C3 Gene Research Articles

Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants

Abstract Gene regulatory networks (GRNs) based on transcription factors (TFs) control development and environmental responses. In this study, GRNs were inferred computationally using random forest decision tree-based regression. Networks were constructed for the grasses barley, maize, wheat, brachypodium, sorghum and rice. When compared with Arabidopsis thaliana and alga networks, they show substantial conservation. The degree of conservation depends on phylogenetic closeness. The processes are conserved between all species include basic cellular functions while the processes conserved only in the grasses are annotated with more specific gene ontology terms. In the three species with a carbon concentration mechanism, photorespiration is partially dissociated from photosynthetic regulation. In contrast, in the C4 species, the regulation of C4 genes is associated with photosynthetic regulation. The comparative analyses reveal conserved TFs that control photosynthesis in seed plants but not in the alga. The analyses resulted in a pipeline for the general transfer of information between the small dicot A. thaliana and the commercially relevant grasses.

A pilot study of childhood-onset Takayasu arteritis using whole exome sequencing suggests oligogenic inheritance involving classical complement, collagen, and autoinflammatory pathways.

Takayasu arteritis (TA) is a chronic granulomatous inflammatory disease affecting the aorta and its branches. Paediatric TA (pTA) may present from 6months after birth till the adolescent age group. Genetics and pathogenesis of pTA are not fully understood. Earlier studies reported monogenic mutation in NOD2, XIAP, and STAT1 genes in patients with pTA. TA, a relatively rare disease, is more common in geographical pockets, including India. We hypothesized that South Asian patients with pTA, namely, those of Indian subcontinent origin, may have clinically relevant and unique pathogenic variants involving one or more genes, especially those linked to genetically driven vasculitic illnesses, including autoinflammatory pathologies. Children with pTA fulfilling EULAR/PRINTO/PReS classification criteria and presenting with clinical symptoms to the Paediatric Rheumatology clinic of Christian Medical College, Vellore, were included. Blood samples were collected after getting informed consent from parents or guardians and assent forms from children. DNA was extracted from whole blood using the Qiagen DNA extraction kit. Initially, the common variant in Indian population, namely, ADA2 c.139G > A; p.Gly47Arg, was screened, followed by whole exome sequencing. Fourteen children were recruited for the study. Median age of patients was 11years (4months-14years) with a male-to-female ratio of 4:10. Distribution of angiographic subsets by Numano's classification of included children were as follows: type 5 (n = 7), type 4 (n = 5), and type 3 (n = 2). We identified novel variants in ten different genes. This include variants in genes of classical complement pathway, namely, C2, C3, C6, C7, and C9, and other genes, namely, CYBA, SH3BP2, GUCY2C, CTC1, COL5A1, and NLPR3. Two of 14 patients have heterozygous pathogenic variants; this implies that combination of heterozygous variants in C3 and COL5A1 might lead to disease development, suggesting digenic inheritance. One patient has a homozygous variant in CYBA. None of the patients were identified to have ADA2 variants. Whole exome sequencing reveals combination of rare variants in genes C3, COL5A1, and CYBA associated with disease development in children with Takayasu Arteritis. Key Points • We identified novel variants in genes of classical complement pathway, namely, C2, C3, C6, C7, and C9, and other genes, namely, CYBA, SH3BP2, GUCY2C, CTC1, COL5A1, and NLPR3. • Two of 14 patients have heterozygous pathogenic variants in C3 and COL5A1; this may have implications in disease development, suggesting digenic inheritance. • One patient has homozygous variant in CYBA. • None of the patients were identified to have ADA2 variants.

Immunomodulatory effects of single and combined exposure to ZnO and TiO2 nanoparticles on rainbow trout challenged with Aeromonas salmonicida achromogenes

