Differential Expression Of Transcription Factors Research Articles

Gene Expression Patterns and Phenotypic Associations in Chondrogenesis: Insights into Skeletal Dysplasia Nosology

The differentiation of mesenchymal stem cells (MSCs) into chondrocytes, known as chondrogenesis, is a complex process that plays a fundamental role in cartilage formation and skeletal development. This study elucidates the transcriptional dynamics and phenotypic correlations at various stages of chondrogenesis (early, mid, and late) using RNA-seq data. We focused on the differential expression of transcription factors (TFs) and RNA-binding proteins (RBPs). We identified critical genes during their highest expression periods and generated heatmaps to visualize these temporal patterns. Additionally, we conducted a comprehensive analysis of skeletal dysplasia nosology genes, determining their highest expression periods and phenotypic implications using the DisGeNET database. Our findings reveal that early-stage (D1) gene expression is linked to craniofacial development and limb formation anomalies, primarily involving genes responsible for extracellular matrix (ECM) organization and signal transduction. Mid-stage (D7) genes are associated with cartilage matrix composition and skeletal growth, highlighting roles in chondrocyte proliferation and matrix deposition. Late-stage (D21) genes are implicated in bone mineral density, cartilage integrity, and joint formation, ensuring the maturation and functionality of cartilage tissue. This study provides a detailed analysis of gene expression regulators and their phenotypic correlations during chondrogenesis, offering insights into the molecular mechanisms driving cartilage development and skeletal dysplasias. Understanding these temporal gene expression patterns enhances our knowledge of chondrogenesis and aids in developing targeted therapies for cartilage-related diseases. These findings underscore the significance of time-point analyses in capturing the dynamic regulation of gene expression throughout the differentiation process.

Gene Expression Patterns and Phenotypic Associations in Chondrogenesis: Insights into Skeletal Dysplasia Nosology

The differentiation of mesenchymal stem cells (MSCs) into chondrocytes, known as chondrogenesis, is a complex process that plays a fundamental role in cartilage formation and skeletal development. This study elucidates the transcriptional dynamics and phenotypic correlations at various stages of chondrogenesis (early, mid, and late) using RNA-seq data. We focused on the differential expression of transcription factors (TFs) and RNA-binding proteins (RBPs). We identified critical genes during their highest expression periods and generated heatmaps to visualize these temporal patterns. Additionally, we conducted a comprehensive analysis of skeletal dysplasia nosology genes, determining their highest expression periods and phenotypic implications using the DisGeNET database. Our findings reveal that early-stage (D1) gene expression is linked to craniofacial development and limb formation anomalies, primarily involving genes responsible for extracellular matrix (ECM) organization and signal transduction. Mid-stage (D7) genes are associated with cartilage matrix composition and skeletal growth, highlighting roles in chondrocyte proliferation and matrix deposition. Late-stage (D21) genes are implicated in bone mineral density, cartilage integrity, and joint formation, ensuring the maturation and functionality of cartilage tissue. This study provides a detailed analysis of gene expression regulators and their phenotypic correlations during chondrogenesis, offering insights into the molecular mechanisms driving cartilage development and skeletal dysplasias. Understanding these temporal gene expression patterns enhances our knowledge of chondrogenesis and aids in developing targeted therapies for cartilage-related diseases. These findings underscore the significance of time-point analyses in capturing the dynamic regulation of gene expression throughout the differentiation process.

Physiological, Biochemical, and Molecular Analyses Reveal Dark Heartwood Formation Mechanism in Acacia melanoxylon.

