IL-19 Is a Novel Lymphangiocrine Factor Inducing Lymphangiogenesis and Lymphatic Junctional Regulation

BACKGROUND

The lymphatic system functions by removing fluid, macromolecules, and immune cells to maintain tissue homeostasis. The structural organization of junctional protein complexes is vital to lymphatic function where initial lymphatics have permeable button junctions and collecting lymphatics have relatively impermeable zipper junctions. During inflammation, this junctional morphology appears to reverse, contributing to overall lymphatic malfunction. Little is known about the effects of immunomodulatory cytokines on lymphatic vessel formation and function during inflammation. The purpose of this study is to test the hypothesis that IL (interleukin)-19 promotes lymphangiogenesis and proper lymphatic function during inflammation.

METHODS

We used cultured human dermal lymphatic endothelial cells to determine IL-19 expression and its effects on lymphangiogenesis assays. Immunocytochemistry and electric cell-substrate impedance sensing determined effects on junctional morphology as it relates to permeability in vitro. RNA sequencing determined the effects of IL-19 on gene expression. Il19-/-Ldlr-/- double knockout mice were used to determine IL-19 effects on lymphatic function and lymphatic vessel visualization in vivo.

RESULTS

Endogenous IL-19 expression is induced by exogenous IL-19 and VEGF (vascular endothelial growth factor) C stimulation. IL-19 is lymphangiogenic, increasing human dermal lymphatic endothelial cell migration, network formation, and proliferation. IL-19 induces expression of transcription factors and permeability-associated genes. IL-19 induces rapid VE-cadherin (vascular endothelial cadherin) phosphorylation, increases permeability of human dermal lymphatic endothelial cell monolayers, and mitigates oxidized low-density lipoprotein-associated decrease in human dermal lymphatic endothelial cell permeability. In vivo, Il19-/-Ldlr-/- double knockout mice on a high-fat diet have impaired lymphatic drainage, decreased lymphatic branch points, and increased percentage of zippered junctions compared with control mice.

CONCLUSIONS

Taken together, these data show that IL-19 has potent effects on lymphatic vessel formation and function in vitro and that IL-19 regulates lymphatic drainage in vivo. IL-19 may represent an immunomodulatory cytokine with therapeutic potential for improving impaired lymphatic function consequent to inflammation.

Targeting Acetyl-CoA Carboxylase Suppresses De Novo Lipogenesis and Tumor Cell Growth in Multiple Myeloma

PURPOSE

In multiple myeloma, tumor cells reprogram metabolic pathways to sustain growth and monoclonal immunoglobulin production. This study examines acetyl-CoA carboxylase 1 (ACC1), the enzyme driving the rate-limiting step in de novo lipogenesis, in multiple myeloma metabolic reprogramming, particularly in c-MYC (MYC)-driven subtypes.

EXPERIMENTAL DESIGN

ACC1 expression was evaluated across multiple myeloma genetic subgroups, focusing on MYC translocations. Functional studies using ACC1 inhibitors and genetic knockdown assessed multiple myeloma cell growth, lipid synthesis, and metabolic homeostasis in vitro and in vivo. The role of MYC overexpression in ACC1 sensitivity was examined, with palmitate rescue experiments. Lipidomic analysis and assessments of endoplasmic reticulum (ER) stress, protein translation, and oxidative damage elucidated underlying mechanisms.

RESULTS

ACC1 was overexpressed in MYC-translocated multiple myeloma. Its inhibition or knockdown reduced multiple myeloma cell growth in vitro and in vivo, particularly in MYC-overexpressing cells. ACC1 knockdown suppressed de novo lipid synthesis, partially rescued by palmitate. Lipidomic disruptions increased cholesterol ester desaturation and altered phospholipid ratios, inducing ER stress, impaired translation, protein carbonylation, oxidative damage, and apoptosis.

CONCLUSIONS

ACC1 is a metabolic vulnerability in MYC-driven multiple myeloma. Inhibiting ACC1 disrupts lipid homeostasis, induces ER stress, and causes oxidative damage, impairing cell survival. Targeting lipid synthesis pathways, especially in MYC-dependent subtypes, offers a promising therapeutic strategy for multiple myeloma.

TP53 mutations and TET2 deficiency cooperate to drive leukemogenesis and establish an immunosuppressive environment

Mutations and deletions in TP53 are associated with adverse outcomes in patients with myeloid malignancies, and there is an urgent need for the development of improved therapies for TP53-mutant leukemias. Here, we identified mutations in TET2 as the most common co-occurring mutation in patients with TP53-mutant acute myeloid leukemia (AML). In mice, combined hematopoietic-specific deletion of TET2 and TP53 resulted in enhanced self-renewal compared with deletion of either gene alone. Tp53/Tet2 double-KO mice developed serially transplantable AML. Both mice and patients with AML with combined TET2/TP53 alterations upregulated innate immune signaling in malignant granulocyte-monocyte progenitors, which had leukemia-initiating capacity. A20 governs the leukemic maintenance by triggering aberrant noncanonical NF-κB signaling. Mice with Tp53/Tet2 loss had expansion of monocytic myeloid-derived suppressor cells (MDSCs), which impaired T cell proliferation and activation. Moreover, mice and patients with AML with combined TP53/TET2 alterations displayed increased expression of the TIGIT ligand, CD155, on malignant cells. TIGIT-blocking antibodies augmented NK cell-mediated killing of Tp53/Tet2 double-mutant AML cells, reduced leukemic burden, and prolonged survival in Tp53/Tet2 double-KO mice. These findings describe a leukemia-promoting link between TET2 and TP53 mutations and highlight therapeutic strategies to overcome the immunosuppressive bone marrow environment in this adverse subtype of AML.

FGF8 promotes lipid droplet accumulation via the FGFR1/p-p38 axis in chondrocytes

Chondrocytes store lipids in the form of lipid droplets (LDs) and maintain cartilage lipid metabolic homeostasis by consuming or regenerating LDs. This modulation is largely mediated by a series of biochemical factors. Fibroblast growth factor 8 (FGF8) is one of the most important factors involved in the proliferation, differentiation, and migration of chondrocytes and has attracted increasing attention in the physiology and pathology of cartilage. However, the effect of FGF8 on LD accumulation in chondrocytes remains unclear. This study aims to elucidate the role of FGF8 in LDs and explore the underlying biomechanism involved. The results reveal that FGF8 promotes LD accumulation in chondrocytes by upregulating perilipin1 (Plin1) expression. FGF8 activates the cytoplasmic p-p38 signaling pathway via fibroblast growth factor receptor 1 (FGFR1) to increase LD accumulation in chondrocytes. Subsequent experiments with siRNAs and specific inhibitors further confirm the importance of the FGFR1/p38 axis for LD accumulation in chondrocytes exposed to FGF8. The results increase our understanding of the role of FGF8 in the lipid metabolic homeostasis of chondrocytes and provide insights into the physiology and pathology of cartilage.

Longitudinal changes in body composition during palliative systemic chemotherapy and survival outcomes in metastatic colorectal cancer

BACKGROUND

In patients with metastatic colorectal cancer, chemotherapy may lead to changes in body composition, including skeletal muscle quantity and quality, and body fat area and distribution. Longitudinal follow-up data in a homogeneous population are required to understand these changes better.

AIM

To comprehensively evaluate changes in body composition and their prognostic value in patients with metastatic colorectal cancer undergoing palliative chemotherapy.

METHODS

This retrospective study included patients with recurrent or metastatic colorectal cancer who received palliative chemotherapy between 2008 and 2017. Computed tomography scans were analyzed at multiple time points (before each new chemotherapy regimen and after discontinuing all chemotherapy). Body composition was analyzed from each scan using artificial intelligence software (AID-UTM, iAID Inc.), and its association with survival was evaluated through time-dependent Cox regression to adjust for time-varying effects.

RESULTS

This analysis included 1805 patients, with a median age at diagnosis of 57 years, and 62% were male. At first-line chemotherapy initiation, 4.7%, 30.9%, 36.5%, and 37.1% of the patients had sarcopenia, myosteatosis, and visceral and subcutaneous obesity, respectively. During treatment, approximately 54.5% of the patients experienced significant changes in body composition, with 9.1% and 19.2% developing new sarcopenia and myosteatosis, respectively. Sarcopenia and myosteatosis were associated with poorer survival outcomes [hazard ratio (HR) for sarcopenia, 2.55 (95%CI: 2.06-3.16, P < 0.001; HR for myosteatosis, 2.37 (95%CI: 2.00-2.82), P < 0.001]. In contrast, visceral and subcutaneous obesity were associated with improved survival [HR for visceral obesity, 0.69 (95%CI: 0.57-0.82), P < 0.001; HR for subcutaneous obesity, 0.78 (95%CI: 0.64-0.95), P = 0.015], with no negative impacts observed at higher fat levels. These changes correlated with end-of-life survival time.

CONCLUSION

Abnormalities and body composition changes were frequently observed during palliative chemotherapy for advanced colorectal cancer; myosteatosis was common. Comprehensive body composition assessment offers valuable prognostic insights without requiring additional testing.

