Downregulation Of Genes Research Articles

Systemic low-dose anti-fibrotic treatment attenuates ovarian aging in the mouse.

The female reproductive system is one of the first to age in humans, resulting in infertility and endocrine disruptions. The aging ovary assumes a fibro-inflammatory milieu which negatively impacts gamete quantity and quality as well as ovulation. Here, we tested whether the systemic delivery of anti-inflammatory (Etanercept) or anti-fibrotic (Pirfenidone) drugs attenuates ovarian aging in mice. We first evaluated the ability of these drugs to decrease the expression of fibro-inflammatory genes in primary ovarian stromal cellstreated with a pro-fibrotic or a pro-inflammatory stimulus. Whereas Etanercept did not block Tnf expression in ovarian stromal cells, Pirfenidone significantly reduced Col1a1 expression. We then tested Pirfenidone in vivo where the drug was delivered systemically via mini-osmotic pumps for 6weeks. Pirfenidone mitigated the age-dependent increase in ovarian fibrosis without impacting overall health parameters. Ovarian function was improved in Pirfenidone-treated mice as evidenced by increased follicle and corpora lutea number, AMH levels, and improved estrous cyclicity. Transcriptomic analysis revealed that Pirfenidone treatment resulted in an upregulation of reproductive function-related genes at 8.5months and a downregulation of inflammatory genes at 12months of age. These findings demonstrate that reducing the fibroinflammatory ovarian microenvironment improves ovarian function, thereby supporting modulating the ovarian environment as a therapeutic avenue to extend reproductive longevity.

Deciphering avian hematopoietic stem cells by surface marker screening and gene expression profiling

BackgroundAvian species have played a pivotal role in developmental hematopoiesis research, leading to numerous critical discoveries. Avian influenza, particularly the H5N1 strain, poses a significant threat to poultry and has zoonotic potential for humans. Infections often result in abnormal hematologic profiles, highlighting the complex interplay between avian diseases and hematopoiesis. Many avian diseases can suppress immune cells in the bone marrow (BM), impacting immune responses. Studying hematopoietic stem cells (HSCs) in avian BM is crucial for understanding these processes and developing effective vaccines and protection strategies for both avian and human health. MethodsThis study adapted methods from mouse studies to isolate avian HSCs as Lineage-negative (Lin-) cells. These isolated cells were further identified as Lin-Sca1+c-Kit+ (LSK) and were found to be more prevalent than in control groups. RT-PCR analyses were conducted, showing that genes like MEIS1 and TSC1 were upregulated, while SIRT1, FOXO1, and AHR were downregulated in these stem cells. Screening for LSK markers revealed ten unique surface antigens in the Sca1+c-Kit+ cell populations, including highly enriched antigens such as CD178, CD227, and CD184. Additionally, studies on quail HSCs demonstrated that similar labeling techniques were effective in quail BM. ResultsThe research demonstrated that the identification of avian HSC-specific surface antigens provides valuable insights into the pathogenesis of avian influenza and other diseases, enhancing our understanding of how these diseases suppress HSC function. Notably, the upregulation of MEIS1 and TSC1 genes in LSK cells underscores their critical roles in regulating hematopoietic processes. Conversely, the downregulation of SIRT1, FOXO1, and AHR genes provides important clues about their roles in differentiation and immune response mechanisms. DiscussionThe findings of this study deepen our understanding of the effects of avian diseases on the immune system by identifying surface markers specific to avian HSCs. The suppression of HSC function by pathogens such as influenza highlights the importance of understanding these cells in developing targeted vaccines. These results represent a significant step towards improving global health security by mitigating risks associated with avian pathogens.

The adipose tissue melanocortin 3 receptor is targeted by ghrelin and leptin and may be a therapeutic target in obesity