Acacia melanoxylon is highly valued for its commercial applications, with the heartwood exhibiting a range of colors from dark to light among its various clones. The underlying mechanisms contributing to this color variation, however, have not been fully elucidated. In an effort to understand the factors that influence the development of dark heartwood, a comparative analysis was conducted on the microstructure, substance composition, differential gene expression, and metabolite profiles in the sapwood (SW), transition zone (TZ), and heartwood (HW) of two distinct clones, SR14 and SR25. A microscopic examination revealed that heartwood color variations are associated with an increased substance content within the ray parenchyma cells. A substance analysis indicated that the levels of starches, sugars, and lignin were more abundant in SP compared to HW, while the concentrations of phenols, flavonoids, and terpenoids were found to be higher in HW than in SP. Notably, the dark heartwood of the SR25 clone exhibited greater quantities of phenols and flavonoids compared to the SR14 clone, suggesting that these compounds are pivotal to the color distinction of the heartwood. An integrated analysis of transcriptome and metabolomics data uncovered a significant accumulation of sinapyl alcohol, sinapoyl aldehyde, hesperetin, 2', 3, 4, 4', 6'-peptahydroxychalcone 4'-O-glucoside, homoeriodictyol, and (2S)-liquiritigenin in the heartwood of SR25, which correlates with the up-regulated expression of CCRs (evm.TU.Chr3.1751, evm.TU.Chr4.654_667, evm.TU.Chr4.675, evm.TU.Chr4.699, and evm.TU.Chr4.704), COMTs (evm.TU.Chr13.3082, evm.TU.Chr13.3086, and evm.TU.Chr7.1411), CADs (evm.TU.Chr10.2175, evm.TU.Chr1.3453, and evm.TU.Chr8.1600), and HCTs (evm.TU.Chr4.1122, evm.TU.Chr4.1123, evm.TU.Chr8.1758, and evm.TU.Chr9.2960) in the TZ of A. melanoxylon. Furthermore, a marked differential expression of transcription factors (TFs), including MYBs, AP2/ERFs, bHLHs, bZIPs, C2H2s, and WRKYs, were observed to be closely linked to the phenols and flavonoids metabolites, highlighting the potential role of multiple TFs in regulating the biosynthesis of these metabolites and, consequently, influencing the color variation in the heartwood. This study facilitates molecular breeding for the accumulation of metabolites influencing the heartwood color in A. melanoxylon, and offers new insights into the molecular mechanisms underlying heartwood formation in woody plants.

Potential Roles of Specific Subclasses of Premotor Interneurons in Spinal Cord Function Recovery after Traumatic Spinal Cord Injury in Adults.

The differential expression of transcription factors during embryonic development has been selected as the main feature to define the specific subclasses of spinal interneurons. However, recent studies based on single-cell RNA sequencing and transcriptomic experiments suggest that this approach might not be appropriate in the adult spinal cord, where interneurons show overlapping expression profiles, especially in the ventral region. This constitutes a major challenge for the identification and direct targeting of specific populations that could be involved in locomotor recovery after a traumatic spinal cord injury in adults. Current experimental therapies, including electrical stimulation, training, pharmacological treatments, or cell implantation, that have resulted in improvements in locomotor behavior rely on the modulation of the activity and connectivity of interneurons located in the surroundings of the lesion core for the formation of detour circuits. However, very few publications clarify the specific identity of these cells. In this work, we review the studies where premotor interneurons were able to create new intraspinal circuits after different kinds of traumatic spinal cord injury, highlighting the difficulties encountered by researchers, to classify these populations.

Transcriptomic characterization of Trichoderma harzianum T34 primed tomato plants: assessment of biocontrol agent induced host specific gene expression and plant growth promotion

In this study, we investigated the intricate interplay between Trichoderma and the tomato genome, focusing on the transcriptional and metabolic changes triggered during the late colonization event. Microarray probe set (GSE76332) was utilized to analyze the gene expression profiles changes of the un-inoculated control (tomato) and Trichoderma-tomato interactions for identification of the differentially expressed significant genes. Based on principal component analysis and R-based correlation, we observed a positive correlation between the two cross-comaparable groups, corroborating the existence of transcriptional responses in the host triggered by Trichoderma priming. The statistically significant genes based on different p-value cut-off scores [(padj-values or q-value); padj-value < 0.05], [(pcal-values); pcal-value < 0.05; pcal < 0.01; pcal < 0.001)] were cross compared. Through cross-comparison, we identified 156 common genes that were consistently significant across all probability thresholds, and showing a strong positive corelation between p-value and q-value in the selected probe sets. We reported TD2, CPT1, pectin synthase, EXT-3 (extensin-3), Lox C, and pyruvate kinase (PK), which exhibited upregulated expression, and Glb1 and nitrate reductase (nii), which demonstrated downregulated expression during Trichoderma-tomato interaction. In addition, microbial priming with Trichoderma resulted into differential expression of transcription factors related to systemic defense and flowering including MYB13, MYB78, ERF2, ERF3, ERF5, ERF-1B, NAC, MADS box, ZF3, ZAT10, A20/AN1, polyol sugar transporter like zinc finger proteins, and a novel plant defensin protein. The potential bottleneck and hub genes involved in this dynamic response were also identified. The protein–protein interaction (PPI) network analysis based on 25 topmost DEGS (pcal-value < 0.05) and the Weighted Correlation Gene Network Analysis (WGCNA) of the 1786 significant DEGs (pcal-value < 0.05) we reported the hits associated with carbohydrate metabolism, secondary metabolite biosynthesis, and the nitrogen metabolism. We conclude that the Trichoderma-induced microbial priming re-programmed the host genome for transcriptional response during the late colonization event and were characterized by metabolic shifting and biochemical changes specific to plant growth and development. The work also highlights the relevance of statistical parameters in understanding the gene regulatory dynamics and complex regulatory networks based on differential expression, co-expression, and protein interaction networks orchestrating the host responses to beneficial microbial interactions.

