Tissue Profile Research Articles

Transcriptomic profiling with vascular tension analyses reveals molecular targets and phenotypes in preeclamptic placental vasculature.

The placental vascular system plays an important role in the development of pregnancy hypertension in preeclampsia. The gene profiles of whole placental tissue (containing blood vessels and many other structural components) and pure vascular tissue should be very different. All previous reports using RNA-seq analysis in the placenta have tested its whole tissue or the villous part, and thus the gene profiles in the pure placental blood vessels are unknown. This study was the first to address this point with RNA-seq in human placenta at the transcript level. Isolated placental micro-vessels from normal and preeclamptic pregnancies were used for RNA-seq analysis, real-time quantitative polymerase chain reaction (RT-qPCR) verification, and vascular function tests. Furthermore, a vascular function-centric core network was constructed to show the gene-gene interactions and gene-function associations in the placental vessel system. Differential expression analysis identified a total of 486 significantly changed transcripts. Bioinformatics analysis further confirmed that multiple genes were highly related to blood vessel and placental phenotypes. Several hub genes, including ELMO1, YWHAE, and IL6ST, were significantly reduced in the placental vessels in preeclampsia. Vascular tension experiments showed that angiotensin II-mediated vasoconstriction and exogenous NO donor sodium nitroprusside-induced vasodilation were decreased, while phenylephrine-mediated vascular responses were unchanged in placental micro-vessels in preeclampsia. The results provide important insights into the pathological process in the placental vasculature in preeclampsia and offer great potential for further investigation of these molecular targets in the human placental vascular system.

Abstract 4137833: The plasma cell-free transcriptome non-invasively profiles the immune response and myocardial damage in immune checkpoint inhibitor-induced myocarditis.

Introduction: Immune checkpoint inhibitor-induced myocarditis (ICI-m) is a severe complication of cancer immunotherapy, marked by cardiac inflammation. Despite its high mortality rate, diagnosing ICI-m remains challenging due to the lack of sensitive and non-invasive diagnostic modalities. Plasma cell-free mRNA (cf-mRNA) has recently been highlighted as a promising tool for non-invasive tissue profiling. Hypothesis: The plasma cf-mRNA profile contains disease-specific immune and tissue transcriptomic signatures of ICI-m that can be leveraged for disease-specific precision diagnostics. Aims: To establish and validate a novel cf-mRNA bench and bioinformatic pipeline for noninvasive profiling of the immune and tissue landscape of patients with ICI-m. Methods: We isolated, DNase-treated, and sequenced bulk cfRNA from frozen plasma of patients with ICI-treated cancer patients with no autoimmunity (group A, n=5), extracardiac autoimmunity (group B, n=7), and ICI-m with or without extracardiac autoimmunity (group C, n=10). Publicly available healthy control cfRNA was downloaded (n=30) as external controls. We used cell type-specific gene panels curated from single-cell RNA-sequencing datasets of circulating immune cells and cardiac cells for cellular deconvolution of the cf-mRNA. Signature scores of the sum of the counts of each cell type-specific gene were used to compare cell type contributions between patient groups. Results: Cancer and inflammatory gene pathways were significantly enriched in the cf-mRNA of all ICI-treated cancer patients. Cardiac pathways and conduction genes were significantly enriched in group C vs. A and B patients. Signature scores of Temra CD8+ T cells and cardiomyocytes, and gene expression of CCL5 and MYH6 were elevated in group C patients. Our custom ICI-m classifier containing 3 cardiac- and 3 immune cell-specific genes differentiated group C from A (AUC 0.903, 95% CI 0.858-0.903) and B patients (AUC 0.983, 95% CI 0.970-0.983) effectively, outperforming a diagnostic classifier obtained from unsupervised feature selection from all differentially expressed genes. Conclusions: Using our novel plasma cf-mRNA platform, we developed a diagnostic classifier that captures the disease-specific immune and tissue transcriptomic signatures of ICI-m, highlighting the advantages of this disease-specific approach over conventional biomarker discovery, and demonstrating the broader implications of the platform for the field of precision diagnostics.

