The CCCH-type zinc finger transcription factor Zc3h8 represses NF-κB-mediated inflammation in digestive organs in zebrafish

An integrated approach to identifying sex-specific genes, transcription factors, and pathways relevant to Alzheimer's disease

BACKGROUND

Age represents a significant risk factor for the development of Alzheimer's disease (AD); however, recent research has documented an influencing role of sex in several features of AD. Understanding the impact of sex on specific molecular mechanisms associated with AD remains a critical challenge to creating tailored therapeutic interventions.

METHODS

The exploration of the sex-based differential impact on disease (SDID) in AD used a systematic review to first select transcriptomic studies of AD with data regarding sex in the period covering 2002 to 2021 with a focus on the primary brain regions affected by AD - the cortex (CT) and the hippocampus (HP). A differential expression analysis for each study and two tissue-specific meta-analyses were then performed. Focusing on the CT due to the presence of significant SDID-related alterations, a comprehensive functional characterization was conducted: protein-protein network interaction and over-representation analyses to explore biological processes and pathways and a VIPER analysis to estimate transcription factor activity.

RESULTS

We selected 8 CT and 5 HP studies from the Gene Expression Omnibus (GEO) repository for tissue-specific meta-analyses. We detected 389 significantly altered genes in the SDID comparison in the CT. Generally, female AD patients displayed more affected genes than males; we grouped said genes into six subsets according to their expression profile in female and male AD patients. Only subset I (repressed genes in female AD patients) displayed significant results during functional profiling. Female AD patients demonstrated more significant impairments in biological processes related to the regulation and organization of synapsis and pathways linked to neurotransmitters (glutamate and GABA) and protein folding, Aβ aggregation, and accumulation compared to male AD patients. These findings could partly explain why we observe more pronounced cognitive decline in female AD patients. Finally, we detected 23 transcription factors with different activation patterns according to sex, with some associated with AD for the first time. All results generated during this study are readily available through an open web resource Metafun-AD (https://bioinfo.cipf.es/metafun-ad/).

CONCLUSION

Our meta-analyses indicate the existence of differences in AD-related mechanisms in female and male patients. These sex-based differences will represent the basis for new hypotheses and could significantly impact precision medicine and improve diagnosis and clinical outcomes in AD patients.

Extensive jejunal injury is repaired by migration and transdifferentiation of ileal enterocytes in zebrafish

A major cause of intestinal failure (IF) is intestinal epithelium necrosis and massive loss of enterocytes, especially in the jejunum, the major intestinal segment in charge of nutrient absorption. However, mechanisms underlying jejunal epithelial regeneration after extensive loss of enterocytes remain elusive. Here, we apply a genetic ablation system to induce extensive damage to jejunal enterocytes in zebrafish, mimicking the jejunal epithelium necrosis that causes IF. In response to injury, proliferation and filopodia/lamellipodia drive anterior migration of the ileal enterocytes into the injured jejunum. The migrated fabp6⁺ ileal enterocytes transdifferentiate into fabp2⁺ jejunal enterocytes to fulfill the regeneration, consisting of dedifferentiation to precursor status followed by redifferentiation. The dedifferentiation is activated by the IL1β-NFκB axis, whose agonist promotes regeneration. Extensive jejunal epithelial damage is repaired by the migration and transdifferentiation of ileal enterocytes, revealing an intersegmental migration mechanism of intestinal regeneration and providing potential therapeutic targets for IF caused by jejunal epithelium necrosis.

Ronidazole Is a Superior Prodrug to Metronidazole for Nitroreductase-Mediated Hepatocytes Ablation in Zebrafish Larvae

The liver plays a very important role in physiological processes of the human body. Liver regeneration has developed into an important area of study in liver disease. The Mtz (metronidazole)/NTR (nitroreductase)-mediated cell ablation system has been widely used to study the processes and mechanisms of liver injury and regeneration. However, high concentrations and toxic side effects of Mtz severely limit the application of the Mtz/NTR system. Therefore, screening new analogs to replace Mtz has become an important means to optimize the NTR ablation system. In this study, we screened five Mtz analogs including furazolidone, ronidazole, ornidazole, nitromide, and tinidazole. We compared their toxicity on the transgenic fish line Tg(fabp10a: mCherry-NTR) and their specific ablation ability on liver cells. The results showed that Ronidazole at a lower concentration (2 mM) had the same ability to ablate liver cells comparable with that of Mtz (10 mM), almost without toxic side effects on juvenile fish. Further study found that zebrafish hepatocyte injury caused by the Ronidazole/NTR system achieved the same liver regenerative effect as the Mtz/NTR system. The above results show that Ronidazole can replace Mtz with NTR to achieve superior damage and ablation effects in zebrafish liver.

