TC-1 (c8orf4) enhances aggressive biologic behavior in lung cancer through the Wnt/β-catenin pathway

Accurate and efficient integrative reference-informed spatial domain detection for spatial transcriptomics

Spatially resolved transcriptomics (SRT) studies are becoming increasingly common and large, offering unprecedented opportunities in mapping complex tissue structures and functions. Here we present integrative and reference-informed tissue segmentation (IRIS), a computational method designed to characterize tissue spatial organization in SRT studies through accurately and efficiently detecting spatial domains. IRIS uniquely leverages single-cell RNA sequencing data for reference-informed detection of biologically interpretable spatial domains, integrating multiple SRT slices while explicitly considering correlations both within and across slices. We demonstrate the advantages of IRIS through in-depth analysis of six SRT datasets encompassing diverse technologies, tissues, species and resolutions. In these applications, IRIS achieves substantial accuracy gains (39-1,083%) and speed improvements (4.6-666.0) in moderate-sized datasets, while representing the only method applicable for large datasets including Stereo-seq and 10x Xenium. As a result, IRIS reveals intricate brain structures, uncovers tumor microenvironment heterogeneity and detects structural changes in diabetes-affected testis, all with exceptional speed and accuracy.

Elevated phagocytic capacity directs innate spinal cord repair

Immune cells elicit a continuum of transcriptional and functional states after spinal cord injury (SCI). In mammals, inefficient debris clearance and chronic inflammation impede recovery and overshadow pro-regenerative immune functions. We found that, unlike mammals, zebrafish SCI elicits transient immune activation and efficient debris clearance, without causing chronic inflammation. Single-cell transcriptomics and inducible genetic ablation showed zebrafish macrophages are highly phagocytic and required for regeneration. Cross-species comparisons between zebrafish and mammalian macrophages identified transcription and immune response regulator ( tcim ) as a macrophage-enriched zebrafish gene. Genetic deletion of zebrafish tcim impairs phagocytosis and regeneration, causes aberrant and chronic immune activation, and can be rescued by transplanting wild-type immune precursors into tcim mutants. Conversely, genetic expression of human TCIM accelerates debris clearance and regeneration by reprogramming myeloid precursors into activated phagocytes. This study establishes a central requirement for elevated phagocytic capacity to achieve innate spinal cord repair.

Transcriptomic profiles of age-related genes in female trachea and bronchus

Background: Studies demonstrated that age-related cellular and functional changes of airway significantly contribute to the pathogenesis of many airway diseases. However, our understanding on the age-related molecular alterations of human airway remains inadequate.

Methods: Airway (trachea and bronchus) brushing specimens were collected from 14 healthy, female non-smokers with ages ranging from 20 to 60 years. Bulk RNA sequencing was performed on all the specimens (n = 28). Airway cell types and their relative proportions were estimated using CIBERSORTx. The cell type proportions were compared between the younger (age 20–40) and elder group (age 40–60) in the trachea and bronchus respectively. The linear association between cell type proportion and age was assessed using the Pearson correlation coefficient. Differentially expressed genes (DEGs) between the two age groups were identified using DESeq2. Three kinds of enrichment analysis of the age-related DEGs were performed, including Gene ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and disease enrichment analysis.

Results: Sixteen and thirteen cell types were separately identified in tracheal and bronchial brushings, with the airway epithelial cells (including suprabasal, submucosal gland (SMG) goblet, serous, secretory, multiciliated, cycling.basal, basal cells) accounting for 85.1% in the trachea and 92.5% in the bronchus. The lymphatic cell and NK cells had a higher abundance ratio in the trachea, compared with the bronchus. The proportion of basal cells was negatively related to age both in the trachea and bronchus. Thirty-one and fifty-two age-related DEGs (p < 0.1) were identified in the trachea and bronchus, respectively. Among them, five common DEGs (CXCL2, CXCL8, TCIM, P4HA3, AQP10) were identified. Pathway enrichment analysis showed both tracheal and bronchial age-related DEGs were primarily involved in immune regulatory signaling pathways (TNF, NF-kappa B, IL-17 et al.). Disease enrichment analysis suggested that tracheal age-related DEGs significantly related to asthmatic pulmonary eosinophilia, and chronic airflow obstruction et al., and that bronchial age-related DEGs were enriched in airflow obstruction, bronchiectasis, pulmonary emphysema, and low respiratory tract infection et al.

