Specific Pathways Research Articles

Malassezia globosa Induces Differentiation of Pathogenic Th17 Cells by Inducing IL-23 Secretion by Keratinocytes.

Malassezia, the most abundant fungal commensal on the mammalian skin, has been linked to several inflammatory skin diseases such as atopic dermatitis, seborrheic dermatitis and psoriasis. This study reveals that epicutaneous application with Malassezia globosa (M. globosa) triggers skin inflammation in mice. RNA-sequencing of the resulting mouse lesions indicates activation of Interleukin-17 (IL-17) signaling and T helper 17 (Th17) cells differentiation pathways by M. globosa. Furthermore, our findings demonstrate a significant upregulation of IL-23, IL-23R, IL-17A, and IL-22 expressions, along with an increase in the proportion of Th17 and pathogenic Th17 cells in mouse skin exposed to M. globosa. In vitro experiments illustrate that M. globosa prompts human primary keratinocytes to secrete IL-23 via TLR2/MyD88/NF-κB signaling. This IL-23 secretion by keratinocytes is shown to be adequate for inducing the differentiation of pathogenic Th17 cells in the skin. Overall, these results underscore the significant role of Malassezia in exacerbating skin inflammation by stimulating IL-23 secretion by keratinocytes and promoting the differentiation of pathogenic Th17 cells.

Investigating immune dysregulation and hub genes in septic cardiomyopathy development

Septic cardiomyopathy is a life-threatening heart dysfunction caused by severe infection. Considering the complexity of pathogenesis and high mortality, the identification of efficient biomarkers are needed to guide clinical practice. Based on multimicroarray analysis, this study aimed to explore the pathogenesis of septic cardiomyopathy and the related immune landscape. The results showed that septic cardiomyopathy resulted in organ dysfunction due to extreme pro- and anti-inflammatory effects. In this process, KLRG1, PRF1, BCL6, GAB2, MMP9, IL1R1, JAK3, IL6ST, and SERPINE1 were identified as the hub genes regulating the immune landscape of septic cardiomyopathy. Nine transcription factors regulated the expression of these genes: SRF, STAT1, SP1, RELA, PPARG, NFKB1, PPARA, SMAD3, and STAT3. The hub genes activated the Th17 cell differentiation pathway, JAK-STAT signaling pathway, and cytokine‒cytokine receptor interaction pathway. These pathways were mainly involved in regulating the inflammatory response, adaptive immune response, leukocyte-mediated immunity, cytokine-mediated immunity, immune effector processes, myeloid cell differentiation, and T-helper cell differentiation. These nine hub genes could be considered biomarkers for the early prediction of septic cardiomyopathy.

Steroid hormone-deprived sex reversal in cyp11a1 mutant XX tilapia experiences an ovary-like stage at molecular level

Fish sex is largely influenced by steroid hormones, especially sex hormones. Here, we established a steroid hormone-free genetic model by mutation of cyp11a1 in Nile tilapia, which was confirmed by EIA assay. Gonadal phenotype and transcriptome analyses showed that the XX mutants displayed sex reversal from female to male but with defective spermatogenesis. Despite the sex reversal, the aromatase encoding gene cyp19a1a was continuously expressed in the gonads of the XX mutants, which might be caused by androgen deficiency. Whole-mount fluorescence in situ hybridization and transcriptome analysis showed that the gonads of the XX mutants firstly developed towards ovary but shifted to testis between 10 to 15 days after hatching. Detailed expression analysis of key sex differentiation pathway genes foxl3 and dmrt1 combined with apoptosis analysis revealed transdifferentiation of germ cells from female to male during sex reversal. Rescue experiments showed that both P5 and E2 treatment rescued the sex reversal of cyp11a1 mutant XX fish. Overall, our results revealed a transient ovary-like stage and transdifferentiation of germ cells from female to male in the early gonads of the steroid hormone-deprived cyp11a1 mutant XX fish.

PSIV-24 Evaluation of different colostrum feeding volumes on serum immunoglobulin G concentration and metabolic profiles of calves in high altitude area