Effects of polystyrene microparticles exposures on spermatogenic cell differentiation and reproductive endpoints in male mice

The widespread distribution of microplastics in the environment has raised concerns about their potential implications for human health. Microplastics accumulate in animals and humans, but the risks associated with these pollutants are not fully understood. This study aimed to investigate the effects of polystyrene microplastics on the male reproductive system. The 0.1 μm polystyrene (PS) could accumulate in the testicular tissue and spermatogonia GC-1, while 1 μm PS was not easy to enter and accumulate in the testicular tissue and cells. Mice continuously exposed for 3-months to 0.1 μm PS demonstrated lower fertility and inhibited spermatogonium differentiation compared to control mice. The 0.1 μm PS were dispersed throughout the seminiferous tubule of the testis. Metabolic reprogramming was found to be involved in these processes. Histone methylation and autophagy-related pathways showed significant differences following PS treatment in testis tissue and GC-1 cells. Our findings suggest that chronic exposure to 0.1 μm PS inhibited spermatogenic cell differentiation and impaired fertility in male mice. We propose that abnormal epigenetic modifications in 0.1 μm PS exposed mice contributed to the dysregulation of glycolytic enzymes, and that the impaired autophagic pathway exacerbated the accumulation of glycolytic enzymes further. Glycolysis plays a critical role in the regulation of spermatogenic cell differentiation, and its regulation partially alleviated the impairments associated with PS exposure. In conclusion, our findings suggest that chronic exposure to nanoplastics PS inhibited spermatogenic cell differentiation and impaired fertility in male mice via disrupted epigenetic modification and metabolic dysregulation.

P.1 and P.2 SARS-CoV-2 Brazilian variants activate the unfolded protein response with a time and pathway specificity

COVID-19 is a human respiratory syndrome caused by the infection of the SARS-CoV-2 virus that has a high rate of infection and mortality. Viruses modulate the host machinery by altering cellular mechanisms that favor their replication. One of the mechanisms that viruses exploit is the protein folding and processing of post-translational modifications that occur in the endoplasmic reticulum (ER). When ER function is impaired, there is an accumulation of misfolded proteins leading to endoplasmic reticulum stress (ER stress). To maintain homeostasis, cells trigger an adaptive signaling mechanism called the Unfolded Protein Response (UPR) which helps cells deal with stress, but under severe conditions, can activate the apoptotic cell death mechanism. This study elucidated an activation of a diversity of molecular mechanisms by Brazilian variants of SARS-CoV-2 by a time-resolved and large-scale characterization of SARS-CoV-2-infected cells proteomics and immunoblotting. Furthermore, it was shown that pharmacological UPR modulation could reduce viral release by counteracting the different viral activations of its cellular response. Analysis of human clinical specimens and disease outcomes focusing on ER stress reinforces the importance of UPR modulation as a host regulatory mechanism during viral infection and could point to novel therapeutic targets. SIGNIFICANCE: Since the emergence of SARS-CoV-2 and the consequent COVID-19 pandemic, the rapid emergence of variants of this new coronavirus has been a cause for concern since many of them have significantly higher rates of transmissibility and virulence, being called Variants of Concern (VOC). In this work, we studied the VOCs Gamma (P.1) and Zeta (P.2), also known as Brazilian variants. Constant evidence has reported that there are particularities related to each variant of SARS-CoV-2, with different rates of transmissibility, replication and modulation of host biological processes being observed, in addition to the mutations present in the variants. For this reason, this work focused on infections caused by the Brazilian variants of SARS-CoV-2 in different cell lines, in which we were able to observe that the infections caused by the variants induced endoplasmic reticulum stress in the infected cells and activated the UPR pathways, presenting specific modulations of each variant in this pathway. Furthermore, transcriptome analysis of patients revealed a correlation between ER-related genes and COVID-19 progression. Finally, we observed that the use of UPR modulators in host cells decreased viral release of all variants without affecting cell viability. The data presented in this work complement the observations of other studies that aim to understand the pathogenicity of SARS-CoV-2 VOCs and possible new therapeutic strategies, mainly targeting biological processes related to the endoplasmic reticulum.

Comparative Perspectives on Neuropeptide Function and Social Isolation

Chronic social isolation alters behavior across animal species. Genetic model organisms such as mice and flies provide crucial insight into the molecular and physiological effects of social isolation on brain cells and circuits. Here, we comparatively review recent findings regarding the function of conserved neuropeptides in social isolation in mice and flies. Analogous functions of 3 classes of neuropeptides-tachykinins, cholecystokinins, and neuropeptide Y/F-in the two model organisms suggest that these molecules may be involved in modulating behavioral changes induced by social isolation across a wider range of species, including humans. Comparative approaches armed with tools to dissect neuropeptidergic function can lead to an integrated understanding of the impacts of social isolation on brain circuits and behavior.

SPDL1 inhibition enhances colorectal cancer progression via epidermal growth factor receptor/extracellular signal-regulated kinase pathways

BACKGROUND

In patients with colorectal cancer (CRC), tumour metastasis is the leading cause of death. The search for key genes involved in metastasis of CRC is imperative for improved prognoses and treatments. SPDL1 has been implicated in the development of CRC, however, its mechanism of action remains unclear.

AIM

To investigate the role and mechanism of action by which SPDL1 inhibits the development and metastasis of CRC.

METHODS

In this study, we examined the relationship between SPDL1 expression and CRC prognosis using immunohistochemistry. Survival analyses were performed using Kaplan-Meier analysis and log-rank test. After knocking down SPDL1 in the HCT116 cancer cell line changes in cell viability, migration, invasion, and gene expression were examined using a cell counting kit 8 assay, Transwell assay, and Western blot. The effect of SPDL1 on the cell cycle was assessed using flow cytometry. RNA sequencing was used to analyse the effect of SPDL1 on gene expression of CRC cells. The mechanism of action of SPDL1 in CRC was further clarified using U0126, an inhibitor of the mitogen-activated protein kinase signaling pathway.

RESULTS

SPDL1 is expressed at low levels in tissues of patients with CRC, and this reduced expression is associated with poor prognosis. Functionally, low expression of SPDL1 in CRC promotes cell proliferation, migration, invasion, and affects the cell cycle. Mechanistically, SPDL1 affects the progression of CRC through its regulation of the process of epithelial-mesenchymal transition (EMT) and of the epidermal growth factor receptor (EGFR)/ extracellular signal-regulated kinase (ERK) signaling pathways.

CONCLUSION

This study showed that the loss of SPDL1 may induce EMT and promote cell migration and invasion in CRC through the EGFR/ERK pathway.

AARS2 ameliorates myocardial ischemia via fine-tuning PKM2-mediated metabolism

AARS2, an alanyl-tRNA synthase, is essential for protein translation, but its function in mouse hearts is not fully addressed. Here, we found that cardiomyocyte-specific deletion of mouse AARS2 exhibited evident cardiomyopathy with impaired cardiac function, notable cardiac fibrosis, and cardiomyocyte apoptosis. Cardiomyocyte-specific AARS2 overexpression in mice improved cardiac function and reduced cardiac fibrosis after myocardial infarction (MI), without affecting cardiomyocyte proliferation and coronary angiogenesis. Mechanistically, AARS2 overexpression suppressed cardiomyocyte apoptosis and mitochondrial reactive oxide species production, and changed cellular metabolism from oxidative phosphorylation toward glycolysis in cardiomyocytes, thus leading to cardiomyocyte survival from ischemia and hypoxia stress. Ribo-Seq revealed that Aars2 overexpression increased pyruvate kinase M2 (PKM2) protein translation and the ratio of PKM2 dimers to tetramers that promote glycolysis. Additionally, PKM2 activator TEPP-46 reversed cardiomyocyte apoptosis and cardiac fibrosis caused by AARS2 deficiency. Thus, this study demonstrates that AARS2 plays an essential role in protecting cardiomyocytes from ischemic pressure via fine-tuning PKM2-mediated energy metabolism, and presents a novel cardiac protective AARS2-PKM2 signaling during the pathogenesis of MI.

The Notch Signaling Pathway: A Potential Target for Mental Disorders

The highly conserved Notch signaling pathway plays a critical role in cell fate determination during metazoan development through cell-to-cell communication. The classical pathway consists of Notch receptors, ligands, intracellular effectors, DNA-binding proteins, and other regulatory molecules. Recent research has highlighted its involvement in the pathogenesis of several diseases. In autism, bipolar disorder, and schizophrenia, the Notch signaling pathway is implicated in key processes such as neuronal development and synaptic plasticity. Furthermore, it has been shown to play significant roles in other mental health conditions, including anxiety, depression, post-traumatic stress disorder, and neurocognitive disorders. However, the precise mechanisms underlying the contribution of Notch to these conditions remain poorly understood. This review examines the current understanding of the Notch signaling pathway in mental disorders, highlighting its role in their pathophysiology and summarizing therapeutic strategies aimed at modulating this pathway to improve mental health outcomes.

Induced clustering of SHP2-depleted tumor cells in vascular islands restores sensitivity to MEK/ERK inhibition

Allosteric inhibitors of the tyrosine phosphatase Src homology 2 domain-containing protein tyrosine phosphatase 2 (SHP2) hold therapeutic promise in cancers with overactive RAS/ERK signaling, but adaptive resistance to SHP2 inhibitors may limit benefits. Here, we utilized tumor cells that proliferate similarly with or without endogenous SHP2 to explore means to overcome this growth independence from SHP2. We found that SHP2 depletion profoundly altered the output of vascular regulators, cytokines, chemokines, and other factors from SHP2 growth-resistant cancer cells. Tumors derived from inoculation of SHP2-depleted, but SHP2 growth-independent, mouse melanoma and colon carcinoma cell lines displayed a typically subverted architecture, in which proliferative tumor cells surrounding a remodeled vessel formed "vascular islands", each limited by surrounding hypoxic and dead tumor tissue, where inflammatory blood cells were limited. Although vascular islands generally reflect protected sanctuaries for tumor cells, we found that vascular island-resident, highly proliferative, SHP2-depleted tumor cells acquired an increased sensitivity to blockage of MEK/ERK signaling, resulting in reduced tumor growth. Our results show that the response to targeted therapies in resistant tumor cells was controlled by tumor cell-induced vascular changes and tumor architectural reorganization, providing a compelling approach to elicit tumor responses by exploiting tumor- and endothelium-dependent biochemical changes.

