The Force is Strong with This Epigenome: Chromatin Structure and Mechanobiology

All life forms sense and respond to mechanical stimuli. Throughout evolution, organisms develop diverse mechanosensing and mechanotransduction pathways, leading to fast and sustained mechanoresponses. Memory and plasticity characteristics of mechanoresponses are thought to be stored in the form of epigenetic modifications, including chromatin structure alterations. These mechanoresponses in the chromatin context share conserved principles across species, such as lateral inhibition during organogenesis and development. However, it remains unclear how mechanotransduction mechanisms alter chromatin structure for specific cellular functions, and if altered chromatin structure can mechanically affect the environment. In this review, we discuss how chromatin structure is altered by environmental forces via an outside-in pathway for cellular functions, and the emerging concept of how chromatin structure alterations can mechanically affect nuclear, cellular, and extracellular environments. This bidirectional mechanical feedback between chromatin of the cell and the environment can potentially have important physiological implications, such as in centromeric chromatin regulation of mechanobiology in mitosis, or in tumor-stroma interactions. Finally, we highlight the current challenges and open questions in the field and provide perspectives for future research.     

LINC01140 regulates osteosarcoma proliferation and invasion by targeting the miR-139-5p/HOXA9 axis

Osteosarcoma is one of the commonest metastatic tumor in children and teenagers, and has a hopeless, prognosis. Long non-coding RNA (lncRNA) acts momentous roles as a regulator on the proliferation and migration of cancer. Here, we performed GEO database analysis and qPCR to identify differentially expressed lncRNAs in osteosarcoma cells. Knockdown of lncRNA LINC01140 was used to detect the effect of LINC01140 on the proliferation, invasion, and epithelial-mesenchymal transition (EMT) of osteosarcoma cells. Bioinformatics analysis and qPCR identified the LINC01140/miR-139-5p/Homeobox A9 (HOXA9) regulatory axis. RNA immunoprecipitation assay, Dual-luciferase assay, and rescue experiments confirmed the interaction of LINC01140/miR-139-5p/HOXA9 in osteosarcoma. LINC01140 was overexpressed in osteosarcoma and knocking down LINC01140 restrained the proliferation and invasion of osteosarcoma cells and EMT. In Saos2 and MG63 cells, LINC01140 sponged miR-139-5p, and a miR-139-5p inhibitor overturned the suppression of LINC01140 knockdown on the proliferation and migration of osteosarcoma cells. Moreover, miR-139-5p depressed the invasion, proliferation, and EMT of osteosarcoma cells via targeting HOXA9. Our results indicate that LINC01140 downregulation inhibits the invasion, proliferation, and EMT in osteosarcoma cells through targeting the miR-139-5p/HOXA9 axis. Therefore, LINC01140 is a potential therapeutic target for osteosarcoma.     

5′-CMP and 5′-UMP promote myogenic differentiation and mitochondrial biogenesis by activating myogenin and PGC-1α in a mouse myoblast C2C12 cell line

Ribonucleotides are basic monomeric building blocks for RNA considered as conditionally essential nutrients. They are normally produced in sufficient quantity, but can become insufficient upon stressful challenges. The administration of pyrimidine nucleotides, such as cytidine-5′-monophosphate (5′-CMP) and uridine-5′-monophosphate (5′-UMP), enables rats to endure prolonged exercise. However, the underlying mechanisms have remained elusive. To investigate these mechanisms, we studied the effect of 5′-CMP and 5′-UMP on muscular differentiation and mitochondrial biogenesis in myoblast C2C12 cells. 5′-CMP and 5′-UMP were found to increase the mRNA levels of myogenin, which is a myogenic regulatory protein expressed during the final differentiation step and fusion of myoblasts into myotubes. 5′-CMP and 5′-UMP also promoted myoblast differentiation into myotube cells. 5′-CMP and 5′-UMP further increased the mRNA levels of PGC-1α which regulates mitochondrial biogenesis and skeletal muscle fiber type. In addition, 5′-CMP and 5′-UMP increased mitochondrial DNA copy number and enhanced mRNA levels of slow-muscle myosin heavy chains. Moreover, cytidine and uridine, nucleosides corresponding to 5′-CMP and 5′-UMP, markedly promoted myotube formation in C2C12 cells. Considering the metabolism and absorption of nucleotides, the active bodies underlying the effects observed with 5′-CMP and 5′-UMP could be cytidine and uridine. In conclusion, our results indicate that 5′-CMP and 5′-UMP can promote myogenic differentiation and mitochondrial biogenesis, as well as increase slow-twitch fiber via the activation of myogenin and PGC-1α. In addition, 5′-CMP and 5′-UMP may be considered as safe and effective agents to enhance muscle growth and improve the endurance in skeletal muscles.     

