Pitx genes in development and disease

PITX2 functions as a transcription factor for GPX4 and protects pancreatic cancer cells from ferroptosis

Ferroptosis inhibits tumor progression in pancreatic cancer cells, while PITX2 is known to function as a pro-oncogenic factor in various tumor types, protecting them from ferroptosis and thereby promoting tumor progression. In this study, we sought to investigate the regulatory role of PITX2 in tumor cell ferroptosis within the context of pancreatic cancer. We conducted PITX2 knockdown experiments using lentiviral infection in two pancreatic cancer cell lines, namely PANC-1 and BxPC-3. We assessed protein expression through immunoblotting and mRNA expression through RT-PCR. To confirm PITX2 as a transcription factor for GPX4, we employed Chromatin Immunoprecipitation (ChIP) and Dual-luciferase assays. Furthermore, we used flow cytometry to measure reactive oxygen species (ROS), lipid peroxidation, and apoptosis and employed confocal microscopy to assess mitochondrial membrane potential. Additionally, electron microscopy was used to observe mitochondrial structural changes and evaluate PITX2's regulation of ferroptosis in pancreatic cancer cells. Our findings demonstrated that PITX2, functioning as a transcription factor for GPX4, promoted GPX4 expression, thereby exerting an inhibitory effect on ferroptosis in pancreatic cancer cells and consequently promoting tumor progression. Moreover, PITX2 enhanced the invasive and migratory capabilities of pancreatic cancer cells by activating the WNT signaling pathway. Knockdown of PITX2 increased ferroptosis and inhibited the proliferation of PANC-1 and BxPC-3 cells. Notably, the inhibitory effect on ferroptosis resulting from PITX2 overexpression in these cells could be countered using RSL3, an inhibitor of GPX4. Overall, our study established PITX2 as a transcriptional regulator of GPX4 that could promote tumor progression in pancreatic cancer by reducing ferroptosis. These findings suggest that PITX2 may serve as a potential therapeutic target for combating ferroptosis in pancreatic cancer.

Genetic network analysis indicate that individuals affected by neurodevelopmental conditions have genetic variations associated with ophthalmologic alterations: A critical review of literature

Changes in the nervous system are related to a wide range of mental disorders, which include neurodevelopmental disorders (NDD) that are characterized by early onset mental conditions, such as schizophrenia and autism spectrum disorders and correlated conditions (ASD). Previous studies have shown distinct genetic components associated with diverse schizophrenia and ASD phenotypes, with mostly focused on rescuing neural phenotypes and brain activity, but alterations related to vision are overlooked. Thus, as the vision is composed by the eyes that itself represents a part of the brain, with the retina being formed by neurons and cells originating from the glia, genetic variations affecting the brain can also affect the vision. Here, we performed a critical systematic literature review to screen for all genetic variations in individuals presenting NDD with reported alterations in vision. Using these restricting criteria, we found 20 genes with distinct types of genetic variations, inherited or de novo, that includes SNP, SNV, deletion, insertion, duplication or indel. The variations occurring within protein coding regions have different impact on protein formation, such as missense, nonsense or frameshift. Moreover, a molecular analysis of the 20 genes found revealed that 17 shared a common protein-protein or genetic interaction network. Moreover, gene expression analysis in samples from the brain and other tissues indicates that 18 of the genes found are highly expressed in the brain and retina, indicating their potential role in adult vision phenotype. Finally, we only found 3 genes from our study described in standard public databanks of ophthalmogenetics, suggesting that the other 17 genes could be novel target for vision diseases.

The Critical Role of the Shroom Family Proteins in Morphogenesis, Organogenesis and Disease

The Shroom (Shrm) family of actin-binding proteins has a unique and highly conserved Apx/Shrm Domain 2 (ASD2) motif. Shroom protein directs the subcellular localization of Rho-associated kinase (ROCK), which remodels the actomyosin cytoskeleton and changes cellular morphology via its ability to phosphorylate and activate non-muscle myosin II. Therefore, the Shrm-ROCK complex is critical for the cellular shape and the development of many tissues, including the neural tube, eye, intestines, heart, and vasculature system. Importantly, the structure and expression of Shrm proteins are also associated with neural tube defects, chronic kidney disease, metastasis of carcinoma, and X-link mental retardation. Therefore, a better understanding of Shrm-mediated signaling transduction pathways is essential for the development of new therapeutic strategies to minimize damage resulting in abnormal Shrm proteins. This paper provides a comprehensive overview of the various Shrm proteins and their roles in morphogenesis and disease.

