Homeobox Research Articles

DLX4 promotes the expression of PD-L1 through GATA1 in Gestational Trophoblastic Neoplasia

Gestational Trophoblastic Neoplasia (GTN) is a highly malignant tumor that originates from trophoblastic cells during embryonic development. In this study, we observed that DLX4, a member of the Distal-Less Homeobox (Dlx) gene family, was upregulated in GTN tissues and cell lines. Bioinformatic analysis showed that DLX4 was highly expressed in most cancers and had a poor survival prognosis in certain tumors; further analysis showed that DLX4 was significantly associated with genes of immune pathways and immune infiltration. Functional analyses revealed that DLX4 overexpression or knockdown did not affect GTN cell proliferation; however, we observed that DLX4 could regulate PD-L1 expression via GATA1. The luciferase reporter activity of the wild-type construct increased after overexpression of GATA1, whereas the mutation of the binding sites abolished the transcriptional increase. In conclusion, our findings suggest that DLX4 regulates PD-L1 expression via GATA1 in GTN and may be a new target for antitumor therapy.

Evolutionary plasticity in nematode Hox gene complements and genomic loci arrangement

Hox genes are central to metazoan body plan formation, patterning and evolution, playing a critical role in cell fate decisions early in embryonic development in invertebrates and vertebrates. While the archetypical Hox gene cluster consists of members of nine ortholog groups (HOX1-HOX9), arrayed in close linkage in the order in which they have their anterior-posterior patterning effects, nematode Hox gene sets do not fit this model. The Caenorhabditis elegans Hox gene set is not clustered and contains only six Hox genes from four of the ancestral groups. The pattern observed in C. elegans is not typical of the phylum, and variation in orthologue set presence and absence and in genomic organisation has been reported. Recent advances in genome sequencing have resulted in the availability of many novel genome assemblies in Nematoda, especially from taxonomic groups that had not been analysed previously. Here, we explored Hox gene complements in high-quality genomes of 80 species from all major clades of Nematoda to understand the evolution of this key set of body pattern genes and especially to probe the origins of the “dispersed” cluster observed in C. elegans. We also included the recently available high-quality genomes of some Nematomorpha as an outgroup. We find that nematodes can have Hox genes from up to six orthology groups. While nematode Hox “clusters” are often interrupted by unrelated genes we identify species in which the cluster is intact and not dispersed.

Multiple Displacement Amplification Facilitates SMRT Sequencing of Microscopic Animals and the Genome of the Gastrotrich Lepidodermella squamata (Dujardin, 1841).

Obtaining adequate DNA for long-read genome sequencing remains a roadblock to producing contiguous genomes from small-bodied organisms, hindering understanding of phylogenetic relationships and genome evolution. Multiple displacement amplification (MDA) leverages Phi29 DNA polymerase to produce micrograms of DNA from picograms of input. MDA's inherent biases in amplification related to GC and repeat content and chimera production are a problem for long-read genome assembly, which has been little investigated. We explored the utility of MDA for generating template DNA for HiFi sequencing directly from living cells of Caenorhabditis elegans (Nematoda) and Lepidodermella squamata (Gastrotricha) containing one order of magnitude less DNA than required for the PacBio Ultra-Low DNA Input Workflow. HiFi sequencing of libraries prepared from MDA DNA resulted in highly contiguous and complete genomes for both C. elegans (102 Mbp assembly; 336 contigs; N50=868 Kbp; L50=39; BUSCO_nematoda_nucleotide: S:96.1%, D:2.8%) and L. squamata (122 Mbp assembly; 157 contigs; N50=3.9 Mbp; L50=13; BUSCO_metazoa_nucleotide: S:80.8%, D:2.8%). Coverage uniformity for reads from MDA DNA (Gini Index: 0.14, normalized mean across all 100 Kbp blocks: 0.49) and reads from pooled nematode DNA (Gini Index: 0.16, normalized mean across all 100 Kbp blocks: 0.49) proved similar. Using this approach, we sequenced the genome of the microscopic invertebrate Lepidodermella squamata (Gastrotricha), the first of its phylum. Using the newly sequenced genome, we infer Gastrotricha's long-debated phylogenetic position as the sister taxon of Platyhelminthes and conduct a comparative analysis of the Hox cluster.

