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1.
Nihon Yakurigaku Zasshi ; 159(3): 160-164, 2024.
Article Ja | MEDLINE | ID: mdl-38692880

The 2019 Nobel Prize in Physiology or Medicine was awarded to Dr. William G. Kaelin Jr, Dr. Peter J. Ratcliffe, and Dr. Gregg L. Semenza for their elucidation of new physiological mechanisms "How cells sense and adapt to oxygen availability". Moreover, two different drugs, HIF-PH inhibitors and HIF-2 inhibitors were also developed based on the discovery. Interestingly, those three doctors have different backgrounds as a medical oncologist, a nephrologist, and a pediatrician, respectively. They have started the research based on their own unique perspectives and eventually merged as "the elucidation of the response mechanism of living organisms to hypoxic environments". In this review, we will explain how the translational research that has begun to solve unmet clinical needs successfully contributed to the development of innovative therapeutic drugs.


Hypoxia , Humans , Hypoxia/drug therapy , Hypoxia/metabolism , Animals , Drug Development , Molecular Targeted Therapy , Basic Helix-Loop-Helix Transcription Factors/metabolism
2.
J Cell Mol Med ; 28(9): e18361, 2024 May.
Article En | MEDLINE | ID: mdl-38722283

Hypoxia and Ferroptosis are associated with the malignant behaviour of cervical cancer. Endothelial PAS domain-containing protein 1 (EPAS1) contributes to the progression of cervical cancer. EPAS1 plays important roles in hypoxia and ferroptosis. Using the GEO dataset, machine-learning algorithms were used to screen for hypoxia- and ferroptosis-related genes (HFRGs) in cervical cancer. EPAS1 was identified as the hub gene. qPCR and WB were used to investigate the expression of EPAS1 in normal and cervical cancer tissues. The proliferation, invasion and migration of EPAS1 cells in HeLa and SiHa cell lines were detected using CCK8, transwell and wound healing assays, respectively. Apoptosis was detected by flow cytometry. A dual-luciferase assay was used to analyse the MALAT1-miR-182-5P-EPAS1 mRNA axis and core promoter elements of the super-enhancer. EPAS1 was significantly overexpressed in cervical cancer tissues. EPAS1 could increase the proliferation, invasion, migration of HeLa and SiHa cells and reduce the apoptosis of HeLa and SiHa cell. According to the double-luciferase assay, EPAS1 expression was regulated by the MALAT1-Mir-182-5p-EPAS1 mRNA axis. EPAS1 is associated with super-enhancers. Double-luciferase assay showed that the core elements of the super-enhancer were E1 and E3. EPAS1, an HFRG, is significantly overexpressed in cervical cancer. EPAS1 promotes malignant behaviour of cervical cancer cells. EPAS1 expression is regulated by super-enhancers and the MALAT1-miR-182-5P- EPAS1 mRNA axis. EPAS1 may be a target for the diagnosis and treatment of cervical cancer.


Apoptosis , Basic Helix-Loop-Helix Transcription Factors , Cell Movement , Cell Proliferation , Ferroptosis , Gene Expression Regulation, Neoplastic , Uterine Cervical Neoplasms , Humans , Uterine Cervical Neoplasms/genetics , Uterine Cervical Neoplasms/pathology , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Female , Ferroptosis/genetics , Cell Proliferation/genetics , Cell Movement/genetics , Apoptosis/genetics , MicroRNAs/genetics , MicroRNAs/metabolism , Cell Line, Tumor , HeLa Cells , RNA, Long Noncoding/genetics , RNA, Competitive Endogenous
3.
Front Immunol ; 15: 1390261, 2024.
Article En | MEDLINE | ID: mdl-38726001

Objective: The aim of this study was to identify the molecular subtypes of breast cancer based on chromatin regulator-related genes. Methods: The RNA sequencing data of The Cancer Genome Atlas-Breast Cancer cohort were obtained from the official website, while the single-cell data were downloaded from the Gene Expression Omnibus database (GSE176078). Validation was performed using the Molecular Taxonomy of Breast Cancer International Consortium dataset. Furthermore, the immune characteristics, tumor stemness, heterogeneity, and clinical characteristics of these molecular subtypes were analyzed. The correlation between chromatin regulators and chemotherapy resistance was examined in vitro using the quantitative real-time polymerase chain reaction (qRT-PCR) and Cell Counting Kit-8 (CCK8) assays. Results: This study identified three stable molecular subtypes with different prognostic and pathological features. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction analyses revealed that the differentially expressed genes were associated with disease processes, such as mitotic nuclear division, chromosome segregation, condensed chromosome, and specific chromosome region. The T stage and subtypes were correlated with the clinical features. Tumor heterogeneity (mutant-allele tumor heterogeneity, tumor mutational burden, purity, and homologous recombination deficiency) and tumor stemness (RNA expression-based stemness score, epigenetically regulated RNA expression-based stemness score, DNA methylation-based stemness score, and epigenetically regulated DNA methylation-based stemness score) significantly varied between the three subtypes. Furthermore, Western blotting, qRT-PCR, and CCK8 assays demonstrated that the expression of ASCL1 was positively correlated with chemotherapy resistance in breast cancer. Conclusion: This study identified the subtypes of breast cancer based on chromatin regulators and analyzed their clinical features, gene mutation status, immunophenotype, and drug sensitivity. The results of this study provide effective strategies for assessing clinical prognosis and developing personalized treatment strategies.