Metabolite and transcriptomic changes reveal the ripening process in Sinopodophyllum hexandrum fruit

Sinopodophyllum hexandrum is a perennial herb that produces an aryl-tetralin-type lignan, podophyllotoxin (PPT) isolated from rhizomes and used as a tumor inhibitor. Fruit from the plant, also called Himalayan Mayapple, is used as well in traditional Chinese medicine with biologically active metabolites including lignans, flavonoids, phenolics, and polysaccharides. During fruit maturation, a significant alteration in metabolite composition occurs. To characterize and monitor formation and turnover of metabolites during ripening, solvent-extractions of fruit were analyzed via UPLC-ESI-MS/MS during four developmental stages: young- (S1), expansion- (S2), mature- (S3) and softened-fruit (S4). To study enzymatic processes involving fruit ripening, Mayapple transcripts were monitored by RNA-seq and validated by qRT-PCR. PPT content significantly decreased while total flavonoid and polysaccharide content increased during ripening. Twenty-five differentially accumulated flavonoids (DAFs) and 1775 differentially expressed genes (DEGs) were observed during one or more of the developmental stages. Based on functional annotation, there were 116 and 82 DEGs associated with phenylpropanoid metabolism (i.e., PPT and flavonoids) and glycometabolism (e.g., starch, sucrose, and glucose), respectively. Additionally, differential expression of transcription factors (TFs) (e.g., MYB, bHLH, and WRKY) in fruits supported the phenylpropanoid metabolism and glycometabolism. Gene expression levels associated with PPT biosynthesis (e.g., DIRs, PLRs, and SDHs), flavonoids (e.g., CHSs, F3′Hs, and F3′5′Hs), and polysaccharides (e.g., INV, GOLS2, and AGLU), as well as TFs (e.g., MYB1, BLH2, and WRKY65) were consistent with changing levels of metabolites detected during ripening. These findings track dynamic alterations in ripening from bitter to sweet during fruit maturation. Moreover, these results allow for the prediction of metabolite occurrence and abundance during Mayapple fruit maturation.

A TGF-β-dominant chemoresistant phenotype of hepatoblastoma associated with aflatoxin exposure in children.

Hepatoblastoma (HB) is the most common liver cancer in children, posing a serious threat to children's health. Chemoresistance is the leading cause of mortality in patients with HB. A more explicit definition of the features of chemotherapy resistance in HB represents a fundamental urgent need. We performed an integrative analysis including single-cell RNA sequencing, whole-exome sequencing, and bulk RNA sequencing in 180 HB samples, to reveal genomic features, transcriptomic profiles, and the immune microenvironment of HB. Multicolor immunohistochemistry staining and in vitro experiments were performed for validation. Here, we reported four HB transcriptional subtypes primarily defined by differential expression of transcription factors. Among them, the S2A subtype, characterized by strong expression of progenitor ( MYCN , MIXL1 ) and mesenchymal transcription factors ( TWIST1 , TBX5 ), was defined as a new chemoresistant subtype. The S2A subtype showed increased TGF-β cancer-associated fibroblast and an immunosuppressive microenvironment induced by the upregulated TGF-β of HB. Interestingly, the S2A subtype enriched SBS24 signature and significantly higher serum aflatoxin B1-albumin (AFB1-ALB) level in comparison with other subtypes. Functional assays indicated that aflatoxin promotes HB to upregulate TGF-β. Furthermore, clinical prognostic analysis showed that serum AFB1-ALB is a potential indicator of HB chemoresistance and prognosis. Our studies offer new insights into the relationship between aflatoxin and HB chemoresistance and provide important implications for its diagnosis and treatment.

