Homeostasis Research Articles

Mitochondrial genome-derived circRNAs: Orphan epigenetic regulators in molecular biology

Mitochondria are vital for cellular activities, influencing ATP production, Ca2+ signaling, and reactive oxygen species generation. It has been proposed that nuclear genome-derived circular RNAs (circRNAs) play a role in biological processes. For the first time, this study aims to comprehensively explore experimentally confirmed human mitochondrial genome-derived circRNAs (mt-circRNAs) via in-silico analysis. We utilized wide-ranging bioinformatics tools to anticipate their roles in molecular biology, involving miRNA sponging, protein antagonism, and peptide translation. Among five well-characterized mt-circRNAs, SCAR/mc-COX2 stands out as particularly significant with the potential to sponge around 41 different miRNAs, which target several genes mostly involved in endocytosis, MAP kinase, and PI3K-Akt pathways. Interestingly, circMNTND5 and mecciND1 specifically interact with miRNAs through their unique back-splice junction sequence. These exclusively targeted miRNAs (has-miR-5186, 6888-5p, 8081, 924, 672-5p) are predominantly associated with insulin secretion, proteoglycans in cancer, and MAPK signaling pathways. Moreover, all mt-circRNAs intricately affect the P53 pathway through miRNA sequestration. Remarkably, mc-COX2 and circMNTND5 appear to be involved in the RNA’s biogenesis by antagonizing AGO1/2, EIF4A3, and DGCR8. All mt-circRNAs engaged with IGF2BP proteins crucial in redox signaling, and except mecciND1, they all potentially generate at least one protein resembling the immunoglobulin heavy chain protein. Given P53′s function as a redox-sensitive transcription factor, and insulin’s role as a crucial regulator of energy metabolism, their indirect interplay with mt-circRNAs could influence cellular outcomes. However, due to limited attention and infrequent data availability, it is advisable to conduct more thorough investigations to gain a deeper understanding of the functions of mt-circRNA.

The epigenetic modification of DNA methylation in neurological diseases.

Methylation, a key epigenetic modification, is essential for regulating gene expression and protein function without altering the DNA sequence, contributing to various biological processes, including gene transcription, embryonic development, and cellular functions. Methylation encompasses DNA methylation, RNA methylation and histone modification. Recent research indicates that DNA methylation is vital for establishing and maintaining normal brain functions by modulating the high-order structure of DNA. Alterations in the patterns of DNA methylation can exert significant impacts on both gene expression and cellular function, playing a role in the development of numerous diseases, such as neurological disorders, cardiovascular diseases as well as cancer. Our current understanding of the etiology of neurological diseases emphasizes a multifaceted process that includes neurodegenerative, neuroinflammatory, and neurovascular events. Epigenetic modifications, especially DNA methylation, are fundamental in the control of gene expression and are critical in the onset and progression of neurological disorders. Furthermore, we comprehensively overview the role and mechanism of DNA methylation in in various biological processes and gene regulation in neurological diseases. Understanding the mechanisms and dynamics of DNA methylation in neural development can provide valuable insights into human biology and potentially lead to novel therapies for various neurological diseases.

CDS2 expression regulates de novo phosphatidic acid synthesis.

CDS enzymes (CDS1 and 2 in mammals) convert phosphatidic acid (PA) to CDP-DG, an essential intermediate in the de novo synthesis of PI. Genetic deletion of CDS2 in primary mouse macrophages resulted in only modest changes in the steady-state levels of major phospholipid species, including PI, but substantial increases in several species of PA, CDP-DG, DG and TG. Stable isotope labelling experiments employing both 13C6- and 13C6D7-glucose revealed loss of CDS2 resulted in a minimal reduction in the rate of de novo PI synthesis but a substantial increase in the rate of de novo PA synthesis from G3P, derived from DHAP via glycolysis. This increased synthesis of PA provides a potential explanation for normal basal PI synthesis in the face of reduced CDS capacity (via increased provision of substrate to CDS1) and increased synthesis of DG and TG (via increased provision of substrate to LIPINs). However, under conditions of sustained GPCR-stimulation of PLC, CDS2-deficient macrophages were unable to maintain enhanced rates of PI synthesis via the 'PI cycle', leading to a substantial loss of PI. CDS2-deficient macrophages also exhibited significant defects in calcium homeostasis which were unrelated to the activation of PLC and thus probably an indirect effect of increased basal PA. These experiments reveal that an important homeostatic response in mammalian cells to a reduction in CDS capacity is increased de novo synthesis of PA, likely related to maintaining normal levels of PI, and provides a new interpretation of previous work describing pleiotropic effects of CDS2 deletion on lipid metabolism/signalling.