Basic Helix-Loop-Helix Transcription Factors , Breast Neoplasms , Drug Resistance, Neoplasm , Gene Expression Regulation, Neoplastic , Humans , Breast Neoplasms/genetics , Breast Neoplasms/drug therapy , Drug Resistance, Neoplasm/genetics , Female , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Chromatin/genetics , Prognosis , Biomarkers, Tumor/genetics , Cell Line, Tumor , Gene Expression Profiling
4.
Int J Mol Sci ; 25(9)2024 May 01.
Article En | MEDLINE | ID: mdl-38732175

Drought stress globally poses a significant threat to maize (Zea mays L.) productivity and the underlying molecular mechanisms of drought tolerance remain elusive. In this study, we characterized ZmbHLH47, a basic helix-loop-helix (bHLH) transcription factor, as a positive regulator of drought tolerance in maize. ZmbHLH47 expression was notably induced by both drought stress and abscisic acid (ABA). Transgenic plants overexpressing ZmbHLH47 displayed elevated drought tolerance and ABA responsiveness, while the zmbhlh47 mutant exhibited increased drought sensitivity and reduced ABA sensitivity. Mechanistically, it was revealed that ZmbHLH47 could directly bind to the promoter of ZmSnRK2.9 gene, a member of the subgroup III SnRK2 kinases, activating its expression. Furthermore, ZmSnRK2.9-overexpressing plants exhibited enhanced ABA sensitivity and drought tolerance, whereas the zmsnrk2.9 mutant displayed a decreased sensitivity to both. Notably, overexpressing ZmbHLH47 in the zmsnrk2.9 mutant closely resembled the zmsnrk2.9 mutant, indicating the importance of the ZmbHLH47-ZmSnRK2.9 module in ABA response and drought tolerance. These findings provided valuable insights and a potential genetic resource for enhancing the environmental adaptability of maize.


Abscisic Acid , Droughts , Gene Expression Regulation, Plant , Plant Proteins , Stress, Physiological , Zea mays , Zea mays/genetics , Zea mays/physiology , Zea mays/metabolism , Abscisic Acid/metabolism , Abscisic Acid/pharmacology , Plant Proteins/genetics , Plant Proteins/metabolism , Stress, Physiological/genetics , Plants, Genetically Modified/genetics , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Drought Resistance
5.
Gut Microbes ; 16(1): 2347722, 2024.
Article En | MEDLINE | ID: mdl-38706205

The intestine is prone to radiation damage in patients undergoing radiotherapy for pelvic tumors. However, there are currently no effective drugs available for the prevention or treatment of radiation-induced enteropathy (RIE). In this study, we aimed at investigating the impact of indole-3-carboxaldehyde (I3A) derived from the intestinal microbiota on RIE. Intestinal organoids were isolated and cultivated for screening radioprotective tryptophan metabolites. A RIE model was established using 13 Gy whole-abdominal irradiation in male C57BL/6J mice. After oral administration of I3A, its radioprotective ability was assessed through the observation of survival rates, clinical scores, and pathological analysis. Intestinal stem cell survival and changes in the intestinal barrier were observed through immunofluorescence and immunohistochemistry. Subsequently, the radioprotective mechanisms of I3A was investigated through 16S rRNA and transcriptome sequencing, respectively. Finally, human colon cancer cells and organoids were cultured to assess the influence of I3A on tumor radiotherapy. I3A exhibited the most potent radioprotective effect on intestinal organoids. Oral administration of I3A treatment significantly increased the survival rate in irradiated mice, improved clinical and histological scores, mitigated mucosal damage, enhanced the proliferation and differentiation of Lgr5+ intestinal stem cells, and maintained intestinal barrier integrity. Furthermore, I3A enhanced the abundance of probiotics, and activated the AhR/IL-10/Wnt signaling pathway to promote intestinal epithelial proliferation. As a crucial tryptophan metabolite, I3A promotes intestinal epithelial cell proliferation through the AhR/IL-10/Wnt signaling pathway and upregulates the abundance of probiotics to treat RIE. Microbiota-derived I3A demonstrates potential clinical application value for the treatment of RIE.


