Changes In Expression Patterns Research Articles

Sucrose-delaying flower color fading associated with delaying anthocyanin accumulation decrease in cut chrysanthemum

As fresh ornamental crops, vase life and post-harvested quality of cut flowers have attracted much attention. Flower color fading is the prominent defect in red and purple cut flowers, especially in cut chrysanthemum which have a relative long vase life. Here, the effect of sucrose on change in anthocyanin contents during the vase life of ‘Dante Purple’ cut chrysanthemum was studied. Results showed that 500 mM sucrose as holding solution could significantly delay the decrease in anthocyanin content and maintain the ornamental value for as long as 38 vase days. Moreover, the sucrose also increased the flower diameter, soluble sugar contents and total antioxidant capacity, while decreasing the malondialdehyde contents. Further studies suggested that the transcript levels of anthocyanin biosynthetic genes and transcription factors, CmMYB6 and CmMYB#7, had continuously decreased during the vase life. The changes in these genes expression patterns was retarded by the sucrose treatment, except for CmMYB#7 which is a repressor of anthocyanin biosynthesis gene expression. The decline in relative expression of CmMYB#7 was accelerated by sucrose. These results have supplied clues to study the mechanism whereby sucrose serves as a signal molecule to regulate anthocyanin biosynthesis.

RNAseq of diverse spring wheat cultivars released during last 110 years

Here, we performed RNA-seq based expression analysis of root and leaf tissues of a set of 24 historical spring wheat cultivars representing 110 years of temporal genetic variations. This huge 130 tissues RNAseq dataset was initially used to study expression pattern of 97 genes regulating root growth and development in wheat. Root system architecture (RSA) is an important target for breeding stress-resilient and high-yielding wheat cultivars under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research due to their below ground presence. We also validated the dataset by performing correlation analysis between expression of RSA related genes in roots and leaves with 25 root traits analyzed under varying moisture conditions and 10 yield-related traits. The Pearson’s correlation coefficients between root phenotypes and expression of root-specific genes varied from −0.72 to 0.78, and strong correlations with genes such as DRO1, TaMOR, ARF4, PIN1 was observed. The presented datasets have multiple uses such as a) studying the change in expression pattern of genes during time, b) differential expression of genes in two very important tissues of wheat i.e., leaf and roots, and c) studying customized expression of genes associated with important phenotypes in diverse wheat cultivars. The initial findings presented here provided key insights into understanding the transcriptomic basis of phenotypic variability of RSA in wheat cultivars.

Knockouts of TNFRSF1A and TNFRSF1B Genes in K562 Cell Line Lead to Diverse Long-Lasting Responses to TNF-α.

This research delves into the intricate landscape of tumor necrosis factor-alpha (TNF-α) signaling, a multi-functional cytokine known for its diverse cellular effects. Specifically, we investigate the roles of two TNF receptors, TNFR1 and TNFR2, in mediating TNF-α-induced transcriptional responses. Using human K562 cell lines with TNFR1 and TNFR2 knockouts, we explore changes in gene expression patterns following TNF-α stimulation. Our findings reveal distinct transcriptional profiles in TNFR1 and TNFR2 knockout cells, shedding light on the unique contributions of these receptors to TNF-α signaling. Notably, several key pathways associated with inflammation, apoptosis, and cell proliferation exhibit altered regulation in the absence of TNFR1 or TNFR2. This study provides valuable insights into the intricate mechanisms governing TNF-α signaling and its diverse cellular effects, with potential implications for targeted therapeutic strategies.

Inhibition of focal adhesion kinase 2 results in a macrophage polarization shift to M2 which attenuates local and systemic inflammation and reduces heterotopic ossification after polysystem extremity trauma.