The increasing release of engineered nanoparticles (ENPs) in aquatic ecosystems stresses the need for stringent investigations of nanoparticle mixture toxicity towards aquatic organisms. Here, the individual and combined immunotoxicity of two of the most consumed ENPs, the ZnO and the TiO2 ones, was investigated on rainbow trout juveniles (Oncorhynchus mykiss). Fish were exposed to environmentally realistic concentrations (21 and 210 µg L−1 for the ZnO and 210 µg L−1 for the TiO2) for 28 days, and then challenged with the pathogenic bacterium, Aeromonas salmonicida achromogenes. Antioxidant and innate immune markers were assessed before and after the bacterial infection. None of the experimental conditions affected the basal activity of the studied innate immune markers and the redox balance. However, following the bacterial infection, the expression of genes coding for pro and anti-inflammatory cytokines (il1β and il10), as well as innate immune compounds (mpo) were significantly reduced in fish exposed to the mixture. Conversely, exposure to ZnO NPs alone seemed to stimulate the immune response by enhancing the expression of the IgM and c3 genes for instance. Overall, our results suggest that even though the tested ENPs at their environmental concentration do not strongly affect basal immune functions, their mixture may alter the development of the immune response when the organism is exposed to a pathogen by interfering with the inflammatory response.

Dietary supplementation of Astragalus fermentation products improves the growth performance, immunological characteristics, and disease resistance of crucian carp (Carassius auratus)

The fermentation products of Astragalus have been acknowledged for their ability to enhance immune functions. This study assessed the impact of incorporating Astragalus, fermented with Lactobacillus plantarum and Bacillus coagulans, on crucian carp’s growth, disease resistance, and immunological characteristics. The experimental groups were fed with common feed (C), C + Astragalus (A), A + Lactobacillus plantarum (AL), A + Bacillus coagulans (AB), and AL + Bacillus coagulans (ALB). The fermented products were mixed with common feed at a 1:99 ratio, and crucian carp were fed 2% of their body weight for four weeks, with sampling conducted on days 3, 7, 14, 21, and 28. Disease resistance was evaluated using Aeromonas hydrophila (A. hydrophila) at a concentration of 0.2 mL (1.0×107 CFU/mL). The final weights in the AL, AB, and ALB groups significantly increased compared to the C group. The ALB group exhibited elevated serum albumin levels, alkaline phosphatase, intestinal lipase, protease enzyme, C3, and IgM gene expression compared to the C group. At the same time, alanine aminotransferase, aspartate aminotransferase, and glucose contents were significantly reduced. The survival rate significantly increased in all experimental groups after treatment with A. hydrophila. In conclusion, Astragalus products fermented with Lactobacillus plantarum and Bacillus coagulans could effectively improve crucian carp’s growth, disease resistance, and immune response.

#623 One-year outcome of kidney transplant recipients harbouring complement regulatory gene mutation

Abstract Background and Aims Thrombotic Microangiopathy (TMA) is associated with genetic abnormalities in complement regulatory pathways. The impact of complement regulatory gene (CRG) mutation on post-transplant TMA in Indian kidney transplant recipients (KTR) is unknown. This study was conducted to ascertain an association between post-transplant renal limited TMA and the risk of graft failure in KTRs harbouring mutations in genes encoding complement-regulatory proteins. Method A Single Centre, Prospective Cohort Study was undertaken to assess the incidence of post-transplant renal limited TMA in KTRs with mutations in genes encoding complement regulatory proteins. Patients enrolled over one year were followed up for one-year post-transplantation. Genetic testing was performed with MLPA and Clinical exome sequencing. Results 138 KTRs with a mean age of 36.39 ± 12.39 years were enrolled. CRG mutation was seen in 96/138 (69.6%) KTRs. Duplication of the CFHR gene (n = 72) was most prevalent followed by mutations in CFH (n = 6), CFI (n = 2), MCP (n = 2), and DGKE (n = 1). Mutations in CFB, C3, and THBD genes were not detected. The Incidence of Post transplant renal limited TMA in KTRs with CRG mutations is 9.37% (9/96). Mutation related to aHUS was seen in 9 out of 11 patients who developed TMA. There was no significant difference in eGFR of patients with or without CRG mutation at the end of 1 year. Conclusion The prevalence of CRG mutation in KTRs is high and the majority of patients with post-transplant de novo TMA had CRG mutations. The graft functions at the end of 1 year were similar in patients with or without CRG gene mutation. This study suggests that the presence of CRG mutation should not preclude the option of Kidney transplantation in a patient with ESRD.

Lupus Nephritis with Autoantibodies to Complement Alternative Pathway Proteins and C3 Gene Mutation

Lupus Nephritis with Autoantibodies to Complement Alternative Pathway Proteins and C3 Gene Mutation

Analysis of schizophrenia-associated genetic markers in the HLA region as risk factors for tardive dyskinesia.

