuropeptides, also regulates bone mass and secretion of hypothalamo-pituitary-adrenal hormones. In the periphery, increases basal metabolism, influences reproductive function, regulates pancreatic beta-cell function and insulin secretion, is pro-angiogenic for endothelial cell and affects innate and adaptive immunity (By similarity) (PubMed:11460888, PubMed:19688109, PubMed:24340098, PubMed:25060689, PubMed:8589726). In the arcuate nucleus of the hypothalamus, activates by depolarization POMC neurons inducing FOS and SOCS3 expression to release anorexigenic peptides and inhibits by hyperpolarization NPY neurons inducing SOCS3 with a consequent reduction on release of orexigenic peptides (By similarity). In addition to its known satiety inducing effect, has a modulatory role in nutrient absorption. In the intestine, reduces glucose absorption by enterocytes by activating PKC and leading to a sequential activation of p38, PI3K and ERK signaling pathways which exerts an inhibitory effect on glucose absorption (PubMed:24340098). Acts as a growth factor on certain tissues, through the activation of different signaling pathways increases expression of genes involved in cell cycle regulation such as CCND1, via JAK2-STAT3 pathway, or VEGFA, via MAPK1/3 and PI3K-AKT1 pathways (By similarity) (PubMed:17344214). May also play an apoptotic role via JAK2-STAT3 pathway and up-regulation of BIRC5 expression (PubMed:18242580). Pro-angiogenic, has mitogenic activity on vascular endothelial cells and plays a role in matrix remodeling by regulating the expression of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) (PubMed:11460888). In innate immunity, modulates the activity and function of neutrophils by increasing chemotaxis and the secretion of oxygen radicals. Increases phagocytosis by macrophages and enhances secretion of pro-inflammatory mediators. Increases cytotoxic ability of NK cells (PubMed:12504075). Plays a pro-inflammatory role, in synergy with IL1B, by inducing NOS2 which promotes the production of IL6, IL8 and Prostaglandin E2, through a signaling pathway that involves JAK2, PI3K, MAP2K1/MEK1 and MAPK14/p38 (PubMed:15899045, PubMed:19688109). In adaptive immunity, promotes the switch of memory T-cells towards T helper-1 cell immune responses (By similarity). Increases CD4(+)CD25(-) T-cell proliferation and reduces autophagy during TCR (T-cell receptor) stimulation, through MTOR signaling pathway activation and BCL2 up-regulation (PubMed:25060689)

Evaluation of Synergic Effects of Molybdenum Disulfide Treatment and Near-Infrared Radiation on Human Mesenchymal Stem Cells.

Abstract: Introduction: Molybdenum disulfide (MoS2), as an anticancer reagent, can absorb near-infrared (NIR) wavelengths in phototherapy. In the present study, the synergic effect of MoS2 (in nanostructure) and NIR radiation on human mesenchymal stem cells (hMSCs) was evaluated via protein-protein interaction (PPI) network analysis. Methods: Gene expression profiles of hMSCs were extracted from the Gene Expression Omnibus (GEO) database and analyzed via PPI network analysis. The validity of findings was assessed via the Kaplan-Meier Plotter. Results: FN1, ACTA2, CCL2, CXCL8, FBN1, and LEP genes were selected as hub genes among 121 recognized differentially expressed genes (DEGs) as the targeted genes by the synergic effects of MoS2 and NIR radiation. Kaplan-Meier Plotter analysis demonstrated that FN1 suppression by MoS2 and NIR radiation can significantly increase the overall survival of patients with gastric cancer, lung cancer, ovarian cancer, and myeloma. Conclusion: In conclusion, findings indicate that the anticancer property of MoS2 is intensified in the condition of NIR radiation. Therefore, MoS2 is a suitable photosensitizer reagent in photodynamic therapy.

Adherence to the EAT-Lancet Diet, plasma proteomics, and risk of venous thromboembolism: a large-scale prospective cohort study.

Abstract: The EAT Lancet diet is increasingly recognized for its simultaneous benefits to human and planetary health. Its key components are known to exert anti-inflammatory and antiplatelet effects; however, the potential association between adherence to the EAT‑Lancet diet and incident venous thromboembolism (VTE), as well as the underlying biological mechanisms, remains unclear. This prospective study involved 201,695 UK Biobank participants who were free of VTE at baseline, and integrated large-scale Olink plasma proteomics to identify diet-related molecular signatures. Adherence to the EAT-Lancet diet was quantified using two validated indices. Cox models were employed to evaluate associations between EAT-Lancet diet, plasma proteins, and incident VTE (including deep vein thrombosis [DVT] and pulmonary embolism [PE]). Mediation analyses quantified the role of plasma proteins. During a median follow-up of 13.77 years, participants in the highest adherence group of the Stubbendorff index showed lower risks of VTE (HR = 0.809, 95% CI: 0.750-0.874), DVT (HR = 0.856, 95% CI: 0.781-0.938), and PE (HR = 0.754, 95% CI: 0.678-0.838). Consistent protective associations were observed with the Knuppel index. Mediation analyses identified 94 shared plasma protein mediators, with mediation proportions ranging from - 4.77% to 8.45% of the association, among which FABP4, LEP, and ENPP6 were the top-ranked mediators. The overall proteomic signature mediated 59.19% (95% CI: 27.02%-92.15%) and 40.10% (95% CI: 14.53%-65.96%) of the associations between the Stubbendorff and Knuppel index and incident VTE, respectively. Higher adherence to the EAT-Lancet diet is significantly associated with a reduced risk of incident VTE, DVT, and PE, with plasma proteins potentially mediating this effect.

Insulin-stimulated glucose uptake is impaired in senescent human adipocytes.

Abstract: Cell senescence, a state of cell cycle arrest induced by intrinsic or extrinsic stress, is linked to aging and aging-associated diseases. Senescence markers are elevated in adipose tissue with age and in obesity. Recently, it was shown that human mature adipocytes can undergo senescence in response to hyperinsulinemia. However, the functional consequences of adipocyte cell senescence remain poorly understood. To study the impact of cellular senescence on human adipocyte function, we induced senescence in differentiated primary human preadipocytes (referred to as human adipocytes) using nutlin-3a, doxorubicin and etoposide. Expression of senescence markers, insulin receptor signaling, response to lipolytic stimuli and insulin mediated glucose uptake were investigated. The senescence-inducing compounds increased expression of senescence markers p21, p53, activity of senescence-associated β-galactosidase (SA-βgal) and secretion of senescence-associated secreted factors (SASP). We showed that insulin-stimulated glucose uptake, but not basal glucose uptake, was significantly reduced in senescent adipocytes. Insulin receptor signaling was largely unaffected, while expression of insulin receptor signaling proteins and especially GLUT4 expression were reduced. Expression of some adipocyte marker genes, including ADIPOQ, LEP, PNPLA2, LIPE and PPARγ2, and secretion of adiponectin were reduced in the senescent adipocytes. In contrast, lipolytic capacity of senescent adipocytes was largely unaffected. Our findings indicate that cellular senescence impairs insulin-stimulated glucose uptake but not lipolytic capacity; changes that may contribute to impaired glucose control and ectopic fat accumulation.

Leptin-dependent fat accumulation triggers autophagy in metabolic dysfunction-associated steatohepatitis model.

Translational gastroenterology and hepatology

Abstract: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a metabolic syndrome characterized by increased fat storage in hepatocytes. In the hepatocytes, autophagy protects against cytotoxic stress and harmful cellular conditions. In the hepatic stellate cells (HSCs), autophagy exerts pro-fibrotic properties and promotes the release of pro-inflammatory metabolites. We investigated the modulation of autophagy as a therapeutic approach for MASLD. Murine liver tissue and human hepatic cells were analyzed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot. Real time fluorescence was performed to monitor the autophagy maturation process. Accumulation of fat was detected by Oil Red O staining. Collagen fibers were detected by picrosirius staining under polarized light. The loss of leptin in obese mice affected by metabolic dysfunction-associated steatohepatitis (MASH) promoted the over-expression of Becn1, Map1lc3b, Sqstm1, Uvrag and Prkaa1_2 and the accumulation of their proteins. The oleic acid caused an accumulation of fat, followed by the reduction of the autophagy proteins and the increase of the P-AMPK-α in LEP-/- HepG2 cells and the maturation of autophagosome vesicles in LEP-/- Hep3B cells. Oleic acid increased the accumulation of fat in human HSCs and the COL1A1 transcript level, but not the collagen I fibers. BECN1 and MAP1LC3B were up-regulated. Instead, all the autophagy proteins were downregulated, but not P-AMPK-α. Instead, the treatment with caffeine prompted neither the transactivation nor the autophagy. Leptin loss contributes to the autophagy process in obese mice. The administration of oleic acid in LEP-/- cells prompted autophagy not only in hepatocyte-like cells but also in human HSCs.

The Influence of Cisplatin on Functionality and Surface Characteristics of Mesenchymal Stromal Cells In Vitro.

