Tissue Patterning Research Articles

Interactions between the gut microbiome and DNA methylation patterns in blood and visceral adipose tissue in subjects with different metabolic characteristics

BackgroundThe gut microbiome has been reported to induce epigenetic modifications in the host, which may be involved in the pathophysiology of metabolic diseases.ObjectiveTo evaluate the potential interactions between the gut microbiome and DNA methylome in subjects with different metabolic characteristics.MethodsSixty-four participants with different metabolic characteristics (i.e., participants without obesity -healthy controls-, and participants with obesity and normal insulin sensitivity/insulin resistance/ type 2 diabetes-T2DM-) were included in this study. A machine learning approach was performed in order to identify distinctive patterns in three omics (gut microbiome, blood DNA methylome, and visceral adipose tissue-VAT- DNA methylome) according to the different study groups.ResultsRobust distinctive distribution patterns of the three different omics were found between healthy controls and patients with obesity; participants with and without T2DM, and patients with obesity with and without insulin resistance. Importantly, strong correlations between the gut microbiome (including Odoribacteriaceae and Christensenllaceae families) and both blood and VAT DNA methylome were found. Moreover, in the entire study population, three main bacterial genera (Sutterella, Collinsella and Eubacterium) were related to the epigenetic regulation of different genes involved in distinct processes related to cellular metabolism and metabolic diseases, including small ubiquitin-related modifier (SUMO) transferase activity or lipid binding.ConclusionWe show that distinctive interactions between the gut microbiome and DNA methylome may occur in subjects with different metabolic characteristics. Further research is needed to elucidate the potential role of these interactions in the pathophysiology of obesity and related comorbidities.

Dynamic Shifts in Antibiotic Residues and Gut Microbiome Following Tilmicosin Administration to Silkie Chickens

Tilmicosin, an antibiotic widely used in animal husbandry to prevent and treat bacterial infections, raises concerns due to its residual accumulation, which impacts both animal health and food safety. In this study, we conducted a comprehensive analysis of tilmicosin clearance patterns in different tissues, assessed physiological impacts through blood biochemistry, and investigated changes in gut microbial composition with 16S rRNA sequencing of the tilmicosin-treated Silkie chickens. Initially, we observed rapid peaks in tilmicosin residues in all tissues within 1 day after treatment, but complete metabolism took longer, extending beyond 9 days. Moreover, tilmicosin treatment significantly decreased serum levels of total bile acid, blood urea nitrogen, and uric acid, while increasing the levels of direct bilirubin, total bilirubin, and glutathione peroxidase at day 3, followed by a decrease from day 5 onwards. The effects of tilmicosin use on microbial composition and diversity lasted for an extended period, with the relative abundance of Proteobacteria remaining significantly different between the control and tilmicosin-treated groups at 120 days. Additionally, correlation analysis revealed a strong positive correlation between Mucispirillum_schaedleri and tilmicosin residue in all tissues, while Parabbacteroide_distasonis, Faecalibacterium_prausnitzii, and others exhibited negative correlations with tilmicosin residue. Overall, our study indicates a significant correlation between intestinal microbes and antibiotic residues, providing a theoretical basis for guiding the withdrawal period after antibiotic use.

Visium spatial transcriptomics and proteomics identifies novel hepatic cell populations and transcriptomic signatures of alcohol-associated hepatitis.

