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Background: Slow transit constipation (STC) is highly prevalent and has rising incidence. Shouhui Tongbian capsule (SHTB) is a traditional Chinese Medicine formula with extensive and highly efficacious usage in STC treatment, however, its mechanism of action, especially the regulation of microbiome and lipid metabolites, remains unclear. Methods: After quality control of SHTB using LC‒MS to obtain its material basis, we tried to elucidate the cohesive modulatory network of SHTB against STC using hyphenated methods from microbiomics, lipidomics, mass spectrometry imaging (MSI) and molecular methods. Results: SHTB could repair intestinal barrier damage, reduce systemic inflammation and increase intestinal motility in a diphenoxylate-induced STC rat model. Based on 16S rDNA sequencing results, SHTB rehabilitated the abnormal changes in Alloprevotella, Coprococcus, Marvinbryantia, etc., which were associated with STC symptoms. Meanwhile, microbial functional prediction showed that lipid metabolism was improved with SHTB administration. The differential lipids, including fatty acids, lysophosphatidylcholine, phosphatidylcholine, sphingomyelin triglyceride and ceramide, that are closely related to STC disease and SHTB efficacy. Furthermore, SHTB significantly reversed the abnormal expression of these key target enzymes in colon samples, including CTP-phosphocholine cytidylyltransferase, CTP-phosphoethanolamine cytidylyltransferase, phosphatidic acid phosphatase, acid sphingomyelinase etc. Conclusions: Combined analysis demonstrated that SHTB reducing lipid accumulation and recovery of intestinal microbial homeostasis was the critical mechanism by which SHTB treats STC. [ABSTRACT FROM AUTHOR]

The conserved Rad2/XPG family 5′–3′ exonuclease, exonuclease 1 (Exo1), plays many roles in DNA metabolism including during resolution of DNA double-strand breaks via homologous recombination. Prior studies provided evidence that the end resection activity of Exo1 is downregulated in yeast and mammals by Cdk1/2 family cyclin-dependent and checkpoint kinases, including budding yeast kinase Rad53 which functions in mitotic cells. Here, we provide evidence that the master meiotic kinase Mek1 , a paralog of Rad53 , limits 5′–3′ single-strand resection at the sites of programmed meiotic DNA breaks. Mutational analysis suggests that the mechanism of Exo1 suppression by Mek1 differs from that of Rad53. [ABSTRACT FROM AUTHOR]

The T-box (Tbx) proteins have a 180–230 amino acid DNA-binding domain, first reported in the Brachyury (T) protein. They are highly conserved among metazoans. They regulate a multitude of cellular functions in development and disease. Here, we report posttranscriptional and translational regulation of midline (mid), a Tbx member in Drosophila. We found that the 3′UTR of mid has mRNA degradation elements and AT-rich sequences. In Schneider S2 cells, mid- mRNA could be detected only when the transgene was without the 3′UTR. Similarly, the 3′UTR linked to the Renilla luciferase reporter significantly reduced the activity of the Luciferase, whereas deleting only the degradation elements from the 3′UTR resulted in reduced activity, but not as much. Overexpression of mid in MP2, an embryonic neuroblast, showed no significant difference in the levels of mid- mRNA between the 2 transgenes, with and without the 3′UTR, indicating the absence of posttranscriptional regulation of mid in MP2. Moreover, while elevated mid- RNA was detected in MP2 in nearly all hemisegments, only a fifth of those hemisegments had elevated levels of the protein. Overexpression of the 2 transgenes resulted in MP2-lineage defects at about the same frequency. These results indicate a translational/posttranslational regulation of mid in MP2. The regulation of ectopically expressed mid in the wing imaginal disc was complex. In the wing disc, where mid is not expressed, the ectopic expression of the transgene lacking the 3′UTR had a higher level of mid- RNA and the protein had a stronger phenotypic effect. These results indicate that the 3′UTR can subject mid -mRNA to degradation in a cell- and tissue-specific manner. We further report a balancer-mediated transgenerational modifier effect on the expression and gain of function effects of the 2 transgenes. [ABSTRACT FROM AUTHOR]

Background: DNA biomarkers are useful for the assessment of tumor cell proliferation. The authors aimed to synthesize a thiopurine-based ligand for evaluation of nuclear uptake and tumor localization. Materials and Methods: A 2-hydroxypropyl spacer was incorporated between a chelator (cyclam) and thiopurine ligand to produce SC-06-L1. In vitro cellular uptake and the cell/media ratios of [99mTc]Tc-SC-06-L1 were assessed in breast (MCF-7, MDA-MB-231) and ovarian (TOV-112D, OVCAR3) cancer cells. The nuclear and cytosolic uptake ratio of [99mTc]Tc-SC-06-L1 was determined in OVCAR-3 and MCF-7 cells. Cytotoxicity assays and flow cytometric analysis of cell cycle apoptosis were conducted in cancer cells treated with SC-06-L1. Imaging was conducted in tumor-bearing mice; fluorine-18-2′-fluorodeoxyglucose ([18F]FDG) was used as a control. Results: The radiochemical purity of [99mTc]Tc-SC-06-L1 was >95%. [99mTc]Tc-SC-06-L1 exhibited higher cell-to-media ratios than [18F]FDG in cancer cells. [99mTc]Tc-SC-06-L1 had high uptake in the nuclear fractions in OVCAR-3 and MCF-7 cells, with nuclear/cytosolic ratios of 8 and 2, respectively. Cytotoxicity assays showed that SC-06-L1 was non-toxic compared with azathioprine in breast and ovarian cancer cells. Conclusions: [99mTc]Tc-SC-06-L1 was stable and involved in nuclear activities. [99mTc]Tc-SC-06-L1 showed non-toxic to cancer cells and exhibited fast kinetic uptake patterns for tumor imaging. [99mTc]Tc-SC-06-L1 represents a promising biomarker for imaging purine pathway-directed systems. [ABSTRACT FROM AUTHOR]

Simple Summary: Predicting which patients will respond to therapy or experience disease relapse can help clinicians select treatments that could slow down or prevent the spread of cancer. Clinicians have routinely used imaging to measure the size of the tumor to assess whether or not it is responding to treatment. A recent development for monitoring tumors involves a test to detect mutated DNA shed by tumors into the blood, called circulating tumor DNA (ctDNA). The authors searched the scientific literature to find studies that have combined imaging and ctDNA to build tools that can predict treatment response or patient survival. The authors noted that only a few studies have been reported, indicating that this field is new and needs further exploration. These early studies, however, showed that combining these two clinical tests (imaging + ctDNA) may improve the prediction of tumors' response to therapy and the return of cancer. While promising, these tools need to be refined to improve the accuracy of the predictions and the results confirmed in more extensive studies. Biomarkers for evaluating tumor response to therapy and estimating the risk of disease relapse represent tremendous areas of clinical need. To evaluate treatment efficacy, tumor response is routinely assessed using different imaging modalities like positron emission tomography/computed tomography or magnetic resonance imaging. More recently, the development of circulating tumor DNA detection assays has provided a minimally invasive approach to evaluate tumor response and prognosis through a blood test (liquid biopsy). Integrating imaging- and circulating tumor DNA-based biomarkers may lead to improvements in the prediction of patient outcomes. For this mini-review, we searched the scientific literature to find original articles that combined quantitative imaging and circulating tumor DNA biomarkers to build prediction models. Seven studies reported building prognostic models to predict distant recurrence-free, progression-free, or overall survival. Three discussed building models to predict treatment response using tumor volume, pathologic complete response, or objective response as endpoints. The limited number of articles and the modest cohort sizes reported in these studies attest to the infancy of this field of study. Nonetheless, these studies demonstrate the feasibility of developing multivariable response-predictive and prognostic models using regression and machine learning approaches. Larger studies are warranted to facilitate the building of highly accurate response-predictive and prognostic models that are generalizable to other datasets and clinical settings. [ABSTRACT FROM AUTHOR]

