Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

P-glycoprotein inhibits the MAPK/NF-KB pathway and activates autophagy and oxidative stress to improve GPS resistance in vivo and in vitro

Glaesserella parasuis (Gps) is an important pathogen that causes polyserositis, peritonitis and meningitis in pigs, causing considerable economic losses to the pig industry worldwide. In recent years, due to the abuse of antibiotic drugs, Gps drug resistance and multi-drug resistance have become increasingly serious, especially for macrolides. Thus, by inducing Tydigrosin resistant bacteria, we found that PgtP is a Gps-produced virulence gene that plays a crucial role in the disease, but its interaction in host cells remains unclear. To characterize the function of the PgtP gene in Gps, we constructed ΔPgtP mutants. Notably, deletion of the PgtP gene resulted in increased adhesion to mouse macrophages, suggesting that PgtP is essential for adhesion of Gps. In addition, as a member of the cell membrane transporter family, PgtP links activated inflammation with autophagy and oxidative stress metabolism. To further investigate the role of PgtP, we infected mouse macrophages with ΔPgtP mutants and wild strains respectively. We found that ΔPgtP mutations can reduce the level of intracellular reactive oxygen species (ROS), up-regulate the number of intracellular autophagosomes, and down-regulate the expression of cytokines IL-6 and TNF-a. Further mechanistic studies showed that PGTP-associated p38 mitogen-activated protein kinase (MAPK) and NF-κB signaling pathways were involved in autophagy and oxidative stress and demonstrated that the related signaling pathways were also activated in mice. These results highlight the potential of PgtP as a target for therapeutic intervention and provide important new insights into how it contributes to the aggressiveness and persistence of Gps.

An inulin-type fructan CP-A from Codonopsis pilosula combined with 5-Fluorouracil alleviates colitis-associated tumorigenesis via inhibition of EGFR/AKT/ERK signaling pathway and regulation of intestinal flora

Inulin-type fructan CP-A, the main component of Codonopsis pilosula polysaccharides, has been found to have therapeutic effects on ulcerative colitis (UC). Herein, we established a colitis-associated cancer (CAC) mouse model by azomethane (AOM) and dextran sulfate sodium (DSS) and selected mouse colon cancer cells CT-26 to explore the therapeutic effects of the combined administration of CP-A and 5-fluorouracil (5-FU) in vivo and in vitro. High-throughput transcriptomics sequencing technology was used to identify differentially expressed genes (DEGs) in the mouse colon and enrich related pathways. 16S rRNA gene sequencing technology was used for gut microbiota research to identify microbial changes in mouse feces. Short-chain fatty acid (SCFA) content was identified in the mouse colon using gas chromatography-mass spectroscopy (GC-MS). In vivo experiments showed that compared with untreated CAC mice, those treated with the combined administration of CP-A and 5-FU had significantly restored body weight, fewer tumors, smaller tumor volume, and reduced disease activity index (DAI) and histopathological scores. The combination of CP-A and 5-FU increased the anti-inflammatory cytokine interleukin 10 (IL-10) and inhibited the expression of pro-inflammatory cytokines interleukin 6 (IL-6), tumor necrosis factor-α (TNF-α), and interferon-gamma (IFN-γ). In vitro experiments indicated that a combination of CP-A and 5-FU promoted the apoptosis of CT-26 cells. The results of transcriptomics studies suggested that the therapeutic effect of the combined administration of CP-A and 5-FU on CAC may be related to the EGFR/AKT/ERK pathway. Both in vivo and in vitro experiments verified the regulatory effect of the combined administration of CP-A and 5-FU on the EGFR/AKT/ERK pathway. Moreover, the intestinal flora experiment manifested that compared with untreated CAC mice, the combined CP-A and 5-FU group had a more stable intestinal microbiota composition, and the combined administration of CP-A and 5-FU increased the abundance of SCFAs. Our experimental findings have demonstrated that the combination of CP-A and 5-FU exhibits promising efficacy in the treatment of CAC, warranting further clinical investigation in the future.

Whole-transcriptome sequencing reveals the effects of acupuncture on early embryos post-IVF-ET in poor ovarian response

BACKGROUND

Poor ovarian response (POR) refers to a pathological condition where the ovaries respond inadequately to gonadotropin stimulation during ovulation induction. The decline in both the quantity and quality of available oocytes makes achieving pregnancy through IVF-ET more challenging. Several studies have demonstrated that acupuncture can improve embryo quality, increase the number of high-quality embryos, and enhance pregnancy outcomes in IVF-ET patients, although the underlying mechanisms remain unclear. Therefore, this study aimed to investigate the molecular mechanisms by which acupuncture influences early embryo development in POR mice after IVF-ET through whole-transcriptome sequencing.

METHODS

We established POR mice model and performed acupuncture treatment. Fresh denuded oocytes were retrieved and transplanted via IVF-ET into new donor female mice to obtain early-stage embryo tissues. Vaginal smear tests were conducted to monitor estrous cycle changes, while oocyte retrieval, ovarian wet weight, and ovarian index were assessed. Serum concentrations of anti-Müllerian hormone (AMH), follicle-stimulating hormone (FSH), estradiol (E2), and luteinizing hormone (LH) were measured via ELISA. Histopathological changes and apoptosis in the ovaries were evaluated using HE and TUNEL staining. Whole-transcriptome sequencing was employed to establish expression profiles of differentially expressed mRNAs (DEmRNAs), DEmiRNAs, DElncRNAs, and DEcircRNAs. The circ/lncRNA-miRNA-mRNA network was constructed to analyze the biological functions and potential mechanisms of acupuncture on early embryo development post-IVF-ET in POR mice.

RESULTS

Our results demonstrated that acupuncture improved ovarian function in POR mice, corrected serum hormone imbalances, and alleviated abnormal apoptosis in ovarian granulosa cells. Through whole-transcriptome sequencing, we identified 685 DEmRNAs, 13 DEmiRNAs, 325 DElncRNAs, and 4 DEcircRNAs exhibiting regulatory trends. By constructing the circ/lncRNA-miRNA-mRNA network, we found that miR-291a-3p, miR-294-3p, and miR-295-3p may serve as key targets influencing early embryo development via multiple pathways, including the Toll-like receptor signaling pathway and p53 signaling pathway.

CONCLUSION

Overall, our study is the first to reveal the molecular mechanisms by which acupuncture improves early embryo development under POR conditions, providing new evidence for the use of acupuncture in assisted reproduction.

Transcriptome reveals the roles and potential mechanisms of CeRNA in the regulation of salivary gland development in the tick Rhipicephalus haemaphysaloides

Introduction

The salivary glands of female ticks rapidly degenerate after feeding. The mechanism involves programmed cell death mediated by an ecdysteroid receptor. A competing endogenous RNA (ceRNA) network has been established using miRNA and the competitive binding of three types of RNA (lncRNA, circRNA, and mRNA), that were demonstrated to be involved in the regulation of biological processes. However, the comprehensive expression profile and competing endogenous RNA (ceRNA) regulatory network between mRNAs and ncRNAs involved in salivary gland development remain unclear.

Methods

In the current study, we employed whole-transcriptome sequencing (RNA sequencing) at various stages of feeding to identify differentially expressed lncRNAs, circRNAs, miRNAs, and mRNAs. The ceRNA networks combining lncRNAs, circRNAs, miRNAs, and mRNAs were predicted and constructed based on the miRanda and TargetScan databases. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for target mRNAs with significantly different expression levels.

Results

We identified several pathways related to organ growth and development: Insulin secretion, the Hippo signaling pathway, the Pl3K-Akt signaling pathway, the FoxO signaling pathway, and the Ferroptosis pathway in the lncRNA-miRNA-mRNA network, and Steroid biosynthesis, Cholesterol metabolism, the FoxO signaling pathway, and the Ferroptosis pathway in the circRNA-miRNA-mRNA network, each of which involved insulin and ecdysteroid regulation.

Discussion

Our findings have advanced our understanding of the underlying mechanisms of salivary gland development and degeneration.

Transcriptomics, single-cell sequencing and spatial sequencing-based studies of cerebral ischemia

With high disability and mortality rate as well as highly complex pathogenesis, cerebral ischemia is highly morbid, prone to recurrence. To comprehensively understand the pathophysiological process of cerebral ischemia and to find new therapeutic strategies, a new approach to cerebral ischemia transcriptomics has emerged in recent years. By integrating data from multiple levels of transcriptomics, such as transcriptomics, single-cell transcriptomics, and spatial transcriptomics, this new approach can provide powerful help in revealing the molecular mechanisms of cerebral ischemia occurrence and development. Key findings highlight the critical roles of inflammation, blood-brain barrier dysfunction, and mitochondrial dysregulation in cerebral ischemia, offering potential biomarkers and therapeutic targets for early diagnosis and personalized treatment. A review of the research progress of cerebral ischemic injury mechanism under the analysis of the comprehensive transcriptomics research method was presented in this article, aiming to study the potential mechanism to provide new, innovative therapeutic strategies for this disease.

PD98059 inhibit the proliferation and differentiation of osteoblasts in the formation of tympanosclerosis via ERK1/2-MAPK signaling pathway

Tympanosclerosis (TS) has become a common pathological condition of the middle ear, but the underlying mechanism of it is still ambiguous. It was found that osteoprotegerin/receptor activator of nuclear factor kappa B ligand (OPG/RANKL) axis played an important role in the development of TS and was regulated by the extracellular signal regulated kinase 1/2-mitogen activated protein kinase (ERK1/2-MAPK) pathway. However, whether ERK1/2-MAPK pathway mediates the occurrence of TS by regulating OPG/RANKL axis has not been reported. In this study, MAPK and calcium pathway were found significantly activated in TS model. In vivo, the expression of p-ERK1/2 in TS model was significantly increased. In vitro, osteoblasts were isolated from auditory vesicles of neonatal rats for the first time, and then cultured with ERK1/2-MAPK pathway inhibitor PD98059. As results, PD98059 showed inhibitory effects on the phosphorylation of ERK1/2 and proliferation of osteoblasts. Besides, different concentrations of PD98059 showed different inhibitory effects on mRNA expression of osteocalcin (Ocn), bone sialoprotein (Bsp), runt-related transcription factor 2 (Runx2), bone morphogenetic protein 2 (Bmp2) and OPG. Therefore, it was speculated that the ERK1/2-MAPK pathway may affect the formation of TS by regulating the proliferation and differentiation of osteoblasts, which may be helpful for the study of drug target for tympanosclerosis.