The role of transcription factors in shaping regulatory T cell identity.

Forkhead box protein 3-expressing (FOXP3+) regulatory T cells (Treg cells) suppress conventional T cells and are essential for immunological tolerance. FOXP3, the master transcription factor of Treg cells, controls the expression of multiples genes to guide Treg cell differentiation and function. However, only a small fraction (<10%) of Treg cell-associated genes are directly bound by FOXP3, and FOXP3 alone is insufficient to fully specify the Treg cell programme, indicating a role for other accessory transcription factors operating upstream, downstream and/or concurrently with FOXP3 to direct Treg cell specification and specialized functions. Indeed, the heterogeneity of Treg cells can be at least partially attributed to differential expression of transcription factors that fine-tune their trafficking, survival and functional properties, some of which are niche-specific. In this Review, we discuss the emerging roles of accessory transcription factors in controlling Treg cell identity. We specifically focus on members of the basic helix-loop-helix family (AHR), basic leucine zipper family (BACH2, NFIL3 and BATF), CUT homeobox family (SATB1), zinc-finger domain family (BLIMP1, Ikaros and BCL-11B) and interferon regulatory factor family (IRF4), as well as lineage-defining transcription factors (T-bet, GATA3, RORγt and BCL-6). Understanding the imprinting of Treg cell identity and specialized function will be key to unravelling basic mechanisms of autoimmunity and identifying novel targets for drug development.

A multifunctional hydrogel loaded with two nanoagents improves the pathological microenvironment associated with radiation combined with skin wounds.

Persistent oxidative stress and recurring waves of inflammation with excessive reactive oxygen species (ROS) and free radical accumulation could be generated by radiation. Exposure to radiation in combination with physical injuries such as wound trauma would produce a more harmful set of medical complications, which was known as radiation combined with skin wounds (RCSWs). However, little attention has been given to RCSW research despite the unsatisfactory therapeutic outcomes. In this study, a dual-nanoagent-loaded multifunctional hydrogel was fabricated to ameliorate the pathological microenvironment associated with RCSWs. The injectable, adhesive, and self-healing hydrogel was prepared by crosslinking carbohydrazide-modified gelatin (Gel-CDH) and oxidized hyaluronic acid (OHA) through the Schiff-base reaction under mild condition. Polydopamine nanoparticles (PDA-NPs) and mesenchymal stem cell-secreted small extracellular vesicles (MSC-sEV) were loaded to relieve radiation-produced tissue inflammation and oxidation impairment and enhance cell vitality and angiogenesis individually or jointly. The proposed PDA-NPs@MSC-sEV hydrogel enhanced cell vitality, as shown by cell proliferation, migration, colony formation, and cell cycle and apoptosis assays in vitro, and promoted reepithelization by attenuating microenvironment pathology in vivo. Notably, a gene set enrichment analysis of proteomic data revealed significant enrichment with adipogenic and hypoxic pathways, which play prominent roles in wound repair. Specifically, target genes were predicted based on differential transcription factor expression. The results suggested that MSC-sEV- and PDA-NP-loaded multifunctional hydrogels may be promising nanotherapies for RCSWs. STATEMENT OF SIGNIFICANCE: The small extracellular vesicle (sEV) has distinct advantages compared with MSCs, and polydopamine nanoparticles (PDA-NPs), known as the biological materials with good cell affinity and histocompatibility which have been reported to scavenge ROS free radicals. In this study, an adhesive, injectable, self-healing, antibacterial, ROS scavenging and amelioration of the radiation related microenvironment hydrogel encapsulating nanoscale particles of MSC-sEV and PDA-NPs (PDA-NPs@MSC-sEV hydrogel) was synthesized for promoting radiation combined with skin wounds (RCSWs). GSEA analysis profiled by proteomics data revealed significant enrichments in the regulations of adipogenic and hypoxic pathways with this multi-functional hydrogel. This is the first report of combining this two promising nanoscale agents for the special skin wounds associated with radiation.

TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors.

