Chordin-like 1 is a novel prognostic biomarker and correlative with immune cell infiltration in lung adenocarcinoma

Exploration of Toxins from a Marine Annelid: An Analysis of Phyllotoxins and Accompanying Bioactives

Proteinaceous toxins are peptides or proteins that hold great biotechnological value, evidenced by their ecological role, whether as defense or predation mechanisms. Bioprospecting using bioinformatics and omics may render screening for novel bioactives more expeditious, especially considering the immense diversity of toxin-secreting marine organisms. Eulalia sp. (Annelida: Phyllodocidae), a toxin bearing marine annelid, was recently shown to secrete cysteine-rich protein (Crisp) toxins (hitherto referred to as 'phyllotoxins') that can immobilize its prey. By analyzing and validating transcriptomic data, we narrowed the list of isolated full coding sequences of transcripts of the most abundant toxins or accompanying bioactives secreted by the species (the phyllotoxin Crisp, hyaluronidase, serine protease, and peptidases M12A, M13, and M12B). Through homology matching with human proteins, the biotechnological potential of the marine annelid's toxins and related proteins was tentatively associated with coagulative and anti-inflammatory responses for the peptidases PepM12A, SePr, PepM12B, and PepM13, and with the neurotoxic activity of Crisp, and finally, hyaluronidase was inferred to bear properties of an permeabilizing agent. The in silico analysis succeeded by validation by PCR and Sanger sequencing enabled us to retrieve cDNAs can may be used for the heterologous expression of these toxins.

Transcriptome characteristics of epithelial cells from advanced non-small cell lung cancer were revealed by single-cell RNA sequencing

BACKGROUND

Lung adenocarcinoma (LUAD) is the prevalent malignancy worldwide. The aim is to explore differentially expressed genes (DEGs) associated with immune infiltration and survival time of LUAD patients, and predict transcriptional factors for shedding new light on molecular mechanisms and individual therapy of LUAD.

METHOD

ScRNA-seq data of LUAD patients was downloaded from GSE148071 and analyzed by R packages. The clustering and protein-protein interaction network were constructed for screening DEGs. Gene Set Enrichment Analysis (GSEA) and GO enrichment analysis were performed in epithelial cell subgroups with high differentiation potential. Potential regulatory transcription factors were predicted.

RESULTS

Sixteen epithelial cell types were required and top 20 genes were identified on cell subgroup Epi4 with the highest differentiation potential associated with poor prognosis of LUAD in PPI network. GSEA and GO annotation results showed that cell subgroup Epi4 was enriched in the biological processes of cell proliferation and energy metabolism, and positively regulated the function of cell proliferation. TPI1 was significantly highly expressed in LUAD samples (p < .0001). TPI1 demonstrated a negative correlation with the infiltration levels of CD8+ T cells, CD4+ T cells, B cells, and activated mast cells, whilst manifesting a positive correlation with the infiltration levels of resident mast cells, Th2 cells, and MDSC. Epi4 was regulated by transcription factors MXD3 and GATA4.

CONCLUSION

Overexpression of TPI1 was identified as a novel biomarker for LUAD, and potential regulatory transcription factors MXD3 and GATA4 regulated the proliferation of LUAD with the poor prognosis, which may serve as potential targets to suppress the proliferation of LUAD.

A prognostic model based on regulatory T-cell-related genes in gastric cancer: Systematic construction and validation

Human gastrointestinal tumours have been shown to contain massive numbers of tumour infiltrating regulatory T cells (Tregs), the presence of which are closely related to tumour immunity. This study was designed to develop new Treg-related prognostic biomarkers to monitor the prognosis of patients with gastric cancer (GC). Treg-related prognostic genes were screened from Treg-related differentially expressed genes in GC patients by using Cox regression analysis, based on which a prognostic model was constructed. Then, combined with RiskScore, survival curve, survival status assessment and ROC analysis, these genes were used to verify the accuracy of the model, whose independent prognostic ability was also evaluated. Six Treg-related prognostic genes (CHRDL1, APOC3, NPTX1, TREML4, MCEMP1, GH2) in GC were identified, and a 6-gene Treg-related prognostic model was constructed. Survival analysis revealed that patients had a higher survival rate in the low-risk group. Combining clinicopathological features, we performed univariate and multivariate regression analyses, with results establishing that the RiskScore was an independent prognostic factor. Predicted 1-, 3- and 5-year survival rates of GC patients had a good fit with the actual survival rates according to nomogram results. In addition patients in the low-risk group had higher tumour mutational burden (TMB) values. Gene Set Enrichment Analysis (GSEA) demonstrated that genes in the high-risk group were significantly enriched in pathways related to immune inflammation, tumour proliferation and migration. In general, we constructed a 6-gene Treg-associated GC prognostic model with good prediction accuracy, where RiskScore could act as an independent prognostic factor. This model is expected to provide a reference for clinicians to estimate the prognosis of GC patients.

