Kruppel-like factor family genes are expressed during Xenopus embryogenesis and involved in germ layer formation and body axis patterning

Spatial molecular anatomy of germ layers in the gastrulating cynomolgus monkey embryo

During mammalian embryogenesis, spatial regulation of gene expression and cell signaling are functionally coupled with lineage specification, patterning of tissue progenitors, and germ layer morphogenesis. While the mouse model has been instrumental for understanding mammalian development, comparatively little is known about human and non-human primate gastrulation due to the restriction of both technical and ethical issues. Here, we present a spatial and temporal survey of the molecular dynamics of cell types populating the non-human primate embryos during gastrulation. We reconstructed three-dimensional digital models from serial sections of cynomolgus monkey (Macaca fascicularis) gastrulating embryos at 1-day temporal resolution from E17 to E21. Spatial transcriptomics identifies gene expression profiles unique to the germ layers. Cross-species comparison reveals a developmental coordinate of germ layer segregation between mouse and primates, and species-specific transcription programs during gastrulation. These findings offer insights into evolutionarily conserved and divergent processes during mammalian gastrulation.

Adrenergic receptor signaling induced by Klf15, a regulator of regeneration enhancer, promotes kidney reconstruction

Despite the recent discovery of tissue regeneration enhancers in highly regenerative animals, upstream and downstream genetic programs connected by these enhancers still remain unclear. Here, we performed a genome-wide analysis of enhancers and associated genes in regenerating nephric tubules of Xenopus laevis. Putative enhancers were identified using assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) analyses. Their target genes were predicted based on their proximity to enhancers on genomic DNA and consistency of their transcriptome profiles to ATAC-seq/ChIP-seq profiles of the enhancers. Motif enrichment analysis identified the central role of Krüppel-like factors (Klf) in the enhancer. Klf15, a member of the Klf family, directly binds enhancers and stimulates expression of regenerative genes, including adrenoreceptor alpha 1A (adra1a), whereas inhibition of Klf15 activity results in failure of nephric tubule regeneration. Moreover, pharmacological inhibition of Adra1a-signaling suppresses nephric tubule regeneration, while its activation promotes nephric tubule regeneration and restores organ size. These results indicate that Klf15-dependent adrenergic receptor signaling through regeneration enhancers plays a central role in the genetic network for kidney regeneration.

Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing

The Krüppel-like factor (Klf) gene family encodes transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation and development in bilaterians. Although Klf genes have been shown to specify functionally various cell types in non-bilaterian animals, their role in early-diverging animal lineages has not been assessed. Thus, the ancestral activity of these transcription factors in animal development is not well understood. The ctenophore Mnemiopsis leidyi has emerged as an important non-bilaterian model system for understanding early animal evolution. Here, we characterize the expression and functional role of Klf genes during M. leidyi embryogenesis. Zygotic Klf gene function was assessed with both CRISPR/Cas9-mediated genome editing and splice-blocking morpholino oligonucleotide knockdown approaches. Abrogation of zygotic Klf expression during M. leidyi embryogenesis resulted in abnormal development of several organs, including the pharynx, tentacle bulbs and apical organ. Our data suggest an ancient role for Klf genes in regulating endodermal patterning, possibly through regulation of cell proliferation.

Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates

During vertebrate gastrulation, mesoderm is induced in pluripotent cells, concomitant with dorsal‐ventral patterning and establishing of the dorsal axis. We applied single‐cell chromatin accessibility and transcriptome analyses to explore the emergence of cellular heterogeneity during gastrulation in Xenopus tropicalis. Transcriptionally inactive lineage‐restricted genes exhibit relatively open chromatin in animal caps, whereas chromatin accessibility in dorsal marginal zone cells more closely reflects transcriptional activity. We characterized single‐cell trajectories and identified head and trunk organizer cell clusters in early gastrulae. By integrating chromatin accessibility and transcriptome data, we inferred the activity of transcription factors in single‐cell clusters and tested the activity of organizer‐expressed transcription factors in animal caps, alone or in combination. The expression profile induced by a combination of Foxb1 and Eomes most closely resembles that observed in the head organizer. Genes induced by Eomes, Otx2, or the Irx3‐Otx2 combination are enriched for maternally regulated H3K4me3 modifications, whereas Lhx8‐induced genes are marked more frequently by zygotically controlled H3K4me3. Taken together, our results show that transcription factors cooperate in a combinatorial fashion in generally open chromatin to orchestrate zygotic gene expression.