Alcohol-associated hepatitis (AH) is the clinical manifestation of alcohol-associated liver disease (ALD). AH is a complex disease encompassing the dysregulation of many cells and cell subpopulations. This study used a hepatic spatial transcriptomic and proteomic approach (10X Genomics Visium) to identify hepatic cell populations and their associated transcriptomic and proteomic alterations in human AH. Formalin-fixed paraffin-embedded liver tissue from AH patients (n = 2) and non-ALD controls (donors) (n = 2) were used for Visium spatial transcriptomic and proteomic analysis. AH cell clusters and cell markers were drastically different in regard to tissue pattern and number of cell types compared to non-ALD controls. Cholangiocytes, endothelial cells, macrophages, and stellate cells were more profuse in AH relative to non-ALD controls. Transcriptionally, proliferating cell nuclear antigen-positive (PCNA+) hepatocytes in AH more closely resembled cholangiocytes suggesting they were non-functional hepatocytes derived from cholangiocytes. Furthermore, mitochondria protein-coding genes were reduced in AH versus non-ALD control hepatocytes, suggesting reduced functionality and loss of regenerative mechanisms. Macrophages in AH exhibited elevated gene expression involved in exosomes as compared to non-ALD controls. The most upregulated macrophage genes observed in AH were those involved in exosome trafficking. Gene and protein signatures of disease-associated hepatocytes (ANXA2+/CXCL1+/CEACAM8+) were elevated in AH and could visually identify a pre-malignant lesion. This study identified global cell type alterations in AH and distinct transcriptomic changes between AH and non-ALD controls. These findings characterize cellular plasticity and profuse transcriptomic and proteomic changes that are apparent in AH and contribute to the identification of novel therapeutics.

Genome-wide analysis of fatty acid desaturase genes in moso bamboo (Phyllostachys edulis) reveal their important roles in abiotic stresses responses

BackgroundBamboo is an important nontimber forestry product worldwide, while growth, development and geographic distribution of bamboo are often affected by abiotic stresses. Fatty acid desaturases have important roles in regulating plant abiotic stress tolerance, especially low-temperature. However, there is no report on genome-wide of FAD genes in bamboo under abiotic stresses.ResultsA toltal of 43 PeFAD genes were identified in moso bamboo genome, which were unevenly located in 17 scaffolds. Phylogenetic analysis indicated that PeFAD genes were divided into 6 groups and ADS/FAD5 group was absence in momo bamboo, and gene structure and histidine-motifs remained highly conserved in each group. The expansion of PeFAD genes was mainly caused by tandem and segmental duplications of SAD/FAB2 group. We also identified 59 types of miRNAs targeting PeFAD genes. RNA-seq data indicated that PeFAD genes were transcribed in various organs/tissues with different degrees, and responded to abiotic stresses and hormone treatments, including cold, salt, drought, SA, ABA, BR, NAA and GA. Co-expression analysis under cold stress showed that PeCBF3 might directly bind the promoter of top cold-responsive PeSLD1 gene that contained LTR cis-element and DRE core element. The qRT-PCR assay also validated the expression pattern of PeSLD1 and its upstream regulatory gene PeCBF3.ConclusionIn this study, we performed comprehensive genome-wide survey of PeFAD genes in moso bamboo and analyzed their expression patterns in various tissues and organs, and under abiotic stresses and phytohormones treatment. The qRT-PCR assay validated the cold inducibility of PeSLD1 and PeCBF3. This work showed critical roles of PeFAD genes in abiotic stresses responses. This is the first report on genome-wide analysis of PeFAD genes in moso bamboo, which will provide critical gene resources for molecular breeding of stress-toleranct moso bamboo.

The role of the SOX2 gene in cervical cancer: focus on ferroptosis and construction of a predictive model

BackgroundThe intricate interplay between stemness markers and cell death pathways significantly influences the pathophysiology of cervical cancer. SOX2, a pivotal regulator of stem cell pluripotency, has recently been implicated in the modulation of ferroptosis, a specialized form of iron-dependent cell death, in cancer dynamics. This study delineates the role of SOX2 in the ferroptotic landscape of cervical carcinoma.ObjectiveTo delineate the association between SOX2 expression and ferroptosis in cervical cancer and develop a robust, SOX2-centric model for predicting prognosis and enhancing personalized treatment.MethodsA multidimensional approach integrating advanced bioinformatics, comprehensive molecular profiling, and state-of-the-art machine learning algorithms was employed to assess SOX2 expression patterns and their correlation with ferroptosis marker expression patterns in cervical cancer tissues. A prognostic model incorporating the expression levels of SOX2 and ferroptosis indicators was meticulously constructed.ResultsThis investigation revealed a profound and intricate correlation between SOX2 expression and ferroptotic processes in cervical cancer, substantiated by robust molecular evidence. The developed predictive model based on SOX2 expression exhibited superior prognostic accuracy and may guide therapeutic decision-making.ConclusionThis study underscores the critical role of SOX2 in orchestrating the ferroptosis pathway in cervical cancer and presents a novel prognostic framework. The SOX2-centric predictive model represents a significant advancement in prognosis evaluation, offering a gateway to personalized treatment for gynaecologic cancers.

