Upregulated LAMB3 increases proliferation and metastasis in thyroid cancer

CRABP2 promotes cell migration and invasion by activating PI3K/AKT and MAPK signalling pathways via upregulating LAMB3 in prostate cancer

Prostate cancer (PCa) has become a worldwide health burden among men. Previous studies have suggested that cellular retinoic acid binding protein 2 (CRABP2) significantly affects the regulation of cell proliferation, motility and apoptosis in multiple cancers; however, the effect of CRABP2 on PCa is poorly reported. CRABP2 expression in different PCa cell lines and its effect on different cellular functions varied. While CRABP2 promotes cell migration and invasion, it appears to inhibit cell proliferation specifically in PC-3 cells. However, the proliferation of DU145 and 22RV1 cells did not appear to be significantly affected by CRABP2. Additionally, CRABP2 had no influence on the cell cycle distribution of PCa cells. The RNA-seq assay showed that overexpressing CRABP2 upregulated laminin subunit beta-3 (LAMB3) mRNA expression, and the enrichment analyses revealed that the differentially expressed genes were enriched in the phosphoinositide 3-kinase (PI3K)/activated protein kinase B (AKT) and mitogen-activated protein kinase (MAPK) signalling pathways. The following western blot experiments also confirmed the upregulated LAMB3 protein level and the activation of the PI3K/AKT and MAPK signalling pathways. Moreover, overexpressing CRABP2 significantly inhibited tumour growth in vivo. In conclusion, CRABP2 facilitates cell migration and invasion by activating PI3K/AKT and MAPK signalling pathways through upregulating LAMB3 in PCa.

LAMB3: Central role and clinical significance in neoplastic and non-neoplastic diseases

Recently, topics related to targeted gene therapy and diagnosis have become increasingly important in disease research. The progression of many diseases is associated with specific gene signaling pathways. Therefore, the identification of precise gene targets in various diseases is crucial for the development of effective treatments. Laminin subunit beta 3 (LAMB3), a component of laminin 5, functions as an adhesive protein in the extracellular matrix and plays a vital role in regulating cell proliferation, migration, and cell cycle in certain diseases. Previous studies have indicated that LAMB3 is highly expressed in numerous tumorous and non-tumorous conditions, including renal fibrosis; squamous cell carcinoma of the skin, thyroid, lung, pancreatic, ovarian, colorectalr, gastric, breast, cervical, nasopharyngeal, bladder, prostate cancers; and cholangiocarcinoma. Conversely, it is underexpressed in other conditions, such as hepatocellular carcinoma, epidermolysis bullosa, and amelogenesis imperfecta. Consequently, LAMB3 may serve as a molecular diagnostic and therapeutic target for various diseases through its involvement in critical gene signaling pathways. This paper reviews the research status of LAMB3 and its role in related diseases.

Integrated transcriptome sequencing and weighted gene co-expression network analysis reveals key genes of papillary thyroid carcinomas

Objective

Papillary thyroid carcinoma (PTC) accounts for the majority of thyroid cancers and has a high recurrence rate. We aimed to screen key genes involved in PTC to provide novel insights into the mechanisms of PTC.

Methods

Seven microarray datasets of PTC were downloaded from gene expression omnibus database. Differentially expressed genes (DEGs) between PTC and normal samples were screened in the merged dataset. Then, protein-protein interaction (PPIs) functional modules analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify PTC-associated key genes. The identified key genes were then characterized from various aspects, including gene set enrichment analysis (GSEA) and the associations with immune infiltration, methylation levels and prognosis.

Results

A large numbers of DEGs were identified, and these DEGs are involved in several cancer pathways. Nine key genes (including down-regulated genes GNA14, AVPR1A, and WFS1, and up-regulated genes LAMB3, PLAU, MET, MFGE8, PRSS23, and SERPINA1) were identified. Patients in the AVPR1A and GNA14 high expression groups had better disease-free survival (DFS) than those in the low expression group. Key genes were mainly involved in P53 pathway, estrogen response, apoptosis, glycolysis, NOTCH signaling, epithelial mesenchymal transition, WNT_beta catenin signaling, and inflammatory response. The expression of key genes was associated with immune cell infiltration and corresponding methylation levels. The verification results of key gene proteins and mRNA expression levels using external validation datasets were consistent with our expectations, implying the involvements of key genes in PTC.

Conclusion

The key genes may serve as potential therapeutic targets for PTC. This study provides novel insights into the mechanisms underlying PTC development.

Downregulation of LAMB3 Altered the Carcinogenic Properties of Human Papillomavirus 16-Positive Cervical Cancer Cells

Nearly all cervical cancer cases are caused by infection with high-risk human papillomavirus (HR-HPV) types. The mechanism of cervical cell transformation is related to the powerful action of viral oncoproteins and cellular gene alterations. Transcriptomic data from cervical cancer and normal cervical cells were utilized to identify upregulated genes and their associated pathways. The laminin subunit beta-3 (LAMB3) mRNAwas overexpressed in cervical cancer and was chosen for functional analysis. The LAMB3 was predominantly expressed in the extracellular region and the plasma membrane, which play a role in protein binding and cell adhesion molecule binding, leading to cell migration and tissue development. LAMB3 was found to be implicated in the pathway in cancer and the PI3K-AKT signaling pathway. LAMB3 knockdown decreased cell migration, invasion, anchorage-dependent and anchorage-independent cell growth and increased the number of apoptotic cells. These effects were linked to a decrease in protein levels involved in the PI3K-AKT signaling pathway and an increase in p53 protein. This study demonstrated that LAMB3 could promote cervical cancer cell migration, invasion and survival.