PATH-13. MOLECULAR AND BIOLOGY CORRELATIVE RESULTS FROM THE PHASE 1B TRIAL OF UNESBULIN (PTC596) WITH RADIOTHERAPY IN CHILDREN NEWLY-DIAGNOSED WITH DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG) AND HIGH-GRADE GLIOMA (HGG): A REPORT FROM THE COLLABORATIVE NETWORK FOR NEURO-ONCOLOGY CLINICAL TRIALS (CONNECT)

Abstract BACKGROUND Within the CONNECT1702 trial of unesbulin (tubulin-binding agent causing BMI-1 modulation) with radiotherapy in patients with DIPG/HGG, tumor tissue was analyzed at diagnosis and/or autopsy for biology correlatives, enabling comprehensive, longitudinal molecular characterization. METHODS Whole genome sequencing, RNA-sequencing, and Western blot analyses were performed on tumor, normal brain, and peripheral blood mononuclear cells (PBMCs). RESULTS Tumor tissue from diagnosis (n=11) and/or autopsy (n=7) was analyzed for 16 patients (DIPG=9; HGG=7). Western blot analyses demonstrated 1) BMI-1 overexpression in baseline tumor compared to normal brain and 2) primary on-target effect of BMI1-modulation causing M-phase mitotic arrest when comparing pre- and post-treated PBMCs (increased H3S10-phosphorylation). Among 9 DIPG patients, alterations in the following genes were identified: H3-3A (H3.3) (n=5), H3C2 (H3.1) (n=2, both with co-occurring ACVR1 and PIK3CA mutations), TP53 (n=5), ATRX (n=2), and PPM1D (n=2). Tumors from two longer DIPG survivors were H3.1-, ACVR1-mutant (overall survival [OS]=26 months) and MET-amplified (OS=18 months); one patient with H3.3K27M-DIPG had germline MSH6 mutation (Lynch syndrome) (OS=12.6 months). Among 7 HGG patients, alterations in the following genes were identified: H3-3A (n=5), TP53 (n=3), NF1 (n=3), PDGFRA (n=1), EGFR (n=1), and PIK3CA (n=1). A BRAFV600E mutation was observed in the thalamic HGG patient (H3.3K27M) with greatest progression-free survival (>23 months). Early leptomeningeal metastases occurred in one DIPG patient with BCOR alteration and one HGG patient, with MYCN amplification identified in the spinal metastasis, but not intracranial disease. From gene set enrichment analyses, pathways enriched in patients with longer survival included telomerase regulation and ATP synthesis, whereas pathways enriched in patients with shorter survival included interneuron development, neuron semaphorin signaling, and gamma aminobutyric signaling. CONCLUSIONS Comprehensive molecular profiling of diagnostic and post-mortem tumor tissue provides valuable early biological insight, elucidating potential genomic biomarkers predictive of outcome and response to M-phase alteration and BMI-1 modulation in DIPG/HGG.

Integration of mRNA and miRNA Analysis Sheds New Light on the Muscle Response to Heat Stress in Spotted Sea Bass (Lateolabrax maculatus).

Temperature is a crucial environmental factor for fish. Elevated temperatures trigger various physiological and molecular responses designed to maintain internal environmental homeostasis and ensure the proper functioning of the organism. In this study, we measured biochemical parameters and performed mRNA-miRNA integrated transcriptomic analysis to characterize changes in gene expression profiles in the muscle tissue of spotted sea bass (Lateolabrax maculatus) under heat stress. The measurement of biochemical parameters revealed that the activities of nine biochemical enzymes (ALP, γ-GT, AST, GLU, CK, ALT, TG, LDH and TC) were significantly affected to varying degrees by elevated temperatures. A total of 1940 overlapping differentially expressed genes (DEGs) were identified among the five comparisons in the muscle tissue after heat stress. Protein-protein interaction (PPI) analysis of DEGs indicated that heat shock protein genes (HSPs) were deeply involved in the response to heat stress. In addition, we detected 462 differential alternative splicing (DAS) events and 618 DAS genes, which are closely associated with sarcomere assembly in muscle, highlighting the role of alternative splicing in thermal response regulation. Moreover, 32 differentially expressed miRNAs (DEMs) were identified in response to heat stress, and 599 DEGs were predicted as potential target genes of those DEMs, generating 846 DEG-DEM negative regulatory pairs potentially associated with thermal response. Function enrichment analysis of the target genes suggested that lipid metabolism-related pathways and genes were regulated by miRNAs. By analyzing PPIs of target genes, we identified 28 key negative regulatory pairs, including 13 miRNAs (such as lma-miR-122, lma-miR-200b-5p and novel-miR-444) and 15 target genes (such as hspa13, dnaja1, and dnajb1a). This study elucidates the molecular mechanisms of response to high-temperature stress and offers valuable information for the selection and breeding of heat-tolerant strains of spotted sea bass.