ObjectiveObesity is linked to perturbations in energy balance mechanisms, including ghrelin and leptin actions at the hypothalamic circuitry of neuropeptide Y (NPY) and melanocortin. However, information about the regulation of this system in the periphery is still scarce. Our objective was to study the regulation of the NPY/melanocortin system in the adipose tissue (AT) and evaluate its therapeutic potential for obesity and type 2 diabetes. MethodsThe expression of the NPY/melanocortin receptors’ levels was assessed in the visceral AT of individuals with obesity and altered metabolism. Protein levels of these receptors were evaluated in cultured adipocytes incubated with ghrelin (30 and 100 ng/mL) and leptin (1 and 10 nM) and in the AT of an animal model with a mutation in the leptin receptor (ZSF1 rat), to understand their regulation by leptin and ghrelin. The vertical sleeve gastrectomy animal model was used to evaluate the putative therapeutic potential of the NPY/melanocortin system. ResultsIn this study, we unravelled that leptin (1 nM and 10 nM) selectively reduced the levels of NPY5R and MC3R but no other NPYR/MCRs in cultured adipocytes. In turn, acylated ghrelin (100 ng/mL) significantly increased NPY1R, but the inhibition of its receptor also abrogates MC3R levels. However, in the Lepr-deficient ZSF1 rat, both NPY5R and MC3R levels were reduced, along with other NPYRs and MCRs, suggesting that leptin resistance negatively affects NPY and melanocortin signalling. In human adipose tissue, we found a downregulation of genes encoding the NPY and melanocortin receptors in the visceral AT of individuals with obesity and insulin resistance, being correlated with genes regulating metabolic activity. Additionally, diabetic obese rats submitted to vertical sleeve gastrectomy showed increased levels of NPY, melanocortin, ghrelin, and leptin receptors in the AT, including MC3R, suggesting it may constitute a therapeutic target in obesity. ConclusionsOur results suggest that the AT NPY/melanocortin system, particularly the MC3R, may be involved in the neuroendocrine regulation of adipocyte metabolism. Altogether, our work shows MC3R is under the control of the ghrelin/leptin duo, is reduced in patients with obesity and prediabetes, and may constitute a therapeutic target in obesity.

Modulation of osteoblastogenesis by NRF2: NRF2 activation suppresses osteogenic differentiation and enhances mineralization in human bone marrow-derived mesenchymal stromal cells.

Mesenchymal stromal stem cells (MSCs) or skeletal stem cells (SSCs) play a major role in tissue repair due to their robust ability to differentiate into osteoblasts, chondrocytes, and adipocytes. Complex cell signaling cascades tightly regulate this differentiation. In osteogenic differentiation, Runt-related transcription factor 2 (RUNX2) and ALP activity are essential. Furthermore, during the latter stages of osteogenic differentiation, mineral formation mediated by the osteoblast occurs with the secretion of a collagenous extracellular matrix and calcium deposition. Activation of nuclear factor erythroid 2-related factor 2 (NRF2), an important transcription factor against oxidative stress, inhibits osteogenic differentiation and mineralization via modulation of RUNX2 function; however, the exact role of NRF2 in osteoblastogenesis remains unclear. Here, we demonstrate that NRF2 activation in human bone marrow-derived stromal cells (HBMSCs) suppressed osteogenic differentiation. NRF2 activation increased the expression of STRO-1 and KITLG (stem cell markers), indicating NRF2 protects HBMSCs stemness against osteogenic differentiation. In contrast, NRF2 activation enhanced mineralization, which is typically linked to osteogenic differentiation. We determined that these divergent results were due in part to the modulation of cellular calcium flux genes by NRF2 activation. The current findings demonstrate a dual role for NRF2 as a HBMSC maintenance factor as well as a central factor in mineralization, with implications therein for elucidation of bone formation and cellular Ca2+ kinetics, dystrophic calcification and, potentially, application in the modulation of bone formation.

The Impact of Ten Days of Periodic Fasting on the Modulation of the Longevity Gene in Overweight and Obese Individuals: A Quasi-Experimental Study.

Fasting potentially alters the aging process induced by obesity by regulating telomere integrity, which is related to longevity genes. However, the impact of periodic fasting (PF) on the expression of longevity genes, particularly Forkhead Box O Transcription Factors (FOXO3a) and the Human Telomerase Reverse Transcriptase (hTERT), is not fully understood. This study aimed to analyze the effects of PF, specifically on FOXO3a, hTERT expression, and other associated factors. A quasi-experimental 10-day study was conducted in Surabaya, East Java, Indonesia. This study consisted of an intervention group (PFG), which carried out PF for ten days using a daily 12 h time-restricted eating protocol, and a control group (CG), which had daily meals as usual. FOXO3a and hTERT expression were analyzed by quantitative real-time qPCR. A paired t-test/Wilcoxon test, independent t-test/Mann-Whitney U-test, and Spearman's correlation test were used for statistical analysis. Thirty-six young men participated in this study. During the post-test period, FOXO3a expression in the PFG increased 28.56 (±114.05) times compared to the pre-test, but the difference was not significant. hTERT expression was significantly higher in both the CG and PFG. The hTERT expression in the PFG was 10.26 (±8.46) times higher than in the CG, which was only 4.73 (±4.81) times higher. There was also a positive relationship between FOXO and hTERT in the CG. PF significantly increased hTERT expression in the PFG; however, no significant increase was found in FOXO3a expression. PF regimens using the 12 h time-restricted eating approach may become a potential strategy for preventing obesity-induced premature aging by regulating longevity gene expression.