The developmental gene Chordin is amplified and expressed in human cancers

Chordin (CHRD) is a secreted protein important in early development, yet a role for CHRD in human disease has not been identified. In this study we investigated CHRD in cancer and normal adult tissues using the wealth of genome-wide data available in public databases. We found that Chordin is amplified in the DNA of specific cancers such as lung squamous cell and others, although copy number variation did not strictly correlate with higher mRNA expression. In some cancers, such as renal and stomach carcinomas, increased CHRD expression significantly correlated with poor survival. In normal adult human tissues, CHRD mRNA was highest in hepatocytes. Crossveinless-2/BMPER, a component of the Chordin morphogenetic pathway expressed at the opposite side in embryos, was expressed in liver stellate cells. This raises the intriguing possibility that a BMP gradient might be established in the extracellular matrix of the space of Disse that surrounds portal sinusoid capillaries.

Bioinformatics identify the role of chordin-like 1 in thyroid cancer

The abnormal expression of chordin-like 1 (CHRDL1) is identified in many cancers, while the effect of CHRDL1 in thyroid cancer (THCA) remains unclear. The University of California Santa Cruz, Gene Expression Profiling Interactive Analysis, University of Alabama at Birmingham Cancer, and Gene Expression Omnibus database (GSE33570, GSE33630, and GSE60542) were used for determining the mRNA and methylation expression of CHRDL1 in tumor and normal tissues. Human Protein Atlas was used for exploring the protein expression level of CHRDL1. The genes correlated to CHRDL1 were assessed by cBioPortal database. The prognostic value of CHRDL1 was evaluated through Kaplan-Meier method, cox regression, and nomogram analysis. Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and gene set enrichment analysis were used for predicting potential function of CHRDL1. The relationship between CHRDL1 and immune cell infiltration was determined by Pearson method. The downregulated mRNA and protein expressions of CHRDL1 were identified in THCA through the analysis of data from The Cancer Genome Atlas, Gene Expression Omnibus, and Human Protein Atlas database. The survival analysis showed that the CHRDL1 expression significantly affected disease-free interval (DFI) and progression-free interval, and CHRDL1 was an independent predictor of DFI. Besides, we found that C-C motif chemokine ligand 21 could significantly affect DFI time when it was co-expressed with CHRDL1. Additionally, the function of CHRDL1 was enriched in cell migration, apoptosis, and immune cell receptor. The downregulated expression of CHRDL1 was observed in THCA and caused poor prognosis. CHRDL1 may be involved in signal pathway related to cancer development and immune response, which suggested it could be a potential biomarker.

Chordin-Like 2: A Possible Therapeutic Target for Gastric Cancer by Affecting Cell Cycle and Proliferation

PURPOSE

This study aimed to examine the role of chordin-like 2 (CHRDL2) in gastric cancer.

METHODS

The Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) datasets were screened and the differentially expressed gene CHRDL2 was identified. The CHRDL2 expression was examined in the Human Protein Atlas and TCGA. Clinical data on gastric cancer were evaluated for their association with CHRDL2 by using TCGA and KM-plotter databases. The possible relationship amongst CHRDL2, immune cells, and related genes was investigated via the TIMER database. Enrichment analysis was performed using GO and KEGG pathways to explore the mechanisms.

RESULTS

Screening of databases revealed that CHRDL2 was a differentially expressed gene. An increase in cytoplasmic CHRDL2 expression was found in cancer tissues compared with the surrounding normal tissues. The data, together with those from TCGA and the KM-plotter databases, showed that patients with gastric cancer with high level of CHRDL2 have worse prognosis than those with low expression. A strong correlation was found between CHRDL2 expression and T stage, race, pathological grade, and pathological type according to clinical data analysis. CHRDL2 expression is linked to immune infiltration, as shown by the TIMER database. The data suggested that CHRDL2 plays a pivotal role in the tumor microenvironment of gastric cancer and might help tumor cells evade the immune system. Gene set enrichment analysis showed that CHRDL2 is involved in the chemokine signaling route, the intestinal immune network, the MAPK pathway, cell cycle, and the PI3K-Akt signaling system that are associated with the pathological processes of gastric cancer.

CONCLUSION

Patients with gastric cancer with decreased CHRDL2 levels have dramatically improved OS, PFS, and PPS. CHRDL2 plays a pivotal role in enabling tumor cell immune evasion in tumor microenvironment, suggesting a function of this gene in the development of gastric cancer and its immune infiltration. Interfering with CHRDL2 may slow down the development of this malignancy by affecting cell cycle and apoptosis pathways.