Abstract Qinghai-Tibet Plateau is the highest plateau in the world, reputed as “the roof of the world” and “the world’s third pole”. Its ecological environment is characterized by low atmospheric oxygen pressure, cold, and limited feed supplies. This study aimed to investigate the serum immunoglobulin G (IgG) concentration and metabolic profiles of calves in high altitude area (3,650 m) fed different volumes of colostrum [8, 12, or 15% of birth body weight (BW)] using untargeted metabolomics strategies. Neonatal Holstein hybrid heifer calves (n = 44) were randomly divided into 1 of the 3 colostrum feeding amounts: 8% of birth BW (Low volume, L), 12% of birth BW (Middle volume, M), and 15% of birth BW (High volume, H) in colostrum. To safeguard the efficiency of colostrum intake, the colostrum was fed to calves within 0.5 h and 6 h after birth. The serum samples at 24 h after birth were collected for IgG concentration determination by indirect enzyme-linked immunosorbent assay (ELISA) and for LC-MS/MS metabonomic analysis. As the volumes of colostrum increased, there was a linearly increased in the serum IgG concentration (P < 0.01). Differential metabolites were selected according to the following 3 conditions: minimum fold change (FC) > 2, P-value < 0.01 in single-dimensional statistical analysis, and variable importance in projection (VIP) > 1 in the OPLS-DA model. Multivariate statistical analyses were performed to visualize differences among groups. Based on the screening criteria, a total of 3 differential metabolites (22 alpha-Hydroxy-campesterol, N-Myristoyl Histidine, and Calcitetrol) were detected between L and M, of which all differential metabolites were down-regulated. Six differential metabolites were detected between M and H, of which PC[P-18:1(11Z)/18:1(12Z)-2OH(9,10)] was up-regulated and 5 differential metabolites including 1-arachidonoyl-2-hydroxy-sn-glycero-3-phosphate, propanoyl phosphate, ascorbic acid 6-palmitate, 20-hydroxyecdysone, and 6’’’-deamino-6’’’-hydroxyparomomycin II were down-regulated. There were 28 differed metabolites (including leucyl-tryptophan, calcitetrol, 3’’-Oxoribostamycin) between L and H, of which 9 differential metabolites were up-regulated and 19 differential metabolites were down-regulated (Figure 1). Based on KEGG metabolic enrichment pathway analysis and pathway topology analysis, porphyrin metabolism was identified as the most impacted pathway between L and H (Figure 2). In conclusion, increasing colostrum volumes significantly increased serum IgG concentrations at 24 h after birth, favoring the success of the transfer of passive immunity. Alterations in serum metabolome of calves in the Qinghai-Tibet Plateau fed different volumes of colostrum were successfully revealed by untargeted metabolomics. The role of the identified differential metabolites and enriched pathway in the transfer of passive immunity in calves at high altitude deserves further investigation. Keywords: calf, colostrum volumes, high altitude area

PSIII-2 Exploring differential gene expression and pathways associated with pregnancy outcomes in beef heifers

Abstract Heifer fertility is a key factor in the success of beef production systems, as the reproductive performance of a heifer correlates with her stayability in the breeding herd. However, despite being reproductively mature and physically healthy, 5 to 15% of these heifers fail to conceive within a designated breeding season. The underlying physiological mechanisms preventing these heifers from achieving pregnancy remain elusive. Therefore, this study aimed to determine differentially expressed genes (DEGs) and biological pathways associated with pregnancy outcomes in beef heifers. Angus-Simmental crossbred heifers were subjected to an estrus synchronization and fixed-time artificial insemination (AI) program (7-d CO-Synch + CIDR) and blood samples were collected at the time of AI for isolation of peripheral white blood cells (PWBC). After pregnancy check, heifers were classified as pregnant (P) and non-pregnant (NP). Based on that, 6 animals per group were randomly selected for total RNA isolation from the PWBC samples, and genome-wide expression was measured through RNA sequencing. The RNA-Seq data were analyzed using an in-house bioinformatics pipeline, with filtered reads aligned to the Bos taurus reference genome using STAR. DEGs were identified using DESeq2, followed by functional analysis using ShinyGO. Our approach unveiled 230 DEGs, comprising 102 up and 128 downregulated genes in the NP group (P-value ≤ 0.05 and |log2FC| > 0.5). Upregulated genes included those from the cytochrome P450 superfamily (CYP27B1 and CYP2U1). The genes SCML2, USIG2, and FBP1 were upregulated and have been associated with immune response and increased PWBC counts. This may be related to the over-representation of biological processes involved in cell division based on the upregulated genes. KEGG pathway over-representation analysis of DEGs retrieved allograft rejection, graft-versus-host disease, type I Diabetes Mellitus, insulin signaling pathway, and transcriptional misregulation of cancer. These pathways included genes such as BOLA-DQB, PRKAR1B, CALML4 and JUP, which were reported as downregulated during times of inflammatory response. Another downregulated gene was GZMB, which is needed for proper cell targeting during immune response. This finding may provide a link between immune function and early pregnancy failure. However, the relationship between the immune system and pregnancy warrants further investigation. Our results shed light on the molecular mechanisms underlying reproductive performance in beef heifers and support previous studies associating immune function with pregnancy outcomes. These differentially expressed genes may be further explored as potential avenues for enhancing fertility in beef production systems.