UNC-30/PITX coordinates neurotransmitter identity with postsynaptic GABA receptor clustering

Terminal selectors are transcription factors that control neuronal identity by regulating the expression of key effector molecules, such as neurotransmitter (NT) biosynthesis proteins, ion channels and neuropeptides. Whether and how terminal selectors control neuronal connectivity is poorly understood. Here, we report that UNC-30 (PITX2/3), the terminal selector of GABA motor neuron identity in C. elegans , is required for NT receptor clustering, a hallmark of postsynaptic differentiation. Animals lacking unc-30 or madd-4B, the short isoform of the MN-secreted synapse organizer madd-4 ( Punctin/ADAMTSL ), display severe GABA receptor type A (GABA A R) clustering defects in postsynaptic muscle cells. Mechanistically, UNC-30 acts directly to induce and maintain transcription of madd-4B and GABA biosynthesis genes (e.g., unc-25/GAD , unc-47/VGAT ). Hence, UNC-30 controls GABA A R clustering on postsynaptic muscle cells and GABA biosynthesis in presynaptic cells, transcriptionally coordinating two critical processes for GABA neurotransmission. Further, we uncover multiple target genes and a dual role for UNC-30 both as an activator and repressor of gene transcription. Our findings on UNC-30 function may contribute to our molecular understanding of human conditions, such as Axenfeld-Rieger syndrome, caused by PITX2 and PITX3 gene mutations.

Exome sequencing in 16 patients with pituitary stalk interruption syndrome: A monocentric study

Pituitary stalk interruption syndrome (PSIS) is a rare disorder characterized by an absent or ectopic posterior pituitary, absent or interrupted pituitary stalk and anterior pituitary hypoplasia on magnetic resonance imaging (MRI), as well in some cases a range of heterogeneous somatic anomalies. The triad can be incomplete. Here, we performed exome sequencing on 16 sporadic patients, aged 0.4 to 13.7 years diagnosed with isolated or complex PSIS. Growth hormone deficiency was isolated in 10 cases, or associated with thyrotropin deficiency in 6 others (isolated (2 cases), associated with adrenocorticotropin deficiency (1 case), gonadotropins deficiency (1 case), or multiple deficiencies (2 cases)). Additional phenotypic anomalies were present in six cases (37.5%) including four with ophthalmic disorders. In 13 patients variants were identified that may contribute to the phenotype. However, only a single individual carried a variant classified as pathogenic. This child presented with the typical clinical presentation of Okur-Chung neurodevelopmental syndrome due to a CSNK2A1 missense variant. We also identified variants in the holoprosencephaly associated genes GLI2 and PTCH1. A likely pathogenic novel splice site variant in the GLI2 gene was observed in a child with PSIS and megacisterna magna. In the remaining 11 cases 26 variants in genes associated with pituitary development or function were identified and were classified of unknown significance. Compared with syndromic forms the diagnostic yield in the isolated forms of PSIS is low. Although we identified rare or novel missense variants in several hypogonadotropic hypogonadism genes (e.g. FGF17, HS6ST1, KISS1R, CHD7, IL17RD) definitively linking them to the PSIS phenotype is premature. A major challenge remains to identify pathogenic variants in cases with isolated PSIS.

CellNeighborEX: deciphering neighbor-dependent gene expression from spatial transcriptomics data

Cells have evolved their communication methods to sense their microenvironments and send biological signals. In addition to communication using ligands and receptors, cells use diverse channels including gap junctions to communicate with their immediate neighbors. Current approaches, however, cannot effectively capture the influence of various microenvironments. Here, we propose a novel approach to investigate cell neighbor-dependent gene expression (CellNeighborEX) in spatial transcriptomics (ST) data. To categorize cells based on their microenvironment, CellNeighborEX uses direct cell location or the mixture of transcriptome from multiple cells depending on ST technologies. For each cell type, CellNeighborEX identifies diverse gene sets associated with partnering cell types, providing further insight. We found that cells express different genes depending on their neighboring cell types in various tissues including mouse embryos, brain, and liver cancer. Those genes are associated with critical biological processes such as development or metastases. We further validated that gene expression is induced by neighboring partners via spatial visualization. The neighbor-dependent gene expression suggests new potential genes involved in cell-cell interactions beyond what ligand-receptor co-expression can discover.