Systematic Analysis and Identification of Molecular Subtypes of TRP-Related Genes and Prognosis Prediction in Lung Adenocarcinoma

Background. Transient receptor potential channel (TRP) is a superfamily of nonselective cation channels, which is a member of calcium ion channels with a vital role in different calcium ion signal transduction pathways. TRP channel expression is often changed in the tumor, although the role of TRP proteins in lung cancer is unknown. Methods. Molecular Signatures Database (MsigDB) provided the TRP gene set. Univariate Cox regression analysis was performed on The Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) data collection set employing the coxph function of R package survival to find prognosis-related genes. The R package ConsumusClusterPlus was employed for doing the consistency cluster analysis of TCGA-LUAD samples according to the prognosis-related TRP gene. The R-package limma was utilized for investigating the differential expression of TRP subtypes. According to the differentially expressed genes between subtypes, the least absolute shrinkage and selection operator (LASSO) regression was employed to find the major genes and develop the risk model. CIBERPORT algorithm, R package maftools, gene set variation analysis (GSVA), and pRRophetic of R-package were employed for measuring the proportion of immune cells among subtypes, genomic mutation difference, pathway enrichment score, and drug sensitivity analysis. Results. A total of 15 TRP-related genes associated with the prognosis of lung adenocarcinoma were found. According to the expression value of 15 genes, lung adenocarcinoma can be sorted into two subcategories. The prognosis of cluster1 is considerably better in comparison with that of cluster2. There were 123 differentially expressed genes between C1 and C2 subtypes, including 6 up- and 117 downregulated genes. There were major variations in the tumor microenvironment between C1 and C2 subtypes. The proportion of CD8 T cells in the C1 subtype was considerably enhanced in comparison with that in the C2 subtype. We further discovered 123 differentially expressed genes among subtypes, and 8 key genes were obtained at the end. The risk score (RS) model developed by the 8-gene signature had good strength in the TCGA validation set, overall set, and Gene Expression Omnibus (GEO) external dataset. There were major variations in immune checkpoint gene expression, patient sensitivity to immunotherapeutic drugs, immune infiltration, and genomic mutations between high and low groups on the basis of RS. Conclusions. The risk model developed on the basis of TRP-related genes can help in predicting the prognosis of patients suffering from lung adenocarcinoma and guide immunotherapy.

Identification of Potential Prognostic Biomarkers Associated with Monocyte Infiltration in Lung Squamous Cell Carcinoma

The five-year survival rate of lung squamous cell carcinoma is significantly lower than that of other cancer types. It is therefore urgent to discover novel prognosis biomarkers and therapeutic targets and understand their correction with infiltrating immune cells to improve the prognosis of patients with lung squamous cell carcinoma. In this study, we employed robust rank aggregation algorithms to overcome the shortcomings of small sizes and potential bias in each Gene Expression Omnibus dataset of lung squamous cell carcinoma and identified 513 robust differentially expressed genes including 220 upregulated and 293 downregulated genes from six microarray datasets. Functional enrichment analysis showed that these robust differentially expressed genes were obviously involved in the extracellular matrix and structure organization, epidermis development, cell adhesion molecule binding, p53 signaling pathway, and interleukin-17 signaling pathway to affect the progress of lung squamous cell carcinoma. We further identified six hub genes from 513 robust differentially expressed genes by protein-protein interaction network and 10 topological analyses. Moreover, the results of immune cell infiltration analysis from six integrated Gene Expression Omnibus datasets and our sequencing transcriptome data demonstrated that the abundance of monocytes was significantly lower in lung squamous cell carcinoma compared to controls. Immune correlation analysis and survival analysis of hub genes suggested that three hub genes, collagen alpha-1(VII) chain, mesothelin, and chordin-like protein 1, significantly correlated with tumor-infiltrating monocytes as well as may be potential prognostic biomarkers and therapy targets in lung squamous cell carcinoma. The investigation of the correlation of hub gene markers and infiltrating monocytes can also improve to well understand the molecular mechanisms of lung squamous cell carcinoma development.

Chordin-Like 1 Regulates Epithelial-to-Mesenchymal Transition and Metastasis via the MAPK Signaling Pathway in Oral Squamous Cell Carcinoma

Background

Accumulating evidence suggests that dysregulation of Chordin-like 1 (CHRDL1) is associated with malignant biological behaviors in multiple cancers. However, the exact function and molecular mechanism of CHRDL1 in oral squamous cell carcinoma (OSCC) remain unclear.

Methods

The expression levels of CHRDL1 in OSCC tissues and CAL27 cells were determined by RT-qPCR. Immunohistochemical staining was applied to detect CHRDL1 protein expression in sample tissues from OSCC patients. Gain of function and knockdown by lentivirus were further used to examine the effects of CHRDL1 on cell proliferation, migration, invasion, and adhesion in OSCC. Tail vein injection of CAL27 cells with dysregulated CHRDL1 expression was further used to examine the effect of CHRDL1 on lung colonization. RNA sequencing was performed to explore the molecular mechanisms of CHRDL1 that underlie the progression of OSCC.

Results

CHRDL1 was significantly downregulated in OSCC tissues and CAL27 cells compared to controls. CHRDL1 knockdown enhanced migration, invasion, adhesion, and EMT, but not proliferation, in CAL27 cells. Overexpression of CHRDL1 had the opposite effects. Moreover, CHRDL1 was proven to inhibit tumor metastasis in vivo. Mechanistically, MAPK signaling pathway components, including ERK1/2, p38, and JNK, were found to regulate the malignant biological behaviors of CAL27 cells.

Conclusions

Our results suggest that CHRDL1 has an inhibitory effect on OSCC metastasis via the MAPK signaling pathway, which provides a new possible potential therapeutic target against OSCC.