Epigenetic regulation of HOXA3 and its impact on oral squamous cell carcinoma progression

ObjectiveThe role of homeobox A3 (HOXA3) in cancer progression is gaining prominence, however, to date, no studies have investigated its regulatory function in oral cancer. In this study, we explored the role of HOXA3 through epigenetic mechanisms. MethodsClinical samples were collected from 25 potentially malignant oral lesions and 50 oral squamous cell carcinoma (OSCC) patients, categorized into low-stage and high-stage tumors. The promoter activity of HOXA3 was determined through cloning and luciferase assays. CpG methylation patterns across the gene were identified using methyl-capture sequencing. Gene expression was analysed using RT‒qPCR. The Survminer R package was used to assess the clinical significance of 3′ UTR methylation associated with overall survival. RNA‒RNA interactions were analysed using RNAInter and TargetScan v8.0. ResultsHOXA3 expression was upregulated in dysplasia and downregulated in advanced cancer stages, showing an inverse correlation with promoter methylation, suggesting epigenetic regulation by DNA methylation. Hypermethylation of the 3′ UTR was associated with poor overall survival in advanced stages. Long non-coding RNAs and microRNAs may post-transcriptionally modulate HOXA3 in oral carcinogenesis. ConclusionCpG-specific hypermethylation in the 3′ UTR may serve as a potential biomarker in OSCC. Statement of Clinical RelevanceLocus-specific CpG hypermethylation in the 3′ UTR was significantly associated with poor overall survival and patient stratification based on OSCC progression.

Annotation of transcription factors, chromatin-associated factors, and basal transcription machinery in the pea aphid, Acyrthosiphon pisum, and development of the ATFdb database, a resource for studies of transcriptional regulation

The pea aphid, Acyrthosiphon pisum, is an emerging model system in functional and comparative genomics, in part due to the availability of new genomic approaches and the different sequencing and annotation efforts that the community has dedicated to this important crop pest insect. The pea aphid is also used as a model to study fascinating biological traits of aphids, such as their extensive polyphenisms, their bacteriocyte-confined nutritional symbiosis, or their adaptation to the highly unbalanced diet represented by phloem sap. To get insights into the molecular basis of all these processes, it is important to have an appropriate annotation of transcription factors (TFs), which would enable the reconstruction/inference of gene regulatory networks in aphids. Using the latest version of the A. pisum genome assembly and annotation, which represents the first chromosome-level pea aphid genome, we annotated the complete repertoire of A. pisum TFs and complemented this information by annotating genes encoding chromatin-associated and basal transcription machinery proteins. These annotations were done combining information from the model Drosophila melanogaster, for which we also provide a revisited list of these proteins, and de novo prediction. The comparison between the two model systems allowed the identification of major losses or expansions in each genome, while a deeper analysis was made of ZNF TFs (with certain families expanded in the pea aphid), and the Hox gene cluster (showing reorganization in gene position in the pea aphid compared to D. melanogaster). All annotations are available to the community through the Aphid Transcription Factors database (ATFdb), consolidating the various annotations we generated. ATFdb serves as a valuable resource for gene regulation studies in aphids.

A new cancer/testis long noncoding RNA, the OTP-AS1 RNA

The orthopedia homeobox (OTP) gene encodes a homeodomain-containing transcription factor involved in brain development. OTP is mapped to human chromosome 5q14.1. Earlier we described transcription in the second intron of this gene in wide variety of tumors, but among normal tissues only in testis. In GeneBank these transcripts are represented by several 300–400 nucleotide long AI267901-like ESTs. We assumed that the AI267901-like ESTs belonged to the longer transcript(s). We used the Rapid Amplification of cDNA Ends (RACE) approach and other methods to find the full-length transcript. The transcript we found was a 2436 nucleotide polyadenylated sequence in antisense to OTP gene. The corresponding gene consisted of two exons separated by an intron of 2961 bp. The first exon was found to be 91 bp long and located in the third exon of OTP. The second exon was 2345 bp long and located in the second intron of OTP. We have shown the expression of this gene in many human tumors but as few as a single sample of normal testis. The transcript lacked significant ORFs suggesting that we discovered a new antisense cancer/testis (CT) sequence OTP-AS1 (OTP—antisense RNA 1), which belongs to the class of long noncoding RNAs (lncRNAs). According to our findings we assume that OTP-AS1 and OTP genes may be a CT-coding gene/CT-ncRNA pair, or sense-antisense gene pair involved in regulatory interactions.

