Immunomodulatory Roles of IL-15 in Immune Cells and its Potential for Cancer Immunotherapy.

Interleukin-15 (IL-15) was identified in 1994 as a T-cell growth factor with the capability to mimic the functions of IL-2. IL-15 engages with the IL-15Rα subunit expressed on the surface of antigen-presenting cells (APCs) and, through a trans-presentation mechanism, activates the IL-2/IL-15Rßγ complex receptor on the surface of natural killer (NK) cells and CD8+ T cells. This interaction initiates a cascade of downstream signaling pathways, playing a pivotal role in the activation, proliferation, and anti-apoptotic processes in NK cells, CD8+ T cells, and B cells. It provides a substantial theoretical foundation and potential therapeutic targets for tumor immunotherapy. Whether through active or passive immunotherapeutic strategies, IL-15 has emerged as a critical molecule for stimulating anti-tumor cell proliferation.

Investigating the mechanisms of inflammation and immune alterations in Parkinson's disease using spatial transcriptomics techniques.

In recent years, overwhelming evidence has emphasized the crucial role of inflammation in the pathogenesis of PD. However, the exact mechanisms by which inflammation damages dopaminergic neurons in PD are still unclear. Therefore, we generated a MPTP-induced PD mouse model and performed spatial transcriptomic sequencing to provide more insight into the process of PD development at specific brain regions. Our results indicate that the pathological changes of PD are mainly manifested in the midbrain, especially in the substantia nigra region, with significant reductions in oligodendrocytes and Agt-labeled astrocytes and an increase in Gfap-labeled astrocytes. Macrophages displayed an increasing trend in the PD environment, indicating a pattern of immune modulation induced by PD. Moreover, pathway analysis revealed significant impairments in ion migration ability, abnormal Ca2+ channels, cAMP signaling, and synaptic damage in PD. Significant downregulation of Mt1 and Mt2 and upregulation of Atp1b2, Gpi1, and Cox6a1 in PD further underscored the occurrence of intense inflammation and immune alterations. On the basis of these findings, we have validated the significant accumulation of Ca2+ in the midbrain tissue in the PD environment by measuring its content. Additionally, we have demonstrated a close association between the reduction of dopaminergic neurons, represented by the midbrain region, and ferroptosis by evaluating the iron content, malondialdehyde (MDA) levels, and the protein expression of GPX4 and TH in the tissue. We propose the hypothesis that PD-related inflammation and immune changes can induce neuronal and oligodendrocyte damage through the induction of ferroptosis, thereby further accelerating the progression of PD.

Obesity-derived macrophages upregulate TNF-α to induce apoptosis in glial cell via the NF-κB/PHLPP1 axis.

Macrophages in obese adipose tissue have been shown to damage nerve fibers, however, the mechanism underlying how macrophages cause glial cell damage remains unknown. This study aimed to characterize the mechanism by which macrophages induce apoptosis in glial cell during obesity formation in mice by single-nucleus RNA sequencing (snRNA-seq). Cells obtained from paraepididymal adipose tissue in obese mice underwent snRNA-seq. Eighteen different clusters were identified, and 12 cell types were annotated, including glial cells, macrophages, and fibroblasts. There was a negative correlation between the number of glial cells and macrophages in mouse adipose tissue during the formation of obesity. The pro-apoptotic factor PHLPP1 was identified in GO Terms. The interaction between adipose tissue glial cells and macrophages was revealed via in-depth analysis, and the cell-cell communication mechanism between the TNF-α and NF-KB/PHLPP1 axes was perfected. Apoptosis of glial cell by upregulation of TNF-α via obesity-derived macrophages and activation of the NF-κB/PHLPP1 axis. We further revealed how macrophages induce apoptosis in glial cells during obesity formation, as well as different changes in the two cell populations. This study provides valuable resources and foundations for understanding the mechanistic effects of macrophages and glial cells during obesity formation, as well as diseases and potential interventions.

Research trends and hotspot evolution of exercise-regulated myokines: a bibliometric analysis from 2003 to 2023.