Hypothetical protein FoDbp40 influences the growth and virulence of Fusarium oxysporum by regulating the expression of isocitrate lyase

Fungal growth is closely related to virulence. Finding the key genes and pathways that regulate growth can help elucidate the regulatory mechanisms of fungal growth and virulence in efforts to locate new drug targets. Fusarium oxysporum is an important plant pathogen and human opportunistic pathogen that has research value in agricultural and medicinal fields. A mutant of F. oxysporum with reduced growth was obtained by Agrobacterium tumefaciens-mediated transformation, the transferred DNA (T-DNA) interrupted gene in this mutant coded a hypothetical protein that we named FoDbp40. FoDbp40 has an unknown function, but we chose to explore its possible functions as it may play a role in fungal growth regulatory mechanisms. Results showed that F. oxysporum growth and virulence decreased after FoDbp40 deletion. FOXG_05529 (NCBI Gene ID, isocitrate lyase, ICL) was identified as a key gene that involved in the reduced growth of this mutant. Deletion of FoDbp40 results in a decrease of more than 80% in ICL expression and activity, succinate level, and energy level, plus a decrease in phosphorylated mammalian target of rapamycin level and an increase in phosphorylated 5′-adenosine monophosphate activated protein kinase level. In summary, our study found that the FoDbp40 regulates the expression of ICL at a transcriptional level and affects energy levels and downstream related pathways, thereby regulating the growth and virulence of F. oxysporum.

Mcm5 Represses Endodermal Migration through Cxcr4a-itgb1b Cascade Instead of Cell Cycle Control

Minichromosome maintenance protein 5 (MCM5) is a critical cell cycle regulator; its role in DNA replication is well known, but whether it is involved in the regulation of organogenesis in a cell cycle-independent way, is far from clear. In this study, we found that a loss of mcm5 function resulted in a mildly smaller liver, but that mcm5 overexpression led to liver bifida. Further, the data showed that mcm5 overexpression delayed endodermal migration in the ventral–dorsal axis and induced the liver bifida. Cell cycle analysis showed that a loss of mcm5 function, but not overexpression, resulted in cell cycle delay and increased cell apoptosis during gastrulation, implying that liver bifida was not the result of a cell cycle defect. In terms of its mechanism, our data proves that mcm5 represses the expression of cxcr4a, which sequentially causes a decrease in the expression of itgb1b during gastrulation. The downregulation of the cxcr4a-itgb1b cascade leads to an endodermal migration delay during gastrulation, as well as to the subsequent liver bifida during liver morphogenesis. In conclusion, our results suggest that in a cell cycle-independent way, mcm5 works as a gene expression regulator, either partially and directly, or indirectly repressing the expression of cxcr4a and the downstream gene itgb1b, to coordinate endodermal migration during gastrulation and liver location during liver organogenesis.

Potential neurotoxicity, immunotoxicity, and carcinogenicity induced by metribuzin and tebuconazole exposure in earthworms (Eisenia fetida) revealed by transcriptome analysis

Metribuzin and tebuconazole have been widely used in agriculture for several decades. Apart from endocrine disruption, little is known about their toxicological effects on organisms without thyroid organs, at the transcriptional level. To explore this toxicity, model earthworm species Eisenia fetida, hatched from the same cocoon and cultured under identical environmental conditions, were independently exposed to the two chemicals at non-lethal concentrations in OECD artificial soil for 48 h after exposure. RNA-seq technology was used to analyze and compare the gene expression profiles of earthworms exposed to metribuzin and tebuconazole. The functions of differentially expressed genes and their standard response patterns of upregulated and downregulated expression for both pesticides were verified. The findings demonstrated that metribuzin and tebuconazole are both potentially toxic to earthworms. Toxicological effects mainly involved the nervous system, immune system, and tumors, at the transcriptional level, as well as the induction of cytochrome P450-dependent detoxification and oxidative stress. In addition, the mitogen-activated protein kinase kinase kinase gene was identified as a biomarker, and the mitogen-activated protein kinase signaling pathway was verified to be a part of the adverse outcome pathway of metribuzin and tebuconazole and their structural analogs.

