Tissue-specific Responses Research Articles

Autophagy, apoptosis, and inflammation response of Sebastiscus marmoratus to different concentrations of hydroxychloroquine

Hydroxychloroquine (HCQ) is an important public health therapeutic agent widely used in the prevention and treatment of malaria and autoimmune diseases, with some antiviral effects, as well as a common autophagy inhibitor. Its autophagy-inhibiting effect attracts great research interest in mammals but is still little studied in fish. We even have no idea about the effects of HCQ on different tissues of fish and what concentrations should be used for safety studies. This study investigated the effect of different concentration of HCQ treatments on the survival, tissue structure, and expressions of genes related to autophagy, apoptosis, and inflammation in the gill, spleen, testis, and ovary of Sebastiscus marmoratus. The results showed that the higher HCQ concentration (77.40 and 154.80 mg/mL) led to mass mortality within an hour. The half-lethal concentration (LC50, 24 h) of HCQ for S. marmoratus was approximately 48.95 mg/mL. When exposed to 30.96 mg/mL HCQ for 24 hours, autophagy was blocked as revealed by electron microscopy from gill, spleen and testis of fish. The expressions of autophagy-related genes (LC3/Cx43), apoptosis-related genes (Cas3/p53), and inflammation-related genes (TNF-α/IL8) exhibited tissue-specific and dose-dependent responses. The gonads showed preferential expression of all these genes and were found to be sensitive and regular after HCQ treatment. For example, at a concentration of 30.96 mg/mL, the testis demonstrated a regularity that suggests it is an ideal candidate tissue for studying the role of HCQ or autophagy. This study systematically revealed the response of S. marmoratus to different concentrations of HCQ and provided optional assay concentrations for key tissues, serving as an important reference for the future studies on HCQ and autophagy in S. marmoratus. Furthermore, the potential crosstalk between autophagy, apoptosis, and inflammatory pathways initially identified in this study could be helpful for the future research on autophagy regulation in marine fish.

Repeat treatment of organotypic airway cultures with ethyl methanesulfonate causes accumulation of somatic cell mutations without expansion of bronchial-carcinoma-specific cancer driver mutations

The human in vitro organotypic air-liquid-interface (ALI) airway tissue model is structurally and functionally similar to the human large airway epithelium and, as a result, is being used increasingly for studying the toxicity of inhaled substances. Our previous research demonstrated that DNA damage and mutagenesis can be detected in human airway tissue models under conditions used to assess general and respiratory toxicity endpoints. Expanding upon our previous proof-of-principle study, human airway epithelial tissue models were treated with 6.25–100 µg/mL ethyl methanesulfonate (EMS) for 28 days, followed by a 28-day recovery period. Mutagenesis was evaluated by Duplex Sequencing (DS), and clonal expansion of bronchial-cancer-specific cancer-driver mutations (CDMs) was investigated by CarcSeq to determine if both mutation-based endpoints can be assessed in the same system. Additionally, DNA damage and tissue-specific responses were analyzed during the treatment and following the recovery period. EMS exposure led to time-dependent increases in mutagenesis over the 28-day treatment period, without expansion of clones containing CDMs; the mutation frequencies remained elevated following the recovery. EMS also produced an increase in DNA damage measured by the CometChip and MultiFlow assays and the elevated levels of DNA damage were reduced (but not eliminated) following the recovery period. Cytotoxicity and most tissue-function changes induced by EMS treatment recovered to control levels, the exception being reduced proliferating cell frequency. Our results indicate that general, respiratory-tissue-specific and genotoxicity endpoints increased with repeat EMS dosing; expansion of CDM clones, however, was not detected using this repeat treatment protocol. DisclaimerThis article reflects the views of its authors and does not necessarily reflect those of the U.S. Food and Drug Administration. Any mention of commercial products is for clarification only and is not intended as approval, endorsement, or recommendation.