Obesity prevention by different exercise protocols (HIIT or MICT) involves beige adipocyte recruitment and improved mitochondrial dynamics in high-fat-fed mice

AIM

This study evaluated the effects of high-intensity interval training (HIIT) and moderate-intensity continuous training (MICT) on UCP1-dependent and UCP1-independent thermogenic and mitochondrial dynamics markers in the inguinal sWAT of high-fat-fed mice.

METHODS

Sixty male C57BL/6 mice (3 months old) were divided into six experimental groups: control diet (C), C + HIIT (C-HIIT), C + MICT (C-MICT), high-fat diet (HF), HF + HIIT (HF-HIIT) and HF + MICT (HF-MICT). The diet and exercise protocols started simultaneously and lasted ten weeks.

RESULTS

HIIT and MICT prevented body mass gain and fat pad expansion, improved insulin sensitivity, and induced browning in C-fed and HF-fed animals. Chronic intake of a HF diet caused adipocyte hypertrophy with a proinflammatory adipokine profile and impaired the expression of thermogenic and mitochondrial dynamics markers. However, both exercise intensities increased anti-inflammatory adipokine concentrations and improved gene markers of mitochondrial dynamics, resulting in sustained UCP1-dependent and UCP1-independent thermogenic markers and maintenance of the beige phenotype in inguinal sWAT. The principal component analysis placed all trained groups opposite the HF group and near the C group, ensuring the effectiveness of HIIT and MICT to prevent metabolic alterations.

CONCLUSIONS

This study provides reliable evidence that, regardless of intensity, exercise is a strategy to prevent obesity by reducing body fat accumulation and inducing browning. The anti-inflammatory adipokine profile and the increased expression of UCP1-dependent and UCP1-independent thermogenic markers sustained active beige adipocytes and mitochondrial enhancement to halt metabolic disturbances due to HF-feeding in exercised mice.

Trypanosoma cruzi cell cycle progression exhibits minimal variation in histone PTMs with unique histone H4 acetylation pattern

Histones are crucial proteins in eukaryotic cells that undergo extensive posttranslational modifications (PTMs) such as methylation, acetylation, and phosphorylation, which are associated to chromatin structure, gene expression, DNA damage/repair and cell cycle. In Trypanosoma cruzi, the primary sequence of histones differs from that of other eukaryotes. Despite this, they display a vast range of PTMs, though their modulation throughout the cell cycle remains largely unexplored. In this study, we investigated the dynamic modulation of histone PTMs across G1/S, S, and G2/M phases of T. cruzi cell cycle using hydroxyurea- synchronized parasites. We applied a workflow that included histone derivatization, trypsin digestion followed by a high-resolution mass spectrometry and data independent analysis. Quantitative analysis of 141 histone peptide isoforms revealed that there are only minor variations in histone PTM levels throughout the cell cycle. The H3K76 trimethylation remained predominant throughout all phases, with an increase in monomethylation during G2/M. Additionally, hyperacetylation of the N-terminal region of histone H4 was observed, particularly at lysine residues 2, 5, and 10, suggesting their importance in cell cycle progression. Striking, acetylation of histone H4 at K2 and K5 increases during the S-phase, mirroring the H4K5acK12ac pattern observed in mammals, which are related to histone nuclear import and chromatin deposition. Overall, the results suggest that the T. cruzi cell cycle maintains stable global levels of histone PTMs, relying on variations in only a few specific PTMs. Further investigations are warranted to elucidate the functional significance of these PTMs and their impact on cell cycle regulation and chromatin dynamics in T. cruzi. SIGNIFICANCE: Histone posttranslational modifications (PTMs) are key regulators of chromatin architecture and cellular processes such as gene expression and cell cycle control. In Trypanosoma cruzi, the etiological agent of Chagas disease, histones have a distinct primary structure compared to other eukaryotes, yet they display a wide variety of PTMs. This study provides a comprehensive analysis of histone PTM dynamics across the G1/S, S, and G2/M phases of the T. cruzi cell cycle, revealing that global histone PTM levels remain largely stable, with variations in a few specific marks. Notably, the study highlights the increased acetylation of histone H4 at lysines 2 and 5 during the S-phase, contrasting with the well-conserved acetylation at lysines 5 and 12 observed in mammals involved in nuclear import and chromatin assembly. These findings underscore the evolutionary divergence and functional specificity of histone modifications and provide a foundation for further investigations into their roles in parasite biology, with potential implications for understanding chromatin dynamics and identifying novel therapeutic targets.

Silencing of SCEL promotes progression of oral squamous cell carcinoma via activating TGF-β/Smad pathway

OBJECTIVE

SCEL serves as a precursor protein for the cornified envelope (CE), and its abnormal expression has been identified in various malignancies. Despite this, the functional role and detailed mechanisms of SCEL in oral squamous cell carcinoma (OSCC) remain to be clarified.

METHODS

mRNA and protein expression of SCEL in OSCC cell lines and patient tissues were examined by qRT-PCR and IHC. In vitro and in vivo experiments assessed SCEL's influence on proliferation, apoptosis, cell cycle, ROS production, migration, and invasion. Western blotting was used to analyze SCEL's effect on various signaling pathways, and a dual-luciferase reporter assay identified the miRNA that targets SCEL.

RESULTS

SCEL is downregulated in OSCC, which correlates with reduced tumor cell differentiation and lymph node metastasis. SCEL inhibits OSCC proliferation, induces cell cycle arrest, apoptosis, and ROS production. SCEL suppresses the TGF-β/Smad pathway, inhibiting migration and invasion. SCEL also triggers MET and downregulates VEGFC, reducing lymph node metastasis probability. miR-5696 inhibitor effectively inhibits OSCC proliferation and invasion by targeting SCEL.

CONCLUSION

SCEL acts as a tumor suppressor in OSCC, influencing its progression and potential metastasis. Loss of SCEL facilitates OSCC progression by activating TGF-β/Smad signaling. Upregulating SCEL and silencing miR-5696 hold therapeutic promise for OSCC.

Reactivation of CTLA4-expressing T cells accelerates resolution of lung fibrosis in a humanized mouse model

Tissue regenerative responses involve complex interactions between resident structural and immune cells. Recent reports indicate that accumulation of senescent cells during injury repair contributes to pathological tissue fibrosis. Using tissue-based spatial transcriptomics and proteomics, we identified upregulation of the immune checkpoint protein, cytotoxic T lymphocyte-associated protein 4 (CTLA4), on CD8+ T cells adjacent to regions of active fibrogenesis in human idiopathic pulmonary fibrosis and in a repetitive bleomycin lung injury murine model of persistent fibrosis. In humanized CTLA4-knockin mice, treatment with ipilimumab, an FDA-approved drug that targets CTLA4, resulted in accelerated lung epithelial regeneration and diminished fibrosis from repetitive bleomycin injury. Ipilimumab treatment resulted in the expansion of Cd3e+ T cells, diminished accumulation of senescent cells, and robust expansion of type 2 alveolar epithelial cells, facultative progenitor cells of the alveolar epithelium. Ex vivo activation of isolated CTLA4-expressing CD8+ cells from mice with established fibrosis resulted in enhanced cytolysis of senescent cells, suggesting that impaired immune-mediated clearance of these cells contributes to persistence of lung fibrosis in this murine model. Our studies support the concept that endogenous immune surveillance of senescent cells may be essential in promoting tissue regenerative responses that facilitate the resolution of fibrosis.

Regulation of autophagy: Insights into O-GlcNAc modification mechanisms

Autophagy is a "self-eating" biological process that degrades cytoplasmic contents to ensure cellular homeostasis. Its response to stimuli occurs in two stages: Within a few to several hours of exposure to a stress condition, autophagic flow rapidly increases, which is mediated by post-translational modification (PTM). Subsequently, the transcriptional program is activated and mediates the persistent autophagic response. O-linked β-N-acetylglucosamine (O-GlcNAc) modification is an inducible and dynamically cycling PTM; mounting evidence suggests that O-GlcNAc modification participates in the total autophagic process, including autophagy initiation, autophagosome formation, autophagosome-lysosome fusion, and transcriptional process. In this review, we summarize the current knowledge on the emerging role of O-GlcNAc modification in regulating autophagy-associated proteins and explain the different regulatory effects on autophagy exerted by O-GlcNAc modification.

ZLN005, a PGC-1α agonist, delays photoreceptor degeneration by enhancing mitochondrial biogenesis in a murine model of retinitis pigmentosa

Retinitis pigmentosa (RP) is a hereditary neurodegenerative disease characterized by the degeneration of photoreceptors caused by mutations in various genes. Increasing evidence suggests that mitochondrial biogenesis plays a critical role in many neurodegenerative diseases. This study investigated the role of mitochondrial biogenesis in rd1 mice, a widely recognized model of RP. Male C57BL/6 mice and age-matched rd1 mice were used for in vivo experiments, while H2O2 was employed on 661w cells to establish an in vitro model. Our findings revealed that mitochondrial biogenesis and the regulatory PGC-1α/NRF-1/TFAM pathway were significantly downregulated in rd1 mice. Treatment with ZLN005, a PGC-1α agonist, markedly improved visual function in rd1 mice and alleviated thinning of the retinal outer nuclear layer. Additionally, ZLN005 enhanced mitochondrial biogenesis and restored mitochondrial function in photoreceptors. Further analysis in vitro confirmed that ZLN005 rescued photoreceptor degeneration by promoting mitochondrial biogenesis through the PGC-1α/NRF-1/TFAM pathway. In summary, our results highlight the critical role of mitochondrial biogenesis and the PGC-1α/NRF-1/TFAM pathway in the progression of RP. This offers a potential strategy to delay photoreceptor degeneration in RP by maintaining mitochondrial function and could be combined with existing therapies for improving treatment outcomes through synergistic pathways.