International journal of molecular sciences

Abstract: Mesenchymal stromal cells (MSCs) are multipotent and play an important role in regenerative processes such as wound healing. Data on possible changes and functional restrictions of MSCs due to cisplatin chemotherapy, for example, in the treatment of head and neck cancer, diverge. The aim of this study was to evaluate the influence of cisplatin on MSCs with regard to their defining characteristics and their ability to differentiate and to migrate. MSCs from four human donors (a 59-year-old man, a 63-year-old woman, a 70-year-old man, and a 61-year-old man) were cultured in vitro with and without cisplatin for 24 h, and toxic and subcytotoxic concentrations were determined using an MTT. We then examined the surface phenotype markers (flow cytometry), migration (scratch assay), histological differentiation markers (adipo-, chondro-, osteogenic), and the expression of selected line-associated genes in real-time quantitative PCR (RT-qPCR) (LEP, SOX9, RUNX2). These characteristics were evaluated after treatment with different subcytotoxic, clinically relevant doses of cisplatin. Flow cytometry confirmed the presence of MSCs-characteristic surface markers, which remained stable under treatment with subcytotoxic doses of cisplatin. Cisplatin exposure reduced the mRNA abundance of leptin (a marker for adipogenic differentiation) but increased SOX9 mRNA abundance (chondrogenic differentiation). RUNX (osteogenic differentiation) did not change post cisplatin exposure. Histological analysis showed no difference with regard to osteogenic, chondrogenic, and adipogenic differentiation at doses up to 10 μM cisplatin. Cell migration was not restricted by cisplatin exposure under the conditions used here. The characteristics of MSCs were not different to controls post cisplatin exposure. mRNA analysis suggested induced changes by cisplatin, although this effect was not histologically detectable even at high doses. Based on the single-molecule markers used here, indications for an inhibitory effect of cisplatin on adipogenic differentiation and a rather enhancing effect on chondrogenic and osteogenic differentiation may be hypothesized. The process observed here could further aggravate the already serious problem of malnutrition in head and neck cancer patients, for example. Taken together though, our study confirms overall MSCs tolerance towards cisplatin.


Receptor for hormone LEP/leptin (Probable) (PubMed:22405007). On ligand binding, mediates LEP central and peripheral effects through the activation of different signaling pathways such as JAK2/STAT3 and MAPK cascade/FOS. In the hypothalamus, LEP acts as an appetite-regulating factor that induces a decrease in food intake and an increase in energy consumption by inducing anorexinogenic factors and suppressing orexigenic neuropeptides, also regulates bone mass and secretion of hypothalamo-pituitary-adrenal hormones (By similarity) (PubMed:9537324). In the periphery, increases basal metabolism, influences reproductive function, regulates pancreatic beta-cell function and insulin secretion, is pro-angiogenic and affects innate and adaptive immunity (PubMed:12504075, PubMed:25060689, PubMed:8805376). Control of energy homeostasis and melanocortin production (stimulation of POMC and full repression of AgRP transcription) is mediated by STAT3 signaling, whereas distinct signals regulate NPY and the control of fertility, growth and glucose homeostasis. Involved in the regulation of counter-regulatory response to hypoglycemia by inhibiting neurons of the parabrachial nucleus. Has a specific effect on T lymphocyte responses, differentially regulating the proliferation of naive and memory T -ells. Leptin increases Th1 and suppresses Th2 cytokine production (By similarity) May transport LEP across the blood-brain barrier. Binds LEP and mediates LEP endocytosis. Does not induce phosphorylation of and activate STAT3 Antagonizes Isoform A and isoform B-mediated LEP binding and endocytosis

Systemic and Local Adiposity in the Bone Marrow Microenvironment Associated With Improved Prognosis in Hodgkin Lymphoma: Imaging and Molecular Analysis.

Abstract: Excess adiposity has been associated with Hodgkin lymphoma (HL) development, but its implications remain unclear. Bone marrow (BM), a frequent extranodal involvement site, contains both red and fatty yellow marrow. We investigated whether obesity influences HL outcomes and characterized the BM and cytokine profiles. In this retrospective study, HL patients were analyzed to assess the association between obesity with relapse and mortality. Yellow and red marrow composition were evaluated using CT imaging and correlated with HL outcomes. A nested study analyzed cytokines in the interstitial marrow fluid (IMF) and in circulation of HL patients, in comparison to a control group of healthy blood donors. Further, in vitro functional analyses were performed. Overweight/obesity in HL patients was associated with lower rates of BM involvement, disease relapse, and mortality. Moreover, dense yellow marrow was related to increased risk of death. HL subjects had elevated levels of adiponectin in IMF compared to marrow donors, whereas higher insulin, interleukin 8, and osteoprotegerin levels in IMF were associated with shorter time to relapse. At the molecular level in BM, HL patients had overexpression of LEPR and IGFBP3 in adipocytes, while stromal cells overexpressed IGF-axis receptors. In in vitro studies, human recombinant IGF-1 significantly induced the L428 HL cell line proliferation, which when combined with IGFBP-3 modified apoptosis. The current findings suggest that obesity is associated with a lower incidence of BM involvement and mortality in patients with HL. The obesity together with HL mechanistically influences systemic and local BM cytokine production, thereby impacting HL fate.

Leptin Receptor Fibroblasts Are Preferential Contributors to Cardiac Fibrosis.

Abstract: Cardiac fibrosis, a hallmark of heart failure and an unmet clinical need, arises from pathological activation of preexisting cardiac fibroblasts (CFs), but the contribution of CF heterogeneity to this process remains unclear. Murine models were used to lineage trace or deplete a specific sub-population of CFs at baseline and after myocardial infarction. Transcriptional and epigenetic differences between fibroblast subsets were assessed using next-generation sequencing. Conservation in humans was evaluated through single-cell RNA-seq data sets and histological examination. In mice, fibroblasts were the sole cardiac cell type expressing the signaling-capable isoform of the LepR (leptin receptor). LepR+ CFs emerged neonatally, occupied a defined niche in the coronary adventitia, exhibited enhanced hedgehog signaling, and responded to leptin. After myocardial infarction, LepR-Cre+ CFs proliferated more than interstitial CFs, became a predominant fibroblast lineage in the scar, and their genetic ablation reduced fibrosis while improving function. LepR+ CFs were also detected in the human heart, where they were embedded in an adipocyte-rich niche. These findings identify adventitial fibroblasts as key drivers of pathological remodeling and demonstrate that fibroblasts, rather than cardiomyocytes, are the principal responders to leptin in the heart, redefining how this major endocrine pathway influences cardiac remodeling and disease.

Unraveling the Molecular Pathways of Insulin-Producing Cells Derived From Placenta Multipotent Stem Cells via Multi-Omics Analysis.

Abstract: Stem cell-derived insulin-producing cells (Ins-PCs) hold great promise for diabetes treatment. Placenta-derived multipotent stem cells (PMSCs) are considered an ideal source of Ins-PC generation due to their immunomodulatory and differentiation properties. However, the cellular and molecular pathways underlying PMSC differentiation to Ins-PCs have not been fully elucidated. In this study, PMSCs were isolated from human placenta and successfully differentiated into Ins-PCs using miRNA-181a mimics. Differentiated Ins-PCs produced a significant amount of insulin and upregulation of C-peptide, insulin, and MAFA expression, compared to undifferentiated control PMSCs. RNA sequencing and LC-MS/MS were performed to uncover the pathways involved in the Ins-PC differentiation process. RNA sequencing revealed the transcriptional landscape of PMSC-derived Ins-PC differentiation. Pathway analysis identified important pathways involved in the differentiation process, including Notch and Wnt/ß-catenin, and so forth. Proteomics analysis further affirmed the presence of key insulin pathway-related proteins involved in the differentiation of PMSCs into Ins-PCs, including LEPR, STC2, MAP2K2, and so forth. Moreover, integrated transcriptomic and proteomic analyses further highlighted LEPR as a potential key regulator for Ins-PC differentiation. These findings demonstrated the feasibility of generating Ins-PCs from PMSCs and identified potential signaling pathways and regulators underlying Ins-PC differentiation, supporting PMSCs as a promising stem cell source of cell-based therapy for diabetes treatment.


Precursor protein of pituitary hormones that are involved in diverse physiological processes, including the regulation of energy balance, stress response, immune function and skin pigmentation Functions as a ligand for the melanocortin receptors MC1R, MC2R, MC3R and MC5R (PubMed:8396929, PubMed:8463333, PubMed:8636348). Activation of MC1R increases melanogenesis in melanocytes found in the skin and hair (PubMed:9620771). Binding to MC2R stimulates the adrenal glands to secrete cortisol (PubMed:8636348). Contributes to the regulation of energy homeostasis through activation of MC3R (Probable). Involved in the regulation exocrine gland function through MC5R activation (By similarity) Serves as a ligand for the melanocortin receptors MC1R, MC3R, MC4R and MC5R (PubMed:8392067, PubMed:8396929, PubMed:8463333). Activation of MC1R promotes melanogenesis in melanocytes of the skin and hair (PubMed:10403794, PubMed:9620771). Contributes to the regulation of energy homeostasis through activation of MC3R (Probable). Through MC4R activation, functions as an anorexigenic peptide (PubMed:8392067). Promotes immunosuppression and involved in the regulation exocrine gland function through MC5R activation (By similarity) Functions as a ligand for the melanocortin receptors MC1R, MC3R, MC4R and MC5R (PubMed:8396929, PubMed:8463333). Activation of MC1R increases melanogenesis in melanocytes found in the skin and hair (Probable). Contributes to the regulation of energy homeostasis through activation of MC3R (Probable). Through MC4R activation, functions as an anorexigenic peptide (PubMed:8392067). Involved in the regulation exocrine gland function through MC5R activation (By similarity) Functions as a ligand for the melanocortin receptors MC1R, MC3R, MC4R and MC5R (PubMed:8396929, PubMed:8463333). Activation of MC1R increases melanogenesis in melanocytes found in the skin and hair (Probable). Contributes to the regulation of energy homeostasis through activation of MC3R (Probable). Binds to MC4R with low potency (PubMed:8392067). Involved in the regulation exocrine gland function through MC5R activation (By similarity) Endogenous orexigenic opiate Endogenous opiate

Scalable hypothalamic neuron differentiation from human pluripotent stem cells suitable for modeling metabolic disorders.