Gene expression in heart, kidney, and liver identifies possible mechanisms underpinning fetal resistance and susceptibility to in utero PRRSV infection

Porcine reproductive and respiratory syndrome (PRRS) is one of the costliest diseases to pork producers worldwide. We tested samples from the pregnant gilt model (PGM) to better understand the fetal response to in-utero PRRS virus (PRRSV) infection. Our goal was to identify critical tissues and genes associated with fetal resilience or susceptibility. Pregnant gilts (N=22) were infected with PRRSV on day 86 of gestation. At 21 days post maternal infection, the gilts and fetuses were euthanized, and fetal tissues collected. Fetuses were characterized for PRRS viral load in fetal serum and thymus, and preservation status (viable or meconium stained: VIA or MEC). Fetuses (N=10 per group) were compared: uninfected (UNIF; <1 log/µL PRRSV RNA), resilient (HV_VIA, >5 log virus/µL but viable), and susceptible (HV_MEC, >5 log virus/µL with MEC). Gene expression in fetal heart, kidney, and liver was investigated using NanoString transcriptomics. Gene categories investigated were hypothesized to be involved in fetal response to PRRSV infection: renin- angiotensin-aldosterone, inflammatory, transporter and metabolic systems. Following PRRSV infection, CCL5 increased expression in heart and kidney, and ACE2 decreased expression in kidney, each associated with fetal PRRS susceptibility. Liver revealed the most significant differential gene expression: CXCL10 decreased and IL10 increased indicative of immune suppression. Increased liver gene expression indicated potential associations with fetal PRRS susceptibility on several systems including blood pressure regulation (AGTR1), energy metabolism (SLC16A1 and SLC16A7), tissue specific responses (KL) and growth modulation (TGFB1). Overall, analyses of non-lymphoid tissues provided clues to mechanisms of fetal compromise following maternal PRRSV infection.

Sex-Related Differences in Oxidant and Antioxidant Profiles of Murine Kidney and Brain: A Focus on Sirt3-Mediated Regulation

Background: Sirt3 is a mitochondrial deacetylase with an important role in maintainance of cellular redox and metabolic homeostasis and mitochondrial function. As growing evidence support the existence of sex-specific responses to metabolic and oxidative stress, we aimed to investigate sex- and organ-specific effects of Sirt3 loss. Materials and methods: Expression of Sirt3, PGC-1a, CuZnSOD, MnSOD and Cat proteins in kidneys and brains of Sirt3-wild type (Sirt3 WT) and Sirt3-knockout (Sirt3 KO) mice was assessed by Western blotting. Protein carbonylation and lipid peroxidation levels were measured using ELISA and fluorometric assays, respectively. SOD and Cat activities were determined using standard enzymatic assays. Results: Significant sex- and organ- specific differences in response to Sirt3 loss were detected. Sirt3 knockout affected kidneys more than brain tissue, with females showing lower levels PC and LPO. In kidneys, female KO showed higher MnSOD, but lower CuZnSOD and Cat activity compared to males. In brains, WT females show higher activities of these enzymes than males, suggesting a sex-specific protection mechanism, but female KO brains show a larger decrease in these parameters. Conclusion: Our study provides comprehensive insights into the complex interplay of Sirt3, oxidative stress, and antioxidant defenses in murine kidney and brain. The observed differences between the two organs and the impact of sex highlight the need for studying Sirt3 function in diverse physiological contexts. The tissue-specific responses and sex-related variations underscore the importance of considering these factors in the development of therapeutic strategies targeting mitochondrial function and redox homeostasis.

Immune response to IL6 gradient in a diffusion-based microfluidic labchip

Cell migration plays a crucial role in uncovering many physiological phenomena and predicting several pathologies, such as immune cell trafficking, tissue-specific immunological responses, wound healing, cancer metastasis, etc. A controlled approach to cellular migration has been explored through microfluidic devices. In order to create multiple dilutions of interleukin 6, a symmetric microfluidic labchip is well-designed. Eight chambers for cell culture and two for collecting migrated T cells were considered. This research will focus on mimicking immune cell movement or chemotaxis in a diffusion-based microfluidic device with different chemokine concentration gradients. Immune cells co-cultured with fibroblasts migrate in response to different gradients of interleukin 6. Immune cell migration is spatially controlled for 48 h by monitoring immune cell migration time and dose dependency. The microfluidic chip developed in this research aims to study immune cell movement in response to the concentration gradient of chemokine in cancer studies and clinical applications.