Single-cell RNA sequencing analysis of peripheral blood mononuclear cells in PD-1-induced renal toxicity in patients with lung cancer

BackgroundAlthough the patient survival rate for many malignancies has been improved with immune checkpoint inhibitors (ICIs), some patients experience various immune-related adverse events (irAEs). IrAEs impact several organ systems, including the kidney. With anti-programmed cell death protein 1 (PD-1) therapy (pembrolizumab), kidney-related adverse events occur relatively rarely compared with other irAEs. However, the occurrence of AKI usually leads to anti-PD-1 therapy interruption or discontinuation. Therefore, there is an urgent need to clarify the mechanisms of renal irAEs (R-irAEs) to facilitate early management. This study aimed to analyse the characteristics of peripheral blood mononuclear cells (PBMCs) in R-irAEs.MethodsPBMCs were collected from three patients who developed R-irAEs after anti-PD-1 therapy and three patients who did not. The PBMCs were subjected to scRNA-seq to identify cell clusters and differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analyses were performed to investigate the most active biological processes in immune cells.ResultsFifteen cell clusters were identified across the two groups. FOS, RPS26, and JUN were the top three upregulated genes in CD4+ T cells. The DEGs in CD4+ T cells were enriched in Th17 differentiation, Th1 and Th2 cell differentiation, NF-kappa B, Nod-like receptor, TNF, IL-17, apoptosis, and NK cell-mediated cytotoxicity signaling pathways. RPS26, TRBV25-1, and JUN were the top three upregulated genes in CD8+ T cells. The DEGs in CD8+ T cells were enriched in Th17 cell differentiation, antigen processing and presentation, natural killer cell-mediated cytotoxicity, the intestinal immune network for IgA production, the T-cell receptor signalling pathway, Th1 and Th2 cell differentiation, the phagosome, and cell adhesion molecules.ConclusionsIn conclusion, R-irAEs are associated with immune cell dysfunction. DEGs and their enriched pathways identified in CD4+ T cells and CD8+ T cells play important roles in the development of renal irAEs related to anti-PD-1 therapy. These findings offer fresh perspectives on the pathogenesis of renal damage caused by anti-PD-1 therapy.

Effects of exposure to 17α-methyltestosterone on hepatic lipid metabolism in Gobiocypris rarus

This study aimed to investigate the effects of 17α-Methyltestosterone (MT) on hepatic lipid metabolism in Gobiocypris rarus. G. rarus was exposed to varying concentrations of MT (0, 25, 50, and 100 ng/L) for durations of 7, 14, and 21 d. Biochemical and transcriptomic analyses were conducted using methods, such as ELISA, RT-qPCR, Western Blotting, and RNA-seq, to decipher the key signals and molecular mechanisms triggered by MT in vivo. The results revealed that MT induced hepatomegaly in G. rarus and markedly increased the hepatic steatosis index (HSI). After 14 d of exposure, significant increase in PPARγ mRNA expression was observed, whereas after 21 d, PPARα mRNA expression was significantly reduced. The expression pattern of SREBP1C mRNA initially decreased before increasing, mirroring the trend observed for SREBP1C protein expression. Furthermore, MT increased the levels of key lipid synthesis enzymes, including HSL, CPT1, GPAT, and FAS, thereby fostering lipid accumulation. RNA-seq analysis revealed that MT modulated hepatic bile acid metabolism via the PPAR pathway, consequently influencing cholesterol and lipid metabolism. Considering the differential metabolic pathways of MT across genders, it is postulated that MT may undergo aromatization to estrogen within G. rarus, thereby exerting estrogenic effects. These findings provide crucial experimental insights into the detrimental effects of MT in aquatic settings, underscoring its implications for safeguarding aquatic organisms and human health.

Metabolomics-Based Study of the Protective Effect of 4-Hydroxybenzyl Alcohol on Ischemic Astrocytes.