Inferring DNA methylation in non-skeletal tissues of ancient specimens.

Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes.

Genome-Wide Analysis of the Multidrug and Toxic Compound Extrusion Gene Family in the Tea Plant

The multidrug and toxic compound extrusion (MATE) family is the latest class of novel secondary transporters discovered in plants. However, there is currently no comprehensive analysis of the MATE gene family in the tea plant. In this study, 68 CsMATE genes were identified from the tea plant genome using bioinformatic methods. In general, we analyzed the evolutionary relationships, intron–exon structure, distribution in chromosomes, conserved domains, and gene expression patterns in different tissues and stresses of the CsMATE gene family. The 68 CsMATEs were phylogenetically divided into four major clusters (Class I to Class IV). The CsMATE genes within the same class exhibit similar structural features, while displaying certain distinctions across different classes. Evolutionary analysis indicated that the CsMATE gene family expanded mainly through gene duplication events, in addition to proximal duplication. Through the analysis of cis-acting elements, it was found that CsMATE genes may be involved in the growth, development, and stress response. Furthermore, we observed that certain CsMATE genes could be induced to exhibit expression under abiotic stress conditions such as low temperature, high salinity (NaCl), osmotic stress (PEG), and methyl jasmonate treatment (MeJA). The findings presented herein offer a crucial theoretical foundation for elucidating the biological functions of CsMATE genes, particularly in response to abiotic stress, and furnish valuable potential genetic resources for tea plant resistance breeding.

Oxindole derivatives alleviate paracetamol-induced nephrotoxicity and hepatotoxicity: biochemical, histological, and computational expressions.

Oxindole is a nature-derived heteroaromatic nucleus with a history of preclinical uses in various conditions. In this study, oxindole derivatives, 6-chloro-3-(3-hydroxybenzylidene) indolin-2-one (3OH) and 6-chloro-3-(4-hydroxybenzylidene) indolin-2-one (4OH) were evaluated for nephroprotective and hepatoprotective effects. Paracetamol-induced nephrotoxicity and hepatotoxicity model was used in mice. Tissue histology and serum biochemistry were carried out to further support in vivo activity. Compound 3OH reduced serum urea and creatinine levels by 51.8% and 64.6%, respectively (p < 0.0001). Excretion of creatinine by 3OH 10mg was 52.8% as compared to silymarin. In case of urinary excretion of urea, the significant rise in excretion was observed in 4OH 15mg (30.4%; p < 0.05) and 3OH 10mg group (29.24%; p < 0.05). The compound 3OH exhibited restorative pattern of the renal tissues with slight inflammatory infiltrations. In case of hepatoprotective activity, 3OH reduced (59.9%; p < 0.0001) serum ALT at 5mg even more than silymarin and all other doses of oxindole derivatives. In case of serum AST, all treatment groups produced significant (p < 0.0001) reduction except 3OH 15mg.Computational studies supported the results as both derivatives were found to have promising interactions with enzymes at lower binding energies. Compound 3OH which possesses a hydroxyl group based on aromatic ring at meta position was the most successful drug candidate throughout this study. In a nutshell, the selected compounds elicited significant nephroprotective and hepatoprotective-like effects in mice.

Mechano-gradients drive morphogen-noise correction to ensure robust patterning.

Morphogen gradients instruct cells to pattern tissues. Although the mechanisms by which morphogens transduce chemical signals have been extensively studied, the roles and regulation of the physical communication between morphogen-receiver cells remain unclear. Here, we show that the Wnt/β-catenin-morphogen gradient, which patterns the embryonic anterior-posterior (AP) axis, generates intercellular tension gradients along the AP axis by controlling membrane cadherin levels in zebrafish embryos. This "mechano-gradient" is used for the cell competition-driven correction of noisy morphogen gradients. Naturally and artificially generated unfit cells, producing noisy Wnt/β-catenin gradients, induce local deformation of the mechano-gradients that activate mechanosensitive calcium channels in the neighboring fit cells, which then secrete annexin A1a to kill unfit cells. Thus, chemo-mechanical interconversion-mediated competitive communication between the morphogen-receiver cells ensures precise tissue patterning.