Partial substitution of organic nitrogen with synthetic nitrogen enhances rice yield,grain starch metabolism and related genes expression under the dual cropping system

Improving grain filling in the presernt farming systems is crucial where grain filling is a concern due to the extreme use of chemical fertilizers (CF). A field experiment was conducted at the experimental station of Guangxi University, China in 2019 to test the hypothesis that cattle manure (CM) and poultry manure (PM) combined with CF could improve rice grain filling rate, yield, biochemical and qualitative attributes. A total of six treatments, i.e., no fertilizer (T₁), 100% CF (T₂), 60% CM + 40% CF (T₃), 30% CM + 70% CF (T₄), 60% PM + 40% CF (T₅), and 30% PM + 70% CF (T₆) were used in this study. Results showed that the combined treatment T₆increased starch metabolizing enzymes activity (SMEs), such as ADP-glucose phosphorylase (ADGPase) by 8 and 12%, soluble starch synthase (SSS) by 7 and 10%, granule bound starch synthesis (GBSS) by 7 and 9%, and starch branching enzyme (SBE) by 14 and 21% in the early and late seasons, respectively, compared with T₂. Similarly, higher rice grain yield, grain filling rate, starch, and amylose content were also recorded in combined treatments. In terms of seasons, higher activity of SMEs , grain starch, and amylose content was noted in the late-season compared to the early season. The increment in these traits was mainly attributed to a lower temperature in the late season during the grain filling period. Furthermore, our results suggested that an increment in starch accumulation and grain filling rate were mainly associated with the enhanced sink capacity by regulating key enzyme activities involved in Suc-to-starch conversion. In-addition, RT-qPCR analysis showed higher expression levels of AGPS2b, SSS1, GBSS1, and GBSE11b genes, which resultantly increased the activities of SMEs during the grain filling period under combined treatments. Linear regression analysis revealed that the activity of ADGPase, SSS, GBSS, and SBE were highly positively correlated with starch and amylose accumulation. Thus, we concluded that a combination of 30% N from PM or CM with 70% N from CF is a promising option in terms of improving rice grain yield and quality. Our study provides a sustainable fertilizer management strategy to enhance rice grain yield and quality at the lowest environmental cost.     

Is the Neutrophil-to-Lymphocyte Ratio an Exceptional Indicator for Metabolic Syndrome Disease and Outcomes?

ObjectivesTo show that there is relation between neutrophil-to-lymphocyte ratio (NLR) and metabolic syndrome and also, its components.FindingsMetabolic syndrome is associated with elevated fasting blood glucose, increased blood pressure, central obesity, decreased high-density lipoprotein, and increased triglyceride levels. Because of its growing incidence and prevalence and the effect that it has on developing other noncommunicable diseases, the importance gets even more value. The prediction and control of this disease in its early stages and in the most inexpensive way is of crucial need. Due to the role of chronic low-grade inflammation in metabolic syndrome, cytokines and inflammatory factors (like interleukin-6 and tumor necrosis factor-α) play a critical role on this phenomenon. The NLR is an inflammatory marker that has an unchallenging availability and has a reasonable cost. The NLR is related to obesity, type 2 diabetes, hypertension, and blood cholesterol levels.ConclusionThis suggests that there may be a relationship between the NLR and metabolic syndrome. The NLR, as a low-grade inflammation marker, indicates a positive relationship with central obesity. Also, studies indicate that the incidence of diabetes, its severity, and its control are related to the NLR. Hypertension and hyperlipidemia can both be noticed with higher NLRs. This rapid review assesses the association between metabolic syndrome and the NLR.     

Hypoxia Is a Dominant Remodeler of the Effector T Cell Surface Proteome Relative to Activation and Regulatory T Cell Suppression

