LAMC1 is a prognostic factor and a potential therapeutic target in endometrial cancer

Exploring the promise of regulator of G Protein Signaling 20: insights into potential mechanisms and prospects across solid cancers and hematological malignancies

RGS (Regulator of G protein signaling) proteins have long captured the fascination of researchers due to their intricate involvement across a wide array of signaling pathways within cellular systems. Their diverse and nuanced functions have positioned them as continual subjects of scientific inquiry, especially given the implications of certain family members in various cancer types. Of particular note in this context is RGS20, whose clinical relevance and molecular significance in hepatocellular carcinoma we have recently investigated. These investigations have prompted questions into the prevalence of pathogenic mutations within the RGS20 gene and the intricate network of interacting proteins that could contribute to the complex landscape of cancer biology. In our study, we aim to unravel the mutations within the RGS20 gene and the multifaceted interplay between RGS20 and other proteins within the context of cancer. Expanding on this line of inquiry, our research is dedicated to uncovering the intricate mechanisms of RGS20 in various cancers. In particular, we have redirected our attention to examining the role of RGS20 within hematological malignancies, with a specific focus on multiple myeloma and follicular lymphoma. These hematological cancers hold significant promise for further investigation, as understanding the involvement of RGS20 in their pathogenesis could unveil novel therapeutic strategies and treatment avenues. Furthermore, our exploration has extended to encompass the latest discoveries concerning the potential involvement of RGS20 in diseases affecting the central nervous system, thereby broadening the scope of its implications beyond oncology to encompass neurobiology and related fields.

Circ_100549 promotes tumor progression in lung adenocarcinoma through upregulation of BIRC6

Lung adenocarcinoma (LUAD) is a subtype of lung cancer with high incidence and mortality globally. Emerging evidence suggests that circular RNAs (circRNAs) exert critical functions in human cancers, including LUAD. CircRNA_100549 (circ_100549) has been reported to be significantly upregulated in non-small cell lung cancer (NSCLC) samples, while its role in modulating LUAD progression remains to be explored. The current study aims at investigating the functional roles of circ_100549 in LUAD and its downstream molecular mechanism. First, we found that the expression of circ_100549 was higher in LUAD cell lines. Loss-of-function assays verified that depletion of circ_100549 repressed LUAD cell proliferation but accelerated cell apoptosis. Furthermore, in vivo experiments demonstrated that silencing of circ_100549 suppressed tumor growth. Subsequently, based on database analysis, we carried out a series of experiments to explore the mechanisms and effects of circ_100549 underlying LUAD progression, including RNA-binding protein immunoprecipitation (RIP), RNA/DNA pull-down, luciferase reporter, and chromatin immunoprecipitation (ChIP) assays. The results indicated that circ_100549 serves as a ceRNA by sponging miR-95-5p to upregulate BPTF expression, thus upregulating BIRC6 expression at a transcriptional level in LUAD. In summary, our study demonstrated that circ_100549 facilitates LUAD progression by upregulating BIRC6 expression.

HIF-1α-mediated LAMC1 overexpression is an unfavorable predictor of prognosis for glioma patients: evidence from pan-cancer analysis and validation experiments

BACKGROUND

Laminin subunit gamma-1 (LAMC1) is a major extracellular matrix molecule involved in the tumor microenvironment. Knowledge of the biological features and clinical relevance of LAMC1 in cancers remains limited.

METHODS

We conducted comprehensive bioinformatics analysis of LAMC1 gene expression and clinical relevance in pan-cancer datasets of public databases and validated LAMC1 expression in glioma tissues and cell lines. The association and regulatory mechanism between hypoxia inducible factor-1α (HIF-1α) and LAMC1 expression were explored.

RESULTS

LAMC1 expression in most cancers in The Cancer Genome Atlas (TCGA) including glioma was significantly higher than that in normal tissues, which had a poor prognosis and were related to various clinicopathological features. Data from the Chinese Glioma Genome Atlas also showed high expression of LAMC1 in glioma associated with poor prognoses. In clinical glioma tissues, LAMC1 protein was highly expressed and correlated to poor overall survival. LAMC1 knockdown in Hs683 glioma cells attenuated cell proliferation, migration, and invasion, while overexpression of LAMC1 in U251 cells leads to the opposite trend. Most TCGA solid cancers including glioma showed enhancement of HIF-1α expression. High HIF-1α expression leads to adverse prognosis in gliomas, besides, HIF-1α expression was positively related to LAMC1. Mechanistically, HIF-1α directly upregulated LAMC1 promotor activity. Hypoxia (2% O2)-treated Hs683 and U251 cells exhibited upregulated HIF-1α and LAMC1 expression, which was significantly attenuated by HIF-1α inhibitor YC-1 and accompanied by attenuated cell proliferation and invasion.

CONCLUSIONS

High expression of LAMC1 in some solid tumors including gliomas suggests a poor prognosis. The hypoxic microenvironment in gliomas activates the HIF-1α/LAMC1 signaling, thereby promoting tumor progression. Targeted intervention on the HIF-1α/LAMC1 signaling attenuates cell growth and invasion, suggesting a new strategy for glioma treatment.

CCDC58 is a potential biomarker for diagnosis, prognosis, immunity, and genomic heterogeneity in pan-cancer

Coiled-coil domain-containing 58 (CCDC58) is a member of the CCDC protein family. Similar to other members, CCDC58 exhibits potential tumorigenic roles in a variety of malignancies. However, there is no systematic and comprehensive pan-cancer analysis to investigate the diagnosis, prognosis, immune infiltration, and other related functions of CCDC58. We used several online websites and databases, such as TCGA, GTEx, UALCAN, HPA, CancerSEA, BioGRID, GEPIA 2.0, TIMER 2.0, and TISIDB, to extract CCDC58 expression data and clinical data of patients in pan-cancer. Then, the relationship between CCDC58 expression and diagnosis, prognosis, genetic alterations, DNA methylation, genomic heterogeneity, and immune infiltration level were determined. In addition, the biological function of CCDC58 in liver hepatocellular carcinoma (LIHC) was investigated. Pan-cancer analysis results showed that CCDC58 was differentially expressed in most tumors and showed excellent performance in diagnosis and prediction of prognosis. The expression of CCDC58 was highly correlated with genetic alterations, DNA methylation, and genomic heterogeneity in some tumors. In addition, the correlation analysis of CCDC58 with the level of immune infiltration and immune checkpoint marker genes indicated that CCDC58 might affect the composition of the tumor immune microenvironment. Enrichment analysis showed that CCDC58-related genes were mainly linked to mitosis, chromosome, and cell cycle. Finally, biological function experiments demonstrated that CCDC58 plays an important role in tumor cell proliferation and migration. CCDC58 was first identified as a pan-cancer biomarker. It may be used as a potential therapeutic target to improve the prognosis of patients in the future.

Comprehensive pan-cancer analysis reveals CCDC58 as a carcinogenic factor related to immune infiltration

CCDC58, a member of the CCDC protein family, has been primarily associated with the malignant progression of hepatocellular carcinoma (HCC) and breast cancer, with limited research conducted on its involvement in other tumor types. We aimed to assess the significance of CCDC58 in pan-cancer. We utilized the TCGA, GTEx, and UALCAN databases to perform the differential expression of CCDC58 at both mRNA and protein levels. Prognostic value was evaluated through univariate Cox regression and Kaplan-Meier methods. Mutation and methylation analyses were conducted using the cBioPortal and SMART databases. We identified genes interacting with and correlated to CCDC58 through STRING and GEPIA2, respectively. Subsequently, we performed GO and KEGG enrichment analyses. To gain insights into the functional status of CCDC58 at the single-cell level, we utilized CancerSEA. We explored the correlation between CCDC58 and immune infiltration as well as immunotherapy using the ESTIMATE package, TIMER2.0, TISIDB, TIDE, TIMSO, and TCIA. We examined the relationship between CCDC58 and tumor heterogeneity, stemness, DNA methyltransferases, and MMR genes. Lastly, we constructed a nomogram based on CCDC58 in HCC and investigated its association with drug sensitivity. CCDC58 expression was significantly upregulated and correlated with poor prognosis across various tumor types. The mutation frequency of CCDC58 was found to be increased in 25 tumors. We observed a negative correlation between CCDC58 expression and the methylation sites in the majority of tumors. CCDC58 showed negative correlations with immune and stromal scores, as well as with NK T cells, Tregs, CAFs, endothelial cells, and immunomodulators. Its value in immunotherapy was comparable to that of tumor mutational burden. CCDC58 exhibited positive correlations with tumor heterogeneity, stemness, DNA methyltransferase genes, and MMR genes. In HCC, CCDC58 was identified as an independent risk factor and demonstrated potential associations with multiple drugs. CCDC58 demonstrates significant clinical value as a prognostic marker and indicator of immune response across various tumor types. Its comprehensive analysis provides insights into its potential implications in pan-cancer research.