Abstract: The hypothalamus, composed of multiple nuclei, is essential for maintaining the body's homeostasis. Within the mediobasal hypothalamus, the arcuate nucleus (ARC) contains key neuronal populations, including appetite-suppressing pro-opiomelanocortin (POMC) neurons that regulate energy and glucose balance. Here, we present a chemically defined, scalable method for differentiating human pluripotent stem cells (hPSCs) into hypothalamic neurons enriched for POMC cells, compatible with robotic cell culture platforms for high-throughput use. Neuronal identity was validated by MERFISH single-cell transcriptomics, RNA-Seq, ATAC-Seq, and comparison to human hypothalamus. The method is robust across multiple hPSC lines, showing consistent induction of ventral diencephalon and hypothalamic markers. Derived neurons display metabolic disease-relevant features, including body mass index (BMI)-associated gene enrichment, and ATAC-Seq identifies potential candidate regulatory regions linked to hypothalamic development and metabolic traits. Functional assays reveal neuronal responses to insulin and the GLP-1 receptor agonist Exendin-4, and transcriptional responses to altered glucose conditions. This platform delivers a physiologically relevant model of human hypothalamic neurons that enables deeper mechanistic and therapeutic studies of metabolic disease.

Biomarkers of hypothalamic melanocortin activity in human energy balance.

Abstract: The hypothalamic melanocortin system, comprised of proopiomelanocortin (POMC) and agouti-related protein (AgRP) neurons, regulates energy balance but studies in humans are limited by lack of biomarkers to assess brain melanocortin activity. Previous studies evaluated POMC concentrations in human CSF in relation to BMI and leptin and to weight loss, including pharmacotherapy with lorcaserin which targets POMC neurons, showing that lower baseline POMC predicted a better weight loss response to lorcaserin. We performed a retrospective analysis of baseline CSF POMC levels in 139 healthy weight-stable individuals without diabetes or neurologic disease who participated in previous studies, including a subgroup analysis of 70 subjects spread equally across the BMI spectrum (19.2-57.3) and in 97 subjects with obesity. POMC was measured in CSF and AgRP was measured in CSF and plasma by sensitive 2-site ELISAs. Mean CSF POMC was lower in individuals with elevated versus normal BMI (200 vs. 269 fmol/mL; p = .0003) and strong negative correlations between CSF POMC and both BMI and leptin were found in 70 subjects across the BMI spectrum (p < .0001); this remained significant in all 139 subjects but not in 97 with obesity. The cohort with obesity included some very low CSF POMC levels (bottom 10%) that do not overlap with non-obese subjects. Strong positive correlations were noted between CSF POMC and AgRP in both CSF and plasma in all groups, including the subgroup with obesity, providing evidence that activities of both sets of neurons may be linked independently of leptin and BMI. Importantly CSF POMC levels remained remarkably constant when nine weight-stable subjects were studied twice over several years. In summary, CSF POMC was lower in individuals with elevated BMI and correlated negatively with BMI and leptin across the BMI spectrum but not within a cohort with obesity. However, the cohort with obesity contained subjects with very low CSF POMC levels that may indicate POMC deficiency and predict treatment response to melanocortin agonists. It remains to be determined if alternative biomarkers associated with low CSF POMC can be identified for use in the clinical setting.

Generation and characterization of POMC-tdTomato reporter human pluripotent stem cell lines.

Abstract: Proopiomelanocortin (POMC) is a precursor polypeptide that undergoes extensive, tissue-specific post-translational processing. It is expressed in several tissues, including pituitary gland, hypothalamus, brain stem, and skin. The hypothalamic POMC neurons in the arcuate nucleus are major neuronal populations involved in the regulation of body weight. In these neurons, POMC is processed into several peptides, among them the anorexigenic alpha-melanocyte stimulating hormone. Thus, the POMC neurons in the ARC have been named "satiety" neurons and are highly desirable drug targets. Here, we performed CRISPR/Cas9-mediated insertion of tdTomato reporter at the endogenous POMC locus, enabling direct visualization of POMC expression through tdTomato fluorescence in human pluripotent stem cell (hPSC)-derived hypothalamic neurons. This reporter line enables real-time visualization of POMC neuron differentiation, and selective enrichment of these populations for molecular, functional, and pharmacological studies. This line is readily available as new alternative method (NAM) platform, to support disease modeling and drug discovery in metabolic and neuroendocrine disorders within a human context.


Transcriptional factor that may have pleiotropic effects during embryogenesis and in the adult

Rare variation in non-coding regions with evolutionary signatures contributes to autism spectrum disorder risk.

Abstract: Little is known about the role of non-coding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of non-coding regions: human accelerated regions (HARs), which show signatures of positive selection in humans; experimentally validated neural VISTA enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole-genome analysis of >16,600 samples and >4,900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly contribute, if at all, in simplex family structures. We identified multiple patient variants in HARs near IL1RAPL1 and in VEs near OTX1 and SIM1 and showed that they change enhancer activity. Our results implicate both human-evolved and evolutionarily conserved non-coding regions in ASD risk and suggest potential mechanisms of how regulatory changes can modulate social behavior.

Rare variation in noncoding regions with evolutionary signatures contributes to autism spectrum disorder risk.

medRxiv : the preprint server for health sciences

Abstract: Little is known about the role of noncoding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of noncoding regions: Human Accelerated Regions (HARs), which show signatures of positive selection in humans; experimentally validated neural Vista Enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole genome analysis of >16,600 samples and >4900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly, if at all, in simplex family structures. We identified multiple patient variants in HARs near IL1RAPL1 and in a VE near SIM1 and showed that they change enhancer activity. Our results implicate both human-evolved and evolutionarily conserved noncoding regions in ASD risk and suggest potential mechanisms of how changes in regulatory regions can modulate social behavior.

SUMO-3 promotes the ubiquitin-dependent turnover of TRIM55.

Biochemistry and cell biology = Biochimie et biologie cellulaire

Abstract: Human muscle-specific RING fingers (MURFs) are members of the tripartite motif (TRIM) family of proteins characterized by their C-terminal subgroup one signature domain. MURFs play a role in sarcomere formation and microtubule dynamics. It was previously established that some TRIMs undergo post-translational modification by small ubiquitin-like modifier (SUMO). In this study, we explored the putative SUMOylation of MURF proteins as well as their interactions with SUMO. MURF proteins (TRIM54, TRIM55, and TRIM63) were not found to be SUMOylated. However, TRIM55 turnover by proteasomal and lysosomal degradation was higher upon overexpression of SUMO-3 but not of SUMO-1. Furthermore, it is predicted that TRIM55 contains two potential SUMO-interacting motifs (SIMs). We found that SIM1- and SIM2-mutated TRIM55 were more stable than the wild-type (WT) protein partly due to decreased degradation. Consistently, SIM-mutated TRIM55 was less polyubiquitinated than the WT protein, despite similar monoubiquitination levels. Using IF microscopy, we observed that SIM motifs influenced TRIM55 subcellular localization. In conclusion, our results suggest that SUMO-3 or SUMO-3-modified proteins modulate the localization, stability, and RING ubiquitin ligase activity of TRIM55.

Rare Variant Analysis of Obesity-Associated Genes in Young Adults With Severe Obesity From a Consanguineous Population of Pakistan.

Abstract: Recent advances in genetic analysis have significantly helped in progressively attenuating the heritability gap of obesity and have brought into focus monogenic variants that disrupt the melanocortin signaling. In a previous study, next-generation sequencing revealed a monogenic etiology in ∼50% of the children with severe obesity from a consanguineous population in Pakistan. Here we assess rare variants in obesity-causing genes in young adults with severe obesity from the same region. Genomic DNA from 126 randomly selected young adult obese subjects (BMI 37.2 ± 0.3 kg/m2; age 18.4 ± 0.3 years) was screened by conventional or augmented whole-exome analysis for point mutations and copy number variants (CNVs). Leptin, insulin, and cortisol levels were measured by ELISA. We identified 13 subjects carrying 13 different pathogenic or likely pathogenic variants in LEPR, PCSK1, MC4R, NTRK2, POMC, SH2B1, and SIM1. We also identified for the first time in the human, two homozygous stop-gain mutations in ASNSD1 and IFI16 genes. Inactivation of these genes in mouse models has been shown to result in obesity. Additionally, we describe nine homozygous mutations (seven missense, one stop-gain, and one stop-loss) and four copy-loss CNVs in genes or genomic regions previously linked to obesity-associated traits by genome-wide association studies. Unexpectedly, in contrast to obese children, pathogenic mutations in LEP and LEPR were either absent or rare in this cohort of young adults. High morbidity and mortality risks and social disadvantage of children with LEP or LEPR deficiency may in part explain this difference between the two cohorts.

Clinical Significance of

Abstract: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney tumors, accounting for the majority of deaths from genitourinary cancers. The currently used nomograms for predicting patient outcomes are based on clinical-pathological characteristics only; however, a significant number of ccRCC survivors with similar radiological and histological features still demonstrate a different clinical course of the disease. This study aimed at the identification of novel DNA methylation biomarkers for the monitoring of patients with ccRCC. Gene expression profiling by SurePrint G3 Human GE 8×60K Microarrays was performed in 4 ccRCC tissues and adjacent non-cancerous renal tissue (NRT) samples. Four down-regulated genes were selected for further DNA methylation status analysis in 123 ccRCC and 45 NRT samples using methylation-specific PCR (MSP). DNA methylation changes of ADAMTS19, BMP7, SIM1, and SFRP1 were cancer-specific with significantly (P<0.050) higher methylation frequency (37%, 20%, 18%, and 42%, respectively) in tumor tissues. The methylated status of at least one gene was significantly related to various clinical-pathological parameters, including tumor size, Fuhrman and WHO/ISUP grades, intravascular invasion, and necrosis. Moreover, the methylated status of multimarker panel ADAMTS19, BMP7 & SFRP1 was predictive for poorer overall survival (HR, 4.11; 95% CI, 1.22-13.86). In conclusion, DNA methylation of the three-gene panel consisting of ADAMTS19, BMP7 & SFRP1 supposedly predicts the outcome of patients diagnosed with ccRCC and possibly might be used to enrich the current prognostic tools.