Eukaryotic gene expression is controlled by cis-regulatory elements (CREs), including promoters and enhancers, which are bound by transcription factors (TFs). Differential expression of TFs and their binding affinity at putative CREs determine tissue- and developmental-specific transcriptional activity. Consolidating genomic datasets can offer further insights into the accessibility of CREs, TF activity, and, thus, gene regulation. However, the integration and analysis of multimodal datasets are hampered by considerable technical challenges. While methods for highlighting differential TF activity from combined chromatin state data (e.g., chromatin immunoprecipitation [ChIP], ATAC, or DNase sequencing) and RNA sequencing data exist, they do not offer convenient usability, have limited support for large-scale data processing, and provide only minimal functionality for visually interpreting results. We developed TF-Prioritizer, an automated pipeline that prioritizes condition-specific TFs from multimodal data and generates an interactive web report. We demonstrated its potential by identifying known TFs along with their target genes, as well as previously unreported TFs active in lactating mouse mammary glands. Additionally, we studied a variety of ENCODE datasets for cell lines K562 and MCF-7, including 12 histone modification ChIP sequencing as well as ATAC and DNase sequencing datasets, where we observe and discuss assay-specific differences. TF-Prioritizer accepts ATAC, DNase, or ChIP sequencing and RNA sequencing data as input and identifies TFs with differential activity, thus offering an understanding of genome-wide gene regulation, potential pathogenesis, and therapeutic targets in biomedical research.

Temporal Analysis Reveals the Transient Differential Expression of Transcription Factors That Underlie the Trans-Differentiation of Human Monocytes to Macrophages.

The activation of monocytes and their trans-differentiation into macrophages are critical processes of the immune response. Prior work has characterized the differences in the expression between monocytes and macrophages, but the transitional process between these cells is poorly detailed. Here, we analyzed the temporal changes of the transcriptome during trans-differentiation of primary human monocytes into M0 macrophages. We find changes with many transcription factors throughout the process, the vast majority of which exhibit a maximally different expression at the intermediate stages. A few factors, including AP-1, were previously known to play a role in immunological transitions, but most were not. Thus, these findings indicate that this trans-differentiation requires the dynamic expression of many transcription factors not previously discussed in immunology, and provide a foundation for the delineation of the molecular mechanisms associated with healthy or pathological responses that involve this transition.

Oligodendrocyte origin and development in the zebrafish visual system.

Oligodendrocytes are the myelinating cells in the central nervous system. In birds and mammals, the oligodendrocyte progenitor cells (OPCs) originate in the preoptic area (POA) of the hypothalamus. However, it remains unclear in other vertebrates such as fish. Thus, we have studied the early progression of OPCs during zebrafish visual morphogenesis from 2 days post fertilization (dpf) until 11 dpf using the olig2:EGFP transgenic line; and we have analyzed the differential expression of transcription factors involved in oligodendrocyte differentiation: Sox2 (using immunohistochemistry) and Sox10 (using the transgenic line sox10:tagRFP). The first OPCs (olig2:EGFP/Sox2) were found at 2 dpf in the POA. From 3 dpf onwards, these olig2:EGFP/Sox2 cells migrate to the optic chiasm, where they invade the optic nerve (ON), extending toward the retina. At 5 dpf, olig2:EGFP/Sox2 cells in the ON also colocalize with sox10:tagRFP. When olig2:EGFP cells differentiate and present more projections, they become positive only for sox10:tagRFP. olig2:EGFP/sox10: tagRFP cells ensheath the ON by 5 dpf when they also become positive for a myelin marker, based on the mbpa:tagRFPt transgenic line. We also found olig2:EGFP cells in other regions of the visual system. In the central retina at 2 dpf, they are positive for Sox2 but later become restricted to the proliferative germinal zone without this marker. In the ventricular areas of the optic tectum, olig2:EGFP cells present Sox2 but arborized ones sox10:tagRFP instead. Our data matches with other models, where OPCs are specified in the POA and migrate to the ON through the optic chiasm.

Transcriptome Analysis Reveals Gene Expression Changes during Repair from Mechanical Wounding in Aquilaria sinensis