Background and Aim: There are still risks of contamination of seafood by the common pathogens such as bacteria and viruses, despite significant achievements in the food security and environmental protection in recent years. The aim of this study was to investigate the prevalence of pathogenic viruses linked to the seafood hygiene in the raw seafood samples collected from the seafood retailers in Tehran, Iran. Materials and Methods: In general, 200 samples (100 fish and 100 shrimps) were collected from the seafood retailers in Tehran, Iran. For the RNA viruses, the RNA was extracted from the samples and subjected to cDNA synthesis and polymerase chain reaction (PCR) to amplify the target genes. For the adenovirus, DNA genome was extracted and directly used in PCR. Data were analyzed using the SPSS Statistics 29.0.10. Results: From 100 fish samples, 48, 24, 32, 35, 56 and 55 samples were contaminated with adenovirus, astrovirus, hepatitis A virus, hepatitis E virus, rotavirus and norovirus, respectively. From 100 shrimp samples, 51, 47, 28, 47, 49 and 47 samples were contaminated with adenovirus, astrovirus, hepatitis A virus, hepatitis E virus, rotavirus and norovirus, respectively. Conclusion: In conclusion, raw seafood can still be a major public health concern. Therefore, it is strongly recommended to use the organized monitoring systems and improved hygiene measurements to decrease the risks of the seafood contaminations and hence foodborne diseases and outbreaks in consumers. [ABSTRACT FROM AUTHOR]

Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities—often central to the protein function—thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein–DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field. [ABSTRACT FROM AUTHOR]

Simple Summary: As a tumor grows, DNA fragments from cancer cells shed into the bloodstream. Known as circulating tumor DNA (ctDNA), these fragments can be used to inform on cancer diagnosis, treatment, and prognosis. However, despite the potential for these uninavasive liquid biopsies to revolutionize cancer monitoring and treatment, ctDNA can show poor genetic concordance between blood and the main tumor tissue, hampering its general clinical utility. For liquid biopsy technologies and ctDNA analyses to transform cancer care, from early screening and diagnosis through treatment and long-term follow-up, we need to better understand how to interpret the genetic diversity measured in the blood and how it can be used to describe the true composition of the tumor tissue. In this work we study the evolutionary processes that can lead to genetic discordance between a blood sample and the main tumor tissue and specifically, how tumor spatial heterogeneity shapes these genetic differences. We find that spatial heterogeneity in apoptosis and cellular shedding across different regions of a tumor can significantly bias the mutational composition of ctDNA and emphasize important directions for further theoretical and clinical investigation into the effect of the microenvironment on ctDNA origin and quantification. Circulating tumor DNA (ctDNA) monitoring, while sufficiently advanced to reflect tumor evolution in real time and inform cancer diagnosis, treatment, and prognosis, mainly relies on DNA that originates from cell death via apoptosis or necrosis. In solid tumors, chemotherapy and immune infiltration can induce spatially variable rates of cell death, with the potential to bias and distort the clonal composition of ctDNA. Using a stochastic evolutionary model of boundary-driven growth, we study how elevated cell death on the edge of a tumor can simultaneously impact driver mutation accumulation and the representation of tumor clones and mutation detectability in ctDNA. We describe conditions in which invasive clones are over-represented in ctDNA, clonal diversity can appear elevated in the blood, and spatial bias in shedding can inflate subclonal variant allele frequencies (VAFs). Additionally, we find that tumors that are mostly quiescent can display similar biases but are far less detectable, and the extent of perceptible spatial bias strongly depends on sequence detection limits. Overall, we show that spatially structured shedding might cause liquid biopsies to provide highly biased profiles of tumor state. While this may enable more sensitive detection of expanding clones, it could also increase the risk of targeting a subclonal variant for treatment. Our results indicate that the effects and clinical consequences of spatially variable cell death on ctDNA composition present an important area for future work. [ABSTRACT FROM AUTHOR]

Aging is the major risk factor in most of the leading causes of mortality worldwide, yet its fundamental causes mostly remain unclear. One of the clear hallmarks of aging is mitochondrial dysfunction. Mitochondria are best known for their roles in cellular energy generation, but they are also critical biosynthetic and signaling organelles. They also undergo multiple changes with organismal age, including increased genetic errors in their independent, circular genome. A key group of studies looking at mice with increased mtDNA mutations showed that premature aging phenotypes correlated with increased deletions but not point mutations. This generated an interest in mitochondrial deletions as a potential fundamental cause of aging. However, subsequent studies in different models have yielded diverse results. This review summarizes the research on mitochondrial deletions in various organisms to understand their possible roles in causing aging while identifying the key complications in quantifying deletions across all models. [ABSTRACT FROM AUTHOR]

Objective. Adult skeletal stem cells (SSCs) that give rise to chondrocytes, osteocytes, and stromal cells as progeny have been shown to contribute to cartilage regeneration in osteoarthritis (OA). Understanding extrinsic and intrinsic regulators of SSC fate and function can therefore identify putative candidate factors to enhance cartilage regeneration. This study explores how the DNA hydroxymethylase Tet1 regulates SSC function in OA. Methods. We investigated the differences in the SSC lineage tree and differentiation potential in neonatal and adult Tet1+/+ and Tet1−/− mice with and without injury and upon OA induction and progression. Using RNA sequencing, the transcriptomic differences between SSCs and bone cartilage stroma progenitor cells (BCSPs) were identified in Tet1+/+ mice and Tet1−/− mice. Results. Loss of Tet1 skewed the SSC lineage tree by expanding the SSC pool and enhanced the chondrogenic potential of SSCs and BCSPs. Tet1 inhibition led to enhanced chondrogenesis in human SSCs and chondroprogenitors isolated from human cartilage. Importantly, TET1 inhibition in vivo in late stages of a mouse model of OA led to increased cartilage regeneration. Transcriptomic analyses of SSCs and BCSPs lacking Tet1 revealed pathway alterations in transforming growth factor β signaling, melatonin degradation, and cartilage development–associated genes. Lastly, we report that use of the hormone melatonin can dampen inflammation and improve cartilage health. Conclusion. Although Tet1 is a broad epigenetic regulator, melatonin can mimic the inhibition ability of TET1 to enhance the chondrogenic ability of SSCs. Melatonin administration has the potential to be an attractive stem cell– based therapy for cartilage regeneration. [ABSTRACT FROM AUTHOR]

Simple Summary: Many cancers exhibit compromised 5′-3′-exoribonuclease 2 (XRN2) expression. XRN2 is a major regulator of RNA polymerase II (RNAPII) at the transcription termination sites of protein-coding genes. Deregulated transcription termination facilitates the formation of triple-stranded nucleic acid structures known as R-loops (RNA–DNA hybrids with displaced single-strand DNA). Elevated levels of unscheduled R-loops promote genomic instability. In the absence of XRN2, R-loop levels increase and promote DNA damage that activates DNA damage surveillance protein poly(ADP-ribose) polymerase 1 (PARP1). Previously, we discovered that the simultaneous absence of XRN2 and PARP1 compromises the survival of non-cancer and cancer cells; however, the underlying cellular stress response remained unknown. Here, we aimed to uncover the molecular consequences of concurrent XRN2 depletion and PARP1 inhibition. Our findings provide a mechanistic understanding of why cancer cells rely on PARP1 when XRN2 is absent and strengthen the translational aspect of targeting XRN2 cancer vulnerabilities using PARP inhibitors. R-loops (RNA–DNA hybrids with displaced single-stranded DNA) have emerged as a potent source of DNA damage and genomic instability. The termination of defective RNA polymerase II (RNAPII) is one of the major sources of R-loop formation. 5′-3′-exoribonuclease 2 (XRN2) promotes genome-wide efficient RNAPII termination, and XRN2-deficient cells exhibit increased DNA damage emanating from elevated R-loops. Recently, we showed that DNA damage instigated by XRN2 depletion in human fibroblast cells resulted in enhanced poly(ADP-ribose) polymerase 1 (PARP1) activity. Additionally, we established a synthetic lethal relationship between XRN2 and PARP1. However, the underlying cellular stress response promoting this synthetic lethality remains elusive. Here, we delineate the molecular consequences leading to the synthetic lethality of XRN2-deficient cancer cells induced by PARP inhibition. We found that XRN2-deficient lung and breast cancer cells display sensitivity to two clinically relevant PARP inhibitors, Rucaparib and Olaparib. At a mechanistic level, PARP inhibition combined with XRN2 deficiency exacerbates R-loop and DNA double-strand break formation in cancer cells. Consistent with our previous findings using several different siRNAs, we also show that XRN2 deficiency in cancer cells hyperactivates PARP1. Furthermore, we observed enhanced replication stress in XRN2-deficient cancer cells treated with PARP inhibitors. Finally, the enhanced stress response instigated by compromised PARP1 catalytic function in XRN2-deficient cells activates caspase-3 to initiate cell death. Collectively, these findings provide mechanistic insights into the sensitivity of XRN2-deficient cancer cells to PARP inhibition and strengthen the underlying translational implications for targeted therapy. [ABSTRACT FROM AUTHOR]