Gender‐specific genetic influence of rs1111875 on diabetes risk: Insights from the Taiwan biobank study

ABSTRACTBackgroundThis study investigates the gender‐specific genetic influence of the single nucleotide polymorphism (SNP) rs1111875 on diabetes risk within the Taiwanese population using data from the Taiwan Biobank. Diabetes mellitus, particularly type 2 diabetes (T2D), is influenced by genetic factors, and the rs1111875 SNP near the hematopoietically expressed homeobox (HHEX) gene has been linked to T2D susceptibility.MethodsThe study included 69,272 participants after excluding those from arsenic‐polluted areas and those with incomplete data. Logistic regression models were used for analyses.ResultsThe analyses revealed that the CT genotype of rs1111875 was associated with an increased risk of diabetes (OR = 1.092, 95% CI = 1.030–1.157, P = 0.003), as was the TT genotype (OR = 1.280, 95% CI = 1.165–1.407, P < 0.001). The effect was more pronounced in women (CT: OR = 1.118, 95% CI = 1.036–1.207, P = 0.004; TT: OR = 1.404, 95% CI = 1.243–1.585, P < 0.001). Men exhibited a higher overall risk of diabetes (OR = 1.565, 95% CI = 1.445–1.694, P < 0.001) and had a higher prevalence (12.71% vs 7.80%, P < 0.001) compared to women.ConclusionsThe findings underscore the importance of considering gender differences in genetic studies of diabetes and suggest that personalized diabetes management strategies should account for both genetic and gender‐specific risk factors. This research contributes to the broader understanding of genetic determinants of diabetes and their interaction with gender, aiming to enhance personalized healthcare strategies for diabetes prevention and treatment.

Abstract 4119262: Anti-atherosclerotic Potential of M2 Macrophage-Derived Exosomes by Promoting Cholesterol Efflux of Foam Cell-Like Vascular Smooth Muscle Cells via the PPARγ-LXRα-ABCA1/ ABCG1 Pathway

Background: Impediment in the excretion of lipid deposits within SMC-derived foam cells (SMC-FCs) is one of the reasons for the continuous expansion of the plaque necrotic core. This study aims to explore the effect and underlying mechanimsm of exosomes secreted by M2 macrophage (M2-exos) on SMC-FCs lipid metabolism and plaque stability. Methods: First, immunofluorescence was used to detect the expression levels of CD45 (a recognized differentially expressed molecule of myeloid and SMC-FCs) and the key proteins of cholesterol efflux pathway, ABCA1 and ABCG1, in human early and late plaques. Exosomes derived from M0 and M2 macrophages were purified by sucrose density gradient centrifugation, and characterized based on specific morphology and surface markers. Western blot, Oil red O staining and cell total cholesterol assay were used to assess the effects of M2-exos on the lipid mechanism of SMC-FCs. RNA-seq was used to detect the miRNA profiles of M2-exos. Quantitative real-time PCR was used to identify candidate miRNAs. The dual-luciferase reporting system was utilized to assess the regulatory effect of candidate miRNA on target gene. Then, the effect of M2-exos on the progression and stability of plaques in ApoE -/- mice was evaluated using Oil red O, H&E, Masson, Movat and immunohistochemistry. Results: Immunofluorescence revealed that compared with early plaques, VSMC-FCs (CD45 - ) were significantly increased in late plaques, and the expression levels of ABCG1 and ABCA1 were marked lower than those in macrophage-derived foam cells (CD45 + ). Purified M2-exos treatment significantly promoted the cholesterol efflux of SMC-FCs in vitro. In high-fat-fed ApoE -/- mice, M2-exos significantly reduced the VSMC-FCs, delayed the progression of plaques, decreased necrotic core area and enhanced plaque stability. MiRNA profiling and comprehensive analysis of signaling pathways showed that M2-exos were rich in miR-7683-3p, which played a key role in regulating SMC-FCs lipid metabolism through PPARγ-LXRα-ABCA1/ABCG1 pathway. Dual-luciferase reporting assay showed that miR-7683-3p can specifically bind to the promoter region of homeobox genes A1(HoxA1), an inhibitor of PPARγ-LXRα-ABCA1/ABCG1 pathway. Conclusion: M2-exos exerted an obvious atherosclerotic protective effect, and the underlying mechanism was closely related to MiR-7683-3p, which targeted the 3’UTR of HoxA1 mRNA and activated the PPARγ-LXRα-ABCA1/ABCG1 mediated cholesterol efflux in SMC-FCs.