Meniscus gene expression profiling of inner and outer zone meniscus tissue compared to cartilage and passaged monolayer meniscus cells

Meniscus injuries are common and while surgical strategies have improved, there is a need for alternative therapeutics to improve long-term outcomes and prevent post-traumatic osteoarthritis. Current research efforts in regenerative therapies and tissue engineering are hindered by a lack of understanding of meniscus cell biology and a poorly defined meniscus cell phenotype. This study utilized bulk RNA-sequencing to identify unique and overlapping transcriptomic profiles in cartilage, inner and outer zone meniscus tissue, and passaged inner and outer zone meniscus cells. The greatest transcriptomic differences were identified when comparing meniscus tissue to passaged monolayer cells (> 4,600 differentially expressed genes (DEGs)) and meniscus tissue to cartilage (> 3,100 DEGs). While zonal differences exist within the meniscus tissue (205 DEGs between inner and outer zone meniscus tissue), meniscus resident cells are more similar to each other than to either cartilage or passaged monolayer meniscus cells. Additionally, we identified and validated LUM, PRRX1, and SNTB1 as potential markers for meniscus tissue and ACTA2, TAGLN, SFRP2, and FSTL1 as novel markers for meniscus cell dedifferentiation. Our data contribute significantly to the current characterization of meniscus cells and provide an important foundation for future work in meniscus cell biology, regenerative medicine, and tissue engineering.

CD1a affects the recurrence and prognosis of ovarian cancer.

Explored the correlation between CD1a expression in recurrence and prognosis of ovarian cancer (OV). The CD1a expression profile in OV, recurrent OV, and normal tissues, as well as corresponding clinical data, were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), Gene Expression Omnibus (GEO), and Genotype Tissue Expression (GTEx) databases. Meanwhile, immunohistochemical detection of CD1a expression in normal and OV tissues. Kaplan-Meier curves were plotted to estimate the hazard ratio (HR) of survival in OV. In addition, the correlation between CD1a and immune cells in OV, as well as the CD1a expression profile and corresponding survival time in pan-cancer were obtained from TCGA database. CD1a was overexpressed in OV and was significantly under-expressed in recurrent OV (TCGA-OV, p < 0.0001 and ICGC-OV, p < 0.0001). CD1a immunohistochemistry is significantly overexpressed in OV compared to normal tissue (p < 0.05). Recurrent OV (ICGC, p < 0.001; GSE17260, p < 0.001; GSE32062, p < 0.05). The prognosis in OV was significantly better when CD1a is overexpressed compared to under-expressed (HR [low], 1.426: 95% confidence interval [CI], 0.912-2.128; p = 0.050). Meanwhile, the overexpression of CD1a has a better prognosis than low expression in OV and recurrent OV (p = 0.004, HR [low] = 2.462, 95%CI [1.346-4.504] and p = 0.011, HR [low] = 2.199, 95%CI [1.202-4.024]). In addition, CD1a expression was closely correlated with immune cells, the CD8+ T cells, macrophages, and NK cells, while uncharacterized cells were significantly different (p = 2.65e-6, p = 7.52e-13, p = 8.28e-12, and p = 5.89e-8, respectively). Moreover, CD1a expression affected the prognosis in various other cancers. CD1a expression affected the recurrence and prognosis of OV and is closely related to various immune cell levels.