Abstract A019: Black race and CA 19-9 nonproduction is associated with limited pathologic response to neoadjuvant chemotherapy in patients with localized pancreatic cancer

Abstract Introduction: Black patients with pancreatic ductal adenocarcinoma (PDAC) are less likely to have major pathologic response (MPR) following induction chemotherapy. Our previous study suggested a lower baseline CA 19-9 among Black patients. We aimed to determine if CA 19-9 nonproduction contributes to racial differences in neoadjuvant chemotherapy (NAC) response. We then investigated the biological mechanisms underlying reduced response in CAnonprod with multi-omic analysis. Methods: Black and White patients with PDAC receiving ≥ 2 cycles of NAC followed by pancreatectomy at 7 high-volume centers were reviewed. Patients were categorized as CAproducers (CAprod, CA 19-9 > 5 U/mL) or CAnonprod (CA 19-9 ≤ 5 U/mL). Uni- and multi-variable models evaluated differences in rates of CAnonprod by race, and the association of CAnonprod with MPR (CAP 0/1). The Pancreatic Cancer Action Network SPARK platform was queried for patients with CA 19-9 and genomic data. Fisher’s exact test was used to compare differentially mutated genes between CAnonprod and CAprod. Differential gene expression (DEG) analysis identified significantly differentially expressed genes using an absolute fold change of ≥ 2 and p-adj < 0.05 as a cutoff. quanTIseq computational pipeline was used for immune cell deconvolution analysis of the two groups. Results: Our cohort included 385 CAprod and 30 CAnonprod. CAnonprod had a significantly higher rate of Black patients (50% vs 13%, p<0.01). Compared with CAprod, CAnonprod received similar rates of FOLFIRINOX (60% vs. 57%, p=0.27) and duration of NAC (4 vs 5 cycles, p=0.83). Rate of MPR was higher among CAprod compared to CAnonprod (26% vs 8%, p=0.03). No CAnonprod patient had a complete pathologic response vs 28 (7%) of CAprod (p=0.12). CAnonprod was independently associated with decreased odds of MPR (OR 0.21, CI [0.04-0.99]). Black race was independently associated with increased odds of CAnonprod (OR 8.66, CI [3.81 – 19.7]). When CA 19-9 production status was matched by race, there was no difference between rate of MPR between White and Black CAnonprod; both experienced low rates of MPR (12% and 9%, respectively, (p=0.68)). CAnonprod had higher rates of SWI/SNF alterations (50% CAnonprod vs 33% CAprod, p< 0.01; P-adj=ns), and ARID1B was the most frequently mutated gene in CAnonprod (28% vs 11%, p< 0.01; P-adj=ns). DEG analysis showed the LIPF gene was significantly downregulated in CAnonprod compared to CAprod. There was no difference in immune cell distribution between CAprod and CAnonprod. Conclusion: CA 19-9 non-production is more prevalent in Black patients and potentially mediates the lower rates of MPR following NAC. CA 19-9 non-production is associated with higher rates of SWI/SNF alterations and a downregulation of the LIPF gene encoding gastric lipase, unveiling a potential biologic or metabolomic difference in response to chemotherapy between races. Citation Format: Mary P. Martos, Erin M. Dickey, Kawther Abdilleh, Syed A. Ahmad, Shishir K. Maithel, Chet W. Hammill, Hong Jin Kim, Daniel E. Abbott, David A. Kooby, Alexander A. Parikh, Peter J. Hosein, Nipun B. Merchant, Jashodeep Datta, Caitlin A. Hester. Black race and CA 19-9 nonproduction is associated with limited pathologic response to neoadjuvant chemotherapy in patients with localized pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A019.

Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis in C. elegans.

Caenorhabditis elegans males undergo sex-specific tail tip morphogenesis (TTM) under the control of the DM-domain transcription factor DMD-3. To find genes regulated by DMD-3, we performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males versus dmd-3(-) males and hermaphrodites. The transcription profile of dmd-3(-) tail tips is similar to that in hermaphrodites. For validation, we analyzed transcriptional reporters for 49 genes and found male-specific or male-biased expression for 26 genes. Only 11 DE genes overlapped with genes found in a previous RNAi screen for defective TTM. GO enrichment analysis of DE genes finds upregulation of genes within the unfolded protein response pathway and downregulation of genes involved in cuticle maintenance. Of the DE genes, 40 are transcription factors, indicating that the gene network downstream of DMD-3 is complex and potentially modular. We propose modules of genes that act together in TTM and are co-regulated by DMD-3, among them the chondroitin synthesis pathway and the hypertonic stress response.