Background: The lack of physical activity is a common issue in modern society and is considered a major risk factor for various chronic non-communicable diseases. Bioactive factors secreted by skeletal muscle during exercise play a crucial role in inter-organ interactions. Since the concept of "myokines" was proposed in 2004, hundreds of regulatory myokines have been identified. Visual analysis of research on exercise-regulated myokines is significant to explore research hotspots and frontiers in this field. Methods: Research literature on exercise-regulated myokines from 2003 to 2023 in the "Web of Science" database was used as the data source. Knowledge maps were drawn using "VOS Viewer, CiteSpace, and R-bibliometrix" software. Results: A total of 1,405 papers were included, showing a fluctuating yet slow growth in annual publications. The United States and China led in the number of publications and collaboration networks. Harvard University ranked first with 120 publications. CIBER (centrality 0.16) and the University of California System (centrality 0.16) were pivotal in advancing this field. PEDERSEN BK led author rankings with 41 publications and 1,952 citations. FRONTIERS IN PHYSIOLOGY ranked first among journals with 64 publications and the highest g-index (39), while PLoS One had the highest h-index (25) and most citations (2,599). Key co-cited reference clusters included #1 skeletal muscle dysfunction, #2 obesity, #6 ASCs, and #7 adaptive immunocytes. Pontus Boström's paper had a notable citation burst intensity of 77.37. High-frequency keywords were "exercise" (509), "skeletal muscle" (452), and "expression" (293), with long-term keywords such as #0 irisin, #2 insulin resistance, #3 transcription, and #6 physical activity. Recently, keywords like "physical exercise," "resistance exercise," "aerobic exercise," "insulin," and "oxidative stress" have emerged. Conclusion: Research in the field of exercise-regulated myokines shows an overall upward trend. The focus areas include myokines mediated by different types of exercise, the interaction of irisin-mediated muscle with other organs, and the important role of myokine-mediated oxidative stress in exercise simulation.

The effect of multi-component exercise on cognition function in patients with diabetes: A systematic review and meta-analysis.

BACKGROUND: This meta-analysis investigated the influence of exercise on cognitive function in people living with diabetes. METHODS: Stringent criteria for literature inclusion and exclusion were defined. Searches were conducted across four English databases to gather randomized controlled trials investigating exercise interventions for cognitive function in people living with diabetes. Outcome indicators from 1193 subjects across 12 articles were analyzed using RevMan 5.4 software. RESULTS: Exercise intervention demonstrated the ability to mitigate cognitive decline in people living with diabetes, with a combined effect size (standardized mean difference) of 0.91, 95% CI: 0.28, 1.54, P < 0.00001. The intervention effect showed significant modulation by intervention content (I2 = 95%), intervention duration (I2 = 95%), intervention frequency (I2 = 95%), and intervention cycle (I2 = 96%). Among these factors, multi-component exercise, sessions >40 minutes, exercise frequency >4 times per week, and sustained exercise for >6 months were paramount, all with P < 0.05. CONCLUSION: Exercise intervention emerges as a viable strategy for delaying cognitive decline in people living with diabetes. Its efficacy is subject to modulation by various variables. Optimal intervention includes multi-component exercise, individual sessions lasting 40-60 minutes, exercising >4 times a week, and continuous exercise for over 6 months.

Single-nucleus RNA transcriptome profiling reveals murine adipose tissue endothelial cell proliferation gene networks involved in obesity development.