The pathology of Tardive Dyskinesia (TD) has yet to be fully understood, but there have been proposed hypotheses for the cause of this condition. Our team previously reported a possible association of TD with the Complement Component C4 gene in the HLA region. In this study, we explored the HLA region further by examining two previously identified schizophrenia-associated HLA-region single-nucleotide polymorphisms (SNPs), namely rs13194504 and rs210133. The SNPs rs13194504 and rs210133 were tested for association with the occurrence and severity of TD in a sample of 172 schizophrenia patients who were recruited for four studies from three different clinical sites in Canada and USA. The rs13194504 AA genotype was associated with decreased severity for TD as measured by Abnormal Involuntary Movement Scale (AIMS) scores (p=0.047) but not for TD occurrence. SNP rs210133 was not significantly associated with either TD occurrence or AIMS scores. Our findings suggest that the rs13194504 AA genotype may play a role in TD severity, while SNP rs210133 may not have a major role in the risk or severity of TD.

Effects on growth performance and immunity of Monopterus albus after high temperature stress.

To investigate the impact of the effect of high temperature stimulation on Monopterus albus larvae after a certain period of time, five experimental groups were established at different temperatures. Then, the M. albus under high temperature stress was fed at 30°C for 70days. After that, the growth index of the M. albus was counted and analyzed. In terms of growth index, high temperature stress had significant effects on FCR, FBW, WGR, and SGR of M. albus (p < 0.05). The SR increased after being stimulated by temperature (p < 0.1). The study revealed that liver cells of M. albus were harmed by elevated temperatures of 36°C and 38°C. In the experimental group, the activities of digestive enzymes changed in the same trend, reaching the highest point in the 32°C group and then decreasing, and the AMS activity in the 38°C group was significantly different from that in the 30°C group (p < 0.05). The activities of antioxidase in liver reached the highest at 34°C, which was significantly different from those at 30°C (p < 0.05). In addition, the expression levels of TLR1, C3, TNF-α, and other genes increased in the experimental group, reaching the highest point at 34°C, and the expression level of the IL-1β gene reached the highest point at 32°C, which was significantly different from that at 30°C (p < 0.05). However, the expression level of the IRAK3 gene decreased in the experimental group and reached its lowest point at 34°C (p < 0.05). The expression level of the HSP90α gene increased with the highest temperature stimulus and reached its highest point at 38°C (p < 0.05). In the α diversity index of intestinal microorganisms in the experimental group, the observed species, Shannon, and Chao1 indexes in the 34°C group were the highest (p < 0.05), and β diversity analysis revealed that the intestinal microbial community in the experimental group was separated after high temperature stimulation. At the phylum level, the three dominant flora are Proteus, Firmicutes, and Bacteroides. Bacteroides and Macrococcus abundance increased at the genus level, but Vibrio and Aeromonas abundance decreased. To sum up, appropriate high-temperature stress can enhance the immunity and adaptability of M. albus. These results show that the high temperature stimulation of 32°C-34°C is beneficial to the industrial culture of M. albus.

Roles of Single Nucleotide Polymorphisms of C3 Gene in Patients with Coronary Artery Disease.