Abstract A052: Silencing MICAL2 Expression in Pancreatic Cancer Cells rewires the tumor microenvironment through the IL1-a/p38 MAP kinase/STAT-3 axis and Sensitizes Tumors to Immune Checkpoint Blockade therapy

Abstract Introduction: PDAC is marked by a fibroinflammatory stroma and thrives on interactions between cancer cells and their microenvironment, including CAFs and immune cells, driving disease progression and treatment resistance. Using ChIP-seq on resected human PDAC samples, we identified MICAL2 as a super-enhancer-associated gene and its role in tumor progression. MICAL2 is a flavin monooxygenase that promotes actin depolymerization and SRF transcription. Here, we evaluated how tumor cell-expressed MICAL2 rewires the PDAC microenvironment through the IL1-a/p38 MAP kinase/STAT3 axis. Methods: KPC-Shcontrol (ShCNT) and MICAL2 (M2KD) were orthotopically injected to assess tumor growth. Sc-RNA seq, immunophenotyping, and immunohistochemistry were performed on ShCNT and M2KD tumors. Atomic force microscopy was done to assess tissue stiffness. CD8+ specific antibodies were used for T-cell depletion. Adoptive transfer of CD8+ T cells enriched from M2KD tumors was performed by tail vein injection. Anti-PD1 and anti-IL-1a antibodies were injected IP. RNA-Seq analysis was performed on human PDAC cells (AsPC-1 ShCNT and M2KD) and validation of IL-1α and IL-1R expression was done in human and mouse pancreas control, KD, OE cancer cell lines, and PSCs by q-PCR. We exposed PSCs to conditioned media from cancer cells with and without MICAL2 and checked the expression of genes related to inflammation and fibrosis by qPCR. Results: Orthotopic injections of KPC-M2KD cells led to decreased tumor growth compared to ShCNT (0.26 gm vs. 1 gm, p = 0.008). Sc-RNA and immunohistochemistry revealed reduced PDPN+ and a-SMA+ CAFs in M2KD tumors. We also observed less collagen and fibronectin deposition in M2KD tumors resulting in reduced tissue stiffness as measured by atomic force microscopy. Flow cytometry and immunofluorescence showed increased intertumoral infiltration of cytotoxic and effector CD8+T cells in M2KD tumors. CD8+T cell depletion reversed growth inhibition in M2KD tumors. Adoptive transfer of CD8+T cells enriched from M2KD tumors impeded control tumor growth. RNA-seq revealed decreased IL1-α expression in M2KD cells (p<0.05). IL1R expression was reduced on PSCs when cocultured with M2KD vs. control cell media. PSCs co-cultured with M2KD cancer cells also showed significant downregulation of genes including IL-6, Cxcl1, and LIF changes that were rescued by adding recombinant IL-1α in M2KD cells. Western blot showed MICAL2 regulates the phosphorylation of p38 MAP kinase which in turn regulates the expression of IL1-α and STAT3 activation confirmed by treating dox-inducible ShCNT and ShM2KD cancer cells with p38 inhibitor. Treating M2KD tumors with immune checkpoint blockade PD-1 alone significantly reduced tumor size and 50% of M2KD tumor-bearing mice had complete tumor regression after treatment with PD-1 and neutralizing IL-1a antibodies. Conclusion: MICAL2 mediates tumor-stromal crosstalk through the IL1-a/p38/STAT3 axis and creates an immunosuppressive environment in PDAC. MICAL2 may be a potential immunomodulatory target for pancreatic cancer therapy. Citation Format: Bharti Garg, Evangeline Mose, Edgar Esparaza, Jay Patel, Rithika Medari, Alexei Martsinkovskiy, Carrie Bishop, Gissele Gonzalez, Adam Engler, Parag Katira, Herve Tiriac, Andrew M Lowy. Silencing MICAL2 Expression in Pancreatic Cancer Cells rewires the tumor microenvironment through the IL1-a/p38 MAP kinase/STAT-3 axis and Sensitizes Tumors to Immune Checkpoint Blockade therapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A052.

Azacitidine and cytarabine induce sustained lymphopenia with abnormal differentiation of common lymphoid progenitors and prolonged suppression of Dnmt3a and Dnmt3b expression in mice.

Myelosuppression is a major side effect of chemotherapy. Although decreased blood cells are restored with the recovery of bone marrow cells, insufficient recovery of decreased lymphocytes was observed in mice given azacitidine (AZA), a DNA methyltransferase (DNMT) inhibitor, even following the restoration of bone marrow cells. To understand the mechanisms behind this sustained lymphopenia, we examined AZA's impact on the hematopoietic progenitor cells and the expression of Dnmts and differentiation-related genes. An antimetabolite of cytidine analog, cytarabine (Ara-C), was used as a reference compound. Decreases in almost all blood parameters and common lymphoid progenitors (CLPs) and the downregulation of Dnmts and differentiation-related genes in Lineage-Sca-1+c-kit+ (LSK) cells were observed in mice administered AZA or Ara-C for 7 d. In the posttreatment observation, all parameters, except for lymphocytes and monocytes, exhibited recovery within 3 wk after the final dosing in both treated groups. However, no recovery from the decreases in lymphocytes, especially B cells, and monocytes occurred even after 5 wk. The number of CLPs was elevated after 3 wk. There was a tendency toward recovery from the decreased expression of Dnmt1 and differentiation-related genes, but the expression levels of Dnmt3a and Dnmt3b did not fully recover even 5 wk after the final dosing. Taken together, the findings revealed that the mechanism of sustained lymphopenia observed in mice treated with AZA or Ara-C is associated, at least in part, with the abnormal differentiation of CLPs into B cells accompanied by the prolonged suppression of Dnmt3a and Dnmt3b expression on LSK cells.

