Associations of genetic variants in endocytic trafficking of epidermal growth factor receptor super pathway with risk of nonsyndromic cleft lip with or without cleft palate

Exploring the therapeutic mechanisms of Coptidis Rhizoma in gastric precancerous lesions: a network pharmacology approach

BACKGROUND

Gastric precancerous lesions are a critical stage in the development of gastric cancer or gastric adenocarcinoma, and their outcome plays an important role in the malignant progression of gastric cancer. Coptidis Rhizoma has a good effect on Gastric precancerous lesions. However, the specific mechanisms of its action remain incompletely elucidated.

METHODS

Network pharmacology and molecular docking techniques were used to explore the active ingredients and molecular mechanism of Coptidis Rhizoma in treating gastric precancerous lesions. The active compounds of Coptidis Rhizoma and their potential gastric precancerous lesions related targets were obtained from TCMSP, GeneCards, and OMIM databases. An interaction network based on protein-protein interactions (PPIs) was constructed to visualize the interactions between hub genes. Analysis of GO enrichment and KEGG pathway were conducted using the DAVID database. An investigation of interactions between active compounds and potential targets was carried out by molecular docking. Finally, animal experiments were conducted to verify the effect and mechanism of Coptidis Rhizoma in treating precancerous lesions of gastric cancer.

RESULTS

A total of 11 active compounds and 95 anti-gastric precancerous lesions targets of Coptidis Rhizoma were screened for analysis. GO enrichment analysis showed that the mechanism of Coptidis Rhizoma acting on gastric precancerous lesions involves gene expression regulation and apoptosis regulation. KEGG pathway enrichment analysis showed that Coptidis Rhizoma against gastric precancerous lesions involving the AKT /HIF-1α/VEGF signalling pathway. Molecular docking simulations indicated potential interactions between these compounds and core targets involved in anti-gastric precancerous lesions activity. In addition, it was confirmed in vivo that Berberine and Coptidis Rhizoma may reverse atrophy and potential intestinal metaplasia by inhibiting the expression of p-AKT, HIFA, and VEGF.

CONCLUSION

Bioactive compounds in Coptidis Rhizoma have the potential to prevent atrophy and intestinal metaplasia. These compounds function by regulating the proteins implicated in AKT /HIF-1α/VEGF signalling pathways that are crucial in gastric epithelial cell differentiation, proliferation and maturation.

Expression of Rab25 is down-regulated in the foreskin of children with hypospadias

BACKGROUND

Hypospadias, a congenital malformation of the penis, is one of the newborns' most common developmental defects. The incidence of hypospadias is increasing yearly, and its pathogenesis is closely related to genetic susceptibility and environmental exposure to endocrine disruptors. Exploring the hypospadias' key molecular regulatory mechanism is crucial to reducing its incidence.

OBJECTIVE

To examine the differential expression of Rab25 in hypospadias and normal penile tissue and to identify whether it is a candidate gene for exploring the mechanism of hypospadias.

STUDY DESIGN

This study included 18 children aged 1-6 years undergoing hypospadias repair surgery at the Children's Hospital of Chongqing Medical University, and foreskin samples were collected. Children diagnosed with cryptorchidism, intersex status, or endocrine abnormalities were excluded from this study. Another 18 children aged 3-8 years with phimosis were included in the control group. The specimens were used for immunohistochemistry, western blotting, immunofluorescence, and polymerase chain reaction to assess the expression of Rab25.

RESULTS

Rab25 protein expression was lower in the hypospadias group than in the control group [ (2.101 ± 0.1845), (0.7506 ± 0.1779), p = 0.0008 < 0.05). The hypospadias group showed decreased expression of Rab25 protein in the epithelial cell layer. Rab25 mRNA levels were downregulated in the foreskin of children with hypospadias compared with controls [(1.697 ± 0.2005), (0.7687 ± 0.2130), p = 0.0053 < 0.05)].

DISCUSSION

Rab25 mRNA and protein expressions in the hypospadias group were significantly downregulated compared with the control group. This was consistent with the results of single-cell sequencing of fetal mice reproductive nodules at 15.5 days of gestation (Zhang Z, Liu Z, Zhang Q, et al., unpublished observations). Our study represents the first report of abnormal Rab25 expression in the foreskin tissue of patients with hypospadias. More detailed research on the relationship between Rab25 and urethral development could be conducted to reveal the molecular mechanism of hypospadias.