Construction and Validation of a Prognostic Model Based on Pyroptosis-related Genes in Bladder Cancer

BACKGROUND

Bladder cancer (BCa) is a highly prevalent disease with a poor prognosis. There is no better forecasting method for it yet. Current studies demonstrate that pyroptosis is involved in the development and progression of various cancers.

METHODS

This study employed bioinformatics techniques to analyze the data of BCa patients obtained from the TCGA and GEO databases in order to construct a prognostic risk model. The TCGA dataset was used for the training set, and the multiple external datasets (including GSE13507, GSE31684, GSE48075, IMvigor210, and GSE32894) were applied as the validation sets. Prognostic-associated pyroptosis genes screened by univariate Cox regression analysis were utilized to construct the lasso Cox regression model. GO and KEGG analysis results identified the selected genes that are primarily involved in the inflammation and cell death processes. The related patients were grouped into low- and high-risk groups. Kaplan-Meier survival analysis was performed to compare survival differences between the risk groups. The accuracy of this risk prediction model was assessed by ROC. We also applied the Human Protein Atlas (HPA) to detect the protein expression of these genes. Subsequently, qRT-PCR was performed to verify the expression of these model genes.

RESULTS

There are 29 pyroptosis-related genes with significant expression differences between BCa and corresponding adjacent tissues, and 11 genes (SH2D2A, CHMP4C, MRFAP1L1, GBP2, EHBP1, RAD9A, ANXA1, TMEM109, HEYL, APOL2, ORMDL1) were picked by univariate and LASSO Cox regression analysis. Immunological cell infiltration and ssGSEA results further indicated that the low and high-risk groups were substantially correlated with the immune status of BCa patients. According to TCGA and multiple external datasets, Kaplan-Meier survival curves showed the overall survival rate of the high-risk group to be decreased. ROC curves showed the model established to be accurate and reliable. Moreover, the HPA database also demonstrated the verification of the modeled genes' expression in BCa and normal bladder tissue using the HPA database. qRT-PCR results also suggested the up-regulated EHBP1 and down-regulated RAD9A mRNA expression levels to be confirmed in 15 pairs of BCa and corresponding adjacent tissues.

CONCLUSION

This study presents the development and validation of a novel gene signature associated with pyroptosis, which holds the potential for predicting patient outcomes in BCa and providing insights into the immune microenvironment of BCa.

Circ_0124208 Promotes the Progression of Hepatocellular Carcinoma by Regulating the miR-338-3p/LAMC1 Axis

Hundreds of circular RNAs (circRNAs) have been identified as key regulators in biological processes; however, only few of these circRNAs have been functionally described to participate in the development of hepatocellular carcinoma (HCC). The present study aimed to reveal the function and molecular mechanisms of circ_0124208 in HCC. Real-time quantitative PCR revealed the upregulation of circ_0124208 in HCC tissues and cells. Based on cell functional experiments, silencing circ_0124208 attenuated proliferation and migration, but boosted the apoptosis of Hep 3B and Huh7 cells in vitro. The in vivo experiment further validated the repression of tumor growth via circ_0124208 knockdown. RNA immunoprecipitation and dual-luciferase reporter assays showed that circ_0124208 sponged miR-338-3p and reduced its expression. miR-338-3p inhibition was found to partially reverse the tumor-suppressive effects caused by circ_0124208 in Hep 3B and Huh7 cells. Furthermore, miR-338-3p directly targeted laminin subunit gamma 1 (LAMC1). The malignancy of Hep 3B and Huh7 cell was decreased by LAMC1 knockdown, and this effect was mitigated by miR-338-3p suppression. Overall, circ_0124208 was demonstrated for the first time to play a crucial role as an oncogene in HCC, implying that it could be a useful biomarker for HCC diagnosis. Furthermore, the circ_0124208/miR-338-3p/LAMC1 axis can be used as a potential therapeutic target for HCC treatment.

LncRNA SNHG6 role in clinicopathological parameters in cancers

RNA sequencing has revealed that a substantial portion of the human genome undergoes transcription, yet a minimal fraction of these transcripts translates into proteins. LncRNAs, RNA molecules less than 200 nt in length, once deemed as transcriptional noise, have now emerged as crucial regulators of numerous cellular processes. This review focuses on the lncRNA SNHG6, aiming to elucidate its biogenesis, the pivotal roles it plays, and its mechanisms in facilitating the hallmarks of cancer. A comprehensive literature review and analysis were undertaken to delve into the biogenesis of SNHG6, its roles in cellular processes, and the mechanisms through which it contributes to the hallmarks of cancer. SNHG6 is a notable lncRNA, observed to be overexpressed in various cancer types; its perturbation has been linked to tumor progression, emphasizing its significance in oncogenesis. This lncRNA contributes to a range of cellular aberrations, influencing transcriptional, post-transcriptional, and epigenetic processes of mRNA, ultimately driving cancerous transformations. LncRNA SNHG6 serves as a potential biomarker and therapeutic target due to its association with tumorigenesis. Understanding its mechanism and role in cancer can pave the way for novel diagnostic and therapeutic strategies.

Deep learning of 2D-Restructured gene expression representations for improved low-sample therapeutic response prediction

Clinical outcome prediction is important for stratified therapeutics. Machine learning (ML) and deep learning (DL) methods facilitate therapeutic response prediction from transcriptomic profiles of cells and clinical samples. Clinical transcriptomic DL is challenged by the low-sample sizes (34-286 subjects), high-dimensionality (up to 21,653 genes) and unordered nature of clinical transcriptomic data. The established methods rely on ML algorithms at accuracy levels of 0.6-0.8 AUC/ACC values. Low-sample DL algorithms are needed for enhanced prediction capability. Here, an unsupervised manifold-guided algorithm was employed for restructuring transcriptomic data into ordered image-like 2D-representations, followed by efficient DL of these 2D-representations with deep ConvNets. Our DL models significantly outperformed the state-of-the-art (SOTA) ML models on 82% of 17 low-sample benchmark datasets (53% with >0.05 AUC/ACC improvement). They are more robust than the SOTA models in cross-cohort prediction tasks, and in identifying robust biomarkers and response-dependent variational patterns consistent with experimental indications.

NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1

PURPOSE

Gliomas and their surrounding microenvironment constantly interact to promote tumorigenicity, yet the underlying posttranscriptional regulatory mechanisms that govern this interplay are poorly understood.

METHODS

Utilizing our established PAC-seq approach and PolyAMiner bioinformatic analysis pipeline, we deciphered the NUDT21-mediated differential APA dynamics in glioma cells.