Plants repair their mechanical wounds by reprogramming secondary metabolism. However, which genes are reprogrammed during this repair process in Aquilaria sinensis has rarely been studied. Here, we used high-throughput RNA sequencing to explore the changes in the transcriptome of Aquilaria’s xylem, six months after the stem was subjected to mechanical wounding. In total, 1165 transcripts were differentially accumulated, of which 1002 transcripts were increased and 163 were decreased in their abundances (|log2 (fold change)| ≥ 1 and FDR ≤ 0.05). The majority of these genes encode products involved in plant secondary metabolism, transcription regulation, and phytohormone metabolism and signaling. The up-regulated genes were classified into 15 significantly enriched GO terms and were involved in 83 pathways, whereas the down-regulated genes were classified into 5 significantly enriched GO terms and represented 43 pathways. Gene annotation demonstrated that 100 transcripts could encode transcription factors (TFs), such as WRKY, AP2, MYB, and Helix-loop-helix (HLH) TFs. We inferred that the differential expression of TFs, genes associated with plant hormones, phenylpropanoid biosynthesis, and sesquiterpenoid biosynthesis may contribute to the repair of the stem after mechanical wounding in A. sinensis. Using co-expression analysis and prediction of TF binding sites, a TF–gene regulatory network for Aquilaria lignin biosynthesis was constructed. This included the MYB, HLH, WRKY, and AP2 TFs, and the COMT1, 4CLL7, and CCR1 genes. The changes in 10 candidate genes were validated by quantitative reverse-transcription PCR, indicating significant differences between the treated and untreated areas. Our study provides global gene expression patterns under mechanical wounding and would be valuable to further studies on the molecular mechanisms of plant repair in A. sinensis.

Chemosensitivity of gastric cancer: analysis of key pathogenic transcription factors.

We aimed to screen the key pathogenic transcription factors of gastric cancer and analyzed the correlation between the expression of transcription factors and chemotherapy drugs in gastric cancer. Gastric cancer RNA sequencing data sets, single nucleotide polymorphism data sets, and corresponding clinical data sets were downloaded from The Cancer Genome Atlas, which is public data. The expression of transcription factors in gastric cancer and normal tissues was analyzed with R software. Pathway enrichment analysis of differentially expressed transcription factors was performed using the Kyoto Encyclopedia of Genes and Genomes database. Univariate Cox analysis was used to explore the correlation between the differential expression of transcription factors and prognosis. The interaction network among differentially expressed transcription factors was constructed using String database. Spearman test was used to explore the correlation between transcription factor mutation and gene expression. The Genomics of Drug Sensitivity in Cancer database was used to examine the relationship between the expression of transcription factors and chemotherapeutic drug sensitivity. A total of 17 differentially expressed transcription factors were screened. The results indicated that CENPA, E2F1, EMX1, HOXA9, FOXM1, and MYBL2 were prognostic risk factors for gastric cancer patients (P<0.05), while RXRG and SOX4 were prognostic protective factors for gastric cancer patients (P<0.05). FDXM1 interacted with E2F7, MYBL2, E2F1, NCAPG, and SOX9. FOXM1 gene mutation was positively correlated with the expression level (P<0.05). Based on the median value of FOXM1, the patients were divided into high expression group and low expression group of FOXM1. There was no significant difference in IC50 of 5-fluorouracil between the FOXM1 high expression group and the FOXM1 low expression group (P>0.05). The IC50 of paclitaxel in the FOXM1 high expression group was higher than that in the FOXM1 low expression group (P<0.001). The expression of IC50 of cisplatin in the FOXM1 high expression group was higher than that in the FOXM1 low expression group (P<0.05). FOXM1 was a highly expressed transcription factor in gastric cancer. High FOXM1 expression was associated with the resistance of gastric cancer patients to paclitaxel and cisplatin. Therefore, FOXM1 is a potential therapeutic target for gastric cancer.

Pigment Epithelia of the Eye: Cell-Type Conversion in Regeneration and Disease.

Pigment epithelial cells (PECs) of the retina (RPE), ciliary body, and iris (IPE) are capable of altering their phenotype. The main pathway of phenotypic switching of eye PECs in vertebrates and humans in vivo and/or in vitro is neural/retinal. Besides, cells of amphibian IPE give rise to the lens and its derivatives, while mammalian and human RPE can be converted along the mesenchymal pathway. The PECs’ capability of conversion in vivo underlies the lens and retinal regeneration in lower vertebrates and retinal diseases such as proliferative vitreoretinopathy and fibrosis in mammals and humans. The present review considers these processes studied in vitro and in vivo in animal models and in humans. The molecular basis of conversion strategies in PECs is elucidated. Being predetermined onto- and phylogenetically, it includes a species-specific molecular context, differential expression of transcription factors, signaling pathways, and epigenomic changes. The accumulated knowledge regarding the mechanisms of PECs phenotypic switching allows the development of approaches to specified conversion for many purposes: obtaining cells for transplantation, creating conditions to stimulate natural regeneration of the retina and the lens, blocking undesirable conversions associated with eye pathology, and finding molecular markers of pathology to be targets of therapy.