Linking metabolism and histone acetylation dynamics by integrated metabolic flux analysis of Acetyl-CoA and histone acetylation sites

ObjectivesHistone acetylation is an important epigenetic modification that regulates various biological processes and cell homeostasis. Acetyl-CoA, a hub molecule of metabolism, is the substrate for histone acetylation, thus linking metabolism with epigenetic regulation. However, still relatively little is known about the dynamics of histone acetylation and its dependence on metabolic processes, due to the lack of integrated methods that can capture site-specific histone acetylation and deacetylation reactions together with the dynamics of acetyl-CoA synthesis. MethodsIn this study, we present a novel proteo-metabo-flux approach that combines mass spectrometry-based metabolic flux analysis of acetyl-CoA and histone acetylation with computational modelling. We developed a mathematical model to describe metabolic label incorporation into acetyl-CoA and histone acetylation based on experimentally measured relative abundances. ResultsWe demonstrate that our approach is able to determine acetyl-CoA synthesis dynamics and site-specific histone acetylation and deacetylation reaction rate constants, and that consideration of the metabolically labelled acetyl-CoA fraction is essential for accurate determination of histone acetylation dynamics. Furthermore, we show that without correction, changes in metabolic fluxes would be misinterpreted as changes in histone acetylation dynamics, whereas our proteo-metabo-flux approach allows to distinguish between the two processes. ConclusionsOur proteo-metabo-flux approach expands the repertoire of metabolic flux analysis and cross-omics and represents a valuable approach to study the regulatory interplay between metabolism and epigenetic regulation by histone acetylation.

The liver as a central "hub" of the immune system: pathophysiological implications

The purpose of this review is to describe the immune function of the liver, guiding the reader from the homeostatic tolerogenic status to the aberrant activation demonstrated in chronic liver disease. An extensive description of the pathways behind the inflammatory modulation of the healthy liver will be provided focusing on the complex immune cell network residing within the liver. The limit of tolerance will be presented in the context of organ transplantation, seizing the limits of homeostatic mechanisms that fail in accepting the graft, progressing eventually toward rejection. The triggers and mechanisms behind chronic activation in metabolic liver conditions and viral hepatitis will be discussed. The last session will be dedicated to one of the greatest paradoxes for a tolerogenic organ, developing autoimmunity. Through the description of the three most common autoimmune liver disease, the autoimmune reaction against hepatocytes and biliary epithelial cells will be dissected.

Rational Design of High-Efficiency Synthetic Small Regulatory RNAs and Their Application in Robust Genetic Circuit Performance Through Tight Control of Leaky Gene Expression.

Synthetic sRNAs show promise as tools for targeted and programmable gene expression manipulation. However, the design of high-efficiency synthetic sRNAs is a challenging task that necessitates careful consideration of multiple factors. Therefore, this study aims to investigate rational design strategies that significantly and robustly enhance the efficiency of synthetic sRNAs. This is achieved by optimizing the following parameters: the sRNA scaffold, mRNA binding affinity, Hfq protein expression level, and mRNA secondary structure. By utilizing optimized synthetic sRNAs within a positive feedback circuit, we effectively addressed the issue of gene expression leakage─an enduring challenge in synthetic biology that undermines the reliability of genetic circuits in bacteria. Our designed synthetic sRNAs successfully prevented gene expression leakage, thus averting unintended circuit activation caused by initial expression noise, even in the absence of signal molecules. This result shows that high-efficiency synthetic sRNAs not only enable precise gene knockdown for metabolic engineering but also ensure the robust performance of synthetic circuits. The strategies developed here hold significant promise for broad applications across diverse biotechnological fields, establishing synthetic sRNAs as pivotal tools in advancing synthetic biology and gene regulation.