Important signaling molecule that activates signaling cascades downstream of NTRK2 (PubMed:11152678). During development, promotes the survival and differentiation of selected neuronal populations of the peripheral and central nervous systems. Participates in axonal growth, pathfinding and in the modulation of dendritic growth and morphology. Major regulator of synaptic transmission and plasticity at adult synapses in many regions of the CNS. The versatility of BDNF is emphasized by its contribution to a range of adaptive neuronal responses including long-term potentiation (LTP), long-term depression (LTD), certain forms of short-term synaptic plasticity, as well as homeostatic regulation of intrinsic neuronal excitability Important signaling molecule that activates signaling cascades downstream of NTRK2. Activates signaling cascades via the heterodimeric receptor formed by NGFR and SORCS2 (PubMed:24908487, PubMed:29909994). Signaling via NGFR and SORCS2 plays a role in synaptic plasticity and long-term depression (LTD). Binding to NGFR and SORCS2 promotes neuronal apoptosis. Promotes neuronal growth cone collapse (By similarity)

Tail-Suspension Model of Simulated Microgravity-Induced Functional Dyspepsia in Rats: Behavioral, Motility, and Brain-Gut Peptide Alterations.

Abstract: Animal models are essential for elucidating human disease mechanisms and advancing translational research. Here, we used a well-established rat tail-suspension model to investigate the pathophysiological changes associated with simulated microgravity-induced functional dyspepsia (FD) and to evaluate its utility for preclinical to clinical translation. Thirty male Wistar rats were randomly assigned to control, simulated weightlessness using hindlimb unloading (HU), and domperidone groups. The HU model was induced by 21-day tail suspension, a widely accepted ground-based platform for simulating microgravity. Behavioral tests (sucrose preference, novelty-suppressed feeding), gastrointestinal motility measurements (gastric emptying, intestinal propulsion), and serum brain-gut peptide levels were assessed. Gastric and hypothalamic gene expression was analyzed by qRT-PCR. The model successfully recapitulated key FD phenotypes, including anxiety/depression-like behaviors, reduced gastric emptying and intestinal propulsion, and systemic brain-gut peptide imbalance-characterized by decreased excitatory peptides [substance P (SP), gastrin (GAS), motilin (MTL), ghrelin] and increased inhibitory peptides [vasoactive intestinal peptide (VIP), cholecystokinin (CCK), calcitonin gene-related peptide (CGRP), nesfatin-1] in serum. Consistent transcriptional dysregulation was observed in gastric and hypothalamic tissues. Hippocampal brain-derived neurotrophic factor (BDNF) was decreased, and colon 5-hydroxytryptamine (5-HT) increased, with no organic gastric lesions. Domperidone treatment significantly ameliorated behavioral abnormalities and gastrointestinal dysmotility, partially reversed brain-gut peptide imbalances at both protein and transcriptional levels, and restored hippocampal BDNF. These findings demonstrate that the rat tail-suspension model provides a reproducible platform for studying microgravity-induced FD, implicating brain-gut axis dysregulation. Domperidone's therapeutic effects highlight the model's utility for evaluating countermeasures against spaceflight-associated digestive dysfunction.

Humanised Environmental Enrichment: Spatial Effects of Cities and Buildings on Adult Hippocampal Neurogenesis in Humans.

Abstract: Adult hippocampal neurogenesis persists throughout the human lifespan, yet declines in Alzheimer's disease and major depression, associated in part with reduced brain-derived neurotrophic factor (BDNF) levels. For rodents, environmental enrichment, dichotomised primarily as physical activity and spatial complexity, robustly promotes adult hippocampal neurogenesis, but no framework has translated these findings to human environments. This review is the first to synthesise evidence across the full translational pathway, arguing that spatial complexity and physically active navigation in neighbourhoods and buildings constitute a humanised form of environmental enrichment. It proposes that standard indoor environments may represent a functionally impoverished condition for the human hippocampus, paralleling standard laboratory caging. An applied model is presented, mapping built environment features onto the neurobiological mechanisms regulating adult hippocampal neurogenesis, with BDNF as the central translatable biomarker linking environmental exposures to neurogenic outcomes. A methodological roadmap for future empirical validation is also outlined. This framework repositions the built environment as a modifiable determinant of adult hippocampal neurogenesis in humans, with implications for mitigating the risk of depression, cognitive impairment, and Alzheimer's disease.

Unlocking Neuroprotection: Exercise-Induced Muscle Secretome (Myokines) as a Therapeutic Avenue Against Alzheimer's Disease Pathogenesis.

Abstract: This review critically evaluates exercise-induced myokines as neuroprotective agents against Alzheimer's disease (AD) and is structured around three thematic sections: (1) mechanistic foundations of myokine neuroprotection, (2) translational barriers to therapeutic development, and (3) a strategic framework for future research. Epidemiological studies associate physical exercise with reduced AD risk (30-45%), yet mechanisms remain incompletely resolved. Preclinical studies demonstrate that exercise-induced myokines (Irisin, BDNF, Cathepsin B) modulate AD pathology by: (1) attenuating amyloid-beta (Aβ)/tau accumulation, (2) suppressing neuroinflammation, and (3) enhancing synaptic plasticity. However, human exercise interventions show conflicting results influenced by APOE genotype, age, and exercise modality. Associative human data suggest that Interleukin-6 (IL-6) exemplifies pleiotropy-affording neuroprotective effects in acute contexts but potentially detrimental effects in states of chronic inflammation. Therapeutic hurdles include blood-brain barrier (BBB) penetration, pleiotropic risks, and patient heterogeneity. Emerging concepts such as combinatorial approaches (nanocarriers, exercise mimetics) and biomarker-driven trials are proposed as hypothetical future strategies; however, these remain unvalidated and require substantial preclinical development before implemented in clinical care. This narrative review is structured around three thematic sections: mechanistic foundations of myokine neuroprotection, translational barriers to therapeutic development, and a strategic framework for future research. The muscle-brain axis represents a compelling but complex therapeutic target. Based on current preclinical and correlational human evidence, future research should prioritize mechanistic rigor, standardized biomarker validation, and clinically viable delivery strategies. Notably, several approaches discussed herein-including nanocarrier delivery systems, exercise mimetics, and combinatorial myokine cocktails-remain speculative and are presented as future research directions rather than established therapeutic interventions.

Neuropsychopharmacological effects of Aronia melanocarpa: A narrative review.

Abstract: This narrative review examines the neuropsychopharmacological effects of Aronia melanocarpa (black chokeberry), focusing on its potential in the prevention and treatment of neuropsychiatric disorders such as anxiety, depression, and cognitive decline. A comprehensive literature search across Web of Science, Scopus, and Google Scholar identified 29 original studies, based on in vitro, animal, and human research. Findings demonstrated that Aronia melanocarpa, rich in polyphenols like anthocyanins and proanthocyanidins, exerts cognitive-enhancing, anxiolytic-like, and antidepressant-like effects. These outcomes are mediated by mechanisms involving antioxidant activity, modulation of neurotransmitter systems, inhibition of monoamine oxidases, reduction of neuroinflammation, modulation of gut microbiota, and upregulation of brain-derived neurotrophic factor (BDNF). Animal models of Alzheimer's disease and stress-induced disorders, along with human clinical trials, corroborated these effects. The review underscores the therapeutic promise of Aronia melanocarpa nutraceuticals in neuropsychiatric health and highlights the need for further clinical validation.

Unveiling the neuroprotective effects of pomegranate extract and/or physical activity against aluminum chloride-induced Alzheimer's disease in rats: modulation of multitude pathways.

Abstract: Alzheimer's disease (AD) is a devastating neurodegenerative malady marked by cognitive dysfunction and increased deposition of amyloid-beta and hyperphosphorylated tau proteins. Aluminum-associated neurotoxicity is well-documented and manifests itself in the form of cognitive dysfunction. Nutraceuticals, such as pomegranate extract (POM) or physical activity (PHA), have been recognized to exert beneficial actions on human wellbeing. This study aimed to mechanistically scrutinize the effects of POM and PHA either separately or in combination on AlCl3-induced AD in rats. Sixty adult male Wistar rats were randomly assigned into five groups: control, AlCl3, AlCl3 + PHA, AlCl3 + POM, and AlCl3 + COMB (POM + PHA) and treated for 5 weeks. PHA and POM, either alone or in combination, exhibited a significant boost in memory and cognitive abilities, evidenced by the significant improvements in behavioral outcomes, elevations in monoamine (DA, NE, 5-HT), LRP1, and neprilysin levels, and reductions in acetylcholinesterase (ACHE) activity, APOE4 levels, and AD markers, relative to the AlCl3-intoxicated group. All treatments significantly ameliorated AlCl3-induced perturbations in antioxidant, neurotrophic, autophagic, inflammatory, endoplasmic reticulum (ER) stress, and apoptotic parameters, along with histopathological and immunohistochemical findings. These effects were demonstrated by the significant increase in antioxidant (Nrf2/HO-1/TAC/SOD), neurotrophic (PI3K/AKT/CREB/BDNF/TrKB), and autophagic (AMPK/SIRT-1/Beclin-1) markers, with significant reduction in neuroinflammatory (P38 MAPK/JNK/NF-κB/JAK-2/STAT-3/TNF-α/IL-1β), ER stress (PERK/CHOP/GRP78), and apoptotic (BAX/P53/caspase-3) markers, relative to the AlCl3-intoxicated group. Interestingly, the combination exerted more favorable actions in all measured parameters and histological findings than the solo-treated groups. This study revealed the superiority of the combined therapy, compared to solo treatments, in alleviation of AlCl3-induced AD in rats, via adjustment of the Nrf2/HO-1, P38 MAPK/JNK/NF-κB/JAK-2/STAT-3, PI3K/AKT/GSK-3β/CREB, AMPK/SIRT-1, PERK/CHOP, and apoptotic hubs.