Gastrointestinal Microbiome , Indoles , Mice, Inbred C57BL , Probiotics , Receptors, Aryl Hydrocarbon , Wnt Signaling Pathway , Animals , Mice , Gastrointestinal Microbiome/drug effects , Male , Humans , Probiotics/administration & dosage , Probiotics/pharmacology , Receptors, Aryl Hydrocarbon/metabolism , Indoles/metabolism , Indoles/pharmacology , Radiation-Protective Agents/pharmacology , Organoids/metabolism , Radiation Injuries/metabolism , Radiation Injuries/prevention & control , Intestinal Mucosa/metabolism , Intestinal Mucosa/microbiology , Intestinal Mucosa/radiation effects , Intestines/microbiology , Intestines/radiation effects , Basic Helix-Loop-Helix Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics
6.
Proc Natl Acad Sci U S A ; 121(20): e2321711121, 2024 May 14.
Article En | MEDLINE | ID: mdl-38713624

During development, neural stem cells in the cerebral cortex, also known as radial glial cells (RGCs), generate excitatory neurons, followed by production of cortical macroglia and inhibitory neurons that migrate to the olfactory bulb (OB). Understanding the mechanisms for this lineage switch is fundamental for unraveling how proper numbers of diverse neuronal and glial cell types are controlled. We and others recently showed that Sonic Hedgehog (Shh) signaling promotes the cortical RGC lineage switch to generate cortical oligodendrocytes and OB interneurons. During this process, cortical RGCs generate intermediate progenitor cells that express critical gliogenesis genes Ascl1, Egfr, and Olig2. The increased Ascl1 expression and appearance of Egfr+ and Olig2+ cortical progenitors are concurrent with the switch from excitatory neurogenesis to gliogenesis and OB interneuron neurogenesis in the cortex. While Shh signaling promotes Olig2 expression in the developing spinal cord, the exact mechanism for this transcriptional regulation is not known. Furthermore, the transcriptional regulation of Olig2 and Egfr has not been explored. Here, we show that in cortical progenitor cells, multiple regulatory programs, including Pax6 and Gli3, prevent precocious expression of Olig2, a gene essential for production of cortical oligodendrocytes and astrocytes. We identify multiple enhancers that control Olig2 expression in cortical progenitors and show that the mechanisms for regulating Olig2 expression are conserved between the mouse and human. Our study reveals evolutionarily conserved regulatory logic controlling the lineage switch of cortical neural stem cells.


Basic Helix-Loop-Helix Transcription Factors , Cerebral Cortex , ErbB Receptors , Hedgehog Proteins , Nerve Tissue Proteins , Neural Stem Cells , Neurogenesis , Oligodendrocyte Transcription Factor 2 , PAX6 Transcription Factor , Animals , Neurogenesis/physiology , Cerebral Cortex/metabolism , Cerebral Cortex/cytology , Basic Helix-Loop-Helix Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics , ErbB Receptors/metabolism , ErbB Receptors/genetics , Mice , Oligodendrocyte Transcription Factor 2/metabolism , Oligodendrocyte Transcription Factor 2/genetics , Nerve Tissue Proteins/metabolism , Nerve Tissue Proteins/genetics , Hedgehog Proteins/metabolism , Hedgehog Proteins/genetics , PAX6 Transcription Factor/metabolism , PAX6 Transcription Factor/genetics , Neural Stem Cells/metabolism , Neural Stem Cells/cytology , Homeodomain Proteins/metabolism , Homeodomain Proteins/genetics , Zinc Finger Protein Gli3/metabolism , Zinc Finger Protein Gli3/genetics , Eye Proteins/metabolism , Eye Proteins/genetics , Repressor Proteins/metabolism , Repressor Proteins/genetics , Paired Box Transcription Factors/metabolism , Paired Box Transcription Factors/genetics , Neuroglia/metabolism , Neuroglia/cytology , Gene Expression Regulation, Developmental , Signal Transduction , Olfactory Bulb/metabolism , Olfactory Bulb/cytology , Cell Lineage , Humans
7.
Genesis ; 62(3): e23601, 2024 Jun.
Article En | MEDLINE | ID: mdl-38703044

HAND2 is a basic helix-loop-helix transcription factor with diverse functions during development. To facilitate the investigation of genetic and functional diversity among Hand2-expressing cells in the mouse, we have generated Hand2Dre, a knock-in allele expressing Dre recombinase. To avoid disrupting Hand2 function, the Dre cDNA is inserted at the 3' end of the Hand2 coding sequence following a viral 2A peptide. Hand2Dre homozygotes can therefore be used in complex crosses to increase the proportion of useful genotypes among offspring. Dre expression in mid-gestation Hand2Dre embryos is indistinguishable from wild-type Hand2 expression, and HandDre efficiently recombines rox target sites in vivo. In combination with existing Cre and Flp mouse lines, Hand2Dre will therefore extend the ability to perform genetic intersectional labeling, fate mapping, and functional manipulation of subpopulations of cells characterized by developmental expression of Hand2.