Immunosuppressive factors in the tumor microenvironment (TME) impair T cell function and limit the antitumor immune response. T cell surface receptors and surface proteins that influence interactions and function in the TME are proven targets for cancer immunotherapy. However, how the entire surface proteome remodels in primary human T cells in response to specific suppressive factors in the TME remains to be broadly and systematically characterized. Here, using a reductionist cell culture approach with primary human T cells and stable isotopic labeling with amino acids in cell culture–based quantitative cell surface capture glycoproteomics, we examined how two immunosuppressive TME factors, regulatory T cells (Tregs) and hypoxia, globally affect the activated CD8⁺ surface proteome (surfaceome). Surprisingly, coculturing primary CD8⁺ T cells with Tregs only modestly affected the CD8⁺ surfaceome but did partially reverse activation-induced surfaceomic changes. In contrast, hypoxia drastically altered the CD8⁺ surfaceome in a manner consistent with both metabolic reprogramming and induction of an immunosuppressed state. The CD4⁺ T cell surfaceome similarly responded to hypoxia, revealing a common hypoxia-induced surface receptor program. Our surfaceomics findings suggest that hypoxic environments create a challenge for T cell activation. These studies provide global insight into how Tregs and hypoxia remodel the T cell surfaceome and we believe represent a valuable resource to inform future therapeutic efforts to enhance T cell function.     

Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand

DNA damage bypass pathways promote the replication of damaged DNA when replication forks stall at sites of DNA damage. Template switching is a DNA damage bypass pathway in which fork-reversal helicases convert stalled replication forks into four-way DNA junctions called chicken foot intermediates, which are subsequently extended by replicative DNA polymerases. In yeast, fork-reversal is carried out by the Rad5 helicase using an unknown mechanism. To better understand the mechanism of Rad5 and its specificity for different fork DNA substrates, we used a FRET-based assay to observe fork reversal in real time. We examined the ability of Rad5 to bind and catalyze the reversal of various fork DNA substrates in the presence of short gaps in the leading or lagging strand as well as in the presence or absence of RPA and RNA primers in the lagging strand. We found that Rad5 preferentially reverses fork DNA substrates with short gaps (10 to 30 nt.) in the leading strand. Thus, Rad5 preferentially reverses fork DNA substrates that form chicken foot intermediates with 5′ overhangs that can be extended by replicative DNA polymerases during the subsequent steps of template switching.     

Distinct roles in phagocytosis of the early and late increases of cell surface calreticulin induced by oxaliplatin

Calreticulin (CRT), a chaperone typically located in the endoplasmic reticulum (ER), is known to translocate to the cell surface in response to anticancer drugs. Cell surface CRT (ecto-CRT) on apoptotic or pre-apoptotic cells serves as an “eat me” signal that can promote phagocytosis. In this study, we observed the biphasic (early transient and late sustained) increase of ecto-CRT on HT-29 cells after treatment with oxaliplatin (L-OHP). To investigate the role of ecto-CRT that accumulates in the early and late phases as “eat me” signals, we examined the phagocytosis of HT-29 cells by macrophage-like cells and dendritic cell (DC) -like cells prepared from THP-1 cells. The results indicated that the early ecto-CRT-expressed cells were phagocytosed by immature DC-like cells, and the late ecto-CRT-expressed cells were phagocytosed primarily by macrophage-like cells, while mature DC-like cells did not respond to the either class of ecto-CRT-expressed cells. Both types of phagocytotic events were inhibited by CRT Blocking Peptide, suggesting that such events depended on the ecto-CRT. Our results suggested that the early increase of ecto-CRT is related to phagocytosis as part of immunogenic cell death (ICD), while the late increase of ecto-CRT is related to the removal of apoptotic cells by macrophages.     

Smash ridge tillage strongly influence soil functionality,physiology and rice yield

The practice of smash-ridging on dry land crop cultivation has shown much promise. However, the mechanism how does soil functionality and root traits can affect rice yield under smash ridge tillage with reduced nitrogen fertilization have not yet been explored. To fill this knowledge gap, we used three tillage methods—smash-ridging 40 cm (S40), smash-ridging 20 cm (S20), and traditional turn-over plowing 20 cm (T)—and two rice varieties (hybrid rice and conventional rice) and measured soil quality, root traits, rice yield and their correlation analysis at different growth stages. Soil physical and chemical properties were significantly improved by smash-ridging, including improvements in root morphological and physiological traits during three growth stages compared with T. S40 had the highest leaf area index (LAI), plant height (PH), and biomass accumulation (BA). Increment in biomass and panicle number (PN) resulted in higher grain yield (GY) of 6.9–9.4% compared with T. Correlation analysis revealed that root total absorption area (RTAA), root active absorption area (RAA), and root area ratio (RAR) were strongly correlated with soil quality. Root injury flow (RIF) and root biomass accumulation (RBA) were strongly correlated with LAI and above-ground plant biomass accumulation (AGBA). Conclusively, S40 is a promising option for improving soil quality, root traits, and consequently GY.     