Conclusion: We found the proportion of basal cells decreased with age in both the trachea and bronchus, suggesting a weakening of their self-renew ability with age. We identified transcriptomic signature genes associated with the early aging process of the human trachea and bronchus, and provided evidence to support that changes in their immune regulatory function may play critical roles in age-related airway diseases.

Exosomal miR-328 originated from pulmonary adenocarcinoma cells enhances osteoclastogenesis via downregulating Nrp-2 expression

Osseous metastases of pulmonary carcinoma and the detailed mechanisms remain unclear, and the effects of exosomes (Exos) originated from pulmonary adenocarcinoma cells in this process have received a lot of attentions. Our study revealed that the Exos secreted from A549 cells (A549-Exos) enhanced osteoclastogenesis and osseous resorption in vitro. In addition, A549-Exos showed a targeted effect on bones to enhance osseous resorption in vivo. A549-exosomal miR-328 enhanced osseous resorption via downregulating neuropilin 2 (Nrp-2) expression, and A549-Exos miR-328 inhibitors suppressed osseous resorption in vivo. Therefore, A549-exosomal miR-328 enhances osteoclastogenesis via downregulating Nrp-2 expression, thus A549-Exos ^{miR-328 inhibitors} can be used as a potential nanodrug for treating osseous metastases.

Thymoquinone inhibits the proliferation and invasion of esophageal cancer cells by disrupting the AKT/GSK-3β/Wnt signaling pathway via PTEN upregulation

Although thymoquinone (TQ) has been reported to exert antitumor activity against various types of human cancers without evident toxicity, limited studies have reported the effects of TQ on esophageal cancer. Here, we showed that TQ induced cell cycle arrest in the G2/M phase and significantly inhibited cell proliferation and invasion. Further investigation of the potential mechanism revealed that TQ increased the levels of p53 and p21 but significantly reduced the expression of Cyclin B1, Cyclin A, and Cyclin E. Moreover, TQ led to a decrease in Bcl-2 and an increase in cleaved caspase-3, cleaved caspase-7, cleaved caspase-9, and Bax, indicating that TQ induced apoptosis by activating the intrinsic mitochondrial apoptosis pathway. Western blotting showed that TQ disrupted the PI3K/AKT pathway by upregulating PTEN, thus modulating GSK-3β activity, increasing β-catenin degradation, and decreasing decreased MMP-2 and MMP-9 levels in Eca109 cells. However, these changes were attenuated by disrupting PTEN function (using a potent inhibitor) or downregulating PTEN expression. In addition, in vivo results showed that the efficacy of TQ as an antitumor agent in a mouse xenograft tumor model. In conclusion, TQ suppressed human esophageal cancer cells proliferation and invasion both in vitro and in vivo and could provide a novel therapeutic approach for esophageal cancer.

Association of C8orf4 expression with its methylation status, aberrant β-catenin expression, and the development of cervical squamous cell carcinoma

Chromosome 8 open reading frame 4 (C8orf4) is an activator of Wnt signaling pathway, and participates in the tumorigenesis and progression of many tumors. The expression levels of C8orf4 and β-catenin were assessed via immunohistochemical staining in 100 cervical squamous cell carcinoma (CSCC) tissues, 50 high-grade squamous intraepithelial lesions (HSILs), 50 low-grade squamous intraepithelial lesions (LSILs), and 50 normal cervical tissues. Bisulfite sequencing polymerase chain reaction analysis was used to examine the methylation status of the C8orf4 locus in CSCC and normal cervical tissues. The expression rates of C8orf4 and β-catenin were significantly higher in CSCCs or HSILs than in LSILs or normal cervical tissues (P < .05). C8orf4 expression was positively correlated with the poor differentiation of CSCCs (P = .009), and with aberrant expression of β-catenin in CSCCs (P = .002) and squamous intraepithelial lesions (P < .001). The methylation rate of C8orf4 in CSCCs was significantly lower than that in normal cervical tissues (P = .001). The Cancer Genome Atlas genomics data also confirmed that the mRNA expression of C8orf4 was positively associated with the copy number alteration of C8orf4 (correlation coefficient = 0.213, P < .001), and negatively correlated with the methylation level of C8orf4 (correlation coefficient = -0.408, P < .001). In conclusion, the expressions of C8orf4 and β-catenin were synergistically increased in CSCCs and HSILs and higher than those in LSILs and normal cervical tissues. The methylation level of C8orf4 is decreased in CSCCs and is responsible for the increased expression of C8orf4.