Alleles , Basic Helix-Loop-Helix Transcription Factors , Gene Knock-In Techniques , Animals , Female , Mice , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Gene Knock-In Techniques/methods , Integrases/genetics , Integrases/metabolism , Male
8.
Ups J Med Sci ; 1292024.
Article En | MEDLINE | ID: mdl-38571885

Objectives: This study aimed to assess the cellular localization and expression levels of hypoxia-inducible factor (HIF) -α proteins (specifically HIF-1α, HIF-2α, and HIF-3α) that play a role in the hypoxia pathway and to determine their correlation with clinicopathological parameters and patient survival in renal cell carcinoma (RCC). Materials and methods: Tissue microarray (TMA) with cores from 150 clear cell RCCs and 31 non-ccRCC samples. HIF-1α, HIF-2α, and HIF-3α antibodies were used for immunohistochemistry (IHC) of TMA to evaluate the cellular localization and expression levels of HIF-α proteins, specifically in relation to the hypoxia pathway. Results: The expression levels of the HIF-α proteins were higher in the nucleus than in the cytoplasm. Furthermore, the nuclear expression levels of all HIF-α proteins were significantly higher in clear cell RCC (ccRCC) than in non-ccRCC. Cytoplasmic HIF-3α expression was also higher in ccRCC than in non-ccRCC, whereas cytoplasmic HIF-1α and HIF-2α expression levels were similar between the different RCC types. In ccRCC, nuclear HIF-1α expression levels correlated with both nuclear HIF-2α and HIF-3α levels, whereas cytoplasmic HIF-3α expression levels were associated with HIF-1α only.In non-ccRCC, there was a positive correlation observed between nuclear HIF-1α and HIF-3α expression, but no correlation was found with HIF-2α. In patients with ccRCC, the nuclear expressions of HIF-1α and HIF-3α was significantly associated with cancer-specific survival (CSS) in univariate analysis. This association was no longer evident in multivariate analysis. Notably, there was no correlation observed between nuclear HIF-2α expression and CSS in these patients. In contrast, cytoplasmic expression levels showed no association with CSS. Conclusion: The expression levels of the three primary HIF-α proteins were found to be higher in the nucleus than in the cytoplasm. Furthermore, the results indicated that HIF-3α and HIF-1α expression levels were significant univariate factors associated with CSS in patients with clear cell RCC. These results highlight the critical role that HIF-3α and HIF-1α play in the hypoxia pathway.


Carcinoma, Renal Cell , Kidney Neoplasms , Humans , Carcinoma, Renal Cell/metabolism , Carcinoma, Renal Cell/pathology , Basic Helix-Loop-Helix Transcription Factors/analysis , Basic Helix-Loop-Helix Transcription Factors/metabolism , Immunohistochemistry , Hypoxia , Hypoxia-Inducible Factor 1, alpha Subunit
9.
Cells ; 13(7)2024 Apr 05.
Article En | MEDLINE | ID: mdl-38607072

The field cancerization theory is an important paradigm in head and neck carcinoma as its oncological repercussions affect treatment outcomes in diverse ways. The aim of this study is to assess the possible interconnection between peritumor mucosa and the process of tumor neoangiogenesis. Sixty patients with advanced laryngeal carcinoma were enrolled in this study. The majority of patients express a canonical HIF-upregulated proangiogenic signature with almost complete predominancy of HIF-1α overexpression and normal expression levels of the HIF-2α isoform. Remarkably, more than 60% of the whole cohort also exhibited an HIF-upregulated proangiogenic signature in the peritumoral benign mucosa. Additionally, the latter subgroup had a distinctly shifted phenotype towards HIF-2α upregulation compared to the one in tumor tissue, i.e., a tendency towards an HIF switch is observed in contrast to the dominated by HIF-1α tumor phenotype. ETS-1 displays stable and identical significant overexpression in both the proangiogenic phenotypes present in tumor and peritumoral mucosa. In the current study, we report for the first time the existence of an abnormal proangiogenic expression profile present in the peritumoral mucosa in advanced laryngeal carcinoma when compared to paired distant laryngeal mucosa. Moreover, we describe a specific phenotype of this proangiogenic signature that is significantly different from the one present in tumor tissue as we delineate both phenotypes, quantitively and qualitatively. This finding is cancer heterogeneity, per se, which extends beyond the "classical" borders of the malignancy, and it is proof of a strong interconnection between field cancerization and one of the classical hallmarks of cancer-the process of tumor neoangiogenesis.


Carcinoma , Laryngeal Neoplasms , Humans , Laryngeal Neoplasms/genetics , Neovascularization, Pathologic/genetics , Mucous Membrane , Basic Helix-Loop-Helix Transcription Factors/metabolism
10.
PLoS One ; 19(4): e0295732, 2024.
Article En | MEDLINE | ID: mdl-38626041

Iron (Fe) is a crucial micronutrient needed in many metabolic processes. To balance needs and potential toxicity, plants control the amount of Fe they take up and allocate to leaves and seeds during their development. One important regulator of this process is POPEYE (PYE). PYE is a Fe deficiency-induced key bHLH transcription factor (TF) for allocation of internal Fe in plants. In the absence of PYE, there is altered Fe translocation and plants develop a leaf chlorosis. NICOTIANAMINE SYNTHASE4 (NAS4), FERRIC-REDUCTION OXIDASE3 (FRO3), and ZINC-INDUCED FACILITATOR1 (ZIF1) genes are expressed at higher level in pye-1 indicating that PYE represses these genes. PYE activity is controlled in a yet unknown manner. Here, we show that a small Fe deficiency-induced protein OLIVIA (OLV) can interact with PYE. OLV has a conserved C-terminal motif, that we named TGIYY. Through deletion mapping, we pinpointed that OLV TGIYY and several regions of PYE can be involved in the protein interaction. An OLV overexpressing (OX) mutant line exhibited an enhanced NAS4 gene expression. This was a mild Fe deficiency response phenotype that was related to PYE function. Leaf rosettes of olv mutants remained smaller than those of wild type, indicating that OLV promotes plant growth. Taken together, our study identified a small protein OLV as a candidate that may connect aspects of Fe homeostasis with regulation of leaf growth.