This study aims to investigate the association between nine tag single nucleotide polymorphisms (SNPs) in the C3 gene locus and the risk of coronary artery disease (CAD) as well as lipid levels in the Chinese population, and to further explore the interactions between SNPs and environmental factors that may be associated with CAD risk. A case-control study was conducted to investigate the association between CAD and C3 gene polymorphisms in a hospital setting. The study consisted of 944 CAD patients with a mean age of 55.97 10.182 years and 897 non-CAD controls with a mean age of 55.94 9.162 years. There were 565 males and 288 females in the CAD group and 583 males and 314 females in the control group. TagSNPs in the C3 gene were identified by employing the improved multiplex ligation detection reaction (iMLDR) technique, and multifactor dimensionality reduction (MDR) analysis was utilized to investigate the C3 gene-environment and gene-gene interactions in relation to the risk of CAD. Results of the polymorphism study indicated that the CC genotype of rs7257062 was more frequent in the CAD group compared to the control group (10.9% vs 7.7%), with a statistically significant difference (p = 0.009). Moreover, the TT and CC + CT genotype groups of rs7257062 in the CAD subgroup showed a significant difference in terms of serum triglyceride levels (2.326 1.889 vs 2.059 1.447, p = 0.019). Analysis of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), apolipoprotein A (ApoA), and apolipoprotein B (ApoB) levels revealed no significant differences between the TT and CC + CT genotypes. Furthermore, no significant differences in serum lipid levels were observed between genotypes of the other SNPs. Multivariable logistic analysis, controlling for gender, age, body mass index (BMI), triglycerides (TG), TC, HDL-C, LDL-C, ApoA and ApoB, demonstrated that rs7257062 was still an independent risk factor of CAD (OR = 1.499, 95% CI: 1.036-2.168, p = 0.032). MDR analysis revealed that the rs7257062 interacted significantly with environmental factors such as smoking, diabetes, hypertension, BMI, and TG (p 0.05). The rs7257062 variation of the C3 gene could be linked to both lipid balance and the risk of CAD. It is conceivable that the interplay between C3 polymorphisms and environmental elements could account for the etiology of CAD.

Identification of tomato C2 gene family and functional analysis of the inflorescence branching regulatory gene SlC2–25

The C2 domain plays an important role in plant growth and development. We performed genome-wide identification of SlC2 gene family members by bioinformatics, and predictive analysis of chromosome distribution, evolutionary relationships, gene structure and colinearity of their family members. The results showed that a total of 103 SlC2 genes were screened, according to the order of their physical coordinates, 103 SlC2 genes were named from SlC2–1 to SlC2–103. The amino acid lengths ranged from 107 to 2133aa, the molecular weights ranged from 12,416.96 to 229,427.7 Da, and the isoelectric points ranged from 4.18 to 9.94. The cluster analysis was divided into six subgroups, and the gene sequences were highly conserved. Based on the pre-laboratory transcriptome data, we screened the SlC2–25 gene, analyzed the expression pattern of SlC2–25 in two kinds of tomato inflorescences by RT-qPCR, and preliminarily explored the function of SlC2–25 in the regulation of tomato inflorescence meristem by using gene editing technology, and found that SlC2–25 was a negative regulator of tomato inflorescence branching. In addition, the endogenous hormone content of tomato inflorescences was determined, and it was hypothesized that the SlC2s genes might be involved in the regulatory process of tomato inflorescence branching by altering the content of endogenous hormones in the plant or by interacting with a variety of proteins.

Transcriptome and small RNA analysis unveils novel insights into the C4 gene regulation in sugarcane.

This study reveals miRNA indirect regulation of C4 genes in sugarcane through transcription factors, highlighting potential key regulators like SsHAM3a. C4 photosynthesis is crucial for the high productivity and biomass of sugarcane, however, the miRNA regulation of C4 genes in sugarcane remains elusive. We have identified 384 miRNAs along the leaf gradients, including 293 known miRNAs and 91 novel miRNAs. Among these, 86 unique miRNAs exhibited differential expression patterns, and we identified 3511 potential expressed targets of these differentially expressed miRNAs (DEmiRNAs). Analyses using Pearson correlation coefficient (PCC) and Gene Ontology (GO) enrichment revealed that targets of miRNAs with positive correlations are integral to chlorophyll-related photosynthetic processes. In contrast, negatively correlated pairs are primarily associated with metabolic functions. It is worth noting that no C4 genes were predicted as targets of DEmiRNAs. Our application of weighted gene co-expression network analysis (WGCNA) led to a gene regulatory network (GRN) suggesting miRNAs might indirectly regulate C4 genes via transcription factors (TFs). The GRAS TF SsHAM3a emerged as a potential regulator of C4 genes, targeted by miR171y and miR171am, and exhibiting a negative correlation with miRNA expression along the leaf gradient. This study sheds light on the complex involvement of miRNAs in regulating C4 genes, offering a foundation for future research into enhancing sugarcane's photosynthetic efficiency.

Low C4A copy numbers and higher HERV gene insertion contributes to increased risk of SLE, with absence of association with disease phenotype and disease activity.