RESULTS

We identified LAMC1 as a critical NUDT21 alternative polyadenylation (APA) target, common in several core glioma-driving signaling pathways. qRT-PCR analysis confirmed that NUDT21-knockdown in glioma cells results in the preferred usage of the proximal polyA signal (PAS) of LAMC1. Functional studies revealed that NUDT21-knockdown-induced 3'UTR shortening of LAMC1 is sufficient to cause translational gain, as LAMC1 protein is upregulated in these cells compared to their respective controls. We demonstrate that 3'UTR shortening of LAMC1 after NUDT21 knockdown removes binding sites for miR-124/506, thereby relieving potent miRNA-based repression of LAMC1 expression. Remarkably, we report that the knockdown of NUDT21 significantly promoted glioma cell migration and that co-depletion of LAMC1 with NUDT21 abolished this effect. Lastly, we observed that LAMC1 3'UTR shortening predicts poor prognosis of low-grade glioma patients from The Cancer Genome Atlas.

CONCLUSION

This study identifies NUDT21 as a core alternative polyadenylation factor that regulates the tumor microenvironment through differential APA and loss of miR-124/506 inhibition of LAMC1. Knockdown of NUDT21 in GBM cells mediates 3'UTR shortening of LAMC1, contributing to an increase in LAMC1, increased glioma cell migration/invasion, and a poor prognosis.

Hsa_circ_0005085 may suppress cutaneous squamous cell carcinoma growth and metastasis through targeting the miR-186-5p/LAMC1 axis

BACKGROUND

Cutaneous squamous cell carcinoma (CSCC) is a severe malignancy derived from the skin. Mounting evidence suggests that circular RNAs (circRNAs) participate in diverse biological functions in human cancers, containing CSCC. However, the biological functions and underlying mechanism of hsa_circ_0005085 in CSCC have not been clearly studied.

METHODS

Expression levels of hsa_circ_0005085, microRNA-186-5p (miR-186-5p), and Laminin subunit gamma 1 (LAMC1) were detected by reverse transcription-quantitative polymerase chain reaction. Cell counting kit-8 assay, colony formation assay, and 5-Ethynyl-2'-deoxyuridine assay were used to assess cell proliferation. Transwell assay was conducted to detect cell migration and invasion. Cell apoptosis was analyzed by flow cytometry. Protein expression of LAMC1, E-cadherin, Snail, and slug were assessed using western blot assay. Using bioinformatics software, the binding between miR-186-5p and hsa_circ_0005085 or LAMC1 was predicted, followed by verification using a dual-luciferase reporter and RNA-Immunoprecipitation. The mouse xenograft model was established to investigate the role of hsa_circ_0005085 in vivo.

RESULTS

Hsa_circ_0005085 level was downregulated in CSCC tissues and cells. Overexpression of hsa_circ_0005085 inhibited cell proliferation, migration, invasion, epithelial-mesenchymal transition (EMT), and promoted cell apoptosis in CSCC. MiR-186-5p could restore the effect of hsa_circ_0005085 overexpression on CSCC cells, and the knockdown of LAMC1 reversed the regulation of the miR-186-5p inhibitor. In mechanism, hsa_circ_0005085 served as a sponge for miR-186-5p to regulate LAMC1 expression. Overexpression of hsa_circ_0005085 reduced growth of tumor via miR-186-5p/LAMC1 axis in vivo.

CONCLUSION

In our study, hsa_circ_0005085 might inhibit CSCC development by targeting the miR-186-5p/LAMC1 axis, which might provide a promising therapeutic target for CSCC.

EPRS1 correlates with malignant progression in hepatocellular carcinoma

BACKGROUND

Glutamyl-prolyl-tRNA synthetase 1 (EPRS1) is an aminoacyl-tRNA synthase involved in the pathology of cancer and other diseases. In this study, we investigated the carcinogenic function, potential mechanism, and clinical significance of EPRS1 in human hepatocellular carcinoma (HCC).

METHODS

The expression, clinical significance, and prognostic value of EPRS1 in HCC were assessed using the TCGA and GEO databases. The function of EPRS1 in HCC cells was detected by CCK-8, Transwell, and hepatosphere formation assays. Immunohistochemistry was used to explore the difference in EPRS1 levels in HCC tissues and peri-cancerous tissues. The mechanism of EPRS1 was studied using a proteomics method. Finally, cBioportal and MEXEPRSS were used to analyze the variations involved in the differential expression of EPRS1.

RESULTS

EPRS1 was frequently upregulated at the mRNA and protein levels in liver cancer. Increased EPRS1 correlated with shortened patient survival. EPRS1 could promote cancer cell proliferation, characteristics of cell stemness, and mobility. Mechanistically, EPRS1 played a carcinogenic role by upregulating several downstream proline-rich proteins, primarily LAMC1 and CCNB1. In addition, copy number variation could contribute to the high expression of EPRS1 in liver cancer.

CONCLUSION

Together, our data imply that enhanced EPRS1 contributes to the development of HCC by increasing the expression of oncogenes in the tumor microenvironment. EPRS1 may be a successful treatment target.

Automatic Text-Mining Approach to Identify Molecular Target Candidates Associated with Metabolic Processes for Myotonic Dystrophy Type 1

Myotonic dystrophy type 1 (DM1) is an autosomal dominant hereditary disease caused by abnormal expansion of unstable CTG repeats in the 3' untranslated region of the myotonic dystrophy protein kinase (DMPK) gene. This disease mainly affects skeletal muscle, resulting in myotonia, progressive distal muscle weakness, and atrophy, but also affects other tissues and systems, such as the heart and central nervous system. Despite some studies reporting therapeutic strategies for DM1, many issues remain unsolved, such as the contribution of metabolic and mitochondrial dysfunctions to DM1 pathogenesis. Therefore, it is crucial to identify molecular target candidates associated with metabolic processes for DM1. In this study, resorting to a bibliometric analysis, articles combining DM1, and metabolic/metabolism terms were identified and further analyzed using an unbiased strategy of automatic text mining with VOSviewer software. A list of candidate molecular targets for DM1 associated with metabolic/metabolism was generated and compared with genes previously associated with DM1 in the DisGeNET database. Furthermore, g:Profiler was used to perform a functional enrichment analysis using the Gene Ontology (GO) and REAC databases. Enriched signaling pathways were identified using integrated bioinformatics enrichment analyses. The results revealed that only 15 of the genes identified in the bibliometric analysis were previously associated with DM1 in the DisGeNET database. Of note, we identified 71 genes not previously associated with DM1, which are of particular interest and should be further explored. The functional enrichment analysis of these genes revealed that regulation of cellular metabolic and metabolic processes were the most associated biological processes. Additionally, a number of signaling pathways were found to be enriched, e.g., signaling by receptor tyrosine kinases, signaling by NRTK1 (TRKA), TRKA activation by NGF, PI3K-AKT activation, prolonged ERK activation events, and axon guidance. Overall, several valuable target candidates related to metabolic processes for DM1 were identified, such as NGF, NTRK1, RhoA, ROCK1, ROCK2, DAG, ACTA, ID1, ID2 MYOD, and MYOG. Therefore, our study strengthens the hypothesis that metabolic dysfunctions contribute to DM1 pathogenesis, and the exploitation of metabolic dysfunction targets is crucial for the development of future therapeutic interventions for DM1.

LncRNA TM4SF19-AS1 exacerbates cell proliferation, migration, invasion, and EMT in head and neck squamous cell carcinoma via enhancing LAMC1 expression

Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous and aggressive tumor with high mortality and unfavorable prognosis. Numerous long non-coding RNAs (lncRNAs) have been confirmed to exert pivotal parts in cancers. Nevertheless, the functions of most lncRNAs in HNSCC need deeper exploration. Our present research tried to clarify the biological role of TM4SF19 antisense RNA 1 (TM4SF19-AS1) and investigate its regulatory mechanism in HNSCC. RT-qPCR analysis was done to test TM4SF19-AS1 expression and identify the up-regulation of TM4SF19-AS1 in HNSCC cells. Loss-of-function assays were also involved, and the data implied that TM4SF19-AS1 knockdown hampered the proliferation, migration, invasion, along with epithelial-mesenchymal transition (EMT) of HNSCC cells. In vivo assays revealed TM4SF19-AS1 depletion restrained HNSCC tumor growth. Additionally, mechanism experiments were implemented to uncover the underlying regulatory mechanism of TM4SF19-AS1 in HNSCC cells. It turned out that TM4SF19-AS1 modulated laminin subunit gamma 1 (LAMC1) expression via sequestering microRNA-153-3p (miR-153-3p) and recruiting heterogeneous nuclear ribonucleoprotein C (HNRNPC) protein. Rescue assays confirmed that TM4SF19-AS1 contributed to HNSCC cell malignant behaviors via up-regulating LAMC1. To summarize, TM4SF19-AS1 played an oncogenic role in HNSCC cells, signifying TM4SF19-AS1 may have the potential to be used as a novel molecular target for HNSCC diagnosis.