The overexpression of R-spondin 3 affects hair morphogenesis and hair development along with the formation and maturation of the hair follicle stem cells.

Mice hair follicles (HFs) are a valuable model for studying various aspects of hair biology, including morphogenesis, development, and regeneration due to their easily observable phenotype and genetic manipulability. The initiation and progression of hair follicle morphogenesis, as well as the hair follicle cycle, are regulated by various signaling pathways, of which the main role is played by the Wingless-type MMTV integration site family (Wnt) and the Bone Morphogenic Protein (BMP). During the hair follicle cycle, the BMP pathway maintains hair follicle stem cells (HFSCs) in a dormant state while the Wnt pathway activates them for hair growth. Given the pivotal role of the Wnt pathway in hair biology and HFSCs regulation, we investigated the influence of the Wnt modulator - R-spondin 3 (Rspo3), in these processes. For this purpose, we developed a transgenic mice model with the overexpression of Rspo3 (Rspo3GOF) in the whole ectoderm and its derivatives, starting from early morphogenesis. Rspo3GOF mice exhibited a distinct phenotype with sparse hair and visible bald areas, caused by reduced proliferation and increased apoptosis of hair matrix progenitor cells, which resulted in a premature anagen-to-catagen transition with a shortened growth phase and decreased overall length of all hair types. In addition, Rspo3GOF promoted induction of auchene and awl, canonical Wnt-dependent hair type during morphogenesis, but the overall hair amount remained reduced. We also discovered a delay in the pre-bulge formation during morphogenesis and prolonged immaturity of the HFSC population in the bulge region postnatally, which further impaired proper hair regeneration throughout the mice's lifespan. Our data supported that Rspo3 function observed in our model works in HFSCs' formation of pre-bulge during morphogenesis via enhancing activation of the canonical Wnt pathway, whereas in contrast, in the postnatal immature bulge, activation of canonical Wnt signaling was attenuated. In vitro studies on keratinocytes revealed changes in proliferation, migration, and colony formation, highlighting the inhibitory effect of constitutive overexpression of Rspo3 on these cellular processes. Our research provides novel insights into the role of Rspo3 in the regulation of hair morphogenesis and development, along with the formation and maturation of the HFSCs, which affect hair regeneration.

20 Trace metal homeostasis in growing cattle

Abstract Apparent trace metal absorption and tissue retention upon incremental levels of supplemental Zn, Cu, and Mn were studied in growing cattle. A total of 60 Holstein bulls were enrolled for the study and fed for 28 d a diet consisting of barley straw (15%), molasses (10%) and pelleted concentrate (75%; Zn = 78 ppm, Cu = 15 ppm, Mn = 91 ppm). Thereafter, 20 bulls were randomly selected and slaughtered for determination of baseline tissue trace metal composition. The remaining 40 bulls [body weight (BW) = 394 ± 20 kg] were then blocked based on BW in 8 blocks of 5 bulls each. Bulls within a block were randomly assigned one of the diets differing in supplemental levels of Zn, Cu, and Mn (all from sulfate form) with the following dietary contents of Zn, Cu and Mn, respectively: No supplement (38, 7, and 47 ppm), Dose 1 (61, 11, and 68 ppm), Dose 2 (78, 15 and 91 ppm), Dose 3 (123, 26, 136 ppm) or Dose 4 (195, 43, and 214 ppm). These diets were fed for 12 wk, and complete collection of feces and urine were performed on wk 4, 8 and 12 for assessment of trace metals balance and apparent absorption. Gastrointestinal tissues, whole organs (heart, liver, spleen, and kidney), bile, cervical vertebra, and tibia were collected at slaughterhouse from all bulls. All samples were dried, ground, and analyzed for minerals. Data were processed using dietary treatment as a continuous variable and also as categorial variable. Both approaches adjusted for the fixed effect of block (Proc Mixed, SAS 9.4). Whole-body Zn, Cu and Mn balance quadratically increased (P < 0.05) with supplementation, with a significantly higher values for Dose 4 compared with all other dietary treatment (Figure 1, P < 0.05). Dose 4 also led to a 2-fold increase in urinary Zn and Cu excretions (P < 0.05), and a 4-fold increase in urinary Mn excretion (P < 0.01). Although magnitudes of change were moderate (8 to 15%), increasing dietary Zn supply linearly increased spleen Zn content (P = 0.03), and tended to increase ruminal and hepatic Zn content (P < 0.10). Hepatic Cu linearly increased from 264 to 667 mg/kg DM with increasing dietary Cu supply (P < 0.01), whereas Cu concentration in bile only increased at Doses 4 and 5 (P < 0.01). Increasing Mn supply resulted in quadratic increase of ruminal and biliary Mn content from 340 to 1140 mg/kg DM, and from 0.32 to 1.38 mg/L, respectively. Small intestine and cecum Mn concentrations linearly and quadratically increased (about 2-fold increase, P < 0.05) with incremental supply of Mn. Homeostatic regulation mechanisms were apparently overwhelmed at the greatest Zn, Cu and Mn supplementation levels evaluated in this study.