PITX1 plays essential functions in cancer

PITX1, also known as the pituitary homeobox 1 gene, has emerged as a key regulator in animal growth and development, attracting significant research attention. Recent investigations have revealed the implication of dysregulated PITX1 expression in tumorigenesis, highlighting its involvement in cancer development. Notably, PITX1 interacts with p53 and exerts control over crucial cellular processes including cell cycle progression, apoptosis, and chemotherapy resistance. Its influence extends to various tumors, such as esophageal, colorectal, gastric, and liver cancer, contributing to tumor progression and metastasis. Despite its significance, a comprehensive review examining PITX1's role in oncology remains lacking. This review aims to address this gap by providing a comprehensive overview of PITX1 in different cancer types, with a particular focus on its clinicopathological significance.

PITX2 in pancreatic stellate cells promotes EMT in pancreatic cancer cells via the Wnt/β-catenin pathway

Since the prognosis of patients with pancreatic cancer is very poor and there is a lack of treatment methods, this study is performed to investigate the function of PITX2 in pancreatic stellate cells (PSCs) in the progression of pancreatic cancer. Scientific hypotheses are proposed according to bioinformatics analysis and tissue microarray analysis. Stable knockdown of PITX2 in PSCs is achieved through lentiviral infection. The relative expressions of PITX2, α-SMA, vimentin, CTNNB1, AXIN1 and LEF1 are measured in wild-type PSCs and PITX2-knockdown PSCs. Proliferative capacity is measured by EdU assay. After coculture with PSCs, the proliferation, invasion and migration capacity of pancreatic cancer cells are tested. EMT and Wnt/β-catenin downstream genes of pancreatic cancer cells are investigated to reveal the potential mechanism. Bioinformatics analysis reveals that the PITX2 gene is highly expressed in stromal cells in pancreatic cancer and is correlated with squamous-type PDAC. Analysis of PDAC tissue microarray further demonstrates that high PITX2 level in stromal cells is correlated with poor prognosis in PDAC. After stable knockdown of PITX2 in PSCs, the relative protein levels of α-SMA, vimentin, CTNNB1, AXIN1 and LEF1 are decreased, and the proliferative capacity of PSCs is also decreased. After coculture with PSCs, in which PITX2 expression is downregulated, the proliferation, invasion and migration capacities of pancreatic cancer cells are inhibited. Thus, our results show that PITX2-silenced PSCs inhibit the growth, migration and invasion of pancreatic cancer cells via reduced EMT and Wnt/β-catenin signaling.

The Crucial Roles of Pitx3 in Midbrain Dopaminergic Neuron Development and Parkinson's Disease-Associated Neurodegeneration

The degeneration of midbrain dopaminergic (mDA) neurons, particularly in the substantia nigra pars compacta (SNc), is one of the most prominent pathological hallmarks of Parkinson's disease (PD). To uncover the pathogenic mechanisms of mDA neuronal death during PD may provide therapeutic targets to prevent mDA neuronal loss and slow down the disease's progression. Paired-like homeodomain transcription factor 3 (Pitx3) is selectively expressed in the mDA neurons as early as embryonic day 11.5 and plays a critical role in mDA neuron terminal differentiation and subset specification. Moreover, Pitx3-deficient mice exhibit some canonical PD-related features, including the profound loss of SNc mDA neurons, a dramatic decrease in striatal dopamine (DA) levels, and motor abnormalities. However, the precise role of Pitx3 in progressive PD and how this gene contributes to mDA neuronal specification during early stages remains unclear. In this review, we updated the latest findings on Pitx3 by summarizing the crosstalk between Pitx3 and its associated transcription factors in mDA neuron development. We further explored the potential benefits of Pitx3 as a therapeutic target for PD in the future. To better understand the transcriptional network of Pitx3 in mDA neuron development may provide insights into Pitx3-related clinical drug-targeting research and therapeutic approaches.