Arabidopsis Proteins , Arabidopsis , Iron Deficiencies , Humans , Iron/metabolism , Basic Helix-Loop-Helix Transcription Factors/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , Gene Expression Regulation, Plant
11.
Methods Mol Biol ; 2795: 161-167, 2024.
Article En | MEDLINE | ID: mdl-38594537

The PHYTOCHROME INTERACTING FACTORs (PIFs) play pivotal roles in regulating thermo- and photo-morphogenesis in Arabidopsis. One of the main hubs in thermomorphogenesis is PIF4, which regulates plant development under high ambient temperature along with other PIFs. PIF4 enhances its own transcription and PIF4 protein is stabilized under high ambient temperature. However, the mechanisms of thermo-stabilization of PIF4 are less understood. Recently, it was shown that SUPPRESSOR OF PHYA-105 1 (SPA1) can function as a serine/threonine kinase to phosphorylate PIF4 in vitro, and the phosphorylated form of PIF4 is more stable under high ambient temperature conditions. In this chapter, we describe the in vitro kinase assay of PIF4 by SPA1. In principle, this protocol can be applied for other putative substrates and kinases.


Arabidopsis Proteins , Arabidopsis , Phytochrome , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Phosphorylation , Arabidopsis/metabolism , Phytochrome/metabolism , Plant Development , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Gene Expression Regulation, Plant , Cell Cycle Proteins/metabolism
12.
Methods Mol Biol ; 2795: 195-212, 2024.
Article En | MEDLINE | ID: mdl-38594540

The phytochrome-interacting factor 4 (PIF4) is a well-known transcription factor that plays a pivotal role in plant thermomorphogenesis, coordinating growth and development in response to temperature changes. As PIF4 functions by forming complexes with other proteins, determining its interacting partners is essential for understanding its diverse roles in plant thermal responses. The GST (glutathione-S-transferase) pull-down assay is a widely used biochemical technique that enables the investigation of protein-protein interactions in vitro. It is particularly useful for studying transient or weak interactions between proteins. In this chapter, we describe the GST pull-down approach to detect the interaction between PIF4 and a known or suspected interacting protein. We provide detailed step-by-step descriptions of the assay procedures, from the preparation of recombinant GST-PIF4 fusion protein to the binding and elution of interacting partners. Additionally, we provide guidelines for data interpretation, quantification, and statistical analysis to ensure robust and reliable results.


Arabidopsis Proteins , Arabidopsis , Phytochrome , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Phytochrome/metabolism , Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Gene Expression Regulation, Plant
13.
Methods Mol Biol ; 2795: 183-194, 2024.
Article En | MEDLINE | ID: mdl-38594539

Phytochromes are red (R) and far-red (FR) light photoreceptors in plants. Upon light exposure, photoactivated phytochromes translocate into the nucleus, where they interact with their partner proteins to transduce light signals. The yeast two-hybrid (Y2H) system is a powerful technique for rapidly identifying and verifying protein-protein interactions, and PHYTOCHROME-INTERACTING FACTOR3 (PIF3), the founding member of the PIF proteins, was initially identified in a Y2H screen for phytochrome B (phyB)-interacting proteins. Recently, we developed a yeast three-hybrid (Y3H) system by introducing an additional vector into this Y2H system, and thus a new regulator could be co-expressed and its role in modulating the interactions between phytochromes and their signaling partners could be examined. By employing this Y3H system, we recently showed that both MYB30 and CBF1, two negative regulators of seedlings photomorphogenesis, act to inhibit the interactions between phyB and PIF4/PIF5. In this chapter, we will use the CBF1-phyB-PIF4 module as an example and describe the detailed procedure for performing this Y3H assay. It will be intriguing and exciting to explore the potential usage of this Y3H system in future research.