Proteomics and phosphoproteomics analysis of acute pancreatitis alleviated by forsythoside B

Acute pancreatitis (AP) is a common acute abdominal condition in clinical practice, associated with high morbidity and mortality rates. Forsythia constitutes a component of traditional Chinese medicinal decoctions used for clinical AP treatment; however, the efficacy of its active monomer in treating AP has yet to be completely substantiated. Here, we engineered an AP cell and mouse model by administering a combination of caerulein and LPS. In vitro experiments utilizing AR42J cells demonstrated that forsythoside B (FST·B) was the most effective monomer in mitigating cellular inflammation. Subsequently, a comprehensive evaluation of FST·B concentrations and efficacy was performed in animal models. Next Mass spectrometry analysis of pancreatic from AP mice treated with 50 mg/kg FST·B was conducted to elucidate its primary regulatory molecular signaling and key targets. FST·B effectively mitigated pathological damage in mice with acute pancreatitis, leading to a reduction in the expression of inflammatory cytokines in both pancreatic tissue and serum. Proteomics and phosphoproteomic profiles revealed that FST·B significantly enhanced the level of oxidative phosphorylation and spliceosome pathway in the AP mice. This research provides initial evidence of the regulatory molecular signals and targets of FST·B in AP, laying a potential foundation for its clinical use in treating AP. SIGNIFICANCE: Acute pancreatitis (AP) is a common acute abdominal condition in clinical practice, associated with high morbidity and mortality rates, and the global incidence of AP has increased by approximately 25 % over the past 15 years. Despite the complexity of AP's causes and the high susceptibility of proteins to degradation during lesions, systems biology studies, such as proteomics, have been limited in investigating the molecular mechanisms involved in its pharmacological treatment. Forsythoside B, a phenylethanol glycoside isolated from the air-dried fruit of forsythia, is a traditional oriental anti-inflammatory drug commonly used in clinical practice. We demonstrated in the AP mouse model that forsythoside B can alleviate pancreatic inflammatory damage in vivo. To elucidate the molecular mechanisms underlying the anti-inflammatory effect of forsythoside B, a comprehensive proteomic and phosphoproteomic analysis was conducted on AP mice models prior to and subsequent to forsythoside B intervention. Finally, 1640 significantly differentially expressed proteins, 1448 significantly differentially expressed phosphoproteins corresponding to 2496 significantly differentially expressed phosphosites were identified. Functional analysis revealed that forsythoside B significantly enhanced the level of oxidative phosphorylation in the AP mice in proteomic profiles, and the spliceosome pathway at the phosphorylation level was significantly affected by forsythoside B. This research provides initial evidence of the regulatory molecular signals and targets of forsythoside B in AP, laying a potential foundation for its clinical use in treating AP.

Quercetin-doped sol-gel coatings on titanium implants: a promising approach for enhanced immune response and cell adhesion

Quercetin (QUE), a natural flavonoid found in various fruits and vegetables, has diverse biological functions, including anti-inflammatory effects, regulation of cell adhesion and oxidative stress mitigation. In this study, sol-gel materials with increasing concentrations of quercetin (0.5, 1 and 2 wt%) were synthesised and applied onto titanium (Ti) surfaces as coatings. The materials were characterised physiochemically, and in vitro responses were examined using HOb osteoblastic cells and THP-1 macrophages. Human serum protein adsorption was evaluated using nLC-MS/MS. The incorporation of quercetin did not affect the sol-gel network cross-linking, and a controlled release of quercetin was achieved. The materials exhibited no cytotoxicity at any concentration. The HOb cells cultured on quercetin-doped materials were more elongated than those grown on QUE-free coatings, with protruding lamellipodia and increased cell surface. QUE-doped surfaces enhanced the expression of BMP-2, RANKL, and cell adhesion-related genes CTNNB1 and β-actin. In the THP-1 cells, pro-inflammatory gene expression (IL-1β, MCP-1 and iNOS) was down-regulated on 0.5QUE material, while it increased on 2QUE, as did the cytokine liberation. These changes correlated with altered protein adsorption patterns. The 2QUE coatings enhanced the adsorption of acute-phase proteins (SAA1, SAA2 and SAA4), indicating an inflammatory response; this behaviour was not seen on 0.5QUE. Moreover, cell adhesion (COF1, PROF1) and oxidative stress proteins (GPX3, SEPP1, AMBP) were preferentially adsorbed onto QUE-doped coatings. These results highlight the significance of optimising quercetin concentration in sol-gel coatings to modulate the immune response and enhance cell adhesion effectively.

Nanomaterial-based scaffolds for bone regeneration with piezoelectric properties

For proper cellular growth, to prepare tissue scaffold mimicking the tissue properties is a significant challenge. Bone is a vital organ supporting the whole human body for its function. The efficiencies in its structure for a variety of reasons should properly be remedied. Bone tissue engineering (BTE) is an emerging field addressing to develop or repair bone tissue for its proper function. The bone is naturally a piezoelectric material and generates electrical stimuli because of mechanical stress. Thus, the use of piezoelectric materials to build bone tissue is of great interest in BTE. Both piezoelectric polymers and nanomaterials (NMs) are investigated for this goal. In this review, we give an overview of the recent advances in piezoelectric NMs to construct piezoelectric scaffolds in BTE.

Calcium-binding protein 39 in with-no-lysine kinase signaling and the modulation of renal tubular transport

PURPOSE OF REVIEW

The regulation of renal tubular transport is essential for maintaining electrolyte balance and blood pressure. Calcium-binding protein 39 (Cab39), also known as mouse protein-25 (MO25), plays a pivotal role in modulating this process through its interaction with WNK (with no lysine) kinases and Ste20-like kinases, including STE20/SPS1-related proline-alanine-rich kinase (SPAK) and oxidative stress response 1 (OSR1). By stabilizing and facilitating the activation of these kinases, Cab39 plays a crucial role in the regulation of key ion transporters, such as the sodium-chloride cotransporter (NCC) and the sodium-potassium-chloride cotransporters (NKCC1 and NKCC2). This review provides a comprehensive analysis of Cab39 structural properties, molecular interactions, and functional roles in renal physiology, emphasizing its significance in ion homeostasis.

RECENT FINDINGS

Studies reveal that Cab39 enhances SPAK activity up to 100-fold. Importantly, the role of Cab39 extends beyond simple kinase activation, as it supports kinase complex assembly and localization, enabling precise control over transporter regulation. Evidence also suggests that Cab39 may influence the regulation of NCC and NKCC2 through similar mechanisms, making it a promising target for therapeutic interventions in disorders such as hypertension and salt-wasting syndromes.

SUMMARY

The discovery of a small-molecule Cab39 inhibitor highlights its potential as a pharmacological target. Understanding the multifaceted functions of Cab39 may unlock novel strategies for managing renal and cardiovascular disorders.

Oncogenic fusions converge on shared mechanisms in initiating astroblastoma

Chromosomal rearrangements and gene fusions are the initial events in the development of many cancers. Astroblastoma (ABM), a brain cancer of unknown cellular origin and challenging to treat, is associated with diverse in-frame gene fusions, including MN1-BEND2 and MN1-CXXC5 (refs. 1,2). However, it remains unclear whether these gene fusions contribute to tumorigenesis. Here we show in mice that these two ABM-associated fusions converge on similar molecular activities and initiate malignancy specifically in ventral telencephalon neural progenitors. BEND2 and CXXC5 recognize similar DNA motifs, which indicates a convergence on downstream gene regulation. Expression of MN1-BEND2 in ventral telencephalon neural progenitors results in aberrant cell proliferation, impaired differentiation, a perivascular occupancy pattern of cells reminiscent of ABM and acquisition of an ABM-associated transcriptional signature. By contrast, MN1-BEND2 expression in dorsal telencephalon neural progenitors leads to extensive cell death. This cell-type-specific malignancy depends on OLIG2 expression. Mechanistically, both ABM-associated fusion proteins (MN1-BEND2 and MN1-CXXC5) induce overlapping transcriptional responses, including the activation of a therapeutically targetable PDGFRα pathway. Collectively, our data suggest that distinct ABM-associated fusions upregulate shared transcriptional networks to disrupt the normal development of ventral telencephalon neural progenitors, which leads to oncogenic transformation. These findings uncover new avenues for targeted ABM treatment.

Integrated Metabolomic and Transcriptomic Analyses of Mouse Liver Reveals the In Vivo Toxicity and Mechanisms of Individual and Combined Toxicants Formed in the Thermal Processing of High-Fat Diets

As a part of a continuous 90 day subchronic toxicology study, integrated metabolomic and transcriptomic approaches were applied to assess the metabolic network changes in the livers of Kunming mice exposed to three typical thermally induced food toxicants, including oxidative derivatives of triacylglycerols (ox-TGs), aldehydes, and 3-monochloropropane-1,2-diol esters (3-MCPDE), as well as their mixtures. Results showed lipid metabolic dysregulation through impaired purine metabolism, PPAR signaling, and bile acid metabolism. Ox-TGs emerged as the most hazardous compound, altering over 10 genes/enzymes. 3-MCPDE exhibited gender-specific effects, significantly upregulating fatty acid metabolism and gluconeogenesis genes in males. Interestingly, toxicant mixtures attenuated the adverse metabolic effects caused by individual compounds, demonstrating complex regulatory mechanisms in fatty acid biosynthesis and oxidation. The metabolomic and transcriptomic analyses conducted in this study revealed that combined exposure to multiple toxicants generated during lipid thermal processing may induce more complex toxicity effects than the simple additive effects of individual toxicants. Certain antagonistic effects were observed when comparing individual toxicants to their mixtures, highlighting the need for further mechanistic verifications in this area.