Ischemic stroke is a common and dangerous disease in clinical practice. Astrocytes (ASs) are essential for maintaining the metabolic balance of the affected regions during the disease process. 4-Hydroxybenzyl alcohol (4HBA) from Gastrodia elata Bl. has potential neuroprotective properties due to its ability to cross the blood-brain barrier. In an in vitro experiment, we replicated the oxygen-glucose deprivation/reoxygenation model, and used methyl thiazoly tertrazolium, flow cytometry, kits, and other technical means to clarify the protective effect of 4HBA on primary ASs. In in vivo experiments, the 2VO model was replicated, and immunofluorescence and immunohistochemistry techniques were used to clarify the protective effect of 4HBA on ASs and the maintenance of the blood-brain barrier. Differential metabolites and related pathways were screened and verified using metabolomics analysis and western blot. 4HBA noticeably amplified AS cell survival, reduced mitochondrial dysfunction, and mitigated oxidative stress. It demonstrated a protective effect on ASs in both environments and was instrumental in stabilizing the blood-brain barrier. Metabolomic data indicated that 4HBA regulated nucleic acid and glutathione metabolism, influencing purines, pyrimidines, and amino acids, and it activated the N-methyl-D-aspartate/p-cAMP-response element binding protein/brain-derived neurotrophic factor signaling pathway via N-methyl-D-aspartate R1/N-methyl-D-aspartate 2C receptors. Our findings suggest that 4HBA is a potent neuroprotective agent against ischemic stroke, enhancing AS cell survival and function while stabilizing the blood-brain barrier. The N-methyl-D-aspartate/p-cAMP-response element binding protein/brain-derived neurotrophic factor signaling pathway is activated by 4HBA.

Single‑cell RNA sequencing analysis of human embryos from the late Carnegie to fetal development

BackgroundThe cell development atlas of transition stage from late Carnegie to fetal development (7–9 weeks) remain unclear. It can be seen that the early period of human embryos (7–9 weeks) is a critical research gap. Therefore, we employed single‑cell RNA sequencing to identify cell types and elucidate differentiation relationships.ResultsThe single‑cell RNA sequencing analysis determines eighteen cell clusters in human embryos during the 7–9 weeks period. We uncover two distinct pathways of cellular development and differentiation. Initially, mesenchymal progenitor cells differentiated into osteoblast progenitor cells and neural stem cells, respectively. Neural stem cells further differentiated into neurons. Alternatively, multipotential stem cells differentiated into adipocyte, hematopoietic stem cells and neutrophil, respectively. Additionally, COL1A2-(ITGA1 + ITGB1) mediated the cell communication between mesenchymal progenitor cells and osteoblast progenitor cells. NCAM1-FGFR1 facilitated the cell communication between mesenchymal progenitor cells and neural stem cells. Notably, NCAM1-NCAM1 as a major contributor mediated the cell communication between neural stem cells and neurons. Moreover, CGA-FSHR simultaneously mediated the communication between multipotential stem cells, adipocyte, hematopoietic stem cells and neutrophil. Distinct cell clusters activated specific transcription factors such as HIC1, LMX1B, TWIST1, and et al., which were responsible for their specific functions. These coregulators, such as HOXB13, VSX2, PAX5, and et al., may mediate cell development and differentiation in human embryos.ConclusionsWe provide the cell development atlas for human embryos (7–9 weeks). Two distinct cell development and differentiation pathways are revealed.

Regulation of drought stress on nutrient cycle and metabolism of rhizosphere microorganisms in desert riparian forest

Microbial communities in desert riparian forest ecosystems have developed unique adaptive strategies to thrive in harsh habitats shaped by prolonged exposure to abiotic stressors. However, the influence of drought stress on the functional and metabolic characteristics of soil rhizosphere microorganisms remains unknown. Therefore, this study aimed to investigate the effects of drought stress on soil biogeochemistry and metabolism and analyze the relationship between the biogeochemical cycle processes and network of differentially-expressed metabolites. Using metagenomics and metabolomics, this study explored the microbial functional cycle and differential metabolic pathways within desert riparian forests. The predominant biogeochemical cycles in the study area were the Carbon and Nitrogen cycles, comprising 78.90 % of C, N, Phosphorus, Sulfur and Iron cycles. Drought led to increased soil C fixation, reduced C degradation and methane metabolism, weakened denitrification, and decreased N fixation. Furthermore, drought can disrupt iron homeostasis and reduce its absorption. The differential metabolic pathways of drought stress include flavonoid biosynthesis, arachidonic acid metabolism, steroid hormone biosynthesis, and starch and sucrose degradation. Network analysis of functional genes and metabolism revealed a pronounced competitive relationship between the C cycle and metabolic network, whereas the Fe cycle and metabolic network promoted each other, optimizing resource utilization. Partial least squares analysis revealed that drought hindered the expression and metabolic processes and functional genes, whereas the rhizosphere environment facilitated metabolic expression and the functional genes. The rhizosphere effect primarily promoted metabolic processes indirectly through soil enzyme activities. The integrated multi-omics analysis further revealed that the effects of drought and the rhizosphere play a predominant role in shaping soil functional potential and the accumulation of metabolites. These insights deepen our comprehension of desert riparian forest ecosystems and offer strong support for the functionality of nutrient cycling and metabolite dynamics.

Effects of 5-Aminolevulinic Acid Supplementation on Gas Production, Fermentation Characteristics, and Bacterial Community Profiles In Vitro.