145 Utilization of 16s sequencing data and physiological measurements to produce a comparative analysis of the equine microbiome

Abstract Rapid advancements in microbiome research, particularly in the technologies associated with next-generation sequencing have enabled unprecedented investigations into the composition of the equine microbiome. The large datasets produced from these studies often present challenges to researchers seeking to understand the applicability of these data to equine physiology. To that end, a multi-year project was conducted with the goal of determining the core bacterial population of the equine hindgut through analysis of rectal swabs collected from thousands of horses and applying logic to the association between these ecologies and equine health. Samples were obtained from horses that varied across a diverse range of considerations including location, breed, age, and diet, amongst other metadata points including disease state, health history, vaccination and deworming status, body condition, and pregnancy status. These data were used in the development of a comparative score, that authors defined as the Microbiome Quotient (MQ score). Rectal swabs were collected, and DNA was extracted using the Quick-DNA Fecal/Soil Microbe Miniprep kit (Zymo Research, Irvine, CA) and the V3-V4 hypervariable region of the 16S rRNA gene was sequenced by following the Illumina 16S Protocol (San Diego, CA). Sequences were denoised using DADA2 within the QIIME2 pipeline to obtain amplicon sequence variant composition. These data were filtered again in R (4.2.2) to remove samples with missing data and low sequencing depth. Sample metadata was used to classify samples as either typical or atypical. The MQ score was calculated by computing the Euclidean distance difference between a sample and the centroids representing typical and atypical microbial ecologies, and then subtracting these distances to obtain the individual score. This score quantifies how similar the microbiome in a sample is to those of typical and atypical horses. These scores were then categorized into tertiles, representing the status of the individual horse’s microbiome. These statuses indicate differences in bacterial ecology among samples and their subsequent relevance to the health of the horse. While a large portion of the equine fecal microbiome is conserved through homeostatic and other mechanisms, there remains a high degree of variability in the lesser abundant genera that may be responsible for the different physiological interactions between the microbes and their hosts. Utilizing this MQ score, feeding and management recommendations can be made, providing veterinarians and horse owners with a tool to support the health and performance of horses through modulation of the bacterial population and its functionality. Further research is necessary to fully elucidate the impact of the various metadata components on the bacterial ecology. Additionally, the function of the metagenome is a critical component of microbiome sciences. Prediction of metagenomic function is likely to provide insight into the regulation of physiological function by the microbial population residing within the host.