Breast cancer type 1 susceptibility protein

E3 ubiquitin-protein ligase that specifically mediates the formation of 'Lys-6'-linked polyubiquitin chains and plays a central role in DNA repair by facilitating cellular responses to DNA damage (PubMed:10500182, PubMed:12887909, PubMed:12890688, PubMed:14976165, PubMed:16818604, PubMed:17525340, PubMed:19261748). It is unclear whether it also mediates the formation of other types of polyubiquitin chains (PubMed:12890688). The BRCA1-BARD1 heterodimer coordinates a diverse range of cellular pathways such as DNA damage repair, ubiquitination and transcriptional regulation to maintain genomic stability (PubMed:12890688, PubMed:14976165, PubMed:20351172). Regulates centrosomal microtubule nucleation (PubMed:18056443). Required for appropriate cell cycle arrests after ionizing irradiation in both the S-phase and the G2 phase of the cell cycle (PubMed:10724175, PubMed:11836499, PubMed:12183412, PubMed:19261748). Required for FANCD2 targeting to sites of DNA damage (PubMed:12887909). Inhibits lipid synthesis by binding to inactive phosphorylated ACACA and preventing its dephosphorylation (PubMed:16326698). Contributes to homologous recombination repair (HRR) via its direct interaction with PALB2, fine-tunes recombinational repair partly through its modulatory role in the PALB2-dependent loading of BRCA2-RAD51 repair machinery at DNA breaks (PubMed:19369211). Component of the BRCA1-RBBP8 complex which regulates CHEK1 activation and controls cell cycle G2/M checkpoints on DNA damage via BRCA1-mediated ubiquitination of RBBP8 (PubMed:16818604). Acts as a transcriptional activator (PubMed:20160719)

Spatiotemporal organisation of residual disease in mouse and human BRCA1-deficient mammary tumours and breast cancer.

Abstract: Breast cancer remains a leading cause of death worldwide. Although chemotherapy reduces primary and metastatic tumour burden, persisting drug-tolerant tumour cell populations, known as minimal residual disease (MRD), pose a significant risk of recurrence and therapy resistance. In this study, we describe the spatiotemporal organisation of therapy response and MRD in BRCA1;p53-deficient mouse mammary tumours and human clinical samples. By integrating single-cell RNA sequencing, spatial transcriptomics, and imaging mass cytometry across multiple treatment timepoints, we characterise dynamic interactions between tumour cell subpopulations and their surrounding microenvironment. Our multiomic analysis uncovers a distinct, chemotherapy-tolerant epithelial-mesenchymal transition (EMT) cancer cell population that displays a conserved expression programme in human BRCA1-deficient tumours, significantly correlates with adverse clinical outcomes, and can be pharmacologically targeted in preclinical models. We reveal the spatial distribution of residual EMT-like tumour cells within discrete anatomical niches, providing a framework for understanding the persistence of MRD and potential therapeutic vulnerabilities.

An instrument-free height readout biosensing device based on gold nanobipyramid-loaded hydrogel for point-of-care detection of acid phosphatase and the BRCA1 gene.

Abstract: Point-of-care testing (POCT) is crucial for disease diagnosis, especially in resource-limited settings with inadequate laboratory infrastructure. Although visual distance-based readout sensors present a promising approach for instrument-free quantification, their widespread application is hindered by complex fabrication processes and dependence on external driving mechanisms. Here we developed a universal, instrument-free visual quantification platform based on a gold nanobipyramid -loaded agarose (AuNBP/agarose) hydrogel encapsulated in a polycarbonate (PC) tube. The iodine-mediated etching of AuNBPs transduced target recognition into a measurable color-changing hydrogel height. The addition of acid phosphatase (ACP) initiated the enzymatic production of ascorbic acid (AA), driving the etching process and generated a height signal proportional to ACP concentration in the range of 0.1-1000 mU/mL, with a detection limit of 9.72 μU/mL. Moreover, it exhibited high selectivity and satisfactory recoveries for ACP in human serum samples. For DNA detection, target hybridization introduced horseradish peroxidase (HRP), which effectively inhibited etching by consuming H2O2. This strategy enabled sensitive detection of the BRCA1 gene within a concentration range of 100-1500 nM, with a detection limit of 270 nM. Both assays enabled quantitative readout using a simple ruler, without the need for complex instrumentation, demonstrating a universal and cost-effective strategy for POCT detection.

Microplastics as a Cross-Disease Driving Risk Factor in Lung Pathogenesis: An Integrative Study Combining In Silico Analysis and Experimental Validation Using Polystyrene Nanoplastics.

Abstract: Microplastics (MPs), as environmental pollutants, have garnered widespread attention. Growing evidence suggests a close association between MP exposure and lung diseases. However, the molecular mechanisms through which MP exposure influences the onset and progression of lung diseases remain unclear. This study positions MP exposure as a cross-disease driving risk factor and employs integrated computational toxicology and bioinformatics approaches to explore potential key targets underlying the impact of MP exposure on the development of lung diseases (COPD, IPF, and LUAD). Common differentially expressed genes (cDEGs) and shared common DEGs (scDEGs) associated with MP exposure and COPD, IPF, and LUAD were identified through database screening and intersection analysis. A protein-protein interaction (PPI) network was constructed using the STRING database, followed by enrichment analysis. The expression patterns and cellular localization of key targets among the shared common differentially expressed genes were validated using single-cell datasets of COPD, IPF, and LUAD. Finally, experimental validation was conducted based on the cell types identified through analysis. MP exposure may influence the occurrence and progression of COPD, IPF, and LUAD through mechanisms involving the cell cycle, mitosis, and DNA repair. Potential key targets identified include CDK1, BRCA1, and CCND1. Validation via database and single-cell analyses suggests that MP exposure may increase the risk of COPD, IPF, and LUAD by upregulating CDK1 expression in pulmonary fibroblasts. Experimental validation in human pulmonary fibroblasts demonstrated that PS-NPs significantly upregulated CDK1 mRNA and protein levels in a dose-dependent manner. CDK1 inhibition experiments confirmed that PS-NP exposure promotes fibrosis in human pulmonary fibroblasts by upregulating CDK1. This study defines MP exposure as a cross-disease driving risk factor and identifies CDK1 as a potential key target mediating the development of MPs-driven lung diseases. This finding offers a new perspective for understanding MPs-related lung diseases and establishes a novel paradigm for exploring the intrinsic connections between pollutant exposure and disease pathogenesis.

Genomic Biomarkers for First-Line Treatment Selection in Metastatic Pancreatic Ductal Adenocarcinoma: A Narrative Review.

Abstract: Metastatic pancreatic ductal adenocarcinoma (PDAC) is typically treated with fluorouracil, leucovorin, irinotecan, and oxaliplatin (FOLFIRINOX) or gemcitabine plus nab-paclitaxel (GnP), but the choice between regimens remains largely empirical. This narrative review summarizes biomarkers with potential to inform first-line selection in metastatic PDAC, emphasizing genomic and transcriptomic correlates of differential benefit. Recent head-to-head trials, particularly Pancreatic Adenocarcinoma Signature Stratification for Treatment (PASS-01) and GENERATE (Japan Clinical Oncology Group [JCOG] 1611), indicate that modified FOLFIRINOX (mFOLFIRINOX) is not uniformly superior to GnP, strengthening the rationale for biomarker-guided selection. The strongest evidence favoring platinum-based/FOLFIRINOX strategies involves homologous recombination repair deficiency (HRD), especially alterations in germline breast cancer gene 1/2 (BRCA1/2) or partner and localizer of BRCA2 (PALB2), as well as broader genomic scar signatures. Transcriptomic subtype and GATA-binding protein 6 (GATA6) expression are promising but remain unsettled because retrospective data favor classical/GATA6-high disease for FOLFIRINOX, whereas PASS-01 suggested better outcomes with GnP in classical tumors. Candidate biomarkers favoring GnP include high human equilibrative nucleoside transporter 1 (hENT1), low class III β-tubulin (TUBB3) expression, and exploratory phosphatidylinositol 3-kinase (PI3K)/KIT/NOTCH pathway mutation signals. Comprehensive molecular profiling also identifies actionable alterations that may redirect patients to targeted therapy or clinical trials rather than standard chemotherapy alone. Importantly, no biomarker has yet been prospectively validated in a biomarker-stratified randomized trial with regimen selection as the primary endpoint; all biomarker-regimen associations described in this review should therefore be considered hypothesis-generating rather than practice-defining. Nevertheless, the convergence of genomic, transcriptomic, and organoid-based approaches makes biologically informed first-line selection increasingly feasible in metastatic PDAC.