Anatomic Genetic Heterogeneity Is Uncovered By Concurrent Cell-Free DNA and Tissue Profiling and Predicts Treatment Resistance in Diffuse Large B-Cell Lymphoma

Anatomic Genetic Heterogeneity Is Uncovered By Concurrent Cell-Free DNA and Tissue Profiling and Predicts Treatment Resistance in Diffuse Large B-Cell Lymphoma

FOXO3 as a potential diagnostic biomarker for autophagy in rheumatoid arthritis: A bioinformatics study

This study aimed to identify genes associated with autophagy and potential diagnostic biomarkers by comparing the gene expression profiles of synovial tissues in patients with rheumatoid arthritis (RA) and healthy individuals, aiming to offer new insights for clinical treatment strategies. We used publicly available datasets to analyze differentially expressed genes (DEGs) between the synovial tissue of RA patients and healthy individuals. Then, we intersected these DEGs with autophagy-related genes to identify autophagy genes in the synovial tissue of RA patients. We further analyzed the biological processes and functions of these genes. Furthermore, we used machine learning to identify characteristic autophagy genes in RA synovial tissue. Finally, we examined the differential expression of these characteristic genes in the blood of RA patients using an external dataset. Our study identified FOXO3 as a potential biomarker for diagnosing RA. FOXO3 gene expression was downregulated in both the synovial tissue and blood of RA patients, suggesting its involvement in multiple biological processes such as local inflammation, oxidative stress, metabolic processes, and immune responses. Our findings suggest that FOXO3 may be a novel biomarker for the clinical diagnosis of RA and may play a crucial role in the pathogenesis of RA. The study provides new insights into the molecular mechanisms of RA and potential new therapeutic targets.

Exploring transcriptomic mechanisms underlying pulmonary adaptation to diverse environments in Indian rams.

The Changthangi sheep thrive at high altitudes in the cold desert regions of Ladakh, India while Muzaffarnagri sheep are well-suited to the low altitude plains of northern India. This study investigates the molecular mechanisms of pulmonary adaptation to diverse environments by analyzing gene expression profiles of lung tissues through RNA sequencing. Four biological replicates of lung tissue from each breed were utilized to generate the transcriptomic data. Differences in gene expression analysis revealed discrete expression profiles in lungs of each breed. In Changthangi sheep, genes related to immune responses, particularly cytokine signaling, were significantly enriched. Pathway analysis highlighted the activation of NF-kB signaling, a key mediator of inflammation and immune response. Additionally, the gene network analysis indicated a strong association between cytokine signaling, hypoxia-inducible factor (HIF) and NF-kB activation, suggesting a coordinated response to hypoxic stress in lungs of Changthangi sheep. In Muzaffarnagri sheep, the gene expression profiles were enriched for pathways related to energy metabolism, homeostasis and lung physiology. Key pathways identified include collagen formation and carbohydrate metabolism, both of which are crucial for maintaining lung function and structural integrity. Gene network analysis further reinforced this by revealing a strong connection between genes associated with lung structure and function. Our findings shed light on the valuable insights into gene expression mechanisms that enable these sheep breeds to adapt to their respective environments and contribute to a better understanding of high altitude adaptation in livestock.

MLLT3 knockdown suppresses proliferation and cell mobility in human lung adenocarcinoma.

Lung cancer is emerging as one of the most frequently encountered malignancies around the world that carries high morbidity and mortality. Lung adenocarcinoma (LUAD) has become the most common subtype of lung cancer. MLLT3 or named AF9 was first characterized in acute myeloid leukemia and can downregulate the expression of several critical genes. The aim of this study was to explore the function of MLLT3 in the progression of LUAD and related molecular mechanisms. Immunohistochemistry was employed to assess MLLT3 expression in LUAD tissues, while quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were utilized to detect MLLT3 expression levels in lung adenocarcinoma cell lines. These results revealed a significant overexpression of MLLT3 in LUAD cell lines and tissues. We further uncovered an association between MLLT3 expression profiles in LUAD tissues and metastasis, as well as TNM stage. Survival analysis showed that elevated MLLT3 correlated with a poorer survival rate. We also found that MLLT3 knockdown repressed LUAD cells invasion, migration, and proliferation in vitro, while inducing cell cycle arrest and apoptosis of LUAD cells. Moreover, knocking down MLLT3 inhibited tumor growth in vivo. Specific markers of apoptosis, cell cycle, epithelial-mesenchymal transition (EMT), and MLLT3-induced signaling were examined by Western blot. We demonstrated that MLLT3 knockdown inhibited the activity of the EGFR-MAPK/ERK signaling pathway, and MLLT3 might be a novel diagnostic biomarker and therapeutic target in lung adenocarcinomas.