Conserved and tissue-specific immune responses to biologic scaffold implantation

Upon implantation into a patient, any biomaterial induces a cascade of immune responses that influences the outcome of that device. This cascade depends upon several factors, including the composition of the material itself and the location in which the material is implanted. There is still significant uncertainty around the role of different tissue microenvironments in the immune response to biomaterials and how that may alter downstream scaffold remodeling and integration. In this study, we present a study evaluating the immune response to decellularized extracellular matrix materials within the intraperitoneal cavity, the subcutaneous space, and in a traumatic skeletal muscle injury microenvironment. All different locations induced robust cellular recruitment, specifically of macrophages and eosinophils. The latter was most prominent in the subcutaneous space. Intraperitoneal implants uniquely recruited B cells that may alter downstream reactivity as adaptive immunity has been strongly implicated in the outcome of scaffold remodeling. These data suggest that the location of tissue implants should be taken together with the composition of the material itself when designing devices for downline therapeutics. Statement of significanceDifferent tissue locations have unique immune microenvironments, which can influence the immune response to biomaterial implants. By considering the specific immune profiles of the target tissue, researchers can develop implant materials that promote better integration, reduce complications, and improve the overall outcome of the implantation process.

Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander

Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.

Sea water acclimation of rainbow trout (Oncorhynchus mykiss) modulates the mucosal transcript immune response induced by Vibrio anguillarum and Aeromonas salmonicida vaccine, and prevents further transcription of stress-immune genes in response to acute stress

Mucosal tissues appear to be more important in fish than in mammals due to living in a microbial-rich aquatic milieu, yet the complex interaction between the immune and the neuroendocrine system in these tissues remains elusive. The aim of this work was to investigate the mucosal immune response in immunized rainbow trout vaccinated with Alpha ject vaccine (bivalent), kept in fresh water (FW) or transferred to seawater (SW), and to evaluate their response to acute stress (chasing). Acute stress resulted in higher levels of plasma cortisol (Sham + Stress and Vaccine + Stress). A similar response was observed in skin mucus, but it was lower in Vaccine + Stress compared with stressed fish. With a few exceptions, minimal alterations were detected in the transcriptomic profile of stress-immune gene in the skin of vaccinated and stressed fish in both FW and SW. In the gills, the stress elicited activation of key stress-immune components (gr1, mr, β-ar, hsp70, c3, lysozyme, α-enolase, nadph oxidase, il1β, il6, tnfα, il10 and tgfβ1) in FW, but fewer immune changes were induced by the vaccine (nadph oxidase, il6, tnfα, il10 and igt) in both SW and FW. In the intestine, an array of immune genes was activated by the vaccine particularly those related with B cells (igm, igt) and T cells (cd8α) in FW with no stimulation observed in SW. Therefore, our survey on the transcriptomic mucosal response demonstrates that the immune protection conferred by the vaccine to the intestine is modulated in SW. Overall, our results showed: i) plasma and skin mucus cortisol showed no additional stress effect induced by prolonged SW acclimation, ii) the stress and immune response were different among mucosal tissues which indicates a tissue-specific response to specific antigens/stressor. Further, the results suggest that the systemic immune organs may be more implicated in infectious events in SW (as few changes were observed in the mucosal barriers of immunized fish in SW) than in FW.

Expression of dehydroshikimate dehydratase in poplar induces transcriptional and metabolic changes in the phenylpropanoid pathway.

Modification of lignin in feedstocks via genetic engineering aims to reduce biomass recalcitrance to facilitate efficient conversion processes. These improvements can be achieved by expressing exogenous enzymes that interfere with native biosynthetic pathways responsible for the production of the lignin precursors. In planta expression of a bacterial 3-dehydroshikimate dehydratase in poplar trees reduced lignin content and altered the monomer composition, which enabled higher yields of sugars after cell wall polysaccharide hydrolysis. Understanding how plants respond to such genetic modifications at the transcriptional and metabolic levels is needed to facilitate further improvement and field deployment. In this work, we acquired fundamental knowledge on lignin-modified poplar expressing 3-dehydroshikimate dehydratase using RNA-seq and metabolomics. The data clearly demonstrate that changes in gene expression and metabolite abundance can occur in a strict spatiotemporal fashion, revealing tissue-specific responses in the xylem, phloem, or periderm. In the poplar line that exhibited the strongest reduction in lignin, we found that 3% of the transcripts had altered expression levels and ~19% of the detected metabolites had differential abundance in the xylem from older stems. The changes affected predominantly the shikimate and phenylpropanoid pathways as well as secondary cell wall metabolism, and resulted in significant accumulation of hydroxybenzoates derived from protocatechuate and salicylate.