Abstract PR011: Advance prostate cancer detection through epigenomic profiling of cell-free DNA

Abstract Introduction: Metastatic castration-resistant prostate cancer (mCRPC) is a heterogeneous disease which can be classified into clinically relevant subtypes based on the expression of genes, such as the androgen receptor (AR) and neuroendocrine markers. Neuroendocrine prostate cancer (NEPC), characterized by gain of stem-like and neuroendocrine features and lack of AR expression is a clinically aggressive variant. Due to the lack of adequate biomarkers, NEPC is usually detected at a very advanced stage. There is mounting evidence that molecular subtype changes seen in NEPC are enforced by widespread epigenetic alterations, in particular DNA methylation changes. In this study, we aim to devise a novel DNA methylation-based assay for molecular subtyping and disease monitoring from cell-free DNA (cfDNA). Methods: We analyzed genome wide methylation patterns in 56 prostate cancer patient-derived xenograft (PDX) and 128 mCRPC tumors using array- and sequencing-based assays. We integrated DNA methylation at promoters, gene bodies and transcription factor binding site (TFBS) to determine the landscape of methylation alterations at key lineage specific genes. Using whole genome methylation derived from tissue with matched expression data we developed a deep learning framework to predict gene expression directly from tissue or cfDNA. Using key marker genes, the model was used to discern tumor molecular phenotypes from tissue and cfDNA in three independent cohorts of mCRPC patients using whole genome bisulfite sequencing and low-pass Enzymatic Methyl-Seq (EM-seq). Results: We observed a tight association between promoter, gene body and TFBS methylation with gene expression. Inferring gene expression from methylation for lineage specific markers such as AR, KLK3, ASCL1, INSM1, SRRM4 and DLL3 we classified molecular subtypes from both tissue and cfDNA. Additionally, for AR and ASCL1, we identified core sets of TFBSs whose differential methylation allowed for accurate assay-independent molecular subtype quantification. Applying the optimized quantitative model to mCRPC patients who underwent comprehensive tissue sampling by rapid autopsy we observed accurate subtype classification from both tissue samples and cfDNA for all cases. A similar analytical performance was observed in additional clinical mCRPC cohorts with cfDNA. Conclusion: Whole-genome methylation analysis of cfDNA allows for the prediction of gene expression patterns in tumor tissues, enabling non-invasive tumor subclassification and assessment of therapeutic targets. Citation Format: Mohamed Adil, Brian Hanratty, Pallabi Mustafi, Chitvan Mittal, Helen Richards, Ilsa Coleman, Radhika Patel, Anna-Lisa Doebley, Robert Patton, Eden Cruikshank, Patricia Galipeau, Ruth Dumpit, Martine Roudier, Jin-Yih Low, Navonil Sarkar, Robert Montgomery, Eva Corey, Colm Morrissey, Peter Nelson, Gavin Ha, Michael Haffner. Advance prostate cancer detection through epigenomic profiling of cell-free DNA [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr PR011.

Transcriptome Signatures for Cognitive Resilience Among Individuals with Pathologically Confirmed Alzheimer Disease.