TMET-32. THE ROLE OF HOXC10 IN DRIVING GLIOBLASTOMA AGGRESSIVENESS

Abstract BACKGROUND Glioblastoma (GBM) is an aggressive malignancy, with a tumor doubling time of just 49.6 days. Despite maximal safe surgical resection, radiation, and temozolomide, median survival is only 14.6 months. Homeobox gene, homeobox C10 (HOXC10), a transcription factor of the HOX10 family, is pivotal in neuronal development, upregulated in several cancers, including glioma, and correlates with poor survival. METHODS RNA sequencing analysis was done on our mouse glioma syngeneic cell lines. HOXC10 expression analysis was done on human and mouse GBM cell lines and tissues by immunoblotting and immunohistochemistry, respectively. HOXC10 and p16-/-silencing were done using 4 unique 29mer shRNA constructs in the GFP vector, respectively. Gene Ontology predicted HOXC10 functions. HOXC10 and pyrroline-5-carboxylic acid reductase 1 (PYCR 1), a proline biosynthetic enzyme co-expression was studied using immunofluorescence analysis. RESULTS HOXC10 is highly expressed in human and mouse GBM tissues. HOXC10 was upregulated only in the high-grade/aggressive cell line [EGFRvIII; p16-/- & GFAP Cre] and demonstrated increased expression with p16 deletion in the mouse glioma cell line. Compellingly, TCGA analysis of GBM correlated the negatively prognostic p16 homozygous deletion (HD) with HOXC10 upregulation. Gene Ontology supports the role of HOXC10 for proline biosynthesis and metabolism. Immunofluorescence on mouse GBM sections revealed co-expression of HOXC10 and PYCR1. HOXC10 silencing significantly decreased GBM cell line proliferation, induced apoptosis, and decreased PYCR1 expression in vitro. CONCLUSIONS HOXC10 expression is increased in GBM and with p16 HD. HOXC10 silencing significantly decreased GBM cell line proliferation and decreased PYCR1 expression. HOXC10-mediated proline biosynthesis may present a novel target to improve GBM survival.

Homeotic and nonhomeotic patterns in the tetrapod vertebral formula

Vertebrate development and phylogeny are intimately connected through the vertebral formula, the numerical distribution of vertebrae along the body axis into different categories such as neck and chest. A key window into this relationship is through the conserved Hox gene clusters. Hox gene expression boundaries align with vertebral boundaries, and their manipulation in model organisms often results in the transformation of one vertebral type into its neighbor, a homeotic transformation. If the variety in the vertebrate body plan is produced by homeotic shifts, then the number of adjacent vertebrae will be inversely related when making interspecies comparisons since the gain in one vertebra is due to the loss in its neighbor. To date, such a pattern across species consistent with homeotic transitions has only been found in the thoracolumbar vertebral count of mammals. To further investigate potential homeotic relationships in other vertebrate classes and along the entire body axis, we compiled a comprehensive dataset of complete tetrapod vertebral formulas and systematically searched for patterns by analyzing combinations of vertebrae. We uncovered mammalian homeotic patterns and found balances between distal vertebrae not anticipated by a Hox-vertebral homeotic relationship, including one that emerged during the progression from theropods to birds. We also identified correlations between vertebral counts and intergenic distances in the HoxB gene cluster which do not align with the common picture of a colinear relationship between Hox expression and vertebral categories. This quantitative approach revises our expectations for the diversity of a Hox-mediated vertebrate body plan.

Unveiling the depths of pelvic organ prolapse: From risk factors to therapeutic methods (Review).

Pelvic organ prolapse (POP) is a condition where one or more pelvic organs (such as the uterus, bladder and rectum) descend from their normal anatomical positions into the vagina, primarily due to the weakening of the pelvic floor support structures. While not life-threatening, POP can substantially diminish the patient's quality of life and lead to serious social and psychological complications. Researchers have explored novel directions regarding the etiology, mechanism and treatment of POP. However, existing literature on the subject often lacks comprehensive and systematic overviews. To address this gap and enhance researchers' understanding of POP, the present study reviewed the risk factors and molecular mechanisms of POP [including matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs, transforming growth factor β, advanced glycation end products (AGEs)/receptor for AGE, phosphoinositide 3-kinase/protein kinase B, fibulin, lysyl oxidase-like 1, homeobox A11, collagen α-1 (XVIII) chain, Wnt signaling pathways and estrogen receptor α], as well as therapeutic approaches, such as lifestyle interventions, physical methods, pharmacotherapy, stem cell transplantation and surgical techniques. The present review aims to provide new insights for future research and contribute to the advancement of diagnosis and treatment strategies for POP.