Endothelial cells play an important role in the metabolism of adipose tissue (AT). This study aimed to analyze the changes that adipose tissue in AT endothelial cells undergo during the development of obesity, using single-nucleus RNA sequence (snRNA-seq). Mouse paraepididymal AT cells were subjected to snRNA-seq with the 10X Genomics platform. The cell types were then clustered using t-distributed stochastic neighbor embedding and unbiased computational informatics analyses. Protein-protein interactions network was established using the STRING database and visualized using Cytoscape. The dataset was subjected to differential gene enrichment analysis. In total, 21,333 cells acquired from 24 mouse paraepididymal AT samples were analyzed using snRNA-seq. This study identified 18 distinct clusters and annotated macrophages, fibroblasts, epithelial cells, T cells, endothelial cells, stem cells, neutrophil cells, and neutrophil cell types based on representative markers. Cluster 12 was defined as endothelial cells. The proportion of endothelial cells decreased with the development of obesity. Inflammatory factors, such as Vegfa and Prdm16 were upregulated in the medium obesity group but downregulated in the obesity group. Genes, such as Prox1, Erg, Flt4, Kdr, Flt1, and Pecam1 promoted the proliferation of AT endothelial cells and maintained the internal environment of AT. This study established a reference model and general framework for studying the mechanisms, biomarkers, and therapeutic targets of endothelial cell dysfunction-related diseases at the single-cell level.

SOCS modulates JAK-STAT pathway as a novel target to mediate the occurrence of neuroinflammation: Molecular details and treatment options.

SOCS (Suppressor of Cytokine Signalling) proteins are intracellular negative regulators that primarily modulate and inhibit cytokine-mediated signal transduction, playing a crucial role in immune homeostasis and related inflammatory diseases. SOCS act as inhibitors by regulating the Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway, thereby intervening in the pathogenesis of inflammation and autoimmune diseases. Recent studies have also demonstrated their involvement in central immunity and neuroinflammation, showing a dual functionality. However, the specific mechanisms of SOCS in the central nervous system remain unclear. This review thoroughly elucidates the specific mechanisms linking the SOCS-JAK-STAT pathway with the inflammatory manifestations of neurodegenerative diseases. Based on this, it proposes the theory that SOCS proteins can regulate the JAK-STAT pathway and inhibit the occurrence of neuroinflammation. Additionally, this review explores in detail the current therapeutic landscape and potential of targeting SOCS in the brain via the JAK-STAT pathway for neuroinflammation, offering insights into potential targets for the treatment of neurodegenerative diseases.

Single cell RNA-sequencing data generated from mouse adipose tissue during the development of obesity.

In recent years, the number of obesity has increased rapidly around the world, and it has become a major public health problem endangering global health [1]. Obesity is caused by excessive calorie intake over a long period of time, and high-fat diet (HFD) is one of the important predisposing factors [2], [3], [4]. Adipose tissue (AT) is an important immune and endocrine organ in the body, and plays an important role in the body [5]. Obesity leads to AT dysfunction, AT dilation and cell hypertrophy. Dysfunctional fat cells are the main source of pro-inflammatory cytokines, which aggravate low-grade systemic inflammation and further promote the development of obesity-related diseases [6], [7], [8]. However, whether AT releases pro-inflammatory cytokines in the early stages of obesity development remains unknown. The AT microenvironment is composed of a variety of cells, including fat cells, immune cells, fibroblasts, and endothelial cells. The immune microenvironment (TIME) and its metabolic imbalance can lead to the secretion or regulation of related hormones, which causes inflammation AT [9]. TIME is very important for maintaining AT homeostasis, which is crucial for the occurrence of obesity [10,11]. This data use single-cell RNA sequencing (sNuc-Seq) to analyze the characteristics of TIME changes in the mouse epididymal adipose tissue during the development of obesity, and the changes of cell types and genes in the tissue.

[Tau Protein Induces Aberrant Alternative Splicing Changes in PS19 Transgenic Mice].