Proteomic Insights into the Effects of Jianweixiaoshi Tablets on Functional Dyspepsia with Spleen Deficiency in Rats.

Jianweixiaoshi tablets (JWXS) is widely used in traditional Chinese medicine for treating functional dyspepsia with spleen deficiency (SD-FD) in China. However, the molecular mechanisms underlying the therapeutic effects of JWXS remain incompletely understood. Functional dyspepsia was induced in rats with spleen deficiency by iodoacetamide in combination with the modified multiple platform method. The SD-FD rats were administered JWXS at both low and high doses, as well as domperidone. We conducted a comprehensive evaluation of the treatment effects of JWXS, including body weight, gastrointestinal motility, immune organ index, biochemical analysis, gastrointestinal hormones, and hematological studies. Quantitative proteomic analysis based on data-independent acquisition (DIA) was used to determine the changes in protein profiles of gastric and duodenal tissues in SD-FD rats and JWXS intervention rats. The results showed that JWXS effectively alleviated gastrointestinal motility disorders in SD-FD rats, as indicated by accelerated gastric emptying and intestinal propulsion, increased levels of gastrin, motilin, and ghrelin, and reduced levels of cholecystokinin-octapeptide, vasoactive intestinal peptide, and somatostatin. Additionally, JWXS increased the spleen and thymus index, increased %lymphocyte in blood, reduced white blood cell count and %neutrophil, and improved immune function. Through quantitative proteomic analysis of gastric tissues, we identified 333 differentially expressed proteins in the JWXS treatment group and the model group. Notably, the mechanism by which JWXS accelerated gastric emptying may be related to PLC-γ and SERCA2 in the calcium signaling pathway. Furthermore, JWXS treatment altered the expression of 732 proteins in rat duodenal samples. The differentially expressed proteins were enriched in immune-related functions and pathways, including antigen processing and presentation, as well as the intestinal immune network for IgA production. In conclusion, JWXS exhibits a multi-faceted impact on various pathways, demonstrating its efficacy in treating SD-FD. These findings provide a foundation for the clinical application of JWXS in managing SD-FD.

Potential involvement of PPARs in the inhibition of mammary lipid synthesis during diet-induced milk fat depression

The objective of this study was to evaluate the possible role of the peroxisome proliferator-activated receptors (PPARs: PPAR-α, PPAR-β/δ, and PPAR-γ) in diet and conjugated linoleic acid (CLA)-induced milk fat depression (MFD) in dairy cows. We hypothesized that the expression of PPARs, which regulate lipid metabolism and bind to polyunsaturated fatty acids, could be modulated by biohydrogenation intermediates that induce MFD, thereby interfering with milk fat synthesis. First, tissue profiling revealed that PPAR-α and PPAR-β/δ had low expression in mammary tissue compared with the liver. A comparison of lactating and nonlactating tissue from the same cows showed that expression of the PPARs did increase during lactation. Mammary expression of the PPARs during MFD was then observed in 9 mid-lactation cows in a 3x3 Latin square design with MFD induced by a 3-d intravenous infusion of trans-10,cis-12 CLA or feeding a high-oil/low-forage diet. The expression of the PPARs remained largely unaltered during CLA and diet-induced MFD, except for an increase in PPAR-α target genes CPT1A and ACADVL that are involved in β-oxidation. The interaction of PPAR-γ chemical agonist Troglitazone and antagonist T0070907 and CLA was then investigated in bovine mammary epithelial cells (MAC-T). The activation and inhibition of PPAR-γ did not overcome trans-10,cis-12 CLA inhibition of lipogenesis despite the agonist stimulating PPAR-γ expression. Furthermore, PPAR-γ activation did not modify the expression of lipogenic genes. Overall, the results fail to support a functional role of the PPARs in the inhibition of lipogenesis during MFD in dairy cows.