Of Wnts and Ribosomes

Wnt proteins are secreted glycoproteins that activate different intracellular signal transduction pathways. They regulate cell proliferation and are required for proper embryonic development. Misregulation of Wnt signaling can result in various diseases including cancer. In most circumstances, cell growth is essential for cell division and thus cell proliferation. Therefore, several reports have highlighted the key role of Wnt proteins for cell growth. Ribosomes represent the cellular protein synthesis machinery and cells need to be equipped with an appropriate number of ribosomes to allow cell growth. Recent findings suggest a role for Wnt proteins in regulating ribosome biogenesis and we here summarize these findings representing a previously unknown function of Wnt proteins. Understanding this role of Wnt signaling might open new avenues to slow down proliferation by drugs for instance in cancer therapy.

PTEN Gene Induces Cell Invasion and Migration via Regulating AKT/GSK-3β/β-Catenin Signaling Pathway in Human Gastric Cancer

BACKGROUND

Abnormality of PTEN gene and Wnt/β-catenin signaling have been strongly implicated in various malignant cancers. Recently, it has been noted that a functional interaction/cross-talk was found between the PTEN/PI3K/AKT and Wnt/β-catenin, which plays a key role in the development of cancers. However, few related studies on gastric cancer are available.

AIM

We examined the expression of PTEN and β-catenin in gastric cancer tissues and detected whether down-regulation of PTEN promotes the migration and invasion in gastric cancer cells along with its underlying mechanism.

MATERIALS AND METHODS

Immunocytochemistry, a wound healing assay, a Matrigel invasion assay, an immunofluorescence staining were performed to detect expression of PTEN and β-catenin in gastric cancer and adjacent normal tissues, cell migration, cell invasion, and the effects of PTEN knockdown on β-catenin in cells, respectively. Further, MMP-2 and MMP-9 activities were analyzed by zymography assay. The changes in related proteins were further quantified by western blotting.

RESULTS

Low expression of PTEN was found in majority of gastric cancer tissues, which showed significant associations with differentiation grade in gastric cancer patients. Further, a negative correlation was revealed between PTEN and β-catenin protein expression in gastric cancer tissues (r = - 0.546, P < 0.01). Additionally, PTEN knockdown promoted the migration and invasion of cells and caused an obvious increase in p-AKT, p-GSK-3β, β-catenin, E-cadherin, MMP-7, MMP-2, and MMP-9 in gastric cancer cells.

CONCLUSION

Our results indicated PTEN gene might induce cell invasion and migration via regulating AKT/GSK-3β/β-catenin signaling pathway, playing a vital role in the progression of gastric cancer.

Thyroid cancer 1 (C8orf4) shows high expression, no mutation and reduced methylation level in lung cancers, and its expression correlates with β-catenin and DNMT1 expression and poor prognosis

Thyroid cancer 1 (TC1, C8orf4) plays important roles in tumors. The aim of this study was to examine the protein expression levels, methylation status, and mutational status of TC1 (C8orf4) in lung cancers, and investigate the correlation between TC1, other members of the Wnt signaling pathway, and lung cancer. TC1 expression levels were assessed via immunohistochemical staining in 179 cases of lung cancer. β-catenin, TCF4, Axin, Disabled-2, Chibby, and DNA methyltransferase-1 (DNMT1) expressions were also examined. Bisulfite sequencing PCR analysis was used to examine the methylation status of the C8orf4 locus, while PCR analysis and direct sequencing were used to determine its mutational status. We found high TC1 expression correlated with poor differentiation, advanced TNM stage, lymphatic metastasis, and poor prognosis in lung cancer patients. TC1 expression also correlated with β-catenin and DNMT1 expressions. No mutations in C8orf4 were detected. However, methylation levels of C8orf4 in lung cancers were lower than in corresponding normal lung tissues. In conclusion, high TC1 expression is implicated in lung cancer progression and correlates with poor prognosis in lung cancer. Reduced methylation levels might be responsible for the elevated TC1 expression levels. TC1, β-catenin, and DNMT1 can synergistically activate Wnt/β-catenin signaling in lung cancers.