Low copy numbers (CNs) of C4 genes are associated with systemic autoimmune disorders and affects autoantibody diversity and disease subgroups. The primary objective of this study was to characterize diversity of complement (C4) and C4-Human Endogenous Retrovirus (HERV) gene copy numbers in SLE. We also sought to assess the association of C4 and C4-HERV CNs with serum complement levels, autoantibodies, disease phenotypes and activity. Finally, we checked the association of C4 and HERV CNs with specific HLA alleles. Genomic DNA from 70 SLE and 90 healthy controls of south Indian Tamil origin were included. Demographic, clinical and serological data was collected in a predetermined proforma. CNs of C4A and C4B genes and the frequency of insertion of 6.4kb HERV within C4 gene (C4AL, C4BL) was determined using droplet digital polymerase chain reaction (ddPCR). A four digit high resolution HLA genotyping was done using next generation sequencing. In our cohort, the total C4 gene copies ranged from 2 to 6. Compared to controls, presence of two or less copies of C4A gene was associated with SLE risk (p = 0.005; OR = 2.79; 95% CI = 1.29-6.22). Higher frequency of HERV insertion in C4A than in C4B increases such risk (p = 0.000; OR = 12.67; 95% CI = 2.80-115.3). AL-AL-AL-BS genotype was significantly higher in controls than SLE (9%vs1%, p = 0.04; OR = 0.15, 95% CI = 0.00-0.16). Distribution of HLA alleles was not different in SLE compared to controls as well as in SLE subjects with ≤ 2 copies and > 2 copies of C4A, but HLA allele distribution was diverse in subjects with C4B ≤ 2 copies and > 2 copies. Finally, there was no correlation between the C4 and the C4-HERV diversity and complement levels, autoantibodies, disease phenotypes and activity. In conclusion, our data show that, low C4A copy number and higher insertion of HERV-K in C4A increases the risk for SLE. C4 and C4-HERV CNs did not correlate with serum complements, autoantibodies, disease phenotypes and activity in SLE. Further validation in a larger homogenous SLE cohort is needed.

Dietary arginine regulates the growth performance, antioxidant capacity, and immune response in Culter alburnus.

Culter alburnus is sensitive to stressors. Arginine is a precursor of nitric oxide, which can effectively relieve the level of oxidative stress and improve the antioxidant and immune capacity of fish. The effect of different arginine levels on topmouth culter (Culter alburnus) fry development performance, liver antioxidant capacity, and immune parameters were investigated in this study. Five diets (1.96%, ARG1, control group; 2.28%, ARG2; 2.52%, ARG3; 2.81%, ARG4; 3.09%, ARG5) were used to feed fry (initial weight 0.31 ± 0.01g) for 8weeks. The data showed that the final weight (FW), weight gain rate (WGR), and specific growth rate (SGR) of the ARG3 and ARG4 groups were significantly improved, while the feed conversion ratio (FCR) reduced significantly. Compared with the ARG1 group, all groups remarkably reduced the crude ash content of the whole body. The activity of hepatic superoxide dismutase (SOD) and the content of hepatic glutathione (GSH) were significantly increased in the ARG3 and ARG4 groups, while the malondialdehyde (MDA) content was significantly decreased. Compared with the ARG1 group, arginine levels in ARG2, ARG3, and ARG4 groups up-regulated the expression levels of Nrf2, down-regulated the gene expression level of Keap1 in the liver. And the expression of Nrf2/Keap1 pathway downstream genes Mn-SOD and CAT was up-regulated in ARG2 and ARG3 groups. Furthermore, the expression levels of MyD88 and IL-1β were down-regulated, and the anti-inflammatory gene TGF-β expression levels were up-regulated in the ARG2, ARG3, and ARG4 groups. Additionally, compared to the ARG1 group, there was a significant increase in the relative expression levels of the C3 and C4 genes in the ARG4 group. In conclusion, 2.28-2.81% dietary arginine levels improved the growth performance, promoted antioxidant capacity, and enhance immune response. The optimal level of arginine was determined by the quadratic regression analysis of SGR and FCR to be 2.55% of diet (5.43% of dietary protein) and 2.53% of diet (5.38% of dietary protein), accordingly.