Comprehensive circular RNA profiling in various sheep tissues

Despite the scientific relevance of circular RNAs (circRNAs), the study of these RNAs in non-model organisms, especially in sheep, is still in its infancy. On the other hand, while some studies have focused on sheep circRNA identification in a limited number of tissues, there is a lack of comprehensive analysis that profile circRNA expression patterns across the tissues not yet investigated. In this study, 61 public RNA sequencing datasets from 12 different tissues were uniformly analyzed to identify circRNAs, profile their expression and investigate their various characteristics. We reported for the first time a circRNA expression landscape with functional annotation in sheep tissues not yet investigated including hippocampus, BonMarrowMacrophage, left-ventricle, thymus, ileum, reticulum and 23-day-embryo. A stringent computational pipeline was employed and 8919 exon-derived circRNAs with high confidence were identified, including 88 novel circRNAs. Tissue-specificity analysis revealed that 3059 circRNAs were tissue-specific, which were also more specific to the tissues than linear RNAs. The highest number of tissue-specific circRNAs was found in kidney, hippocampus and thymus, respectively. Co-expression analysis revealed that expression of circRNAs may not be affected by their host genes. While most of the host genes produced more than one isoform, only one isoform had dominant expression across the tissues. The host genes of the tissue-specific circRNAs were significantly enriched in biological/pathways terms linked to the important functions of their corresponding tissues, suggesting potential roles of circRNAs in modulating physiological activity of those tissues. Interestingly, functional terms related to the regulation and various signaling pathways were significantly enriched in all tissues, suggesting some common regulatory mechanisms of circRNAs to modulate the physiological functions of tissues. Finding of the present study provide a valuable resource for depicting the complexity of circRNAs expression across tissues of sheep, which can be useful for the field of sheep genomic and veterinary research.

Quality control for single-cell analysis of high-plex tissue profiles using CyLinter

Tumors are complex assemblies of cellular and acellular structures patterned on spatial scales from microns to centimeters. Study of these assemblies has advanced dramatically with the introduction of high-plex spatial profiling. Image-based profiling methods reveal the intensities and spatial distributions of 20–100 proteins at subcellular resolution in 103–107 cells per specimen. Despite extensive work on methods for extracting single-cell data from these images, all tissue images contain artifacts such as folds, debris, antibody aggregates, optical aberrations and image processing errors that arise from imperfections in specimen preparation, data acquisition, image assembly and feature extraction. Here we show that these artifacts dramatically impact single-cell data analysis, obscuring meaningful biological interpretation. We describe an interactive quality control software tool, CyLinter, that identifies and removes data associated with imaging artifacts. CyLinter greatly improves single-cell analysis, especially for archival specimens sectioned many years before data collection, such as those from clinical trials.

Development of a Multiplex PCR Assay to Detect Neofusicoccum parvum and Botryosphaeria dothidea in Walnut.

In walnut orchards, frequent symptoms of cankers and dieback (fruit blight, twig and branch cankers up to tree death) are caused by different agents, in particular by Botryosphaeriaceae, primarily Neofusicoccum parvum and Botryosphaeria dothidea. This study aimed at developing a sensitive, rapid, specific and internally controlled multiplex PCR assay for the detection of these species. The ability of the multiplex PCR, with an internal inhibition control (i.e. E. coli DNA), to specifically and successfully detect members of the two targeted species was validated using 11 different isolates for each fungal target (inclusivity) and 20 tree-associated fungal species different from B. dothidea or N. parvum (exclusivity). Applicability to plant materials was further investigated and showed an absence of amplification for asymptomatic husk or twig samples while the amplification profiles of symptomatic tissues ranged from no amplification to amplification of both species, in correlation with the observed fungal contamination level. In conclusion, we developed a rapid diagnostic tool for simultaneous detection of two major fungal pathogens of walnut. Although this protocol was tailored for walnut husks and twigs, applicability to any plant sample contaminated by these pathogens can be considered.

Ginsenoside Rg1 Promotes Wound Healing in Mice with Superficial Second-Degree Burns Through Energy Metabolism, Cell Migration, and Cell Adhesion Pathways.