Limited success to date in development of drugs that target hallmark Alzheimer disease (AD) proteins as a means to slow AD-related cognitive decline has sparked interest in approaches focused on cognitive resilience. We sought to identify transcriptome signatures among brain donors with neuropathologically confirmed AD that distinguish those with cognitive impairment from those that were cognitively intact. We compared gene expression patterns in brain tissue from donors in four cohorts who were cognitively and pathologically normal (controls), met clinical and pathological criteria for AD (SymAD), or were cognitively normal prior to death despite pathological evidence of AD (cognitively resilient or AsymAD). Differentially expressed genes (DEGs) at the transcriptome-wide significance (TWS) level (P<10 -6 ) in the total sample and nominally significant (P<0.05) in at least two datasets were further evaluated in analyses testing association of gene expression with co-calibrated and harmonized cognitive domain scores and AD-related neuropathological traits. We identified 52 TWS DEGs, including 14 that surpassed a significance threshold of P<5×10 -8 . The three most significant DEGs, ADAMTS2 (Log2 fold change [Log2FC]=0.46, P=2.94×10 -14 ), S100A4 (Log2FC=0.61, P=3.98×10 -11 ) and NRIP2 (Log2FC=0.32, P=9.52×10 -11 ) were up-regulated in SymAD compared to AsymAD brains. ADAMTS2 and SLC6A9 were also significantly and nominally differentially expressed between AsymAD cases and controls (FDR P=0.45 and FDR P=0.57, respectively). Significant associations (P<0.0038) were identified for executive function with expression of ADAMTS2 (P=4.15×10 -8 ) and ARSG (P=1.09×10 -3 ), and for memory with PRELP (P=3.92×10 -5 ) and EMP3 (P=7.75×10 -4 ), and for language with SLC38A2 (P=6.76×10 -5 ) and SLC6A9 (P=2.13 ×10 -3 ). Expression of ARSG and FHIP1B were associated with measures of Tau pathology (AT8: P=1.5×10 -3 , and pTau181: P=3.64×10 -3 , respectively), and SLC6A9 expression was associated with multiple pTau isoforms including pTau181 (P=1.5×10 -3 ) and pTau396 (P=2.05×10 -3 ). PRELP expression was associated with synaptic density (PSD.95: P=6.18 ×10 -6 ). DEGs were significantly enriched in pathways involving E2F targets, cholesterol homeostasis, and oxidative phosphorylation. We identified multiple DEGs that differentiate neuropathologically confirmed AD cases with and without cognitive impairment prior to death. Expression of several of these genes was also associated with measures of cognitive performance and AD-related neuropathological traits, thus providing important insights into cognitive resilience mechanisms and strategies for delaying clinical symptoms of AD.

INNV-15. A PIVOTAL, MULTICENTER TRIAL OF FOCUSED ULTRASOUND FOR BLOOD-BRAIN BARRIER DISRUPTION FOR PLASMA-BASED LIQUID BIOPSY IN PATIENTS WITH GLIOBLASTOMA (LIBERATE)

Abstract BACKGROUND Liquid biopsy in glioblastoma (GBM) is hindered by insufficient requisite circulating-tumor (ct) and cell-free (cf) DNA in blood due to blood-brain barrier (BBB). This limits the identification of blood-based tumor biomarkers along with biomarker-driven systemic therapies. Real-time image-guided low-intensity focused ultrasound (LIFU) plus IV microbubble oscillators, leads to non-invasive BBB disruption. METHODS LIBERATE is an ongoing, prospective, multi-center, self-controlled, pivotal trial investigating safety and technical efficacy of LIFU-based BBB disruption for increasing blood ctDNA and cfDNA levels in adult GBM patients (aged 18-80 years). Patients with suspected GBM planned for biopsy/resection at ten US centers are being enrolled. Patients with multifocal tumors or tumors arising from deep midline, thalamus, cerebellum, or brainstem are excluded. Patients are administered IV microbubbles for enhanced sonication effects, after which MR-guided BBB disruption using 220kHz LIFU device is performed with real-time acoustic-feedback-control for effective microbubble activation. Pre- and post-LIFU, phlebotomy and MRI brain are performed. Primary study endpoint is defined, per subject, as ratio between their blood cfDNA level 1-hour post-LIFU procedure compared to blood cfDNA pre-procedure. Primary study hypothesis is that BBB disruption leads to ≥2-fold rise in blood cfDNA. Secondary hypothesis is that there exists ≥75% agreement between biomarker pattern in blood cfDNA sample obtained 1-hour post-LIFU and biomarker pattern in tumor tissue obtained later. Trial is powered to evaluate both primary and secondary hypotheses. Based on assumed true agreement rate of 91% and one-sided alpha=0.025, an exact test for binomial proportions provides N=50 with 84% power for secondary hypothesis. Exploratory endpoints include (1) sensitivity of detection of specific somatic mutations in ctDNA from blood collected pre- and post-LIFU, (2) ctDNA estimation in samples collected at 30-minutes, 1-hour, 2-hour, and 3-hour post-LIFU to determine time of greatest yield, (3) correlation of MRI parameters related to grading of BBB disruption and ctDNA-based biomarkers from post-LIFU blood samples. Patient enrollment commenced in 2022 and remains ongoing (NCT05383872).