Preparation of Cell-Cultured Fish Fat via Adipogenic Transdifferentiation of Larimichthys crocea Muscle Satellite Cells

Cell-cultured fish fat (CCF) has the potential to enhance the flavor and texture of cell-cultured fish meat (CCM). Herein, CCF was developed through the adipogenic transdifferentiation of Larimichthys crocea muscle satellite cells (LCMSCs). A low-serum culture system and a large-scale culture system were established. A rapid transdifferentiation medium was also developed, and the mechanisms in promoting adipogenic transdifferentiation were preliminarily analyzed. The results indicated that the proliferation rate and morphology of cells were not significantly affected by serum reduction following domestication. These cells can be cultured in bioreactors, achieving a 10-fold increase in density. The combination of horse serum and oleic acid enabled adipogenic transdifferentiation within 8 days. Transcriptomic and metabolomic analyses revealed significant changes in gene expression and lipid metabolism, with enrichment of pathways related to fatty acid metabolism. Five inducers were quantified to assess the quality of CFF. This study provides a feasible method for CCF production and lays the theoretical basis for the development of CCM.

Transcriptome Data Combined With Mendelian Randomization Analysis Identifies Key Genes Associated With Mitochondria and Programmed Cell Death in Intervertebral Disc Degeneration

Background

Intervertebral disc degeneration (IDD) is a major cause of cervical and lumbar diseases, significantly impacting patients' quality of life. Mitochondria and cell death have been implicated in IDD, but the key related genes remain unknown.

Methods

Differentially expressed genes (DEGs) between IDD and control samples were identified using GSE70362. Mitochondria-related genes (MRGs) and programmed cell death-related genes (PCDRGs) were intersected with DEGs to find DE-MRGs and DE-PCDRGs. Weighted gene co-expression network analysis (WGCNA) identified key module genes, and the overlap with DEGs revealed candidate genes. Mendelian randomization (MR) analysis was used to determine genes causally linked to IDD. Machine learning and expression validation further refined key genes, which were then used to build a nomogram to predict IDD risk. Additionally, gene set enrichment analysis (GSEA), immune infiltration, and single-cell analysis were performed.

Results

A total of 515 DEGs were intersected with 224 key module genes, yielding 31 candidate genes. Six genes-BCKDHB, BID, TNFAIP6, VRK1, CAB39L, and TMTC1-showed a causal relationship with IDD. BID, TNFAIP6, and TMTC1 were further identified as key genes through machine learning and validation. A nomogram was developed based on these genes. GSEA revealed BID and TMTC1 were enriched in N-glycan biosynthesis, TNFAIP6 and TMTC1 in aminoacyl tRNA biosynthesis, and BID and TMTC1 in ribosomal pathways. Activated dendritic cells, CD56dim natural killer cells, monocytes, and other immune cells were elevated in IDD, with TNFAIP6 strongly correlating with activated dendritic cells. Key genes were expressed at higher levels in degraded samples.

Conclusion

BID, TMTC1, and TNFAIP6 were identified as key genes linked to mitochondria and cell death in IDD, offering new insights for diagnosis and treatment.

Genomic and transcriptomic analyses reveal the genetic basis of leg diseases in laying hens

In recent years, while monitoring commercial laying hens during the brooding period, we noticed that some chicks exhibited an abnormal lameness phenomenon. Systematic tests were carried out for pathogens including, but not limited to, common diseases such as viral arthritis, mycoplasma synoviae, Marek's disease and encephalomyelitis. However, the absence of these pathogens in these chicks rules out these common diseases as a direct cause of limping and points to genetic factors. Leg disorders in laying hens pose significant welfare challenges and result in considerable economic losses within the poultry industry. To address this issue, we conducted a comprehensive genomic and transcriptomic analysis to uncover the genetic basis of leg diseases in laying hens. Our study involved 74 laying hens with leg diseases and 60 healthy controls from three different strains. Radiographic identification and resequencing were performed to analyze genetic loci and candidate genes. Transcriptomic analysis was also conducted on cartilage tissues from both groups. Four potential single nucleotide polymorphism (SNP) loci located on chromosomes 4 and 33 were identified through genome-wide association studies (GWAS). Notably, the functional candidate gene SORCS2 has been particularly implicated in the pathogenesis of leg disease. A total of 1,515 differentially expressed genes (DEGs) were identified through transcriptomic analysis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed significant enrichment in pathways such as cytoskeletal protein binding, cell cycle regulation, and muscle cell cytoskeleton organization. Notably, the calcium signaling and the extracellular matrix (ECM)-receptor interaction pathways were associated with the development of leg diseases. The integration of genomic and transcriptomic data identified key genetic loci and candidate genes associated with leg health, providing a genetic foundation for improving disease resistance in laying hens. Our findings offer valuable insights for the development of selective breeding strategies to reduce the incidence of leg disorders in laying hens, thereby enhancing their welfare and productivity.

Sedanolide alleviates DSS-induced colitis by modulating the intestinal FXR-SMPD3 pathway in mice

INTRODUCTION

Inflammatory bowel disease (IBD) is a global disease with limited therapy. It is reported that sedanolide exerts anti-oxidative and anti-inflammatory effects as a natural phthalide, but its effects on IBD remain unclear.

OBJECTIVES

In this study, we investigated the impacts of sedanolide on dextran sodium sulfate (DSS)-induced colitis in mice.

METHODS

The mice were administered sedanolide or vehicle followed by DSS administration, after which colitis symptoms, inflammation levels, and intestinal barrier function were evaluated. Transcriptome analysis, 16S rRNA sequencing, and targeted metabolomics analysis of bile acids and lipids were performed.

RESULTS

Sedanolide protected mice from DSS-induced colitis, suppressed the inflammation, restored the weakened epithelial barrier, and modified the gut microbiota by decreasing bile salt hydrolase (BSH)-expressing bacteria. The downregulation of BSH activity by sedanolide increased the ratio of conjugated/unconjugated bile acids (BAs), thereby inhibiting the intestinal farnesoid X receptor (FXR) pathway. The roles of the FXR pathway and gut microbiota were verified using an intestinal FXR-specific agonist (fexaramine) and germ-free mice, respectively. Furthermore, we identified the key effector ceramide, which is regulated by sphingomyelin phosphodiesterase 3 (SMPD3). The protective effects of ceramide (d18:1/16:0) against inflammation and the gut barrier were demonstrated in vitro using the human cell line Caco-2.

CONCLUSION

Sedanolide could reshape the intestinal flora and influence BA composition, thus inhibiting the FXR-SMPD3 pathway to stimulate the synthesis of ceramide, which ultimately alleviated DSS-induced colitis in mice. Overall, our research revealed the protective effects of sedanolide against DSS-induced colitis in mice, which indicated that sedanolide may be a clinical treatment for colitis. Additionally, the key lipid ceramide (d18:1/16:0) was shown to mediate the protective effects of sedanolide, providing new insight into the associations between colitis and lipid metabolites.

The phytohormone brassinosteroid (BR) promotes early seedling development via auxin signaling pathway in rapeseed

The phytohormone brassinosteroid (BR) regulate various developmental and physiological processes in plants. However, the function of BR during early seedling development stage in rapeseed is largely unknown. To understand the effects of exogenous BR during early seedling development, the ZS11 and BR-INSENSITIVE (bin2) mutants were treated with BR before seed sowing and seed germination stage under 16/8 hours light/dark cycle. The phenotype results indicated that BR promotes only seedling establishment but not seed germination stage in ZS11, while no function in bin2 mutants. Since BRs play a crucial role in regulation of developmental transition between growth in the dark (skotomorphogenesis) and growth in the light (photomorphogenesis), the ZS11 and bin2 mutants were treated with BR under continuous light and dark. The BR treatment also showed the same functions as 16/8 hours light/dark cycle. To understand the function of BR on expression levels, the differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) between mock- and BR-treated seedlings were explored. A total of 234 significantly DEGs were identified between the mock- and BR-treated groups by transcriptomic analyses. These DEGs were markedly enriched in BR biosynthesis, pentose and glucuronate interconversions and plant hormone signal transduction pathways. Meanwhile, a total of 145 DEMs were identified through metabolomics analyses, with a significant enrichment in lipid substances. Interestingly, some genes and metabolites associated with auxin pathway were identified, which exhibited up-regulation in both DEGs and DEMs after BR treatment. Subsequently, functional enrichment analyses revealed that the majority of DEGs and DEMs were primarily enriched in ascorbate and aldehyde metabolism, arginine and proline metabolism, tryptophan metabolism (the main route for auxin synthesis) and cyanogenic amino acid metabolism. Furthermore, it was found that glutamate was up-regulated in nitrogen metabolism, glyoxylate and dicarboxylate metabolism, and arginine and proline metabolism pathways. These indicated that the glutamate signaling pathway was a key regulatory pathway for exogenous BR to induce seedling establishment. These evidence implied that exogenous BR treatment lead to up-regulation of auxin-related genes expression, then promoted seedling establishment in rapeseed.

CD177, MYBL2, and RRM2 Are Potential Biomarkers for Musculoskeletal Infections

BACKGROUND

Biomarkers of infection are measurable indicators that reflect the presence of an infection in the body. They are particularly valuable for detecting infections and tracking treatment responses. Previous transcriptome analysis of peripheral blood mononuclear cells (PBMCs) collected from patients during the active phase of diabetic foot infection identified the upregulation of several genes, including a neutrophil-specific cell surface glycoprotein, CD177, an Myb-related transcription factor 2 (MYBL2), and ribonucleotide reductase regulatory subunit M2 (RRM2). We aimed to investigate whether these observations in diabetic foot infections could be extrapolated to other musculoskeletal infections.

QUESTIONS/PURPOSES

(1) Are the protein concentrations of CD177, MYBL2, and RRM2 elevated in serum or PBMCs of patients with musculoskeletal infections? (2) Do serum and PBMC concentrations of CD177, MYBL2, and RRM2 decrease in response to antibiotic therapy? (3) Can these biomarkers give diagnostic accuracy and differentiate patients with musculoskeletal infections from controls?

METHODS

From April 2023 to June 2024, we treated 26 patients presenting with clinical symptoms and signs of acute musculoskeletal infections, including elevated inflammatory markers (white blood cell [WBC] and C-reactive protein [CRP]) and local changes such as swelling, erythema, tenderness or pain, warmth, purulent drainage, sinus tract, or wound leading to bone or hardware. Diagnosis included periprosthetic joint infection (PJI), foot and ankle infection (FAI), fracture-related infection (FRI), and septic arthritis of the native joints. Patients with chronic recurrent osteomyelitis, PJI, or FRI were excluded from the study. Among the 26 patients deemed potentially eligible, 19% (5) were excluded for the following reasons: prison inmate (1), unable to provide consent because of severe sepsis (1), mental illness (1), and declined to participate (2). Of the 81% (21) of patients who provided consent, cultures from 9.5% (2) were negative. These two patients were ultimately diagnosed with inflammatory arthritis: gout (1) and rheumatoid arthritis (1); thus, the musculoskeletal infection group for analysis consisted of 73.1% (19 of 26) of patients. A control group of 21 patients undergoing elective foot or ankle deformity correction surgery without infections or systemic inflammation was included. Because foot or ankle deformity is highly unlikely to influence the immunologic profile of the subjects, we believed that these patients would serve as an appropriate control group. Other than the absence of infection and the lower prevalence of diabetes mellitus, the control group was comparable to the study group in terms of demographics and clinical factors, including age and sex distribution. We collected blood samples from both patients and controls and quantified CD177, MYBL2, and RRM2 RNA transcription levels in the PBMC using qRT-PCR. We also assessed protein concentrations in the serum and PBMC using an enzyme-linked immunosorbent assay. A comparative analysis of the three biomarkers was performed on 19 patients with musculoskeletal infections with positive cultures and 21 controls to assess their diagnostic potential using the unpaired nonparametric t-test with the Mann-Whitney test. We obtained 8-week follow-up blood samples from seven patients with musculoskeletal infections who clinically healed. Healing was defined by normalization of inflammatory markers (WBC and CRP) and absence of swelling, erythema, local tenderness or pain, warmth, purulent drainage, sinus tract, or open wound. We performed a comparative analysis of the seven patients during active infection and after treatment to determine a change in the level of CD177, MYBL2, and RRM2 in their serum and PBMCs. These findings were also compared with those of the control group. We evaluated the diagnostic accuracy of CD177, MYBL2, and RRM2 for musculoskeletal infections using receiver operating characteristic (ROC) curve analysis.