Construction of a transcription factor-miRNA-mRNA interactive network elucidates underlying pathogenesis for osteosarcoma and validation by qRT-PCR

PURPOSE

Osteosarcoma is characterized by features of rapid growth and early metastasis with a poor prognosis. The aim of our research is to investigate the potential transcription factor (TF)-miRNA-mRNA regulatory mechanism in osteosarcoma utilizing bioinformatics methods and validate by qRT-PCR.

METHODS

The microRNA (miRNA) expression profiling datasets (GSE28423 and GSE65071) and mRNA expression profiling dataset GSE33382 were collected from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs) were screened using the limma package. Then, the TransmiR v2.0, miRDB, and Targetscan 7.2 database were applied for the acquisition of TF-miRNA and miRNA-mRNA interaction relationships, respectively. Finally, we built a TF-miRNA-mRNA interactive network. Furthermore, survival analysis was performed to identify sub-network with prognostic value and validate through qRT-PCR.

RESULTS

Eight overlapping DEMs and 682 DEGs were identified. Based on bioinformatics methods, 30 TF-miRNA interaction pairs and 25 miRNA-mRNA interaction pairs were screened. Finally, we constructed a TF-miRNA-mRNA regulatory network. Furthermore, laminin subunit gamma 1 (LAMC1) and thrombospondin-1 (THBS1), which involved in the network, were determined to have prognostic value and the corresponding subnetwork was identified. qRT-PCR results showed that LAMC1 mRNA expression was higher in osteosarcoma cells.

CONCLUSION

Based on the survival analysis, a TF-miRNA-mRNA sub-network, that is TFs (SPI1, HEY1, and CEBPB)-hsa-miR-338-3p-target genes (LAMC1 and THBS1) was established. In conclusion, the construction of a potential TF-related regulatory network will help elucidate the underlying pathological mechanisms of osteosarcoma, and may provide novel insights for the diagnosis and treatment of osteosarcoma.

Comprehensive analysis of LAMC1 expression and prognostic value in kidney renal papillary cell carcinoma and clear cell carcinoma

Background: Laminin subunit gamma 1 (LAMC1) protein is associated with tumor cell invasion and metastasis. However, its role in kidney cancer remains unclear. In this work, we sought to probe the expression as well as its carcinogenic mechanisms of LAMC1 in kidney renal papillary cell carcinoma (KIRP) and kidney renal clear cell carcinoma (KIRC).

Methods: Public databases including TIMER, Oncomine, UALCAN, TISIDB, TCGA, Kaplan–Meier plotter, UCSC Xena, cBioPortal, SurvivalMeth, KEGG, GeneMANIA, Metascape, GSCALite and GDSC were adopted, and the expression, clinical pathological correlation, prognostic signatures, dominant factors influencing LAMC1 expression, DNA methylation levels, gene mutations, copy number variations, functional networks, and drug sensitivity were analyzed. Expression of LAMC1 protein in clinical KIRP and KIRC was validated using tissue array.

Results:LAMC1 expression in KIRP and KIRC were significantly higher than those in normal tissues. High LAMC1 expression indicated poor overall survival in KIRP patients and better overall survival in KIRC patients. Through the univariate and multivariate Cox analysis, we found that high LAMC1 expression was a potential independent marker for poor prognosis in KIRP, however it implied a better prognosis in KIRC by univariate Cox analysis. In addition, the LAMC1 expression in KIRP and KIRC was negatively correlated with methylation levels of LAMC1 DNA. Interestingly, LAMC1 expression was positively correlated with the infiltration of CD8⁺ T cells, dendritic cells and neutrophils in KIRP; however, it was positively correlated with the infiltration of CD4⁺ T cells, macrophages and neutrophils but negatively correlated with B cells in KIRC. Moreover, high level of CD8⁺ T cells is beneficial for KIRC prognosis but opposite for KIRP. LAMC1 may participate in signaling pathways involved in formation of adherens junction and basement membrane in KIRP and KIRC, and the high expression of LAMC1 is resistant to most drugs or small molecules of the Genomics of Drug Sensitivity in Cancer database.

Conclusion: Enhanced LAMC1 expression suggests a poor prognosis in KIRP while a better prognosis in KIRC, and these opposite prognostic signatures of LAMC1 may be related to different immune microenvironments.

Comprehensive analysis of tissue proteomics in patients with papillary thyroid microcarcinoma uncovers the underlying mechanism of lymph node metastasis and its significant sex disparities

Background

Lymph node metastasis (LNM) in papillary thyroid microcarcinoma (PTMC) is associated with an increased risk of recurrence and poor prognosis. Sex has been regarded as a critical risk factor for LNM. The present study aimed to investigate the molecular mechanisms underlying LNM and its significant sex disparities in PTMC development.

Methods

A direct data-independent acquisition (DIA) proteomics approach was used to identify differentially expressed proteins (DEPs) in PTMC tumorous tissues with or without LNM and from male and female patients with LNM. The functional annotation of DEPs was performed using bioinformatics methods. Furthermore, The Cancer Genome Atlas Thyroid Carcinoma (TCGA-THCA) dataset and immunohistochemistry (IHC) were used to validate selected DEPs.

Results

The proteomics profile in PTMC with LNM differed from that of PTMC without LNM. The metastasis-related DEPs were primarily enriched in categories associated with mitochondrial dysfunction and may promote tumor progression by activating oxidative phosphorylation and PI3K/AKT signaling pathways. Comparative analyses of these DEPs revealed downregulated expression of specific proteins with well-established links to tumor metastasis, such as SLC25A15, DIRAS2, PLA2R1, and MTARC1. Additionally, the proteomics profiles of male and female PTMC patients with LNM were dramatically distinguishable. An elevated level of ECM-associated proteins might be related to more LNM in male PTMC than in female PTMC patients. The upregulated expression levels of MMRN2 and NID2 correlated with sex disparities and showed a positive relationship with unfavorable variables, such as LNMs and poor prognosis.

Conclusions

The proteomics profiles of PTMC show significant differences associated with LNM and its sex disparities, which further expands our understanding of the functional networks and signaling pathways related to PTMC with LNM.