Objective: To explore through big data analysis whether aberrant alternative splicing (AS) events precede tau P301S-induced neurodegenerative phenotype in 6-month-old PS19 mice. Methods: The original sequencing files of the GSE182170 dataset was downloaded from the European Nucleotide Archive (ENA) database with axel, aligned to the reference genome of the ENSEMBL database by using STAR software, and common AS event analysis and visualization were performed with rMATS and rmats2sashimiplot R packages. RSEM software was utilized for gene transcript quantification, Deseq2, edgeR, and limma R packages were used for differential expression analysis, and clusterProfiler R package was applied for GO enrichment analysis. String and Cytoscape were used for protein-protein interaction (PPI) analysis. Gene expression correlation analysis was performed with ggcorrplot R package. AS events were validated using PCR followed by agarose electrophoresis. Results: A total of 8 079 AS events were identified with rMATS and 117 significant AS events (ΔPSI>0.1, sequencing coverage >1) were selected eventually. The most frequent type of AS event was skipped exon (SE) (50.43%), followed by alternative 3' splice site (A3SS) and mutually exclusive exons (MXE). GO enrichment analysis revealed that synapse organization genes were aberrantly spliced in SE events and spliceosome genes were spliced in A3SS events. PPI and correlation analyses showed that the splicing factor Snrpn was significantly associated with the largest number of transcripts. Agarose electrophoresis confirmed the aberrant AS event of the Lrp8 gene in PS19 mice. Conclusion: Dysregulated splicing factors may contribute to tau P301S-induced aberrant AS changes. The study also increases the understanding of the cycling of tau protein and splicing factors in tauopathies.

Bioinformatics analysis of copper death gene in diabetic immune infiltration.

BACKGROUND: Copper plays an important role in the human body and is potentially related to the development of diabetes. The mechanism of copper death gene regulating immune infiltration in diabetes has not been studied. METHODS: Download microarray data from healthy normal and diabetic patients from the GEO database. The identification of differentially expressed genes (DEGs) was analyzed by gene enrichment. Using String online database and Cytoscape software to interact with the protein interaction network and make visual analysis. Using Wilcox analyze the correlation between the copoer death gene and diabetic mellitus. Analysis of the correlation between immune penetration cells and functions, and the difference between the diabetes group and the control group, screening the copper death gene associated with diabetes, and predicting the upper top of microRNA (miRNA) through the Funrich software. RESULTS: According to the identification of differential genes in 25 samples of GSE25724 and GSE95849 data sets, 328 differential genes were identified by consensus, including 190 up-regulated genes and 138 down-regulated genes (log2FC = 2, P < .01). KEGG results showed that neurodegeneration-multiple disease pathways were most significantly upregulated, followed by Huntington disease. According to Cytohubba, the TOP10 genes HCK, FPR1, MNDA, AQP9, TLR8, CXCR1, CSF3R, VNN2, TLR4, and CCR5 are down-regulated genes, which are mostly enriched in neutrophils. Immunoinfiltration-related heat maps show that Macrophage was strongly positively correlated with Activated dendritic cell, Mast cell, Neutrophil, and Regulatory T cell showed a strong positive correlation. Neutrophil was strongly positively correlated with Activated dendritic cell, Mast cell, and Regulatory T cell. Differential analysis of immune infiltration showed that Neutroph, Mast cell, Activated B cell, Macrophage and Eosinophil were significantly increased in the diabetic group. Central memory CD4 T cell (P < .001), Plasmacytoid dendritic cell, Immature dendritic cell, and Central memory CD8 T cell, etal were significantly decreased. DBT, SLC31A1, ATP7A, LIAS, ATP7B, PDHA1, DLST, PDHB, GCSH, LIPT1, DLD, FDX1, and DLAT genes were significantly associated with one or more cells and their functions in immune invasion. Forty-one miRNA. CONCLUSIONS: Copper death is closely related to the occurrence of diabetes. Copper death genes may play an important role in the immune infiltration of diabetes.

Effects of fatigue on balance and ankle proprioception during drop landing among individuals with and without chronic ankle instability.

This study aimed to explore the effects of fatigue on the balance and ankle proprioception during drop landing of individuals with chronic ankle instability (CAI). A total of 35 participants with unilateral CAI and 35 healthy participants participated in this study. A static balance test, dynamic balance test, and ankle proprioception test were conducted before and after fatigue. Fatigue was induced with turn back runs and vertical jumps protocol. Sway distance of the center of pressure (COP), root mean square of the COP (RMS), total excursions (TOTEX), mean velocity (MVELO), 95% confidence ellipse area of the COP movements (95% AREA), Normalise Reach Distance in the anterior (ANT), posteromedial (PM), and posterolateral (PL) directions, and the area under the curve (AUC) were calculated and analyzed. There were significant group by fatigue interactions for static balance variables, normalise reach distance in the PM and PL directions, and AUC. Fatigue reduced balance and ankle proprioception in individuals with CAI. After fatigue, static and dynamic balance and ankle proprioception during drop landing were significantly worse in the CAI group than in the control group. Fatigue had a significant negative effect on balance and ankle proprioception in CAI patients. Therefore, fatigue may be an important factor causing repeated ankle sprain in CAI patients.