Copper nanoparticles: Green synthesis and managing fruit rot disease of chilli caused by Colletotrichum capsici

The present study was focused on synthesis and characterization of copper nanoparticles to evaluate their efficacy against fruit rot pathogen of chilli crop. The green synthesis of nanoparticles was carried out by using extracts of Eucalyptus and Mint leaves. The synthesis of copper nanoparticles was confirmed by XRD, PSA, SEM and TEM. The average size of these particles synthesized by Eucalyptus leaf extract (CuNP-E) ranged from 10 to 130 nm, while as size of Mint leaf extract synthesized particles (CuNP-M) ranged from 23 to 39 nm, thus confirming their nano size. These green synthesized copper nanoparticles were evaluated against Colletotrichum capsici where Carbendazim 50 WP @ 500 ppm and copper oxychloride 50 WP @ 2500 ppm served as standard checks. The mycelia inhibition of Colletotrichum capsici caused by copper nanoparticles was studied on PDA medium. CuNP-M @ 1000 ppm showed highest mycelial inhibition of 99.78% followed by 93.75% at 500 ppm and CuNP-E @ 1000 ppm compared to standard fungicides, carbendazim 50 WP @ 500 ppm (72.82%), and copper oxychloride 50 WP @ 2500 ppm (85.85%). The CuNP-M @ 500 ppm were significantly superior to carbendazim 50 WP @ 500 ppm and copper oxychloride 50 WP @ 2500 ppm, but was statistically at par with CuNP-E @ 1000 ppm. This shows effectiveness of much lower concentration of copper nanoparticles compared to conventional fungicides. In detached fruit method, nanoparticles applied before inoculation of pathogen showed better results with regard to incubation period, lesion number and lesion size than after inoculation of pathogen. The present study reveals a simple, convenient, non-toxic and cost-efficient technique for the synthesis of nanoparticles and their effectiveness against Colletotrichum capsici. CuNP-M first time synthesized and evaluated against Colletotrichum capsici performed better than CuNP-E.     

Arterial Stiffness,Carotid Intima-Media Thickness,Endocan, and A Disintegrin and Metalloproteinase With Thrombospondin Type I Motif 9 Levels and Their Relationship With Disease Activity in Patients With Acromegaly With and Without Cardiovascular Risk Factors

ObjectiveCardiovascular complications such as cardiomyopathy and endothelial dysfunction, which are frequently seen in patients with acromegaly, are among the most important causes of morbidity and mortality. In this study, we aimed to investigate arterial stiffness, carotid intima-media thickness, endocan level, and A disintegrin and metalloproteinase with thrombospondin type I motif 9 level and their relationship with disease activity in patients with acromegaly with and without cardiovascular risk factors.MethodsA total of 60 patients with acromegaly—25 with active disease, 26 with well-controlled disease, and 9 with newly diagnosed disease—and 60 age-, sex-, and body mass index (BMI)-matched healthy control subjects were enrolled in this study. All the subjects’ height, weight, BMI, systolic blood pressure (SBP), diastolic blood pressure (DBP), fasting plasma glucose (FPG) level, insulin, hemoglobin A1C (HbA1C), C-reactive protein , lipid, endocan, A disintegrin and metalloproteinase with thrombospondin type I motif 9 levels, pulse wave velocity (PWV), and carotid intima-media thickness were measured.ResultsThe SBP, DBP, FPG level, HbA1C level, and PWV of the acromegaly group were higher than those of the control group. In patients with acromegaly with cardiovascular disease (CVD) risk factors, the PWV was higher than that in the control group, and in patients with acromegaly without CVD risk factors, the PWV was similar to that in the control group. In a correlation analysis, a positive correlation was found between PWV and age, BMI, SBP, DBP, FPG level, and HbA1C level in the acromegaly group.ConclusionIn our study, we found that arterial stiffness increased in patients with acromegaly with CVD risk factors and that increased arterial stiffness was associated with hemodynamic (SBP and DBP) and metabolic (BMI, FPG level, and HbA1C level) parameters.     