The SSB protein of Escherichia coli functions to bind single-stranded DNA wherever it occurs during DNA metabolism. Depending upon conditions, SSB occurs in several different binding modes. In the course of its function, SSB diffuses on ssDNA and transfers rapidly between different segments of ssDNA. SSB interacts with many other proteins involved in DNA metabolism, with 22 such SSB-interacting proteins, or SIPs, defined to date. These interactions chiefly involve the disordered and conserved C-terminal residues of SSB. When not bound to ssDNA, SSB can aggregate to form a phase-separated biomolecular condensate. Current understanding of the properties of SSB and the functional significance of its many intermolecular interactions are summarized in this review. [ABSTRACT FROM AUTHOR]

Human Replication Protein A (RPA) was historically discovered as one of the six components needed to reconstitute simian virus 40 DNA replication from purified components. RPA is now known to be involved in all DNA metabolism pathways that involve single-stranded DNA (ssDNA). Heterotrimeric RPA comprises several domains connected by flexible linkers and is heavily regulated by post-translational modifications (PTMs). The structure of RPA has been challenging to obtain. Various structural methods have been applied, but a complete understanding of RPA's flexible structure, its function, and how it is regulated by PTMs has yet to be obtained. This review will summarize recent literature concerning how RPA is phosphorylated in the cell cycle, the structural analysis of RPA, DNA and protein interactions involving RPA, and how PTMs regulate RPA activity and complex formation in double-strand break repair. There are many holes in our understanding of this research area. We will conclude with perspectives for future research on how RPA PTMs control double-strand break repair in the cell cycle. [ABSTRACT FROM AUTHOR]

Background: Carissa bispinosa (L.) Desf. ex Brenan is one of the plants used traditionally to treat oral infections. However, there is limited data validating its therapeutic properties and photochemistry. The aim of this study was to investigate the protective efficacy of the leaf and stem extracts of C. bispinosa against oral infections. Methods: The phenolic and tannin contents were measured using Folin-Ciocalteau method after extracting with different solvents. The minimum inhibitory concentrations (MIC) of the extracts were assessed using the microdilution method against fungal (Candida albicans and Candida glabrata) and bacterial (Streptococcus pyogenes, Staphylococcus aureus and Enterococcus faecalis) strains. The 2-diphenyl-1-picrylhydrazyl (DPPH) and ferric reducing power (FRP) models were utilised to assess the antioxidant potential of the extracts. Cytotoxicity of the leaf acetone extract was evaluated using the methylthiazol tetrazolium assay. Results: The methanol leaf extract had the highest phenolic content (113.20 mg TAE/g), whereas hexane extract displayed the highest tannin composition of 22.98 mg GAE/g. The acetone stem extract had the highest phenolic content (338 mg TAE/g) and the stem extract yielded the highest total tannin content (49.87 mg GAE/g). The methanol leaf extract demonstrated the lowest MIC value (0.31 mg/mL), whereas the stem ethanol extract had the least MIC value of 0.31 mg/mL. The stem methanol extract had the best DPPH free radical scavenging activity (IC50, 72 µg/mL) whereas the stem ethanol extract displayed maximum FRP with absorbance of 1.916. The leaf acetone extract had minimum cytotoxicity with the lethal concentration (LC50) of 0.63 mg/mL. Conclusions: The results obtained in this study validated the protective effect of C. bispinosa against oral infections. [ABSTRACT FROM AUTHOR]

Background: Rotator cuff repair is a common orthopaedic procedure, yet the rate of failure to heal after surgery is high. Repair site rupture is due to poor tendon-to-bone healing and lack of regeneration of the native fibrocartilaginous enthesis. During development, the enthesis is formed and mineralized by a pool of progenitors activated by hedgehog signaling. Furthermore, hedgehog signaling drives regenerative enthesis healing in young animals, in contrast to older animals, in which enthesis injuries heal via fibrovascular scar and without participation of hedgehog signaling. Hypothesis: Hedgehog activation improves tendon-to-bone healing in an animal model of rotator cuff repair. Study Design: Controlled laboratory study. Methods: A total of 78 adult Sprague-Dawley rats were used. Supraspinatus tendon injury and repair were completed bilaterally, with microsphere-encapsulated hedgehog agonist administered to right shoulders and control microspheres administered to left shoulders. Animals were sacrificed after 3, 14, 28, or 56 days. Gene expression and histological, biomechanical, and bone morphometric analyses were conducted. Results: At 3 days, hedgehog signaling pathway genes Gli1 (1.70; P =.029) and Smo (2.06; P =.0173), as well as Runx2 (1.69; P =.0386), a transcription factor of osteogenesis, were upregulated in treated relative to control repairs. At 14 days, transcription factors of tenogenesis, Scx (4.00; P =.041), and chondrogenesis, Sox9 (2.95; P =.010), and mineralized fibrocartilage genes Col2 (3.18; P =.031) and Colx (1.85; P =.006), were upregulated in treated relative to control repairs. Treatment promoted fibrocartilage formation at the healing interface by 28 days, with improvements in tendon-bone maturity, organization, and continuity. Treatment led to improved biomechanical properties. The material property strength (2.43 vs 1.89 N/m2; P =.046) and the structural property work to failure (29.01 vs 18.09 mJ; P =.030) were increased in treated relative to control repairs at 28 days and 56 days, respectively. Treatment had a marginal effect on bone morphometry underlying the repair. Trabecular thickness (0.08 vs 0.07 mm; P =.035) was increased at 28 days. Conclusion: Hedgehog agonist treatment activated hedgehog signaling at the tendon-to-bone repair site and prompted increased mineralized fibrocartilage production. This extracellular matrix production and mineralization resulted in improved biomechanical properties, demonstrating the therapeutic potential of hedgehog agonism for improving tendon-to-bone healing after rotator cuff repair. Clinical Relevance: This study demonstrates the therapeutic potential of hedgehog agonist treatment for improving tendon-to-bone healing after rotator cuff injury and repair. [ABSTRACT FROM AUTHOR]

Aim: To explore whether hyperglycaemia plays a role in periodontal inflamm‐aging by inducing phenotypical transformation of macrophages, as well as the potential mechanism via SET domain‐bifurcated histone lysine methyltransferase 1 (SETDB1). Materials and Methods: A hyperglycaemic mouse model was established using streptozotocin injection. The alveolar bone was analysed using micro‐computed tomography. Periodontal inflamm‐aging was detected using western blotting, quantitative real‐time PCR and immunohistochemical analysis. In vitro, RAW 264.7 macrophages were incubated with various doses of glucose. siRNA or overexpression plasmids were used to determine the regulatory mechanism of SETDB1 in macrophage senescence and inflamm‐aging under hyperglycaemic conditions. Expression and distribution of SETDB1 and long interspersed element 1 (LINE‐1) in gingival tissues of patients with or without diabetes were detected using immunofluorescent staining. Results: SETDB1 expression in the periodontal tissues of patients and mice with diabetes was down‐regulated compared with that in non‐diabetic controls. SETDB1 deficiency induced senescence‐like phenotypical changes in macrophages, which aggravated periodontal inflamm‐aging in diabetic mice. Furthermore, metformin treatment rejuvenated SETDB1 activity and alleviated the hyperglycaemia‐induced periodontal inflamm‐aging. Conclusions: The findings of this study show that SETDB1 regulates senescence‐like phenotypical switching of macrophages and is a potential candidate for the treatment of diabetes‐induced periodontal inflamm‐aging. [ABSTRACT FROM AUTHOR]

Background: Laryngeal tumor is the most commonly identified malignancy in head and neck cancers, containing 2.4% of all cancers, and is the 11th most prevalent and fatal cancer in the world. Previous research has revealed that microRNAs (miRNAs) have a significant role in the progression of laryngeal tumors. Additionally, research focuses on the association with the clinical function of miRNA in malignancy. Objectives: Based on previous research, miR-132, miR-302, miR-126, and miR-205 have potential roles in the tumor development of the LSCC. Then, in the current study, we pointed to study if there are any significant alters in the expression of microRNAs and whether they have any significant possibility as a diagnostic or prognostic factor for laryngeal squamous cell carcinoma. Methods: From 30 LSCC patients, we have collected tumor and marginal healthy tissues through laryngectomy. Total RNA extraction from the marginal healthy and malignancy tissues was done. Next, we control the quality of the RNAs and, then, synthesize cDNA. Lastly, the expression of the miRNAs was evaluated by qPCR. The expression level of genes and their association with the patient's clinicopathological features were studied, using related statistical tests. Results: miR-132 (P = 0.0001, fold change: 1.28) and miR-302 (P = 0.0001, fold change: l.o5) are significantly up-regulated in tumor tissues compared to normal peripheral tissues. Furthermore, we revealed that miR-205 (P < 0.0001, fold change: 0.241) and miR-126 (P = 0.0001, fold change: 0.251) are low expressed in LSCC cancer tissue. Between these miRNAs, gust expression of the miR-205 had no relationship with clinical-pathological characteristics in malignancy tissue. Conclusions: The results of the current study showed the possibility of miR-302, miR-132, miR-126, and miR-205 as diagnostic or prognostic factors in LSCC. [ABSTRACT FROM AUTHOR]