Allosteric network of dynamic coupling within BAP1-UCH revealed by methyl NMR.

Abstract: BRCA1-associated protein 1 (BAP1) is a tumor suppressor whose deubiquitinase (DUB) activity is essential for transcriptional regulation and is frequently compromised in cancer by mutations clustered in its ubiquitin carboxyl-terminal hydrolase (UCH) domain. The structural and dynamic bases of these oncogenic mutations remain elusive. Here, we introduce 22 cancer mutations and additional methyl mutations on the other 22 cancer mutation sites of BAP1-UCH to map their effects on the methyl chemical shifts. This analysis reveals an allosteric coupling network centered on a conserved leucine (L49) shared across human UCH paralogs. Strikingly, a single-carbon side-chain truncation in the L49V variant abolishes DUB activity, coinciding with disruption of correlated μs-ms timescale motions within a phenylalanine cluster that undergoes concerted motions within the L49 hub. These findings uncover how BAP1-UCH sustains its catalytic competence through a delicately tuned dynamic network and how minute alterations can collapse this allosteric balance, providing a mechanistic link between subtle structural perturbations and oncogenesis.


Breast cancer type 2 susceptibility protein

Tumor suppressor protein that maintains genome stability primarily by repairing damaged DNA through homologous recombination (HR) (PubMed:11239456, PubMed:12442171, PubMed:15115758, PubMed:15199141, PubMed:15671039, PubMed:15937124, PubMed:17515903, PubMed:17515904, PubMed:18317453, PubMed:19303847, PubMed:20729832, PubMed:20729858, PubMed:20729859, PubMed:21719596, PubMed:27941124, PubMed:37499663, PubMed:37515771). Facilitates the repair of double-strand breaks (DSBs) by binding and mediating the loading of the RAD51 protein onto single-stranded DNA (ssDNA), thereby promoting the activity of RAD51, which catalyzes DNA strand exchange (PubMed:11239456, PubMed:12442171, PubMed:15937124, PubMed:17515903, PubMed:17515904, PubMed:18317453, PubMed:19303847, PubMed:20729832, PubMed:20729858, PubMed:20729859, PubMed:27941124, PubMed:37499663). BRCA2 nucleates and stabilizes RAD51 on ssDNA directly and delivers RAD51 to ssDNA-double-stranded DNA (dsDNA) junctions by sliding along dsDNA backbone (PubMed:12442171, PubMed:19303847, PubMed:37499663). RAD51 targeting to ssDNA promotes removal of replication protein-A (RPA) from ssDNA and stabilization of RAD51-ssDNA filaments by blocking ATP hydrolysis (PubMed:20729859). May play a role in the extension step after strand invasion at replication-dependent DNA double-strand breaks; together with PALB2 is involved in both POLH localization at collapsed replication forks and DNA polymerization activity (PubMed:24485656). Required to prevent R-loop-associated DNA damage and thus transcription-associated genomic instability (PubMed:24896180). Silencing of BRCA2 promotes R-loop accumulation at actively transcribed genes in replicating and non-replicating cells, suggesting that BRCA2 mediates the control of R-loop associated genomic instability, independently of its known role in homologous recombination (PubMed:24896180). Also promotes RAD51 loading to telomeric regions, facilitating telomere replication and capping (PubMed:21076401). Also required for homologous recombination during meiosis by promoting the recruitment of RAD51 and DMC1 recombinases to meiotic DSB sites, enabling proper chromosome pairing and crossing over (PubMed:26976601). Also promotes homologous recombination by inactivating the FIGNL1-FIRRM complex to protect RAD51 filament from premature disassembly (PubMed:37515771). Together with NPM1, may also regulate centrosome duplication (PubMed:21084279)

DNA-contact mutant p53 displaces BRCA2 from chromatin and drives R-loop-associated genome instability.

Abstract: Mutations in the tumor suppressor p53 are among the most frequent events in human cancers. Mutant p53 acquires oncogenic activities beyond the loss of tumor suppressive function. However, how different mutation subtypes differ in their contributions to tumorigenesis remains incompletely understood. Through pan-cancer TCGA analysis, we find that patients with p53 DNA contact mutations exhibit worse clinical outcomes than those carrying conformational mutations. Mechanistically, we demonstrate that the DNA contact mutation p53-R273H forms aberrant condensates that sequester BRCA2 and displace it from chromatin, leading to R-loop accumulation and genomic instability. We further identify the DEAD-box helicase DDX3X as a critical factor required for BRCA2-dependent R-loop resolution. Pharmacological inhibition of DDX3X with RK-33 synergizes with the PARP inhibitor Olaparib, enhancing therapeutic efficacy in p53 DNA contact mutant cancer cells. Our study establishes a pathogenic axis through which the clinically aggressive p53 DNA contact mutations drive genomic instability by dislodging BRCA2 from chromatin and disrupting R-loop homeostasis. These findings suggest a potential therapeutic avenue for treating cancers harboring high-risk p53 DNA contact mutations.

Molecular architecture of the tumor microenvironment caused by

Abstract: Homologous recombination repair (HRR) deficiency is associated with improved immunotherapy responses in non-small cell lung cancer (NSCLC) patients. The HRR genes BRCA1/2 are key regulators of DNA repair, yet their impact on the tumor microenvironment (TME) in lung adenocarcinoma (LUAD) remains unclear. Using single-cell sequencing and multi-omics data, we characterized BRCA1/2 mutation-associated transcriptional programs, immune cell composition, and functional alterations in T cells, investigating the molecular and immune architecture of BRCA-mutant LUAD patients. BRCA1/2 mutations were associated with increased genomic instability and poor prognosis in LUAD patients, but predicted better clinical outcomes following immune checkpoint blockade (ICB) treatment. BRCA1 mutations correlated with an upregulated type I IFN/IFN-γ signature and CD8+ T cell activation. BRCA2 mutations were associated with alveolar/stress/inflammatory responses and enhanced MHC-II antigen presentation, linked to CD4+ T cell differentiation. Both alterations coincided with reduced CD28 co-stimulation and CTL activity, hinting at immune evasion. We identified two tissue-resident memory T cell (Trm) subsets as predictors of clinical outcomes and ICB response. BRCA1 mutations were associated with CD8+ Trm expansion, whereas BRCA2 mutations were linked to tumor CD4+ Trm expansion and peripheral T/NK cell cytotoxicity. Furthermore, a cancer-promoting program activated by BRCA1 mutation was vulnerable to histone deacetylase inhibitors, which inhibited LUAD tumor growth. This study provides a preliminary characterization of the BRCA-mutant TME in LUAD patients, revealing distinct transcriptional and immune patterns that highlight differences in BRCA1/2-associated molecular architecture and offer a framework for improving therapy efficacy in LUAD.

Adjuvant olaparib real world data for

Journal of oncology pharmacy practice : official publication of the International Society of Oncology Pharmacy Practitioners

Abstract: IntroductionSince 2023 olaparib has been commissioned in the United Kingdom for breast cancer for patients with breast cancer gene 1 and 2 (BRCA1 and 2) positive, human epidermal growth factor receptor 2 (HER2)-negative, high-risk early disease after chemotherapy. Our study describes tolerability and adverse effects, to understand continued applicability of the OlympiA trial analyses through comparison to available real-world data.Materials and methodsThis was a retrospective observational study using secondary real-world data for 47 patients who received olaparib between April 2023 and March 2024 from 11 NHS and HSC hospitals. Anonymised data was collected from electronic patient records for eligible patients. A standardised data collection tool was utilised capturing key metrics. Statistical analysis included descriptive statistics and comparisons of adverse events with the OlympiA trial using Chi-square or Fisher's exact tests (p < 0.05).ResultsThe research sample at baseline had broader age range including patients in their 60s, compared to the OlympiA patient population which lacked those aged over 49. It also has a more even distribution of BRCA1/BRCA2 mutations, higher rates of hormone receptor positive HER2-negative cancers and a greater use of neoadjuvant and platinum-based treatments. Adverse events were similar between the two populations. Fatigue was significantly more prevalent compared to OlympiA (p < 0.05). Nineteen patients had dose reductions due to adverse effects and four patients discontinued treatment early.ConclusionAdjuvant olaparib was well tolerated in our real-world UK population study, with toxicity profiles similar to the OlympiA trial. Fatigue was significantly more prevalent in the real-world cohort.

Clinical variant interpretation comparing two saturation genome editing-based functional studies for

Abstract: Two saturation genome editing (SGE) studies for BRCA2 using haploid human HAP1 cells and mouse embryonic stem cells, respectively, demonstrated contradictory functional results in 16.9% (1,052/6,208) of the variants. We performed clinical variant interpretation and tried to address the discordance by comparing two studies combined with 24 years of clinicopathological data collected at a single institution. Retrospectively, we collected data from patients with BRCA2 variants evaluated in the SGE studies. The variants were reassessed according to the ClinGen BRCA1/2 guidelines and/or multifactorial likelihood analysis. For variants with concordant SGE functional results, either PS3 or BS3 was assigned. Major error rates were compared for variants with discordant results. Among the 88 variants from 526 patients, 13, including three potentially hypomorphic variants, showed discordant results. Major error rates were lower for HAP1-SGE dataset, but without statistical significance. Among the 75 variants with concordant results, 28 and 47 were assigned PS3 and BS3, respectively. Consequently, 93.1% (27/29) of the variants of uncertain significance were reclassified as likely pathogenic (n = 3) or likely benign (n = 24). Concordant SGE results are clinically useful for variant reclassification. When discordant results are present, functional evidence should not be assigned, but HAP1-SGE dataset is suggested to be more consistent with patient-specific data. Further segregation analysis and long-term follow-up are needed to resolve discordant cases.