Heterotopic ossification (HO) is a complex pathology often observed in combat injured casualties who have sustained severe, high energy polytraumatic extremity injuries. Once HO has developed, prophylactic therapies are limited outside of surgical excision. Tourniquet-induced ischemia injury (IR) exacerbates trauma-mediated musculoskeletal tissue injury, inflammation, osteogenic progenitor cell development and HO formation. Others have shown that focal adhesion kinase-2 (FAK2) plays a key role in regulating early inflammatory signaling events. Therefore, we hypothesized that targeting FAK2 prophylactically would mitigate extremity trauma induced IR inflammation and HO formation. We tested whether the continuous infusion of a FAK2 inhibitor (Defactinib, PF-573228; 6.94 µg/kg/min for 14 days) can mitigate ectopic bone formation (HO) using an established blast-related extremity injury model involving femoral fracture, quadriceps crush injury, three hours of tourniquet-induced limb ischemia, and hindlimb amputation through the fracture site. Tissue inflammation, infiltrating cells, osteogenic progenitor cell content were assessed at POD-7. Micro-computed tomography imaging was used to quantify mature HO at POD-56. In comparison to vehicle control-treated rats, FAK2 administration resulted in no marked wound healing complications or weight loss. FAK2 treatment decreased HO by 43%. At POD-7, marked reductions in tissue proinflammatory gene expression and assayable osteogenic progenitor cells were measured, albeit no significant changes in expression patterns of angiogenic, chondrogenic and osteogenic genes. At the same timepoint, injured tissue from FAK-treated rats had fewer infiltrating cells. Additionally, gene expression analyses of tissue infiltrating cells resulted in a more measurable shift from an M1 inflammatory to an M2 anti-inflammatory macrophage phenotype in the FAK2 inhibitor-treated group. Our findings suggest that FAK2 inhibition may be a novel strategy to dampen trauma-induced inflammation and attenuate HO in patients at high risk as a consequence of severe musculoskeletal polytrauma.

Abstract LB_A24: Baicalein suppresses tumorigenesis of the ER𝛼 positive of breast cancer cells by targeting multiple signaling pathways

Abstract The anti-tumor properties of baicalein, a flavonoid compound, have been extensively documented. However, the specific effects of baicalein on ER𝛼 positive breast cancer cell lines, namely T47-D and MCF-7, are less well-known. In this study, we conducted comprehensive in vitro experiments to elucidate the comparative impacts of baicalein on these two cell lines. Our results demonstrate that baicalein exerts robust anti-cancer effects, inducing morphological changes, reducing colony formation, and inhibiting cell proliferation in both T47-D and MCF-7 cells. These effects were more pronounced at higher concentrations. Additionally, baicalein treatment impeded the migratory capabilities of both cell lines, as shown by wound healing assays. Furthermore, our data show that baicalein triggers apoptosis, leading to an increase in early apoptotic, late apoptotic, and dead cells. This apoptotic process appears to be caspase 3/7-dependent. Interestingly, the pro-apoptotic effects were more potent in T47-D cells, accompanied by significant upregulation of pro-apoptotic genes and downregulation of anti-apoptotic markers. Baicalein treatment also induced oxidative stress and DNA damage, evidenced by an increase in reactive oxygen species (ROS) and phosphorylation of ATM and H2A.X. Importantly, baicalein inhibited the PI3K signaling pathway, a key mediator of cancer progression. Genome-wide transcriptomic analysis revealed significant changes in gene expression patterns, with baicalein treatment causing both upregulation and downregulation of several genes. Pathway analysis revealed that cell cycle and ferroptosis pathways were activated in both cell lines upon baicalein treatment. In conclusion, our findings highlight the potential of baicalein as a therapeutic agent against breast cancer, while also revealing nuanced differences in response between the T47-D and MCF-7 breast cancer cell lines. Citation Format: Besa Xhabija, Aidan J. McLaughlin, Ibiere Lovelyn Epelle, Tristan H. Nielson, Elisabeta Ujeniuc, Mariam I. Duhaini. Baicalein suppresses tumorigenesis of the ER𝛼 positive of breast cancer cells by targeting multiple signaling pathways [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_A24.

Abstract C092: PRMT1 promotes pancreatic cancer development and resistance to chemotherapy

Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal types of cancer due to the lack of early diagnostic markers and effective therapeutic options. While epigenetic gene regulation is critically involved in the development of various types of cancer, its role in development of PDAC and the potential of therapeutically targeting epigenetic regulators remains underexplored. To identify a targetable epigenetic regulator, we utilized public datasets of pancreatic cancer and show that protein arginine methyl transferase 1 (PRMT1) is highly expressed in pancreatic cancer cells and that high expression of PRMT1 is a poor prognosis factor. Using loss of function studies in vitro and in vivo, we show that PRMT1 is essential for promoting cancer cell proliferation and tumorigenesis. We also demonstrate that the loss of PRMT1 relates to global changes in chromatin accessibility and gene expression pattern. Notably, we revealed that high PRMT1 negatively correlates with gemcitabine sensitivity and exhibit that pharmacological inhibition of PRMT1 in combination with gemcitabine had a greater anticancer effect on pancreatic cancer cells. Collectively, we suggest PRMT1 as a key factor of pancreatic cancer development and a potential candidate of chemotherapy. Citation Format: Bomin Ku, David Eisenbarth, Dae-Sik Lim. PRMT1 promotes pancreatic cancer development and resistance to chemotherapy [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C092.