Dynamic DNA methylation modifications in the cold stress response of cassava

Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.

Homeostatic T helper 17 cell responses triggered by complex microbiota are maintained in ex vivo intestinal tissue slices.

Segmented filamentous bacteria (SFB) are members of the commensal intestinal microbiome. They are known to contribute to the postnatal maturation of the gut immune system, but also to augment inflammatory conditions in chronic diseases such as Crohn's disease. Living primary tissue slices are ultrathin multicellular sections of the intestine and provide a unique opportunity to analyze tissue-specific immune responses ex vivo. This study aimed to investigate whether supplementation of the gut flora with SFB promotes T helper 17 (Th17) cell responses in primary intestinal tissue slices ex vivo. Primary tissue slices were prepared from the small intestine of healthyTaconic mice with SFB-positive and SFB-negative microbiomes and stimulated with anti-CD3/CD28 or Concanavalin A. SFB-positive and -negative mice exhibited distinct microbiome compositions and Th17 cell frequencies in the intestine and complex microbiota including SFB induced up to 15-fold increase in Th17 cell-associated mediators, serum amyloid A (SAA), and immunoglobulin A (IgA) responses ex vivo. This phenotype could be transmitted by co-housing of mice. Our findings highlight that changes in the gut microbiome can be observed in primary intestinal tissue slices ex vivo. This makes the system very attractive for disease modeling and assessment of new therapies.

Genetic loci associated with tissue-specific resistance to powdery mildew in octoploid strawberry (Fragaria × ananassa).

Powdery mildew is one of the most problematic diseases in strawberry production. To date, few commercial strawberry cultivars are deemed to have complete resistance and as such, an extensive spray programme must be implemented to control the pathogen. Here, a large-scale field experiment was used to determine the powdery mildew resistance status of leaf and fruit tissues across a diverse panel of strawberry genotypes. This phenotypic data was used to identify Quantitative Trait Nucleotides (QTN) associated with tissue-specific powdery mildew resistance. In total, six stable QTN were found to be associated with foliar resistance, with one QTN on chromosome 7D associated with a 61% increase in resistance. In contrast to the foliage results, there were no QTN associated with fruit disease resistance and there was a high level of resistance observed on strawberry fruit, with no genetic correlation observed between fruit and foliar symptoms, indicating a tissue-specific response. Beyond the identification of genetic loci, we also demonstrate that genomic selection can lead to rapid gains in foliar resistance across genotypes, with the potential to capture >50% of the genetic foliage resistance present in the population. To date, breeding of robust powdery mildew resistance in strawberry has been impeded by the quantitative nature of natural resistance and a lack of knowledge relating to the genetic control of the trait. These results address this shortfall, through providing the community with a wealth of information that could be utilized for genomic informed breeding, implementation of which could deliver a natural resistance strategy for combatting powdery mildew.

A longitudinal study of queen health in honey bees reveals tissue specific response to seasonal changes and pathogen pressure

The health of honey bee queens is crucial for colony success, particularly during stressful periods like overwintering. To accompany a previous longitudinal study of colony and worker health, we explored niche-specific gut microbiota, host gene expression, and pathogen prevalence in honey bee queens overwintering in a warm southern climate. We found differential gene expression and bacterial abundance with respect to various pathogens throughout the season. Biologically older queens had larger microbiotas, particularly enriched in Bombella and Bifidobacterium. Both Deformed Wing Virus A and B subtypes were highest in the fat body tissue in January, correlating with colony Varroa levels, and Deformed Wing Virus titers in workers. High viral titers in queens were associated with decreased vitellogenin expression, suggesting a potential trade-off between immune function and reproductive capacity. Additionally, we found a complex and dynamic relationship between these viral loads and immune gene expression, indicating a possible breakdown in the coordinated immune response as the season progressed. Our study also revealed a potential link between Nosema and Melissococcus plutonius infections in queens, demonstrating that seasonal opportunism is not confined to just workers. Overall, our findings highlight the intricate interplay between pathogens, metabolic state, and immune response in honey bee queens. Combined with worker and colony-level metrics from the same colonies, our findings illustrate the social aspect of queen health and resilience over the winter dearth.