Structural basis of phosphorylation-independent nuclear import of CIRBP by TNPO3

Transportin 3 (TNPO3) is a nuclear import receptor known for its broad substrate specificity, often recognizing arginine-serine (SR/RS) repeat-rich nuclear localization signals (NLS) in SRSF proteins. While serine phosphorylation or glutamate presence has been associated with these NLSs, recent proteomic studies identified TNPO3 cargoes lacking SR/RS repeats. One such example is the cold-inducible RNA-binding protein (CIRBP), which contains a non-classical RSY-NLS. Using X-ray crystallography, here we investigate the TNPO3-CIRBP interaction and find that tyrosines within the RSY-NLS play a key role in binding, independent of phosphorylation. Surprisingly, serine and tyrosine phosphorylation in CIRBP's NLS inhibits TNPO3 binding, suggesting a regulatory mechanism for nuclear import. Our study reveals a non-conventional nuclear import mechanism mediated by TNPO3, which may extend to other known or yet undiscovered TNPO3 cargoes.

OCT-2 Is Associated With Pro-Metastatic Epigenomic Properties of Triple-Negative Breast Cancer Cells

Triple-negative breast cancer (TNBC) is a malignant type of breast cancer. Owing to the lack of expression of receptors that serve as molecular targets for standard therapy for breast cancer, conventional cytotoxic chemotherapy is the primary treatment option for TNBC. However, TNBC exhibits a high degree of genomic heterogeneity, rendering it resistant to chemotherapy. Therefore, there is an urgent need to identify novel therapeutic targets for the treatment of TNBC. Advances in massively parallel sequencing technology have enabled the identification of cancer cell-specific gene expression patterns and epigenetic alterations that regulate their expression. Cancer cell-specific super-enhancers (SEs) have been identified as effective therapeutic targets for cancer. In this study, we identified the functional roles of epigenetic changes and their regulatory mechanisms in TNBC cells. TNBC cell-specific SEs were formed near several genes that contribute to malignant cancer cell acquisition. We found that the transcription factor OCT-2 (encoded by POU2F2) was responsible for the formation of SEs and the expression of genes encoded in the vicinity of the SE regions. Overexpression of POU2F2 enhances the metastasis of TNBC cells in mice, and its expression is highly correlated to poor prognosis of TNBC patients. Our findings provide a new insight into cancer cell-specific epigenetic changes induced by OCT-2, which trigger the progression of TNBC, and suggest possible candidates that could be targeted for the treatment of TNBC.

MicroRNA nanoformulation: a promising approach to anti-tumour activity

Cancer is a major cause of morbidity and mortality, making it one of the most debilitating diseases in our time. Despite advancements in therapeutic strategies, the development of chemoresistance and the occurrence of secondary tumours pose significant challenges. While several promising anti-tumour agents have been identified, their clinical utility is often limited due to toxicity and associated side effects. MicroRNAs (mi-RNAs) are critical regulators of gene expression, and their altered levels are closely linked to cancer development and progression. Although some microRNAs have shown potential as biomarkers for cancer detection, their integration into routine clinical practice has yet to be realized. Numerous candidate microRNAs exhibit therapeutic potential for cancer treatment; however, further research is needed to create efficient, patient-compliant, and customized drug delivery systems. In recent decades, various nanotechnology platforms have successfully transitioned to clinical trials, particularly in the field of RNA nanotechnology. Several RNA nanoparticles have been developed to address key challenges in vivo for targeting cancer, demonstrating favourable biodistribution characteristics. Studies have shown that RNA nanoparticles, characterized by precise stoichiometry and homogeneity, can effectively target tumour cells while avoiding aggregation in normal, healthy tissues following systemic injection. Animal models have demonstrated that RNA nanoparticles can deliver therapeutics such as siRNA and anti-microRNA, effectively inhibiting tumour growth. Using nanoparticles conjugated with antibodies and/or peptides enhances the targeted delivery and sustained release of microRNAs and anti-microRNAs, which may reduce the required therapeutic dosage and minimize systemic and cellular damage. This review focuses on developing microRNA nanoformulations to improve cellular uptake, bioavailability, and accumulation at tumour sites, assessing their potential anti-tumour efficacy against various types of malignancies. The significance of these advancements in clinical oncology cannot be overstated.

An antisense RNA regulates production of DnaA and affects sporulation in Bacillus subtilis

DnaA is the replication initiator and a transcription factor in virtually all bacteria. Although the synthesis and activity of DnaA are highly regulated, the mechanisms of regulation vary between organisms. We found that production of DnaA in Bacillus subtilis is regulated by an antisense RNA that overlaps with the 5' untranslated region upstream of the dnaA open reading frame. We initially observed this RNA in in vitro transcription experiments and found that its production was inhibited by DnaA. This RNA, now called ArrA for antisense RNA repressor of dnaA, is made in vivo. We identified the arrA promoter and made a mutation that greatly reduced (or eliminated) production of ArrA RNA in vitro and in vivo. In vivo, this arrA promoter mutation caused an increase in the amount of mRNA and protein from dnaA and dnaN, indicating that arrA expression normally inhibits expression of the dnaA-dnaN operon. The arrA mutation also caused a delay in sporulation that was alleviated by loss of sda, a sporulation-inhibitory gene that is directly activated by DnaA. arrA appears to be conserved in some members of the Bacillus genus, indicating that arrA has evolved in at least some endospore-forming bacteria to modulate production of DnaA and enable timely and robust sporulation.

Solid phase transitions as a solution to the genome folding paradox

Ultra-long-range genomic contacts, which are key components of neuronal genome architecture1-3, constitute a biochemical enigma. This is because regulatory DNA elements make selective and stable contacts with DNA sequences located hundreds of kilobases away, instead of interacting with proximal sequences occupied by the exact same transcription factors1,4. This is exemplified in olfactory sensory neurons (OSNs), in which only a fraction of LHX2-, EBF1- and LDB1-bound sites interact with each other, converging into highly selective multi-chromosomal enhancer hubs5. To obtain biochemical insight into this process, here we assembled olfactory receptor (OR) enhancer hubs in vitro with recombinant proteins and enhancer DNA. Cell-free reconstitution of enhancer hubs revealed that OR enhancers form nucleoprotein condensates with unusual, solid-like characteristics. Assembly of these solid condensates is orchestrated by specific DNA motifs enriched in OR enhancers, which are likely to confer distinct homotypic properties on their resident LHX2-EBF1-LDB1 complexes. Single-molecule tracking and pulse-chase experiments in vivo confirmed that LHX2 and EBF1 assemble OR-transcription-competent condensates with solid properties in OSN nuclei, under physiological concentrations of protein. Thus, homophilic nucleoprotein interactions that are influenced by DNA sequence generate new types of biomolecular condensate, which might provide a generalizable explanation for the stability and specificity of long-range genomic contacts across cell types.

Characterizing differences in the muscle transcriptome between cattle with alternative LCORL-NCAPG haplotypes

BACKGROUND

The LCORL-NCAPG locus is a major quantitative trait locus (QTL) on bovine chromosome 6 (BTA6) that influences growth and carcass composition in cattle. To further understand the molecular mechanism responsible for the phenotypic changes associated with this locus, twenty-four Charolais-sired calves were selected for muscle transcriptome analysis based on alternative homozygous LCORL-NCAPG haplotypes (i.e., 12 "QQ" and 12 "qq", where "Q" is a haplotype harboring variation associated with increased growth). At 300 days of age, a biopsy of the longissimus dorsi muscle was collected from each animal for RNA sequencing.

RESULTS

Gene expression analysis identified 733 genes as differentially expressed between QQ and qq animals (q-value < 0.05). Notably, LCORL and genes known to be important regulators of growth such as IGF2 were upregulated in QQ individuals, while genes associated with adiposity such as FASN and LEP were downregulated, reflecting the increase in lean growth associated with this locus. Gene set enrichment analysis demonstrated QQ individuals had downregulation of pathways associated with adipogenesis, alongside upregulation of transcripts for cellular machinery essential for protein synthesis and energy metabolism, particularly ribosomal and mitochondrial components.

CONCLUSIONS

The differences in the muscle transcriptome between QQ and qq animals imply that muscle hypertrophy may be metabolically favored over accumulation of fat in animals with the QQ haplotype. Our findings also suggest this haplotype could be linked to a difference in LCORL expression that potentially influences the downstream transcriptional effects observed, though further research will be needed to confirm the molecular mechanisms underlying the associated changes in phenotype.

Molecular machineries shaping the mitochondrial inner membrane

Mitochondria display intricately shaped deep invaginations of the mitochondrial inner membrane (MIM) termed cristae. This peculiar membrane architecture is essential for diverse mitochondrial functions, such as oxidative phosphorylation or the biosynthesis of cellular building blocks. Conserved protein nano-machineries such as F1Fo-ATP synthase oligomers and the mitochondrial contact site and cristae organizing system (MICOS) act as adaptable protein-lipid scaffolds controlling MIM biogenesis and its dynamic remodelling. Signal-dependent rearrangements of cristae architecture and MIM fusion events are governed by the dynamin-like GTPase optic atrophy 1 (OPA1). Recent groundbreaking structural insights into these nano-machineries have considerably advanced our understanding of the functional architecture of mitochondria. In this Review, we discuss how the MIM-shaping machineries cooperate to control cristae and crista junction dynamics, including MIM fusion, in response to cellular signalling pathways. We also explore how mutations affecting MIM-shaping machineries compromise mitochondrial functions.

Emerging trends and hotspots of tRNA-derived small RNAs in tumours: a bibliometric analysis via VOSviewer and CiteSpace

INTRODUCTION

TRNA-derived small RNAs(tsRNAs) play an important role in many biological processes, and their dysregulation is closely related to the progression of cancer, but the research trend and future direction are not clear. This study aims to identify the leading contributors, collaboration networks, and emerging research trends in tsRNAs and their role in oncology, providing a more comprehensive and intuitive reference for researchers in this field.