Ferroptosis increases obesity: Crosstalk between adipocytes and the neuroimmune system.

Ferroptosis requires not only the accumulation of iron ions, but also changes in many ferroptosis-related regulators, including a decrease in GPX4 and inhibition of SLC7A11 for classical ferroptosis, a deletion of FSP1 or GCH1. Surprisingly, adipose tissue (AT) in the obesity conditions is also accompanied by iron buildup, decreased GSH, and increased ROS. On the neurological side, the pro-inflammatory factor released by AT may have first caused ferroptosis in the vagus nerve by inhibiting of the NRF2-GPX4 pathway, resulting in disorders of the autonomic nervous system. On the immune side, obesity may cause M2 macrophages ferroptosis due to damage to iron-rich ATMs (MFehi) and antioxidant ATMs (Mox), and lead to Treg cells ferroptosis through reductions in NRF2, GPX4, and GCH1 levels. At the same time, the reduction in GPX4 may also trigger the ferroptosis of B1 cells. In addition, some studies have also found the role of GPX4 in neutrophil autophagy, which is also worth pondering whether there is a connection with ferroptosis. In conclusion, this review summarizes the associations between neuroimmune regulation associated with obesity and ferroptosis, and on the basis of this, highlights their potential molecular mechanisms, proposing that ferroptosis in one or more cells in a multicellular tissue changes the fate of that tissue.

Bile acids-gut microbiota crosstalk contributes to the improvement of type 2 diabetes mellitus.

Type 2 diabetes mellitus (T2DM) occurs that cannot effectively use the insulin. Insulin Resistance (IR) is a significant characteristic of T2DM which is also an essential treatment target in blood glucose regulation to prevent T2DM and its complications. Bile acids (BAs) are one group of bioactive metabolites synthesized from cholesterol in liver. BAs play an important role in mutualistic symbiosis between host and gut microbiota. It is shown that T2DM is associated with altered bile acid metabolism which can be regulated by gut microbiota. Simultaneously, BAs also reshape gut microbiota and improve IR and T2DM in the bidirectional communications of the gut-liver axis. This article reviewed the findings on the interaction between BAs and gut microbiota in improving T2DM, which focused on gut microbiota and its debinding function and BAs regulated gut microbiota through FXR/TGR5. Meanwhile, BAs and their derivatives that are effective for improving T2DM and other treatments based on bile acid metabolism were also summarized. This review highlighted that BAs play a critical role in the glucose metabolism and may serve as therapeutic targets in T2DM, providing a reference for discovering and screening novel therapeutic drugs.

Crosstalk between the CBM complex/NF-κB and MAPK/P27 signaling pathways of regulatory T cells contributes to the tumor microenvironment.

Regulatory T cells (Tregs), which execute their immunosuppressive functions by multiple mechanisms, have been verified to contribute to the tumor microenvironment (TME). Numerous studies have shown that the activation of the CBM complex/NF-κB signaling pathway results in the expression of hypoxia-inducible factor-1 (HIF-1α) and interleukin-6 (IL-6), which initiate the TME formation. HIF-1α and IL-6 promote regulatory T cells (Tregs) proliferation and migration through the MAPK/CDK4/6/Rb and STAT3/SIAH2/P27 signaling pathways, respectively. IL-6 also promotes the production of HIF-1α and enhances the self-regulation of Tregs in the process of tumor microenvironment (TME) formation. In this review, we discuss how the crosstalk between the CARMA1-BCL10-MALT1 signalosome complex (CBM complex)/NF-κB and MAPK/P27 signaling pathways contributes to the formation of the TME, which may provide evidence for potential therapeutic targets in the treatment of solid tumors.