Conformational characterization of the intrinsically disordered protein Chibby: Interplay between structural elements in target recognition

The protein Chibby (Cby) is an antagonist of the Wnt signaling pathway, where it inhibits the binding between the transcriptional coactivator β-catenin and the Tcf/Lef transcription factors. The 126 residue Cby is partially disordered; its N-terminal half is unstructured while its C-terminal half comprises a coiled-coil domain. Previous structural analyses of Cby using NMR spectroscopy suffered from severe line broadening for residues within the protein's C-terminal half, hindering detailed characterization of the coiled-coil domain. Here, we use hydrogen/deuterium exchange-mass spectrometry (HDX-MS) to examine Cby's C-terminal half. Results reveal that Cby is divided into three structural elements: a disordered N-terminal half, a coiled-coil domain, and a C-terminal unstructured extension consisting of the last ∼ 25 residues (which we term C-terminal extension). A series of truncation constructs were designed to assess the roles of individual structural elements in protein stability and Cby binding to TC-1, a positive regulator of the Wnt signaling pathway. CD and NMR data show that Cby maintains coiled-coil structure upon deletion of either disordered region. NMR and ITC binding experiments between Cby and TC-1 illustrate that the interaction is retained upon deletion of either Cby's N-terminal half or its C-terminal extension. Intriguingly, Cby's C-terminal half alone binds to TC-1 with significantly greater affinity compared to full-length Cby, implying that target binding of the coiled-coil domain is affected by the flanking disordered regions.

Knockdown of TC-1 enhances radiosensitivity of non-small cell lung cancer via the Wnt/β-catenin pathway

Thyroid cancer 1 (TC-1, C8ofr4) is widely expressed in vertebrates and associated with many kinds of tumors. Previous studies indicated that TC-1 functions as a positive regulator in the Wnt/β-catenin signaling pathway in non-small cell lung cancer (NSCLC). However, its exact role and regulation mechanism in radiosensitivity of NSCLC are still unclear. The expression level of TC-1 was measured by qRT-PCR and western blot in NSCLC cell lines. Proliferation and apoptosis of NSCLC cells in response to TC-1 knockdown or/and radiation were determined by MTT assay and flow cytometry, respectively. The activation of the Wnt/β-catenin signaling pathway was further examined by western blot in vitro and in vivo. Compared to TC-1 siRNA or radiotherapy alone, TC-1 silencing combined with radiation inhibited cell proliferation and induced apoptosis in NSCLC cell lines by inactivating of the Wnt/β-catenin signaling pathway. Furthermore, inhibition of the Wnt/β-catenin signaling pathway by XAV939, a Wnt/β-catenin signaling inhibitor, contributed to proliferation inhibition and apoptosis induction in NSCLC A549 cells. Combinative treatment of A549 xenografts with TC-1 siRNA and radiation caused significant tumor regression and inactivation of the Wnt/β-catenin signaling pathway relative to TC-1 siRNA or radiotherapy alone. The results from in vitro and in vivo studies indicated that TC-1 silencing sensitized NSCLC cell lines to radiotherapy through the Wnt/β-catenin signaling pathway.

Summary: TC-1 silencing inhibited cell proliferation and induced apoptosis in non-small cell lung cancer (NSCLC) both in vitro and in vivo through the Wnt/β-catenin signaling pathway, thereby increasing the susceptibility of NSCLC to radiotherapy.