Abstract Background With the advent of metagenomic next-generation sequencing (mNGS), the time of DNA metabolism can be explored after bacteria be killed. In this study, we applied mNGS in investigation of the clearance profile of circulating bacteria DNA. Methods All of the rabbits were injected with the inactivated Escherichia coli. Using mNGS, we analyzed serial samples of plasma collected from rabbits to detect clearance profile of circulating E. coli DNA. Results In this study, we found that the of E. coli DNA could still be detected 6 h after injecting killed bacteria. The clearance half-lives associated with the 2 phases are 0.37 and 1.81 h. We also explored there is no correlation between the disease severity with the E. coli DNA reads in circulation. Conclusions After the bacteria were completely killed, their DNA could still be detected in the blood circulation. The metabolism of bacterial DNA in the circulation had two phases: fast and slow phases, and there were no correlations between the level of bacteria reads with the severity of patients’ disease after the bacteria have been completely killed.

The highly active family of Mutator (Mu) DNA transposons has been widely used for forward and reverse genetics in maize. There are examples of Mu-suppressible alleles that result in conditional phenotypic effects based on the activity of Mu. Phenotypes from these Mu-suppressible mutations are observed in Mu-active genetic backgrounds, but absent when Mu activity is lost. For some Mu-suppressible alleles, phenotypic suppression likely results from an outward-reading promoter within Mu that is only active when the autonomous Mu element is silenced or lost. We isolated 35 Mu alleles from the UniformMu population that represent insertions in 24 different genes. Most of these mutant alleles are due to insertions within gene coding sequences, but several 5′ UTR and intron insertions were included. RNA-seq and de novo transcript assembly were utilized to document the transcripts produced from 33 of these Mu insertion alleles. For 20 of the 33 alleles, there was evidence of transcripts initiating within the Mu sequence reading through the gene. This outward-reading promoter activity was detected in multiple types of Mu elements and does not depend on the orientation of Mu. Expression analyses of Mu-initiated transcripts revealed the Mu promoter often provides gene expression levels and patterns that are similar to the wild-type gene. These results suggest the Mu promoter may represent a minimal promoter that can respond to gene cis-regulatory elements. Findings from this study have implications for maize researchers using the UniformMu population, and more broadly highlight a strategy for transposons to co-exist with their host. [ABSTRACT FROM AUTHOR]

Objectives: Zinc sulfide nanoparticles (ZnS NPs), as one of the quantum dots less than 10 nm, possess unique size‐dependent autofluorescence. Excitation of their valence electrons by energy higher than the bandgap reveals the ZnS NPs' inherited photocatalysis with additive cytotoxic consequences of reactive oxygen species (ROS) release. Coupling the cytotoxicity of photoactivated ZnS NPs with their autofluorescence would be a novel theranostic modality, combating superficially accessible carcinoma. Material and methods: After synthesizing and characterization of ZnS NPs, we verified their photocatalysis and electron donation upon UV excitation in degrading organic dye and DNA cleavage, respectively. We then tested the efficacy of UV‐activated ZnS NPs to induce ROS‐dependent apoptosis in squamous cell carcinoma and breast cancer cell lines. Results: The energetic electron–hole pairs generated upon UV excitation of ZnS NPs with the consequent cascade of ROS release revealed potent apoptotic cancer cell deaths, compared with single treatment modalities of nonexcited nanoparticles and UV. Moreover, the inherited luminescence of ZnS NPs enabled visualization of their predominant intracytoplasmic uptake with tracking of their cellular response. Conclusion: The intensified luminescence and the fortified cytotoxicity of photoactivated ZnS NPs enhance their theranostic qualifications, boosting their antitumorigenic use. [ABSTRACT FROM AUTHOR]

Objective: Schizophrenia is a serious mental disorder with complex clinical manifestations, while its pathophysiological mechanism is not fully understood. Accumulated evidence suggested the alteration in epigenetic pathway was associated with clinical features and brain dysfunctions in schizophrenia. DNA methyltransferases (DNMTs), a key enzyme for DNA methylation, are related to the development of schizophrenia, whereas the current research evidence is not sufficient. The aim of study was to explore the effects of gene polymorphisms of DNMTs on the susceptibility and symptoms of schizophrenia. Methods: The study was case–control study that designed and employed the Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition (DSM-5) as the diagnostic standard. 134 hospitalized patients with schizophrenia in the Third People's Hospital of Zhongshan City from January 2018 to April 2020 (Case group) as well as 64 healthy controls (Control group) from the same region were involved. Single nucleotide polymorphisms (SNPs) of DNMT1 genes (r s2114724 and rs 2228611) and DNMT3B genes (rs 2424932, rs 1569686, rs 6119954 and rs 2424908) were determined with massARRAY. Linkage disequilibrium analysis and haplotype analysis were performed, and genotype and allele frequencies were compared. The Hardy–Weinberg equilibrium was tested by the Chi-square test in SPSS software (version 20.0, SPSS Inc., USA). The severity of clinical symptoms was assessed by the Positive and Negative Syndrome Scale (PANSS). The correlation between DNMT1 genes (rs 2114724 and rs 2228611) and DNMT3B genes (rs2424932, rs1569686, rs6119954 and rs2424908) and clinical features was analyzed. Results: There were no significant differences in genotype, allele frequency and haplotype of DNMT1 genes (rs 2114724 and rs 2228611) and DNMT3B genes (rs 2424932, rs 1569686, rs 6119954 and rs 2424908) between the case and healthy control group. There were significant differences in the PANSS total positive symptom scores, P3 (hallucinatory behavior), P6 (suspicious/persecution), G7 (motor retardation), and G15 (preoccupation) in patients with different DNMT1 gene rs 2114724 and rs 2228611 genotypes. The linkage disequilibrium analysis of gene polymorphic loci revealed that rs 2114724–rs 2228611 was complete linkage disequilibrium, and rs 1569686–rs 2424908, rs 2424932–rs 1569696 and rs 2424932–rs 2424908 were strongly linkage disequilibrium. Conclusion: The polymorphisms alteration in genetic pathway may be associated with development of specific clinical features in schizophrenia. [ABSTRACT FROM AUTHOR]

Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression that together ensure the correct number of chromosomes is delivered to the next generation. Studies in the budding yeast Saccharomyces cerevisiae have established essentially all fundamental paradigms of meiosis-specific chromosome metabolism and have uncovered components and molecular mechanisms that underlie these conserved processes. Here, we provide an overview of all stages of meiosis in this key model system and highlight how basic mechanisms of genome stability, chromosome architecture, and cell cycle control have been adapted to achieve the unique outcome of meiosis. [ABSTRACT FROM AUTHOR]

Objectives Recently, the involvement of basophils and IgE-type autoantibodies in the pathogenesis of SLE has been elucidated using mouse models; however, few studies have been conducted in humans. In this study, the role of basophils and anti-double-stranded DNA (dsDNA) IgE in SLE was examined using human samples. Methods The correlation between disease activity and serum levels of anti-dsDNA IgE in SLE was evaluated using enzyme-linked immunosorbent assay. Cytokines produced by IgE-stimulated basophils from healthy subjects were assessed using RNA sequences. The interaction of basophils and B cells to promote B cell differentiation was investigated using a co-culture system. The ability of basophils from patients with SLE with anti-dsDNA IgE to create cytokines that may be involved in B cell differentiation in response to dsDNA was examined using real-time PCR. Results Anti-dsDNA IgE levels in the serum of patients with SLE correlated with disease activity. Healthy donor basophils produced IL-3, IL-4 and TGF-β1 after anti-IgE stimulation. Co-culture of B cells with anti-IgE-stimulated basophils increased plasmablasts which were cancelled by neutralizing IL-4. After encountering the antigen, basophils released IL-4 more quickly than follicular helper T cells. Basophils isolated from patients with anti-dsDNA IgE promoted IL-4 expression by adding dsDNA. Conclusions These results suggest that basophils contribute to the pathogenesis of SLE by promoting B cell differentiation via dsDNA-specific IgE in patients similar to the process described in mouse models. [ABSTRACT FROM AUTHOR]