Significant beneficial effects of 12-weeks add-on yoga therapy on antipsychotic-stabilized schizophrenia patients through epigenetic modulation: novel findings from a randomized controlled study

IntroductionComplementary and alternative therapy, especially yoga, is emerging as an important treatment modality for various complex disorders. Yoga therapy has reportedly been demonstrated to exhibit clinical benefits in schizophrenia. However, the modulatory effects of yoga therapy on the pathobiological pathways of schizophrenia are inadequately explored. Immune dysregulation is a widely recognized etiopathological construct of schizophrenia. It is not precisely known whether yoga therapy can modulate the expression of immune molecules by regulating gene expression and epigenetic processes in schizophrenia.ObjectivesTo understand the impact of 12-weeks add-on yoga therapy on the immune-inflammatory pathway in schizophrenia by examining plasma levels and gene expression levels of cytokines and complement proteins as well as by profiling promoter DNA methylation pattern of genes coding for cytokines and complement proteins.MethodsFifty-seven schizophrenia patients fulfilling DSM-V criteria were recruited into the study and randomized into Yoga therapy (n=28) and waitlist control (n=29) groups. Plasma levels of IL-1β, IL-6, IL-10, IL-17, C1q, C2, C3, C4, C5, C5a, Factor B and Factor H by Multiplex Suspension Assay, quantification of gene expression of Il1b, Il6, Il10, IL17, C3, C4 and C5 genes by quantitative PCR and promoter DNA methylation of Il1b, Il6, Il10, Il17, C3, C4 and C5 genes by pyrosequencing were carried out in all the study participants.ResultsPlasma levels of IL-1β (Z score= 2.42, p=0.02) dropped significantly and C2 (Z score= 2.24, p=0.03) levels increased after 12-weeks of yoga therapy. The expression of Il1b (Z score=2.45, p=0.01) and Il6 (Z score=2.07, p=0.04) genes were significantly downregulated, while the levels of C4 (Z score=2.23, p=0.03) gene was upregulated in schizophrenia patients of yoga therapy group. Two CpG sites in the promoter region of Il1b (all p≤0.05) and Il6 (all p≤0.05) genes and three CpG sites in the promoter region of C4 (all p&lt;0.05) gene were hypermethylated, while two CpG sites in the gene body of Il6 (all p≤0.05) gene and two CpG sites in the promoter region of Il10 (all p ≤0.05) gene were hypomethylated after 12-weeks of yoga therapy in schizophrenia patients.ConclusionsOur findings provide important insights into the mode of action of yoga therapy in schizophrenia. This study for the first time reports the epigenetic effects of yoga therapy on immune-inflammatory pathway in schizophrenia.Disclosure of InterestNone Declared

Detecting Polymorphism of Myosin-binding Protein C3 Gene in Persian Breed Cat With and Without Hypertrophic Cardiomyopathy

Background: In cats, hypertrophic cardiomyopathy (HCM) stands out as a prevailing heart disease. The mutations in the gene that encodes cardiac myosin-binding protein C (MYBPC3) have been detected in the Ragdoll and Maine Coon breeds. Objectives: HCM is believed to be hereditary in other breeds, too. Methods: Blood samples were collected for DNA extraction from 2 unaffected and 7 affected Persian breed cats with HCM. Besides accomplishing conventional polymerase chain reaction, DNA sequencing was performed. The sequence changes were utilized to detect single nucleotide polymorphisms in the MYBPC3 gene and predict amino acid substitutions based on the Acc. No. XM_019812396.1 and comparisons with the literature on identified breed variants and control samples. Results: Although many single nucleotide polymorphisms were found in the affected and unaffected Persian cats, no causative mutation for HCM was observed. Conclusion: In this breed, HCM does not seem to be caused solely by mutations in this cardiac gene. Potential cardiac genes should be investigated to uncover other genetic reasons for this cardiac disease in the Persian cat breed.

Molecular expression of Forkhead Box C2 gene (FOXC2) and Prospero homeobox gene (PROX-1) in oral squamous carcinoma and their correlation with clinicopathological parameters: A prospective cohort study.