Immune Response and Transcriptome Analysis of the Head Kidney to Different Concentrations of Aeromonas veronii in Common Carp (Cyprinus carpio).

The common carp (Cyprinus carpio), a major economic freshwater fish, is suffering from a variety of bacterial infectious diseases because of its high-density, factory and intensive farming patterns. Aeromonas veronii is the causative agent of high mortality in common carp, causing severe economic losses in aquaculture. However, the regulatory mechanisms involved in the response of common carp to this bacterial infection remain poorly understood. In this study, we compared mortality, blood serum LZM (Lysozyme) and IgM (Immunoglobulin M) levels and transcriptome patterns of head kidney tissues after infection with different concentrations of Aeromonas veronii. We observed that mortality increased progressively with an increasing pathogen concentration. The concentrations of blood serum LZM and IgM significantly increased after infection. A total of 13 and 925 differentially expressed genes (DEGs) were identified after infection with low (T4) and high (T9) concentrations of bacterial suspension, respectively. KEGG and GO analyses of the DEGs highlighted multiple immune-related signaling pathways. Weighted gene co-expression network analysis (WGCNA) revealed that 136 and 83 hub genes were related to blood serum LZM and IgM, respectively. Finally, the gene expression in the head kidney was validated via RT-qPCR to be consistent with the transcriptome. These results provide insights into the mechanisms of the immune response to infection with different concentrations of Aeromonas veronii and offer useful information for further studies on immune defense mechanisms in common carp.

Normal tissue transcriptional signatures for tumor-type-agnostic phenotype prediction

Cancer transcriptional patterns reflect both unique features and shared hallmarks across diverse cancer types, but whether differences in these patterns are sufficient to characterize the full breadth of tumor phenotype heterogeneity remains an open question. We hypothesized that these shared transcriptomic signatures reflect repurposed versions of functional tasks performed by normal tissues. Starting with normal tissue transcriptomic profiles, we use non-negative matrix factorization to derive six distinct transcriptomic phenotypes, called archetypes, which combine to describe both normal tissue patterns and variations across a broad spectrum of malignancies. We show that differential enrichment of these signatures correlates with key tumor characteristics, including overall patient survival and drug sensitivity, independent of clinically actionable DNA alterations. Additionally, we show that in HR+/HER2- breast cancers, metastatic tumors adopt transcriptomic signatures consistent with the invaded tissue. Broadly, our findings suggest that cancer often arrogates normal tissue transcriptomic characteristics as a component of both malignant progression and drug response. This quantitative framework provides a strategy for connecting the diversity of cancer phenotypes and could potentially help manage individual patients.

MicroRNAs as Regulators, Biomarkers, and Therapeutic Targets in Autism Spectrum Disorder.

The pathogenesis of autism spectrum disorder (ASD) is complex and is mainly influenced by genetic and environmental factors. Some research has indicated that environmental aspects may interplay with genetic aspects to enhance the risk, and microRNAs (miRNAs) are probably factors in explaining this link between heredity and the environment. MiRNAs are single-stranded noncoding RNAs that can regulate gene expression at the posttranscriptional level. Some research has indicated that miRNAs are closely linked to neurological diseases. Many aberrantly expressed miRNAs have been observed in autism, and these dysregulated miRNAs are expected to be potential biomarkers and provide new strategies for the treatment of this disease. This article reviews the research progress of miRNAs in autism, including their biosynthesis and function. It is found that some miRNAs show aberrant expression patterns in brain tissue and peripheral blood of autistic patients, which may serve as biomarkers of the disease. In addition, the article explores the novel role of exosomes as carriers of miRNAs with the ability to cross the blood-brain barrier and unique expression profiles, offering new possibilities for diagnostic and therapeutic interventions in ASD. The potential of miRNAs in exosomes as diagnostic markers for ASD is specifically highlighted, as well as the prospect of using engineered exosome-encapsulated miRNAs for targeted therapies.

Evolution and development of complex floral displays.