Innate lymphoid cell characterization in the rat and their correlation to gut commensal microbes.

Innate lymphoid cells (ILCs) are important for tissue immune homeostasis, and are thoroughly characterized in mice and humans. Here, we have performed in-depth characterization of rat ILCs. Rat ILCs were identified based on differential expression of transcription factors and lack of lineage markers. ILC3s represented the major ILC population of the small intestine, while ILC2s were infrequent but most prominent in liver and adipose tissue. Two major subsets of group 1 ILCs were defined. Lineage- T-bet+ Eomes+ cells were identified as conventional NK cells, while lineage- T-bet+ Eomes- cells were identified as the probable rat counterpart of ILC1s based on their selective expression of the ILC marker CD200R. Rat ILC1s were particularly abundant in liver and intestinal tissues, and were functionally similar to NK cells. Single-cell transcriptomics of spleen and liver cells confirmed the main division of NK cells and ILC1-like cells, and demonstrated Granzyme A as an additional ILC1 marker. We further report differential distributions of NK cells and ILCs along the small and large intestines, and the association of certain bacterial taxa to frequencies of ILCs. In conclusion, we provide a framework for future studies of ILCs in diverse rat experimental models, and novel data on the potential interplay between commensals and intestinal ILCs.

Ammonium regulates the development of pine roots through hormonal crosstalk and differential expression of transcription factors in the apex.

Ammonium is a prominent source of inorganic nitrogen for plant nutrition, but excessive amounts can be toxic for many species. However, most conifers are tolerant to ammonium, a relevant physiological feature of this ancient evolutionary lineage. For a better understanding of the molecular basis of this trait, ammonium-induced changes in the transcriptome of maritime pine (Pinus pinaster Ait.) root apex have been determined by laser capture microdissection and RNA sequencing. Ammonium promoted changes in the transcriptional profiles of multiple transcription factors, such as SHORT-ROOT, and phytohormone-related transcripts, such as ACO, involved in the development of the root meristem. Nano-PALDI-MSI and transcriptomic analyses showed that the distributions of IAA and CKs were altered in the root apex in response to ammonium nutrition. Taken together, the data suggest that this early response is involved in the increased lateral root branching and principal root growth, which characterize the long-term response to ammonium supply in pine. All these results suggest that ammonium induces changes in the root system architecture through the IAA-CK-ET phytohormone crosstalk and transcriptional regulation.

RNA Biological Characteristics at the Peak of Cell Death in Different Hereditary Retinal Degeneration Mutants.

Purpose: The present work investigated changes in the gene expression, molecular mechanisms, and pathogenesis of inherited retinal degeneration (RD) in three different disease models, to identify predictive biomarkers for their varied phenotypes and to provide a better scientific basis for their diagnosis, treatment, and prevention. Methods: Differentially expressed genes (DEGs) between retinal tissue from RD mouse models obtained during the photoreceptor cell death peak period (Pde6b rd1 at post-natal (PN) day 13, Pde6b rd10 at PN23, Prph rd2 at PN29) and retinal tissue from C3H wild-type mice were identified using Illumina high-throughput RNA-sequencing. Co-expression gene modules were identified using a combination of GO and KEGG enrichment analyses and gene co-expression network analysis. CircRNA-miRNA-mRNA network interactions were studied by genome-wide circRNA screening. Results: Pde6b rd1 , Pde6b rd10 , and Prph rd2 mice had 1,926, 3,096, and 375 DEGs, respectively. Genes related to ion channels, stress, inflammatory processes, tumor necrosis factor (TNF) production, and microglial cell activation were up-regulated, while genes related to endoplasmic reticulum regulation, metabolism, and homeostasis were down-regulated. Differential expression of transcription factors and non-coding RNAs generally implicated in other human diseases was detected (e.g., glaucoma, diabetic retinopathy, and inherited retinal degeneration). CircRNA-miRNA-mRNA network analysis indicated that these factors may be involved in photoreceptor cell death. Moreover, excessive cGMP accumulation causes photoreceptor cell death, and cGMP-related genes were generally affected by different pathogenic gene mutations. Conclusion: We screened genes and pathways related to photoreceptor cell death. Additionally, up-stream regulatory factors, such as transcription factors and non-coding RNA and their interaction networks were analyzed. Furthermore, RNAs involved in RD were functionally annotated. Overall, this study lays a foundation for future studies on photoreceptor cell death mechanisms.