Natural products are known to have distinct roles in the treatment of various diseases. However, the potential role of ginsenoside Rg1 (GRg1) in the context of scald injuries remains unclear. This study aimed to elucidate the effects of GRg1 on scald wound healing by utilizing a mouse scald wound model and administering varying concentrations of GRg1 orally. RNA sequencing (RNA-seq) was employed to identify the signaling pathways and key genes influenced by GRg1 in the wound healing process. Our findings indicate that mice treated with a low concentration of GRg1 exhibited a significantly higher wound healing rate compared with the model group and other treatment groups. Through RNA-seq, we observed that the gene expression profile in the wound tissues of the low-concentration-treated group was consistent with that of the normal control group. Furthermore, a low concentration of GRg1 was found to maintain cellular energy metabolism homeostasis by enhancing mitochondrial aerobic respiration and the tricarboxylic acid cycle. In addition, GRg1 facilitated wound healing by restoring the expression of genes associated with cell migration and adhesion. Confirming the appropriate concentration of GRg1 that accelerates tissue healing at scald sites and enhances our understanding of the efficacy and molecular mechanisms underlying the therapeutic effects of natural products in disease treatment.

Capturing the mechanosensitivity of cell proliferation in models of epithelium

Despite the primary role of cell proliferation in tissue development and homeostatic maintenance, the interplay between cell density, cell mechanoresponse, and cell growth and division is not yet understood. In this article, we address this issue by reporting on an experimental investigation of cell proliferation on all time- and length-scales of the development of a model tissue, grown on collagen-coated glass or deformable substrates. Through extensive data analysis, we demonstrate the relation between mechanoresponse and probability for cell division, as a function of the local cell density. Motivated by these results, we construct a minimal model of cell division in tissue environment that can recover the data. By parameterizing the growth and the dividing phases of the cell cycle, and introducing such a proliferation model in dissipative particle dynamics simulations, we recover the mechanoresponsive, time-dependent density profiles in 2D tissues growing to macroscopic scales. The importance of separating the cell population into growing and dividing cells, each characterized by a particular time scale, is further emphasized by calculations of density profiles based on adapted Fisher-Kolmogorov equations. Together, these results show that the mechanoresponse on the level of a constitutive cell and its proliferation results in a matrix-sensitive active pressure. The latter evokes massive cooperative displacement of cells in the invading tissue and is a key factor for developing large-scale structures in the steady state.

Histological and Biochemical Effects of Lutein on Paraquat-induced Renal Toxicity in Wistar Rats

Introduction: Paraquat (PQ) poisoning in humans predominantly results from the generation of reactive oxygen species (ROS). To date, no proven antidote exists for PQ poisoning, which is characterized by severe kidney injury and high mortality rates globally. However, free radical scavengers and antioxidant agents have shown potentials to mitigate PQ toxicity. Aim: The study is aimed at investigating lutein, an antioxidant, for possible mitigation of paraquat-induced renal toxicity. Study Design: Preclinical experimental study. Place and Duration of Study: Department of Anatomy, Obafemi Awolowo University (OAU), Nigeria, between 2022 and 2023. Methods: Forty wistar rats weighing 150-180 grammes were randomly grouped (A to E) for this study. Paraquat (PQ) toxicity was induced in groups B to E. Lutein was administered at graded doses of 50 mg/kg, 100 mg/kg and 150 mg/kg to groups C to E for twenty-one days respectively. Group A (positive control) was given only normal saline, while group B had paraquat only. Twenty-four hours after the last administration, urine and blood samples were collected and the animals were sacrificed before the excision of the kidneys. Results: A marked histological distortion, which was characterized by compromised Bowman's space and renal tubule dimensions, was observed in Group B. In contrast, the lutein-treated groups exhibited dose-dependent improvements, with outcomes comparable to the control group. Notably, Group B showed significant elevations in plasma creatinine (P = 0.003) and urine protein (P = 0.001), accompanied by reduced plasma protein (P = 0.004), relative to the treated groups. However, Group E, which received the highest lutein dose, demonstrated substantial improvement in histoarchitectural and biochemical findings similar to the control group." Conclusion: This study demonstrated significant alterations in the histoarchitecture and biochemical profiles of renal tissue following paraquat exposure. Notably, the lutein-treated groups exhibited substantial improvement, with results comparable to the control group. These findings suggest that lutein may possess potential therapeutic properties to mitigate paraquat-induced renal toxicity.