MATERIALS AND METHODS

Related publications related to tsRNA in the field of oncology from 1990 to 2022 were collected from the Science Citation Index Expanded through the Web of Science Core Collection (WOSCC) database on 6 December 2022.

RESULTS

There were 2,108 publications related to tsRNAs in oncology. The articles came from 69 countries/regions, 2,218 institutions, 11,340 authors, and 200 journals, and included 9,530 keywords. The annual total number of papers and total global citation score increased steadily every year over the study period. Among the articles related to tsRNAs in oncology, the United States had the highest number of publications with 732 articles, and the United States, China, Japan, Canada, and South Korea had the highest number of collaborations. Seoul National University Sun and the journal Nucleic Acids Research had the most publications at 81 and 63 articles, respectively, and the keyword "tRF" was a hotspot.

CONCLUSION

This study provides an in-depth analysis of the research status and development trends of tsRNAs in the field of cancer from a bibliometric perspective. Offering possible guidance for researchers to explore hot topics and frontiers, select suitable journals, and partners in this field.

Biochemical mapping reveals a conserved heme transport mechanism via CcmCD in System I bacterial cytochrome c biogenesis

Heme is a redox-active cofactor for essential processes across all domains of life. Heme's redox capabilities are responsible for its biological significance but also make it highly cytotoxic, requiring tight intracellular regulation. Thus, the mechanisms of heme trafficking are still not well understood. To address this, the bacterial cytochrome c biogenesis pathways are being developed into model systems to elucidate mechanisms of heme trafficking. These pathways function to attach heme to apocytochrome c, which requires the transport of heme from inside to outside of the cell. Here, we focus on the System I pathway (CcmABCDEFGH) which is proposed to function in two steps: CcmABCD transports heme across the membrane and attaches it to CcmE. HoloCcmE then transports heme to the holocytochrome c synthase, CcmFH, for attachment to apocytochrome c. To interrogate heme transport across the membrane, we focus on CcmCD, which can form holoCcmE independent of CcmAB, leading to the hypothesis that CcmCD is a heme transporter. A structure-function analysis via cysteine/heme crosslinking identified a heme acceptance domain and heme transport channel in CcmCD. Bioinformatic analysis and structural predictions across prokaryotic organisms determined that the heme acceptance domains are structurally variable, potentially to interact with diverse heme delivery proteins. In contrast, the CcmC transmembrane heme channel is structurally conserved, indicating a common mechanism for transmembrane heme transport. We provide direct biochemical evidence mapping the CcmCD heme channel and providing insights into general mechanisms of heme trafficking by other putative heme transporters.

IMPORTANCE

Heme is a biologically important cofactor for proteins involved with essential cellular functions, such as oxygen transport and energy production. Heme can also be toxic to cells and thus requires tight regulation and specific trafficking pathways. As a result, much effort has been devoted to understanding how this important, yet cytotoxic, molecule is transported. While several heme transporters/importers/exporters have been identified, the biochemical mechanisms of transport are not well understood, representing a major knowledge gap. Here, the bacterial cytochrome c biogenesis pathway, System I (CcmABCDEFGH), is used to elucidate the transmembrane transport of heme via CcmCD. We utilize a cysteine/heme crosslinking approach, which can trap endogenous heme in specific domains, to biochemically map the heme transport channel in CcmCD, demonstrating that CcmCD is a heme transporter. These results suggest a model for heme trafficking by other heme transporters in both prokaryotes and eukaryotes.

Appearance of transient heteromorphic large chromosome in glyphosate-resistant Amaranthus tuberculatus

Glyphosate resistance in crop weeds is commonly attributed to rapid evolution through the amplification of the target gene, EPSPS (5-enolpyruvylshikimate-3-phosphate synthase). This amplification typically occurs through mechanisms such as unequal recombination, segmental duplications within the target chromosome, or the formation of ring chromosomes and extrachromosomal circular (ecc) DNA elements containing EPSPS. However, structural abnormalities in chromosomes not directly associated with EPSPS amplification have not been documented in the glyphosate-resistant weed population. Here, we describe the presence of a large chromosome found exclusively in the glyphosate-resistant Amaranthus tuberculatus (waterhemp) population but absent in susceptible counterparts. This large chromosome (~ 6 μm) is approximately twice the size of normal chromosomes (~ 2-3 μm) and is present in both male and female euploid plants (2n = 32) in a heteromorphic state. It aroses through pericentromeric heterochromatin expansion and duplications of the 5S rDNA locus but notably lacks the EPSPS gene. The large chromosome pairs with its normal homolog but was not transmitted to progeny in controlled greenhouse matings, suggesting a fitness cost in the absence of glyphosate selection pressure. This large chromosome offers a potential resource for the investigation of chromosome evolution of adaptive traits for glyphosate resistance in A. tuberculatus.

Protein Arginine Methyltransferases from Regulatory Function to Clinical Implication in Central Nervous System

Arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), is a regulatory key mechanism involved in various cellular processes such as gene expression, RNA processing, DNA damage repair. Increasing evidence highlights the crucial role of PRMTs in human diseases, including cancer, cardiovascular and metabolic diseases. Here, this review focuses on the latest findings regarding PRMTs in the central nervous system (CNS), emphasizing their regulatory roles in neural stem cells, neurons, and glial cells. Additionally, we examine the connection between PRMTs dysregulation and neurological diseases affecting the CNS, including brain tumors, neurodegenerative diseases, and neurodevelopmental disorders. Therefore, this review aims to deepen our understanding of PRMTs-mediated arginine methylation in CNS and open avenues for developing novel therapeutic strategies for neurological diseases.

Hidden origami in Trypanosoma cruzi nuclei highlights its non-random 3D genomic organization

The protozoan Trypanosoma cruzi is the causative agent of Chagas disease and is known for its polycistronic transcription, with about 50% of its genome consisting of repetitive sequences, including coding (primarily multigenic families) and non-coding regions (such as ribosomal DNA, spliced leader [SL], and retroelements, etc). Here, we evaluated the genomic features associated with higher-order chromatin organization in T. cruzi (Brazil A4 strain) by extensive computational processing of high-throughput chromosome conformation capture (Hi-C). Through the mHi-C pipeline, designed to handle multimapping reads, we demonstrated that applying canonical Hi-C processing, which overlooks repetitive DNA sequences, results in a loss of DNA-DNA contacts, misidentifying them as chromatin-folding (CF) boundaries. Our analysis revealed that loci encoding multigenic families of virulence factors are enriched in chromatin loops and form shorter and tighter CF domains than the loci encoding core genes. We uncovered a non-random three-dimensional (3D) genomic organization in which nonprotein-coding RNA loci (transfer RNAs [tRNAs], small nuclear RNAs, and small nucleolar RNAs) and transcription termination sites are preferentially located at the boundaries of the CF domains. Our data indicate 3D clustering of tRNA loci, likely optimizing transcription by RNA polymerase III, and a complex interaction between spliced leader RNA and 18S rRNA loci, suggesting a link between RNA polymerase I and II machineries. Finally, we highlighted a group of genes encoding virulence factors that interact with SL-RNA loci, suggesting a potential regulatory role. Our findings provide insights into 3D genome organization in T. cruzi, contributing to the understanding of supranucleosomal-level chromatin organization and suggesting possible links between 3D architecture and gene expression.IMPORTANCEDespite the knowledge about the linear genome sequence and the identification of numerous virulence factors in the protozoan parasite Trypanosoma cruzi, there has been a limited understanding of how these genomic features are spatially organized within the nucleus and how this organization impacts gene regulation and pathogenicity. By providing a detailed analysis of the three-dimensional (3D) chromatin architecture in T. cruzi, our study contributed to narrowing this gap. We deciphered part of the origami structure hidden in the T. cruzi nucleus, showing the unidimensional genomic features are non-randomly 3D organized in the nuclear organelle. We uncovered the role of nonprotein-coding RNA loci (e.g., transfer RNAs, spliced leader RNA, and 18S RNA) in shaping genomic architecture, offering insights into an additional epigenetic layer that may influence gene expression.

Chaperone-mediated autophagy manipulates PGC1α stability and governs energy metabolism under thermal stress

Thermogenic proteins are down-regulated under thermal stress, including PGC1α· However, the molecular mechanisms are not fully understood. Here, we addressed that chaperone-mediated autophagy could regulate the stability of PGC1α under thermal stress. In mice, knockdown of Lamp2a, one of the two components of CMA, in BAT showed increased PGC1α protein and improved metabolic phenotypes. Combining the proteomics of brown adipose tissue (BAT), structure prediction, co-immunoprecipitation- mass spectrum and biochemical assays, we found that PARK7, a Parkinson's disease causative protein, could sense the temperature changes and interact with LAMP2A and HSC70, respectively, subsequently manipulate the activity of CMA. Knockout of Park7 specific in BAT promoted BAT whitening, leading to impaired insulin sensitivity and energy expenditure at thermoneutrality. Moreover, inhibiting the activity of CMA by knockdown of LAMP2A reversed the effects induced by Park7 ablation. These findings suggest CMA is required for BAT to sustain thermoneutrality-induced whitening through degradation of PGC1α.