Endothelial‐Cell Modifications in Murine Collecting Lymphatic Vessels in Obesity

The presence of edema within tissues and cavities presented by patients afflicted with obesity suggests that lymphatic dysfunction may be a contributing factor during the onset and/or development of the various ailments associated with this disease. Importantly, obesity has been shown to significantly increase the chances of developing type-2 diabetes, cardiovascular diseases, and lymphedema in breast cancer patients undergoing surgical intervention and radiotherapy. In obesity, vascular endothelial dysfunction is known to result as a consequence of the chronic systemic inflammation. Relevant to this study, the extent of lymphatic endothelial dysfunction in obesity and type-2 diabetes remains to be fully assessed. In order to 1) elucidate the root cause of lymphatic dysfunction and subsequent impaired lymph transport in obesity, and 2) determine if this dysfunction involves an endothelial component; it is essential to isolate the various cell types in the lymphatic wall and compare the specific genetic and proteomic makeup in health and disease. Here we focus on the study and understanding of the disease-driven modifications to lymphatic endothelial cells (LECs). We hypothesize that LECs of collecting lymphatic vessels from obese mice will exhibit differential expression of transcription factors commonly associated with endothelial dysfunction (i.e. LEC specification, valve dysfunction, and barrier disruption). We utilized a diet-induced obesity mouse model. Obesity was induced by feeding C57BL/6J male mice a western diet (ResearchDiets Inc. Cat.No. D12079Bi) for 14 weeks starting at 5 weeks of age. Consistent with previous studies, diet-induced obese animals gained twice as much weight when compared to aged-matched animals fed a control diet (weight gain 18.8 g vs 9.7 g). Non-fasted blood glucose levels were 41.6±10.6% higher in obese animals, which also displayed increased skin moisture content, 45.1±4.7% (obese) vs 32.6±4.8% (control), as determined by a wet-to-dry weight ratio. Our preliminary qRT-PCR results on fluorescence-activated cell sorting (FACS) purified LECs show that diet-induced obesity results in decreased expression of the transcription factor, and LEC marker, Prox1. We have developed a novel protocol for establishing cell cultures of primary LECs from collecting lymphatic vessels isolated from different species. Notably, the same protocol with minor modifications can be used to establish cultures of primary endothelial cells from blood vessels. Preliminary characterization of murine primary LECs using RT-PCR, immunofluorescence, and confocal microscopy suggests that these cultures could be a useful novel tool for lymphatic research. Currently, we are using these cultured primary LECs from db/db mice and a proteomics approach to further assess the effects of obesity and type-2 diabetes in the lymphatic endothelium of collecting lymphatics. We anticipate that these studies will provide critical information to identify novel mechanisms of lymphatic endothelial dysfunction in obesity, type-2 diabetes, and lymphedema, and propose novel therapeutic targets to ameliorate lymphatic dysfunction in these diseases.

Dissecting the complexity of heart infiltrates in post-infectious myocarditis induced with CVB3 infection by single-cell RNA sequencing analysis

Abstract Viral myocarditis is a predominant cause of heart failure in children and young adolescents that can lead to dilated cardiomyopathy (DCM). Experimentally, Coxsackievirus B3 (CVB) is commonly employed to study the pathogenesis of myocarditis. Post-infectiously, affected mice can develop DCM, and viral RNA may be present with or without inflammation raising a question as to the events culminating in the development of DCM. To dissect this complexity, we sought to characterize heart infiltrates from CVB infected mice by single-cell RNA sequencing and compared the profiles with healthy mice. These analyses revealed 26 subtypes of cells with fibroblasts, T cells and macrophages as the major constituents. Other cell types include endothelial cells (EC), smooth muscle cells, granulocytes, B cells, and innate lymphoid cells. By analyzing the transcriptomes, we noted differential expression of transcription factors (TFs) in various cell types. One such cell type is EC, in which, activating transcription factor 4, interferon regulatory factor 1 (IRF1) and signal transducer and activator of transcription 6 (STAT6) that have a role in apoptosis and inflammation were upregulated. Correspondingly, expression of Myc and nuclear factor erythroid-derived 2-like 2 implicated in EC survival and angiogenesis was downregulated. The data suggests the ECs may play a role in the pathogenesis of CVB infection through a proinflammatory transcriptional program.