To investigate the effect of 5-aminolevulinic acid (5-ALA) on in vitro rumen gas production, fermentation characteristics, and bacterial community profiles, five levels of 5-ALA (0, 100, 500, 1000, and 5000 mg/kg DM) were supplemented into a total mixed ration (concentrate/forage = 40:60) as substrate in an in vitro experiment. Results showed that as the supplementation level of 5-ALA increased, asymptotic gas production (b) decreased linearly and quadratically (p < 0.01) while the dry matter degradation rate increased quadratically (p < 0.01). Meanwhile, the propionate concentration of 72 h incubation fluid increased linearly (p = 0.03) and pH value increased linearly and quadratically (p < 0.01), while the concentrations of butyrate, isobutyrate, valerate, isovalerate, and NH3-N and the ratio of acetate/propionate (A/P) decreased linearly and quadratically (p < 0.05). There was no significant difference in any alpha diversity indices of bacterial communities among the various 5-ALA levels (p < 0.05). PCoA and PERMANOVA analysis revealed that the bacterial profiles showed a statistical difference between the treatment 5-ALA at 1000 mg/kg DM and the other levels except for 5000 mg/kg DM (p < 0.05). Taxonomic classification revealed a total of 18 and 173 bacterial taxa at the phylum and genus level with relative abundances higher than 0.01% in at least half of the samples, respectively. LEfse analysis revealed that 19 bacterial taxa were affected by 5-ALA levels. Correlation analysis showed that Actinobacteriota was positively correlated with the gas production parameter b, the ratio of A/P, and the concentration of butyrate, isovalerate, and NH3-N (p < 0.05) and negatively correlated with pH (p < 0.05). WPS-2 exhibited a negative correlation with the gas production parameter b, the ratio of A/P, and the concentration of butyrate, valerate, isobutyrate, isovalerate, and NH3-N (p < 0.05), along with a weaker positive correlation with pH (p = 0.04). The Bacteroidales BS11 gut group was negatively correlated with the concentration of propionate but positively correlated with gas production parameter b and the concentration of butyrate and NH3-N (p < 0.05). The Lachnospiraceae NK3A20 group was found to have a positive correlation with gas production parameter b, the ratio of A/P, and the concentration of butyrate, isobutyrate, isovalerate, valerate, total VFA, and NH3-N (p < 0.05), but a highly negative correlation with pH (p < 0.01). Differential metabolic pathways analysis suggested that metabolic pathways related to crude protein utilization, such as L-glutamate degradation VIII (to propanoate), L-tryptophan degradation IX, and urea cycle, increased with 5-ALA levels. In summary, including 5-ALA in the diet might improve energy and protein utilization by reducing the abundance of Actinobacteriota, the Bacteroidales BS11 gut group, the Lachnospiraceae NK3A20 group, and certain pathogenic bacteria and increasing the abundance of WPS-2.

Functional Insights in PLS3-Mediated Osteogenic Regulation.

Plastin-3 (PLS3) encodes T-plastin, an actin-bundling protein mediating the formation of actin filaments by which numerous cellular processes are regulated. Loss-of-function genetic defects in PLS3 are reported to cause X-linked osteoporosis and childhood-onset fractures. However, the molecular etiology of PLS3 remains elusive. Functional compensation by actin-bundling proteins ACTN1, ACTN4, and FSCN1 was investigated in zebrafish following morpholino-mediated pls3 knockdown. Primary dermal fibroblasts from six patients with a PLS3 variant were also used to examine expression of these proteins during osteogenic differentiation. In addition, Pls3 knockdown in the murine MLO-Y4 cell line was employed to provide insights in global gene expression. Our results showed that ACTN1 and ACTN4 can rescue the skeletal deformities in zebrafish after pls3 knockdown, but this was inadequate for FSCN1. Patients' fibroblasts showed the same osteogenic transdifferentiation ability as healthy donors. RNA-seq results showed differential expression in Wnt1, Nos1ap, and Myh3 after Pls3 knockdown in MLO-Y4 cells, which were also associated with the Wnt and Th17 cell differentiation pathways. Moreover, WNT2 was significantly increased in patient osteoblast-like cells compared to healthy donors. Altogether, our findings in different bone cell types indicate that the mechanism of PLS3-related pathology extends beyond actin-bundling proteins, implicating broader pathways of bone metabolism.