OsWRKY70 Plays Opposite Roles in Blast Resistance and Cold Stress Tolerance in Rice

The transcription factor WRKYs play pivotal roles in the adapting to adverse environments in plants. Prior research has demonstrated the involvement of OsWRKY70 in resistance against herbivores and its response to abiotic stress. Here, we reported the functional analysis of OsWRKY70 in immunity against fungal diseases and cold tolerance. The results revealed that OsWRKY70 was induced by various Magnaporthe oryzae strains. Knock out mutants of OsWRKY70, which were generated by the CRISPR/Cas9 system, exhibited enhanced resistance to M. oryzae. This was consistent with fortifying the reactive oxygen species (ROS) burst after inoculation in the mutants, elevated transcript levels of defense-responsive genes (OsPR1b, OsPBZ1, OsPOX8.1 and OsPOX22.3) and the observation of the sluggish growth of invasive hyphae under fluorescence microscope. RNA sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR) validations demonstrated that differentially expressed genes were related to plant-pathogen interactions, hormone transduction and MAPK cascades. Notably, OsbHLH6, a key component of the JA signaling pathway, was down-regulated in the mutants compared to wild type plants. Further investigation confirmed that OsWRKY70 bound to the promoter of OsbHLH6 by semi-in vivo chromatin immunoprecipitation (ChIP). Additionally, the loss-function of OsWRKY70 impaired cold tolerance in rice. The enhanced susceptibility in the mutants characterized by excessive ROS production, elevated ion leakage rate and increased malondialdehyde content, as well as decreased activity of catalase (CAT) and peroxidase (POD) under low temperature stress was, which might be attributed to down-regulation of cold-responsive genes (OsLti6b and OsICE1). In conclusion, our findings indicate that OsWRKY70 negatively contributes to blast resistance but positively regulates cold tolerance in rice, providing a strategy for crop breeding with tolerance to stress.

Mechanistic insights to Paenibacillus lentimorbus mediated biocontrol of Alternaria solani in Solanum lycopersicum L. through carbohydrate reallocation and sweet immunity suppression

Researchers envisaged that PGPR (plant growth promoting rhizobacteria) has vast possibilities as a bioinoculant that will lead to revolution. However, it's still very far from becoming commercially successful. Here, the information regarding the root colonization of PGPR in host plants and plant response towards PGPR is inadequate. It can provide valuable information for developing successful biofertilizers and biocontrol agents. PGPR (Paenibacillus lentimorbus NRRL B-30488 or CHM12) has been previously reported as a successful commercial biofertilizer and biocontrol agent. However, the exact mechanism of plant growth promotion and biocontrol is poorly studied. So, CHM12 was appraised for biotic stress amelioration of pathogen Alternaria solani in Tomato (Solanum lycopersicum L.) var. S-22 plants. PGPR CHM12 was assessed for various plant growth parameters such as proline, sugar content, etc. in pathogen A. solani (AS) challenged plants and compared with the CHM12 treated plants in a greenhouse study. Then, the metabolomics tool (GC-MS) was used to identify metabolites and their respective genes playing pivotal roles in colonization tactics availed by PGPR. Further, gene expression analysis was done to affirm the involvement of various genes related to metabolites providing biotic stress tolerance in Tomato plants. The current research discerned that PGPR CHM12 revealed significant differences in different plant growth parameters studied. There were 33 distinct metabolites identified, which stipulated the involvement of carbohydrate metabolism mainly in combating biotic stress in this study. Thus, our study reconfirmed very few reported previous results through gene expression analysis, suggesting the downregulation of carbohydrate metabolism genes in PGPR-treated plants. This downregulation of carbohydrate genes might be the critical factor for suppressing the plant's immune response to gaining entry inside the host plant. This also helps in retaining and reallocating carbohydrates in plant cells to reduce pathogen proliferation.