A multi-omic survey of black cottonwood tissues highlights coordinated transcriptomic and metabolomic mechanisms for plant adaptation to phosphorus deficiency.

Phosphorus (P) deficiency in plants creates a variety of metabolic perturbations that decrease photosynthesis and growth. Phosphorus deficiency is especially challenging for the production of bioenergy feedstock plantation species, such as poplars (Populus spp.), where fertilization may not be practically or economically feasible. While the phenotypic effects of P deficiency are well known, the molecular mechanisms underlying whole-plant and tissue-specific responses to P deficiency, and in particular the responses of commercially valuable hardwoods, are less studied. We used a multi-tissue and multi-omics approach using transcriptomic, proteomic, and metabolomic analyses of the leaves and roots of black cottonwood (Populus trichocarpa) seedlings grown under P-deficient (5 µM P) and replete (100 µM P) conditions to assess this knowledge gap and to identify potential gene targets for selection for P efficiency. In comparison to seedlings grown at 100 µM P, P-deficient seedlings exhibited reduced dry biomass, altered chlorophyll fluorescence, and reduced tissue P concentrations. In line with these observations, growth, C metabolism, and photosynthesis pathways were downregulated in the transcriptome of the P-deficient plants. Additionally, we found evidence of strong lipid remodeling in the leaves. Metabolomic data showed that the roots of P-deficient plants had a greater relative abundance of phosphate ion, which may reflect extensive degradation of P-rich metabolites in plants exposed to long-term P-deficiency. With the notable exception of the KEGG pathway for Starch and Sucrose Metabolism (map00500), the responses of the transcriptome and the metabolome to P deficiency were consistent with one another. No significant changes in the proteome were detected in response to P deficiency. Collectively, our multi-omic and multi-tissue approach enabled the identification of important metabolic and regulatory pathways regulated across tissues at the molecular level that will be important avenues to further evaluate for P efficiency. These included stress-mediating systems associated with reactive oxygen species maintenance, lipid remodeling within tissues, and systems involved in P scavenging from the rhizosphere.

Effect of lazaroid U-74389G and Sildenafil, alone or in combination, on pulmonary function during ischamia-reperfusion injury of myocardium: An exploratory study

Background: This experimental study was designed to evaluate the effects of the pharmaceutical substances U-74389G (Lazaroid) and Sildenafil, administered separately or in combination, during anaesthesia in relation to pulmonary function, in a myocardial ischaemia-reperfusion procedure. Methods: We sought to determine the effect of sildenafil and lazaroid U-74389G maleate, alone or in combination, on systemic and pulmonary tissue inflammation and oxidative stress in a pig model of myocardial ischaemia-reperfusion injury. A total of 56 pigs were divided into seven groups according to the use of sildenafil, lazaroid, or their combination, and the time of administration (prior to the induction of myocardial ischaemia or after reperfusion). Results: Both sildenafil and lazaroid U-74389G maleate, administered either 10 minutes before the induction of myocardial ischaemia or immediately after the start of reperfusion, resulted in a significant effect on several markers of systemic inflammation (p&lt;0.05). In addition, a significant reduction in lung tissue expression of tumour necrosis factor-alpha (TNF-a) (p&lt;0.05) was observed with sildenafil, lazaroid U-74389G maleate, and their combination, when administered either before the induction of myocardial ischaemia or after the induction of reperfusion. However, no effect on tissue oxidative stress was demonstrated. Conclusion: Sildenafil, lazaroid U-74389G maleate, and their combination led to a significant amelioration of both systemic and pulmonary tissue-specific inflammatory responses. Notably, they did not exert any significant effect against tissue oxidative stress in this model. Human mechanistic studies are required to confirm these observations.