Flowering plants - angiosperms - display an astounding diversity of floral features, which have evolved in response to animal pollination and have resulted in the most species-rich plant clade. Combinations of macroscale (e.g. colour, symmetry, organ number) and microscale (e.g. cell type, tissue patterning) features often lead to highly elaborate floral displays. Most studies have focused on model species with simple floral displays to uncover the genetic and evolutionary mechanisms involved in flower evolution, yet few studies have focused on complex floral displays. Here, we review current knowledge on the development and evolution of complex floral displays. We review gene regulatory networks involved in four developmental pathways contributing to overall floral display (inflorescence architecture, organ identity, flower symmetry and flower colour) in classical plant models. We then discuss how evolutionary modification of one or more of these pathways has resulted in the production of a range of complex floral displays. Finally, we explore modular systems in which multiple pathways have been modified simultaneously, generating the most elaborate floral displays.

Senescence in Intervertebral Disc Degeneration: A Comprehensive Analysis Based on Bioinformatic Strategies.

Intervertebral disc degeneration (IDD) is a major cause for low back pain. Studies showed the association between senescence and degenerative diseases. Cell senescence can promote the occurrence and development of degenerative diseases through multiple mechanisms including inflammatory stress, oxidative stress and nutritional deprivation. The roles of senescence and senescence-associated genes (SAGs) remains unknown in IDD. Four differently expressed SAGs were identified as hub SAGs using "limma" package in R. We then calculated the immune infiltration of IDD patients, and investigated the relation between hub SAGs and immune infiltration. Enrichment analysis was performed to explore the functions of hub SAGs in IDD. Nomogram and LASSO model based on hub SAGs was constructed to predict the risk of severe degeneration (SD) for IDD patients. Subsequently, single cell analysis was conducted to describe the expression pattern of hub SAGs in intervertebral disc tissue. We identified ASPH, CCND1, IGFBP3 and SGK1 as hub SAGs. Further analysis demonstrated that the hub SAGs might mediate the development of IDD by regulating immune infiltration and multiple pathways. The LASSO model based on the four hub SAGs showed good performance in predicting the risk of SD. Single cell analysis revealed that ASPH, CCND1 and SGK1 mainly expressed in nucleus pulposus cells, while IGFBP3 mainly expressed in epithelial cells. Eleven candidate drugs targeting hub SAGS were predicted for IDD patients through Comparative Toxicogenomics Database (CDT). PCR and immunohistochemical analysis showed that the levels of four hub SAGs were higher in SD than MD (mild degeneration) patients. We performed a comprehensive analysis of SAGs in IDD, which revealed their functions and expression pattern in intervertebral disc tissue. Based on hub SAGs, we established a predictive model and explored the potential drugs. These findings provide new understandings of SAG mechanism and promising therapeutic strategies for IDD.

Characterization of Human Melanoma Skin Cancer Models: A step towards Model-Based Melanoma Research

Advancing 3D in vitro human tissue models is crucial for biomedical research and drug development to address the ethical and biological limitations of animal testing. Recently, 3D skin models have proven to be effective for studying serious skin conditions, such as melanoma. For these advanced models to be applicable in preclinical studies, thorough characterization is essential to understand their applicability and limitations.In this study, we used bioimaging and RNA sequencing to assess the architecture and transcriptomic profiles of skin models, including models with melanoma. Our results indicated that these models closely mimicked skin morphology and gene expression patterns. The full-thickness (FT) model shows a superior resemblance to the human skin, particularly in basement membrane formation and cellular interactions.The integrity of the skin-like properties and gene expression signatures of both skin and melanoma cells were preserved upon the integration of melanoma cells, establishing these models as robust platforms for cancer research. The responsiveness of the FT melanoma models to vemurafenib treatment was successfully monitored, demonstrating their validity as a reliable, reproducible, and humane tool for pharmacological testing and drug development. Furthermore, the transcriptomic data showed that skin models with cancer spheroids had upregulated genes linked to aggressive and resilient cancer behavior compared to spheroids alone. This emphasizes the importance of the microenvironment in cancer progression and suggests that 3D skin models can serve to uncover mechanisms and therapeutic targets that are not detectable in simpler systems. Statement of SignificanceThis study introduces advanced, ethically sound skin and melanoma models as alternatives to animal testing in drug discovery. By thoroughly characterizing these models using bioimaging and RNA sequencing, we demonstrate their close resemblance to human skin, particularly in full-thickness models. These models not only replicate the complex cellular interactions and gene expression patterns of human tissue but also maintain robustness after melanoma integration. Our findings highlight the potential of these models in revealing cancer mechanisms and therapeutic targets, offering a significant impact on melanoma research and preclinical testing.