Regulation and involvement of matrix metalloproteinases in vascular diseases

Matrix metalloproteinases (MMPs) are a family of zinc dependent endopeptidases whose main function is to degrade and deposit structural proteins within the extracellular matrix (ECM). A dysregulation of MMPs is linked to vascular diseases. MMPs are classified into collagenases, gelatinases, membrane-type, metalloelastase, stromelysins, matrilysins, enamelysins, and unclassified subgroups. The production of MMPs is stimulated by factors such as oxidative stress, growth factors and inflammation which lead to its up- or down-regulation with subsequent ECM remodeling. Normally, excess activation of MMPs is controlled by their endogenous inhibitors, tissue inhibitors of metalloproteinases (TIMPs). An imbalance of MMPs and TIMPs has been implicated in hypertension, atherosclerotic plaque formation and instability, aortic aneurysms and varicose vein wall remodeling. Also, recent evidence suggests epigenetic regulation of some MMPs in angiogenesis and atherosclerosis. Over the years, pharmacological inhibitors of MMPs have been used to modify or prevent the development of the disease with some success. In this review, we discuss recent advances in MMP biology, and their involvement in the manifestation of vascular disease.

Gene expression and pathway analysis of human hepatocellular carcinoma cells treated with cadmium

Cadmium (Cd) is a toxic and carcinogenic metal naturally occurring in the Earth's crust. A common route of human exposure is via diet and cadmium accumulates in the liver. The effects of Cd exposure on gene expression in human hepatocellular carcinoma (HepG2) cells were examined in this study. HepG2 cells were acutely-treated with 0.1, 0.5, or 1.0 μM Cd for 24h; or chronically-treated with 0.01, 0.05, or 0.1 μM Cd for three weeks and gene expression analysis was performed using Affymetrix GeneChip® Human Gene 1.0 ST Arrays. Acute and chronic exposures significantly altered the expression of 333 and 181 genes, respectively. The genes most upregulated by acute exposure included several metallothioneins. Downregulated genes included the monooxygenase CYP3A7, involved in drug and lipid metabolism. In contrast, CYP3A7 was upregulated by chronic Cd exposure, as was DNAJB9, an anti-apoptotic J protein. Genes downregulated following chronic exposure included the transcriptional regulator early growth response protein 1. Ingenuity Pathway Analysis revealed that the top networks altered by acute exposure were lipid metabolism, small molecule biosynthesis, cell morphology, organization, and development; while top networks altered by chronic exposure were organ morphology, cell cycle, cell signaling, and renal and urological diseases/cancer. Many of the dysregulated genes play important roles in cellular growth, proliferation, and apoptosis, and may be involved in carcinogenesis. In addition to gene expression changes, HepG2 cells treated with cadmium for 24h indicated a reduction in global levels of histone methylation and acetylation that persisted 72 h post-treatment.

Human Thyroid Cancer-1 (TC-1) is a vertebrate specific oncogenic protein that protects against copper and pro-apoptotic genes in yeast

The human Thyroid Cancer-1 (hTC-1) protein, also known as C8orf4 was initially identified as a gene that was up-regulated in human thyroid cancer. Here we show that hTC-1 is a peptide that prevents the effects of over-expressing Bax in yeast. Analysis of the 106 residues of hTC-1 in available protein databases revealed direct orthologues in jawed-vertebrates, including mammals, frogs, fish and sharks. No TC-1 orthologue was detected in lower organisms, including yeast. Here we show that TC-1 is a general pro-survival peptide since it prevents the growth- and cell death-inducing effects of copper in yeast. Human TC-1 also prevented the deleterious effects that occur due to the over-expression of a number of key pro-apoptotic peptides, including YCA1, YBH3, NUC1, and AIF1. Even though the protective effects were more pronounced with the over-expression of YBH3 and YCA1, hTC-1 could still protect yeast mutants lacking YBH3 and YCA1 from the effects of copper sulfate. This suggests that the protective effects of TC-1 are not limited to specific pathways or processes. Taken together, our results indicate that hTC-1 is a pro-survival protein that retains its function when heterologously expressed in yeast. Thus yeast is a useful model to characterize the potential roles in cell death and survival of cancer related genes.

Digested disorder, Quarterly intrinsic disorder digest (October-November-December, 2013)

This is the 4th issue of the Digested Disorder series that represents reader's digest of the scientific literature on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the fourth quarter of 2013; i.e. during the period of October, November, and December of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.