Engineering fibronectin-templated multi-component fibrillar extracellular matrices to modulate tissue-specific cell response

Cells assemble fibronectin, the major extracellular matrix (ECM) protein, into fibrillar matrices, which serve as 3D architectural scaffolds to provide, together with other ECM proteins tissue-specific environments. Although recent approaches enable to bioengineer 3D fibrillar fibronectin matrices in vitro, it remains elusive how fibronectin can be co-assembled with other ECM proteins into complex 3D fibrillar matrices that recapitulate tissue-specific compositions and cellular responses. Here, we introduce the engineering of fibrillar fibronectin-templated 3D matrices that can be complemented with other ECM proteins, including vitronectin, collagen, and laminin to resemble ECM architectures observed in vivo. For the co-assembly of different ECM proteins, we employed their innate fibrillogenic mechanisms including shear forces, pH-dependent electrostatic interactions, or specific binding domains. Through recapitulating various tissue-specific ECM compositions and morphologies, the large scale multi-composite 3D fibrillar ECM matrices can guide fibroblast adhesion, 3D fibroblast tissue formation, or tissue morphogenesis of epithelial cells. In other examples, we customize multi-composite 3D fibrillar matrices to support the growth of signal propagating neuronal networks and of human brain organoids. We envision that these 3D fibrillar ECM matrices can be tailored in scale and composition to modulate tissue-specific responses across various biological length scales and systems, and thus to advance manyfold studies of cell biological systems.

Proteasome inhibition triggers tissue-specific immune responses against different pathogens in C. elegans.

Protein quality control pathways play important roles in resistance against pathogen infection. For example, the conserved transcription factor SKN-1/NRF up-regulates proteostasis capacity after blockade of the proteasome and also promotes resistance against bacterial infection in the nematode Caenorhabditis elegans. SKN-1/NRF has 3 isoforms, and the SKN-1A/NRF1 isoform, in particular, regulates proteasomal gene expression upon proteasome dysfunction as part of a conserved bounce-back response. We report here that, in contrast to the previously reported role of SKN-1 in promoting resistance against bacterial infection, loss-of-function mutants in skn-1a and its activating enzymes ddi-1 and png-1 show constitutive expression of immune response programs against natural eukaryotic pathogens of C. elegans. These programs are the oomycete recognition response (ORR), which promotes resistance against oomycetes that infect through the epidermis, and the intracellular pathogen response (IPR), which promotes resistance against intestine-infecting microsporidia. Consequently, skn-1a mutants show increased resistance to both oomycete and microsporidia infections. We also report that almost all ORR/IPR genes induced in common between these programs are regulated by the proteasome and interestingly, specific ORR/IPR genes can be induced in distinct tissues depending on the exact trigger. Furthermore, we show that increasing proteasome function significantly reduces oomycete-mediated induction of multiple ORR markers. Altogether, our findings demonstrate that proteasome regulation keeps innate immune responses in check in a tissue-specific manner against natural eukaryotic pathogens of the C. elegans epidermis and intestine.

Regulation of GeCu/Zn-SOD, GeMn-SOD, GeHsp90, and GeMT in Gymnocypris eckloni in Response to Copper and Lead Ion Challenges

The contamination of aquatic environments by heavy metals can have detrimental effects on fish, impacting their growth and overall health, including the regulation of antioxidant genes. An investigation was carried out to assess the distribution and habitat of Gymnocypris eckloni in the Yellow River basin. Simultaneously, heavy metal concentrations in its habitat and in selected locations within the upper Yellow River were measured. In an effort to explore the potential roles of specific genes in antioxidant responses, G. eckloni was exposed to low concentrations of copper (Cu2+) and lead (Pb2+) for varying durations (12, 24, and 48 hours). The mRNA levels of GeCu/Zn-SOD, GeMn-SOD, GeHsp90, and GeMT were quantified in the gills, kidneys, and liver through qRT-PCR. The findings suggest that the habitat of G. eckloni is generally safe; however, occasional exceedances of safety standards could pose a potential threat to its growth. Importantly, the expression of GeCu/Zn-SOD, GeMn-SOD, GeHsp90, and GeMT exhibited responses to the low concentrations of copper-induced and lead-induced stress. Notably, GeCu/Zn-SOD, GeMn-SOD, and GeMT demonstrated heightened sensitivity to lead compared to copper. Furthermore, the expression of these genes displayed tissue-specific responses under identical metal stress conditions. These results indicate that GeCu/Zn-SOD, GeMn-SOD, GeHsp90, and GeMT genes have the potential to serve as early, sensitive biomarkers for the detection of metal toxicity induced by Cu2+ and Pb2+. This study also provides valuable insights into the functioning of antioxidant genes under oxidative stress in fish.