RESULTS

The musculoskeletal infections group showed a larger increased serum and PBMC concentrations of CD177, MYBL2, and RRM2 proteins compared with the control group. The mean protein concentrations of CD177, MYBL2, and RRM2 were increased in the serum and PBMC of the musculoskeletal infections group compared with the controls. Serum levels of all biomarkers investigated were higher in musculoskeletal infections group compared with the control group (CD177 227 [155 to 432] versus 54 [10 to 100], difference of medians 173, p < 0.01; MYBL2 255 [231 to 314] versus 180 [148 to 214], difference of medians 75, p < 0.01; RRM2 250 [216 to 305] versus 190 [148 to 255], difference of medians 60, p < 0.01). Similarly, PBMC levels of all biomarkers were higher in the musculoskeletal infections group (CD177 55.3 [39.1 to 80.5] versus 17.5 [10.5 to 27.5], difference of medians 37.8, p < 0.01; MYBL2 144 [114 to 190] versus 91 [70 to 105], difference of medians 53, p < 0.01; RRM2 168 [143 to 202] versus 100 [77.5 to 133], difference of medians 68, p < 0.01). Additionally, serum levels of all biomarkers decreased in seven patients with musculoskeletal infections after infection treatment (CD177 3080 [2690 to 3320] versus 4250 [3100 to 8640], difference of medians 1170, p < 0.01; MYBL2 4340 [4120 to 4750] versus 5010 [4460 to 5880], difference of medians 670, p < 0.01; RRM2 4350 [3980 to 5000] versus 5025 [4430 to 6280], difference of medians 675, p = 0.01). Similarly, PBMC levels of all biomarkers were lower after infection treatment (CD177 805 [680 to 980] versus 1025 [750 to 1610], difference of medians 220, p < 0.01; MYBL2 2300 [2100 to 2550] versus 2680 [2220 to 3400], difference of medians 380, p = 0.02; RRM2 2720 [2500 to 3200] versus 3350 [2825 to 4030], difference of medians 630, p < 0.01). The area under the ROC curve for diagnosing musculoskeletal infections in the serum and PBMC was as follows: CD177 95% confidence interval [CI] > 0.99 and > 0.99, MYBL2 95% CI > 0.99 and > 0.99, and RRM2 95% CI = 0.96 and > 0.99, respectively.

CONCLUSION

We may utilize blood-based tests for CD177, MYBL2, and RRM2 to aid in the diagnosis of musculoskeletal infections, particularly when arthrocentesis or obtaining tissue culture is challenging. They may also assist in monitoring treatment response. As some of these biomarkers may also be elevated in other inflammatory conditions, a large-scale clinical study is needed to confirm their reliability in differentiating musculoskeletal infections from other inflammatory conditions.

CLINICAL RELEVANCE

CD177, MYBL2, and RRM2 proteins in blood samples may serve as novel biomarkers for diagnosing and monitoring treatment response in musculoskeletal infections.

FUNCTIONAL IMMUNOPHENOTYPING FOR PRECISION THERAPIES IN SEPSIS

ABSTRACT

Sepsis remains a significant cause of morbidity and mortality worldwide. Although many more patients are surviving the acute event, a substantial number enters a state of persistent inflammation and immunosuppression, rendering them more vulnerable to infections. Modulating the host immune response has been a focus of sepsis research for the past 50 years, yet novel therapies have been few and far between. Although many septic patients have similar clinical phenotypes, pathways affected by the septic event differ not only between individuals but also within an individual over the course of illness. These differences ultimately impact overall immune function and response to treatment. Defining the immune state, or endotype, of an individual is critical to understanding which patients will respond to a particular therapy. In this review, we highlight current approaches to define the immune endotype and propose that these technologies may be used to "prescreen" individuals to determine which therapies are most likely to be beneficial.

The functions and clinical implications of hsa_circ_0032462-miR-488-3p-SLC7A1 axis in human osteosarcoma

BACKGROUND

Osteosarcoma, as the most common primary malignant bone tumor, has become one of the main causes of cancer-related deaths in adolescents and children. This study thus proposes new biomarkers for OS based on whole-transcriptome re-analysis and experimental confirmation.

METHODS

We find two circRNA dataset related to OS, from tissue and cell perspectives respectively, from the GEO database. Analysis of the tumor group and control group data used GEO2R, to obtain the differentially expressed (DE) circRNAs and take the intersection. The downstream miRNAs were predicted and subsequently the targeted mRNAs for these miRNAs were collected. These targeted mRNAs intersected with prognostic mRNAs reported in previous literature. CircRNA/miRNA/mRNA and circRNA/miRNA/mRNA/key pathway networks were constructed and GO and KEGG analyses were done. The prognostic values of hsa_circ_0032462, miR-488-3p, and SLC7A were confirmed in OS using Kaplan-Meier analyses and univariate/multivariate analyses. And the cellular functions of these three factors in OS were further explored through cell experiments.

RESULTS

Five DEcircRNAs were obtained, targeting 42 miRNAs and linking 67 prognostic-related mRNA. GO analysis and KEGG analysis indicate that the mRNAs in the network were involved in various biological processes and signaling pathways related to OS. The luciferase report validated the targeting relationship of hsa_circ_0032462, miR-488-3p, and SLC7A. Cell survival, migration, and invasion experiments found that hsa_circ_0032462 and SLC7A promoted OS, while miR-488-3p inhibited OS.

CONCLUSION

Aberrantly expressed circRNAs in OS are involved in OS progression via the ceRNA network. Hsa_circ_0032462-miR-488-3p-SLC7A1 axis can be developed to be alternative therapeutic targets for OS.

Transcriptome Sequencing Reveals Effects of Artificial Feed Domestication on Intestinal Performance and Gene Expression of Carnivorous Mandarin Fish (Siniperca chuatsi) and Related Mechanisms

Mandarin fish (Siniperca chuatsi) is a voracious carnivorous species, usually consuming only live bait fish, but dietary acclimation enables it to accept artificial feed. However, the effects of dietary acclimation on intestinal performance and gene expression in mandarin fish and related mechanisms remain largely unknown. Therefore, this study investigated the effects of artificial feed on intestinal physicochemical and biochemical performance and gene expression in mandarin fish. Mandarin fish were sampled on day 10 after feeding with live dace (LD), at day 40 after subsequent feeding with dead dace plus artificial feed (DD + AF) from day 11 to day 40, and at day 90 after continuous feeding with artificial feed (AF) alone from day 41 to day 90 for transcriptome sequencing. The biochemical analysis results indicated that artificial feed significantly increased the activity of antioxidant enzymes glutathione peroxidase and superoxide dismutase in the intestine, liver, and stomach. Histological analysis demonstrated intestinal damage in mandarin fish fed with artificial feed. The GO and KEGG enrichment analyses indicated that the DEGs in AF vs. DD + AF were significantly enriched in the pentose phosphate pathway, and the DEGs in AF vs. LD were mainly significantly enriched in glycolysis/gluconeogenesis and PPAR signaling pathways. Nineteen feed acclimation-related key genes such as gene pfkfb4a and scd were identified in the intestine and found to exhibit upregulated expressions. These results revealed that artificial feed domestication enhanced the antioxidant capacity of the mandarin fish intestine and reduced hepatic lipid deposition by upregulating the related gene expression of mandarin fish and that the regulation of carbon metabolisms, including sugar, lipid, and steroid metabolisms, might be fundamental mechanisms for mandarin fish to acclimatize to dietary changes. These findings provide novel insights into the feed acclimation mechanism of mandarin fish, holding implications for promoting large-scale artificial feed aquaculture of mandarin fish and improving economic efficiency.

Genome-wide DNA methylation and transcriptome sequencing analyses of lens tissue in an age-related mouse cataract model

DNA methylation is known to be associated with cataracts. In this study, we used a mouse model and performed DNA methylation and transcriptome sequencing analyses to find epigenetic indicators for age-related cataracts (ARC). Anterior lens capsule membrane tissues from young and aged mice were analyzed by MethylRAD-seq to detect the genome-wide methylation of extracted DNA. The young and aged mice had 76,524 and 15,608 differentially methylated CCGG and CCWGG sites, respectively. The Pearson correlation analysis detected 109 and 33 differentially expressed genes (DEGs) with negative methylation at CCGG and CCWGG sites, respectively, in their promoter regions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses showed that DEGs with abnormal methylation at CCGG sites were primarily associated with protein kinase C signaling (Akap12, Capzb), protein threonine kinase activity (Dmpk, Mapkapk3), and calcium signaling pathway (Slc25a4, Cacna1f), whereas DEGs with abnormal methylation at CCWGG sites were associated with ribosomal protein S6 kinase activity (Rps6ka3). These genes were validated by pyrosequencing methylation analysis. The results showed that the ARC group (aged mice) had lower Dmpk and Slc25a4 methylation levels and a higher Rps6ka3 methylation than the control group (young mice), which is consistent with the results of the joint analysis of differentially methylated and differentially expressed genes. In conclusion, we confirmed the genome-wide DNA methylation pattern and gene expression profile of ARC based on the mouse cataract model with aged mice. The identified methylation molecular markers have great potential for application in the future diagnosis and treatment of ARC.

Comparative transcriptomic and phenotypic analysis of monoclonal and polyclonal Populus deltoides genotypes

Populus species are highly valued for bioenergy and bioproducts due to their rapid growth and productivity. Polyclonal plantings, or mixtures of Populus clones, have shown the potential to enhance resource utilization and productivity, likely due to phenotypic differences arising from niche differentiation. In this study, we investigated gene expression and productivity in monoclonal and polyclonal stands of P. deltoides. Phenotypic results showed that polyclonal plots exhibited higher leaf area index (LAI; p < 0.01, 2.96 ± 0.057 m2) and total biomass (p < 0.01, 2.74 ± 0.06) compared to monoclonal plots, indicating superior productivity. RNA sequencing revealed upregulation of key genes such as exocyst subunit exo70 family protein H7 (EXO70H7), NDH-dependent cyclic electron flow 5 (NDF5), and expansin-like A3 (EXLA3). We also observed enrichment in phenylalanine metabolism and other secondary metabolic pathways in clone S7C8. Phenotypic results, upregulated genes and enriched biological pathways identified in this study may explain the enhanced productivity, increased nitrate content, and expanded canopy in polyclonal plantings. Overall, this study provides a foundation for future research to enhance forest productivity by linking molecular mechanisms to practical applications in field plantings.