A modular mRNA vaccine platform encoding antigen-presenting capsid virus-like particles enhances the immunogenicity of the malaria antigen Pfs25

The COVID-19 pandemic has emphasized the potential of mRNA vaccines in fighting pandemics, owing to their rapid development, strong immunogenicity and adaptability. However, a drawback is their dose-limiting reactogenicity and inability to generate durable humoral immunity. Here we introduce a modular nucleotide vaccine platform combining the advantages of genetic and capsid virus-like-particle-based vaccines. This platform allows for the display of various antigens on different capsid virus-like particles, improving the magnitude, quality and longevity of the vaccine-induced immune responses. We applied this technology to enhance the immunogenicity of the Pfs25 antigen. Immunization with lipid-nanoparticle-formulated mRNA encoding Pfs25 capsid virus-like particles resulted in higher and potentially more durable anti-Pfs25 antibody responses, along with enhanced functional activity, compared with an mRNA vaccine encoding soluble Pfs25. By improving both humoral and cellular immune responses, this approach may reduce the dose and number of administrations required for effective protection. As a result, it can improve the feasibility of both DNA- and mRNA-based vaccines targeting pandemic and endemic infectious diseases.

HSC70 Promotes Breast Cancer Progression via PTEN Autophagic Degradation and PI3K/AKT/mTOR Activation

Heat shock cognate protein 70 (HSC70) functions as a molecular chaperone and plays a crucial role in the regulation of intracellular protein modifications that are involved in tumor autophagy. However, its expression and mechanism in breast cancer have not been studied. The expression of HSC70 was verified by TCGA database and breast cancer patient tissue. We established breast cancer cell models and mouse models using knockdown HSC70. The expression and mechanism of HSC70 in breast cancer were investigated by immunocoprecipitation, protein stability, RNA stability, flow cytometry and biogenic analysis. In this study, we found that HSC70 is highly expressed in breast cancer and that high HSC70 expression positive correlated with poor prognosis using TCGA database and patient tissue verification. Subsequent experimental verification demonstrated that HSC70 drives cell cycle progression and promotes proliferation in breast cancer. Further studies revealed that HSC70 significantly promoted the phosphorylation of PI3K, AKT and mTOR but did not affect the total protein levels. Additionally, the AKT agonist SC79 reversed the effects of HSC70 knockdown on proliferation and cell cycle progression of breast cancer cells. Mechanistically, HSC70 reduces the protein stability of PTEN but does not change its mRNA level, suggesting that HSC70 binds to PTEN and promotes its autophagic degradation. More importantly, in vivo experiments demonstrated that HSC70 knockdown results in slower tumor proliferation and growth. In conclusion, HSC70 can bind to PTEN and promote its autophagic degradation, thereby activating the PI3K/AKT/mTOR signaling pathway to promote cell cycle progression and proliferation in breast cancer. These findings suggest that HSC70 may be a feasible target for breast cancer treatment.

Narciclasine enhances cisplatin-induced apoptotic cell death by inducing unfolded protein response-mediated regulation of NOXA and MCL1

BACKGROUND

Platinum-based chemotherapy is commonly used to treat non-small cell lung cancer (NSCLC); however, innate and acquired resistance is clinically seen in many patients. Hence, a combinatorial approach with novel therapeutic agents to overcome chemoresistance is a promising option for improving patient outcomes. We investigated the combinational anticancer efficacy of cisplatin and narciclasine in three-dimensional NSCLC tumor spheroids.

METHODS

To assess the efficacy of cisplatin and narciclasine, cell viability assays, live/dead cell staining, cell death enzyme-linked immunosorbent assay (ELISA), western blot analysis for proteins related to apoptosis, and in vivo xenograft experiments were performed. The synergistic effects of cisplatin and narciclasine were elucidated through transcriptomic analysis and subsequent validation of candidate molecules by regulating their expression. To clarify the underlying molecular mechanisms, the activation of unfolded protein responses and kinetics of a candidate protein were assessed.

RESULTS

Narciclasine inhibited viability of NSCLC tumor spheroids and augmented the sensitivity of cisplatin-resistant tumor spheroids to cisplatin by inducing apoptosis. After conducting bioinformatic analysis using RNA sequencing data and functional validation experiments, we identified NOXA as a key gene responsible for the enhanced apoptosis observed with the combination of cisplatin and narciclasine. This treatment dramatically increased NOXA while downregulating anti-apoptotic MCL1 levels. Silencing NOXA reversed the enhanced apoptosis and restored MCL1 levels, while MCL1 overexpression protected tumor spheroids from combination treatment-induced apoptosis. Interestingly, narciclasine alone and in combination with cisplatin induced unfolded protein response and inhibited general protein synthesis. Furthermore, the combination treatment increased NOXA expression through the IRE1α-JNK/p38 axis and the activation of p53. Cisplatin alone and in combination with narciclasine destabilized MCL1 via NOXA-mediated proteasomal degradation.

CONCLUSIONS

We identified a natural product, narciclasine, that synergizes with cisplatin. The combination of cisplatin and narciclasine induced NOXA expression, downregulated MCL1, and ultimately induced apoptosis in NSCLC tumor spheroids. Our findings suggest that narciclasine is a potential natural product for combination with cisplatin for treatment of NSCLC.

Paediatric Cardiac Tumours: A National Population Study

Paediatric cardiac tumours are rare. The most common tumour is a rhabdomyoma, a benign tumour of the myocardium associated with Tuberous Sclerosis Complex (TSC), a rare genetic condition caused by constitutional pathogenic variants in either the TSC1 or TSC2 genes. Although benign, complications related to obstructed flow through the heart or intractable arrhythmias occur. A 23-year retrospective study of patients referred to the National Scottish Paediatric Cardiology service with evidence of a cardiac tumour. 51 patients identified; 12 prenatally, 8 live born. Of the 47 patients born alive, 44 (93.6%) patients had a benign cardiac tumour and 3 (6.4%) a malignant tumour. Rhabdomyomas were shown to be the most common tumour type in patients with TSC (p = 0.000861) and overall. 8/44 (18%) benign tumours had a documented arrhythmia, 50% requiring treatment with beta blockade. 7 patients with rhabdomyomas received an mTOR inhibitor, 6 were recorded as TSC 2 genotype. There was significant extra cardiac symptom burden for the TSC subtypes (p = 0.00105), particularly TSC2, related to renal and neurological complications. The natural history of rhabdomyomas is slow regression and if no significant mass or rhythm disturbances in early childhood, a positive cardiovascular prognosis. Identifying cases associated with TSC is important to counsel families regarding the longer-term implications related to morbidity and mortality particularly in TSC2 associated cases, which typically have a more severe phenotype. Targeted medical therapy is indicated and shown to be effective for the treatment of benign cardiac tumours causing significant rhythm or mass effect. mTOR inhibitors should be considered in the treatment of rhabdomyomas and beta blockade for haemangiomas.

METTL1-mediated m7G tRNA modification drives papillary thyroid cancer progression and metastasis by regulating the codon-specific translation of TNF-α

N7-methylguanosine (m7G) modification of transfer RNA (tRNA) is essential for the biological functions of tRNAs and has been found to play a regulatory role in a variety of human cancers. However, the biological function of METTL1-mediated m7G tRNA modification in papillary thyroid cancer (PTC) is unclear. Here, we found that METTL1 is significantly upregulated in PTC tissues compared to normal control tissues and is associated with poor PTC prognosis. Functional analysis confirmed that METTL1 promotes the proliferation and metastasis of PTC cells in a manner dependent on its tRNA methyltransferase activity. Mechanistically, METTL1 knockdown leads to a decrease in the abundance of certain m7G-modified tRNAs, which suppresses the m7G tRNA modification-mediated codon-specific translation of TNF-α. Furthermore, exogenous supplementation with TNF-α partially reversed the decrease in the proliferation and metastasis of PTC cells induced by METTL1 deletion. Positive correlations between METTL1, WDR4, and TNF-α expression, which affect the proliferation and metastasis of PTC, were confirmed via analysis of microarrays containing PTC tissues. These results demonstrate the oncogenic role of METTL1-mediated m7G tRNA modification in regulating codon-specific translation efficiency in PTC and suggest that targeting METTL1 may be a promising therapeutic approach for overcoming PTC progression by inhibiting PTC cell proliferation and metastasis.

Regulation of elevated expression of Mcl-1 in hepatocellular carcinoma - a review

Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors worldwide. Mcl-1 (myeloid cell leukemia-1) is highly expressed in HCC cells and plays a critical role in chemotherapy resistance and is a major contributor to chemotherapy failure in HCC. The purpose of this study is to review the recent research progress that explores the key factors in regulating Mcl-1 overexpression in HCC cells, contributing to chemotherapy resistance. The related studies from the past decade on agents targeting Mcl-1 to inhibit HCC were also reviewed to provide insights into overcoming chemotherapy resistance in HCC. Mcl-1 overexpression in HCC is mainly regulated by transcription factors (such as STAT3, p53), non-coding RNAs (such as miRNA, lncRNA), cell cycle proteins, mitochondrial dynamics, and the hypoxic microenvironment. Targeting Mcl-1, alongside multi-target combination therapies, may overcome HCC chemotherapy resistance and improve outcomes. Future research should focus on strategies addressing multiple pathways to minimize monotherapy resistance risks and offer enhanced treatment options for the betterment of human health.

WDR62 affects the progression of ovarian cancer by regulating the cell cycle

BACKGROUND

Ovarian Cancer (OC) is a gynecological malignant tumor with an extremely high mortality rate, seriously endangering women's health. Due to its insidious clinical manifestations, most patients are diagnosed in the advanced stage of the disease. The currently clinically relied CA125 has limited specificity for the early diagnosis of ovarian cancer. Hence, identifying new promising biomarkers is crucial for the early screening, diagnosis, and treatment of ovarian cancer. Based on differential expression analysis, WGCNA and survival analysis, we identified a centromere-associated gene, WDR62, which is highly expressed in ovarian cancer and highly correlated with ovarian cancer, as well as the poor prognosis of ovarian cancer patients with high expression, suggesting that WDR62 may be a potential biomarker for ovarian cancer. Previous studies have shown that WDR62 is closely associated with the occurrence, development and prognosis of a variety of tumors. However, its role in ovarian cancer has not been studied in depth.