Regulation of gene expression in the bovine blastocyst by colony-stimulating factor 2 is disrupted by CRISPR/Cas9-mediated deletion of CSF2RA

Colony-stimulating factor 2 (CSF2) functions in the reproductive tract to modulate the function of the preimplantation embryo. The β subunit of the CSF2 receptor (CSF2RB) is not expressed in the embryo, and signal transduction is therefore different than for myeloid cells where the receptor is composed of α (CSF2RA) and β subunits. Here, we produced embryos in which exons 5 and 6 of CSF2RA were disrupted using the CRISPR/Cas 9 system to test whether CSF2RA signaling was essential for actions of CSF2 in the bovine embryo. Wild-type and CSF2RA knockout embryos were treated with 10 ng/mL CSF2 or vehicle at day 5 of development. Blastocysts were harvested at day 8 to determine transcript abundance of 90 genes by real-time polymerase chain reaction (PCR). Responses in female blastocysts were examined separately from male blastocysts because actions of CSF2 are sex-dependent. For wild-type embryos, CSF2 altered expression of 10 genes in females and 20 in males. Only three genes were affected by CSF2 in a similar manner for both sexes. Disruption of CSF2RA prevented the effect of CSF2 on expression for 9 of 10 CSF2-regulated genes in females and 19 of 20 genes in males. The results confirm the importance of CSF2RA for regulation of gene expression by CSF2 in the blastocyst.

The role of Krüppel-like factor 8 in cancer biology: Current research and its clinical relevance

Cancer is one of the leading causes of mortality worldwide, ranked second after heart disease. Despite recent advancements in diagnosis and treatment, there are still numerous problems associated with cancer progression, disease recurrence, and therapeutic resistance that are partially explored. Several studies have recently revealed that Krüppel-like factor 8 (KLF8) regulates transcription of genes linked with diverse biological processes, including proliferation, epithelial to mesenchymal transition (EMT), migration, invasion, and inflammation. KLF8 is expressed ubiquitously in mammalian cells, and its aberrant expression has been manifested with several cancer types. Earlier studies demonstrated the crucial role of KLF8 in DNA repair and resistance to apoptosis in numerous cancer types. Hence, studying the function of KLF8 from the perspective of cancer progression and therapy resistance would help develop a new therapeutic avenue. In this review, we summarize the clinical relevance of KLF8 expression in various malignancies, focusing on recent updates in EMT, cellular signaling, and cancer stem cells. We also address the contribution of KLF8 in development, DNA repair, chemoresistance, and its clinical utility as a predictive biomarker.

The landscape of accessible chromatin in bovine oocytes and early embryos

Chromatin reorganization governs the regulation of gene expression during preimplantation development. However, the landscape of chromatin dynamics in this period has not been explored in bovine. In this study, we constructed a genome-wide map of accessible chromatin in bovine oocytes and early embryos using an improved assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) which revealed unique features of the accessible chromatin during bovine early embryo development. We found that chromatin accessibility is low in oocytes and 2-/4-cell embryos, followed by a significant increase in embryos during major embryonic genome activation (EGA), and peaked in elongating day 14 embryos. Genome-wide characteristics of open chromatin showed that ATAC-seq signals in both transcription start sites (TSS) and transcription end sites (TES) were strong. Additionally, the distal ATAC-seq peaks were enriched in repeat elements in a type-specific and stage-specific manner. We further unveiled a series of transcription factor (TF) motifs with distinct variation of enrichment from distal ATAC-seq peaks. By integrated analysis of chromatin accessibility with transcriptomes and DNA methylomes in bovine early embryos, we showed that promoter accessibility was positively correlated with gene expression, especially during major EGA, and was strongly correlated to DNA methylation and CpG density. Finally, we identified the critical chromatin signatures and TFs that differ between in vivo and in vitro derived blastocysts, which provides insights to the potential mechanisms leading to low quality of embryos produced in vitro. Together, this comprehensive analysis revealed critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development.