CONCLUSION

The expression of Rab25 in foreskin tissue was lower in the hypospadias group than in the control group. Rab25 is involved in the formation of the urethral seam and the occurrence of hypospadias. The potential mechanism by which Rab25 affects the canalization of the urethral plate needs to be further investigated.

Cardiofacioneurodevelopmental syndrome: Report of a novel patient and expansion of the phenotype

The cardiofacioneurodevelopmental syndrome (CFNDS) is characterized by craniofacial anomalies including bilateral cleft lip and palate, cardiac, skeletal, and neurodevelopmental features and additional variable manifestations. Whole-exome sequencing revealed homozygous loss-of-function variants in CCDC32 (alternative name: C15orf57) in both previously described patients. ccdc32 deletion in zebrafish suggests a ciliary contribution to the pathomechanism. We report a 9-year-old female patient with CFNDS caused by a homozygous 32,583-bp deletion affecting CCDC32. Independent of the affected CCDC32 transcript variant this deletion likely leads to loss of the encoded protein. The patient had intellectual disability, marked hypertelorism, bilateral cleft lip and palate, and short stature. She had bilateral conductive hearing loss, small hands and feet, and finger abnormalities. Brain imaging disclosed hypoplastic corpus callosum. We describe a core phenotype comprising developmental delay and bilateral cleft lip and palate in the three individuals with CFNDS. Variable abnormalities of the face, brain, heart, fingers, and toes and postnatal growth retardation or microcephaly can be present. Possible involvement of the uncharacterized CCDC32 protein in the adapter protein 2 (AP2) complex regulating clathrin-mediated endocytosis has been reported. Cleft palate and cardiac defects observed in mice deficient of different AP2 subunits support a CCDC32 function in the AP2 complex.

Target sequencing reveals the association between variants in VAX1 and NSCL/P in Chinese population

OBJECTIVE

A significant genetic association between rs7078160 in VAX1 and NSCL/P has been established through genome-wide association studies (GWAS), and we previously replicated the association in the Chinese population. The critical issue in the post-GWAS era is to identify functional variations that have a real impact on disease in the susceptible regions highlighted by GWAS. This study aimed to elucidate functional variants in VAX1 fully.

MATERIALS AND METHODS

Firstly, target sequencing was performed on 159 NSCL/P patients, followed by association analysis to discover disease-associated single nucleotide polymorphisms (SNPs); we then replicated the findings using a larger sample (1626 cases, 2255 controls) and investigated how candidate SNPs affect disease occurrence using extensive annotation databases. Additionally, we compared the genetic profiles of NSCL/P subtypes.

RESULTS

In this study, 6 SNPs in VAX1 were identified to be associated with NSCL/P in the Western Han Chinese population. Five of them were predicted to influence transcriptional factor biding ability and were expression quantitative trait loci (eQTLs) of nearby genes in multiple tissues.

CONCLUSION

The previously reported association between rs7078160 and NSCL/P was successfully replicated. Moreover, our findings firstly revealed that 5 SNPs in VAX1 are associated with NSCL/P in the Western Han Chinese population.

Role of adaptin protein complexes in intracellular trafficking and their impact on diseases

Adaptin proteins (APs) play a crucial role in intracellular cell trafficking. The 'classical' role of APs is carried out by AP1‒3, which bind to clathrin, cargo, and accessory proteins. Accordingly, AP1-3 are crucial for both vesicle formation and sorting. All APs consist of four subunits that are indispensable for their functions. In fact, based on studies using cells, model organism knockdown/knock-out, and human variants, each subunit plays crucial roles and contributes to the specificity of each AP. These studies also revealed that the sorting and intracellular trafficking function of AP can exert varying effects on pathology by controlling features such as cell development, signal transduction related to the apoptosis and proliferation pathways in cancer cells, organelle integrity, receptor presentation, and viral infection. Although the roles and functions of AP1‒3 are relatively well studied, the functions of the less abundant and more recently identified APs, AP4 and AP5, are still to be investigated. Further studies on these APs may enable a better understanding and targeting of specific diseases.APs known or suggested locations and functions.

Evaluation of TGF-β1 and EGFR in Cleft Affected Lip Mucosa

Background.