METHODS

Using combined TCGA and GTEx datasets from the UCSC database, along with WGCNA, and survival analysis, WDR62 was identified as a potential biomarker. GEPIA2 database, GEO database, qRT-PCR, and Western blot proved the expression of WDR62. Enrichment analysis, cell transfection, Western blots and CCK8 demonstrated the regulatory mechanism of WDR62, and the detailed mechanism of WDR62 involvement in the occurrence and development of ovarian cancer was predicted by interaction analysis and correlation analysis.

RESULTS

WDR62 was highly expressed in ovarian cancer cells compared to normal ovarian epithelial cells, both at the RNA and protein levels. Patients with high WDR62 expression had a poor survival prognosis. Upon WDR62 knockdown, the expression of cell cycle-related proteins CDK1 and C-Myc decreased in ovarian cancer cells, and the cell proliferative capacity was decreased. Based on bioinformatic analysis, it was hypothesized that WDR62 might mediate the JNK signaling pathway by interacting with MAPK8, thus affecting ovarian cancer progression through cell cycle regulation.

CONCLUSIONS

WDR62 is overexpressed in ovarian cancer and is closely related to the prognosis of ovarian cancer patients. WDR62 promotes ovarian cancer progression by regulating the cell cycle and may influence its development through interaction with MAPK8 to mediate the JNK signaling pathway. These findings suggest that WDR62 could be a potential target for the early screening, diagnosis, and treatment of ovarian cancer.

Epithelioid Hemangioendothelioma: Treatment Landscape and Innovations for an Ultra-Rare Sarcoma

OPINION STATEMENT

Epithelioid hemangioendothelioma (EHE) is an ultra-rare sarcoma with a paucity of data on best practices for management. Pathogenic translocations involving the YAP or TAZ genes lead to constitutive activation of TEAD and TEAD-associated pathways. As our understanding of the molecular drivers of EHE has advanced, investigational treatment strategies have shifted away from cytotoxic chemotherapy toward more targeted approaches. This review focuses on the historical context and evolving landscape of systemic therapies for patients with EHE. For newly diagnosed patients, we recommend consultation at a high-volume sarcoma center whenever possible. If the disease is localized and resectable, surgical excision by a sarcoma-focused surgical oncologist is preferred. When the disease is unresectable, we first assess for disease progression to determine whether active surveillance is appropriate. Some patients may experience indolent, asymptomatic disease for years-or even decades-without requiring intervention. In patients with progressive or symptomatic unresectable disease, systemic therapy is warranted. Setting realistic expectations about the goals of treatment is essential, as no current systemic therapies reliably reduce tumor burden. However, molecular profiling and ongoing correlative studies from clinical trials may soon identify more effective therapeutic targets. For this reason, we encourage referral to centers that routinely perform molecular profiling and offer clinical trials with eligibility criteria for EHE, even to be considered as a first-line approach. Outside of a clinical trial, cytotoxic chemotherapy remains the frontline standard of care for patients who require systemic treatment. Importantly, treatment decisions must incorporate patient preferences and recognition that symptomatic improvement alone can be a meaningful outcome for preserving quality of life.

The aryl hydrocarbon receptor: a new frontier in male reproductive system

BACKGROUND

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor historically recognized for its role in the regulation of toxicity mediated by environmental chemicals. Recent research points to AhR's critical participation in male reproductive physiology, particularly in spermatogenesis, hormone signaling, and the maintenance of sperm quality. Both endogenous ligands (e.g., dietary and gut microbiota-derived metabolites) and exogenous pollutants (e.g., dioxins and benzo-α-pyrene) influence AhR-mediated pathways, making it a key link between environmental exposures and male fertility.

RESULTS

This review highlights AhR's influence on the male reproductive system, emphasizing the role of endogenous AhR ligands and AhR expression in the maturation and function of male reproductive organs. Environmental AhR agonists have been shown to induce oxidative stress, hormonal imbalance, and sperm DNA damage, which impact harmfully on the spermatogenesis process, which leads to reproductive abnormalities. Conversely, certain natural compounds such as resveratrol, curcumin, and lycopene appear to antagonize AhR activation and reduce its negative effects, thus offering potential protective benefits against male reproductive toxicity. Nevertheless, discrepancies persist regarding the exact interplay between AhR signaling and critical reproductive hormones such as testosterone and LH, and it remains unclear how transgenerational epigenetic changes triggered by AhR activation might affect long-term male fertility.

CONCLUSION

AhR is pivotal in male reproductive physiology, influencing spermatogenesis, sperm quality, and hormone regulation through its interactions with both endogenous and environmental ligands. Persistent pollutants such as dioxins and polycyclic aromatic hydrocarbons cause oxidative damage and hormonal disturbances via AhR, contributing to reduced sperm quality and fertility.

Fibroblasts in immune responses, inflammatory diseases and therapeutic implications

Once regarded as passive bystander cells of the tissue stroma, fibroblasts have emerged as active orchestrators of tissue homeostasis and disease. From regulating immunity and controlling tissue remodelling to governing cell growth and differentiation, fibroblasts assume myriad roles in guiding normal tissue development, maintenance and repair. By comparison, in chronic inflammatory diseases such as rheumatoid arthritis, fibroblasts recruit and sustain inflammatory leukocytes, become dominant producers of pro-inflammatory factors and catalyse tissue destruction. In other disease contexts, fibroblasts promote fibrosis and impair host control of cancer. Single-cell studies have uncovered striking transcriptional and functional heterogeneity exhibited by fibroblasts in both normal tissues and diseased tissues. In particular, advances in the understanding of fibroblast pathology in rheumatoid arthritis have shed light on pathogenic fibroblast states in other chronic diseases. The differentiation and activation of these fibroblast states is driven by diverse physical and chemical cues within the tissue microenvironment and by cell-intrinsic signalling and epigenetic mechanisms. These insights into fibroblast behaviour and regulation have illuminated therapeutic opportunities for the targeted deletion or modulation of pathogenic fibroblasts across many diseases.

Infection-relevant conditions dictate differential versus coordinate expression of Salmonella chaperones and cochaperones

Molecular chaperones are critical for protein homeostasis. In bacteria, chaperone trigger factor (TF) folds proteins co-translationally, and chaperone DnaK requires a J-domain cochaperone and nucleotide exchange factor GrpE to fold proteins largely post-translationally. However, when the pathogen Salmonella enterica serovar Typhimurium faces the infection-relevant condition of cytoplasmic Mg2+ starvation, DnaK reduces protein synthesis independently. This raises the possibility that bacteria differentially express chaperones and cochaperones. We now report that S. Typhimurium responds to cytoplasmic Mg2+ starvation by increasing mRNA amounts of dnaK while decreasing those of the TF-encoding gene tig and J-domain cochaperone genes dnaJ and djlA. This differential strategy requires the master regulator of Mg2+ homeostasis and virulence PhoP, which increases dnaK mRNA amounts by lowering the ATP concentration, thereby hindering proteolysis of the alternative sigma factor RpoH responsible for dnaK transcription. We also establish that DnaK exerts negative feedback on the RpoH protein and RpoH-dependent transcripts independently of J-domain cochaperones. Thus, bacteria express chaperones and cochaperones coordinately or differentially depending on the specific stress perturbing protein homeostasis.IMPORTANCEMolecular chaperones typically require cochaperones to fold proteins and to prevent protein aggregation, and the corresponding genes are thus coordinately expressed. We have now identified an infection-relevant stress condition in which the genes specifying chaperone DnaK and cochaperone DnaJ are differentially expressed despite belonging to the same operon. This differential strategy requires the master regulator of Mg2+ homeostasis and virulence in the pathogen Salmonella enterica serovar Typhimurium. Moreover, it likely reflects that Salmonella requires dnaK, but not J-domain cochaperone-encoding genes, for survival against cytoplasmic Mg2+ starvation and expresses genes only when needed. Thus, the specific condition impacting protein homeostasis determines the coordinate versus differential expression of molecular chaperones and cochaperones.

Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF?

Lens epithelium-derived growth factor (LEDGF) is a chromatin-binding protein. It regulates gene transcription and is associated with acquired immunodeficiency syndrome and cancer. Its PWWP domain binds to histone H3 at K36 (H3K36). The binding affinity depends on H3K36 methylation. To investigate this dependency, we performed molecular dynamics simulations of the PWWP domain and histone fragments. We found that not only hydrophobic interaction but also electrostatic interaction is important. The binding is not maintained with nonmethylated and monomethylated H3K36 because the tips of these H3K36s form hydrogen bonds with water molecules, while dimethylated and trimethylated H3K36 form no such hydrogen bond, making this binding stable.

Systematic transcriptomics analysis of calorie restriction and rapamycin unveils their synergistic interaction in prolonging cellular lifespan

Aging is a multifaceted biological process marked by the decline in both mitotic and postmitotic cellular function, often central to the development of age-related diseases. In the pursuit of slowing or even reversing the aging process, a prominent strategy of significant interest is calorie restriction (CR), also known as dietary restriction, and the potential influence of a drug called rapamycin (RM). Both CR and RM have demonstrated the capacity to extend healthspan and lifespan across a diverse array of species, including yeast, worms, flies, and mice. Nevertheless, their individual and combined effects on mitotic and postmitotic cells, as well as their comparative analysis, remain areas that demand a thorough investigation. In this study, we employ RNA-sequencing methodologies to comprehensively analyze the impact of CR, RM, and their combination (CR + RM) on gene expression in yeast cells. Our analysis uncovers distinctive, overlapping, and even contrasting patterns of gene regulation, illuminating the unique and shared effects of CR and RM. Furthermore, the transcriptional synergistic interaction of CR + RM is validated in extending the lifespan of both yeast and human cells.