Identifying biomarkers associated with the diagnosis of ulcerative colitis via bioinformatics and machine learning

BACKGROUND

Ulcerative colitis (UC) is an idiopathic inflammatory disease with an increasing incidence. This study aimed to identify potential UC biomarkers and associated immune infiltration characteristics.

METHODS

Two datasets (GSE87473 and GSE92415) were merged to obtain 193 UC samples and 42 normal samples. Using R, differentially expressed genes (DEGs) between UC and normal samples were filtered out, and their biological functions were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Promising biomarkers were identified using least absolute shrinkage selector operator regression and support vector machine recursive feature elimination, and their diagnostic efficacy was evaluated through receiver operating characteristic (ROC) curves. Finally, CIBERSORT was used to investigate the immune infiltration characteristics in UC, and the relationship between the identified biomarkers and various immune cells was examined.

RESULTS

We found 102 DEGs, of which 64 were significantly upregulated, and 38 were significantly downregulated. The DEGs were enriched in pathways associated with interleukin-17, cytokine-cytokine receptor interaction and viral protein interactions with cytokines and cytokine receptors, among others. Using machine learning methods and ROC tests, we confirmed DUOX2, DMBT1, CYP2B7P, PITX2 and DEFB1 to be essential diagnostic genes for UC. Immune cell infiltration analysis revealed that all five diagnostic genes were correlated with regulatory T cells, CD8 T cells, activated and resting memory CD4 T cells, activated natural killer cells, neutrophils, activated and resting mast cells, activated and resting dendritic cells and M0, M1 and M2 macrophages.

CONCLUSIONS

DUOX2, DMBT1, CYP2B7P, PITX2 and DEFB1 were identified as prospective biomarkers for UC. A new perspective on understanding the progression of UC may be provided by these biomarkers and their relationship with immune cell infiltration.

Investigating the Clinical Characteristics and PITX3Mutations of a Large Chinese Family with Anterior Segment Mesenchymal Dysgenesis and Congenital Posterior Polar Cataract

Objective

To investigate the clinical characteristics and pathogenic genetic mutations of a Chinese family with anterior segment mesenchymal dysgenesis and congenital posterior polar cataract.

Methods

Through family investigation, the family members were examined via slit lamp anterior segment imaging and screened for eye and other diseases by eye B-ultrasound. Genetic test was performed on the blood samples of the fourth family generation (23 people) via whole exome sequencing (trio-WES) and Sanger sequencing.

Results

Among the 36 members in four family generations, there were 11 living cases with different degrees of ocular abnormalities, such as cataracts, leukoplakia, and small cornea. All patients who received the genetic test had the heterozygous frameshift mutation c.640_656dup (p.G220Pfs∗95) on exon 4 of the PITX3 gene. This mutation was cosegregated with the clinical phenotypes in the family and thus might be one of the genetic factors that cause the corresponding ocular abnormalities in this family.

Conclusion

The congenital posterior polar cataract with or without anterior interstitial dysplasia (ASMD) of this family was inherited in an autosomal dominant manner, and the frameshift mutation (c.640_656dup) in the PITX3 gene was the cause of ocular abnormalities observed in this family. This study is of great significance for guiding prenatal diagnosis and disease treatment.

Developmental pathways linked to the vulnerability of adult midbrain dopaminergic neurons to neurodegeneration