Arabidopsis Proteins , Arabidopsis , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors , Phytochrome , Saccharomyces cerevisiae Proteins , Phytochrome B/genetics , Phytochrome B/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Saccharomyces cerevisiae/metabolism , Light , Phytochrome/genetics , Phytochrome/metabolism , Gene Expression Regulation, Plant , Transcription Factors/genetics , Transcription Factors/metabolism , Trans-Activators/metabolism , Saccharomyces cerevisiae Proteins/metabolism
14.
Mol Biol Rep ; 51(1): 479, 2024 Apr 05.
Article En | MEDLINE | ID: mdl-38578511

BACKGROUND: GLABRA3 (GL3) and ENHANCER OF GLABRA3 (EGL3) genes encode a typical helix-loop-helix (bHLH) transcription factors that primarily regulate trichome branching and root hair development, DNA endoreduplication, trichoblast size, and stomatal formation. The functions of GL3 genes in cotton crop have been poorly characterized. In this study, we performed comprehensive genome-wide scans for GL3 and EGL3 homologs to enhance our comprehension of their potential roles in trichome and fiber development in cotton crop. METHODS AND RESULTS: Our findings paraded that Gossypium hirsutum and G. barbadense have 6 GL3s each, unevenly distributed on 4 chromosomes whereas, G. arboreum, and G. raimondii have 3 GL3s each, unevenly distributed on 2 chromosomes. Gh_A08G2088 and Gb_A09G2187, despite having the same bHLH domain as the other GL3 genes, were excluded due to remarkable short sequences and limited number of motifs, indicating a lack of potential functional activity. The phylogenetic analysis categorized remaining 16 GL3s into three subfamilies (Group I-III) closely related to A. thaliana. The 16 GL3s have complete bHLH domain, encompassing 590-631 amino acids, with molecular weights (MWs) ranging from 65.92 to 71.36 kDa. Within each subfamily GL3s depicted shared similar gene structures and motifs, indicating conserved characteristics within respective groups. Promoter region analysis revealed 27 cis-acting elements, these elements were responsive to salicylic acid, abscisic acid (ABA), methyl jasmonate (MeJA), and gibberellin. The expression of GL3 genes was analyzed across 12 tissues in both G. barbadense and G. hirsutum using the publicly available RNA-seq data. Among GL3s, Gb_D11G0219, Gb_D11G0214, and Gb_D08G2182, were identified as relatively highly expressed across different tissues, consequently selected for hormone treatment and expression validation in G. barbadense. RT-qPCR results demonstrated significant alterations in the expression levels of Gb_D11G0219 and Gb_D11G0214 following MeJA, GA, and ABA treatment. Subcellular localization prediction revealed that most GL3 proteins were predominantly expressed in the nucleus, while a few were localized in the cytoplasm and chloroplasts. CONCLUSIONS: In summary, this study lays the foundation for subsequent functional validation of GL3 genes by identifying hormonal regulation patterns and probable sites of action in cotton trichome formation and fiber development. The results stipulate a rationale to elucidate the roles and regulatory mechanisms of GL3 genes in the intricate process of cotton fibre and trichome development.


Arabidopsis Proteins , Arabidopsis , Gossypium/genetics , Gossypium/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Arabidopsis/genetics , Trichomes/genetics , Trichomes/metabolism , Phylogeny , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Gene Expression Regulation, Plant/genetics
15.
Mar Drugs ; 22(4)2024 Mar 23.
Article En | MEDLINE | ID: mdl-38667760

The inadequate vascularization seen in fast-growing solid tumors gives rise to hypoxic areas, fostering specific changes in gene expression that bolster tumor cell survival and metastasis, ultimately leading to unfavorable clinical prognoses across different cancer types. Hypoxia-inducible factors (HIF-1 and HIF-2) emerge as druggable pivotal players orchestrating tumor metastasis and angiogenesis, thus positioning them as prime targets for cancer treatment. A range of HIF inhibitors, notably natural compounds originating from marine organisms, exhibit encouraging anticancer properties, underscoring their significance as promising therapeutic options. Bioprospection of the marine environment is now a well-settled approach to the discovery and development of anticancer agents that might have their medicinal chemistry developed into clinical candidates. However, despite the massive increase in the number of marine natural products classified as 'anticancer leads,' most of which correspond to general cytotoxic agents, and only a few have been characterized regarding their molecular targets and mechanisms of action. The current review presents a critical analysis of inhibitors of HIF-1 and HIF-2 and hypoxia-selective compounds that have been sourced from marine organisms and that might act as new chemotherapeutic candidates or serve as templates for the development of structurally similar derivatives with improved anticancer efficacy.


Antineoplastic Agents , Aquatic Organisms , Biological Products , Neoplasms , Signal Transduction , Humans , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Animals , Signal Transduction/drug effects , Neoplasms/drug therapy , Neoplasms/pathology , Biological Products/pharmacology , Biological Products/chemistry , Biological Products/therapeutic use , Hypoxia-Inducible Factor 1/antagonists & inhibitors , Hypoxia-Inducible Factor 1/metabolism , Basic Helix-Loop-Helix Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/antagonists & inhibitors
16.
Front Immunol ; 15: 1330228, 2024.
Article En | MEDLINE | ID: mdl-38680496