Technical and Biological Biases in Bulk Transcriptomic Data Mining for Cancer Research

Cancer research has been significantly advanced by the integration of transcriptomic data through high-throughput sequencing technologies like RNA sequencing (RNA-seq). This paper reviews the transformative impact of transcriptomics on understanding cancer biology, focusing on the use of extensive datasets such as The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). While transcriptomic data provides crucial insights into gene expression patterns and disease mechanisms, the analysis is fraught with technical and biological biases. Technical biases include issues related to microarray, RNA-seq, and nanopore sequencing methods, while biological biases arise from factors like tumor heterogeneity and sample purity. Additionally, misinterpretations often occur when correlational data is erroneously assumed to imply causality or when bulk data is misattributed to specific cell types. This review emphasizes the need for researchers to understand and mitigate these biases to ensure accurate data interpretation and reliable clinical outcomes. By addressing these challenges, the paper aims to enhance the robustness of cancer research and improve the application of transcriptomic data in developing effective therapies and diagnostic tools.

Multi-Omics Research Reveals the Effects of the ABA-Regulated Phenylpropanoid Biosynthesis Pathway on the UV-B Response in Rhododendron chrysanthum Pall

The growing depletion of the ozone layer has led to increased ultraviolet B (UV-B) radiation, prompting plants like the alpine Rhododendron chrysanthum Pall. (R. chrysanthum) to adapt to these harsh conditions. This study explored how abscisic acid (ABA) signaling influences R. chrysanthum's metabolic responses under UV-B stress. R. chrysanthum was treated with UV-B radiation and exogenous ABA for widely targeted metabolomics, transcriptomics, and proteomics assays, and relevant chlorophyll fluorescence parameters were also determined. It was observed that UV-B stress negatively impacts the plant's photosynthetic machinery, disrupting multiple metabolic processes. Multi-omics analysis revealed that ABA application mitigates the detrimental effects of UV-B on photosynthesis and bolsters the plant's antioxidant defenses. Additionally, both UV-B exposure and ABA treatment significantly influenced the phenylpropanoid biosynthesis pathway, activating key enzyme genes, such as 4CL, CCR, and HCT. The study also highlighted the MYB-bHLH-WD40 (MBW) complex's role in regulating this pathway and its interaction with ABA signaling components. These findings underscore ABA's crucial function in improving plant resistance to UV-B stress and offer novel insights into plant stress biology.

Effect of leucine on mitochondria and oxidative stress to reduce virulence and pathogenicity of Acinetobacter baumannii

Elucidating the virulence mechanisms of A. baumannii is essential for developing strategies to mitigate pathogenicity. Although high-virulent strains are associated with increased mortality rate in severely infected patients, the underlying mechanisms remains not well understood. Our analysis revealed leucine as a pivotal biomarker, with the 11dP and paaK being significant contributors to virulence. The ATP-dependent activity and antioxidant activity were identified as the most important pathways in distinguishing the virulence of A. baumannii. Exogenous leucine was found to modulate mitochondria dysfunction and oxidative stress, thereby diminishing the pathogenicity of A. baumannii towards Beas 2B cells. Moreover, leucine reduced the virulence of A. baumannii to Galleria mellonella (G. mellonella) and alleviated pathological damage to lung tissues in mice. Our study offers a novel treatment strategy based on metabolomics, which may assist in the exploration and management of infections caused by highly virulent pathogens. It sets a new course for reducing the impact of highly virulent A. baumannii infections and has significant implications for the development of future therapeutic interventions.

Apoptosis-Inducing and Proliferation-Inhibiting Effects of Doramectin on Mz-ChA-1 Human Cholangiocarcinoma Cells

Cholangiocarcinoma is a malignant tumor that emerges in the intrahepatic or extrahepatic bile ducts. Doramectin (DOR), a third-generation derivative of avermectins (AVMs), is renowned for its low toxicity and high efficiency. However, no research has hitherto focused on the anti-cholangiocarcinoma effects of these drugs. In this study, we undertook a preliminary exploration of the mechanism through which DOR inhibits the viability of human cholangiocarcinoma cells (Mz-ChA-1) via transcriptome analysis and molecular validation at the cellular level. The results indicated that DOR could suppress the growth and proliferation of Mz-ChA-1 cells in a dose-dependent manner. Moreover, it significantly diminished their migration and invasion abilities. Cell cycle analysis disclosed arrest in the G1 phase, accompanied by an increase in p21 expression and a decrease in the levels of the cyclin E1 and CDK2 proteins. Additionally, DOR induced apoptosis via the ROS-triggered mitochondrial pathway. This was attested by an elevation in the BAX/BCL-2 ratio, the activation of caspase 3/7 and the cleavage of PARP1. These mechanistic insights underscore DOR's potential as a therapeutic agent against cholangiocarcinoma.

RNA-seq analysis and in vivo experiments identified the protective effect of kaempferol on idiopathic pulmonary fibrosis by regulating the PPARG/TNC signaling pathway to reduce ECM deposition

Idiopathic pulmonary fibrosis (IPF) is a chronic age-related lung disease with a high mortality rate. Kaempferol (KMP), an active ingredient in common plants and foods with anti-inflammatory, antioxidant and immunomodulatory properties, has been shown to be effective against fibrotic diseases. However, the molecular mechanisms underlying the treatment of IPF with KMP remain unclear. Therefore, IPF mice were established by intratracheal instillation of bleomycin (BLM) to explore the efficacy and underlying mechanism of KMP in the treatment of IPF. We found that KMP improved the body weight changes of BLM-induced IPF mice, alleviated inflammatory infiltration and collagen deposition, and decreased the expression levels of hydroxyproline, α-SMA, Col3a1, Mmp2, Timp1, Vim, Fn, TNF-α, TGF-β1, IL-6 and IL-8, while up-regulating the expression E-cadherin in lung tissues. The transcriptomic results showed that KMP may exert therapeutic effects against IPF by regulating the PPARG/TNC signaling pathway to reduce extracellular matrix (ECM) deposition. Interestingly, ROC curve analysis suggested that TNC and PPARG had good diagnostic performance for IPF, and TF prediction revealed that PPARG is an important upstream gene regulating TNC, and the IF experiment confirmed the co-localization of TNC and PPARG. Molecular docking showed that KMP bound well to PPARG and TNC, and IF results revealed that KMP significantly reduced the interaction between PPARG and TNC. Furthermore, RT-PCR, WB, IHC and IF experiments confirmed that KMP elevated the expression of PPARG and inhibited the expression of TNC, thus inhibiting the ECM-receptor interaction pathway and ultimately serving as a therapeutic treatment for IPF mice. These findings revealed that KMP reduced inflammatory infiltration and collagen deposition in the lungs of IPF mice and that the PPARG/TNC signaling pathway may be an important mechanism for the treatment of IPF with KMP, which provides a new perspective for the development of therapeutic approaches for IPF.

Construction of a cell cycle-specific lncRNA-miRNA-mRNA network reveals novel key lncRNAs in colorectal cancer

OBJECTIVE

The current study aimed to determine the roles of pivotal and novel lncRNAs associated with the cell cycle in the occurrence and development of Colorectal cancer (CRC).

METHODS

The TCGA-COAD project related to CRC was downloaded, and differential expression analysis was performed to identify differentially expressed lncRNAs, miRNAs, and mRNAs. A cell cycle-associated lncRNA-miRNA-mRNA regulatory network was constructed, and two novel lncRNAs were selected. Two subnetworks were constructed for selected lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were illustrated for the genes in each sub-network. qPCR analysis was used to validate the expression levels of the selected lncRNAs in CRC tissues compared to those adjacent normal tissues.

RESULTS

The differential expression analysis identified 416 lncRNAs, 317 miRNAs, and 117 mRNAs. The ceRNA subnetwork genes were associated with different pathways, including cellular senescence, DNA replication, human T-cell leukemia virus 1 infection, and oocyte meiosis. The bioinformatic results based on the TCGA project indicated the dysregulation of two novel lncRNAs, MIR29B2CHG and HELLPAR, in CRC tissues compared to adjacent normal tissues. Moreover, qPCR confirmed the dysregulation of lncRNAs in the CRC tissues. ROC curves revealed that both selected lncRNAs had acceptable specificity and sensitivity as biomarkers.

CONCLUSION

In conclusion, novel cell cycle-associated lncRNAs have the potential to be understood as the underlying molecular mechanisms that influence CRC. Therefore, these lncRNAs can be considered as promising biomarkers for the diagnosis and treatment of CRC.

Whole-transcriptome analysis reveals the effect of retinoic acid on small intestinal mucosal injury in cage-stressed young laying ducks

Retinoic acid (RA) is an active derivative of vitamin A and is involved in a variety of physiological processes, including cell growth, antioxidant, and inflammation. However, the role of RA in intestinal oxidative stress injury in caged-stressed laying ducks is unknown. In this study, we analyzed the effect and underlying mechanism of RA supplementation on intestinal damage in cage-stressed young laying ducks. One hundred and sixty laying ducks were divided into 5 treatment groups, including a control group (CR) and 4 treatment groups exposed to different RA concentrations (2,500, 5,000, 7,500 and 10,000 IU/kg, TG1 to TG4). The experimental period comprised a 7-d prefeeding period and a 10-d experimental feeding period, for a total of 17 d. Phenotypic analysis revealed that compared with the control group, RA addition increased the intestinal villus height and the villus-to-crypt ratio; decreased the crypt depth (P < 0.01); decreased the serum diamine oxidase and D-lactate concentrations (P < 0.05); increased the serum antioxidant capacity and intestinal antioxidant gene expression levels (P < 0.05); and increased the expression levels of tight junction-related genes, with the greatest effect observed in TG2 group. Our further whole-transcriptome analysis of duodenum tissues from CR and TG2 ducks revealed 706 differentially expressed mRNAs (DEmRNAs), 357 differentially expressed lncRNAs (DElncRNAs), 14 differentially expressed circRNAs (DEcircRNAs), and 4 differentially expressed miRNAs (DEmiRNAs). These DEGs are involved in calcium signaling, NOD-like receptor signaling, pyruvate metabolism, Jak-STAT signaling, Wnt signaling, riboflavin metabolism, and the adherens junction and tight junction pathways. The results of omics and marker gene expression analysis suggested that RA treatment may play a role in endoplasmic reticulum stress (ERS) and apoptosis. In conclusion, the addition of RA to the diet improved intestinal injury by improving the redox homeostasis of intestinal cells associated with ERS, enhancing the intestinal tight junction structure and alleviating the apoptosis of intestinal epithelial cells; moreover, 5,000 IU/kg RA was determined to be the most appropriate concentration for supplementation.