MobiChIP: a compatible library construction method of single-cell ChIP-seq based droplets.

To illustrate epigenetic heterogeneity, versatile tools of single-cell ChIP-seq (scChIP-seq) are essential for both convenience and accuracy. We developed MobiChIP, a compatible ChIP-seq library construction method based on current sequencing platforms for single-cell applications. MobiChIP efficiently captures fragments from tagmented nuclei across various species and allows sample mixing from different tissues or species. This strategy offers robust nucleosome amplification and flexible sequencing without customized primers. MobiChIP reveals regulatory landscapes of chromatin with active (H3K27ac) and repressive (H3K27me3) histone modification in peripheral blood mononuclear cells (PBMCs) and accurately identifies epigenetic repression of the Hox gene cluster, outperforming ATAC-seq. Meanwhile, we also integrated scChIP-seq with scRNA-seq to further illustrate cellular genetic and epigenetic heterogeneity.

PRDM16 suppresses ferroptosis to protect against sepsis-associated acute kidney injury by targeting the NRF2/GPX4 axis

Acute kidney injury (AKI) constitutes a significant public health issue. Sepsis accounts for over 50 % of AKI cases in the ICU. Recent findings from our research indicated that the PRD1-BF1-RIZ1 homeodomain protein 16 (PRDM16) inhibited the progression of diabetic kidney disease (DKD). However, its precise role and regulatory mechanism in sepsis-induced AKI remain obscure. This study reveals that lipopolysaccharide (LPS) and cecum ligation and puncture (CLP) instigated PRDM16 expression in Boston University mouse proximal tubule (BUMPT) cells and mouse kidneys, respectively. Functionally, PRDM16 curtailed LPS-induced ferroptosis. Mechanistically, PRDM16 associates with the promoter regions of nuclear factor-erythroid 2-related factor-2 (NRF2) and augments its expression, subsequently enhancing glutathione peroxidase 4 (GPX4) expression. Additionally, PRDM16 directly engages with the promoter regions of GPX4, stimulating its expression. Notably, these observations were corroborated in human renal tubular epithelial (HK-2) cells. Furthermore, the ablation of PRDM16 from kidney proximal tubules in mice inhibited NRF2 and GPX4 expression, leading to decreased glutathione (GSH)/oxidized glutathione (GSSG) ratio, increased Fe2+ and reactive oxygen species (ROS) production, exacerbated ferroptosis, and AKI progression. Conversely, PRDM16 knock-in exhibited the opposite effects. Ultimately, adenovirus (ADV)-PRDM16 plasmid or poly (lactide-glycolide acid) (PLGA)-encapsulated formononetin not only mitigated sepsis-induced AKI but also alleviated liver, cardiac, and lung injury. In summary, PRDM16 inhibits ferroptosis via the NRF2/GPX4 axis or GPX4 to prevent sepsis-induced multi-organ injury, including AKI. PLGA-encapsulated formononetin presents a promising therapeutic approach.

Molecular cloning of PRD-like homeobox genes expressed in bovine oocytes and early IVF embryos.