Introduction: Aryl hydrocarbon receptor (AhR) is a transcription factor that performs various functions upon ligand activation. Several studies have explored the role of AhR expression in tumor progression and immune surveillance. Nevertheless, investigations on the distribution of AhR expression, specifically in cancer or immune cells in the tumor microenvironment (TME), remain limited. Examining the AhR expression and distribution in the TME is crucial for gaining insights into the mechanism of action of AhR-targeting anticancer agents and their potential as biomarkers. Methods: Here, we used multiplexed immunohistochemistry (mIHC) and image cytometry to investigate the AhR expression and distribution in 513 patient samples, of which 292 are patients with one of five solid cancer types. Additionally, we analyzed the nuclear and cytosolic distribution of AhR expression. Results: Our findings reveal that AhR expression was primarily localized in cancer cells, followed by stromal T cells and macrophages. Furthermore, we observed a positive correlation between the nuclear and cytosolic expression of AhR, indicating that the expression of AhR as a biomarker is independent of its localization. Interestingly, the expression patterns of AhR were categorized into three clusters based on the cancer type, with high AhR expression levels being found in regulatory T cells (Tregs) in non-small cell lung cancer (NSCLC). Discussion: These findings are anticipated to serve as pivotal evidence for the design of clinical trials and the analysis of the anticancer mechanisms of AhR-targeting therapies.


Neoplasms , Receptors, Aryl Hydrocarbon , Tumor Microenvironment , Receptors, Aryl Hydrocarbon/metabolism , Humans , Tumor Microenvironment/immunology , Neoplasms/immunology , Neoplasms/metabolism , Neoplasms/pathology , Biomarkers, Tumor/metabolism , Basic Helix-Loop-Helix Transcription Factors/metabolism
17.
Biomolecules ; 14(4)2024 Apr 04.
Article En | MEDLINE | ID: mdl-38672460

A considerable effort has been spent in the past decades to develop targeted therapies for the treatment of demyelinating diseases, such as multiple sclerosis (MS). Among drugs with free radical scavenging activity and oligodendrocyte protecting effects, Edaravone (Radicava) has recently received increasing attention because of being able to enhance remyelination in experimental in vitro and in vivo disease models. While its beneficial effects are greatly supported by experimental evidence, there is a current paucity of information regarding its mechanism of action and main molecular targets. By using high-throughput RNA-seq and biochemical experiments in murine oligodendrocyte progenitors and SH-SY5Y neuroblastoma cells combined with molecular docking and molecular dynamics simulation, we here provide evidence that Edaravone triggers the activation of aryl hydrocarbon receptor (AHR) signaling by eliciting AHR nuclear translocation and the transcriptional-mediated induction of key cytoprotective gene expression. We also show that an Edaravone-dependent AHR signaling transduction occurs in the zebrafish experimental model, associated with a downstream upregulation of the NRF2 signaling pathway. We finally demonstrate that its rapid cytoprotective and antioxidant actions boost increased expression of the promyelinating Olig2 protein as well as of an Olig2:GFP transgene in vivo. We therefore shed light on a still undescribed potential mechanism of action for this drug, providing further support to its therapeutic potential in the context of debilitating demyelinating conditions.


Antioxidants , Edaravone , NF-E2-Related Factor 2 , Receptors, Aryl Hydrocarbon , Signal Transduction , Zebrafish , Receptors, Aryl Hydrocarbon/metabolism , Edaravone/pharmacology , Animals , Signal Transduction/drug effects , Humans , Mice , Antioxidants/pharmacology , NF-E2-Related Factor 2/metabolism , Molecular Docking Simulation , Cell Line, Tumor , Basic Helix-Loop-Helix Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics , Molecular Dynamics Simulation
18.
Ecotoxicol Environ Saf ; 276: 116287, 2024 May.
Article En | MEDLINE | ID: mdl-38579532

Benzo(a)pyrene (BaP) can be detected in the human placenta. However, little is known about the effects of BaP exposure on different placental cells under various conditions. In this study, we aimed to investigate the effects of BaP on mitochondrial function, pyrin domain-containing protein 3 (NLRP3) inflammasome, and apoptosis in three human trophoblast cell lines under normoxia, hypoxia, and inflammatory conditions. JEG-3, BeWo, and HTR-8/SVneo cell lines were exposed to BaP under normoxia, hypoxia, or inflammatory conditions for 24 h. After treatment, we evaluated cell viability, apoptosis, aryl hydrocarbon receptor (AhR) protein and cytochrome P450 (CYP) gene expression, mitochondrial function, including mitochondrial DNA copy number (mtDNAcn), mitochondrial membrane potential (ΔΨm), intracellular adenosine triphosphate (iATP), and extracellular ATP (eATP), nitric oxide (NO), NLPR3 inflammasome proteins, and interleukin (IL)-1ß. We found that BaP upregulated the expression of AhR or CYP genes to varying degrees in all three cell lines. Exposure to BaP alone increased ΔΨm in all cell lines but decreased NO in BeWo and HTR-8/SVneo, iATP in HTR-8/SVneo, and cell viability in JEG-3, without affecting apoptosis. Under hypoxic conditions, BaP did not increase the expression of AhR and CYP genes in JEG-3 cells but increased CYP gene expression in two others. Pro-inflammatory conditions did not affect the response of the 3 cell lines to BaP with respect to the expression of CYP genes and changes in the mitochondrial function and NLRP3 inflammasome proteins. In addition, in HTR-8/SVneo cells, BaP increased IL-1ß secretion in the presence of hypoxia and poly(I:C). In conclusion, our results showed that BaP affected mitochondrial function in trophoblast cell lines by increasing ΔΨm. This increased ΔΨm may have rescued the trophoblast cells from activation of the NLRP3 inflammasome and apoptosis after BaP treatment. We also observed that different human trophoblast cell lines had cell type-dependent responses to BaP exposure under normoxia, hypoxia, or pro-inflammatory conditions.