Multifunctional transcription factor that induces cell cycle arrest, DNA repair or apoptosis upon binding to its target DNA sequence (PubMed:11025664, PubMed:12524540, PubMed:12810724, PubMed:15186775, PubMed:15340061, PubMed:17317671, PubMed:17349958, PubMed:19556538, PubMed:20673990, PubMed:20959462, PubMed:22726440, PubMed:24051492, PubMed:24652652, PubMed:35618207, PubMed:36634798, PubMed:38653238, PubMed:9840937). Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type (PubMed:11025664, PubMed:12524540, PubMed:12810724, PubMed:15186775, PubMed:15340061, PubMed:17189187, PubMed:17317671, PubMed:17349958, PubMed:19556538, PubMed:20673990, PubMed:20959462, PubMed:22726440, PubMed:24051492, PubMed:24652652, PubMed:38653238, PubMed:9840937). Negatively regulates cell division by controlling expression of a set of genes required for this process (PubMed:11025664, PubMed:12524540, PubMed:12810724, PubMed:15186775, PubMed:15340061, PubMed:17317671, PubMed:17349958, PubMed:19556538, PubMed:20673990, PubMed:20959462, PubMed:22726440, PubMed:24051492, PubMed:24652652, PubMed:9840937). One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression (PubMed:12524540, PubMed:17189187). Its pro-apoptotic activity is activated via its interaction with PPP1R13B/ASPP1 or TP53BP2/ASPP2 (PubMed:12524540). However, this activity is inhibited when the interaction with PPP1R13B/ASPP1 or TP53BP2/ASPP2 is displaced by PPP1R13L/iASPP (PubMed:12524540). In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA-Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-BMAL1-mediated transcriptional activation of PER2 (PubMed:24051492)

Network pharmacology of Sijunzi decoction in pancreatic cancer.

Abstract: Sijunzi decoction (SJZD) is a traditional Chinese medicine (TCM) commonly used for pancreatic ductal adenocarcinoma (PDAC), but its mechanisms remain unclear. This study investigates its molecular basis using network pharmacology and molecular docking. Active compounds and targets of SJZD were identified via Traditional Chinese Medicine Systems Pharmacology (TCMSP) Database and Analysis Platform, and PDAC-related targets were retrieved from Online Mendelian Inheritance in Man (OMIM) and GeneCards. Protein-protein interaction (PPI) networks, Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and tissue distribution analyses were conducted. Molecular docking evaluated binding affinities between compounds and targets. The anti-PDAC effects of SJZD were evaluated in vitro using human pancreatic cancer cell lines (CFPAC-1 and MiaPaCa-2) and in vivo using a patient-derived xenograft (PDX) mouse model. SJZD comprises 131 compounds and 260 targets, with key targets such as AKT serine/threonine kinase 1 (AKT1), BCL2 associated agonist of cell death (BAD), BCL2 apoptosis regulator (BCL2), and tumor protein p53 ( TP53) identified through PPI analysis. Enrichment analyses highlighted the phosphatidylinositide 3-kinases (PI3K)/protein Kinase B (AKT)/mechanistic target of rapamycin kinase (mTOR) and apoptosis pathways as primary therapeutic mechanisms. SJZD exhibited cytotoxic effects against PDAC cells in vitro and suppressed tumor growth in vivo, with mechanistic analyses confirming its regulatory effects on the PI3K/AKT/mTOR and apoptosis pathways. Molecular docking revealed strong binding affinities, particularly for compounds targeting estrogen receptor 1 (ESR1) and estrogen receptor 2 (ESR2). These findings suggest that SJZD exerts anti-PDAC effects via multi-target modulation, primarily through inhibition of the PI3K/AKT/mTOR signaling axis, induction of apoptosis and autophagy, and anti-inflammatory activity. The involvement of classic compounds supports the rationale of its traditional use, while experimental validation provides a mechanistic foundation for future clinical development. This study clarifies the active components, targets, and mechanisms of SJZD in treating PDAC, offering insights into the therapeutic potential of TCM.

Predicting TP53 biomarkers from whole slide images across human solid tumours using weakly supervised learning.

Abstract: Accurate molecular profiling from routine histopathology slides could transform clinical oncology. A Vision Transformer (ViT)-based model was developed to jointly predict the TP53 biomarker, detect 32 solid tumour types, and predict survival directly from Whole Slide Images (WSIs). Over 11K primary tumour data were retrieved from the Pan-Cancer Atlas, along with corresponding somatic mutation, RNA-seq, and clinical outcome data. WSIs underwent tissue masking, quality control, stain normalisation, patch extraction, and feature embedding using a ViT encoder. Seven task heads were developed to generate predictions for cancer type, TP53 mutation status, TP53 RNA expression levels, overall survival, progression-free interval, and their corresponding event times. Model training proceeded in two stages: initial training on tumour-only patches at multiple magnifications, followed by fine-tuning on WSIs using a content-aware strategy. Model performance was evaluated on an independent validation set of 1,729 slides using evaluation metrics, including the area under the receiver operating characteristic curve (AUROC), regression metrics, and the concordance index. An AUROC of 0.766 for TP53 mutation detection on an independent validation set across 32 human solid tumours. In conclusion, the ViT-based model could simultaneously infer TP53 mutation status, TP53 RNA expression levels, and tumour taxonomy directly from WSIs, supporting the existence of reproducible morphologic correlates of TP53 alterations across human cancers, whereas prognostic risk prediction remained limited.

Rising incidence of oral tongue squamous cell carcinoma in young women: Emerging non-traditional etiologic factors and clinical implications: A structured narrative review.

Abstract: Oral squamous cell carcinoma (OSCC) accounts for the majority of oral malignancies worldwide, with oral tongue squamous cell carcinoma (OTSCC) considered one of its most aggressive subtypes. Historically, OSCC has predominantly affected older males with substantial tobacco and alcohol exposure. However, emerging epidemiologic evidence demonstrates a rising incidence of OTSCC among young females, particularly patients aged ≤ 45 years, many of whom lack these traditional risk factors, suggesting distinct etiologic pathways. A structured narrative review using a comprehensive literature search strategy was conducted using PubMed, Scopus, Ovid MEDLINE, and Web of Science, combining terms related to oral cancer, tongue, young patients aged ≤ 45 years, females, incidence, and risk factors. Of 653 records identified, 19 studies met the inclusion criteria after exclusion of non-English articles, conference abstracts, animal studies, and non-oral tongue reports. Population-based and institutional data from North America, Europe, Asia, and Australia consistently report increasing OTSCC incidence among young women, in some regions surpassing rates observed in age-matched men. Many affected patients are non-smokers, non-drinkers, and human papillomavirus (HPV)-negative. Proposed non-traditional contributors include genetic susceptibility, family history of malignancy, hormonal influences, early-life carcinogen exposure, chronic mucosal irritation, metabolic comorbidities, environmental factors, and possible misclassification of HPV-related base-of-tongue tumors. Molecular findings suggest distinct patterns of TP53 alterations and chromosomal instability in younger patients. The growing burden of OTSCC in young women underscores the need for improved early detection and multi-institutional molecular studies to clarify mechanisms and inform tailored prevention and treatment strategies.

A pan-cancer single-cell analysis of intratumoral copy number diversity and evolution.

Abstract: Aneuploidy is a hallmark of human tumors. While patient-level copy number alteration (CNA) differences have been investigated extensively in large cohorts, their intratumoral heterogeneity remains understudied. Here, we conducted a pan-cancer analysis of 94 human tumors at single cell resolution, representing seven cancer types: bladder, breast, colon, glioblastoma, kidney, lung, and ovarian. Single-cell copy number profiling was used to analyze 62,646 aneuploid cells, in addition to bulk exome sequencing of most patients and single-nucleus RNA-seq of 6 samples. In many cancer types, increased subclonal diversity was associated with higher CNA burden, whole genome doubling, TP53 mutations, and increased geographic diversity. Cancer cells from each patient shared a set of truncal CNAs, suggesting evolution from a single ancestral cell. Many tumors accumulated CNAs in bursts of evolution, suggesting that punctuated evolution is common in diverse cancer types. This study greatly improves our knowledge of intratumoral chromosome diversity across human cancers.

TP53 mutation at codon 179 metabolically reprograms cancer cells to promote invasion.

Abstract: Mutations in the tumour suppressor, TP53, are prevalent in human cancers yet their functional implications remain unclear. Through comprehensive pan-cancer database analysis, we identified H179 mutations in TP53 as significantly associated with poor disease-free survival across multiple cancer types. Functional studies in lung, ovarian, and prostate cancer cells over-expressing the p53H179R/Y mutants revealed that these mutants are not only defective in tumour-suppressive functions but also actively promote tumour progression. These mutants drive metabolic reprogramming by increasing neutral lipid levels through de novo fatty acid synthesis (p53H179R/Y) and fatty acid uptake (p53H179Y), accompanied by increased lipid droplets and APOE expression, collectively promoting enhanced invasiveness relative to p53-null cells. Our findings demonstrate that TP53 missense mutations are not functionally equivalent to TP53 loss. Notably, H179 mutations act as oncogenic drivers, and our data highlight APOE and lipid metabolism as potential therapeutic targets, underscoring the clinical relevance of precise TP53 mutation characterisation.