The morphopathogenesis of orofacial cleft development is only partly understood; therefore, it is important to identify factors, which possibly could be involved in it. The aim of the study was to evaluate the distribution of TGF-β1 and EGFR-containing cells in cleft affected lip mucosa.

Materials and Methods.

The study group included lip mucosa tissue samples from 14 patients with orofacial cleft. The control group contained 11 healthy oral mucosa tissue samples. The tissue sections were stained by immunohistochemistry for TGF-β1 and EGFR. The expression of positive structures was graded semiquantitatively. IBM SPSS 26.0 was used for statistical analysis, Spearman`s rank correlation and Mann-Whitney U tests were performed.

Results.

Mostly few to moderate number (+/++) of TGF-β1-containing cells was found in epithelium, also the same number of fibroblasts and macrophages was seen in the lamina propria of cleft affected lip mucosa. Meanwhile, healthy oral mucosa on average demonstrated a moderate number (++) of TGF-β1-containing epithelial cells, fibroblasts, and macrophages. A variable, mostly indistinct number of EGFR-containing cells was seen in the epithelium of cleft affected lip mucosa, meanwhile, mostly no (0) EGFR positive cells were found in the epithelium of healthy mucosa. Statistically significantly less TGF-β1-containing cells were found in the epithelium of cleft affected lip mucosa than in the healthy mucosa (U=33.000; p=0.015). Also, the lamina propria of cleft affected lip mucosa showed statistically significantly less TGF-β1 immunoreactive fibroblasts and macrophages than the healthy mucosa (U=28.500; p=0.006).

Conclusions.

The decreased number of TGF-β1-containing epithelial cells, fibroblasts and macrophages in cleft affected lip mucosa proves the role of problematic tissue remodelation in the cleft pathogenesis. The distribution of EGFR in cleft affected and healthy mucosa is similar and possibly does not play a role in the cleft development of humans.

Integrating GWAS and eQTL to predict genes and pathways for non-syndromic cleft lip with or without palate

OBJECTIVE

To explore susceptibility genes and pathways for non-syndromic cleft lip with or without cleft palate (NSCL/P).

MATERIALS AND METHODS

Two genome-wide association studies (GWAS) datasets, including 858 NSCL/P cases and 1,248 controls, were integrated with expression quantitative trait loci (eQTL) dataset identified by Genotype-Tissue Expression (GTEx) project in whole-blood samples. The expression of the candidate genes in mouse orofacial development was inquired from FaceBase. Protein-protein interaction (PPI) network was visualized to identify protein functions. Go and KEGG pathway analyses were performed to explore the underlying risk pathways.

RESULTS

A total of 233 eQTL single-nucleotide polymorphisms (SNPs) in 432 candidate genes were identified to be associated with the risk of NSCL/P. One hundred and eighty-three susceptible genes were expressed in mouse orofacial development according to FaceBase. PPI network analysis highlighted that these genes involved in ubiquitin-mediated proteolysis (KCTD7, ASB1, UBOX5, ANAPC4) and DNA synthesis (XRCC3, RFC3, KAT5, RHNO1) were associated with the risk of NSCL/P. GO and KEGG pathway analyses revealed that the fatty acid metabolism pathway (ACADL, HSD17B12, ACSL5, PPT1, MCAT) played an important role in the development of NSCL/P.

CONCLUSIONS

Our results identified novel susceptibility genes and pathways associated with the development of NSCL/P.

Effects of small interfering RNA-mediated silencing of susceptibility genes of non-syndromic cleft lip with or without cleft palate on cell proliferation and migration

BACKGROUND

Non-syndrome cleft lip with or without cleft palate (NSCL/P) is the most common congenital defect with a complex etiology involving both genetic and environmental factors. Our previous research has identified susceptibility genes of NSCL/P using whole-exome sequencing. The study was to determine the effects of small interfering RNA (siRNA)-mediated silencing of genes on cell proliferation and migration to confirm the roles of the genes in NSCL/P.

METHODS

We silenced the genes by RNA interference (RNAi) with siRNA in human oral keratinocyte (HOK). We used the Cell Counting Kit-8 (CCK8) assay to determine cell proliferation and the wound healing assay to determine cell migration.