Expression of Krüppel-like factor 9 in breast cancer patients and its effect on prognosis

Expression of Krüppel-like factor 9 (KLF9) in breast cancer tissue and its influence on prognosis was investigated. Sixty-eight patients with breast cancer admitted in Ningde Hospital Affiliated to Fujian Medical University from February 2014 to August 2015 were collected, and the expression level of KLF9 in cancerous tissue (n=68) and normal tissue (n=68) of the patients was measured by quantitative real-time PCR (RT-qPCR). The relationship between the expression and clinical pathological features and prognosis of patients was analyzed. The expression level of KLF9 in cancerous tissue was significantly lower than that in normal tissue (P<0.05). The expression in breast cancer tissue was not significantly correlated with age, height, menstrual status, lymph node metastasis or pathological differentiation (P>0.05), but was significantly correlated with tumor size and clinical stage (P<0.05). The 1-, 2-, and 3-year survival rates in the high expression group were significantly higher than those in the low expression group (P<0.001). Univariate Cox regression analysis was carried out according to the 3-year survival of the patients, and the results showed that tumor size (P=0.009), lymph node metastasis (P=0.002), pathological differentiation (P=0.015), clinical stage (P=0.013), and KLF9 (P=0.018) were factors affecting the survival of breast cancer patients. Subsequently, multivariate Cox regression analysis of the indicators with differences showed that those indicators were independent predictors of survival of breast cancer patients. In conclusion, KLF9 expression is low in breast cancer tissue, and its expression level is related to tumor size and clinical stage. Moreover, tumor size >5 cm, lymph node metastasis, low pathological differentiation, high clinical stage and low expression of KLF9 are all important factors that cause death of patients.

Enhancer activation by FGF signalling during otic induction

Vertebrate ear progenitors are induced by fibroblast growth factor signalling, however the molecular mechanisms leading to the coordinate activation of downstream targets are yet to be discovered. The ear, like other sensory placodes, arises from the pre-placodal region at the border of the neural plate. Using a multiplex NanoString approach, we determined the response of these progenitors to FGF signalling by examining the changes of more than 200 transcripts that define the otic and other placodes, neural crest and neural plate territories. This analysis identifies new direct and indirect FGF targets during otic induction. Investigating changes in histone marks by ChIP-seq reveals that FGF exposure of pre-placodal cells leads to rapid deposition of active chromatin marks H3K27ac near FGF-response genes, while H3K27ac is depleted in the vicinity of non-otic genes. Genomic regions that gain H3K27ac act as cis-regulatory elements controlling otic gene expression in time and space and define a unique transcription factor signature likely to control their activity. Finally, we show that in response to FGF signalling the transcription factor dimer AP1 recruits the histone acetyl transferase p300 to selected otic enhancers. Thus, during ear induction FGF signalling modifies the chromatin landscape to promote enhancer activation and chromatin accessibility.

The Effect and Mechanism of KLF7 in the TLR4/NF-κB/IL-6 Inflammatory Signal Pathway of Adipocytes

Objective

To investigate the role and possible molecular mechanism of Krüppel-like factor 7 (KLF7) in the TLR4/NF-κB/IL-6 inflammatory signaling pathway activated by free fatty acids (FFA).

Methods

The mRNA and protein expression levels of KLF7 and the factors of TLR4/NF-κB/IL-6 inflammatory signal pathways were detected by qRT-PCR and Western blotting after cell culture with different concentrations of palmitic acid (PA). The expression of KLF7 or TLR4 in adipocytes was upregulated or downregulated; after that, the mRNA and protein expression levels of these key factors were detected. KLF7 expression was downregulated while PA stimulated adipocytes, and then the mRNA and protein expressions of KLF7/p65 and downstream inflammatory cytokine IL-6 were detected. The luciferase reporter assay was used to determine whether KLF7 had a transcriptional activation effect on IL-6.

Results

(1) High concentration of PA can promote the expression of TLR4, KLF7, and IL-6 in adipocytes. (2) TLR4 positively regulates KLF7 expression in adipocytes. (3) KLF7 positively regulates IL-6 expression in adipocytes. (4) PA promotes IL-6 expression via KLF7 in adipocytes. (5) KLF7 has a transcriptional activation on IL-6.

Conclusion

PA promotes the expression of the inflammatory cytokine IL-6 by activating the TLR4/KLF7/NF-κB inflammatory signaling pathway. In addition, KLF7 may directly bind to the IL-6 promoter region and thus activate IL-6.

Klf4 could be activated by Pou5f3/Stat3 to induce the expression of Nanog in Japanese flounder

Krüppel-like factor 4 (Klf4) is a zinc finger protein transcription factor of the KLF family and plays an important role in various important biological process, including cell proliferation, differentiation, embryonic development, and cancer formation. In this study, the full length Klf4 cDNA sequence of Japanese flounder (Paralichthys olivaceus) was analyzed. Phylogenetic, gene structure, and synteny analysis revealed that PoKlf4 was conserved to that of teleost. Transcript of PoKlf4 showed that its expression was high during early embryonic development but reduced when gastrulation began, thus indicating its possible role in embryonic development. Tissue expression pattern showed that PoKlf4 was expressed higher in ovaries than in testes. ISH revealed that PoKlf4 was also expressed in spermatogonium, oocytes, and oogonia and in high levels in epithelial and lamellar epithelial cells of gills. Functional characterization of PoKlf4 gene promoter provided valuable information in understanding the molecular regulatory mechanisms of PoKlf4 gene. PoKlf4 could up-regulate Nanog, a gene that prevents ES cells from differentiating and being up-regulated by Pou5f3 and Stat3 genes that could maintain ES cell self-renewal. These results suggested that PoKlf4 maintains the pluripotency of ES cells. This study provides valuable information in exploring the regulatory network of PoKlf4 and lays the foundation for further research on the function of this gene.