28 Integrating homeostasis in practical mineral supplementation recommendations

Abstract A long-established objective in ruminant nutrition is an accurate supply of the 4 main trace metal nutrients Zn, Cu, Mn, and Fe, respecting bioavailability, nutritional interactions, and nutrient tolerance. Although, current dietary supplementation practices, justified by the multiple uncertainties of trace metal supply, results in dietary levels that widely exceed nutritional guidelines. Additionally, reference feeding recommendations are defined assuming fixed and highly conservative uptake coefficients, an approach that disregards the opportunity, and limitations, of absorptive regulation, the main homeostatic mechanism of these nutrients. Mitigating deficiency risks by generous supplementation can result in a generally overlooked risk, exceeding tolerable trace metal availability. Complete nutrient balance studies have recently described the overwhelming homeostatic downregulation of trace metals at dietary levels that are not uncommon in practice. This finding calls for a novel approach to define supplementation that resolves this conundrum of trace metal adequacy. This approach integrated 3 elements: a stochastic analysis of native dietary supply; a stochastic analysis of net nutrient requirements; and the identification of the upper and lower boundaries of homeostatic regulation for these 4 nutrients in the bovine species. This last, aims to resolve the main limitation of current dietary guidelines, using the potential maximum uptake rates in homeostatic upregulation, and the minimum uptake rates achievable by downregulation, instead of assuming fixed uptake rates. As result, this approach delivers dietary supply ranges of adequate supply, instead of a minimum dietary level to meet dietary adequacy. The probability distribution of nutrient supply was determined by dry-matter intake variability, diversity in dietary composition, and variability of nutrient occurrence in feedstuffs. The probability distribution of net nutrient requirements was defined by the variability of the components of a classic factorial requirement approach applied to different animal conditions. A maximum apparent absorption efficiency was determined to define lower supply boundaries using published datasets. Upper boundaries were defined as the dietary supply level beyond which apparent absorption empirically has shown to exceed net requirements. As expected, this risk-based approach resulted in much lower supplementation recommendations than current reference models. However, it supports the value of preventive supplementation of Zn and Cu to growing and lactating animals, and Cu to non-lactating non-growing cows. This assessment also indicates merit in Mn supplementation to growing bovines. Furthermore, it confirms that under all circumstances native dietary Fe meets nutritional needs, but it also illustrates a tolerance risk to native Fe supply under multiple productive scenarios. Most interestingly, this analysis illustrates the risk of exceeding trace metal tolerance boundaries with common levels of supplementation under common conditions. This approach offers a novel perspective to trace metal supplementation, pointing at an opportunity to improve nutritional adequacy by reconsidering supplementation practices.

Gasdermin D-mediated metabolic crosstalk promotes tissue repair.

The establishment of an early pro-regenerative niche is crucial for tissue regeneration1,2. Gasdermin D (GSDMD)-dependent pyroptosis accounts for the release of inflammatory cytokines upon various insults3-5. However, little is known about its role in tissue regeneration followed by homeostatic maintenance. Here we show that macrophage GSDMD deficiency delays tissue recovery but has little effect on the local inflammatory milieu or the lytic pyroptosis process. Profiling of the metabolite secretome of hyperactivated macrophages revealed a non-canonical metabolite-secreting function of GSDMD. We further identified 11,12-epoxyeicosatrienoic acid (11,12-EET) as a bioactive, pro-healing oxylipin that is secreted from hyperactive macrophages in a GSDMD-dependent manner. Accumulation of 11,12-EET by direct supplementation or deletion of Ephx2, which encodes a 11,12-EET-hydrolytic enzyme, accelerated muscle regeneration. We further demonstrated that EPHX2 accumulated within aged muscle, and that consecutive 11,12-EET treatment rejuvenated aged muscle. Mechanistically, 11,12-EET amplifies fibroblast growth factor signalling by modulating liquid-liquid phase separation of fibroblast growth factors, thereby boosting the activation and proliferation of muscle stem cells. These data depict a GSDMD-guided metabolite crosstalk between macrophages and muscle stem cells that governs the repair process, which offers insights with therapeutic implications for the regeneration of injured or aged tissues.

PRC1 Protein Subcomplexes Architecture: Focus on the Interplay between Distinct PCGF Subunits in Protein Interaction Networks.

The six PCGF proteins (PCGF1-6) define the biochemical identity of Polycomb repressor complex 1 (PRC1) subcomplexes. While structural and functional studies of PRC1 subcomplexes have revealed their specialized roles in distinct aspects of epigenetic regulation, our understanding of the variation in the protein interaction networks of distinct PCGF subunits in different PRC1 complexes is incomplete. We carried out an affinity purification mass spectrometry (AP-MS) screening of three PCGF subunits, PCGF1 (NSPC1), PCGF2 (MEL18), and PCGF4 (BMI1), to define their interactome and potential cellular function in pluripotent human embryonal carcinoma cell "NT2". The bioinformatic analysis revealed that these interacting proteins cover a range of functional pathways, often involved in cell biology and chromatin regulation. We also found evidence of mutual regulation (at mRNA and protein level) between three distinct PCGF subunits. Furthermore, we confirmed that the disruption of these subunits results in reduced cell proliferation ability. We reveal an interplay between the compositional diversity of the distinct PCGF containing PRC1 complex and the potential role of PCGF proteins within the wider cellular network.