Functional analysis of cutinase transcription factors in Fusarium verticillioides

Fusarium verticillioides is an important pathogen of maize and causes serious yield losses and food safety issues worldwide. F. verticillioides produces highly toxic mycotoxin Fumonisin B1 (FB1) in infested commodities which makes these food and feeds unsafe for humans and animals. For pathogenic fungi to successfully penetrate its plant hosts, the pathogen secretes hydrolytic enzymes that can facilitate penetration into the plant cutin layer. However, there is limited information on how cutinases transcriptionally regulated to impact F. verticillioides pathogenicity. In this study, our aim is to functionally characterize cutinase transcription factors that regulate key cutinase activities that are directly associated with F. verticillioides pathogenicity and FB1 biosynthesis. Gene deletion of cutinase transcription factor FvCTF1α did not affect the growth and morphology of the fungal mycelia on CMII medium, whereas the conidiation, utilization of sodium acetate and sodium oleate, stress tolerance against cell wall interfering agent, and the cutinase and pectinase activities in the ΔFvctf1α mutant were negatively impacted. FvCtf1α regulates the expression of induced cutinase genes FvCUT1 and FvCUT4 by binding to their GC-rich promoters. In addition, FvCtf1α, containing a novel function in regulating FB1, interacts with the promoter of FvFUM1 and FvFUM6 to down-regulate the expression of FvFUM1 and FvFUM6, resulting in decreased production of FB1 in the ΔFvctf1α strain. ΔFvctf1α exhibited decreased pathogenicity in maize due to the down-regulation of pathogenicity-related genes as well as key downstream cutinase genes FvCUT3 and FvCUT4 in F. verticillioides. We also demonstrated that FvCtf1α regulated FvCUT3 and FvCUT4 differently; FvCUT4 via direct regulation while FvCUT3 via indirect regulation by interacting with FvFarB, a homologous protein of FvCtf1α. Moreover, RNA-seq analysis showed that FvCtf1α was associated with many pathways, such as fatty acid metabolism, carbon source utilization, cell wall integrity, oxidative stress, and fumonisin synthesis in F. verticillioides. Our study demonstrated that FvCtf1α was not only involved in the regulation of cutinases but also a broad spectrum of pathways that ultimately affect F. verticillioides virulence and mycotoxin biosynthesis.

Ex vivo disease modelling of Rett syndrome: the transcriptomic and metabolomic implications of direct neuronal conversion.

Rett syndrome (RTT) is a rare neurodevelopmental disorder that primarily affects females and is characterized by a period of normal development followed by severe cognitive, motor, and communication impairment. The syndrome is predominantly caused by mutations in the MECP2. This study aimed to use comprehensive multi-omic analysis to identify the molecular and metabolic alterations associated with Rett syndrome. Transcriptomic and metabolomic profiling was performed using neuron-like cells derived from the fibroblasts of 3 Rett syndrome patients with different MECP2 mutations (R168X, P152R, and R133C) and 1 healthy control. Differential gene expression, alternative splicing events, and metabolite changes were analyzed to identify the key pathways and processes affected in patients with Rett syndrome. Transcriptomic analysis showed there was significant down-regulation of genes associated with the extracellular matrix (ECM) and cytoskeletal components, which was particularly notable in patient P3 (R133C mutation), who had non-random X chromosome inactivation. Additionally, significant changes in microtubule-related gene expression and alternative splicing events were observed, especially in patient P2 (P152R mutation). Metabolomic profiling showed that there were alterations in metabolic pathways, particularly up-regulation of ketone body synthesis and degradation pathways, in addition to an increase in free fatty acid levels. Integrated analysis highlighted the interplay between structural gene down-regulation and metabolic shifts, underscoring the adaptive responses to cellular stress in Rett neurons. The present findings provide valuable insights into the molecular and metabolic landscape of Rett syndrome, emphasizing the importance of combining omic data to enlighten the molecular pathophysiology of this syndrome.

Environmental fluoxetine promotes skin cell proliferation and wound healing

This study investigates the effects of environmentally-relevant concentrations of fluoxetine (FLX, commercial name: Prozac) on wound healing. Pollution of water systems with pharmaceutical and personal care products, including antidepressants such as FLX and other selective serotonin reuptake inhibitors, is a growing environmental concern. Environmentally-relevant FLX concentrations are known to impact physiological functions and behaviour of aquatic animals, however, the effects of exposure on humans are currently unknown. Using a combination of human skin biopsies and a human keratinocyte cell line, we show that exposure to environmental FLX promotes wound closure. We show dose-dependent increases in wound closure with FLX concentrations from 125 ng/l. Using several –omics and pharmaceutical approaches, we demonstrate that the mechanisms underlying enhanced wound closure are increased cell proliferation and serotonin signalling. Transcriptomic analysis revealed 350 differentially expressed genes after exposure. Downregulated genes were enriched in pathways related to mitochondrial function and metabolism, while upregulated genes were associated with cell proliferation and tissue morphogenesis. Kinase profiling showed altered phosphorylation of kinases linked to the MAPK pathway. Consistent with this, phosphoproteomic analyses identified 235 differentially phosphorylated proteins after exposure, with enriched GO terms related to cell cycle, division, and protein biosynthesis. Treatment of skin biopsies and keratinocytes with ketanserin, a serotonin receptor antagonist, reversed the increase in wound closure observed upon exposure. These findings collectively show that exposure to environmental FLX promotes wound healing through modulating serotonin signalling, gene expression and protein phosphorylation, leading to enhanced cell proliferation. Our results justify a transition from the study of behavioural effects of environmental FLX in aquatic animals to the investigation of effects of exposure on wound healing in aquatic and terrestrial animals, including direct impacts on human health.