Unveiling the mechanism of action of nature-inspired anti-cancer compounds using a multi-omics approach

The 2020 global cancer registry has ranked breast cancer (BCa) as the most commonly diagnosed type of cancer and the most common cause of cancer-related deaths in women worldwide. Increasing resistance and significant side effects continue to limit the efficacy of anti-BCa drugs, hence the need to identify new drug targets and to develop novel compounds to overcome these limitations. Nature-inspired anti-cancer compounds are becoming increasingly popular since they often provide a relatively safe and effective alternative. In this study, we employed multi-omics techniques to gain insights into the relevant mechanism of action of two recently identified new nature-inspired anti-cancer compounds (SIMR3066 and SIMR3058). Discovery proteomics analysis combined with LC-MS/MS-based untargeted metabolomics analysis was performed on compound-treated vs DMSO-treated (control) MCF-7 cells. Downstream protein functional enrichment analysis showed that most of the responsive proteins were functionally associated with antigen processing and neutrophil degranulation, RNA catabolism and protein folding as well as cytoplasmic vesicle lumen and mitochondrial matrix formation. Consistent with the proteomics findings, metabolomic pathway analysis suggested that the differentially abundant compounds indicated altered metabolic pathways such as glycolysis, the Krebs cycle and oxidative phosphorylation. Furthermore, metabolomics-based enriched-for-action pathway analysis showed that the two compounds associate with mercaptopurine, thioguanine and azathioprine related pathways. Lastly, integrated proteomics and metabolomics analysis revealed that treatment of BCa with SIMR3066 disrupts several signaling pathways including p53-mediated apoptosis and the circadian entertainment pathway. Overall, the multi-omics approach we used in this study indicated that it is a powerful tool in probing the mechanism of action of lead drug candidates. SIGNIFICANCE: In this study we adopted a multi-omics (proteomics and metabolomics) strategy to learn more about the molecular mechanisms of action of nature-inspired potential anticancer drugs. Following treatment with SIMR3066 or SIMR3058, the integration of these multi-omics data sets revealed which biological pathways are altered in BCa cells. This study demonstrates that combining proteomics with metabolomics is a powerful method to investigate the mechanism of action of potential anticancer lead drug candidates.

Laminin-integrin a6b4 interaction activates notch signaling to facilitate bladder cancer development

Background

Laminins are high-molecular weight (400 ~ 900 kDa) proteins in extracellular matrix, which serve as major component of the basal lamina, and play a crucial role in promoting tumor cell migration. This study aimed at characterizing the role of laminin in promoting cancer development, and elucidating the mechanism of tumor progression driven by laminin-Notch signaling in bladder cancer.

Methods

2D collagen/laminin culture system was established and CCK-8/transwell assay was conducted to evaluate the proliferation/migration ability of Biu-87 and MB49 cells cultured on 2D gels. Activation of integrins-Notch1 signaling was determined by western blotting. Orthotopic bladder cancer mice model was established to assess the therapeutic effects of Notch inhibitor.

Results

Our study demonstrated that extracellular laminin can trigger tumor cell proliferation/migration through integrin α6β4/Notch1 signaling in bladder cancer. Inhibition of Telomere repeat-binding factor 3 (TRB3)/Jagged Canonical Notch Ligand 1 (JAG1) signaling suppressed Notch signals activation induced by laminin-integrin axis. In MB49 orthotopic bladder cancer mice model, Notch inhibitor SAHM1 efficiently improved tumor suppressive effects of chemotherapy and prolonged survival time of tumor-bearing mice.

Conclusion

In conclusion, we show that, in bladder cancer, extracellular laminin induced the activation of Notch pathway through integrin α6β4/TRB3/JAG3, and disclosed a novel role of laminin in bladder cancer cells proliferation or migration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-022-09645-7.

Comprehensive Analysis of a Novel Lipid Metabolism-Related Gene Signature for Predicting the Prognosis and Immune Landscape in Uterine Corpus Endometrial Carcinoma

Lipid metabolism is important in various cancers. However, the association between lipid metabolism and uterine corpus endometrial carcinoma (UCEC) is still unclear. In this study, we collected clinicopathologic parameters and the expression of lipid metabolism-related genes (LMRGs) from the Cancer Genome Atlas (TCGA). A lipid metabolism-related risk model was built and verified. The risk score was developed based on 11 selected LMRGs. The expression of 11 LMRGs was confirmed by qRT-PCR in clinical samples. We found that the model was an independent prediction factor of UCEC in terms of multivariate analysis. The overall survival (OS) of low-risk group was higher than that in the high-risk group. GSEA revealed that MAPK signaling pathway, ERBB signaling pathway, ECM receptor interaction, WNT pathway, and TGF-β signaling pathway were enriched in the high-risk group. Low-risk group was characterized by high tumor mutation burden (TMB) and showed sensitive response to immunotherapy and chemotherapy. In brief, we built a lipid metabolism gene expression-based risk signature which can reflect the prognosis of UCEC patients and their response to chemotherapeutics and immune therapy.

PAQR5 Expression Is Suppressed by TGFβ1 and Associated With a Poor Survival Outcome in Renal Clear Cell Carcinoma

Background

Renal cell carcinoma (RCC) was sex-hormone responsive, and clinical trials using progesterone significantly reduced the incidence of distal metastasis after radical nephrectomy. Recently membrane-bound progesterone receptors (mPRs) were discovered to mediate the non-genomic effect of progesterone. Aberrant expressions of these mPRs were reported in human breast, ovarian, urinary bladder, brain, uterine, and prostate cancers. However, their expression profiles in RCC are yet to be assessed.

Methods

Multiple datasets from RNA sequencing (RNA-seq), cDNA microarray, and proteomic analysis were used to compare gene expression between cancerous and normal kidney tissues. Immunohistochemistry was conducted to examine protein expression in kidney tissues. Promoter methylation levels were assessed for correlation analysis with gene expression.

Results

Of the seven membrane-bound progesterone receptor genes, the progestin and adipoQ receptor-5 (PAQR5) gene is predominantly expressed in normal kidney tissue but was significantly downregulated in RCC tissues. PAQR5 downregulation correlated with tumor stage, cancer grade, lymph node invasion, and distal metastasis only in clear cell RCC (ccRCC) tissues. PAQR5 downregulation was associated with an increased promoter DNA methylation and a poor survival outcome in ccRCC patients. In addition, PAQR5 expression inversely correlated with transforming growth factor beta-1 (TGFB1) expression, and TGFβ1 treatment significantly reduced PAQR5 gene expression.

Conclusion

PAQR5 is a novel prognostic biomarker in ccRCC and is negatively regulated by the TGFβ1 pathway.

The Endoplasmic Reticulum-Stressed Head and Neck Squamous Cell Carcinoma Cells Induced Exosomal miR-424-5p Inhibits Angiogenesis and Migration of Humanumbilical Vein Endothelial Cells Through LAMC1-Mediated Wnt/β-Catenin Signaling Pathway

Under endoplasmic reticulum (ER) stress, tumor plays multifaceted roles in endothelial cell dysfunction through secreting exosomal miRNAs. However, for the head and neck squamous cell carcinoma (HNSCC), it is still unclear about the impact of ER-stressed HNSCC cell derived exosomes on vascular endothelial cells. To address this gap, herein, systemic research was conducted including isolation and characterization of ER-stressed HNSCC cell (HN4 cell line as an in vitro model) derived exosomes, identification of regulatory exosomal miRNAs, target exploration and downstream signaling pathway investigation of exosomal miRNAs in human umbilical vein endothelial cell (HUVEC). ER-stressed HN4 cell-derived exosomes inhibited angiogenesis and migration of HUVEC cells in vitro. Furthermore, RNA-seq analysis demonstrated that miR-424-5p was highly upregulated in ER-stressed HN4 cell-derived exosomes. Through matrigel tube formation and transwell assays of HUVEC cells, miR-424-5p displayed great capabilities on inhibiting angiogenesis and migration. Finally, based on western blot and luciferase reporter, it was demonstrated that LAMC1 is the target of miR-424-5p which could inhibit the angiogenesis and migration of HUVEC cells by repressing the LAMC1-mediated Wnt/β-catenin signaling pathway. ER-stressed HNSCC cell-induced exosomal miR-424-5p inhibits angiogenesis and migration of HUVEC cells through LAMC1-mediated Wnt/β-catenin signaling pathway. This study offers a new insight for understanding the complicated mechanism behind ER-stress induced anti-angiogenesis of HNSCC.