Optimization of growing conditions for pigments production from microalga Navicula incerta using response surface methodology and its antioxidant capacity

Navicula incerta is a marine microalga distributed in Baja California, México, commonly used in aquaculture nutrition, and has been extended to human food, biomedical, and pharmaceutical industries due to its high biological activity. Therefore, the study aimed to optimize culture conditions to produce antioxidant pigments. A central composite experimental design and response surface methodology (RSM) was employed to analyze the best culture conditions. The medium (nitrogen-deficient concentrations), salinity (PSU = Practical Salinity Unity [g/kg]), age of culture (days), and solvent extraction (ethanol, methanol, and acetone) were the factors used for the experiment. Chlorophyll a (Chl a) and total carotenoids (T-Car), determined spectroscopically, were used as the response variables. The antioxidant capacity was evaluated by DPPH^? and ABTS^?+ radical inhibition, FRAP, and anti-hemolytic activity. According to the overlay plots, the optimum growth conditions for Chl a and T-Car production were the following conditions: medium = 0.44 mol·L^-1 of NaNO₃, salinity = 40 PSU, age of culture: 3.5 days, and solvent = methanol. The pigment extracts obtained in these optimized conditions had high antioxidant activity in ABTS^?+ (86.2–92.1% of inhibition) and anti-hemolytic activity (81.8–96.7% of hemolysis inhibition). Low inhibition (33–35%) was observed in DPPH^?. The highest value of FRAP (766.03 ± 16.62 μmol TE/g) was observed in the acetonic extract. The results demonstrated that RSM could obtain an extract with high antioxidant capacity with potential applications in the biomedical and pharmaceutical industry, which encourages the use of natural resources for chemoprevention of chronic-degenerative pathologies.     

Parathyroidectomy Is Associated With Reversed Nondipping Heart Rate That Impacts Mortality in Chronic Kidney Disease Patients

ObjectiveNondipping heart rate (HR), defined as a night/day HR ratio >0.90, has been associated with increased mortality in epidemiologic studies. However, its prognostic value in stage 5 chronic kidney disease (CKD5) patients and the effects of parathyroidectomy (PTX) on nondipping HR remain unknown.MethodsThis case-control study of 162 healthy controls and 502 CKD5 patients was performed between 2011 and 2018, in which CKD5 patients were further divided into non-PTX (n = 186) and severe secondary hyperparathyroidism (SHPT) with PTX (n = 316) subgroups. Each participant underwent 24-hour Holter monitoring for HR ratio. Mortality was followed up in CKD5 patients (median time: 46.0 months).ResultsThe HR ratio in CKD5 patients was higher than in controls (0.92 ± 0.08 vs 0.81 ± 0.08, P <.001), associated with a 44% increase in mortality risk per 0.1 increment (hazard ratio, 1.44; 95% CI: 1.02-2.03; P =.04), and was positively related to serum intact parathyroid hormone levels (P <.001). PTX reversed nondipping HR in SHPT patients (n = 50, median time: 6.3 months, P <.001). Survival probabilities for PTX (n = 294) were better than non-PTX (n = 47) (hazard ratio, 0.31; 95% CI: 0.14-0.67; P <.01) in SHPT patients (serum intact parathyroid hormone >500.0 pg/mL).ConclusionCKD5 patients displayed a nondipping HR pattern, which is a prognostic marker of all-cause mortality. PTX for SHPT patients was associated with a reversal in nondipping HR ratio, which may mediate a better outcome.     

Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability

Colorectal cancer is the second leading cause of cancer death worldwide, and the incidence of this disease is expected to increase as global socioeconomic changes occur. Immune checkpoint inhibition therapy is effective in treating a minority of colorectal cancer tumors; however, microsatellite stable tumors do not respond well to this treatment. Emerging cancer immunotherapeutic strategies aim to activate a cytotoxic T cell response against tumor-specific antigens, presented exclusively at the cell surface of cancer cells. These antigens are rare and are most effectively identified with a mass spectrometry–based approach, which allows the direct sampling and sequencing of these peptides. Although the few tumor-specific antigens identified to date are derived from coding regions of the genome, recent findings indicate that a large proportion of tumor-specific antigens originate from allegedly noncoding regions. Here, we employed a novel proteogenomic approach to identify tumor antigens in a collection of colorectal cancer–derived cell lines and biopsy samples consisting of matched tumor and normal adjacent tissue. The generation of personalized cancer databases paired with mass spectrometry analyses permitted the identification of more than 30,000 unique MHC I–associated peptides. We identified 19 tumor-specific antigens in both microsatellite stable and unstable tumors, over two-thirds of which were derived from noncoding regions. Many of these peptides were derived from source genes known to be involved in colorectal cancer progression, suggesting that antigens from these genes could have therapeutic potential in a wide range of tumors. These findings could benefit the development of T cell–based vaccines, in which T cells are primed against these antigens to target and eradicate tumors. Such a vaccine could be used in tandem with existing immune checkpoint inhibition therapies, to bridge the gap in treatment efficacy across subtypes of colorectal cancer with varying prognoses. Data are available via ProteomeXchange with identifier PXD028309.