Hypoxia in Human Obesity: New Insights from Inflammation towards Insulin Resistance-A Narrative Review.

Insulin resistance (IR), marked by reduced cellular responsiveness to insulin, and obesity, defined by the excessive accumulation of adipose tissue, are two intertwined conditions that significantly contribute to the global burden of cardiometabolic diseases. Adipose tissue, beyond merely storing triglycerides, acts as an active producer of biomolecules. In obesity, as adipose tissue undergoes hypertrophy, it becomes dysfunctional, altering the release of adipocyte-derived factors, known as adipokines. This dysfunction promotes low-grade chronic inflammation, exacerbates IR, and creates a hyperglycemic, proatherogenic, and prothrombotic environment. However, the fundamental cause of these phenomena remains unclear. This narrative review points to hypoxia as a critical trigger for the molecular changes associated with fat accumulation, particularly within visceral adipose tissue (VAT). The activation of hypoxia-inducible factor-1 (HIF-1), a transcription factor that regulates homeostatic responses to low oxygen levels, initiates a series of molecular events in VAT, leading to the aberrant release of adipokines, many of which are still unexplored, and potentially affecting peripheral insulin sensitivity. Recent discoveries have highlighted the role of hypoxia and miRNA-128 in regulating the insulin receptor in visceral adipocytes, contributing to their dysfunctional behavior, including impaired glucose uptake. Understanding the complex interplay between adipose tissue hypoxia, dysfunction, inflammation, and IR in obesity is essential for developing innovative, targeted therapeutic strategies.

Dynamically adjusted cell fate decisions and resilience to mutant invasion during steady-state hematopoiesis revealed by an experimentally parameterized mathematical model

A major next step in hematopoietic stem cell (HSC) biology is to enhance our quantitative understanding of cellular and evolutionary dynamics involved in undisturbed hematopoiesis. Mathematical models have been and continue to be key in this respect, and are most powerful when parameterized experimentally and containing sufficient biological complexity. In this paper, we use data from label propagation experiments in mice to parameterize a mathematical model of hematopoiesis that includes homeostatic control mechanisms as well as clonal evolution. We find that nonlinear feedback control can drastically change the interpretation of kinetic estimates at homeostasis. This suggests that short-term HSC and multipotent progenitors can dynamically adjust to sustain themselves temporarily in the absence of long-term HSCs, even if they differentiate more often than they self-renew in undisturbed homeostasis. Additionally, the presence of feedback control in the model renders the system resilient against mutant invasion. Invasion barriers, however, can be overcome by a combination of age-related changes in stem cell differentiation and evolutionary niche construction dynamics based on a mutant-associated inflammatory environment. This helps us understand the evolution of e.g., TET2 or DNMT3A mutants, and how to potentially reduce mutant burden.

Kinetic Modeling of In Vivo K+ Distribution and Fluxes with Stable K+ Isotopes: Effects of Dietary K+ Restriction.

Maintaining extracellular potassium (K+) within narrow limits, critical for membrane potential and excitability, is accomplished through the internal redistribution of K+ between extracellular fluid (ECF) and intracellular fluid (ICF) in concert with the regulation of renal K+ output to balance K+ intake. Here we present evidence from high-precision analyses of stable K+ isotopes in rats maintained on a control diet that the tissues and organs involved in the internal redistribution of K+ differ in their speed of K+ exchange with ECF and can be grouped into those that exchange K+ with ECF either rapidly or more slowly ("fast" and "slow" pools). After 10 days of K+ restriction, a compartmental analysis indicates that the sizes of the ICF K+ pools decreased but that this decrease in ICF K+ pools was not homogeneous, rather occurring only in the slow pool (15% decrease, p < 0.01), representing skeletal muscles, not in the fast pool. Furthermore, we find that the dietary K+ restriction is associated with a decline in the rate constants for K+ effluxes from both the "fast" and "slow" ICF pools (p < 0.05 for both). These results suggest that changes in unidentified transport pathways responsible for K+ efflux from ICF to ECF play an important role in buffering the internal redistribution of K+ between ICF and ECF during K+ restriction. Thus, the present study introduces novel stable isotope approaches to separately characterize heterogenous ICF K+ pools in vivo and assess K+ uptake by individual tissues, methods that provide key new tools to elucidate K+ homeostatic mechanisms in vivo.