The long non-coding RNA ASMTL-AS1 promotes hepatocellular carcinoma progression by sponging miR-1343-3p that suppresses LAMC1 (laminin subunit gamma 1)

Long non-coding RNAs (lncRNAs) are critical regulators of hepatocellular carcinoma (HCC) carcinogenesis and development. We aimed to identify the function of the lncRNA ASMTL-AS1 during HCC malignancy. The expression of ASMTL-AS1, miR-1343-3p, and LAMC1 (laminin subunit gamma 1) was assessed in HCC tissues and cells. Cell Counting Kit-8 (CCK8) and Transwell migration assays were performed to determine the effect of ASMTL-AS1 on HCC cell proliferation and migration. Cell apoptosis was identified by detecting Bax and Bcl-2 protein expression using Western blotting, and a xenograft assay was performed to investigate tumor growth in vivo. The interplay between miR-1343-3p and ASMTL-AS1 or LAMC1 was verified through luciferase reporter and RNA immunoprecipitation assays. ASMTL-AS1 and LAMC1 were highly expressed in HCC tissues and cells, whereas miR-1343-3p showed low expression. Clinically, miR-1343-3p expression in HCC tissues showed a negative correlation with ASMTL-AS1 or LAMC1 expression. Functional assays demonstrated that ASMTL-AS1 silencing suppressed HCC cell proliferation and migration and increased cell apoptosis. More interestingly, ASMTL-AS1 sponged miR-1343-3p and miR-1343-3p to target the 3'-UTR of LAMC1, thereby interfering with the malignant behavior of HCC cells. In conclusion, ASMTL-AS1 acts as a carcinogen in HCC through competing endogenous RNA (ceRNA) activity in the miR-1343-3p/LAMC1 axis. Our findings demonstrate that regulating ASMTL-AS1/miR-1343-3p/LAMC1-mediated HCC cell malignancy might be an effective method to interfere with HCC progression.

Downregulation of Smad4 expression confers chemoresistance against imatinib mesylate to chronic myeloid leukemia K562 cells

Objective: Imatinib mesylate (IM), a tyrosine kinase inhibitor, exhibits clinically prominent effects against chronic myeloid leukemia (CML); however, a few patients have shown resistance to IM treatment, resulting in disease progression. Smad4 is a tumor inhibitor that transduces TGF-β signaling and modulates genomic stability. Previous studies have indicated that decreased Smad4 expression played a bidirectional role in chemosensitivity in many types of cancers. Therefore, this study aims to evaluate the association between IM sensitivity and decreased Smad4 expression in human CML K562 cells.Methods: Bone marrow (BM) samples were acquired from the patients prior to treatment. qRT-PCR, Western Blotting (WB), colony formation assay (CFA), and apoptosis assay were used to detect relevant indices.Results: Smad4 expression was downregulated in the bone marrow and plasma of patients with multidrug-resistant CML as well as IM-resistant K562 (K562R) cells compared with samples collected from CML patients and K562 cells. Smad4 overexpression inhibited IM-treated K562R cell proliferation and augmented apoptosis, whereas Smad4 silencing promoted viability and inhibited apoptosis in IM-treated K562 cells. In addition, Smad4 expression was inversely correlated with laminin subunit gamma 1 (LAMC1) expression. The upregulation or downregulation of LAMC1 expression partially abolished the effect of Smad4 overexpression or silencing on the IM resistance of CML cells.Conclusion: The downregulation of Smad4 expression might induce drug resistance in CML cells and displayed a possible mechanism through which Smad4 modulates CML cell survival and apoptosis upon IM treatment.

The Epithelial and Stromal Immune Microenvironment in Gastric Cancer: A Comprehensive Analysis Reveals Prognostic Factors with Digital Cytometry

Gastric cancer (GC) is the third leading cause of cancer-related deaths worldwide. Tumor heterogeneity continues to confound researchers' understanding of tumor growth and the development of an effective therapy. Digital cytometry allows interpretation of heterogeneous bulk tissue transcriptomes at the cellular level. We built a novel signature matrix to dissect epithelium and stroma signals using a scRNA-seq data set (GSE134520) for GC and then applied cell mixture deconvolution to estimate diverse epithelial, stromal, and immune cell proportions from bulk transcriptome data in four independent GC cohorts (GSE62254, GSE15459, GSE84437, and TCGA-STAD) from the GEO and TCGA databases. Robust computational methods were applied to identify strong prognostic factors for GC. We identified an EMEC population whose proportions were significantly higher in patients with stage I cancer than other stages, and it was predominantly present in tumor samples but not typically found in normal samples. We found that the ratio of EMECs to stromal cells and the ratio of adaptive T cells to monocytes were the most significant prognostic factors within the non-immune and immune factors, respectively. The STEM score, which unifies these two prognostic factors, was an independent prognostic factor of overall survival (HR = 0.92, 95% CI = 0.89-0.94, p=2.05×10-9). The entire GC cohort was stratified into three risk groups (high-, moderate-, and low-risk), which yielded incremental survival times (p<0.0001). For stage III disease, patients in the moderate- and low-risk groups experienced better survival benefits from radiation therapy ((HR = 0.16, 95% CI = 0.06-0.4, p<0.0001), whereas those in the high-risk group did not (HR = 0.49, 95% CI = 0.14-1.72, p=0.25). We concluded that the STEM score is a promising prognostic factor for gastric cancer.

circRNA circ_POLA2 increases microRNA-31 methylation to promote endometrial cancer cell proliferation

Circular RNA (circRNA) circ_POLA2 is an oncogene in lung and cervical cancers. However, the role of circ_POLA2 in other types of cancer is unknown. The present study investigated the role of circ_POLA2 in endometrial cancer (EC). The mRNA expression levels of circ_POLA2 and microRNA (miR)-31 in EC and paired adjacent normal tissues were analyzed using reverse transcription-quantitative (RT-qPCR). Overexpression of circ_POLA2 was achieved in the EC cell lines, and its effects on miR-31 mRNA expression level and methylation were evaluated using RT-qPCR and methylation-specific PCR (MSP), respectively. Cell proliferation was assessed using a Cell Counting Kit-8 assay. The results indicated that circ_POLA2 was highly expressed in EC tissue and inversely correlated with miR-31 mRNA expression level. MSP analysis showed that circ_POLA2 overexpression increased miR-31 methylation and RT-qPCR analysis showed that circ_POLA2 overexpression decreased miR-31 mRNA expression level. Furthermore, circ_POLA2 overexpression also increased EC cell proliferation, while miR-31 overexpression decreased cell proliferation. Finally, circ_POLA2 overexpression reduced the effects of miR-31 overexpression. In conclusion, circ_POLA2 may increase miR-31 methylation of miR-31 in EC cells to promote cancer cell proliferation.

PAQR6 Upregulation Is Associated with AR Signaling and Unfavorite Prognosis in Prostate Cancers

Progesterone-induced rapid non-genomic signaling events have been confirmed through several membrane progesterone receptors (mPR). Some mPRs were reported to correlate with cancer progression and patient prognosis. In this study, we conducted a comprehensive analysis of all progesterone receptor (PGR)-related genes in prostate cancer tissues and examined the correlations of their expression levels with disease progression and patient survival outcomes. We utilized multiple RNA-seq and cDNA microarray datasets to analyze gene expression profiles and performed logistics aggression and Kaplan-Meier survival analysis after stratifying patients based on tumor stages and Gleason scores. We also used NCBI GEO datasets to examine gene expression patterns in individual cell types of the prostate gland and to determine the androgen-induced alteration of gene expression. Spearman coefficient analysis was conducted to access the correlation of target gene expression with treatment responses and disease progression status. The classic PGR was mainly expressed in stromal cells and progestin and adipoQ receptor (PAQR) genes were the predominant genes in prostate epithelial cells. Progesterone receptor membrane component-1 (PGRMC1) was significantly higher than PGRMC2 in all prostate cell types. In prostate cancer tissues, PAQR6 expression was significantly upregulated, while all other genes were largely downregulated compared to normal prostate tissues. Although both PAQR6 upregulation and PAQR5 downregulation were significantly correlated with tumor pathological stages, only PAQR6 upregulation was associated with Gleason score, free-prostate-specific antigen (fPSA)/total-PSA (tPSA) ratio, and patient overall survival outcomes. In addition, PAQR6 upregulation and PGR/PGRMC1 downregulation were significantly associated with a quick relapse. Conversely, in neuroendocrinal prostate cancer (NEPC) tissues, PAQR6 expression was significantly lower, but PAQR7/8 expression was higher than castration-resistant prostate cancer (CRPC) tissues. PAQR8 expression was positively correlated with androgen receptor (AR) score and AR-V7 expression levels but inversely correlated with NEPC score in metastatic CRPC tumors. This study provides detailed expression profiles of membrane progesterone receptor genes in primary cancer, CRPC, and NEPC tissues. PAQR6 upregulation in primary cancer tissues is a novel prognostic biomarker for disease progression, overall, and progression-free survival in prostate cancers. PAQR8 expression in CRPC tissues is a biomarker for AR activation.