Transcriptomic era of cancers in females: new epigenetic perspectives and therapeutic prospects

In the era of transcriptomics, the role of epigenetics in the study of cancers in females has gained increasing recognition. This article explores the impact of epigenetic modifications, such as DNA methylation, histone modification, and non-coding RNA, on cancers in females, including breast, cervical, and ovarian cancers (1). Our findings suggest that these epigenetic markers not only influence tumor onset, progression, and metastasis but also present novel targets for therapeutic intervention. Detailed analyses of DNA methylation patterns have revealed aberrant events in cancer cells, particularly promoter region hypermethylation, which may lead to silencing of tumor suppressor genes. Furthermore, we examined the complex roles of histone modifications and long non-coding RNAs in regulating the expression of cancer-related genes, thereby providing a scientific basis for developing targeted epigenetic therapies. Our research emphasizes the importance of understanding the functions and mechanisms of epigenetics in cancers in females to develop effective treatment strategies. Future therapeutic approaches may include drugs targeting specific epigenetic markers, which could not only improve therapeutic outcomes but also enhance patient survival and quality of life. Through these efforts, we aim to offer new perspectives and hope for the prevention, diagnosis, and treatment of cancers in females.

Super-resolution ultrasound and microvasculomics: a consensus statement

This is a summary of a consensus statement on the introduction of "Ultrasound microvasculomics" produced by The Chinese Artificial Intelligence Alliance for Thyroid and Breast Ultrasound. The evaluation of microvessels is a very important part for the assessment of diseases. Super-resolution ultrasound (SRUS) microvascular imaging surpasses traditional ultrasound imaging in the morphological and functional analysis of microcirculation. SRUS microvascular imaging relies on contrast microbubbles to gain sensitivity to microvessels and improves the spatial resolution of ultrasound blood flow imaging for a more detailed depiction of vascular structures and hemodynamics. This method has been applied in preclinical animal models and pilot clinical studies, involving areas including neurology, oncology, nephrology, and cardiology. However, the current quantitative parameters of SRUS images are not enough for precise evaluation of microvessels. Therefore, by employing omics methods, more quantification indicators can be obtained, enabling a more precise and personalized assessment of microvascular status. Ultrasound microvasculomics - a high-throughput extraction of image features from SRUS images - is one novel approach that holds great promise but needs further validation in both bench and clinical settings. CLINICAL RELEVANCE STATEMENT: Super-resolution Ultrasound (SRUS) blood flow imaging improves spatial resolution. Ultrasound microvasculomics is possible to acquire high-throughput information of features from SRUS images. It provides more precise and abundant micro-blood flow information in clinical medicine. KEY POINTS: This consensus statement reviews the development and application of super-resolution ultrasound (SRUS). The shortcomings of the current quantification indicators of SRUS and strengths of the omics methodology are addressed. "Ultrasound microvasculomics" is introduced for a high-throughput extraction of image features from SRUS images.

Individualized responses to acupuncture in premature ovarian insufficiency: A study protocol for a nested case-control trial with transcriptome analysis

Background

Premature ovarian insufficiency (POI), a modifiable cause of infertility with substantial implications for women's well-being, prompts the exploration of efficacious adjunctive treatments. Acupuncture emerges as a promising therapeutic avenue; however, the nuanced effects of acupuncture in POI warrant more comprehensive investigation. The intricate mechanisms dictating individualized responses remain elusive. This trial seeks to assess the effectiveness of acupuncture as an adjunctive treatment for POI, concurrently delving into the impact of transcriptome analysis on peripheral blood to unravel the underpinnings of these individual variations. The overarching objective is to enrich our comprehension of acupuncture's therapeutic potential in the context of POI, with a view to advancing holistic patient care.

Methods/design

Constituting an open-label, nested case-control study, this research endeavors to enroll 108 women diagnosed with POI. Participants will be randomly assigned in a 1:1 ratio to either the study group or the control group, each comprising 54 subjects. Ten patients from each group meeting specific criteria will partake in transcriptome analysis. An additional 10 subjects meeting the study criteria will form a healthy control group. The study group will exclusively undergo acupuncture treatment, while the control group will solely receive Fenmutong. Acupuncture sessions, administered thrice weekly across three menstrual cycles from the fifth day of menstruation, constitute the intervention. Primary outcome measurement rests on Follicle-Stimulating Hormone (FSH) levels, supplemented by secondary assessments encompassing biometric features, hormone biomarkers, anxiety and depression scores, and transcriptome analysis. Baseline measurements precede intervention, with post-intervention evaluations following. The study endeavors to discern specific genes linked to individualized responses to acupuncture. Data analysis, employing SPSS 25.0 software, incorporates a meticulous examination of peripheral blood samples for transcriptome analysis. The investigation aspires to shed light on genetic determinants influencing the effects of acupuncture on women with POI, thereby fostering elevated standards in patient care and management.

Discussion

This study pivots on the principal objective of scrutinizing the efficacy of acupuncture as an adjunctive treatment for POI. Beyond effectiveness, it undertakes an exploration of the intricate mechanisms underlying the diverse responses exhibited by individuals in the context of acupuncture, augmenting the depth of understanding in this therapeutic domain.

Selection and Regulatory Network Analysis of Differential CircRNAs in the Hypothalamus of Goats with High and Low Reproductive Capacity

The objectives of this investigation were to identify differentially expressed circular RNAs (circRNAs) in the hypothalamus of goats with high and low prolificacy and construct a circRNA-mRNA regulatory network to uncover key potential circRNAs that influence goat prolificacy. Transcriptome analysis was performed on hypothalamus samples from low-prolificacy (n = 5) and high-prolificacy (n = 6) Chuanzhong black goats to identify circRNAs that influence prolificacy in these goats. Differential expression analysis identified a total of 205 differentially expressed circRNAs, comprising 100 upregulated and 105 downregulated circRNAs in the high-prolificacy group compared with the low-prolificacy group. Enrichment analysis of these differentially expressed circRNAs indicated significant enrichment in Gene Ontology terms associated with mammalian oogenesis, negative regulation of neurotransmitter secretion, reproductive developmental processes, hormone-mediated signaling pathways, and negative regulation of hormone secretion. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlighted significant enrichment in the oxytocin signaling pathway, GnRH signaling pathway, and hormone-mediated oocyte maturation. The hypothalamus of low- and high-prolificacy goats contains circular RNAs (circRNAs), including chicirc_063269, chicirc_097731, chicirc_017440, chicirc_049641, chicirc_008429, chicirc_145057, chicirc_030156, chicirc_109497, chicirc_030156, chicirc_176754, and chicirc_193363. Chuanzhong black goats have the potential to influence prolificacy by modulating the release of serum hormones from the hypothalamus. A circRNA-miRNA regulatory network was constructed, which determined that miR-135a, miR-188-3p, miR-101-3p, and miR-128-3p may interact with differentially expressed circRNAs, thereby regulating reproductive capacity through the hypothalamic-pituitary-gonadal axis. The results of this study enhance our knowledge of the molecular mechanisms that regulate prolificacy in Chuanzhong black goats at the hypothalamic level.

Importance of Transcript Variants in Transcriptome Analyses

RNA sequencing (RNA-Seq) has become a widely adopted technique for studying gene expression. However, conventional RNA-Seq analyses rely on gene expression (GE) values that aggregate all the transcripts produced under a single gene identifier, overlooking the complexity of transcript variants arising from different transcription start sites or alternative splicing. Transcript variants may encode proteins with diverse functional domains, or noncoding RNAs. This study explored the implications of neglecting transcript variants in RNA-Seq analyses. Among the 1334 transcription factor (TF) genes expressed in mouse embryonic stem (ES) or trophoblast stem (TS) cells, 652 were differentially expressed in TS cells based on GE values (365 upregulated and 287 downregulated, ≥absolute 2-fold changes, false discovery rate (FDR) p-value ≤ 0.05). The 365 upregulated genes expressed 883 transcript variants. Further transcript expression (TE) based analyses identified only 174 (<20%) of the 883 transcripts to be upregulated. The remaining 709 transcripts were either downregulated or showed no significant changes. Meanwhile, the 287 downregulated genes expressed 856 transcript variants and only 153 (<20%) of the 856 transcripts were downregulated. The other 703 transcripts were either upregulated or showed no significant change. Additionally, the 682 insignificant TF genes (GE values < absolute 2-fold changes and/or FDR p-values > 0.05) between ES and TS cells expressed 2215 transcript variants. These included 477 (>21%) differentially expressed transcripts (276 upregulated and 201 downregulated, ≥absolute 2-fold changes, FDR p-value ≤ 0.05). Hence, GE based RNA-Seq analyses do not represent accurate expression levels due to divergent transcripts expression from the same gene. Our findings show that by including transcript variants in RNA-Seq analyses, we can generate a precise understanding of a gene's functional and regulatory landscape; ignoring the variants may result in an erroneous interpretation.

Transcriptomics reveals that NAD(P)H affects the development of the Zig-zag eel (Mastacembelus armatus ♀) × Spiny eel (Sinobdella sinensis ♂) hybrid offspring leading to low hatching rates

Zig-zag eel (Mastacembelus armatus (2 n = 48)) and Spiny eel (Sinobdella sinensis (2 n = 48)) are two species of the Mastacembelidae family commonly found in southern China. Hybridization between the two has a very high deformity rate and a very low hatching rate. In order to investigate the reasons for this, the first hybridization between M. armatus and S. sinensis was carried out using artificial insemination, and the embryonic development of the hybrid offspring was examined using microphotography, and the malformations of the hybrid offspring were investigated by transcriptomics. The experiments showed that the average egg production was 4265.7 ± 322.94 (Mean ± SD), the average fertilization rate of hybrid offspring was 98.67 ± 0.58 % (Mean ± SD), the hatching rate was 12.06 ± 3.44 % (Mean ± SD), the deformity rate was 98.15 ± 3.21 % (Mean ± SD), and the embryonic development successively went through the five main stages of fertilized egg, egg cleavage, embryo formation, organogenesis, and exertion of membranes. Transcriptomics showed that the expression of NAD(P)H-related enzyme activity DEGs was increased, and many DEGs related to cell signaling molecule transmission and metabolic regulation are enriched in KEGG pathways, such as IL-17 signaling pathway, Osteoclast differentiation, TNF signaling pathway and MAPK signaling pathway. etc. The major types of DEGs corresponded to those coding for proteins. This study suggests that the high malformation rate in hybrid offspring may be caused by impaired synthesis of proteins during embryonic development.