Embryonic genome activation (EGA) is a critical step in early embryonic development, as it marks the transition from relying on maternal factors to the initiation of transcription from embryo's own genome. The factors associated with EGA are not well understood and need further investigation. PRD-like (PRDL) homeodomain transcription factors (TFs) are considered to play crucial roles in this early event during development but these TFs have evolved differently, even within mammalian lineages. Different numbers of PRDL TFs have been predicted in bovine (Bos taurus); however, their divergent evolution requires species-specific confirmation and functional investigations. In this study, we conducted molecular cloning of mRNAs for the PRDL TFs ARGFX, DUXA, LEUTX, NOBOX, TPRX1, TPRX2, and TPRX3 in bovine oocytes or in vitro fertilized (IVF) preimplantation embryos. Our results confirmed the expression of PRDL TF genes in early bovine development at the cDNA level and uncovered their structures. For each investigated PRDL TF gene, we isolated at least one homeodomain-encoding cDNA fragment, indicative of DNA binding and thus potential role in transcriptional regulation in developing bovine embryos. Additionally, our cDNA cloning approach allowed us to reveal breed-related differences in bovine, as evidenced by the identification of a high number of single nucleotide variants (SNVs) across the PRDL class homeobox genes. Subsequently, we observed the prediction of the 9aa transactivation domain (9aaTAD) motif in the putative protein sequence of TPRX3 leading us to conduct functional analysis of this gene. We demonstrated that the TPRX3 overexpression in bovine fibroblast induces not only protein-coding genes but also short noncoding RNAs involved in splicing and RNA editing. We supported this finding by identifying a shared set of genes between our and published bovine early embryo development datasets. Providing full-length cDNA evidence for previously predicted homeobox genes that belong to PRDL class improves the annotation of the bovine genome. Updating the annotation with seven developmentally-important genes will enhance the accuracy of RNAseq analysis with datasets derived from bovine preimplantation embryos. In addition, the absence of TPRX3 in humans highlights the species-specific and TF-specific regulation of biological processes during early embryo development.

CTCF-dependent insulation of Hoxb13 and the heterochronic control of tail length

Mammalian tail length is controlled by several genetic determinants, among which are Hox13 genes, whose function is to terminate the body axis. Accordingly, the precise timing in the transcriptional activation of these genes may impact upon body length. Unlike other Hox clusters, HoxB lacks posterior genes between Hoxb9 and Hoxb13, two genes separated by a ca. 70 kb large DNA segment containing a high number of CTCF sites, potentially isolating Hoxb13 from the rest of the cluster and thereby delaying its negative impact on trunk extension. We deleted the spacer DNA to induce a potential heterochronic gain of function of Hoxb13 at physiological concentration and observed a shortening of the tail as well as other abnormal phenotypes. These defects were all rescued by inactivating Hoxb13 in-cis with the deletion. A comparable gain of function was observed in mutant Embryonic Stem (ES) cells grown as pseudoembryos in vitro, which allowed us to examine in detail the importance of both the number and the orientation of CTCF sites in the insulating activity of the DNA spacer. A short cassette containing all the CTCF sites was sufficient to insulate Hoxb13 from the rest of HoxB, and additional modifications of this CTCF cassette showed that two CTCF sites in convergent orientations were already capable of importantly delaying Hoxb13 activation in these conditions. We discuss the relative importance of genomic distance versus number and orientation of CTCF sites in preventing Hoxb13 to be activated too early during trunk extension and hence to modulate tail length.

Role of HOXA10 in pathologies of the endometrium.

HOXA10 belongs to the homeobox gene family and is essential for uterine biogenesis, endometrial receptivity, embryo implantation, and stromal cell decidualization. Available evidence suggests that the expression of HOXA10 is dysregulated in different endometrial disorders like endometrial hyperplasia, endometrial cancer, adenomyosis, endometriosis, recurrent implantation failure, and unexplained infertility. The downregulation of HOXA10 occurs by genetic changes in the HOXA10 gene, methylation of the HOXA10 locus, or selected miRNAs. Endocrine disruptors and organic pollutants also cause the reduced expression of HOXA10 in these conditions. In vivo experiments in mouse models and in vitro studies in human cell lines demonstrate that downregulation of HOXA10 leads to endometrial epithelial cell proliferation, failure of stromal cell decidualization, altered expression of genes involved in cell cycle regulation, immunomodulation, and various signaling pathways. These disruptions are speculated to cause infertility associated with the disorders of the endometrium.

Plant Growth Regulators: An Overview of WOX Gene Family.

The adaptation of plants to land requires sophisticated biological processes and signaling. Transcription factors (TFs) regulate several cellular and metabolic activities, as well as signaling pathways in plants during stress and growth and development. The WUSCHEL-RELATED HOMEOBOX (WOX) genes are TFs that are part of the homeodomain (HD) family, which is important for the maintenance of apical meristem, stem cell niche, and other cellular processes. The WOX gene family is divided into three clades: ancient, intermediate, and modern (WUS) based on historical evolution linkage. The number of WOX genes in the plant body increases as plants grow more complex and varies in different species. Numerous research studies have discovered that the WOX gene family play a role in the whole plant's growth and development, such as in the stem, embryo, root, flower, and leaf. This review comprehensively analyzes roles of the WOX gene family across various plant species, highlighting the evolutionary significance and potential biotechnological applications in stress resistance and crop improvement.