Transcriptome profiling reveals insight into the cold response of perennial ryegrass genotypes with contrasting freezing tolerance

Low freezing tolerance threatens the survival and productivity of perennial ryegrass under northern climate. In this study, we aimed to identify transcriptional changes in plants subjected to low and freezing temperatures as well as to elucidate differences between tolerant and sensitive genotypes. Response to freezing stress was evaluated in a panel of 160 perennial ryegrass genotypes by measuring electrolyte leakage after exposure to -12 °C and -14 °C for 24 h. Two tolerant and two sensitive genotypes were selected for the transcriptome analysis. Crown tissue samples were collected at six treatments: before the start of cold acclimation (control point), at the start of acclimation, after one week of acclimation, after three weeks of acclimation, after freezing at -5 °C and freezing at -10 °C. A total of 11,125 differentially expressed genes (DEGs) were identified in the sensitive and 12,937 DEGs in the tolerant genotypes, when comparing the control vs. each of the acclimation and freezing treatments, as well as the end of acclimation vs. freezing treatments. Among the identified DEGs 3323 were unique to the sensitive genotypes, 5135 were unique to the tolerant genotypes and 7802 were shared. Genes upregulated during cold acclimation and freezing stress were linked to the MAPK signalling pathway, circadian rhythm, starch and sucrose metabolism, plant-pathogen interaction, carbon fixation, alpha-linoleic acid metabolism, carotenoid metabolism, glyoxylate and dicarboxylate metabolism pathways. Downregulated genes were linked to ATP-dependent chromatin remodelling, fatty acid elongation and DNA replication. The downregulation of fatty acid elongation and glutathione metabolism DEGs could indicate that the studied genotypes respond to cold stress in a novel or not yet well-characterized manner.

Functional impacts of PtrMYB203 on phenylpropanoid pathway regulation and wood properties in hybrid poplar

The phenylpropanoid pathway is vital for plant growth and development, producing lignin and flavonoids. This study investigates PtrMYB203, a homolog of MYB repressors of proanthocyanidin (PA) biosynthesis in Populus trichocarpa, as a transcriptional repressor in the phenylpropanoid pathway of hybrid poplar (Populus alba x P. glandulosa). Overexpression of PtrMYB203 (35S::PtrMYB203) in hybrid poplar detrimentally impacted plant growth and development. Histological analysis revealed irregular xylem vessel formation and decreased lignin content, corroborated by Klason lignin assays. Moreover, 35S::PtrMYB203 transgenic poplars exhibited significant decreases in anthocyanin and PA accumulations in callus tissues, even under high light conditions. Quantitative RT-PCR analysis and protoplast-based transcriptional activation assay confirmed the downregulation of lignin and flavonoid biosynthesis genes. This genetic modification also alters the expression of several MYB transcription factors, essential for phenylpropanoid pathway regulation. Remarkably, saccharification efficiency in the 35S::PtrMYB203 poplar was improved by over 34% following hot water treatment alone. These findings suggest PtrMYB203 as a potential genetic target for enhancing wood properties for bioenergy production, providing valuable insights into the manipulation of metabolite pathways in woody perennials to advance wood biotechnology.

Differential immune gene expression in rainbow trout, Oncorhynchus mykiss (walbaum), exposed to five pathogens: Aeromonas salmonicida, Flavobacterium psychrophilum, Vibrio anguillarum, Yersinia ruckeri and Ichthyophthirius multifiliis

Rainbow trout, Oncorhynchus mykiss, originating from the same outbred population and reared under the same conditions, were bath exposed to five different pathogens (Aeromonas salmonicida, Flavobacterium psychrophilum, Vibrio anguillarum, Y. ruckeri, Ichthyophthirius multifiliis). The exposures were conducted as independent experiments with non-exposed fish as time-point controls. At peak of infections, fish showing significant clinical signs, fish without clinical signs, and time-point control fish were euthanized, and gills, spleen, and liver were sampled for gene expression analysis. At the end of the infection course, i.e. a period without any disease signs, surviving fish were sampled as well. Genes encoding 14 cytokines, 5 immune cell markers, 5 immune effector molecules and 3 reference/housekeeping genes were analyzed. The host fish exhibited different reaction patterns dependent on the pathogen. Especially trout infected with I. multifiliis showed a characteristic Th2 expression signature in gills, whereas only innate responses occurred in internal organs. Rainbow trout exposed to F. psychrophilum displayed a relatively lower expression of immune genes contrasting the host responses to A. salmonicida, V. anguillarum and Y. ruckeri. The bacterial pathogens induced a relatively similar expression profile in internal organs of trout with a few exceptions. Thus, F. psychrophilum induced upregulation of genes earlier in gills than internal organs, and A. salmonicida infected fish showed a notable downregulation of immune genes in gills. The differential expression patterns may reflect the different invasion mechanisms and target tissues associated with the five pathogens.