Wnt3a increases the metastatic potential of non-small cell lung cancer cells in vitro in part via its upregulation of Notch3

Metastasis is the leading cause of death in lung cancer. Understanding the mechanisms underlying the process of metastasis is crucial for identifying novel anti-metastatic therapies. Studies indicate that the highly conserved developmental pathways, such as the Wnt and Notch signaling pathways, play important roles in the non-small cell lung cancer (NSCLC) tumorigenesis. However, the roles of both pathways in NSCLC metastasis are unclear. The present study aimed to investigate whether Wnt3a and Notch3, key components of the Wnt and Notch signaling pathways, respectively, regulate the metastatic abilities of NSCLC cells and whether there is some relationship during these regulatory events. Here, we observed that Wnt3a treatment upregulated, not only the protein expression of Notch3, but also the mRNA expression of Notch3 and its downstream genes, HES1 and HEYL. In addition, Wnt3a promoted cell invasion and anchorage-independent growth. Meanwhile, Wnt3a treatment caused epithelial‑mesenchymal transition (EMT)-like morphological changes and F-actin reorganization. The western blotting data showed that Wnt3a treatment decreased the expression of E-cadherin and increased the expression of N-cadherin and vimentin. Compared with Wnt3a treatment, Notch3 shRNA transfection had opposite effects. Furthermore, Notch3 shRNA weakened the effects of Wnt3a treatment on the in vitro cell invasion and EMT. Overall, these observations suggest that Wnt3a and Notch3 may promote the metastasis of NSCLC and Notch3 upregulation is required for the Wnt3a mediated increased metastatic abilities of NSCLC.

PEG10 plays a crucial role in human lung cancer proliferation, progression, prognosis and metastasis

Paternally expressed gene 10 (PEG10) has been identified as a genetic imprinted gene, which is important for apoptosis resistance in cancer cells. Mounting evidence suggests that PEG10 is expressed in the majority of hepatocellular carcinoma (HCC) cells with growth-promoting activity. In the present study, we evaluated the correlation between PEG10 expression and the clinicopathological features of lung, breast and HCC tumors, and predicted the relationship between survival and expression levels of PEG10 in lung cancer patients. Furthermore, we chose non-small cell lung cancer cell line A549 as a model to analyze the function of PEG10 in proliferation and metastasis in vitro. Our results revealed that expression of PEG10 was closely correlated with clinical TNM grade and patient prognosis in lung cancer. PEG10 enhanced cell proliferation and promoted tumor cell migration and invasion by upregulating the expression of β-catenin, MMP-2 and MMP-9, and decreased the expression of E-cadherin in the A549 cells. Our findings provide significant insight into the molecular mechanisms of lung cancer and offer novel ideas for designing new therapeutic targets for lung carcinoma.

Prognostic value of matrix metalloproteinase-7 expression in patients with non-small cell lung cancer

The prognostic value of matrix metalloproteinase-7 (MMP-7) for survival of patients with non-small cell lung cancer (NSCLC) remains controversial. We performed a meta-analysis of the literatures to clarify its impact. Trials were selected for meta-analysis if they provided an independent assessment of MMP-7 in NSCLC and reported the analysis of survival data based on MMP-7 status. Pooled hazard ratio (HR) with 95% confidence interval (95% CI) was used to evaluate the associations between MMP-7 expression and survival of NSCLC patients. Heterogeneity and publication bias were also assessed. Seven studies involving 1,446 patients were identified. The combined HR for all studies was 1.28 (95% CI 0.86-1.91; P = 0.22). Subgroup analysis revealed that MMP-7 overexpression had a favorable impact on survival in Caucasians (HR = 0.74; 95% CI 0.55-0.99; P = 0.043) but showed a poor survival prognosis in Asians (HR = 1.74; 95% CI 1.05-2.88, P = 0.031). Its effect also appeared significant when the analysis was restricted to Asian patients with squamous cell cancer (HR =3.42; 95% CI 1.92-6.11, P = 0.000) and adenocarcinoma (HR = 2.1; 95% CI 1.34-3.29, P = 0.001). Our meta-analysis suggests that there are ethnic differences in the clinical significance of MMP-7 expression for patients with NSCLC.