RNA-seq validation of microRNA expression signatures for precision melanoma diagnosis and prognostic stratification

BackgroundNew diagnostic tools are needed to improve the diagnosis and risk stratification of cutaneous melanoma. Disease-specific microRNA signatures have been previously described via NanoString profiling of solid biopsy tissue and plasma. This study validated these signatures via next-generation sequencing technology and compared their performance against clinical metrics and other published melanoma signatures.MethodsRNA from 64 plasma and 60 FFPE biopsy samples from individuals with invasive melanoma or related benign/control phenotypes was extracted and enriched for microRNA. RNA sequencing was performed to compute MEL38/MEL12 signature scores. The results were evaluated with published NanoString and RNA sequencing datasets, comprising 548 solid tissue samples and 217 plasma samples, to predict disease status and patient outcome.ResultsThe MEL38 diagnostic signature classifies patients into discrete diagnostic groups via RNA sequencing in either solid tissue or plasma (P < 0.001). In solid tissue, the prognostic MEL12 signature stratifies patients into low-, intermediate- and high-risk groups, independent of clinical covariates. The hazard ratios for 10-year overall survival, based on observed survival intervals, were 2.2 (MEL12 high-risk vs low-risk, P < 0.001) and 1.8 (intermediate-risk vs low-risk, P < 0.001), outperforming other published prognostic models. MEL12 also exhibited prognostic significance in the plasma of 42 patients with invasive disease.ConclusionsThe MEL38 and MEL12 signatures can be assessed in either solid tissue or plasma using RNA-seq and are strong predictors of disease state and patient outcome. Compared with other genomic methods, MEL12 was shown to be the strongest predictor of poor prognosis. MicroRNA expression profiling offers objective, accurate genomic information about a patient’s likelihood of invasive melanoma and prognosis.

Lipidomic profiling of serum and liver tissue reveals hepatoprotective mechanism of taxifolin in rats with CCl4-induced subacute hepatic injury based on LC-MS/MS

Currently, the hepatoprotective activity of taxifolin, a flavonoid isolated from Pseudotsuga taxifolia, has been reported in many animal models. However, whether the protective effect of taxifolin on the liver is related to its effect on lipidomics is unclear. Based on the significant therapeutic effect of taxifolin on CCl4 induced subacute hepatic injury, we observed the intervention of taxifolin by lipidomics. The results demonstrate that taxifolin can effectively reverse the damage caused by CCl4, which including hepatocyte vacuolization and necrosis. Lipomic profiling based on liquid chromatography-mass spectrometry showed that taxifolin was able to restore lipidomic changes caused by CCl4, including the levels of lysophosphatidylserine (LPS), phosphatidylcholine (PC), coenzyme (Co), phosphatidylglyceride (PG), phosphatidylserine (PS), dimethylphosphatidylethanolamine (dMePE), ceramide (Cer), sphingosine (So), triglycerides (TG), and monogalactosyl diacylglycerol (MGDG) in the rat liver, and phosphatidylcarbinol (PMe) and phosphatidylethanolamine (PE), plant sphingosine (phSM), glucose ceramide (CerG1), TG, and diglycerides (DG) in serum. Spearman's correlation analysis showed that CerG1, phSM, PE, and PMe in serum, and Cer, dMePE, PG, PS, So, TG, and MGDG in liver were positively correlated with serum levels of aspartate transaminase, alanine transaminase, and liver index; while TG, DG in serum, and Co, LPS, PC in liver were negatively correlated with the parameters. In total, 43 and 34 lipid molecules were altered by taxifolin treatment in the liver and serum, respectively, mainly including glycerophosphoglycerols, glycerophosphocholines, glycerophosphoethanolamines, and linoleic acids and derivatives. Our findings help to provide novel insights into the mechanism of the hepatoprotective effect of taxifolin from a lipidomics approach.