Screening for Genes Related to Meat Production Traits in Duroc × Bama Xiang Crossbred Pigs by Whole Transcriptome Sequencing

The meat production traits of pigs are influenced by the expression regulation of multiple gene types, including mRNAs, miRNAs, and lncRNAs. To study the differences in meat production traits at the transcriptional level among individuals with different growth rates, the longissimus dorsi samples from eight Duroc × Bama Xiang F2 crossbred pigs with a fast growth rate (high gTroup) or a slow growth rate (low group) were selected to perform whole transcriptome sequencing and ceRNA regulatory network construction. This study first analyzed the differences in physiological and biochemical indicators, muscle histological characteristics, and muscle fiber types. A total of 248 mRNAs, 25 miRNAs, and 432 lncRNAs were identified as differentially expressed by whole transcriptome sequencing. Key genes that may influence meat production traits include MTMR14, PPP1R3A, PYGM, PGAM2, MYH1, and MYH7. The ceRNA regulatory network map showed that ENSSSCG00000042061-ssc-mir-208b-MYH7, ENSSSCG00000042223-ssc-mir-146a-MTMR14, ENSSSCG00000045539-ssc-mir-9-3-MYH1, and ENSSSCG00000047852-ssc-mir-103-1-PPP1R3A may be the key factors affecting meat production traits through their regulatory relationships. This study provides valuable insights into the molecular mechanisms underlying porcine muscle development and can aid in improving meat production traits.

Identification of relevant differential genes to the divergent development of pectoral muscle in ducks by transcriptomic analysis

OBJECTIVE

The objective of this study was to identify candidate genes that play important roles in skeletal muscle development in ducks.

METHODS

In this study, we investigated the transcriptional sequencing of embryonic pectoral muscles from two specialized lines: Liancheng white ducks (female) and Cherry valley ducks (male) hybrid Line A (LCA) and Line C (LCC) ducks. In addition, prediction of target genes for the differentially expressed mRNAs was conducted and the enriched gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes signaling pathways were further analyzed. Finally, a protein-to-protein interaction network was analyzed by using the target genes to gain insights into their potential functional association.

RESULTS

A total of 1,428 differentially expressed genes (DEGs) with 762 being up-regulated genes and 666 being down-regulated genes in pectoral muscle of LCA and LCC ducks identified by RNA-seq (p<0.05). Meanwhile, 23 GO terms in the down-regulated genes and 75 GO terms in up-regulated genes were significantly enriched (p<0.05). Furthermore, the top 5 most enriched pathways were ECM-receptor interaction, fatty acid degradation, pyruvate degradation, PPAR signaling pathway, and glycolysis/gluconeogenesis. Finally, the candidate genes including integrin b3 (Itgb3), pyruvate kinase M1/2 (Pkm), insulinlike growth factor 1 (Igf1), glucose-6-phosphate isomerase (Gpi), GABA type A receptorassociated protein-like 1 (Gabarapl1), and thyroid hormone receptor beta (Thrb) showed the most expression difference, and then were selected to verification by quantitative realtime polymerase chain reaction (qRT-PCR). The result of qRT-PCR was consistent with that of transcriptome sequencing.

CONCLUSION

This study provided information of molecular mechanisms underlying the developmental differences in skeletal muscles between specialized duck lines.

Single-cell RNA sequencing reveals that NRF2 regulates vascular smooth muscle cell phenotypic switching in abdominal aortic aneurysm

Abdominal aortic aneurysm (AAA) is a life-threatening disease characterized by extensive membrane destruction in the vascular wall that is closely associated with vascular smooth muscle cell (VSMC) phenotypic switching. A thorough understanding of the changes in regulatory factors during VSMC phenotypic switching is essential for managing AAA therapy. In this study, we revealed the impact of NRF2 on the modulation of VSMC phenotype and the development of AAA based on single-cell RNA sequencing analysis. By utilizing a murine model of VSMC-specific knockout of nuclear factor E2-related factor 2 (NRF2), we observed that the absence of NRF2 in VSMCs exacerbated AAA formation in an angiotensin II-induced AAA model. The downregulation of NRF2 promoted VSMC phenotypic switching, leading to an enhanced inflammatory response. Through genome-wide transcriptome analysis and loss- or gain-of-function experiments, we discovered that NRF2 upregulated the expression of VSMC contractile phenotype-specific genes by facilitating microRNA-145 (miR-145) expression. Our data identified NRF2 as a novel regulator involved in maintaining the VSMC contractile phenotype while also influencing AAA formation through an miR-145-dependent regulatory mechanism.

Multi-omics based artificial intelligence for cancer research

With significant advancements of next generation sequencing technologies, large amounts of multi-omics data, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, have been accumulated, offering an unprecedented opportunity to explore the heterogeneity and complexity of cancer across various molecular levels and scales. One of the promising aspects of multi-omics lies in its capacity to offer a holistic view of the biological networks and pathways underpinning cancer, facilitating a deeper understanding of its development, progression, and response to treatment. However, the exponential growth of data generated by multi-omics studies present significant analytical challenges. Processing, analyzing, integrating, and interpreting these multi-omics datasets to extract meaningful insights is an ambitious task that stands at the forefront of current cancer research. The application of artificial intelligence (AI) has emerged as a powerful solution to these challenges, demonstrating exceptional capabilities in deciphering complex patterns and extracting valuable information from large-scale, intricate omics datasets. This review delves into the synergy of AI and multi-omics, highlighting its revolutionary impact on oncology. We dissect how this confluence is reshaping the landscape of cancer research and clinical practice, particularly in the realms of early detection, diagnosis, prognosis, treatment and pathology. Additionally, we elaborate the latest AI methods for multi-omics integration to provide a comprehensive insight of the complex biological mechanisms and inherent heterogeneity of cancer. Finally, we discuss the current challenges of data harmonization, algorithm interpretability, and ethical considerations. Addressing these challenges necessitates a multidisciplinary collaboration, paving the promising way for more precise, personalized, and effective treatments for cancer patients.

LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue

Whole transcriptome analysis (WTA) using RNA extracted from Formalin Fixed Paraffin Embedded (FFPE) tissue is an invaluable tool to understand the molecular pathology of disease. RNA extracted from FFPE tissue is either degraded and/or in very low quantities hampering gene expression analysis. Earlier studies described protocols applied for cellular RNA using poly-A primer-based linear amplification. The current study describes a method, LINCATRA (LINear amplifiCAtion of RNA for whole TRAnscriptome analysis). It employs random nonamer primer based method which can amplify short, fragmented RNA with high fidelity from as low as 5 ng to obtain enough material for WTA. The two-cycle method significantly amplified RNA at ∼1000 folds (p < 0.0001) improving the mean read lengths (p < 0.05) in WTA. Overall, increased mean read length positively correlated with on-target reads (Pearson's r = 0.71, p < 0.0001) in both amplified and unamplified RNA-seq analysis. Gene expression analysis compared between unamplified and amplified group displayed substantial overlap of the differentially expressed genes (DEGs) (log2 fold change cut-off < -2 and >2, p < 0.05) identified between lung cancer and asthma cohorts validating the method developed. This method is applicable in clinical molecular pathology field for both diagnostics and elucidation of disease mechanisms.

Elucidating the hepatoprotective mechanisms of cholic acid against CCl4-Induced acute liver injury: A transcriptomic and metabolomic study

ETHNOPHARMACOLOGICAL RELEVANCE

Cholic acid (CA) is one of the main active ingredients in Calculus Bovis, a traditional Chinese medicine, which helps to regulate the heart and liver meridians, clearing the heart, opening the mouth, cooling the liver and calming the wind. However, the molecular mechanism of its liver protective effect is still unclear.

AIM OF THE STUDY

Growing attention has been directed towards traditional Chinese medicine (TCM), particularly Calculus Bovis, as a potential solution for liver protection. Despite this interest, a comprehensive understanding of its hepatoprotective mechanisms remains lacking. This research seeks to explore the potential protective properties of cholic acid (CA) against CCl4-induced acute liver injury (ALI) in mice, while also examining the mechanisms involved.

MATERIALS AND METHODS

In the experiment, a mouse model was employed to ALI using CCl4, and the potential therapeutic effects of orally administered CA at varying doses (15, 30, and 60 mg/kg) were assessed. The study employed a multi-faceted approach, integrating liver transcriptomics with serum metabolomics, and conducting thorough analyses of serum biochemical markers and liver histopathological sections.

RESULTS

Oral CA administration markedly reduced the organ indices of the liver, spleen, and thymus in comparison with the model group. It also elevated the expression of superoxide dismutase (SOD) in serum while diminishing the concentrations of ALT, AST, MDA, IL-6, and TNF-α. Moreover, CA ameliorated the pathological damage induced by CCl4. Integrated metabolomic and transcriptomic analyses indicated that the hepatoprotective action of CA on ALI is mediated through the modulation of lipid metabolic pathways-specifically, metabolisms of glycerophospholipid, arachidonic acid, as well as linoleic acid-and by altering the expression of genes such as Ptgr1, PLpp1, Tbxas1, and Cyp2c37.

CONCLUSIONS

The current investigation offers insights into the hepatoprotective mechanisms by which CA mitigates ALI caused by CCl4 exposure, thus supporting the further evaluation and development of CA-based therapeutics for ALI.

Identification of diagnostic biomarkers and potential therapeutic targets for biliary atresia via WGCNA and machine learning methods

Biliary atresia (BA) is a severe and progressive biliary obstructive disease in infants that requires early diagnosis and new therapeutic targets. This study employed bioinformatics methods to identify diagnostic biomarkers and potential therapeutic targets for BA. Our analysis of mRNA expression from Gene Expression Omnibus datasets revealed 3,273 differentially expressed genes between patients with BA and those without BA (nBA). Weighted gene coexpression network analysis determined that the turquoise gene coexpression module, consisting of 298 genes, is predominantly associated with BA. The machine learning method then filtered out the top 2 important genes, CXCL8 and TMSB10, from the turquoise module. The area under receiver operating characteristic curves for TMSB10 and CXCL8 were 0.961 and 0.927 in the training group and 0.819 and 0.791 in the testing group, which indicated a high diagnostic value. Besides, combining TMSB10 and CXCL8, a nomogram with better diagnostic performance was built for clinical translation. Several studies have highlighted the potential of CXCL8 as a therapeutic target for BA, while TMSB10 has been shown to regulate cell polarity, which was related to BA progression. Our analysis with qRT PCR and immunohistochemistry also confirmed the upregulation of TMSB10 at mRNA and protein levels in BA liver samples. These findings highlight the sensitivity of CXCL8 and TMSB10 as diagnostic biomarkers and their potential as therapeutic targets for BA.