Formimidoyltransferase cyclodeaminase prevents the starvation-induced liver hepatomegaly and dysfunction through downregulating mTORC1

The liver is a crucial center in the regulation of energy homeostasis under starvation. Although downregulation of mammalian target of rapamycin complex 1 (mTORC1) has been reported to play pivotal roles in the starvation responses, the underpinning mechanisms in particular upstream factors that downregulate mTORC1 remain largely unknown. To identify genetic variants that cause liver energy disorders during starvation, we conduct a zebrafish forward genetic screen. We identify a liver hulk (lvh) mutant with normal liver under feeding, but exhibiting liver hypertrophy under fasting. The hepatomegaly in lvh is caused by enlarged hepatocyte size and leads to liver dysfunction as well as limited tolerance to starvation. Positional cloning reveals that lvh phenotypes are caused by mutation in the ftcd gene, which encodes the formimidoyltransferase cyclodeaminase (FTCD). Further studies show that in response to starvation, the phosphorylated ribosomal S6 protein (p-RS6), a downstream effector of mTORC1, becomes downregulated in the wild-type liver, but remains at high level in lvh. Inhibition of mTORC1 by rapamycin rescues the hepatomegaly and liver dysfunction of lvh. Thus, we characterize the roles of FTCD in starvation response, which acts as an important upstream factor to downregulate mTORC1, thus preventing liver hypertrophy and dysfunction.

Under starvation, the liver initiates a series of metabolic adaptations to maintain energy homeostasis that is critical for survival. During this process, mTORC1 pathway is downregulated to reduce anabolism and promote catabolism, ensuring adequate usage of limited resources. However, mechanisms underlying the downregulation of mTORC1 remain incompletely understood. In a zebrafish genetic screen aiming to characterize factors important for starvation response in the liver, we identify an ftcd mutation that causes liver hypertrophy and dysfunction under fasting. FTCD acts upstream to inactivate mTORC1 in response to starvation. Our work reveals previously unappreciated roles of FTCD in the responses to energy stress through modulating mTORC1 activities, moreover implicates a potential liver disorder risk of FTCD deficiency under the circumstances of starvation.

Proteins in plasma as a potential biomarkers diagnostic for pelvic organ prolapse

Background

Pelvic organ prolapse (POP) is the most common and widespread type of female pelvic floor dysfunction disease (PFD). At present, the diagnosis of POP is mainly based on a complicated systematic evaluation of the clinical phenotype, medical history, and relevant functional examinations. Rapid and simple tests that are based on biochemical biomarkers that surpass the sensitivity and specificity of the current methods for the diagnosis of POP will greatly facilitate the timely diagnosis and treatment of women with POP.

Methods

A protein array was used to screen plasma samples collected from healthy controls and women with POP. Enzyme-linked immunosorbent assays (ELISAs) were used to determine the levels of three novel and potentially useful analytes: heat shock protein 10 (HSP10), zinc finger CCCH domain-containing protein 8 (ZC3H8), and unc-45 myosin chaperone A (UNC45A). We then determined the diagnostic value of each of these analytes as potential diagnostic biomarkers for clinical application.

Results

The mean levels of HSP10, ZC3H8, and UNC45A, were lower in the plasma samples from 76 patients with POP than in 56 samples from healthy controls (P<0.05). Comparisons between patients with POP and healthy controls demonstrated the sensitivity and specificity of HSP10 (73.7% and 71.4%), ZC3H8 (71.1% and 62.5%), and UNC45A (70.7% and 62.5%).

Conclusions

Analysis indicated that plasma levels of HSP10, ZC3H8, and UNC45A, are sensitive and specific biomarkers for the diagnosis of POP.