Heterodimerizes with PMS2 to form MutL alpha, a component of the post-replicative DNA mismatch repair system (MMR). DNA repair is initiated by MutS alpha (MSH2-MSH6) or MutS beta (MSH2-MSH3) binding to a dsDNA mismatch, then MutL alpha is recruited to the heteroduplex. Assembly of the MutL-MutS-heteroduplex ternary complex in presence of RFC and PCNA is sufficient to activate endonuclease activity of PMS2. It introduces single-strand breaks near the mismatch and thus generates new entry points for the exonuclease EXO1 to degrade the strand containing the mismatch. DNA methylation would prevent cleavage and therefore assure that only the newly mutated DNA strand is going to be corrected. MutL alpha (MLH1-PMS2) interacts physically with the clamp loader subunits of DNA polymerase III, suggesting that it may play a role to recruit the DNA polymerase III to the site of the MMR. Also implicated in DNA damage signaling, a process which induces cell cycle arrest and can lead to apoptosis in case of major DNA damages. Heterodimerizes with MLH3 to form MutL gamma which plays a role in meiosis

Computational Analysis of Differentially Expressed Genes in Arsenic-Induced Carcinogenesis and Their Effect on Human Repair Mechanisms.

Abstract: Arsenic poisoning significantly elevates the risk of cancer and other chronic illnesses. The goal of this research is to identify important genes whose expression changes in response to arsenic toxicity, and the molecular pathways affected by arsenic, using computational analysis of arsenic toxicity profiles. This approach will computationally identify and analyze genes whose expression changes in response to arsenic, thereby elucidating the heightened risk of carcinogenesis in arsenic-exposed individuals. This work employed high-throughput arsenic toxicity profiles to computationally identify and analyze expressed genes (DEGs) differentially in Affymetrix microarray datasets from the Gene Expression Omnibus (GEO) database, which were screened using the GEO2R program. A protein-protein interaction (PPI) network was constructed using STRING to elucidate the functional links between these DEGs and DNA repair genes. Interactions between the seven central genes (E2F1, EXO1, EZH2, FEN1, HIST1H3A, POLA1, and TIMELESS) and the repair genes PARP1, NBN, PMS1, MSH3, XRCC5, XRCC6, MGMT, and MLH1 were discovered. We employed the DAVID and Enrichr-KG platforms to investigate the functions of these genes and their associations with cellular and molecular processes in greater detail. Two hundred eighty-one non-synonymous single-nucleotide polymorphisms (nsSNPs) in the 07 genes linked to arsenic toxicity were found using the COSMIC database. Based on our analysis, mutations in E2F1, EXO1, EZH2, FEN1, HIST1H3A, POLA1, and TIMELESS can hinder DNA repair mechanisms, ultimately leading to cancer. Our computational analysis demonstrated that these non-synonymous SNPs can affect gene function, potentially altering protein stability and activity. Furthermore, according to Metal-Protein docking and protein-protein docking, these genes and their mutations appear to affect interactions with repair proteins substantially. Specific dietary consumption may lessen the detrimental effects of arsenic poisoning on protein function. We hypothesized that the mutations might be reversed by attaching particular molecules to these mutants. The protective effects of six curcumin compounds were examined using molecular docking with AutoDock 4.2.6 to assess protein dynamics and binding interactions. Optimal complexes were selected for dynamics simulation using GROMACS, and potential strategies for long-term cancer prevention related to arsenic exposure were identified.

Mechanism of MutLβ-dependent DNA expansions.

Proceedings of the National Academy of Sciences of the United States of America

Abstract: MutS and MutL proteins and their eukaryotic homologs have important functions in DNA metabolism. MutLβ (MLH1-PMS1 heterodimer) is a poorly understood eukaryotic MutL complex. Recent genetic studies have implicated MutLβ in the process of expansion of the short, tandem DNA repeat tracts that is responsible for the repeat expansion diseases. The function of MutLβ and the mechanism of MutLβ-dependent DNA expansions have not been established. We show here that MutLβ promotes MutSβ- and MutLγ-dependent DNA expansions in human cell extracts and defined systems. Importantly, DNA expansions that occur in human cell extracts in the presence of MutSβ and a low concentration of MutLγ require MutLβ. A MutSβ variant lacking the PCNA-binding motif is proficient in supporting MutLβ-promoted and MutLγ-dependent DNA expansions. We also show that MutLβ enhances the MutSβ-dependent endonuclease activity of MutLγ that incises the loop-lacking strand of loop-containing DNAs. MutLβ also increases the endonuclease activity of MutLγ in the presence of ATP-Mn2+ and physically interacts with MutLγ, MutSβ, and PCNA. In addition, MutLβ suppresses inhibition of DNA expansion by MutSα. An MLH1-F80V substitution in MutLβ causes a defect in the ability of the protein to promote MutSβ- and MutLγ-dependent DNA expansions. Taken together, our findings support a model in which MutLβ is involved in DNA expansions by acting in a MutSβ- and MutLγ-dependent mechanism that includes incision of loop-containing DNAs in the loop-lacking strand.

Targeted native long-read sequencing of DNA methylation alterations following CRISPR-Cas9-induced double-strand breaks in human cells.

Abstract: CRISPR-Cas9 nucleases are widely used to introduce targeted DNA double-strand breaks (DSBs) for genome engineering, but the long-term impact of these lesions on local epigenetic information remains poorly characterized. In a companion research article, we used Cas9-assisted targeted nanopore sequencing (CTS) to reveal that CRISPR-Cas9-induced DSBs can disrupt local epigenetic maintenance across multiple genomic contexts and cell systems. Here, we present a structured description of the raw and minimally processed datasets underlying the study. These datasets provide base-resolution measurements of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at the differentially methylated regions (DMRs) of several imprinted loci, two heterochromatic regions, a cancer-associated promoter epimutation region, and the SNRPN DMR at early/late passages of a clonal line. They enable re-analysis and methodological benchmarking of DSB-associated epigenetic instability. We provide aligned BAM files and per-CpG methylation calls for multiple genomic contexts under both CRISPR-targeted and non-targeting control conditions. Specifically, the collection includes: (i) imprinted loci in human embryonic stem cells (hESCs), including small nuclear ribonucleoprotein polypeptide N (SNRPN), paternally expressed 10 (PEG10), and KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1), (ii) heterochromatic regions in hESCs, including urothelial cancer associated 1 (UCA1), and cysteine rich C-terminal 1 (CRCT1)), (iii) the epimutation locus of MutL homolog 1 (MLH1) in RKO cells, and (iv) the DMR of SNRPN locus in early- and late-passage derivatives of a single hESC clone. For each collection, there is a dataset that includes both the raw aligned Nanopore sequencing reads (BAM) deposited in the NCBI Sequence Read Archive (SRA) and the corresponding processed per-CpG 5mC/5hmC matrices deposited in Zenodo. All higher-level analyses in the research article-such as DMR calling, haplotype-resolved analyses, and structural variant (SV) characterization-are fully reproducible using these deposited data. Additional processed analyses are comprehensively documented in the companion article and are therefore not duplicated here. Together, these datasets offer a rich resource for benchmarking long-read methylation analysis workflows and further investigation of DSB-associated epigenetic instability across diverse genomic contexts.

An accurate cellular assay to determine pathogenicity of coding and noncoding variants in Lynch syndrome genes.

Abstract: Lynch syndrome (LS) is a genetic predisposition to mainly colorectal and endometrial cancer due to heterozygous disruptive germline mutations in the DNA mismatch-repair (MMR) genes MSH2, MSH6, MLH1, or PMS2. Beyond clearly pathogenic mutations, germline sequencing often reveals variants of uncertain significance (VUS), predominantly single base-pair alterations in coding or noncoding regions. These uncertain variants obstruct LS diagnosis, hampering personalized surveillance. To address this challenge, we developed a highly accurate functional assay that interrogates VUS pathogenicity in human cells. Building on a mouse-based cellular assay, we adapted oligonucleotide-directed mutation screening (ODMS) for human cells and introduced a refined approach named "coselection ODMS." To ensure physiological expression, the variant is introduced into the endogenous MMR gene by replication-coupled gene editing. Coselection ODMS demonstrated 100% accuracy in classifying 50 benign and 86 pathogenic variants spanning coding and noncoding regions in all four MMR genes. Among 109 patient-derived VUS, 51 were identified as deleterious for MMR function. Importantly, coselection ODMS delivered 100% concordant results in a clinical diagnostic laboratory. With >93% sensitivity and >92% specificity, coselection ODMS provides a highly reliable functional assay in the diagnosis of enigmatic LS variants, enabling risk assessment and personalized surveillance or treatment for affected families.

DNA mismatch repair mediated by Mlh1-Pms1 endonuclease-catalyzed mispair excision.

Abstract: Eukaryotic DNA mismatch repair (MMR) involves several excision pathways, including those mediated by exonuclease 1 (Exo1) and by the flap endonuclease Rad27 (human FEN1) coupled with DNA polymerase δ. Simultaneous inactivation of both excision mechanisms causes an MMR defect that is at most 5 to 13% of that caused by complete inactivation of MMR. Here, we reconstituted nicked-strand-specific MMR with the Saccharomyces cerevisiae proteins Msh2-Msh6 or Msh2-Msh3, DNA polymerase ε, RFC, PCNA, RPA, and Mlh1-Pms1 (human Mlh1-Pms2) under conditions lacking Exo1, Rad27, or strand-displacement synthesis by DNA polymerase δ. These reactions required the Mlh1-Pms1 endonuclease activity, its activation by RFC and PCNA, and its recruitment by Msh2-Msh6 or Msh2-Msh3. MMR was mediated by nicked-strand-specific excision by Mlh1-Pms1 through formation of single-strand DNA gaps having a broad range of sizes. This reaction is consistent with genetic data demonstrating redundancy between the Exo1, Rad27, and Mlh1-Pms1 excision pathways in MMR.