The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcoma

Osteosarcoma is a form of bone cancer that predominantly impacts osteoblasts, the cells responsible for creating fresh bone tissue. Typical indications include bone pain, inflammation, sensitivity, mobility constraints, and fractures. Utilising imaging techniques such as X-rays, MRI scans, and CT scans can provide insights into the size and location of the tumour. Additionally, a biopsy is employed to confirm the diagnosis. Analysing genes with distinct expression patterns unique to osteosarcoma can be valuable for early detection and the development of effective treatment approaches. In this research, we comprehensively examined the entire transcriptome and pinpointed genes with altered expression profiles specific to osteosarcoma. The study mainly aimed to identify the molecular fingerprint of osteosarcoma. In this study, we processed 90 FFPE samples from PathWest with an almost equal number of osteosarcoma and healthy tissues. RNA was extracted from Paraffin-embedded tissue; RNA was sequenced, the sequencing data was analysed, and gene expression was compared to the healthy samples of the same patients. Differentially expressed genes in osteosarcoma-derived samples were identified, and the functions of those genes were explored. This result was combined with our previous studies based on FFPE and fresh samples to perform a meta-analysis. We identified 1,500 identical differentially expressed genes in PathWest osteosarcoma samples compared to normal tissue samples of the same patients. Meta-analysis with combined fresh tissue samples identified 530 differentially expressed genes. IFITM5, MMP13, PANX3, and MAGEA6 were some of the most overexpressed genes in osteosarcoma samples, while SLC4A1, HBA1, HBB, AQP7 genes were some of the top downregulated genes. Through the meta-analysis, 530 differentially expressed genes were identified to be identical among FFPE (105 FFPE samples) and 36 fresh bone samples. Deconvolution analysis with single-cell RNAseq data confirmed the presence of specific cell clusters in FFPE samples. We propose these 530 DEGs as a molecular fingerprint of osteosarcoma.

Uncovering periodontitis-associated markers through the aggregation of transcriptomics information from diverse sources

Introduction

Periodontitis, a common chronic inflammatory disease, significantly impacted oral health. To provide novel biological indicators for the diagnosis and treatment of periodontitis, we analyzed public microarray datasets to identify biomarkers associated with periodontitis.

Method

The Gene Expression Omnibus (GEO) datasets GSE16134 and GSE106090 were downloaded. We performed differential analysis and robust rank aggregation (RRA) to obtain a list of differential genes. To obtain the core modules and core genes related to periodontitis, we evaluated differential genes through enrichment analysis, correlation analysis, protein-protein interaction (PPI) network and competing endogenous RNA (ceRNA) network analysis. Potential biomarkers for periodontitis were identified through comparative analysis of dual networks (PPI network and ceRNA network). PPI network analysis was performed in STRING. The ceRNA network consisted of RRA differentially expressed messenger RNAs (RRA_DEmRNAs) and RRA differentially expressed long non-coding RNAs (RRA_DElncRNAs), which regulated each other's expression by sharing microRNA (miRNA) target sites.

Results

RRA_DEmRNAs were significantly enriched in inflammation-related biological processes, osteoblast differentiation, inflammatory response pathways and immunomodulatory pathways. Comparing the core ceRNA module and the core PPI module, C1QA, CENPK, CENPU and BST2 were found to be the common genes of the two core modules, and C1QA was highly correlated with inflammatory functionality. C1QA and BST2 were significantly enriched in immune-regulatory pathways. Meanwhile, LINC01133 played a significant role in regulating the expression of the core genes during the pathogenesis of periodontitis.

Conclusion

The identified biomarkers C1QA, CENPK, CENPU, BST2 and LINC01133 provided valuable insight into periodontitis pathology.

Multi-OMICS approaches in cancer biology: New era in cancer therapy

Innovative multi-omics frameworks integrate diverse datasets from the same patients to enhance our understanding of the molecular and clinical aspects of cancers. Advanced omics and multi-view clustering algorithms present unprecedented opportunities for classifying cancers into subtypes, refining survival predictions and treatment outcomes, and unravelling key pathophysiological processes across various molecular layers. However, with the increasing availability of cost-effective high-throughput technologies (HTT) that generate vast amounts of data, analyzing single layers often falls short of establishing causal relations. Integrating multi-omics data spanning genomes, epigenomes, transcriptomes, proteomes, metabolomes, and microbiomes offers unique prospects to comprehend the underlying biology of complex diseases like cancer. This discussion explores algorithmic frameworks designed to uncover cancer subtypes, disease mechanisms, and methods for identifying pivotal genomic alterations. It also underscores the significance of multi-omics in tumor classifications, diagnostics, and prognostications. Despite its unparalleled advantages, the integration of multi-omics data has been slow to find its way into everyday clinics. A major hurdle is the uneven maturity of different omics approaches and the widening gap between the generation of large datasets and the capacity to process this data. Initiatives promoting the standardization of sample processing and analytical pipelines, as well as multidisciplinary training for experts in data analysis and interpretation, are crucial for translating theoretical findings into practical applications.

Molecular mechanism of RBM14-mediated promotion of proliferation, migration, and invasion in osteosarcoma

BACKGROUND

Osteosarcoma (OS) is an exceptionally aggressive bone neoplasm that predominantly impacts the paediatric and adolescent population, exhibiting unfavourable prognosis. The importance of RNA binding motif protein 14 (RBM14) in the aetiology of OS is not well understood, despite its established involvement in several other types of cancer.

METHODS

In this study, we conducted an analysis of the expression profiles of RBM14 in cancer tissues and cell lines. To achieve this, we will utilised data obtained from various databases including The Cancer Genome Atlas Program (TCGA) project, The Genotype-Tissue Expression (GTEx) Project, Gene Expression Omnibus (GEO) database, and cancer cell line encyclopedia (CCLE) data. Furthermore, this study also aims to examine the effects of RBM14 on the proliferation, migration, and invasive properties of OS cells using cell functional gain and loss studies. In this study, we carried out an in-depth investigation to explore possible molecular pathways that underlie the regulation of the malignant phenotype found in OS by RBM14. This investigation involved integrating data from RBM14 overexpression, RBM14 knockdown RNA-seq experiments, and an array comprising 6,096 perturbed genes obtained from the Genetic Perturbation Similarity Analysis Database (GPSAdb). This research offers an opportunity to build a robust conceptual framework for the potential advancement of novel therapeutic approaches that are especially aimed at attacking OS.

RESULTS

RBM14 plays an active role in OS by significantly contributing to the enhancement of cellular proliferation, migration, and invasion. At the molecular level, it is probable that RBM14 exerts control over the malignant characteristics of OS through its modulation of the Hippo signalling system.

CONCLUSIONS

The above-mentioned findings underscore the significant importance of RBM14 as an intriguing target for therapy for the mitigation and management of OS. This particular protein holds an excellent opportunity for the development of novel and efficacious therapeutic approaches that possess the potential to yield favorable results for patients affected with OS.

Transcriptome profiling of immune rejection mechanisms in a porcine vascularized composite allotransplantation model

Background

Vascularized composite allotransplantation (VCA) offers the potential for a biological, functional reconstruction in individuals with limb loss or facial disfigurement. Yet, it faces substantial challenges due to heightened immune rejection rates compared to solid organ transplants. A deep understanding of the genetic and immunological drivers of VCA rejection is essential to improve VCA outcomes.

Methods

Heterotopic porcine hindlimb VCA models were established and followed until reaching the endpoint. Skin and muscle samples were obtained from VCA transplant recipient pigs for histological assessments and RNA sequencing analysis. The rejection groups included recipients with moderate pathological rejection, treated locally with tacrolimus encapsulated in triglycerol-monostearate gel (TGMS-TAC), as well as recipients with severe end-stage rejection presenting evident necrosis. Healthy donor tissue served as controls. Bioinformatics analysis, immunofluorescence, and electron microscopy were utilized to examine gene expression patterns and the expression of immune response markers.

Results

Our comprehensive analyses encompassed differentially expressed genes, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathways, spanning various composite tissues including skin and muscle, in comparison to the healthy control group. The analysis revealed a consistency and reproducibility in alignment with the pathological rejection grading. Genes and pathways associated with innate immunity, notably pattern recognition receptors (PRRs), damage-associated molecular patterns (DAMPs), and antigen processing and presentation pathways, exhibited upregulation in the VCA rejection groups compared to the healthy controls. Our investigation identified significant shifts in gene expression related to cytokines, chemokines, complement pathways, and diverse immune cell types, with CD8 T cells and macrophages notably enriched in the VCA rejection tissues. Mechanisms of cell death, such as apoptosis, necroptosis and ferroptosis were observed and coexisted in rejected tissues.

Conclusion

Our study provides insights into the genetic profile of tissue rejection in the porcine VCA model. We comprehensively analyze the molecular landscape of immune rejection mechanisms, from innate immunity activation to critical stages such as antigen recognition, cytotoxic rejection, and cell death. This research advances our understanding of graft rejection mechanisms and offers potential for improving diagnostic and therapeutic strategies to enhance the long-term success of VCA.

Comparative transcriptomics analysis reveals defense mechanisms of Manihot esculenta Crantz against Sri Lanka Cassava MosaicVirus

BACKGROUND

Cassava mosaic disease (CMD), caused by Sri Lankan cassava mosaic virus (SLCMV) infection, has been identified as a major pernicious disease in Manihot esculenta Crantz (cassava) plantations. It is widespread in Southeast Asia, especially in Thailand, which is one of the main cassava supplier countries. With the aim of restricting the spread of SLCMV, we explored the gene expression of a tolerant cassava cultivar vs. a susceptible cassava cultivar from the perspective of transcriptional regulation and the mechanisms underlying plant immunity and adaptation.

RESULTS

Transcriptomic analysis of SLCMV-infected tolerant (Kasetsart 50 [KU 50]) and susceptible (Rayong 11 [R 11]) cultivars at three infection stages-that is, at 21 days post-inoculation (dpi) (early/asymptomatic), 32 dpi (middle/recovery), and 67 dpi (late infection/late recovery)-identified 55,699 expressed genes. Differentially expressed genes (DEGs) between SLCMV-infected KU 50 and R 11 cultivars at (i) 21 dpi to 32 dpi (the early to middle stage), and (ii) 32 dpi to 67 dpi (the middle stage to late stage) were then identified and validated by real-time quantitative PCR (RT-qPCR). DEGs among different infection stages represent genes that respond to and regulate the viral infection during specific stages. The transcriptomic comparison between the tolerant and susceptible cultivars highlighted the role of gene expression regulation in tolerant and susceptible phenotypes.

CONCLUSIONS

This study identified genes involved in epigenetic modification, transcription and transcription factor activities, plant defense and oxidative stress response, gene expression, hormone- and metabolite-related pathways, and translation and translational initiation activities, particularly in KU 50 which represented the tolerant cultivar in this study.

Whole transcriptome profiling reveals a lncMDP1 that regulates myogenesis by adsorbing miR-301a-5p targeting CHAC1

Myoblast proliferation and differentiation are essential for skeletal muscle development. In this study, we generated the expression profiles of mRNAs, long noncoding RNAs (lncRNAs), and microRNAs (miRNAs) in different developmental stages of chicken primary myoblasts (CPMs) using RNA sequencing (RNA-seq) technology. The dual luciferase reporter system was performed using chicken embryonic fibroblast cells (DF-1), and functional studies quantitative real-time polymerase chain reaction (qPCR), cell counting kit-8 (CCK-8), 5-Ethynyl-2'-deoxyuridine (EdU), flow cytometry cycle, RNA fluorescence in situ hybridization (RNA-FISH), immunofluorescence, and western blotting assay. Our research demonstrated that miR-301a-5p had a targeted binding ability to lncMDP1 and ChaC glutathione-specific gamma-glutamylcyclotransferase 1 (CHAC1). The results revealed that lncMDP1 regulated the proliferation and differentiation of myoblasts via regulating the miR-301a-5p/CHAC1 axis, and CHAC1 promotes muscle regeneration. This study fulfilled the molecular regulatory network of skeletal muscle development and providing an important theoretical reference for the future improvement of chicken meat performance and meat quality.