Combining Gene Mutation with Transcriptomic Data Improves Outcome Prediction in Myelodysplastic Syndromes

Background and Aim. Myelodysplastic syndromes (MDS) are myeloid neoplasms characterized by peripheral blood cytopenias and risk of progression to acute myeloid leukemia (AML). Disease management is challenged by heterogeneity in clinical courses and survival probability. Recently, the genomic screening integration (by Molecular International Prognostic Scoring System, IPSS-M) into patient's assessment has resulted into a significant improvement in predicting clinical outcomes compared to the conventional prognostic score (Revised IPSS, IPSS-R). Many of the consequences of genetic and cytogenetic alterations will affect gene expression by means of transcriptional and epigenetic instability and altered microenviromental signaling. The aim of this project conducted by GenoMed4All and Synthema EU consortia is to link genomic information with transcriptomic data for possibly improving the prediction of clinical outcomes in MDS patients. Patients and Methods.Clinical, cytogenetic, genomic (somatic mutations screening of 31 target genes) and transcriptomic (bulk RNA-seq of CD34 + bone marrow cells) data were collected at diagnosis in 389 MDS patients. Transcriptomic and genomic profiles were processed and the former were normalized before Principal Component Analysis (PCA) dimensionality reduction to mine the interdependency of expression-wide perturbation and recurrent genomic alterations. The prognostic impacts of genetic, cytogenetic, transcriptomic, clinical and demographic features were assessed with a penalized Cox's proportional hazards model [Gerstung M et al, Nat Commun. 2015. 6, 5901] considering the Overall Survival (OS) as primary end point. A 5-fold cross-validating (CV) scheme was exploited to control bias in risk estimation. Model accuracy was assessed using Harrell's concordance index (C-index). An independent validation of the results on 202 patients was planned. Results.We first processed each data layer assessing data robustness, removed not informative variables and scaled quantitative ones. We considered recurrent genomic and cytogenetic lesions (present in ≥5 patients), platelets, hemoglobin and bone marrow blasts (%), age and sex as covariates. To explore the main patterns of expression changes, PCA was performed to reduce multidimensional correlated expression features (20 PCs was selected, explaining 42% of the total transcriptomic variability). To evaluate the prognostic power of each data layer we grouped all available features into five groups: gene mutations (n=15), cytogenetic alterations (n=7), expression data (n=20), blood counts (n=3) and demographic variables (n=2). Within a 5-fold CV we combined these variables in our integrative model to calculate MDS patients risk. The obtained predictive accuracy (C-index) for OS was 0.83, underlying that transcriptomic data significantly improved the current standard prognostic scoring systems. Accordingly, in our patient population, the C-index of the conventional IPSS-R score and the new IPSS-M were 0.68 and 0.76, respectively. A similar improvement by adding transcriptomic data was observed in prediction of the risk of AML evolution. Moreover, by analyzing the contribution of each feature category to the OS probability ( Figure 1), in term of explained variance, the relative impact of transcriptomic is 40%, with the remaining prognostic information distributed among genomic features (somatic gene mutations and cytogenetics lesions, 24%), demographics (20%) and clinical features (15%). An independent validation of these results on 202 patients is currently ongoing. Figure 2 shows an example of personalized survival prediction using patients from the study population. In two subjects with same clinical phenotype and mutations leading to a similar IPSS-M prognosis, the integrative model captures additional prognostic information and efficiently predicts clinical outcome. Given the complexity of our model, specific technological support is needed to combine data at individual patient level and to translate it into a personalized outcome prediction. To this aim, we created a prototype web portal based on our dataset for user-defined genomic/transcriptomic and clinical features. Conclusion. In predicting survival of MDS patients, genomic, transcriptomic and diagnostic clinical variables all have utility, with a significant contribution from the transcriptome.

Small-Molecule U2 Auxiliary Factor Homology Motif (UHM) Domain Inhibitors Cause Splicing Pattern Changes in U2AF1 Mutant Leukemia Cells and Induce Sub-G1 Cell Cycle Arrest