RBN-2397, a PARP7 Inhibitor, Synergizes with Paclitaxel to Inhibit Proliferation and Migration of Ovarian Cancer Cells.

Mono(ADP-ribosyl)ation (MARylation), a post translational modification of proteins, is emerging as an important regulator of the biology of cancer cells. PARP7 (TiPARP), a mono (ADP-ribosyl) transferase (MART), MARylates its substrate α-tubulin in ovarian cancer cells, promoting destabilization of microtubules, cell growth, and migration. Recent development of RBN-2397, a potent inhibitor that selectively acts on PARP7, has provided a new tool for exploring the role of PARP7 catalytic activity in biological processes. In this study, we investigated the role of PARP7 catalytic activity in the regulation of ovarian cancer cell biology via MARylation of α-tubulin. Ovarian cancer cell lines (OVCAR4, OVCAR3) were treated with RBN-2397 and paclitaxel, both separately and in combination. Western blotting and immunoprecipitation confirmed the effects of RBN-2397 on α-tubulin MARylation and stabilization. Cell proliferation and migration were assessed, and α-tubulin stabilization was quantified using immunofluorescent imaging. RNA-sequencing was performed to assess the effects on gene expression changes. RBN-2397 inhibited PARP7 activity, decreasing α-tubulin MARylation, leading to its stabilization, and reducing cancer cell proliferation and migration. The addition of paclitaxel further enhanced these effects, highlighting a synergistic interaction between the two drugs. Mutating the site of PARP7-mediated MARylation on α-tubulin similarly resulted in microtubule stabilization and decreased cell migration in the presence of paclitaxel. This study demonstrates that targeting PARP7 with RBN-2397, particularly in combination with paclitaxel, offers an effective strategy for inhibiting aggressive ovarian cancer cell phenotypes. Our findings underscore the potential of combining PARP7 inhibitors with established chemotherapeutics to enhance treatment efficacy in ovarian cancer.

Pig-derived ECM-SIS provides a novel matrix gel for tumor modeling

The absence of effective extracellular matrix to mimic the natural tumor microenvironment remains a significant obstacle in cancer research. Matrigel, abundant in various biological matrix components, is limited in its application due to its high cost. This has prompted researchers to explore alternative matrix substitutes. Here, we have investigated the effects of the extracellular matrix derived from pig small intestinal submucosa (ECM-SIS) in xenograft tumor modeling. Our results showed that the pig-derived ECM-SIS effectively promotes the establishment of xenograft tumor models, with a tumor formation rate comparable to that of Matrigel. Furthermore, we showed that the pig-derived ECM-SIS exhibited lower immune rejection and fewer infiltrating macrophages than Matrigel. Gene sequencing analysis demonstrated only a 0.5% difference in genes between pig-derived ECM-SIS and Matrigel during the process of tumor tissue formation. These differentially expressed genes primarily participate in cellular processes, biological regulation, and metabolic processes. These findings emphasize the potential of pig-derived ECM-SIS as a cost-effective option for tumor modeling in cancer research.