MicroRNAs and their signaling pathway in mycosis fungoides.

BACKGROUND: Oncogenic microRNAs, a kind of stable epigenetic inhibitors, often deregulated in Mycosis fungoides (MF) which affect the skin and tend to transform and spread. RESULTS: Previous studies investigating the de-expression of microRNA in MF patients skin biopsies identified that they were not only regulated by signaling pathway, but also regulated other signaling pathway. Furthermore, studies have elucidated the molecular mechanisms of the STAT signaling pathway that can promote a great diversity of miRNA expression via cytokine binding receptors, activating Janus kinase-3 and STAT proteins. But some non-STAT signaling pathway with mircoRNA de-expression in MF was incomplete. CONCLUSION: Taken together, these studies demonstrate that microRNA may be used as the prognosis, progression and diagnose of MF, as they can not only control MF cell proliferation, but also induce MF cell apoptosis.

Effects of Tai Chi on the neuromuscular function of the patients with functional ankle instability: a study protocol for a randomized controlled trial.

BACKGROUND: Ankle instability limits physical activities and undermines a person's quality of life. Tai Chi's health benefits have been reported in different population groups. However, the effects of Tai Chi on neuromuscular function among young adults with functional ankle instability (FAI) remain unclear. Therefore, we aim to investigate the effect of Tai Chi on young adults with FAI. METHODS: This study will be conducted as a randomized controlled trial with blinded assessors. A total of 104 young adults with FAI will be recruited and randomly assigned to intervention and control groups. The participants in the simplified Tai Chi exercise program (STCEP) group will receive a 12-week Tai Chi training. The participants in the control group will receive a low-intensity exercise program and health education for 12 weeks. The primary and secondary outcomes will be assessed at baseline, 4th, 8th, and 12th weeks. Primary outcome measures will include the Cumberland Ankle Instability Tool (CAIT) score, kinematics/kinetics data, electromyography during single-leg landing tasks, and the modified Star Excursion Balance Test (mSEBT). Secondary outcome measures will include the total time of Dynamic Leap and Balance Test (DLBT), ankle muscle strength, and ankle proprioception. DISCUSSION: This study will investigate the effects of Tai Chi exercise on the neuromuscular function of patients with FAI, as indicated by ankle joint biomechanics, ankle proprioception, balance, ankle muscle strength, and ankle muscle activation. Results will demonstrate that Tai Chi can be an effective exercise for young adults with FAI. TRIAL REGISTRATION: Chinese Clinical Trial Registry ChiCTR2100044089 . Registered on 10 March 2021.

Nonsurgical spinal decompression system traction combined with electroacupuncture in the treatment of multi-segmental cervical disc herniation: A case report.

RATIONALE: With the spread of computers and mobile phones, cervical spondylosis has become a common occupational disease in clinics, which seriously affects the quality of life of patients. We used a nonsurgical spinal decompression system (SDS) combined with physical therapy electroacupuncture (EA) to treat a case of mixed cervical spondylosis caused by multi-level cervical disc herniation, and we achieved satisfactory results. PATIENT CONCERNS: A 44-year-old Caucasian Asian woman presented with neck pain and numbness on the left side of the limb. MRI showed the patient's C3-C7 segment cervical disc herniation, and the flexion arch of the cervical spine was reversed. DIAGNOSIS: The patient was diagnosed with a mixed cervical spondylosis. INTERVENTIONS: The patient received a month of physical therapy (SDS traction combined with EA). OUTCOMES: Before and after treatment: VAS score of neck pain decreased from 8 to 0; Cervical spine mobility returned to normal; The grip strength of left hand increased from 7.5 kg to 19.2 kg; Cervical curvature index changed from -16.04% to -3.50%; the physiological curvature of the cervical spine was significantly restored. There was no dizziness or neck discomfort at 6 month and 1 year follow-up. LESSONS SUBSETIONS: SDS traction combined with EA is effective for the treatment of cervical disc herniation and can help restore and rebuild the biomechanical balance of the cervical spine.