Mutations in factors involved in the spliceosomal pathway have emerged to be an important contributor to the development of myeloid neoplasms including MDS and secondary AML (sAML). A set of frequently mutated genes encoding RNA splicing factors including SF3B1, U2AF1, SRSF2, and ZRSR2 or haploinsufficiency of LUC7L2 have beenreported, but pharmacological intervention targeting these genes remains limited and under-developed. Combination of mutations of these splicing factors are rarely found in patients indicating that multiple defects in a spliceosome pathway may be deleterious. Heterozygous mutation in U2AF1 found in MDS leads to the acquisition of the neomorphic mutant U2AF1 (U2AF1 wt) that relies on wild-type U2AF1 (U2AF1 wt) to survive and proliferate. To support our hypothesis, we undertook a discovery campaign to identify small-molecule compounds targeting U2AF1. By recognizing the challenge of discovering compounds selectively targeting the mutant zinc-finger domains in U2AF1 found clinically, we devised a tractable intervention strategy to inhibit the UHM domain of U2AF1 (U2AF1-UHM). U2AF1-UHM binds with U2AF2 to form a protein complex (U2AF1/U2AF2) that recognizes the 3' splice site in mRNA processing. U2AF1-UHM inhibitors may decrease the binding between U2AF1 and U2AF2 and abrogate U2AF1/U2AF2 functions to change expression patterns of protein isoforms. To identify hit compounds for development, we performed screening of ~3000 fragment molecules against U2AF1-UHM using the thermal shift assay. Two of the top hits were derivatives of the same chemical scaffold. We verified that both hits inhibited the binding of U2AF1-UHM and U2AF2-ULM (U2AF ligand motifs) in our Homogenous Time-Resolved Fluorescence (HTRF) assay. We next evaluated the top hit, SF-1-8, in our K562-U2AF1 S34F mutant cell line and obtained an IC50 at the micromolar range. In contrast, SF-1-8 had no activity in K562-U2AF1 wt cell line and bone marrow cells obtained from healthy individuals. Based on SF-1-8, we performed chemical modifications to develop structure-activity relationship (SAR) of SF-1-8 and obtained SF-1-50 that was two-fold more potent than SF-1-8. To assess the selectivity of SF-1-8 and analogs to other UHM containing proteins, we further determined the IC50 values of our SF-1-8 analogs to RBM39-UHM, SPF45-UHM, and PUF60-UHM to construct the selectivity profiles of our compounds. The selectivity profiles of SF-1-8 and SF-1-50 showed they were selectively more effective to U2AF1-UHM than RBM39-UHM, SPF45-UHM, and PUF60-UHM. We then studied pathways impacted by these inhibitors in K562-U2AF1 S34F cells by performing RNA-seq in K562-U2AF1 S34F cells treated with SF-1-8 at 5 uM and control. We found that 36 and 63 genes were significantly (p <0.002) up- and down-regulated respectively by SF-1-8 in K562-U2AF1 S34F cells. Downregulated genes included CBL, CBLL1, and a subset of collagen genes ( COL1, COL3, COL5) and upregulated genes included ATF3 and BCL2. When analyzing the transcript changes affected by SF-1-8, we identified substantial protein isoform changes in genes involved with proteosome, endocytosis, apoptosis, extracellular matrix/cell adhesion, histones, and stress response. Primary effects from changes of protein isoform patterns ameliorated the restoration of the trans-Golgi network ( ERGIC3, COPB2), secretory pathway ( RUSC1, AP4E1) and impairment of clathrin mediated endocytosis and endosome-lysosome transport ( CBL, PICALM, VAMP7, ASAP1). NKM-1 cell line was previously characterized to carry U2AF1 mutation. We also found SF-1-50 caused accumulation of sub-G1 cells in NKM-1 cells in a dose-dependent manner. In summary, SF-1-8 caused disruption of extra- and intracellular protein transport in K562-U2AF1 S34F cells and represented a new class of small-molecule inhibitors to target U2AF1-UHM. Further optimization of this class of compounds will allow us to develop effective chemical probes for study in the U2af1 murine models and assess the potential of U2AF1 as a therapeutic target in MDS and sAML.

Identification of antimicrobial peptide genes from transcriptomes in Mandarin fish (Siniperca chuatsi) and their response to infection with Aeromonas hydrophila

Mandarin fish (Siniperca chuatsi) is a valuable freshwater fish species widely cultured in China. Its aquaculture production is challenged by bacterial septicaemia, which is one of the most common bacterial diseases. Antimicrobial peptides (AMPs) play a critical role in the innate immune system of fish, exhibiting defensive and inhibitory effects against a wide range of pathogens. This study aimed to identify the antimicrobial peptide genes in mandarin fish using transcriptomes data obtained from 17 tissue in our laboratory. Through nucleotide sequence alignment and protein structural domain analysis, 15 antimicrobial peptide genes (moronecidin, pleurocidin, lysozyme g, thymosin β12, hepcidin, leap 2, β-defensin, galectin 8, galectin 9, apoB, apoD, apoE, apoF, apoM, and nk-lysin) were identified, of which 9 antimicrobial peptide genes were identified for the first time. In addition, 15 AMPs were subjected to sequence characterization and protein structure analysis. After injection with Aeromonas hydrophila, the number of red blood cells, hemoglobin concentration, and platelet counts in mandarin fish showed a decreasing trend, indicating partial hemolysis. The expression change patterns of 15 AMP genes in the intestine after A. hydrophila infection were examined by using qRT-PCR. The results revealed, marked up-regulation (approximately 116.04) of the hepcidin gene, down-regulation of the piscidin family genes expression. Moreover, most AMP genes were responded in the early stages after A. hydrophila challenge. This study provides fundamental information for investigating the role of the different antimicrobial peptide genes in mandarin fish in defense against A. hydrophila infection.