Genome-wide analysis of the Amorphophallus konjac AkCSLA gene family and its functional characterization in drought tolerance of transgenic arabidopsis

BackgroundAmorphophallus konjac (A. konjac), a perennial tuberous plant, is widely cultivated for its high konjac glucomannan (KGM) content, a heteropolysaccharide with diverse applications. The cellulose synthase-like (CSL) gene family is known to be a group of processive glycan synthases involved in the synthesis of cell-wall polysaccharides and plays an important role in the biological process of KGM. However, in A. konjac the classification, structure, and function of the AkCSLA superfamily have been studied very little.ResultsBioinformatics methods were used to identify the 11 AkCSLA genes from the whole genome of Amorphophallus konjac and to systematically analyze their characteristics, phylogenetic evolution, promoter cis-elements, expression patterns, and subcellular locations. Phylogenetic analysis revealed that the AkCSLA gene family can be divided into three subfamilies (Groups I- III), which have close relationships with Arabidopsis. The promoters of most AkCSLA family members contain MBS elements and ABA response elements. Analysis of expression patterns in different tissues showed that most AkCSLAs are highly expressed in the corms. Notably, PEG6000 induced down-regulation of the expression of most AkCSLAs, including AkCSLA11. Subcellular localization results showed that AkCSLA11 was localized to the plasma membrane, Golgi apparatus and endoplasmic reticulum. Transgenic Arabidopsis experiments demonstrated that overexpression of AkCSLA11 reduced the plant’s drought tolerance. This overexpression also inhibited the expression of drought response genes and altered the sugar components of the cell wall. These findings provide new insights into the response mechanisms of A. konjac to drought stress and may offer potential genetic resources for improving crop drought resistance.ConclusionIn conclusion, the study reveals that the AkCSLA11 gene from A. konjac negatively impacts drought tolerance when overexpressed in Arabidopsis. This discovery provides valuable insights into the mechanisms of plant response to drought stress and may guide future research on crop improvement for enhanced resilience.

Three RLKs integrate SHR-SCR and gibberellins to regulate root ground tissue patterning in Arabidopsis thaliana

Precise regulation of cell division is essential for proper tissue patterning in multicellular organisms. In Arabidopsis, the ground tissue (GT) comprises cortex and endodermis in the early stages of root development. During GT maturation, additional periclinal cell divisions (PCDs) occasionally occur of the endodermis, generating a middle cortex (MC) layer between the cortex and endodermis. Although several regulatory proteins and phytohormones were identified to mediate GT patterning, such as SHORT-ROOT (SHR), SCARECROW (SCR), CYCLIND6;1 (CYCD6;1), and gibberellins (GAs), the interrelationship among these factors is not elucidated. Here, we report that three closely related receptor-like kinases (RLKs), ARH1, FEI1, and FEI2, play crucial roles in mediating a signal transduction pathway from the SHR-SCR module to GA to regulate GT patterning. Two independent triple mutants of these RLKs (tri-1 and tri-2) exhibit increased MC formation compared with wild type. Genetic analysis indicated that all three RLKs regulate MC formation mainly in a cell-autonomous manner. The transcription levels of these RLKs are negatively controlled by SHR and SCR. The altered GT patterns in shr and scr can be partially complemented by tri-1. GA biosynthesis is significantly reduced in the roots of tri-1. The excessive MC formation in tri-1 can be greatly suppressed by the exogenous application of GA3 or by the mutation of CYCD6;1. Our results demonstrate a signaling pathway involving SHR/SCR-ARH1/FEI1/FEI2-GA-CYCD6;1 to govern GT patterning in Arabidopsis thaliana.