The degeneration of dopaminergic and other neurons in the aging brain is considered a process starting well beyond the infantile and juvenile period. In contrast to other dopamine-associated neuropsychiatric disorders, such as schizophrenia and drug addiction, typically diagnosed during adolescence or young adulthood and, thus, thought to be rooted in the developing brain, Parkinson's Disease (PD) is rarely viewed as such. However, evidences have accumulated suggesting that several factors might contribute to an increased vulnerability to death of the dopaminergic neurons at an already very early (developmental) phase in life. Despite the remarkable ability of the brain to compensate such dopamine deficits, the early loss or dysfunction of these neurons might predispose an individual to suffer from PD because the critical threshold of dopamine function will be reached much earlier in life, even if the time-course and strength of naturally occurring and age-dependent dopaminergic cell death is not markedly altered in this individual. Several signaling and transcriptional pathways required for the proper embryonic development of the midbrain dopaminergic neurons, which are the most affected in PD, either continue to be active in the adult mammalian midbrain or are reactivated at the transition to adulthood and under neurotoxic conditions. The persistent activity of these pathways often has neuroprotective functions in adult midbrain dopaminergic neurons, whereas the reactivation of silenced pathways under pathological conditions can promote the survival and even regeneration of these neurons in the lesioned or aging brain. This article summarizes our current knowledge about signaling and transcription factors involved in midbrain dopaminergic neuron development, whose reduced gene dosage or signaling activity are implicated in a lower survival rate of these neurons in the postnatal or aging brain. It also discusses the evidences supporting the neuroprotection of the midbrain dopaminergic system after the external supply or ectopic expression of some of these secreted and nuclear factors in the adult and aging brain. Altogether, the timely monitoring and/or correction of these signaling and transcriptional pathways might be a promising approach to a much earlier diagnosis and/or prevention of PD.

The expression and methylation of PITX genes is associated with the prognosis of head and neck squamous cell carcinoma

Background: The PITX gene family, comprising PITX1, PITX2, and PITX3, is critical in organogenesis and has been evolutionary conserved in animals. PITX genes are associated with the advanced progression and poor prognosis of multiple cancers. However, the relationship between the PITX genes and head and neck squamous cell carcinoma (HNSC) has not been reported.

Methods: We used data from The Cancer Genome Atlas (TCGA) to analyze the association between PITX mRNA expression and clinicopathological parameters of patients with HNSC. The prognostic value of PITX genes was evaluated using the Kaplan-Meier plotter. Multivariate Cox analysis was used to screen out prognosis-associated genes to identify better prognostic indicators. The potential roles of PITX1 and PITX2 in HNSC prognosis were investigated using the protein-protein interaction (PPI) network, Gene Ontology (GO) analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The correlation between PITX1 and PITX2 expression or methylation and immune cell infiltration was evaluated using the tumor-immune system interaction database (TISIDB). MethSurv was used to identify DNA methylation and its effect on HNSC prognosis.

Results:PITX genes expression was correlated with different cancers. PITX1 and PITX2 expression was lower in the patients with HNSC. In HNSC, PITX1 expression was significantly related to the clinical stage, histologic grade, and N stage, while PITX2 expression was only significantly related to the histologic grade. The high expression of PITX3 was significantly related to the histologic grade, T stage, and N stage. Survival analysis revealed that PITX genes had prognostic value in HNSC, which was supported by multivariate Cox analysis. PPI network and enrichment analysis showed that the genes interacting with PITX1 and PITX2 belonged predominantly to signaling pathways associated with DNA binding and transcription. Of the CpG DNA methylation sites in PITX1 and PITX2, 28 and 22 were related to the prognosis of HNSC, respectively. Additionally, PITX1 and PITX2 expression and methylation was associated with tumor-infiltrating lymphocytes (TILs).

Conclusion: The PITX genes were differentially expressed in patients with HNSC, highlighting their essential role in DNA methylation and tumor-infiltrating immune cell regulation, as well as overall prognostic value in HNSC.

Comparative transcriptome profiles of human dental pulp stem cells from maxillary and mandibular teeth