Yam protein ameliorates cyclophosphamide-induced intestinal immunosuppression by regulating gut microbiota and its metabolites

Yam is a dual-purpose crop used in both medicine and food that is commonly used as a dietary supplement in food processing. Since yam proteins are often lost during the production of yam starch, elucidating the functionally active value of yam proteins is an important guideline for fully utilizing yam in industrial production processes. This study aimed to explore the potential protective effect of yam protein (YP) on cyclophosphamide (CTX)-induced immunosuppression in mice. The results showed that YP can reduce immune damage caused by CTX by reversing immunoglobulins (IgA, IgG and IgM), cytokines (TNF-α, IL-6, etc.) in the intestines of mice. Moreover, YPs were found to prevent CTX-induced microbiota dysbiosis by enhancing the levels of beneficial bacteria within the microbiome, such as Lactobacillus, and lowering those of Desulfovibrio_R and Helicobacter_A. Metabolomics analyses showed that YP significantly altered differential metabolites (tryptophan, etc.) and metabolic pathways (ABC transporter protein, etc.) associated with immune responses in the gut. Furthermore, important connections were noted between particular microbiomes and metabolites, shedding light on the immunoprotective effects of YPs by regulating gut flora and metabolism. These findings deepen our understanding of the functional properties of YPs and lay a solid foundation for the utilization of yam.

Histological observations and transcriptome analyses reveal the dynamic changes in the gonads of the blotched snakehead (Channa maculata) during sex differentiation and gametogenesis

BackgroundBlotched snakehead (Channa maculata) displays significant sexual dimorphism, with males exhibiting faster growth rates and larger body sizes compared to females. The cultivation of the all-male population of snakeheads holds substantial economic and ecological value. Nonetheless, the intricate processes governing the development of bipotential gonads into either testis or ovary in C. maculata remain inadequately elucidated. Therefore, it is necessary to determine the critical time window of sex differentiation in C. maculata, providing a theoretical basis for sex control in production practices.MethodsThe body length and weight of male and female C. maculata were measured at different developmental stages to reveal when sexual dimorphism in growth initially appears. Histological observations and spatiotemporal comparative transcriptome analyses were performed on ovaries and testes across various developmental stages to determine the crucial time windows for sex differentiation in each sex and the sex-related genes. Additionally, qPCR and MG2C were utilized to validate and locate sex-related genes, and levels of E2 and T were quantified to understand sex steroid synthesis.ResultsSexual dimorphism in growth became evident starting from 90 dpf. Histological observations revealed that morphological sex differentiation in females and males occurred between 20 and 25 dpf or earlier and 30–35 dpf or earlier, respectively, corresponding to the appearance of the ovarian cavity or efferent duct anlage. Transcriptome analyses revealed divergent gene expression patterns in testes and ovaries after 30 dpf. The periods of 40–60 dpf and 60–90 dpf marked the initiation of molecular sex differentiation in females and males, respectively. Male-biased genes (Sox11a, Dmrt1, Amh, Amhr2, Gsdf, Ar, Cyp17a2) likely play crucial roles in male sex differentiation and spermatogenesis, while female-biased genes (Foxl2, Cyp19a1a, Bmp15, Figla, Er) could be pivotal in ovarian differentiation and development. Numerous biological pathways linked to sex differentiation and gametogenesis were also identified. Additionally, E2 and T exhibited sexual dimorphism during sex differentiation and gonadal development. Based on these results, it is hypothesized that in C. maculata, the potential male sex differentiation pathway, Sox11a–Dmrt1–Sox9b, activates downstream sex-related genes (Amh, Amhr2, Gsdf, Ar, Cyp17a2) for testicular development, while the antagonistic pathway, Foxl2/Cyp19a1a, activates downstream sex-related genes (Bmp15, Figla, Er) for ovarian development.ConclusionsThis study provides a comprehensive overview of gonadal dynamic changes during sex differentiation and gametogenesis in C. maculata, establishing a scientific foundation for sex control in this species.

MRI radiomics and biological correlations for predicting axillary lymph node burden in early-stage breast cancer

Background and aimsPreoperative prediction of axillary lymph node (ALN) burden in patients with early-stage breast cancer is pivotal for individualised treatment. This study aimed to develop a MRI radiomics model for evaluating the ALN burden in early-stage breast cancer and to provide biological interpretability to predictions by integrating radiogenomic data.MethodsThis study retrospectively analyzed 1211 patients with early-stage breast cancer from four centers, supplemented by data from The Cancer Imaging Archive (TCIA) and Duke University (DUKE). MRI radiomic features were extracted from dynamic contrast-enhanced MRI images and an ALN burden-related radscore was constructed by the backpropagation neural network algorithm. Clinical and combined models were developed, integrating ALN-related clinical variables and radscore. The Kaplan–Meier curve and log-rank test were used to assess the prognostic differences between the predicted high- and low-ALN burden groups in both Center I and DUKE cohorts. Gene set enrichment and immune infiltration analyses based on transcriptomic TCIA and TCIA Breast Cancer dataset were used to investigate the biological significance of the ALN-related radscore.ResultsThe MRI radiomics model demonstrated an area under the curve of 0.781–0.809 in three validation cohorts. The predicted high-risk population demonstrated a poorer prognosis (log-rank P < .05 in both cohorts). Radiogenomic analysis revealed migration pathway upregulation and cell differentiation pathway downregulation in the high radscore groups. Immune infiltration analysis confirmed the ability of radiological features to reflect the heterogeneity of the tumor microenvironment.ConclusionsThe MRI radiomics model effectively predicted the ALN burden and prognosis of early-stage breast cancer. Moreover, radiogenomic analysis revealed key cellular and immune patterns associated with the radscore.