Simple Summary: The cell division cycle is tightly regulated to ensure faithful and complete DNA replication. A critical cell cycle phase is G1 in which cells prepare DNA for replication in S phase. Interestingly, stem cells and cancer cells have both similarities and differences in their cell cycle regulatory mechanisms. In this review, we address the role of various cell cycle regulators in controlling the dynamics of G1 phase in stem cells and cancer cells. We also discuss recent advances in understanding how core pluripotency factors regulate the cell cycle and play dual roles in stem cell pluripotency and in cancers where they are aberrantly expressed. A better understanding of these common regulatory networks could offer potential new therapeutic avenues for cancer. G1 cell cycle phase dynamics are regulated by intricate networks involving cyclins, cyclin-dependent kinases (CDKs), and CDK inhibitors, which control G1 progression and ensure proper cell cycle transitions. Moreover, adequate origin licensing in G1 phase, the first committed step of DNA replication in the subsequent S phase, is essential to maintain genome integrity. In this review, we highlight the intriguing parallels and disparities in G1 dynamics between stem cells and cancer cells, focusing on their regulatory mechanisms and functional outcomes. Notably, SOX2, OCT4, KLF4, and the pluripotency reprogramming facilitator c-MYC, known for their role in establishing and maintaining stem cell pluripotency, are also aberrantly expressed in certain cancer cells. In this review, we discuss recent advances in understanding the regulatory role of these pluripotency factors in G1 dynamics in the context of stem cells and cancer cells, which may offer new insights into the interconnections between pluripotency and tumorigenesis. [ABSTRACT FROM AUTHOR]

Objectives Polymorphism in a coding region of deoxyribonuclease I-like III (DNASE1L3), causing amino acid substitution of Arg-206 to Cys (R206C), is a robustly replicated heritable risk factor for SSc and other autoimmune diseases. DNASE1L3 is secreted into the circulation, where it can digest genomic DNA (gDNA) in apoptosis-derived membrane vesicles (AdMVs). We sought to determine the impact of DNASE1L3 R206C on digestion of circulating gDNA in SSc patients and healthy controls (HCs). Methods The ability of DNASE1L3 to digest AdMV-associated gDNA was tested in vitro. The effect of R206C substitution on extracellular secretion of DNASE1L3 was determined using a transfected cell line and primary monocyte-derived dendritic cells from SSc patients. Plasma samples from SSc patients and HCs with DNASE1L3 R206C or R206 wild type were compared for their ability to digest AdMV-associated gDNA. The digestion status of endogenous gDNA in plasma samples from 123 SSc patients and 74 HCs was determined by measuring the proportion of relatively long to short gDNA fragments. Results The unique ability of DNASE1L3 to digest AdMV-associated gDNA was confirmed. Extracellular secretion of DNASE1L3 R206C was impaired. Plasma from individuals with DNASE1L3 R206C had reduced ability to digest AdMV-associated gDNA. The ratio of long: short gDNA fragments was increased in plasma from SSc patients with DNASE1L3 R206C, and this ratio correlated inversely with DNase activity. Conclusion Our results confirm that circulating gDNA is a physiological DNASE1L3 substrate and show that its digestion is reduced in SSc patients with the DNASE1L3 R206C variant. [ABSTRACT FROM AUTHOR]

Saline and hypersaline wetlands account for almost half of the volume of inland water globally. They provide pivotal habitat for a vast range of species, including crucial ecosystem services for humans such as carbon sink storage and extractive resource reservoirs. Despite their importance, effective ecological assessment is in its infancy compared to current conventional surveys carried out in freshwater ecosystems. The integration of environmental DNA (eDNA) analysis and traditional techniques has the potential to transform biomonitoring processes, particularly in remote and understudied saline environments. In this context, this preliminary study aims to explore the potential of eDNA coupled with conventional approaches by targeting five hypersaline lakes at Rottnest Island (Wadjemup) in Western Australia. We focused on the invertebrate community, a widely accepted key ecological indicator to assess the conservational status in rivers and lakes. The combination of metabarcoding with morphology-based taxonomic analysis described 16 taxa belonging to the orders Anostraca, Diptera, Isopoda, and Coleoptera. DNA-based diversity assessment revealed more taxa at higher taxonomic resolution than the morphology-based taxonomic analysis. However, certain taxa (i.e., Ephydridae, Stratyiomidae, Ceratopogonidae) were only identified via net surveying. Overall, our results indicate that great potential resides in combining conventional net-based surveys with novel eDNA approaches in saline and hypersaline lakes. Indeed, urgent and effective conservational frameworks are required to contrast the enormous pressure that these ecosystems are increasingly facing. Further investigations at larger spatial-temporal scales will allow consolidation of robust, reliable, and affordable biomonitoring frameworks in the underexplored world of saline wetlands. [ABSTRACT FROM AUTHOR]

Background: With the advent of metagenomic next-generation sequencing (mNGS), the time of DNA metabolism can be explored after bacteria be killed. In this study, we applied mNGS in investigation of the clearance profile of circulating bacteria DNA. Methods: All of the rabbits were injected with the inactivated Escherichia coli. Using mNGS, we analyzed serial samples of plasma collected from rabbits to detect clearance profile of circulating E. coli DNA. Results: In this study, we found that the of E. coli DNA could still be detected 6 h after injecting killed bacteria. The clearance half-lives associated with the 2 phases are 0.37 and 1.81 h. We also explored there is no correlation between the disease severity with the E. coli DNA reads in circulation. Conclusions: After the bacteria were completely killed, their DNA could still be detected in the blood circulation. The metabolism of bacterial DNA in the circulation had two phases: fast and slow phases, and there were no correlations between the level of bacteria reads with the severity of patients’ disease after the bacteria have been completely killed. [ABSTRACT FROM AUTHOR]

The aim of this paper was to assess the cost-effectiveness of pembrolizumab in first-line for microsatellite-instability-high or mismatch-repair-deficient metastatic colorectal cancer. We have considered the pivotal phase III randomized controlled trial of pembrolizumab in first-line for microsatellite-instability-high mismatch-repair-deficient metastatic colorectal cancer. The last available update of each trial was considered as the original source. Incremental cost-effectiveness ratio was calculated as the ratio between the difference of the costs in the intervention and in the control groups (pharmacy costs) and the difference between the effect in the intervention and in the control groups (progression-free survival). The costs of drugs are at the Pharmacy of the Mater Salutis Hospital of Legnago (VR, Italy) and are expressed in euros (€). Three hundred and seven patients were considered in the pivotal phase III randomized controlled trial. Pembrolizumab obtained a cost per month progression-free survival gained ranged from 6471 € towards mFOLFOX (5-FU, oxaliplatin and leucovorin) plus cetuximab to 7886 € towards mFOLFOX. To sum up, combining pharmacological costs of drugs with the measure of efficacy represented by progression-free survival, at the actual prize pembrolizumab cannot be considered cost-effectiveness for first-line treatment for microsatellite-instability-high mismatch-repair-deficient metastatic colorectal cancer. A reduction in pharmacological costs is mandatory. [ABSTRACT FROM AUTHOR]

The most frequent malignant tumor of the head and neck is head and neck squamous cell carcinoma (HNSCC), which has a high frequency, a poor prognosis in the late stages, and subpar therapeutic results. As a result, early HNSCC diagnosis and treatment are urgently needed; however, there are no good diagnostic biomarkers or efficient therapeutic targets at this time. The long-stranded non-coding RNA HOTAIR may be important in the pathogenesis of cancer, according to recent research. By interactions with DNA, RNA, and proteins, it has been demonstrated that HOTAIR, a >200 nucleotide RNA transcript, plays a role in the biological processes of many types of tumor cells, including proliferation, metastasis, and prognosis of HNSCC. Hence, this review discusses HOTAIR's function and molecular mechanisms in HNSCC. [ABSTRACT FROM AUTHOR]