Apoptosis , Benzo(a)pyrene , Cell Survival , NLR Family, Pyrin Domain-Containing 3 Protein , Placenta , Receptors, Aryl Hydrocarbon , Trophoblasts , Humans , Benzo(a)pyrene/toxicity , Placenta/drug effects , Placenta/cytology , Cell Line , Female , Pregnancy , Apoptosis/drug effects , Trophoblasts/drug effects , Trophoblasts/metabolism , Receptors, Aryl Hydrocarbon/metabolism , Cell Survival/drug effects , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Inflammasomes/drug effects , Inflammasomes/metabolism , Mitochondria/drug effects , Inflammation/chemically induced , Cell Hypoxia/drug effects , Membrane Potential, Mitochondrial/drug effects , Cytochrome P-450 Enzyme System/metabolism , Basic Helix-Loop-Helix Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics
19.
eNeuro ; 11(4)2024 Apr.
Article En | MEDLINE | ID: mdl-38627062

Proprioception, the sense of limb and body position, is required to produce accurate and precise movements. Proprioceptive sensory neurons transmit muscle length and tension information to the spinal cord. The function of excitatory neurons in the intermediate spinal cord, which receive this proprioceptive information, remains poorly understood. Using genetic labeling strategies and patch-clamp techniques in acute spinal cord preparations in mice, we set out to uncover how two sets of spinal neurons, Clarke's column (CC) and Atoh1-lineage neurons, respond to electrical activity and how their inputs are organized. Both sets of neurons are located in close proximity in laminae V-VII of the thoracolumbar spinal cord and have been described to receive proprioceptive signals. We find that a majority of CC neurons have a tonic-firing type and express a distinctive hyperpolarization-activated current (Ih). Atoh1-lineage neurons, which cluster into two spatially distinct populations, are mostly a fading-firing type and display similar electrophysiological properties to each other, possibly due to their common developmental lineage. Finally, we find that CC neurons respond to stimulation of lumbar dorsal roots, consistent with prior knowledge that CC neurons receive hindlimb proprioceptive information. In contrast, using a combination of electrical stimulation, optogenetic stimulation, and transsynaptic rabies virus tracing, we find that Atoh1-lineage neurons receive heterogeneous, predominantly local thoracic inputs that include parvalbumin-lineage sensory afferents and local interneuron presynaptic inputs. Altogether, we find that CC and Atoh1-lineage neurons have distinct membrane properties and sensory input organization, representing different subcircuit modes of proprioceptive information processing.


Proprioception , Spinal Cord , Animals , Proprioception/physiology , Spinal Cord/physiology , Spinal Cord/cytology , Basic Helix-Loop-Helix Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics , Mice, Transgenic , Mice , Male , Female , Action Potentials/physiology , Sensory Receptor Cells/physiology , Patch-Clamp Techniques , Mice, Inbred C57BL , Thoracic Vertebrae
20.
Biochem Biophys Res Commun ; 712-713: 149941, 2024 Jun 18.
Article En | MEDLINE | ID: mdl-38643718

While diosgenin has been demonstrated effective in various cardiovascular diseases, its specific impact on treating heart attacks remains unclear. Our research revealed that diosgenin significantly improved cardiac function in a myocardial infarction (MI) mouse model, reducing cardiac fibrosis and cell apoptosis while promoting angiogenesis. Mechanistically, diosgenin upregulated the Hand2 expression, promoting the proliferation and migration of endothelial cells under hypoxic conditions. Acting as a transcription factor, HAND2 activated the angiogenesis-related gene Aggf1. Conversely, silencing Hand2 inhibited the diosgenin-induced migration of hypoxic endothelial cells and angiogenesis. In summary, these findings provide new insights into the protective role of diosgenin in MI, validating its effect on angiogenic activity and providing a theoretical basis for clinical treatment strategies.


Basic Helix-Loop-Helix Transcription Factors , Diosgenin , Mice, Inbred C57BL , Myocardial Infarction , Neovascularization, Physiologic , Animals , Diosgenin/pharmacology , Diosgenin/therapeutic use , Myocardial Infarction/drug therapy , Myocardial Infarction/metabolism , Myocardial Infarction/pathology , Myocardial Infarction/physiopathology , Neovascularization, Physiologic/drug effects , Basic Helix-Loop-Helix Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics , Male , Mice , Cell Proliferation/drug effects , Cell Movement/drug effects , Apoptosis/drug effects , Endothelial Cells/drug effects , Endothelial Cells/metabolism , Endothelial Cells/pathology , Humans , Human Umbilical Vein Endothelial Cells/drug effects , Human Umbilical Vein Endothelial Cells/metabolism , Angiogenesis
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