Physiological and Molecular Responses of Camellia oleifera Seedlings to Varied Nitrogen Sources

Camellia oleifera Abel. is a unique woody edible oil tree species in China mainly distributed in red soil areas. Nitrogen is one of the important growth-limiting factors for C. oleifera, and the nitrogen form has a vital impact on the growth and development of the plants. Ammonium and nitrate are the two nitrogen forms that are maximally absorbed and utilized by the plants. Here, we used one-year-old seedlings of the main varieties of C. oleifera (‘Xianglin No. 1’, ‘Xianglin No. 27’, and ‘Xianglin No. 210’) to set up six experimental groups treated with different nitrogen forms ([NO3−:NH4+] 0:0, 10:0, 7:3, 5:5, 3:7, and 0:10) and investigated the effects of nitrogen on the vegetative growth and photosynthetic characteristics of the seedlings. This study showed that mixed nitrogen sources could significantly increase the seedling height, ground diameter, biomass accumulation, and photosynthesis efficiency. Transcriptome sequencing analysis led to the identification of 3561 differentially expressed genes in the leaves. Preliminary screening identified several key enzyme genes from nitrogen nutrient metabolic pathways that were differentially expressed among seedlings grown with different nitrogen forms, and their expression pattern changes were further characterized. All the results demonstrate that the same proportion of ammonium nitrate ratio promoted the expression of genes encoding glutamine synthetase and glutamate synthase, thereby improving nitrogen assimilation and utilization efficiency. This study could provide a theoretical basis for scientific and rational fertilization and the improvement of nitrogen utilization efficiency in C. oleifera seedlings.

Effect of IP-10/CXCR3 signaling pathway on rats with diabetic retinopathy.

This study aimed to investigate the effect of the interferon-inducible protein-10 (IP-10)/C-X-C motif chemokine receptor 3 (CXCR3) signaling pathway on rats with diabetic retinopathy. A total of 21 Sprague-Dawley rats were selected as the objects and divided into control (n=7), model (n=7) and inhibitor (n=7) groups. The rats in control group did not receive any treatment. The diabetic retinopathy model was established using streptozotocin and vascular endothelial growth factor in model group, while the rats in inhibitor group were treated with AMG 487, an inhibitor of the IP-10/CXCR3 signaling pathway, based on the treatment in model group. The changes in gene expression patterns in rats with diabetic retinopathy were screened by sequencing. After the differential genes were determined, the pathways mainly related to the complication were obtained via enrichment analysis. The expression of the IP-10/CXCR3 signaling pathway, the apoptotic cells and the expression of inflammatory molecules (IL-6, IL-12, TNF-α and IL-1β) in each group of rats were detected. It was shown in volcano plot that there were some differentially expressed genes (fold change >1.2, P<0.01) in retinal tissues of rats in control and model groups. Meanwhile, the heatmap displayed that there were great differences in the gene expression patterns between control and model groups, and the gene expressions of IP-10 and CXCR3 in model group were higher than those in control group (P<0.05). The differential genes in control and model groupwere enriched in such processes as the cAMP metabolic regulatory pathway, chemotaxis of immunocytes, proliferation of endothelial cells, response of cytokine receptors, apoptosis, mTOR signaling pathway and TGF-β-related signaling pathway. The mRNA expressions of IP-10 and CXCR3 in model group were higher than those in control group (P<0.05), while they were notably lower in inhibitor group than those in model group (P<0.05). Besides, the protein levels of IP-10 and CXCR3 were identical to the mRNA levels. The apoptotic cells were increased markedly in model group compared with those in control group (P<0.05) and inhibitor group (P<0.05). Model group exhibited higher expression levels of IL-6, TNF-α and IL-1β in retinal tissues than control group (P<0.05), while inhibitor group had distinctly lower expression levels of IL-6, TNF-α and IL-1β in retinal tissues than model group (P<0.05). The IP-10/CXCR3 signaling pathway can affect rats with diabetic retinopathy.

Transcriptome Shock in Developing Embryos of a Brassica napus and Brassica rapa Hybrid.

Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes in the hybrid progeny, called 'transcriptome shock'. To better understand the expression pattern after genome merging during the early stages of allopolyploid formation, we performed RNA sequencing analysis on developing embryos of Brassica rapa, B. napus, and their synthesized allotriploid hybrids. Here, we show that the transcriptome shock occurs in the developing seeds of the hybrids. Of the homoeologous gene pairs, 17.1% exhibit expression bias, with an overall expression bias toward B. rapa. The expression level dominance also biases toward B. rapa, mainly induced by the expression change in homoeologous genes from B. napus. Functional enrichment analysis revealed significant differences in differentially expressed genes (DEGs) related to photosynthesis, hormone synthesis, and other pathways. Further study showed that significant changes in the expression levels of the key transcription factors (TFs) could regulate the overall interaction network in the developing embryo, which might be an essential cause of phenotype change. In conclusion, the present results have revealed the global changes in gene expression patterns in developing seeds of the hybrid between B. rapa and B. napus, and provided novel insights into the occurrence of transcriptome shock for harnessing heterosis.

Identification of cell-intrinsic effects of mutated circulating cells due to clonal hematopoiesis in patients with heart failure

Abstract Clonal hematopoiesis of indeterminate potential (CHIP) is caused by somatic mutations in hematopoietic stem cells and is associated with worse prognosis in patients with heart failure with reduced ejection fraction (HFrEF). Circulating immune cells derived from patients with HFrEF harboring CHIP mutations show enhanced proinflammatory signatures. However, it is unclear, whether these signatures are derived from the relatively low number of cells harboring CHIP-driver mutations, or are indicators of a systemic pro-inflammatory activation associated with CHIP. Methods and Results We assessed the cell-intrinsic effects of the most prevalent CHIP-driver gene (DNMT3A) mutant-carrying circulating immune cells in a total of 5 patients with HFrEF. Using an improved protocol to detect mutant cells on a single cell level (MutDetect-Seq), as illustrated in figure 1A, we show that CHIP mutations can be detected in all major immune cell types (e.g. T cells, monocytes, B cells, NK cells). DNMT3A mutant monocytes demonstrated the highest number of significantly upregulated genes relative to other cell types. Specifically, DNMT3A mutant monocytes exhibit altered gene expression profiles associated with inflammation and phagolysosome function (figure 1B). In addition, DNMT3A mutant carrying CD4+, but not CD8+ T cells, showed significant changes in gene expression patterns towards effector cells and away from a naïve T cell state. Finally, increased paracrine signaling pathways involved in amplifying inflammatory circuits are predicted between mutated and non-mutated monocytes. Conclusion This is the first study to decipher the genetic signature of DNMT3A-CHIP-driver mutation carrying circulating immune cells, thereby providing first evidence for the cell intrinsic effects of DNMT3A mutations on peripheral blood cell subsets in patients with HFrEF. The altered gene expression profiles associated with inflammation and phagolysosome function of mutant monocyte as well as the skewing of mutated T cells towards effector cells provide novel insights into how CHIP might promote worse prognosis in heart failure patients.MutDetect-seq

Abstract 13045: Myofibroblasts Revert to an Inactive Phenotype During Regression of Heart Failure

Introduction: The therapy of left ventricular mechanical unloading, such as transcatheter aortic valve replacement(TAVR)and left ventricular assist devices(LVAD)has significantly improved prognosis for patients with heart failure. However, the detailed cellular and/or molecular mechanisms of recovery of cardiac function remain unknown. Objective: We aimed to build a cellular atlas of the heart that experienced stress and de-stress process, with a focus on myofibroblasts, specifically its cell fate of differentiation and function. Methods: We conducted single-cell and ATAC sequencing on non-myocardial cells from mouse heart samples of pressure overload-induced heart failure and recovery, using TAC (transverse aortic arch constriction)/deTAC (with suture for the constriction removed 2 weeks after TAC) model to identify the dynamic changes. Lineage tracing technique was also used to gain further insight into cell fate and reciprocal interactions. Macrophage subgroup was cleared using various approaches to investigate the cross-talk between myofibroblast and macrophage. Results: We generated a TAC/deTAC mouse model which can faithfully simulate a reversal process of functioning for the heart that underwent a pressure overload stress. Multi-omics sequencing reveals the genetic changes and transcriptional regulation of cell populations at different stages. Among the different cell types, significant changes in the gene expression pattern were observed in fibroblasts. Aided by myofibroblast lineage tracing, flow cytometry examinations suggested that remaining in a quiescent state rather than showing a decrease in its number appeared as the main fate of myofibroblasts. Surprisingly, however, simultaneous pressure unloading and macrophage clearance resulted in a significant reduction in the number of myofibroblasts. Conclusions: With a reliable TAC/deTAC mouse model, our multi-omics data revealed dynamic changes in cell populations of the heart that underwent pressure overload followed by unloading, our data demonstrated a quiescent state rather than a reduction in number was the major fate for the activated myofibroblasts for which macrophages were involved. These findings provide a theoretical basis for further treatment.