Folate is hypothesized to accelerate cell proliferation in colorectal cancer (CRC) by supporting DNA synthesis, while alcohol is also linked to gastrointestinal epithelial proliferation, despite biological antagonism of folate. We report associations between folate and alcohol consumption with the proliferation marker Ki67 in CRC tumors from the Southern Community Cohort Study. Tumor samples were obtained from formalin-fixed paraffin-embedded tissue blocks. The percentage of cells expressing Ki67 was measured immunohistochemically. Exposures were assessed via questionnaire pre-diagnosis. Associations were assessed via linear regression. In 248 cases (40–78 years), neither dietary folate, folic acid supplements, nor total folate intake were associated with Ki67. Folic acid supplement use was associated with Ki67 in distal/rectal tumors (β [95% confidence interval]: 7.5 [1.2-13.8], p =.02) but not proximal tumors (-1.4 [-7.1-4.3], p=.62). A positive trend for total folate was observed for distal/rectal tumors (1.6 [0.0-3.3] per 200 μcg, p-trend=.05). Heavy drinking (women: ≥1 drink/day, men: ≥2 drinks/day) was associated with higher Ki67 (6.4 [1.0-11.9], vs. nondrinkers, p=.02), especially for distal/rectal tumors (10.4 [1.6-19.1], p=.02). Negative interaction between alcohol, total folate was observed for distal/rectal tumors (p-interaction=.06). Modest associations between folate, alcohol consumption and distal/rectal tumor Ki67 expression suggest accelerated proliferation, consistent with folate's role in DNA synthesis. [ABSTRACT FROM AUTHOR]

Ageing is a multi-factorial phenomenon which is considered as a major risk factor for the development of neurodegeneration, osteoporosis, cardiovascular disease, dementia, cancer, and other chronic diseases. Phenotypically, ageing is related with a combination of molecular, cellular, and physiological levels like genomic and epi-genomic alterations, loss of proteostasis, deregulation of cellular and subcellular function and mitochondrial dysfunction. Though, no single molecular mechanism accounts for the functional decline of different organ systems in older humans but accumulation of DNA damage or mutations is a dominant theory which contributes largely to the development of ageing and age-related diseases. However, mechanistic, and hierarchical order of these features of ageing has not been clarified yet. Scientific community now focus on the effect of obesity on accelerated ageing process. Obesity is a complex chronic disease that affects multiple organs and tissues. It can not only lead to various health conditions such as diabetes, cancer, and cardiovascular disease but also can decrease life expectancy which shows similar phenotype of ageing. Higher loads of DNA damage were also observed in the genome of obese people. Thus, inability of DNA damage repair may contribute to both ageing and obesity apart from cancer predisposition. The present review emphasizes on the involvement of molecular phenomenon of DNA metabolism in development of obesity and how it accelerates ageing in mammals. [ABSTRACT FROM AUTHOR]

Iron-sulfur (Fe-S) clusters are unique, redox-active co-factors ubiquitous throughout cellular metabolism. Fe-S cluster synthesis, trafficking, and coordination result from highly coordinated, evolutionarily conserved biosynthetic processes. The initial Fe-S cluster synthesis occurs within the mitochondria; however, the maturation of Fe-S clusters culminating in their ultimate insertion into appropriate cytosolic/nuclear proteins is coordinated by a late-acting cytosolic iron-sulfur assembly (CIA) complex in the cytosol. Several nuclear proteins involved in DNA replication and repair interact with the CIA complex and contain Fe-S clusters necessary for proper enzymatic activity. Moreover, it is currently hypothesized that the late-acting CIA complex regulates the maintenance of genome integrity and is an integral feature of DNA metabolism. This review describes the late-acting CIA complex and several [4Fe-4S] DNA metabolic enzymes associated with maintaining genome stability. [ABSTRACT FROM AUTHOR]

Escherichia coli RecBCD helicase–nuclease promotes vital homologous recombination-based repair of DNA double-strand breaks. The RecB nuclease domain (Nuc) is connected to the RecB helicase domain by a 19-amino-acid tether. When DNA binds to RecBCD, published evidence suggests that Nuc moves ∼50 Å from the exit of a RecC tunnel, from which the 3′-ended strand emerges during unwinding, to a distant position on RecC’s surface. During subsequent ATP-dependent unwinding of DNA, Nuc nicks the 3′-ended strand near 5′- GCTGGTGG-3′ (Chi recombination hotspot). Here, we test our model of Nuc swinging on the tether from the RecC tunnel exit to the RecC distant surface and back to the RecC tunnel exit to cut at Chi. We identify positions in a flexible surface loop on RecC and on RecB Nuc with complementary charges, mutation of which strongly reduces but does not eliminate Chi hotspot activity in cells. The recC loop mutation interacts with recB mutations hypothesized to be in the Chi-activated intramolecular signal transduction pathway; the double mutants, but not the single mutants, eliminate Chi hotspot activity. A RecC amino acid near the flexible loop is also essential for full Chi activity; its alteration likewise synergizes with a signal transduction mutation to eliminate Chi activity. We infer that altering the RecC surface loop reduces coordination among the subunits, which is critical for Chi hotspot activity. We discuss other RecBCD mutants with related properties. [ABSTRACT FROM AUTHOR]

Metabolic obstacles of the tumor microenvironment remain a challenge to T-cell-mediated cancer immunotherapies. To better understand the interplay of immune checkpoint signaling and immune metabolism, this study developed and used an optimized metabolite extraction protocol for non-adherent primary human T-cells, to broadly profile in vitro metabolic changes effected by PD-1 signaling by mass spectrometry-based metabolomics and isotopomer analysis. Inhibitory signaling reduced aerobic glycolysis and glutaminolysis. A general scarcity across the panel of metabolites measured supported widespread metabolic regulation by PD-1. Glucose carbon fate analysis supported tricarboxylic acid cycle reliance on pyruvate carboxylation, catabolic-state fluxes into acetyl-CoA and succinyl-CoA, and a block in de novo nucleoside phosphate synthesis that was accompanied by reduced mTORC1 signaling. Nonetheless, exogenous administration of nucleosides was not sufficient to ameliorate proliferation of T-cells in the context of multiple metabolic insufficiencies due to PD-L1 treatment. Carbon fate analysis did not support the use of primarily glucose-derived carbons to fuel fatty acid beta oxidation, in contrast to reports on T-memory cells. These findings add to our understanding of metabolic dysregulation by PD-1 signaling and inform the effort to rationally develop metabolic interventions coupled with immune-checkpoint blockade for increased treatment efficacy.

Iron-sulfur (Fe-S) clusters are unique, redox-active co-factors ubiquitous throughout cellular metabolism. Fe-S cluster synthesis, trafficking, and coordination result from highly coordinated, evolutionarily conserved biosynthetic processes. The initial Fe-S cluster synthesis occurs within the mitochondria; however, the maturation of Fe-S clusters culminating in their ultimate insertion into appropriate cytosolic/nuclear proteins is coordinated by a late-acting cytosolic iron-sulfur assembly (CIA) complex in the cytosol. Several nuclear proteins involved in DNA replication and repair interact with the CIA complex and contain Fe-S clusters necessary for proper enzymatic activity. Moreover, it is currently hypothesized that the late-acting CIA complex regulates the maintenance of genome integrity and is an integral feature of DNA metabolism. This review describes the late-acting CIA complex and several [4Fe-4S] DNA metabolic enzymes associated with maintaining genome stability.

Barley (Hordeum vulgare L.) grass has been recognized as a functional food with a wide spectrum of health-promoting properties. Supplementation with barley grass has the potential to prevent chronic diseases, such as cancer. Here, we investigated whether barley grass could protect against hepatocellular carcinoma (HCC). Our data showed that administration of barley grass juice attenuates tumor development in a hydrodynamic gene delivery-induced model of HCC. The expression levels of the immune cell markers Ptprc and Adgre1 were upregulated in the barley grass juice-treated and normal groups, compared to those in the vehicle group in the HCC model. Immune cells (CD45+, F4/80+, and CLEC4F + iNOS + cells) infiltration in the liver increased following barley grass juice administration. Our results indicate that barley grass could be beneficial for HCC alleviation, partly by regulating immune cell infiltration. The ingredients of barley grass affect immune cell infiltration in HCC, and the detailed mechanism requires further study. [ABSTRACT FROM AUTHOR]

The article presents the discussion on Telomere dysfunction activates the DNA damage checkpoint to induce a cell cycle arrest. Topics include extended period of time where cells can bypass the arrest and undergo cell division despite the persistence of the initial damage, a process called adaptation to DNA damage; and proposing the Cdc5 orchestrates multiple cell cycle pathways to promote adaptation.