Forkhead box C2 gene (FOXC2) acts as an epithelial-mesenchymal transition (EMT) inducer while Prospero homeobox 1 gene (PROX-1) function as a regulator of lymphangiogenesis and angiogenesis in oral squamous cell carcinoma (OSCC). It is presumed that PROX-1 has both tumour-suppressive and oncogenic effects. The main aim of this study is to evaluate the role of PROX-1 and FOXC2 in the invasion and progression of OSCC cases and to correlate their expression with various histopathological parameters. A prospective cohort study was conducted in a total sample size of 52 OSCC tissues and histologically tumour-free margins of 20. mRNA expression and protein levels of FOXC2 and PROX-1 were evaluated using real-time PCR and sandwich enzyme-linked immunosorbent assay techniques. Chi-square analysis and correlation analysis were done. Kaplan-Meier analysis evaluated the survival rate. Mean Ct values of FOXC2 were 1.915 ± 0.519 and PROX-1 was 0.061 ± 0.173. There was a significant 2-fold increase in the FOXC2 expression and a 0.5-fold decrease in the PROX-1 expression in OSCC tissue. Increased levels of FOXC2 protein and decreased levels of PROX-1 with a mean difference of 1.64 ± 0.73 ng/ml and 1.27 ± 0.33 ng/ml were observed in OSCC compared to histologically tumour-free margins. A significant positive correlation was found between the FOXC2 expression and clinicopathological parameters such as staging, perineural invasion (PNI) and lymphovascular invasion (LVI) whereas PROX-1 showed a significant negative correlation with histopathological parameters such as staging, PNI, LVI and tumour staging. There was a significant positive correlation between the PROX-1 and histologically tumour-free margins in disease-free survival patients (P-value = 0.03). FOXC2 and PROX-1 expressions were correlated with lymphovascular invasion, OSCC tumour staging and PNI. Thus, FOXC2 and PROX-1 could be possible therapeutic targets in the treatment of OSCC that can inhibit the EMT in OSCC and thereby favouring a better prognosis.

Exome-Based Amino Acid Optimization: A Dietary Strategy to Satisfy Human Nutritional Demands and Enhance Muscle Strength in Breast Tumor Mice Undergoing Chemotherapy.

Breast cancer patients undergoing chemotherapy often experience muscle wasting and weakness, which impact their quality of life. A potential solution lies in customizing amino acid compositions based on exome-derived formulations (ExAAs). The study hypothesized that tailoring dietary amino acids using ExAAs could enhance muscle health. Theoretical amino acid requirements were calculated from the genome's exome region, and a breast cancer mouse model undergoing paclitaxel treatment was established. The mice were supplemented with a cancer-specific nutritional formula (QJS), and the effects of QJS and amino acid-adjusted QJS (adjQJS) were compared. Both formulations improved the nutritional status without compromising tumor growth. Notably, adjQJS significantly enhanced muscle strength compared to QJS (1.51 ± 0.25 vs. 1.30 ± 0.08 fold change, p < 0.05). Transcriptome analysis revealed alterations in complement and coagulation cascades, with an observed upregulation of C3 gene expression in adjQJS. Immune regulation also changed, showing a decrease in B cells and an increase in monocytes in skeletal muscle with adjQJS. Importantly, adjQJS resulted in a notable increase in Alistipes abundance compared to QJS (10.19 ± 0.04% vs. 5.03 ± 1.75%). This study highlights the potential of ExAAs as valuable guide for optimizing amino acid composition in diets for breast cancer patients undergoing chemotherapy.

Association Between Altered Microbiota Composition and Immune System-Related Genes in COVID-19 Infection.

Microbiota and immunity affect the host's susceptibility to SARS-CoV-2 infection and the severity of COVID-19. This study aimed to identify significant alterations in themicrobiota composition, immune signaling pathways, their potential association, and candidate microRNA in COVID-19 patients using an in silico study model. Enrichment online databases and Python programming were utilized to analyze GSE164805, GSE180594, and GSE182279, as well as NGS data of microbiota composition (PRJNA650244 and PRJNA660302) associated with COVID-19, employing amplicon-based/marker gene sequencing methods. C1, TNF, C2, IL1, and CFH genes were found to have a significant impact on immune signaling pathways. Additionally, we observed a notable decrease in Bacteroides spp. and Faecalibacterium sp., while Escherichia coli, Streptococcus spp., and Akkermansia muciniphila showed increased abundance in COVID-19. Notably, A. muciniphila demonstrated an association with immunity through C1 and TNF, while Faecalibacterium sp. was linked to C2 and IL1. The correlation between E. coli and CFH, as well as IL1 and Streptococcus spp. with C2, was identified. hsa-let-7b-5p was identified as a potential candidate that may be involved in the interaction between the microbiotacomposition, immune response, and COVID-19. In conclusion, integrative in silico analysis shows that these microbiota members are potentially crucial in the immune responses against COVID-19.