Microbially mediated phenolic catabolites exert differential genoprotective activities in normal and adenocarcinoma cell lines

Age-associated decline of nuclear factor erythroid 2-related factor 2 (Nrf2) activity and DNA repair efficiency leads to the accumulation of DNA damage and increased risk of cancer. Understanding the mechanisms behind increased levels of damaged DNA is crucial for developing interventions to mitigate age-related cancer risk. Associated with various health benefits, (poly)phenols and their microbially mediated phenolic catabolites represent a potential means to reduce DNA damage. Four colonic-microbiota-derived phenolic catabolites were investigated for their ability to reduce H2O2-induced oxidative DNA damage and modulate the Nrf2-Antixoidant Response Element (ARE) pathway, in normal (CCD 841 CoN) and adenocarcinoma (HT29) colonocyte cell lines. Each catabolite demonstrated significant (p < .001) genoprotective activity and modulation of key genes in the Nrf2-ARE pathway. Overall, the colon-derived phenolic metabolites, when assessed at physiologically relevant concentrations, reduced DNA damage in both normal and adenocarcinoma colonic cells in response to oxidative challenge, mediated in part via upregulation of the Nrf2-ARE pathway.

The abiotic stress gene (Asg) family member Asg2 as a modulator of plant responses to salt stress

The Abiotic Stress Gene (Asg) family, unique to plants, includes members with the DUF1005 domain of unknown function (DUFs). Although earlier studies have associated members of the Asg gene family and various aspects of plant growth, development, and reactions to abiotic stress, their precise biological roles and underlying mechanisms are not yet well understood. This research found that Asg2 functions not only in regulating root development but also serves as an inhibitor in how the plant responds to salt stress. Overexpression of Asg2 enhances primary root elongation, while gene-edited mutants display the opposite effect. Under salt stress conditions, Arabidopsis lines with increased Asg2 expression exhibit inhibited primary root elongation, reduced seed germination rates, and heightened sensitivity of leaves and seedlings to salt stress. These changes coincide with increased electrolyte leakage, reduced chlorophyll content, decreased antioxidant enzyme activity, and elevated levels of reactive oxygen species (ROS). Transcriptomic analysis revealed that overexpression of Asg2 under salt stress leads to the downregulation of stress resistance genes, thereby increasing sensitivity to salt stress. In conclusion, this research emphasizes the important function of the Asg gene in influencing salt tolerance, providing a foundational framework and genetic resource for comprehending how plants respond to salt stress.

A novel codominant plumage color pattern of white breast patches in WugangTong geese was controlled by EDNRB2

Two basic plumage color patterns are observed in adult geese: solid grey (G) or colorless white (W). However, a Chinese indigenous breed, the Wugangtong goose (WGT), continues to be subject to selective breeding efforts as it displays segregation of plumage colors, including G, W, and a novel color pattern designated Wb (G with white breast circles). The underlying genetic mechanisms responsible for the Wb phenotype are yet to be determined. The current study employed the population differentiation index (FST) to analyze 90 geese exhibiting diverse plumage colors, identifying the fifth intron of EDNRB2 as a particularly noteworthy region with the highest FST values. Sanger sequencing of the region surrounding the EDNRB2 gene identified a 14-bp insertion within exon 3 as the causal mutation. The heterozygosity of this 14-bp insertion and wild-type alleles was completely associated with the Wb phenotype, thereby substantiating the codominant nature of the G and W phenotypes. An inter-species corroborated this finding cross between the graylag (no 14-bp insertion) and the swan goose (homozygous for the 14-bp insertion) breeds, as hybrids from this cross exhibited the Wb phenotype. Transcriptomes from white breast patches and gray dorsal skins of 4 Wb geese were compared. A significant downregulation of genes involved in melanin synthesis and melanocyte development was observed, including EDRNB2 and MLANA. The downregulation of MLANA indicated that the mutated EDNRB2 resulted in melanocyte loss in specific body regions, as MLANA is a marker gene for melanocytes. The findings were corroborated by melanin staining using the Mansson-Fontana method, which revealed no melanin particles deposited in the white breast patches. In summary, the gray plumage color was codominant to the white color in WGT geese, and plumage color variations were controlled by EDNRB2. The findings of our study offer valuable and practical guidance for the purification of plumage colors among WGT, whether through traditional phenotype selection or molecular breeding methods.