Proper repair of DNA double-strand breaks is essential to the maintenance of genomic stability and avoidance of genetic disease. Organisms have many ways of repairing double-strand breaks, including the use of homologous sequences through homology-directed repair. While homology-directed repair is often error free, in single-strand annealing homologous repeats flanking a double-strand break are annealed to one another, leading to the deletion of one repeat and the intervening sequences. Studies in yeast have shown a relationship between the length of the repeat and single-strand annealing efficacy. We sought to determine the effects of homology length on single-strand annealing in Drosophila, as Drosophila uses a different annealing enzyme (Marcal1) than yeast. Using an in vivo single-strand annealing assay, we show that 50 base pairs are insufficient to promote single-strand annealing and that 500–2,000 base pairs are required for maximum efficiency. Loss of Marcal1 generally followed the same homology length trend as wild-type flies, with single-strand annealing frequencies reduced to about a third of wild-type frequencies regardless of homology length. Interestingly, we find a difference in single-strand annealing rates between 500-base pair homologies that align to the annealing target either nearer or further from the double-strand break, a phenomenon that may be explained by Marcal1 dynamics. This study gives insights into Marcal1 function and provides important information to guide the design of genome engineering strategies that use single-strand annealing to integrate linear DNA constructs into a chromosomal double-strand break. [ABSTRACT FROM AUTHOR]

Simple Summary: The role of Tau in genome protection and/or repair in neurons suggests that Tau expression in cancer cells could be involved in resistance to conventional anti-cancer treatments, in particular those inducing DNA damage. Knockdown of Tau in breast cancer cell lines improved the cellular response and resulted in a significant decrease of mouse-xenograft breast tumor volume after DNA damaging agent treatments by impairing the classical nonhomologous end-joining pathway. Tau allows 53BP1 to translocate to the nucleus in response to DNA damage by chaperoning microtubule protein trafficking. Recent reports suggested a role for microtubules in double-strand-DNA break repair. We herein investigated the role of the microtubule-associated protein Tau in radio- and chemotherapy. Noticeably, a lowered expression of Tau in breast cancer cell lines resulted in a significant decrease in mouse-xenograft breast tumor volume after doxorubicin or X-ray treatments. Furthermore, the knockdown of Tau impaired the classical nonhomologous end-joining pathway and led to an improved cellular response to both bleomycin and X-rays. Investigating the mechanism of Tau's protective effect, we found that one of the main mediators of response to double-stranded breaks in DNA, the tumor suppressor p53-binding protein 1 (53BP1), is sequestered in the cytoplasm as a consequence of Tau downregulation. We demonstrated that Tau allows 53BP1 to translocate to the nucleus in response to DNA damage by chaperoning microtubule protein trafficking. Moreover, Tau knockdown chemo-sensitized cancer cells to drugs forming DNA adducts, such as cisplatin and oxaliplatin, and further suggested a general role of Tau in regulating the nuclear trafficking of DNA repair proteins. Altogether, these results suggest that Tau expression in cancer cells may be of interest as a molecular marker for response to DNA-damaging anti-cancer agents. Clinically targeting Tau could sensitize tumors to DNA-damaging treatments. [ABSTRACT FROM AUTHOR]

Background: A simple and effective modified ethanol precipitation-based protocol was described for the extraction of genomic DNA from ancient human bones. The qualitative and quantitative evaluation of genomic DNA was done based on DNA purity (260/280) and the PCR method. Method and Materials: In this study, a total of 50 embalmed ancient bones, including 20 long and 30 hip bone samples, were taken for genomic DNA extraction. The efficiency of the genomic DNA extraction was demonstrated on >50-year-old ancient human HIP and long bone samples. In vitro quantitative and qualitative analysis of extracted genomic DNA was performed by 0.8% agarose gel electrophoresis and PCR amplification. To assess the quality of extracted genomic DNA, a mitochondrial-specific ATPase6 gene primer was used to obtain sequence information of 675 bp. Result: Our data show that a concentration of genomic DNA between 1.6 and 2.0 at 260/280 resulted in successful PCR amplification. Our results demonstrated that the extraction of DNA from ancient bone samples with a manual approach will increase the amplification efficiency of the polymerase chain reaction (PCR). Conclusion: In the present study, a simple, time-saving, and cost-effective protocol is described for the extraction of genomic DNA from ancient human bones. Further, we believe the extraction of genomic DNA from ancient bone samples with this approach will increase the success rate of PCR amplification. [ABSTRACT FROM AUTHOR]

Simple Summary: The transcription factor SOX11 is a member of the SRY box-containing family. Recently, SOX11 research has shifted from embryogenesis to cancer development. Nevertheless, the roles of SOX11 in different cancer types remain controversial. Here, we systematically explored the characteristics of SOX11 by multiple omics analyses. Aberrant SOX11 expression has been observed in many types of human malignant tumors. Moreover, SOX11 expression could serve as an indicator of survival outcomes, tumor progression and cellular immune infiltration. Our work highlights the diverse role of SOX11 in different types of tumors, which points out several directions for future prospective studies on SOX11 in cancer. SRY-box transcription factor 11 (SOX11), as a member of the SOX family, is a transcription factor involved in the regulation of specific biological processes and has recently been found to be a prognostic marker for certain cancers. However, the roles of SOX11 in cancer remain controversial. Our study aimed to explore the various aspects of SOX11 in pan-cancer. The expression of SOX11 was investigated by the Genotype Tissue-Expression (GTEX) dataset and the Cancer Genome Atlas (TCGA) database. The protein level of SOX11 in tumor tissues and tumor-adjacent tissues was verified by human pan-cancer tissue microarray. Additionally, we used TCGA pan-cancer data to analyze the correlations among SOX11 expression and survival outcomes, clinical features, stemness, microsatellite instability (MSI), tumor mutation burden (TMB), mismatch repair (MMR) related genes and the tumor immune microenvironment. Furthermore, the cBioPortal database was applied to investigate the gene alterations of SOX11. The main biological processes of SOX11 in cancers were analyzed by Gene Set Enrichment Analysis (GSEA). As a result, aberrant expression of SOX11 has been implicated in 27 kinds of cancer types. Aberrant SOX11 expression was closely associated with survival outcomes, stage, tumor recurrence, MSI, TMB and MMR-related genes. In addition, the most frequent alteration of the SOX11 genome was mutation. Our study also showed the correlations of SOX11 with the level of immune infiltration in various cancers. In summary, our findings underline the multifaceted role and prognostic value of SOX11 in pan-cancer. [ABSTRACT FROM AUTHOR]

HMGA2 belongs to the non-histone chromosomal high-mobility group (HMG) protein family and binds to DNA at promoter and enhancer regions. The chromatin modifier plays a role in recruiting other factors such as histone acet-ylases, which together with HMGA2 form a structure called the enhanceosome that has impact on local chromatin structure and therefore gene expression. In the cochlea, HMGA2 is tonotopically expressed. However, its relevance for frequency specific hearing remains to be determined. Sonic hedgehog, a tonotopic morphogen, forms an apex-to-base decreasing gradient in the cochlea. To study the impact of hedgehog signaling on HMGA2 expression, the hedgehog pathway was activated in vivo using a gain-of-function mouse model. On the other hand, retinoic acid forms a base-to-apex decreasing morphogen gradient, thereby opposing sonic hedgehog. To modulate retinoic acid levels in vivo, gain- and loss-of-function mouse models were used. Furthermore, conditional knockout of Hmga2 from the otocyst stage was established to study the relevance of HMGA2 using histological staining and hearing measurements. Constitutive activation of the HH pathway resulted in ectopic expression of HMGA2. Retinoic acid in turn was found to limit the extension of the HMGA2 gradient towards the base. This finding indicates that positional information mediated by tonotopic morphogen gradients establish the Hmga2 gradient in vivo. Conditional knockout of Hmga2 did not affect the cellular composition of the organ of Corti. However, adult mice fail to develop normal low-frequency hearing as determined by ABR and DPOAE measurements. In this work, we used different transgenic mouse lines to establish that embryonic patterning via retinoic acid and sonic hedgehog establish the HMGA2 gradient along the tonotopic axis. Also, loss of Hmga2 demonstrated that the chromatin modifier is necessary for the development of low-frequency hearing in the adult animal. Together, these results indicate that HMGA2 is an integral part in mediating tonotopic identity in the mouse cochlea. [ABSTRACT FROM AUTHOR]

Analyses of large-scale cancer sequencing data have revealed that mutagenic processes can create distinctive patterns of base substitutions, called mutational signatures. Interestingly, mutational patterns resembling some of these signatures can also be observed in normal cells. To determine whether similar patterns exist more generally, we analyzed large data sets of genetic variation, including mutations from 7 model species and single nucleotide polymorphisms in 42 species, totaling >1.9 billion variants. We found that base substitution patterns for most species closely match single base substitution (SBS) mutational signature 5 in the Catalog of Somatic Mutations in Cancer (COSMIC) database. SBS5 is ubiquitous in cancers and also present in normal human cells, suggesting that similar patterns of genetic variation across so many species are likely due to conserved biochemistry. We investigated the mechanistic origins of the SBS5-like mutational pattern in Saccharomyces cerevisiae, and show that translesion DNA synthesis and sugar metabolism are directly linked to this form of mutagenesis. We propose that conserved metabolic processes in cells are coupled to continuous generation of genetic variants, which can be acted upon by selection to drive the evolution of biological entities. [ABSTRACT FROM AUTHOR]