Transcriptomic landscape of quiescent and proliferating human corneal stromal fibroblasts

This study analyzed the transcriptional changes in primary human corneal stromal fibroblasts (hCSFs) grown under quiescent (serum-free) and proliferating (serum-supplemented) culture conditions to identify genes, pathways, and protein‒protein interaction networks influencing corneal repair and regeneration. Primary hCSFs were isolated from donor human corneas and maintained in serum-free or serum-laden conditions. RNA was extracted from confluent cultures using Qiagen kit and subjected to RNA sequencing (RNAseq) analysis. Differential gene expression (DGE) and pathway enrichment analyses were conducted using DESeq2 and Gene Set Enrichment Analysis (GSEA), respectively. Protein‒protein interaction (PPI) networks were created exploiting the STRING database and analyzed with Cytoscape and the cytoHubba plugin. RNA-seq revealed 5,181 genes that were significantly differentially expressed/changed among the 18,812 annotated genes (p value ˂0.05). A cutoff value of a log2-fold change of ±1.5 or greater was used to identify 674 significantly upregulated and 771 downregulated genes between quiescent and proliferating hCSFs. Pathway enrichment analysis revealed significant changes in genes linked to cell cycle regulation, inflammatory, and oxidative stress response pathways, such as E2F Targets, G2M Checkpoint, and MYC Targets, TNFA signaling via NF-kB, and oxidative phosphorylation. Protein-protein interaction network analysis highlighted critical hub genes. The FGF22, CD34, ASPN, DPT, LUM, FGF10, PDGFRB, ECM2, DCN, VEGFD, OMD, OGN, ANGPT1, CDH5, and PRELP were upregulated, whereas genes linked to cell cycle regulation and mitotic progression, such as BUB1, TTK, KIF23, KIF11, BUB1B, DLGAP5, NUSAP1, CCNA2, CCNB1, BIRC5, CDK1, KIF20A, AURKB, KIF2C, and CDCA8, were downregulated. The RNA sequences and gene count files have been submitted to the Gene Expression Omnibus (accession # GSE260476). Our study provides a comprehensive information on the transcriptional and molecular changes in hCSFs under quiescent and proliferative conditions and highlights key pathways and hub genes.

Deciphering the dynamic single-cell transcriptional landscape in the ocular surface ectoderm differentiation system

Abstract The ocular surface ectoderm (OSE) is essential for the development of the ocular surface, yet the molecular mechanisms driving its differentiation are not fully understood. In this study, we used single-cell transcriptomic analysis to explore the dynamic cellular trajectories and regulatory networks during the in vitro differentiation of embryonic stem cells (ESCs) into the OSE lineage. We identified nine distinct cell subpopulations undergoing differentiation along three main developmental branches: neural crest, neuroectodermal, and surface ectodermal lineages. Key marker gene expression, transcription factor activity, and signaling pathway insights revealed stepwise transitions from undifferentiated ESCs to fate-specified cell types, including a PAX6 + TP63 + population indicative of OSE precursors. Comparative analysis with mouse embryonic development confirmed the model’s accuracy in mimicking in vivo epiblast-to-surface ectoderm dynamics. By integrating temporal dynamics of transcription factor activation and cell–cell communication, we constructed a comprehensive molecular atlas of the differentiation pathway from ESCs to distinct ectodermal lineages. This study provides new insights into the cellular heterogeneity and regulatory mechanisms of OSE development, aiding the understanding of ocular surface biology and the design of cell-based therapies for ocular surface disorders.

Vitamin D and muscle health: insights from recent studies.