Divalent Metal Transporter 1 Knock-Down Modulates IL-1β Mediated Pancreatic Beta-Cell Pro-Apoptotic Signaling Pathways through the Autophagic Machinery

Pro-inflammatory cytokines promote cellular iron-import through enhanced divalent metal transporter-1 (DMT1) expression in pancreatic β-cells, consequently cell death. Inhibition of β-cell iron-import by DMT1 silencing protects against apoptosis in animal models of diabetes. However, how alterations of signaling networks contribute to the protective action of DMT1 knock-down is unknown. Here, we performed phosphoproteomics using our sequential enrichment strategy of mRNA, protein, and phosphopeptides, which enabled us to explore the concurrent molecular events in the same set of wildtype and DMT1-silenced β-cells during IL-1β exposure. Our findings reveal new phosphosites in the IL-1β-induced proteins that are clearly reverted by DMT1 silencing towards their steady-state levels. We validated the levels of five novel phosphosites of the potential protective proteins using parallel reaction monitoring. We also confirmed the inactivation of autophagic flux that may be relevant for cell survival induced by DMT1 silencing during IL-1β exposure. Additionally, the potential protective proteins induced by DMT1 silencing were related to insulin secretion that may lead to improving β-cell functions upon exposure to IL-1β. This global profiling has shed light on the signal transduction pathways driving the protection against inflammation-induced cell death in β-cells after DMT1 silencing.

Knockout fth1b affects early mineralization of zebrafish pharyngeal teeth

OBJECTIVES

A study was conducted to explore the expression pattern and function of ferritin heavy polypeptide gene (fth1b) in zebrafish pharyngeal teeth development and lay the foundation for subsequent research on teeth development and mineralization.

METHODS

The zebrafish embryos were harvested at 56, 72, 96, and 120 h after fertilization. The expression of fth1b in zebrafish pharyngeal teeth development was detected by whole embryo in situ hybridization and compared with the known pharyngeal teeth marker dlx2b. The specific knockout of fth1b gene was performed using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing technology. The development of zebrafish pharyngeal teeth was detected in the fth1b^-/- mutant.

RESULTS

The expression pattern of fth1b gene was very similar to that of the known zebrafish pharyngeal teeth marker dlx2b and was specifically expressed in the zebrafish pharyngeal teeth during development. After the specific knockout of the gene fth1b, the earliest gene that can be detect in zebrafish pharyngeal teeth-pitx2 was expressed normally during early development. The dlx2b expression was not significantly different from that of wild type zebrafish, but the mineralization of pharyngeal teeth in the mutant was weaker than that of wild type zebrafish.

CONCLUSIONS

The gene fth1b is specifically expressed in zebrafish pharyngeal teeth and acts on their early mineralization.

ZC3H4-a novel Cys-Cys-Cys-His-type zinc finger protein-is essential for early embryogenesis in mice†

Zinc finger domains of the Cys-Cys-Cys-His (CCCH) class are evolutionarily conserved proteins that bind nucleic acids and are involved in various biological processes. Nearly 60 CCCH-type zinc finger proteins have been identified in humans and mice, most have not been functionally characterized. Here, we provide the first in vivo functional characterization of ZC3H4-a novel CCCH-type zinc finger protein. Our results show that although Zc3h4 mutant embryos exhibit normal morphology at E3.5 blastocyst stage, they cannot be recovered at E7.5 early post-gastrulation stage, suggesting implantation failure. Outgrowth assays reveal that mutant blastocysts either fail to hatch from the zona pellucida, or can hatch but do not form a typical inner cell mass colony, the source of embryonic stem cells (ESCs). Although there is no change in levels of reactive oxygen species, Zc3h4 mutants display severe DNA breaks and reduced cell proliferation. Analysis of lineage specification reveals that both epiblast and primitive endoderm lineages are compromised with severe reductions in cell number and/or specification in the mutant blastocysts. In summary, these findings demonstrate the essential role of ZC3H4 during early mammalian embryogenesis.

The Relationship Between Metabolic Syndrome Development and Tissue Trace Elements Status and Inflammatory Markers

Insulin resistance, impaired glucose regulation, dyslipidemia, low-grade inflammation, and elevated blood pressure are main components of the metabolic syndrome (MetS). Trace elements, especially zinc (Zn) and copper (Cu) and cytokines, have physiological importance due to their presence in inflammatory processes and glucose metabolism. Therefore, this study aimed to investigate the potential relationship between cytokine responses and trace elements in different tissues of sucrose-induced MetS rats compared with healthy controls (n:7/groups). Tissue Zn concentrations are found to be decreased in the liver (p = 0.00) and pancreas (p < 0.01) and increased in the kidney (p = 0.00) and heart tissues (p < 0.001) of MetS group. Serum Zn levels were also found to be decreased in MetS compared with control group (p < 0.01), while there was any significant difference in serum Cu concentrations between groups. The Cu concentration (p < 0.01) was found decreased, and Zn/Cu ratio (p < 0.01) was found increased in kidney tissues. TNF-α, IL-6 levels were found increased in MetS tissues. With this study, the Zn and Cu concentrations and their relationships with inflammatory response in different tissues in MetS are reported for the first time in the literature. Serum and tissue Zn levels with diversities in distribution were found to have a higher impact on MetS pathogenesis than Cu levels. It has been concluded that there is a relationship between Zn and Cu concentrations and inflammatory marker levels in MetS pathophysiological mechanisms.