Peculiarities of the Ontogenesis of Bacilli During Development from a Vegetative Cell to a Spore

Understanding the development processes of bacteria, in particular spore-forming ones, has both fundamental and applied importance, since at various stages of this process, the cells of microorganisms perform certain functions that can be regulated by influencing certain factors depending on the tasks. Literature data and the results of our research on the influence of the composition of the nutrient medium, pH, temperature, and aeration on sporulation are analyzed in the article. It isshown that the direction of bacterial cells’ development in certain ways is determined by signals that come from the surrounding environment, affect their genome, and determine the ways of cell development – growth or sporulation. Sporogenesis can also be induced by metabolites formed during microorganism development. It is emphasized that the environmental factors that influence the sporulation of bacteria have been studied in sufficient detail. However, the mechanisms of their action remain debatable. Morphological, genetic, and biochemical changes of spore-forming bacteria under the conditions of macrocyclic and microcyclic ways of their development are also highlighted, which makes it possible to correctly understand the functioning of regulatory mechanisms in the ontogenesis of microbial cells. In particular, the data of our research on the dynamics of morphological changes in the ontogenesis of a specific individual bacterial cell are presented. In addition, factors, including specific terminal products of cell metabolism, such as antibiotics, and genetic mechanisms of sporogenesis regulation of various genera and species of bacteria are described in detail. The nature of the vast majority of "sporogenes" has not been clarified, and there are only a few hypotheses regarding the mechanism of their action. However, most of the biological regulators of sporogenesis were found in the culture liquid, which indicates the cellular nature of their action. Therefore, to obtain more convincing data on the regulation of sporogenesis, studies at the cellular level are needed.

CirSIRT5 induces ferroptosis in bladder cancer by forming a ternary complex with SYVN1/PHGDH

Bladder cancer (BC) represents a prevalent and formidable malignancy necessitating innovative diagnostic and therapeutic strategies. Circular RNAs (circRNAs) have emerged as crucial regulators in cancer biology. In this study, we comprehensively evaluated ferroptosis levels in BC cells utilizing techniques encompassing lipid peroxidation assessment, transmission electron microscopy, and malondialdehyde (MDA) measurement. Additionally, we probed into the mechanistic intricacies by which circRNAs govern BC, employing RNA pull-down, RNA immunoprecipitation (RIP), and immunoprecipitation (IP) assays. Our investigation unveiled circSIRT5, which displayed significant downregulation in BC. Notably, circSIRT5 emerged as a promising prognostic marker, with diminished expression correlating with unfavorable clinical outcomes. Functionally, circSIRT5 was identified as an inhibitor of BC progression both in vitro and in vivo. Mechanistically, circSIRT5 exerted its tumor-suppressive activities through the formation of a ternary complex involving circSIRT5, SYVN1, and PHGDH. This complex enhanced the ubiquitination and subsequent degradation of PHGDH, ultimately promoting ferroptosis in BC cells. This ferroptotic process contributed significantly to the inhibition of tumor growth and metastasis in BC. In addition, FUS was found to accelerate the biogenesis of circSIRT5 in BC. These findings provide valuable insights into the pivotal role of circSIRT5 in BC pathogenesis, underscoring its potential as a diagnostic biomarker and therapeutic target for this malignancy.

TRAF3 regulates STAT6 activation and T-helper cell differentiation by modulating the phosphatase PTP1B

The adaptor protein TNFR associated factor 3 (TRAF3) is a multifaceted regulator of lymphocyte biology that plays key roles in modulation of the molecular signals required for T cell activation and function. TRAF3 regulates signals mediated by the T cell receptor (TCR), costimulatory molecules, and cytokine receptors, which each drive activation of the serine/threonine kinase Akt. The impact of TRAF3 upon TCR/CD28-mediated activation of Akt, and thus on the diverse cellular processes regulated by Akt, including CD4 T cell fate decisions, remains poorly understood. We show here that TRAF3 deficiency led to impaired Akt activation, and thus to impaired in vitro skewing of CD4 T cells into the TH1 and TH2 fates. We investigated the role of TRAF3 in regulation of signaling pathways that drive TH1 and TH2 differentiation, and found that TRAF3 enhanced activation of Signal transducer and activator of transcription 6 (STAT6), thus promoting skewing toward the TH2 fate. TRAF3 promoted STAT6 activation by regulating recruitment of the inhibitory molecule Protein tyrosine phosphatase 1B (PTP1B) to the IL-4R signaling complex, in a manner that required integration of TCR/CD28- and IL-4R-mediated signals. This work reveals a new mechanism for TRAF3-mediated regulation of STAT6 activation in CD4 T cells, and adds to our understanding of the diverse roles played by TRAF3 as an important regulator of T cell biology.