The molecular control of tooth development is different between the maxilla and mandible, contributing to different tooth shapes and locations; however, whether this difference occurs in human permanent teeth is unknown. The aim of this study was to investigate and compare the transcriptome profiles of permanent maxillary and mandibular posterior teeth. Ten participants who had a pair of opposing premolars or molars extracted were recruited. The RNA obtained from cultured dental pulp stem cells underwent RNA-sequencing and qRT-PCR. The transcriptome profiles of two opposing premolar pairs and two molar pairs demonstrated that the upper premolars, lower premolars, upper molars, and lower molars expressed the same top-ranked genes, comprising FN1, COL1A1, COL1A2, ACTB, and EEFIA1, which are involved in extracellular matrix organization, immune system, signal transduction, hemostasis, and vesicle-mediated transport. Comparative transcriptome analyses of each/combined tooth pairs demonstrated that PITX1 was the only gene with different expression levels between upper and lower posterior teeth. PITX1 exhibited a 64-fold and 116-fold higher expression level in lower teeth compared with their upper premolars and molars, respectively. These differences were confirmed by qRT-PCR. Taken together, this study, for the first time, reveals that PITX1 is expressed significantly higher in mandibular posterior teeth compared with maxillary posterior teeth. The difference is more evident in the molars compared with premolars and consistent with its expression pattern in mouse developing teeth. We demonstrate that differences in lower versus upper teeth gene expression during odontogenesis occur in permanent teeth and suggest that these differences should be considered in molecular studies of dental pulp stem cells. Our findings pave the way to develop a more precise treatment in regenerative dentistry such as gene-based therapies for dentin/pulp regeneration and regeneration of different tooth types.

Genetic Factors That Affect Asymmetric Mandibular Growth—A Systematic Review

Facial asymmetry is a feature that occurs to a greater or lesser extent in the general population. As its severity is usually slight, facial asymmetry may not be noticeable to the patient. However, there are cases when severe facial asymmetry not only affects the facial aesthetics by distorting facial proportions, but also contributes to problems related to the function of the stomatognathic system. The nodal signalling pathway appears to be of particular importance in the process of mandibular asymmetry, as it affects not only structures formed from the first pharyngeal arch, but also other organs, such as the heart and lungs. Following the evaluation of the available literature, the inheritance of mandibular asymmetry is a very complex and multifactorial process, and the genes whose altered expression appears to be a more important potential aetiological factor for asymmetry include PITX2, ACTN3, ENPP1 and ESR1. This systematic review attempts to systematise the available literature concerning the impact of signalling pathway disruption, including the disruption of the nodal signalling pathway, on the development of mandibular asymmetry.

A four-gene prognostic signature for predicting the overall survival of patients with lung adenocarcinoma

Background

The prognosis of patients for lung adenocarcinoma (LUAD) is known to vary widely; the 5-year overall survival rate is just 63% even for the pathological IA stage. Thus, in order to identify high-risk patients and facilitate clinical decision making, it is vital that we identify new prognostic markers that can be used alongside TNM staging to facilitate risk stratification.

Methods

We used mRNA expression from The Cancer Genome Atlas (TCGA) cohort to identify a prognostic gene signature and combined this with clinical data to develop a predictive model for the prognosis of patients for lung adenocarcinoma. Kaplan-Meier curves, Lasso regression, and Cox regression, were used to identify specific prognostic genes. The model was assessed via the area under the receiver operating characteristic curve (AUC-ROC) and validated in an independent dataset (GSE50081) from the Gene Expression Omnibus (GEO).

Results

Our analyses identified a four-gene prognostic signature (CENPH, MYLIP, PITX3, and TRAF3IP3) that was associated with the overall survival of patients with T1-4N0-2M0 in the TCGA dataset. Multivariate regression suggested that the total risk score for the four genes represented an independent prognostic factor for the TCGA and GEO cohorts; the hazard ratio (HR) (high risk group vs low risk group) were 2.34 (p < 0.001) and 2.10 (p = 0.017). Immune infiltration estimations, as determined by an online tool (TIMER2.0) showed that CD4+ T cells were in relative abundance in the high risk group compared to the low risk group in both of the two cohorts (both p < 0.001). We established a composite prognostic model for predicting OS, combined with risk-grouping and clinical factors. The AUCs for 1-, 3-, 5- year OS in the training set were 0.750, 0.737, and 0.719; and were 0.645, 0.766, and 0.725 in the validation set. The calibration curves showed a good match between the predicted probabilities and the actual probabilities.

Conclusions

We identified a four-gene predictive signature which represents an independent prognostic factor and can be used to identify high-risk patients from different TNM stages of LUAD. A new prognostic model that combines a prognostic gene signature with clinical features exhibited better discriminatory ability for OS than traditional TNM staging.