Wide-characterization of high and low dry matter kiwifruit through spatiotemporal multi-omic approach

Despite the widespread use of dry matter content (DMC) as an indicator of kiwifruit quality, the physiological and molecular impact of DMC in fruit ripening remains unknown. Herein, the post-harvest physiological, metabolomic, and transcriptomic influence of DMC status on the pericarp and placenta tissue of ‘Hayward’ kiwifruit at harvest and at the onset of post-cold ripening was investigated. A segregation strategy based on DMC in commercially harvested kiwifruit was achieved with near-infrared spectroscopy for the estimation of DMC in individual fruits. Additionally, kiwifruits with distinct DMC levels were treated with 1-methylcyclopropene (1-MCP) and systematically monitored for ripening changes (20°C) at various intervals after cold storage (0°C). Following 90 and 120 days of cold exposure, high DMC kiwifruit generally exhibited superior physiological characteristics, such as increased pericarp and placenta firmness, and soluble solid and starch contents compared to low DMC kiwifruit, regardless of the 1-MCP application. Evidence is also presented for 1-MCP delaying the ripening of low-DMC fruit to the level of the untreated high-DMC kiwifruit. An accumulation of primary metabolites, particularly sugars and polyphenolic compounds, such as catechin, chlorogenic acid and procyanidin B1/B2 was evidenced in the high DMC group. At harvest, gene expression analysis revealed minor differences between DMC groups, with beta-amylase being the highest up-regulated gene in high DMC kiwifruit. Moreover, the gene expression patterns between DMC groups became more distinct after cold storage. Genes related to starch biosynthesis (i.e., glucose-1-phosphate adenyltransferase), water movement (i.e., aquaporin), polyphenolic biosynthesis (i.e., chalcone synthase) and lipid metabolism (i.e., diacylglycerol acyltransferase) showed strong variations between low and high DMC. Interestingly, the placenta tissue displayed almost 4 times more than DMC-affected differentially expressed genes compared to the pericarp, highlighting the key role of the placenta in kiwifruit ripening, notably following 1-MCP treatment. This study provides insights into the tissue-specific ripening response between kiwifruit with distinct DMC, as well as the gene expression influenced by an interaction of 1-MCP and DMC level, thereby helping develop postharvest programs aimed at improving kiwifruit quality traits.

Decoding the transcriptional heterogeneity, differentiation lineage, clinical significance in tissue-resident memory CD8 T cell of the small intestine by single-cell analysis

Resident memory T (Trm) cells which are specifically located in non-lymphoid tissues showed distinct phenotypes and functions compared to circulating memory T cells and were vital for the initiation of robust immune response within tissues. However, the heterogeneity in the transcriptional features, development pathways, and cancer response of Trm cells in the small intestine was not demonstrated. Here, we integrated scRNA-seq and scTCR-seq data pan-tissue T cells to explore the heterogeneity of Trm cells and their development pathways. Trm were enriched in tissue-specific immune response and those in the DUO specially interacted with B cells via TNF and MHC-I signatures. T cell lineage analyses demonstrated that Trm might be derived from the T_CD4/CD8 subset within the same organ or migrated from spleen and mesenteric lymph nodes. We compared the immune repertoire of Trm among organs and implied that clonotypes in both DUO and ILE were less expanded and hydrophilic TRB CDR3s were enriched in the DUO. We further demonstrated that Trm in the intestine infiltrated the colorectal cancer and several effector molecules were highly expressed. Finally, the TCGA dataset of colorectal cancer implied that the infiltration of Trm from the DUO and the ILE was beneficial for overall survival and the response to immune checkpoint blockade.