Roles of ERRα and TGF-ß signaling in stemness enhancement induced by 1 µM bisphenol A exposure via human neural stem cells.

Bisphenol A (BPA) is a common industrial chemical widely used to produce various plastics and is known to impair neural stem cells (NSCs). However, the effects of low-dose BPA exposure on the stemness maintenance and differentiation fate of NSCs remain unclear in the infant brain. The present study demonstrated that 1 µM BPA promoted human NSC proliferation and stemness, without significantly increasing apoptosis. The Chip-seq experiments demonstrated that both the cell cycle and the TGF-ß signaling pathway were accelerated after treatment with 1 µM BPA. Subsequently, estrogen-related receptor α (ERRα) gene knockout cell lines were constructed using CRISPR/Cas9. Further western blotting and chromatin immunoprecipitation-PCR experiments demonstrated that BPA maintained cell stemness by binding to an EERα receptor and activating the TGF-ß1 signaling pathway, including the downstream factors Aurora kinases B and Id2. In conclusion, the stemness of NSCs could be maintained by BPA at 1 µM through the activation of the ERRα and TGF-ß1 signaling pathways and could restrain the differentiation of NSCs into neurons. The present research further clarified the mechanism of BPA toxicity on NSCs from the novel perspective of ERRα and TGF-ß1 signaling pathways regulated by BPA and provided insights into potential novel methods of prevention and therapy for neurogenic diseases.

Effect of high variation in transcript expression on identifying differentially expressed genes in RNA-seq analysis.

Great efforts have been made on the algorithms that deal with RNA-seq data to enhance the accuracy and efficiency of differential expression (DE) analysis. However, no consensus has been reached on the proper threshold values of fold change and adjusted p-value for filtering differentially expressed genes (DEGs). It is generally believed that the more stringent the filtering threshold, the more reliable the result of a DE analysis. Nevertheless, by analyzing the impact of both adjusted p-value and fold change thresholds on DE analyses, with RNA-seq data obtained for three different cancer types from the Cancer Genome Atlas (TCGA) database, we found that, for a given sample size, the reproducibility of DE results became poorer when more stringent thresholds were applied. No matter which threshold level was applied, the overlap rates of DEGs were generally lower for small sample sizes than for large sample sizes. The raw read count analysis demonstrated that the transcript expression of the same gene in different samples, whether in tumor groups or in normal groups, showed high variations, which resulted in a drastic fluctuation in fold change values and adjustedp-values when different sets of samples were used. Overall, more stringent thresholds did not yield more reliable DEGs due to high variations in transcript expression; the reliability of DEGs obtained with small sample sizes was more susceptible to these variations. Therefore, less stringent thresholds are recommended for screening DEGs. Moreover, large sample sizes should be considered in RNA-seq experimental designs to reduce the interfering effect of variations in transcript expression on DEG identification.

Similarities and Differences: A Comparative Review of the Molecular Mechanisms and Effectors of NAFLD and AFLD.

Non-alcoholic fatty liver disease (NAFLD) and alcoholic fatty liver disease (AFLD) are the most prevalent metabolic liver diseases globally. Due to the complex pathogenic mechanisms of NAFLD and AFLD, no specific drugs were approved at present. Lipid accumulation, oxidative stress, insulin resistance, inflammation, and dietary habits are all closely related to the pathogenesis of NAFLD and AFLD. However, the mechanism that promotes disease progression has not been fully elucidated. Meanwhile, the gut microbiota and their metabolites also play an important role in the pathogenesis and development of NAFLD and AFLD. This article comparatively reviewed the shared and specific signaling pathways, clinical trials, and potential intervention effectors of NAFLD and AFLD, revealing their similarities and differences. By comparing the shared and specific molecular regulatory mechanisms, this paper provides mutual reference strategies for preventing and treating NAFLD, AFLD, and related metabolic diseases. Furthermore, it provides enlightenment for discovering novel therapies of safe and effective drugs targeting the metabolic liver disease.