HOXA7 Expression Is an Independent Prognostic Biomarker in Esophageal Squamous Cell Carcinoma.

Background/Objectives: Homeobox (HOX) genes encode conserved transcription factors essential for tissue and organ development and cellular differentiation. In humans, these genes are organized into four clusters: HOXA, HOXB, HOXC, and HOXD. While HOX genes have been extensively studied in cancer biology, their roles in esophageal squamous cell carcinoma (ESCC) remain poorly understood. Given the increasing incidence and high mortality rate of ESCC, exploring the molecular drivers of this tumor is urgent. Methods: Therefore, this study investigated the mutational landscape and expression profiles of HOX genes in ESCC and their differentially expressed targets using ESCC data from The Cancer Genome Atlas (TCGA) and two independent transcriptome datasets. Results: We found that copy number alterations and single nucleotide variations were rare, while seven HOX genes (HOXA2, HOXA7, HOXB13, HOXC9, HOXC10, HOXC13, and HOXD10) were significantly differentially expressed in ESCC compared to paired non-malignant mucosa. Further analysis identified 776 potential HOX target genes differentially expressed in ESCC, many of which are involved in critical cancer pathways such as PI3K-AKT, cell cycle regulation, and epithelial-mesenchymal transition (EMT). The HOXA7 overexpression was associated with poor overall survival rates in ESCC. This finding opens new possibilities for targeted therapies, offering hope for improved patient outcomes. Conclusions: Thus, this study underscored the pivotal role of HOX gene dysregulation in ESCC and classified HOXA7 as a potential prognostic biomarker in this tumor.

Gene expression profile analysis of subregions of the adult female reproductive tract in the brown anole, Anolis sagrei.

The morphological diversity and functional role of the organs of the female reproductive system across tetrapods (limbed vertebrates) are relatively poorly understood. Though some features are morphologically similar, species-specific modification makes comparisons between species and inference about evolutionary origins challenging. In combination with the study of morphological changes, studying differences in gene expression in the adult reproductive system in diverse species can clarify the function of each organ. Here, we use the brown anole, Anolis sagrei, to study gene expression differences within the reproductive tract of the adult female. We generated gene expression profiles of four biological replicates of the three regions of the female reproductive tract, the infundibulum, glandular uterus, and nonglandular uterus by RNA-sequencing. We aligned read to the recently published Anolis sagrei genome and identified significantly differentially expressed genes between the regions using DEseq2. Each organ expressed approximately 14600 genes and comparison of gene expression profiles between organs revealed between 367-883 differentially expressed genes. We identify shared and region-specific transcriptional signatures for the three regions and compare gene expression in the brown anole reproductive tract to known gene expression patterns in other tetrapods. We find that genes in the Hox cluster have an anterior-posterior, colinear expression pattern as has been described in mammals. We also define a secretome for the glandular uterus. These data provide fundamental information for functional studies of the reproductive tract organs in the brown anole as well as an important phylogenetic anchor for comparative study of the evolution of the female reproductive tract.

Genome-wide screening reveals essential roles for HOX genes and imprinted genes during caudal neurogenesis of human embryonic stem cells

Mapping the essential pathways for neuronal differentiation can uncover new therapeutics and models for neurodevelopmental disorders. We thus utilized a genome-wide loss-of-function library in haploid human embryonic stem cells, differentiated into caudal neuronal cells. We show that essential genes for caudal neurogenesis are enriched for secreted and membrane proteins and that a large group of neurological conditions, including neurodegenerative disorders, manifest early neuronal phenotypes. Furthermore, essential transcription factors are enriched with homeobox (HOX) genes demonstrating synergistic regulation and surprising non-redundant functions between HOXA6 and HOXB6 paralogs. Moreover, we establish the essentialome of imprinted genes during neurogenesis, demonstrating that maternally expressed genes are non-essential in pluripotent cells and their differentiated germ layers, yet several are essential for neuronal development. These include Beckwith-Wiedemann syndrome- and Angelman syndrome-related genes, for which we suggest a novel regulatory pathway. Overall, our work identifies essential pathways for caudal neuronal differentiation and stage-specific phenotypes of neurological disorders.