Natural medicinal compounds have gained increasing attention as adjuvants during cancer chemotherapy. The present study demonstrated the chemosensitizing effect of sesamol, a natural phenolic compound, in HeLa cell lines In Vitro. Sesamol-pretreated (10 μM) HeLa cells were exposed to 7.5 nM paclitaxel. The chemosensitization was estimated by MTT-based metabolic assay. Further, oxidative DNA damage, alterations in mitochondrial membrane potential (MMP), and apoptotic morphological changes were analyzed. Sesamol treatment before paclitaxel treatment significantly decreased the IC50 value of paclitaxel (7.5 nM) in a concentration-dependent manner. Further, Sesamol treatment before paclitaxel increased the intracellular ROS levels and enhanced apoptosis through MMP alterations. Moreover, there was an increased % of tail DNA in sesamol + paclitaxel-treated cervical cancer cells compared to paclitaxel alone treatment. The frequency of apoptotic cells were also increased during sesamol + paclitaxel treatment cells compared to paclitaxel alone treatment. Thus, Sesamol treatment before paclitaxel exposure enhanced the apoptotic cell death in the HeLa cell lines. The results of the present study were in support of the usage of natural medicinal compounds for clinical chemotherapy after systematic animal experimentations. [ABSTRACT FROM AUTHOR]

Advanced hepatocellular carcinoma (HCC) is responsive to immune checkpoint inhibitors, but there are currently no known biomarkers to predict treatment benefit. Blood TMB (bTMB) estimation via circulating tumor DNA (ctDNA) profiling can provide a convenient means to estimate HCC TMB. Here we provide the first landscape of bTMB in advanced HCC using a commercially available next-generation sequencing assay, show that it is approximately three times as high as matched tissue TMB, and show that bTMB correlates with NAFLD cirrhosis etiology and the presence of genomic alterations in HTERT and TP53. These results lay the foundation for subsequent studies evaluating bTMB as an immune therapy predictive biomarker in HCC. [ABSTRACT FROM AUTHOR]

Low skeletal muscle mass is associated with cognitive impairment and dementia in older adults. This review describes the possible underlying pathophysiological mechanisms: systemic inflammation, insulin metabolism, protein metabolism, and mitochondrial function. We hypothesize that the central tenet in this pathophysiology is the dysfunctional myokine secretion consequent to minimal physical activity. Myokines, such as fibronectin type III domain containing 5/irisin and cathepsin B, are released by physically active muscle and cross the blood-brain barrier. These myokines upregulate local neurotrophin expression such as brain-derived neurotrophic factor (BDNF) in the brain microenvironment. BDNF exerts anti-inflammatory effects that may be responsible for neuroprotection. Altered myokine secretion due to physical inactivity exacerbates inflammation and impairs muscle glucose metabolism, potentially affecting the transport of insulin across the blood-brain barrier. Our working model also suggests other underlying mechanisms. A negative systemic protein balance, commonly observed in older adults, contributes to low skeletal muscle mass and may also reflect deficient protein metabolism in brain tissues. As a result of age-related loss in skeletal muscle mass, decrease in the abundance of mitochondria and detriments in their function lead to a decrease in tissue oxidative capacity. Dysfunctional mitochondria in skeletal muscle and brain result in the excessive production of reactive oxygen species, which drives tissue oxidative stress and further perpetuates the dysfunction in mitochondria. Both oxidative stress and accumulation of mitochondrial DNA mutations due to aging drive cellular senescence. A targeted approach in the pathophysiology of low muscle mass and cognition could be to restore myokine balance by physical activity. [ABSTRACT FROM AUTHOR]

Background: NETosis is a neutrophil-mediated defense mechanism during which DNA and enzymes are extruded forming a network (NETs) trapping and killing different pathogens. NETosis is reduced in both mice and humans during aging. Aims: We explored the difference in the efficacy of NETs released in elderly (> 65 years) versus adults (20–50 years) subjects in inhibiting Staphylococcus aureus growth and activating the growth of keratinocytes. Methods: Neutrophil granulocytes, obtained from venous blood both in healthy elderly and adult subjects, were stimulated by LPS (0–250 µg/ml) to induce the formation of NET. NETs were quantified by SYBR Green staining and growth inhibition of S. aureus was evaluated by disk diffusion test. Furthermore, NETs (0–500 ng/ml) were added to immortalized human keratinocytes (HaCaT cells), and their proliferation was evaluated by MTT assay after 24 h. Finally, the DNA size of NETs was evaluated by flow cytometry after SYBR Green staining. Results: Greater production of NETs was observed in elderly subjects than in adults, but these NETs showed reduced bactericidal capacity and HaCaT cells' proliferation stimulation. The activities of the NETs are related to the size of the extruded DNA threads, and when NETs size was analyzed, DNA from elderly showed a higher size compared to that obtained by adults. Discussion: Unexpected results showed aging-related NETs structural modification resulting in both a lower antimicrobial activity and keratinocyte proliferation stimulation compared to NETs obtained from adults. Conclusions: The NETs DNA size observed in elderly subjects has not been previously reported and could be part of other pathogenic mechanisms observed in aging. [ABSTRACT FROM AUTHOR]

Dysregulation of DNA methylation is associated with human disease, particularly cancer, and the assessment of aberrant methylation patterns holds great promise for clinical diagnostics. However, DNA polymerases do not effectively discriminate between processing 5-methylcytosine (5 mC) and unmethylated cytosine, resulting in the silencing of methylation information during amplification or sequencing. As a result, current detection methods require multi-step DNA conversion treatments or careful analysis of sequencing data to decipher individual 5 mC bases. To overcome these challenges, we propose a novel DNA polymerase-mediated 5 mC detection approach. Here, we describe the engineering of a thermostable DNA polymerase variant derived from Thermus aquaticus with altered fidelity towards 5 mC. Using a screening-based evolutionary approach, we have identified a DNA polymerase that exhibits increased misincorporation towards 5 mC during DNA synthesis. This DNA polymerase generates mutation signatures at methylated CpG sites, allowing direct detection of 5 mC by reading an increased error rate after sequencing without prior treatment of the sample DNA., (© 2024 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Activin receptor type 1 (ACVR1; ALK2) and activin receptor like type 1 (ACVRL1; ALK1) are transforming growth factor beta family receptors that integrate extracellular signals of bone morphogenic proteins (BMPs) and activins into Mothers Against Decapentaplegic homolog 1/5 (SMAD1/SMAD5) signaling complexes. Several activating mutations in ALK2 are implicated in fibrodysplasia ossificans progressiva (FOP), diffuse intrinsic pontine gliomas, and ependymomas. The ALK2 R206H mutation is also present in a subset of endometrial tumors, melanomas, non-small lung cancers, and colorectal cancers, and ALK2 expression is elevated in pancreatic cancer. Using DNA-encoded chemistry technology, we screened 3.94 billion unique compounds from our diverse DNA-encoded chemical libraries (DECLs) against the kinase domain of ALK2. Off-DNA synthesis of DECL hits and biochemical validation revealed nanomolar potent ALK2 inhibitors. Further structure-activity relationship studies yielded center for drug discovery (CDD)-2789, a potent [NanoBRET (NB) cell IC 50 : 0.54 μM] and metabolically stable analog with good pharmacological profile. Crystal structures of ALK2 bound with CDD-2281, CDD-2282, or CDD-2789 show that these inhibitors bind the active site through Van der Waals interactions and solvent-mediated hydrogen bonds. CDD-2789 exhibits high selectivity toward ALK2/ALK1 in KINOMEscan analysis and NB K192 assay. In cell-based studies, ALK2 inhibitors effectively attenuated activin A and BMP-induced Phosphorylated SMAD1/5 activation in fibroblasts from individuals with FOP in a dose-dependent manner. Thus, CDD-2789 is a valuable tool compound for further investigation of the biological functions of ALK2 and ALK1 and the therapeutic potential of specific inhibition of ALK2., Competing Interests: Competing interests statement:A provisional patent was submitted by R.J., D.M., K.M.B., F.L., J.-Y.L., Z.T. D.W.Y., S.S.P., and M.M.M. from Baylor College of Medicine.