RESULTS

Migration of HOK was inhibited by RNAi-induced silencing of adenosine triphosphate binding cassette transporter A4 (ABCA4), erythropoietin produces hepatocyte A receptor 3 (EPHA3), alpha-parvin (PARVA), and platelet-derived growth factor C (PDGFC). The change of proliferation was not found. Treated with siRNA-mediated silencing of type IV collagen (COL4A2), eukaryotic translation initiation factor 2B subunit (EIF2B3), fibroblast growth factor receptor 2 (FGFR2), kinesin family member 20B (KIF20B), β-lactamase serine-like protein (LACTB), SEC16 homolog A (SEC16A) and thyroid adenoma target gene (THADA) had no effects on cell proliferation and migration of HOK.

CONCLUSIONS

We suggest mutations of the four susceptibility genes ABCA4, EPHA3, PARVA and PDGFC are involved in NSCL/P through inhibiting cell migration. The study provides new candidates for future study of NSCL/P.

Association of Betaine-Homocysteine S-Methyl Transferase (rs3797546 and rs3733890) polymorphisms with non-syndromic cleft lip/palate: A meta-analysis

OBJECTIVE

Non-syndromic cleft lip/palate (NSCL/P) has a multifactorial and polygenic aetiology. The role of genetics in its occurrence has not been fully clarified. The present meta-analysis aimed to evaluate the association of betaine-homocysteine S-methyltransferase (BHMT) polymorphisms (rs3797546 and rs3733890) with the risk of NSCL/P.

MATERIALS AND METHODS

PubMed/Medline, Scopus, Cochrane Library, and Web of Science databases were systematically searched for articles published up until December 2018 with no language restriction. Quality evaluation of each study was performed by the Newcastle-Ottawa Scale (NOS). The crude odds ratio (OR) and 95% confidence interval (CI) were calculated for each study by RevMan 5.3 software, and a funnel plot analysis was performed by the CMA 2.0 software using the Egger's and Begg's tests.

RESULTS

Review of the four selected studies revealed that the CC genotype of rs3797546 polymorphism significantly increased the risk of NSCL/P. No association was noted between NSCL/P risk and rs3733890 polymorphism except in Chinese (elevated risk of NSCL/P) and Polish (decreased risk of NSCL/P) populations.

CONCLUSIONS

According to the present meta-analysis, rs3733890 polymorphism does not play a role in susceptibility to NSCL/P; whereas, rs3797546 polymorphism may play a role in susceptibility to NSCL/P. Future studies are required to examine the association between BHMT polymorphisms and the NSCL/P risk in different ethnicities with a larger sample size.

Associations of genetic variants in endocytic trafficking of epidermal growth factor receptor super pathway with risk of nonsyndromic cleft lip with or without cleft palate

BACKGROUND

The genetic etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P) has not been fully clarified to date. Epidermal growth factor receptor (EGFR) was reportedly involved in its biological establishment and regulation of cell migration during the embryonic stage.

METHODS

We selected a super pathway of endocytic trafficking of EGFR and investigated the associations of single-nucleotide polymorphisms (SNPs) in the super pathway with the risk of NSCL/P by analyzing our published genome-wide association study (GWAS) data from 504 NSCL/P individuals and 455 controls. After the false discovery rate (FDR) control, we conducted linkage disequilibrium (LD) analyses and conditional regression analyses to obtain independent lead SNPs. We performed LD analyses between the lead SNPs and the reported SNPs to find novel ones from our study. We annotated the lead SNPs and investigated their mapped genes in silico.

RESULTS

A total of 82 SNPs showed a statistical association with the risk of NSCL/P after FDR control. They contained three reported SNPs which were g.117068049G>A (rs7078160), g.117086783C>G (rs10886040), and g.117101266G>T (rs17095681). Four independent lead SNPs were obtained, including g.116979803 T>C (rs1905539) and g.117037960A>G (rs7902502) at 10q25.3, g.35720163G>C (rs75656820) at 17q12, and g.156864512G>A (rs1800877) at 1q23.1. Three of them were in low LD (r²  < 0.5) with the reported SNPs except g.117037960A>G (rs7902502), so these three were newly identified. Lead SNPs were mapped to three genes: SHTN1, AP2B1, and NTRK1. The three genes were relatively more highly expressed in the human craniofacial region and in the proximal maxillary location during the craniofacial development stage of the embryonic mouse.

CONCLUSION

Our results suggested that SHTN1, AP2B1, and NTRK1 might be associated with the development of NSCL/P.