Comprehensive Analysis of the Expression and Prognosis for Laminin Genes in Ovarian Cancer

Survival is low in ovarian cancer (OC). Most OC patients demonstrate advanced metastases, and recurrence is common. Dysregulation of laminin interactions is associated with cancer development. However, it is unknown whether laminin subunits can be considered as biomarkers for OC diagnosis, prognosis, and treatment. We used cBioPortal, GEO, ONCOMINE, GEPIA, Human Protein Atlas, Kaplan-Meier Plotter, TIMER, and Metascape to determine the associations among laminin expression, prognosis, and immune cell infiltration in OC. LAMA5, LAMB3, and LAMC2 mRNAs and LAMA3, LAMB1/B2/B3, and LAMC1/C2 proteins were overexpressed in OC tissues compared with normal ovaries. LAMA4, LAMB1, and LAMC1 mRNA upregulation was positively correlated with worse overall survival (OS) and progression-free survival (PFS) in OC. Elevated LAMA2 and LAMC2 mRNA expression levels were related to better PFS or OS, respectively. The results speculated that LAMA5 could potentially be a good prognostic factor in OC. Its expression proves valuable for predicting OS in patients diagnosed with stage Ⅳ and grade 3 OC and PFS in patients diagnosed with all OC stages or grades. LAMB3 and LAMC2 expression was correlated with platinum resistance development. ROC analysis of laminins in OC sets revealed that LAMA2/A4/A5, LAMB1/B2/B3, and LAMC2 could be used to differentiate between malignant tumors and non-neoplastic tissues. LAMA1/A5 and LAMC1 were significantly and negatively correlated with various tumor immune infiltrates (TILs), especially with dendritic cells, CD8⁺ T cells or neutrophil. LAMA4 and LAMB1 might be associated with tumor purity in OC. Overall, LAMA5 and LAMC1 could help predict OC survival and diagnosis and might be deemed important OC oncogenes.

LAMC1 upregulation via TGFβ induces inflammatory cancer-associated fibroblasts in esophageal squamous cell carcinoma via NF-κB-CXCL1-STAT3

Cancer‐associated fibroblasts (CAF) are a heterogeneous cell population within the tumor microenvironment,and play an important role in tumor development. By regulating the heterogeneity of CAF, transforming growth factor β (TGFβ) influences tumor development. Here, we explored oncogenes regulated by TGFβ1 that are also involved in signaling pathways and interactions within the tumor microenvironment. We analyzed sequencing data of The Cancer Genome Atlas (TCGA) and our own previously established RNA microarray data (GSE53625), as well as esophageal squamous cell carcinoma (ESCC) cell lines with or without TGFβ1 stimulation. We then focused on laminin subunit gamma 1 (LAMC1), which was overexpressed in ESCC cells, affecting patient prognosis, which could be upregulated by TGFβ1 through the synergistic activation of SMAD family member 4 (SMAD4) and SP1. LAMC1 directly promoted the proliferation and migration of tumor cells, mainly via Akt–NFκB–MMP9/14 signaling. Additionally, LAMC1 promoted CXCL1 secretion, which stimulated the formation of inflammatory CAF (iCAF) through CXCR2–pSTAT3. Inflammatory CAF promoted tumor progression. In summary, we identified the dual mechanism by which the upregulation of LAMC1 by TGFβ in tumor cells not only promotes ESCC proliferation and migration, but also indirectly induces carcinogenesis by stimulating CXCL1 secretion to promote the formation of iCAF. This finding suggests that LAMC1 could be a potential therapeutic target and prognostic marker for ESCC.

Infiltrating T-cell abundance combined with EMT-related gene expression as a prognostic factor of colon cancer

EMT-related gene expression reportedly exhibits correlation with the anti-tumor immunity of T cells. In the present study, we explored the factors that might affect the efficacy of immunotherapy in colon cancer with treatment. In this regard, RNA-seq and clinical data of 469 colon cancer samples derived from the Cancer Genome Atlas (TCGA) database were used to calculate infiltrating T-cell abundance (ITA), to illustrate a pathway enrichment analysis, and to construct Cox proportional hazards (CPH) regression models. Subsequently, the RNA-seq and clinical data of 177 colon cancer samples derived from the GSE17536 cohort were used to validate the CPH regression models. We found that ITA showed correlation with EMT-related gene expression, and that it was not an independent prognostic factor for colon cancer. However, upon comparison of two groups with the same ITA, higher EMT expression helped predicted a worse prognosis, whereas a higher ITA could help predict a better prognosis upon comparison of two groups with the same EMT. Additionally, seven genes were found to be statistically related to the prognosis of patients with colon cancer. These results suggest that the balance between ITA and EMT-related gene expression is conducive to the prognosis of patients with colon cancer, and TPM1 is necessary to further explore the common target genes of immune checkpoint blockade.

Molecular and Metabolic Reprogramming: Pulling the Strings Toward Tumor Metastasis

Metastasis is a major hurdle to the efficient treatment of cancer, accounting for the great majority of cancer-related deaths. Although several studies have disclosed the detailed mechanisms underlying primary tumor formation, the emergence of metastatic disease remains poorly understood. This multistep process encompasses the dissemination of cancer cells to distant organs, followed by their adaptation to foreign microenvironments and establishment in secondary tumors. During the last decades, it was discovered that these events may be favored by particular metabolic patterns, which are dependent on reprogrammed signaling pathways in cancer cells while they acquire metastatic traits. In this review, we present current knowledge of molecular mechanisms that coordinate the crosstalk between metastatic signaling and cellular metabolism. The recent findings involving the contribution of crucial metabolic pathways involved in the bioenergetics and biosynthesis control in metastatic cells are summarized. Finally, we highlight new promising metabolism-based therapeutic strategies as a putative way of impairing metastasis.

Copy Number Variations of CEP63, FOSL2 and PAQR6 Serve as Novel Signatures for the Prognosis of Bladder Cancer

Background

Finding effective prognostic signatures is of great urgency due to the high risk of recurrence and progression of bladder cancer (BC). Although a lot of genetic alterations are involved in the carcinogenesis, none of them were referred in the current risk group stratifications. In this study, we aimed to find significant copy number variations (CNVs) to predict prognosis for BC patients.

Methods

CNVs with high aberration frequencies in BC were explored by array-based comparative genomic hybridization in 65 tumor samples. Candidates were validated in independent groups of BC tumor samples (n=219) and urine samples (n=123). 3D digital PCR was applied for detecting accurate gene copy numbers in BC urine. In order to explore the prognostic value of candidate CNVs, all enrolled patients were followed up for the disease-free survival (DFS). Cox proportional hazards regression analysis was performed to find the independent prognostic factors for DFS.

Results

CNVs of CEP63, FOSL2 and PAQR6 with high aberration frequencies (67.7%, 56.9% and 60.0%, respectively) were found in BC tumors. Copy numbers of CEP63, FOSL2 and PAQR6 were gained in 219 tumor samples. CNVs of CEP63 and FOSL2 were correlated with advanced tumor stage and high grade. Retrospective analysis (median follow-up time: 69 months) revealed that CNVs of CEP63 and FOSL2 were independent prognostic factors for DFS of non-muscle-invasive bladder cancer (NMIBC) patients, while CNVs of FOSL2 and PAQR6 were independent prognostic factors for DFS of muscle-invasive bladder cancer (MIBC) patients. Models for predicting DFS were constructed based on CNVs of three genes. Patients with high prognostic indexes tended to have poor DFS. Prognostic index can also help to identify those with worse outcomes among high risk NMIBC patients. Copy number gains of CEP63 and FOSL2 in urine were found to be significantly correlated with poor DFS of NMIBC patients.