Macrophage-Derived IL-1β Regulates Emergency Myelopoiesis via the NF-κB and C/ebpβ in Zebrafish

Myeloid phagocytes, neutrophils in particular, are easily consumed when they fight against a large number of invading microbes. Hence, they require efficient and constant replenishment from their progenitors via the well-orchestrated emergency myelopoiesis in the hematopoietic organs. The cellular and molecular details of the danger-sensing and warning processes to activate the emergency myelopoiesis are still under debate. In this study, we set up a systemic infection model in zebrafish (Danio rerio) larvae via circulative administration of LPS. We focused on the cross-talk of macrophages with myeloid progenitors in the caudal hematopoietic tissue. We revealed that macrophages first detected LPS and sent out the emergency message via il1β The myeloid progenitors, rather than hematopoietic stem and progenitor cells, responded and fulfilled the demand to adapt myeloid expansion through the synergistic cooperation of NF-κB and C/ebpβ. Our study unveiled a critical role of macrophages as the early "whistle blowers" to initiate emergency myelopoiesis.

CircRNA ZNF609 in peripheral blood leukocytes acts as a protective factor and a potential biomarker for coronary artery disease

Background

Circular RNAs (circRNAs) have been reported to aberrantly express in coronary artery disease (CAD). Due to their special structures, circRNAs have the potential to be specific and stable markers. We conducted this study to explore circZNF609's function in atherosclerosis and to evaluate its predictive values for CAD.

Methods

About 330 CAD patients and 209 controls were enrolled and the expression of circZNF609 in peripheral blood leukocytes (PBLs) was detected by quantitative real time polymerase chain reaction (RT-PCR). Spearman correlation, multivariate regression, multivariate logistic regression and receiver operating characteristic curve (ROC) were performed. Moreover, circZNF609 was overexpressed in mice macrophage RAW264.7 to investigate its influence on inflammatory cytokines. Finally, bioinformatics analysis was executed to excavate the potential downstream pathway of circZNF609.

Results

The expression level of circZNF609 in PBLs of CAD patients was significantly decreased compared with the controls (the fold changes of 0.4133, P<0.0001). The logistic regression analysis showed that decreased circZNF609 expressions were independently associated with increased risks of CAD. The area under the ROC curve was 0.761 (95% CI: 0.721-0.800, P<0.0001). Furthermore, the circZNF609 expression level was correlated with C-reactive protein (r=-0.138, P=0.026) and lymphocyte counts (r=0.16, P=0.01). After overexpression of circZNF609 in RAW264.7 cells, the expression level of IL-6 (P<0.001) and TNF-α (P<0.01) were significantly decreased and IL-10 was significantly increased (P<0.001). Bioinformatics analysis suggested that the abnormal expression of circZNF609 might probably sponge miRNA to modulate the inflammation cytokines.

Conclusions

CircRNA ZNF609 played an anti-inflammatory role and was an independent protective factor for CAD. It represented a moderate diagnostic value and might provide a new therapeutic target for CAD.

Key Developmental Regulators Suggest Multiple Origins of Pancreatic Beta Cell Regeneration

Extensive efforts have been done to try to restore the lost β cell mass for the cure of diabetes. Animal models have been established to provide evidences of cellular origins and contextual regulators of β cell regeneration. Here, we used a zebrafish β cell ablation and regeneration model to investigate β cell neogenesis in the first few days after a near-total β cell loss. Regeneration of β cells first occurred within 7 h post-treatment. Developmental regulators such as neurod, pdx1, mnx1, and nkx2.2a were active in the regenerating β cells, while at the same time suggesting different subpopulations of regenerative cellular origins. Using Cre/loxP-based lineage tracing, we showed that intrapancreatic ductal cells resisted to give rise to regenerating β cells. Given that transdifferentiation of α cell and δ cell can regenerate β cell, here we have provided further molecular evidence highly suggesting that the regenerating β cells originate from multiple cellular origins.