Opsin Gene Duplication in Lepidoptera: Retrotransposition, Sex Linkage, and Gene Expression.

Color vision in insects is determined by signaling cascades, central to which are opsin proteins, resulting in sensitivity to light at different wavelengths. In certain insect groups, lineage-specific evolution of opsin genes, in terms of copy number, shifts in expression patterns, and functional amino acid substitutions, has resulted in changes in color vision with subsequent behavioral and niche adaptations. Lepidoptera are a fascinating model to address whether evolutionary change in opsin content and sequence evolution are associated with changes in vision phenotype. Until recently, the lack of high-quality genome data representing broad sampling across the lepidopteran phylogeny has greatly limited our ability to accurately address this question. Here, we annotate opsin genes in 219 lepidopteran genomes representing 33 families, reconstruct their evolutionary history, and analyze shifts in selective pressures and expression between genes and species. We discover 44 duplication events in opsin genes across ∼300 million years of lepidopteran evolution. While many duplication events are species or family specific, we find retention of an ancient long-wavelength-sensitive (LW) opsin duplication derived by retrotransposition within the speciose superfamily Noctuoidea (in the families Nolidae, Erebidae, and Noctuidae). This conserved LW retrogene shows life stage-specific expression suggesting visual sensitivities or other sensory functions specific to the early larval stage. This study provides a comprehensive order-wide view of opsin evolution across Lepidoptera, showcasing high rates of opsin duplications and changes in expression patterns.

Distinct Patterns of Gene Expression Changes in the Colon and Striatum of Young Mice Overexpressing Alpha-Synuclein Support Parkinson's Disease as a Multi-System Process.

Evidence supports a role for the gut-brain axis in Parkinson's disease (PD). Mice overexpressing human wild type α- synuclein (Thy1-haSyn) exhibit slow colonic transit prior to motor deficits, mirroring prodromal constipation in PD. Identifying molecular changes in the gut could provide both biomarkers for early diagnosis and gut-targeted therapies to prevent progression. To identify early molecular changes in the gut-brain axis in Thy1-haSyn mice through gene expression profiling. Gene expression profiling was performed on gut (colon) and brain (striatal) tissue from Thy1-haSyn and wild-type (WT) mice aged 1 and 3 months using 3' RNA sequencing. Analysis included differential expression, gene set enrichment and weighted gene co-expression network analysis (WGCNA). At one month, differential expression (Thy1-haSyn vs. WT) of mitochondrial genes and pathways related to PD was discordant between gut and brain, with negative enrichment in brain (enriched in WT) but positive enrichment in gut. Linear regression of WGCNA modules showed partial independence of gut and brain gene expression changes. Thy1-haSyn-associated WGCNA modules in the gut were enriched for PD risk genes and PD-relevant pathways including inflammation, autophagy, and oxidative stress. Changes in gene expression were modest at 3 months. Overexpression of haSyn acutely disrupts gene expression in the colon. While changes in colon gene expression are highly related to known PD-relevant mechanisms, they are distinct from brain changes, and in some cases, opposite in direction. These findings are in line with the emerging view of PD as a multi-system disease.

Bone marrow mesenchymal stem cells to ameliorate experimental autoimmune encephalomyelitis via modifying expression patterns of miRNAs.

Clinical and experimental studies highlighted the significant therapeutic role of Mesenchymal stem cells (MSCs) in neurodegenerative diseases. MSCs possess potent immunomodulatory properties by releasing exosomes, which generate a suitable microenvironment. microRNAs (miRNAs), as one of several effective bioactive molecules of exosomes, influence cellular communication and activities in recipient cells. Recent studies revealed that miRNAs could control the progression of multiple sclerosis (MS) via differentiation and function of T helper cells (Th). Here, we investigated the therapeutic effects of syngeneic-derived BM-MSC in experimental autoimmune encephalomyelitis (EAE) mouse model of MS by evaluating expression profile of miRNAs, pro- and anti-inflammatory in serum and brain tissues. Three-time scheme groups (6th day, 6th & 12th days, and 12th day, of post-EAE induction) were applied to determine the therapeutic effects of intraperitoneally received 1*106 of BM-MSCs. The expression levels of mature isoforms of miR-193, miR-146a, miR-155, miR-21, and miR-326 showed that BM-MSCs treatment attenuated the EAE clinical score and reduced clinical inflammation as well as demyelination. The improved neurological functional outcome associated with enhanced expression of miR-193 and miR-146a, but decreased expression levels of miR-155, miR-21, and miR-326 were followed by suppressing effects on Th1/Th17 immune responses (reduced levels of IFN-γand IL-17 cytokine expression) and induction of Treg cells, immunoregulatory responses (increase of IL-10, TGF-β, and IL-4) in treatment groups. Our findings suggest that BM-MSCs administration might change expression patterns of miRNAs and downstream interactions followed by immune system modulation. However, there is a need to carry out future human clinical trials and complementary experiments.