Conclusions

CNVs of CEP63, FOSL2 and PAQR6 were capable of predicting DFS and may serve as promising signatures for prognosis of BC.

Coiled-Coil Domain-Containing (CCDC) Proteins: Functional Roles in General and Male Reproductive Physiology

The coiled-coil domain-containing (CCDC) proteins have been implicated in a variety of physiological and pathological processes. Their functional roles vary from their interaction with molecular components of signaling pathways to determining the physiological functions at the cellular and organ level. Thus, they govern important functions like gametogenesis, embryonic development, hematopoiesis, angiogenesis, and ciliary development. Further, they are implicated in the pathogenesis of a large number of cancers. Polymorphisms in CCDC genes are associated with the risk of lifetime diseases. Because of their role in many biological processes, they have been extensively studied. This review concisely presents the functional role of CCDC proteins that have been studied in the last decade. Studies on CCDC proteins continue to be an active area of investigation because of their indispensable functions. However, there is ample opportunity to further understand the involvement of CCDC proteins in many more functions. It is anticipated that basing on the available literature, the functional role of CCDC proteins will be explored much further.

Potential Therapeutic Significance of Laminin in Head and Neck Squamous Carcinomas

Simple Summary

Head and neck cancers (HNC) account for approximately 500,000 new cases of tumors annually worldwide and are represented by upper aerodigestive tract malignant neoplasms, which particularly arise in oral cavity, larynx, and pharynx tissues. Thus, due to the biological diversity between the upper aerodigestive organs, and to the heterogeneity of risk factors associated with their malignant transformation, HNC behavior, and prognosis seem to strongly vary according to the tumor site. However, despite to the heterogeneity which characterizes head and neck tumors, squamous cell carcinomas (SCC) represent the predominant histopathologic HNC subtype. In this sense, it has been reported that SCC tumor biology is strongly associated with deregulations within the extracellular matrix compartment. Accordingly, it has been shown that laminin plays a remarkable role in the regulation of crucial events associated with head and neck squamous cell carcinomas (HNSCC) progression, which opens the possibility that laminin may represent a convergence point in HNSCC natural history.

Abstract

Head and neck squamous cell carcinomas (HNSCC) are among the most common and lethal tumors worldwide, occurring mostly in oral cavity, pharynx, and larynx tissues. The squamous epithelia homeostasis is supported by the extracellular matrix (ECM), and alterations in this compartment are crucial for cancer development and progression. Laminin is a fundamental component of ECM, where it represents one of the main components of basement membrane (BM), and data supporting its contribution to HNSCC genesis and progression has been vastly explored in oral cavity squamous cell carcinoma. Laminin subtypes 111 (LN-111) and 332 (LN-332) are the main isoforms associated with malignant transformation, contributing to proliferation, adhesion, migration, invasion, and metastasis, due to its involvement in the regulation of several pathways associated with HNSCC carcinogenesis, including the activation of the EGFR/MAPK signaling pathway. Therefore, it draws attention to the possibility that laminin may represent a convergence point in HNSCC natural history, and an attractive potential therapeutic target for these tumors.

LncRNA SNHG6 promotes breast cancer progression and epithelial-mesenchymal transition via miR-543/LAMC1 axis

PURPOSE

Breast cancer (BC) is the most prevalent cancer in women with an estimated incidence of 10% and the leading cause of mortality due to its heterogenous property and high metastasis rate. Development of novel therapy is very necessary and requires an understanding of molecular mechanisms. We investigated the function of SNHG6/miR-543/LAMC1 axis in BC.

METHODS

Human BC tissues were obtained from diagnosed patients. BC cell lines and normal breast cells were used. QRT-PCR and Western blotting were employed to measure expression levels of SNHG6, miR-543, LAMC1, EMT-related proteins, and PI3K/AKT pathway. Dual-luciferase assay was performed to validate interactions of SNHG6/miR-543 and miR-543/LAMC1. Colony formation assay, flow cytometry, scratch wound healing assay, and transwell assay were utilized to assess the proliferation, apoptosis, migration, and invasion of BC cells. Nude mouse xenograft model was used the evaluate the function of SNHG6/miR-543 in tumor growth in vivo.

RESULTS

SNHG6 and LAMC1 were elevated, but miR-543 was reduced in BC tissues and cells. SNHG6 interacted directly with miR-543, while miR-543 targeted LAMC1. Knockdown of SNHG6 suppressed BC cell proliferation, migration, invasion, EMT, and PI3K/AKT pathway, but promoted cell apoptosis, while miR-543 inhibitor or overexpression of LAMC1 reversed those effects. Overexpression of LAMC1 also blocked the effects of miR-543 on BC cell proliferation, migration, invasion, and EMT. Knockdown of SNHG6 restrained BC growth in vivo, while miR-543 inhibitor inhibited that suppression.

CONCLUSION

SNHG6 promoted EMT and BC cell proliferation and migration by acting as a miR-543 sponge and disinhibiting LAMC1/PI3K/AKT pathway. SNHG6/miR-543/LAMC1 axis could serve as candidates for the development of therapeutic strategies for BC.

miR614 Expression Enhances Breast Cancer Cell Motility

Using a data driven analysis of a high-content screen, we have uncovered new regulators of epithelial-to-mesenchymal transition (EMT) induced cell migration. Our results suggest that increased expression of miR614 can alter cell intrinsic gene expression to enhance single cell and collective migration in multiple contexts. Interestingly, miR614 specifically increased the expression of the EMT transcription factor Slug while not altering existing epithelial character or inducing other canonical EMT regulatory factors. Analysis of two different cell lines identified a set of genes whose expression is altered by the miR614 through direct and indirect mechanisms. Prioritization driven by functional testing of 25 of the miR614 suppressed genes uncovered the mitochondrial small GTPase Miro1 and the transmembrane protein TAPT1 as miR614 suppressed genes that inhibit migration. Notably, the suppression of either Miro1 or TAPT1 was sufficient to increase Slug expression and the rate of cell migration. Importantly, reduced TAPT1 expression correlated with an increased risk of relapse in breast cancer patients. Together, our results reveal how increased miR614 expression and the suppression of TAPT1 and Miro1 modulate the EMT state and migratory properties of breast cancer cells.

The intermembrane space protein Mix23 is a novel stress-induced mitochondrial import factor

The biogenesis of mitochondria requires the import of hundreds of precursor proteins. These proteins are transported post-translationally with the help of chaperones, meaning that the overproduction of mitochondrial proteins or the limited availability of chaperones can lead to the accumulation of cytosolic precursor proteins. This imposes a severe challenge to cytosolic proteostasis and triggers a specific transcription program called the mitoprotein-induced stress response, which activates the proteasome system. This coincides with the repression of mitochondrial proteins, including many proteins of the intermembrane space. In contrast, herein we report that the so-far-uncharacterized intermembrane space protein Mix23 is considerably up-regulated when mitochondrial import is perturbed. Mix23 is evolutionarily conserved and a homolog of the human protein CCDC58. We found that, like the subunits of the proteasome, Mix23 is under control of the transcription factor Rpn4. It is imported into mitochondria by the mitochondrial disulfide relay. Mix23 is critical for the efficient import of proteins into the mitochondrial matrix, particularly if the function of the translocase of the inner membrane 23 is compromised such as in temperature-sensitive mutants of Tim17. Our observations identify Mix23 as a novel regulator or stabilizer of the mitochondrial protein import machinery that is specifically up-regulated upon mitoprotein-induced stress conditions.