Hypoxia‑induced miR‑210 contributes to apoptosis of mouse spermatocyte GC‑2 cells by targeting Kruppel‑like factor 7

The aim of the present study was to investigate the underlying mechanisms of hypoxia-induced microRNA (miR)-210 effects on mouse GC-2spd (GC-2) cells. GC-2 cells were subjected to hypoxia or normoxia for 12, 24, 48 and 72 h. Apoptosis of GC-2 cells was detected using terminal deoxynucleotidyl-transferase-meditated dUTP nick end labeling and flow cytometry. Reverse transcription-quantitative polymerase chain reaction was performed to analyze the expression of miR-210. Hypoxia-inducible factor-1α (HIF-1α), caspase-3, B-cell lymphoma 2, apoptosis regulator BAX and Kruppel-like factor 7 (KLF7) protein expression levels were detected by western blotting. Luciferase reporter gene assays were used to assess the targeting effects of miR-210 on KLF7. Hypoxia induced GC-2 cell apoptosis and increased the expression of HIF-1α and pro-apoptotic proteins; however, decreased anti-apoptotic protein expression levels. Furthermore, hypoxia resulted in the upregulation of miR-210 in GC-2 cells. HIF-1α and miR-210 were involved in the apoptosis of GC-2 cells by mediating the expression of apoptosis-associated proteins. Furthermore, KLF7 was directly targeted by miR-210 to influence the apoptosis of GC-2 cells subjected to hypoxia. The results suggested that hypoxia-induced miR-210 stimulated the activation of the apoptosis signaling pathway and contributed to the apoptosis of GC-2 cells by targeting KLF7.

Missing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status

Within the C-HPP, the Swiss and French teams are responsible for the annotation of proteins from chromosomes 2 and 14, respectively. neXtProt currently reports 1231 entries on chromosome 2 and 624 entries on chromosome 14; of these, 134 and 93 entries are still not experimentally validated and are thus considered as "missing proteins" (PE2-4), respectively. Among these entries, some may never be validated by conventional MS/MS approaches because of incompatible biochemical features. Others have already been validated but are still awaiting annotation. On the basis of information retrieved from the literature and from three of the main C-HPP resources (Human Protein Atlas, PeptideAtlas, and neXtProt), a subset of 40 theoretically detectable missing proteins (25 on chromosome 2 and 15 on chromosome 14) was defined for upcoming targeted studies in sperm samples. This list is proposed as a roadmap for the French and Swiss teams in the near future.

Murine Embryonic Stem Cell Plasticity Is Regulated through Klf5 and Maintained by Metalloproteinase MMP1 and Hypoxia

Mouse embryonic stem cells (mESCs) are expanded and maintained pluripotent in vitro in the presence of leukemia inhibitory factor (LIF), an IL6 cytokine family member which displays pleiotropic functions, depending on both cell maturity and cell type. LIF withdrawal leads to heterogeneous differentiation of mESCs with a proportion of the differentiated cells apoptosising. During LIF withdrawal, cells sequentially enter a reversible and irreversible phase of differentiation during which LIF addition induces different effects. However the regulators and effectors of LIF-mediated reprogramming are poorly understood. By employing a LIF-dependent 'plasticity' test, that we set up, we show that Klf5, but not JunB is a key LIF effector. Furthermore PI3K signaling, required for the maintenance of mESC pluripotency, has no effect on mESC plasticity while displaying a major role in committed cells by stimulating expression of the mesodermal marker Brachyury at the expense of endoderm and neuroectoderm lineage markers. We also show that the MMP1 metalloproteinase, which can replace LIF for maintenance of pluripotency, mimics LIF in the plasticity window, but less efficiently. Finally, we demonstrate that mESCs maintain plasticity and pluripotency potentials in vitro under hypoxic/physioxic growth conditions at 3% O2 despite lower levels of Pluri and Master gene expression in comparison to 20% O2.