Molecular Cloning, Characterization, and Expression of a Receptor for Activated Protein Kinase C1 (RACK1) Gene in Exopalaemon carinicauda Zoea Larvae under Aroclor 1254 Stress.

The receptor for activated protein kinase C1 (RACK1) belongs to the typical WD repeat family, which is extremely conservative and important in multiple signal transduction pathways related to growth and development that coordinate the intracellular role of various life activities. As a novel protein with versatile functions, it was found in a variety of organisms. In a previous study, we identified the RACK1 sequence of white shrimp from transcriptome data. In this study, we employed specialized bioinformatics software to conduct an in-depth analysis of EcRACK1 and compare its amino acid sequence homology with other crustaceans. Furthermore, we investigated the expression patterns of RACK1 at different developmental stages and tissues, as well as at various time points after exposure to Aroclor 1245, aiming to elucidate its function and potential response towards Aroclor 1245 exposure. The length of EcRACK1 is 957 nucleotides, which encodes 318 amino acids. Moreover, there were seven typical WD repeats in EcRACK1, which have more than a 96% sequence identity with the RACK1 proteins of Penaeus. The results of tissue expression and spatiotemporal expression showed that it was significantly increased in the II and IV stages, but had a significant tissue specificity in the hepatopancreas, spermary, and muscle tissues of E. carinicauda, adult stage. Compared to the control, EcRACK1 was significantly induced in E. carinicauda zoea larvae exposed to Aroclor 1254 for 6, 10, 20, and 30 d (p < 0.05). These results suggested that EcRACK1 may play an important role in the larval development and environmental defense of E. carinicauda.

Mitochondrial and Cytosolic One-Carbon Metabolism Is a Targetable Metabolic Vulnerability in Cisplatin-Resistant Ovarian Cancer.

One-carbon (C1) metabolism is compartmentalized between the cytosol and mitochondria with the mitochondrial C1 pathway as the major source of glycine and C1 units for cellular biosynthesis. Expression of mitochondrial C1 genes including SLC25A32, serine hydroxymethyl transferase (SHMT) 2, 5,10-methylene tetrahydrofolate dehydrogenase 2, and 5,10-methylene tetrahydrofolate dehydrogenase 1-like was significantly elevated in primary epithelial ovarian cancer (EOC) specimens compared with normal ovaries. 5-Substituted pyrrolo[3,2-d]pyrimidine antifolates (AGF347, AGF359, AGF362) inhibited proliferation of cisplatin-sensitive (A2780, CaOV3, IGROV1) and cisplatin-resistant (A2780-E80, SKOV3) EOC cells. In SKOV3 and A2780-E80 cells, colony formation was inhibited. AGF347 induced apoptosis in SKOV3 cells. In IGROV1 cells, AGF347 was transported by folate receptor (FR) α. AGF347 was also transported into IGROV1 and SKOV3 cells by the proton-coupled folate transporter (SLC46A1) and the reduced folate carrier (SLC19A1). AGF347 accumulated to high levels in the cytosol and mitochondria of SKOV3 cells. By targeted metabolomics with [2,3,3-2H]L-serine, AGF347, AGF359, and AGF362 inhibited SHMT2 in the mitochondria. In the cytosol, SHMT1 and de novo purine biosynthesis (i.e., glycinamide ribonucleotide formyltransferase, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase) were targeted; AGF359 also inhibited thymidylate synthase. Antifolate treatments of SKOV3 cells depleted cellular glycine, mitochondrial NADH and glutathione, and showed synergistic in vitro inhibition toward SKOV3 and A2780-E80 cells when combined with cisplatin. In vivo studies with subcutaneous SKOV3 EOC xenografts in SCID mice confirmed significant antitumor efficacy of AGF347. Collectively, our studies demonstrate a unique metabolic vulnerability in EOC involving mitochondrial and cytosolic C1 metabolism, which offers a promising new platform for therapy.