Whole-transcriptome RNA sequencing reveals CeRNA regulatory network under long-term space composite stress in Rats

To systematically evaluate the effect of simulated long-term spaceflight composite stress (LSCS) in hippocampus and gain more insights into the transcriptomic landscape and molecular mechanism, we performed whole-transcriptome sequencing based on the control group (Ctrl) and the simulated long-term spaceflight composite stress group (LSCS) from six hippocampus of rats. Subsequently, differential expression analysis was performed on the Ctrl and LSCS groups, followed by enrichment analysis and functional interaction prediction analysis to investigate gene-regulatory circuits in LSCS. In addition, competitive endogenous RNA (ceRNA) network was constructed to gain insights into genetic interaction. The result showed that 276 differentially expressed messenger RNAs (DEmRNAs), 139 differentially expressed long non-coding RNAs (DElncRNAs), 103 differentially expressed circular RNAs (DEcircRNAs), and 52 differentially expressed microRNAs (DEmiRNAs) were found in LSCS samples compared with the controls, which were then subjected to enrichment analysis of Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to find potential functions. PI3K-Akt signaling pathway and MAPK signaling pathway may play fundamental roles in the pathogenesis of LSCS. A ceRNA network was constructed with the predicted 340 DE pairs, which revealed the interaction roles of 220 DEmiRNA-DEmRNA pairs, 76 DEmiRNA-DElncRNA pairs, and 44 DEmiRNA-DEcircRNA pairs. Further, Thrombospondins2 was found to be a key target among those ceRNAs. Overall, we conducted for the first time a full transcriptomic analysis of the response of hippocampus to the LSCS that involved a potential ceRNA network, thus providing a basis to study the underlying mechanism of the LSCS.

Single-Cell Transcriptome Sequencing Reveals Molecular Expression Differences and Marker Genes in Testes during the Sexual Maturation of Mongolian Horses

This study aimed to investigate differences in testicular tissue morphology, gene expression, and marker genes between sexually immature (1-year-old) and sexually mature (10-year-old) Mongolian horses. The purposes of our research were to provide insights into the reproductive physiology of male Mongolian horses and to identify potential markers for sexual maturity. The methods we applied included the transcriptomic profiling of testicular cells using single-cell sequencing techniques. Our results revealed significant differences in tissue morphology and gene expression patterns between the two age groups. Specifically, 25 cell clusters and 10 cell types were identified, including spermatogonial and somatic cells. Differential gene expression analysis highlighted distinct patterns related to cellular infrastructure in sexually immature horses and spermatogenesis in sexually mature horses. Marker genes specific to each stage were also identified, including APOA1, AMH, TAC3, INHA, SPARC, and SOX9 for the sexually immature stage, and PRM1, PRM2, LOC100051500, PRSS37, HMGB4, and H1-9 for the sexually mature stage. These findings contribute to a deeper understanding of testicular development and spermatogenesis in Mongolian horses and have potential applications in equine reproductive biology and breeding programs. In conclusion, this study provides valuable insights into the molecular mechanisms underlying sexual maturity in Mongolian horses.

Review of Personalized Medicine and Pharmacogenomics of Anti-Cancer Compounds and Natural Products

In recent years, the FDA has approved numerous anti-cancer drugs that are mutation-based for clinical use. These drugs have improved the precision of treatment and reduced adverse effects and side effects. Personalized therapy is a prominent and hot topic of current medicine and also represents the future direction of development. With the continuous advancements in gene sequencing and high-throughput screening, research and development strategies for personalized clinical drugs have developed rapidly. This review elaborates the recent personalized treatment strategies, which include artificial intelligence, multi-omics analysis, chemical proteomics, and computation-aided drug design. These technologies rely on the molecular classification of diseases, the global signaling network within organisms, and new models for all targets, which significantly support the development of personalized medicine. Meanwhile, we summarize chemical drugs, such as lorlatinib, osimertinib, and other natural products, that deliver personalized therapeutic effects based on genetic mutations. This review also highlights potential challenges in interpreting genetic mutations and combining drugs, while providing new ideas for the development of personalized medicine and pharmacogenomics in cancer study.

Morphological Changes Induced by TKS4 Deficiency Can Be Reversed by EZH2 Inhibition in Colorectal Carcinoma Cells

BACKGROUND

The scaffold protein tyrosine kinase substrate 4 (TKS4) undergoes tyrosine phosphorylation by the epidermal growth factor receptor (EGFR) pathway via Src kinase. The TKS4 deficiency in humans is responsible for the manifestation of a genetic disorder known as Frank-Ter Haar syndrome (FTHS). Based on our earlier investigation, the absence of TKS4 triggers migration, invasion, and epithelial-mesenchymal transition (EMT)-like phenomena while concurrently suppressing cell proliferation in HCT116 colorectal carcinoma cells. This indicates that TKS4 may play a unique role in the progression of cancer. In this study, we demonstrated that the enhancer of zeste homolog 2 (EZH2) and the histone methyltransferase of polycomb repressive complex 2 (PRC2) are involved in the migration, invasion, and EMT-like changes in TKS4-deficient cells (KO). EZH2 is responsible for the maintenance of the trimethylated lysine 27 on histone H3 (H3K27me3).

METHODS

We performed transcriptome sequencing, chromatin immunoprecipitation, protein and RNA quantitative studies, cell mobility, invasion, and proliferation studies combined with/without the EZH2 activity inhibitor 3-deazanoplanocine (DZNep).

RESULTS

We detected an elevation of global H3K27me3 levels in the TKS4 KO cells, which could be reduced with treatment with DZNep, an EZH2 inhibitor. Inhibition of EZH2 activity reversed the phenotypic effects of the knockout of TKS4, reducing the migration speed and wound healing capacity of the cells as well as decreasing the invasion capacity, while the decrease in cell proliferation became stronger. In addition, inhibition of EZH2 activity also reversed most epithelial and mesenchymal markers. We investigated the wider impact of TKS4 deletion on the gene expression profile of colorectal cancer cells using transcriptome sequencing of wild-type and TKS4 knockout cells, particularly before and after treatment with DZNep. Additionally, we observed changes in the expression of several protein-coding genes and long non-coding RNAs that showed a recovery in expression levels following EZH2 inhibition.

CONCLUSIONS

Our results indicate that the removal of TKS4 causes a notable disruption in the gene expression pattern, leading to the disruption of several signal transduction pathways. Inhibiting the activity of EZH2 can restore most of these transcriptomics and phenotypic effects in colorectal carcinoma cells.

Metabolome and transcriptome analyses reveal changes of rapeseed in response to ABA signal during early seedling development

Seed germination is an important development process in plant growth. The phytohormone abscisic acid (ABA) plays a critical role during seed germination. However, the mechanism of rapeseed in response to ABA is still elusive. In order to understand changes of rapeseed under exogenous ABA treatment, we explored differentially expressed metabolites (DEMs) and the differentially expressed genes (DEGs) between mock- and ABA-treated seedlings. A widely targeted LC-MS/MS based metabolomics were used to identify and quantify metabolic changes in response to ABA during seed germination, and a total of 186 significantly DEMs were identified. There are many compounds which are involved in ABA stimuli, especially some specific ABA transportation-related metabolites such as starches and lipids were screened out. Meanwhile, a total of 4440 significantly DEGs were identified by transcriptomic analyses. There was a significant enrichment of DEGs related to phenylpropanoid and cell wall organization. It suggests that exogenous ABA mainly affects seed germination by regulating cell wall loosening. Finally, the correlation analysis of the key DEMs and DEGs indicates that many DEGs play a direct or indirect regulatory role in DEMs metabolism. The integrative analysis between DEGs and DEMs suggests that the starch and sucrose pathways were the key pathway in ABA responses. The two metabolites from starch and sucrose pathways, levan and cellobiose, both were found significantly down-regulated in ABA-treated seedlings. These comprehensive metabolic and transcript analyses provide useful information for the subsequent post-transcriptional modification and post germination growth of rapeseed in response to ABA signals and stresses.

Cuproptosis-Related Genes MTF1 and LIPT1 as Novel Prognostic Biomarker in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a life-threatening hematologic malignant disease with high morbidity and mortality in both adults and children. Cuproptosis, a novel mode of cell death, plays an important role in tumor development, but the functional mechanisms of cuproptosis-related genes (CRGs) in AML are unclear. The differential expression of CRGs between tumors such as AML and normal tissues in UCSC XENA, TCGA and GTEx was verified using R (version: 3.6.3). Lasso regression, Cox regression and Nomogram were used to screen for prognostic biomarkers of AML and to construct corresponding prognostic models. Kaplan-Meier analysis, ROC analysis, clinical correlation analysis, immune infiltration analysis and enrichment analysis were used to further investigate the correlation and functional mechanisms of CRGs with AML. The ceRNA regulatory network was used to identify the mRNA-miRNA-lncRNA regulatory axis. Cuproptosis-related genes LIPT1, MTF1, GLS and CDKN2A were highly expressed in AML, while FDX1, LIAS, DLD, DLAT, PDHA1, SLC31A1 and ATP7B were lowly expressed in AML. Lasso regression, Cox regression, Nomogram and calibration curve finally identified MTF1 and LIPT1 as two novel prognostic biomarkers of AML and constructed the corresponding prognostic models. In addition, all 12 CRGs had predictive power for AML, with MTF1, LIAS, SLC31A1 and CDKN2A showing more reliable results. Further analysis showed that ATP7B was closely associated with mutation types such as FLT3, NPM1, RAS and IDH1 R140 in AML, while the expression of MTF1, LIAS and ATP7B in AML was closely associated with immune infiltration. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) revealed that biological functions such as metal ion transmembrane transporter activity, haptoglobin binding and oxygen carrier activity, pathways such as interferon alpha response, coagulation, UV response DN, apoptosis, hypoxia and heme metabolism all play a role in the development of AML. The ceRNA regulatory network revealed that 6 lncRNAs such as MALAT1, interfere with MTF1 expression through 6 miRNAs such as hsa-miR-32-5p, which in turn affect the development and progression of AML. In addition, APTO-253 has the potential to become an AML-targeted drug. The cuproptosis-related genes MTF1 and LIPT1 can be used as prognostic biomarkers in AML. A total of six lncRNAs, including MALAT1, are involved in the expression and regulation of MTF1 in AML through six miRNAs such as hsa-miR-32-5p.