The purpose of this review is to critically evaluate the effects of vitamin D on muscle mass and physical/muscle function in middle-aged and older adults, based on recent human studies, including cross-sectional, observational, and intervention studies. Vitamin D, beyond its well established role in bone health, has shown potential in influencing muscle physiology, making it a nutrient of interest in the context of sarcopenia and related chronic conditions. The review states how vitamin D affects muscle function, emphasizing its role in muscle cell proliferation, differentiation, and key signaling pathways. Additionally, the review of recent human studies revealed an inconsistent relationship between vitamin D and sarcopenia and related indices, with mixed results regarding muscle mass and strength. Variability in supplementation dose, duration, and baseline 25-hydroxyvitamin D levels may contribute to these inconsistencies. While animal studies indicate vitamin D's effectiveness in muscle growth, cross-sectional, observational, and intervention studies do not show clear benefits of maintaining efficient vitamin D levels on muscle mass or function in humans. Although vitamin D impacts muscle health, it is insufficient alone, emphasizing the need for a multifaceted approach to sarcopenia prevention and management.

Low-Dose Metformin and Profibrotic Signature in Central Centrifugal Cicatricial Alopecia

Central centrifugal cicatricial alopecia (CCCA) is a scarring alopecia predominantly affecting Black female individuals. Current conventional treatments target inflammation but not the underlying fibrotic processes, often leading to permanent hair loss. To investigate the associations of low-dose oral metformin, an antidiabetic medication with antifibrotic properties, with clinical symptoms and scalp gene expression patterns in patients with CCCA. This retrospective clinical case series and transcriptomic analysis included patients treated at a single tertiary academic medical center between January 2023 and March 2024. All patients had biopsy-confirmed CCCA refractory to standard treatments. Transcriptomic analysis was performed on patients with previously banked, paired scalp biopsies before and after treatment with adjuvant metformin for at least 6 weeks. Extended-release metformin, 500 mg, once daily was added to participants' baseline CCCA treatment regimens. Clinical assessments included pruritus, inflammation, scalp resistance, and hair regrowth. Gene expression profiling via bulk RNA sequencing analysis evaluated differential gene expression and pathway enrichment. A total of 12 Black female participants were included in the study, and transcriptomic analysis was performed in 4 participants. After at least 6 months of metformin treatment, 9 participants experienced improvement in disease, including scalp pain, inflammation, and/or pruritus, and 6 demonstrated clinical evidence of hair regrowth. The addition of metformin led to reversal of many prominent gene pathways previously identified in CCCA. Transcriptomic analysis revealed upregulation of pathways and genes (keratin-associated proteins [KRTAPs]) involved in keratinization, epidermis development, and the hair cycle (absolute log2-fold change > 4), with concomitant downregulation of fibrosis-related pathways and genes (eg, MMP7, COL6A1) (fold change >1.5; all false discovery rate <.05). Gene set analysis showed reduced expression of helper T cell 17 and epithelial-mesenchymal transition pathways and elevated adenosine monophosphate kinase signaling and KRTAPs after metformin treatment. In this case series of patients with treatment-refractory CCCA, low-dose oral metformin was associated with symptomatic improvement and dual modulation of gene expression, stimulating hair growth pathways while suppressing fibrosis and inflammation markers. These findings provide a rationale for future clinical trials studying metformin as a targeted therapy for CCCA and other cicatricial alopecias.

Anti-aging Metabolite-Based Polymeric Microparticles for Intracellular Drug Delivery and Bone Regeneration.

Alpha-ketoglutarate (AKG), a key component of the tricarboxylic acid (TCA) cycle, has attracted attention for its anti-aging properties. Our recent study indicates that locally delivered cell-permeable AKG significantly promotes osteogenic differentiation and mouse bone regeneration. However, the cytotoxicity and rapid hydrolysis of the metabolite limit its application. In this study, we synthesize novel AKG-based polymeric microparticles (PAKG MPs) for sustained release. In vitro data suggest that the chemical components, hydrophilicity, and size of the MPs can significantly affect their cytotoxicity and pro-osteogenic activity. Excitingly, these biodegradable PAKG MPs are highly phagocytosable for nonphagocytic pre-osteoblasts MC3T3-E1 and primary bone marrow mesenchymal stem cells (BMSCs), significantly promoting their osteoblastic differentiation. RNAseq data suggest that PAKG MPs strongly activate Wnt/β-catenin and PI3K-Akt pathways for osteogenic differentiation. Moreover, PAKG enables poly (L-lactic acid) and poly (lactic-co-glycolic acid) MPs (PLLA & PLGA MPs) for efficient phagocytosis. Our data indicate that PLGA-PAKG MPs-mediated intracellular drug delivery can significantly promote stronger osteoblastic differentiation compared to PLGA MPs-delivered phenamil. Notably, PAKG MPs significantly improve large bone regeneration in a mouse cranial bone defect model. Thus, the novel PAKG-based MPs show great promise to improve osteogenic differentiation, bone regeneration, and enable efficient intracellular drug delivery for broad regenerative medicine.