The role of citrate synthase HbCS4 in latex regeneration of Hevea brasiliensis (para rubber tree)

The rubber tree, Hevea brasiliensis, is a tropical rubber-yielding crop with economic importance and provides over 90% of natural rubber (NR) for the global rubber industry. NR biosynthesis belongs to a typical secondary metabolism in laticifers. Definitely, NR production is a huge energy-consuming metabolism, especially during latex regeneration. The tricarboxylic acid (TCA) cycle, as the primary energy source, strongly supports NR synthesis in laticifers. In this study, a mitochondrial citrate synthase (CS) gene named as HbCS4 was isolated from rubber tree and related changes of expression patterns, enzyme activity and metabolites assays in response to tapping and ethephon (ethylene-releasing agent) treatments were compared. These molecular analyses were also conducted in two typical varieties Reyan 7–33–97 and PR107 as well as in HbCS4-overexpressing lines. As a result, the expression characteristics of HbCS4 or its enzyme activity tallied with the energy requirement of rubber synthesis in both treatments and the yielding traits of varieties Reyan 7–33–97 and PR107. In addition, in HbCS4-overexpressing lines, the activities of three key enzymes in TCA cycle, namely CS, NAD-IDH and α-KGDH, were all increased simultaneously. To conclude, these results suggested that HbCS4 is the initial enzyme required for energy supply in laticifers, which greatly contributes to rubber production through changing its expression or enzyme activity.

Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice Subspecies Indica and Japonica.

Changes in gene expression patterns can lead to the variation of morphological traits. This phenomenon is particularly evident in recent evolution events such as crop domestication and responses to environmental stress, where alterations in expression levels can efficiently give rise to domesticated syndromes and adaptive phenotypes. Rice (Oryza sativa L.), one of the world's most crucial cereal crops, comprises two morphologically distinct subspecies, Indica and Japonica. To investigate the morphological divergence between these two rice subspecies, this study planted a total of 315 landrace individuals of both Indica and Japonica under identical cultivation conditions. Out of the 16 quantitative traits measured in this study, 12 exhibited significant differences between the subspecies. To determine the genetic divergence between Indica and Japonica at the whole-genome sequence level, we constructed a phylogenetic tree using a resequencing dataset encompassing 95 rice landrace accessions. The samples formed two major groups that neatly corresponded to the two subspecies, Indica and Japonica. Furthermore, neighbor-joining (NJ) trees based on the expression quantity of effectively expressed genes (EEGs) across five different tissues categorized 12 representative samples into two major clades aligning with the two subspecies. These results imply that divergence in genome-wide expression levels undergoes stabilizing selection under non-stressful conditions, with evolutionary trends in expression levels mirroring sequence variation levels. This study further supports the pivotal role of changes in genome-wide expression regulation in the divergence of the two rice subspecies, Indica and Japonica.

Ralstonia solanacearum Suppresses Tomato Root Growth by Downregulation of a Wall-Associated Receptor Kinase.

The root architecture of a range of host plants is altered in response to Ralstonia solanacearum infection. This work aimed to identify host genes involved in root development during R. solanacearum infection. A deficient mutant of the type III secretion system regulator hrpB was created in R. solanacearum GMI1000. The hrpB mutant was impaired in virulence but showed a similar suppressive effect as wild-type GMI1000 on tomato root development. Based on comparative transcriptome analysis, 209 genes were found that showed the same changed expression pattern in GMI1000 and hrpB mutant infected roots relative to uninoculated roots. Among them, the wall-associated receptor kinase WAKL20 was substantially downregulated in GMI1000 and hrpB mutant infected roots. Knockdown of WAKL20 led to a shorter primary root length and fewer lateral roots in tomato as well as in Nicotiana benthamiana. The WAKL20 is a pivotal target suppressed by R. solanacearum to shape the altered root development during infection.