Identification of Novel Anoikis-Related Gene Signatures to Predict the Prognosis, Immune Microenvironment, and Drug Sensitivity of Breast Cancer Patients

INTRODUCTION

Breast cancer is one of the most prevalent types of cancer and a leading cause of cancer-related death among females worldwide. Anoikis, a specific type of apoptosis that is triggered by the loss of anchoring between cells and the native extracellular matrix, plays a vital role in cancer invasion and metastasis. However, studies that focus on the prognostic values of anoikis-related genes (ARGs) in breast cancer are scarce.

METHODS

Gene expression data were obtained from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) databases. Five anoikis-related signatures (ARS) were selected from ARGs through univariate Cox regression analysis, LASSO regression analysis, and multivariate Cox regression analysis. Subsequently, an ARGs risk score model was established, and breast cancer patients were divided into high and low risk groups. The correlation between risk groups and overall survival (OS), tumor mutation burden (TMB), tumor microenvironment (TME), stemness, and drug sensitivity were analyzed. Moreover, RT-qPCR was performed to verify the gene expression levels of the five ARS in breast cancer tissues. Furthermore, a nomogram model was constructed based on ARGs risk score and clinicopathological factors.

RESULTS

A novel ARGs risk score model was constructed based on five ARS (CEMIP, LAMB3, CD24, PTK6, and PLK1), and breast cancer patients were divided into high and low risk groups. Correlation analysis showed that the high and low risk groups had different OS, TMB, TME, stemness, and drug sensitivity. Both the ARGs risk score model and the nomogram showed promising prognosis predictive value in breast cancer.

CONCLUSION

ARS could be used as promising biomarkers for breast cancer prognosis predication and treatment options selection.

Construction of the metabolic reprogramming-associated gene signature for clear cell renal cell carcinoma prognosis prediction

BACKGROUND

Metabolism reprogramming is a hallmark that associates tumor growth, metastasis, progressive, and poor prognosis. However, the metabolism-related molecular patterns and mechanism in clear cell renal cell carcinoma (ccRCC) remain unclear. Herein, the purpose of this study was to identify metabolism-related molecular pattern and to investigate the characteristics and prognostic values of the metabolism-related clustering.

METHODS

We comprehensively analyzed the differentially expressed genes (DEGs), and metabolism-related genes (MAGs) in ccRCC based on the TCGA database. Consensus clustering was used to construct a metabolism-related molecular pattern. Then, the biological function, molecular characteristics, Estimate/immune/stomal scores, immune cell infiltration, response to immunotherapy, and chemotherapy were analyzed. We also identified the DEGs between subclusters and constructed a poor signature and risk model based on LASSO regression cox analysis and univariable and multivariable cox regression analyses. Then, a predictive nomogram was constructed and validated by calibration curves.

RESULTS

A total of 1942 DEGs (1004 upregulated and 838 downregulated) between ccRCC tumor and normal samples were identified, and 254 MRGs were screened out from those DEGs. Then, 526 ccRCC patients were divided into two subclusters. The 7 metabolism-related pathways enriched in cluster 2. And cluster 2 with high Estimate/immune/stomal scores and poor survival. While, cluster 1 with higher immune cell infiltrating, expression of the immune checkpoint, IFN, HLA, immune activation-related genes, response to anti-CTLA4 treatment, and chemotherapy. Moreover, we identified 295 DEGs between two metabolism-related subclusters and constructed a 15-gene signature and 9 risk factors. Then, a risk score was calculated and the patients into high- and low-risk groups in TCGA-KIRC and E-MTAB-1980 datasets. And the prediction viability of the risk score was validated by ROC curves. Finally, the clinicopathological characteristics (age and stage), risk score, and molecular clustering, were identified as independent prognostic variables, and were used to construct a nomogram for 1-, 3-, 5-year overall survival predicting. The calibration curves were used to verify the performance of the predicted ability of the nomogram.

CONCLUSION

Our finding identified two metabolism-related molecular subclusters for ccRCC, which facilitates the estimation of response to immunotherapy and chemotherapy, and prognosis after treatment.

Multi-omics analysis of LAMB3 as a potential immunological and biomarker in pan-cancer

Laminin Subunit Beta 3 (LAMB3) is a transcription factor and participates in the coding of laminin. It plays an important role in cell proliferation, adhesion, and transfer by regulating various target genes and signaling pathways. However, the role of LAMB3 in human pan-cancer immunology and prognosis is still poorly understood. The TCGA, GTEx, CCLE, and HPA databases were utilized for the analysis of LAMB mRNA and protein expression. The expression of LAMB3 in various immune and molecular subtypes of human cancer was examined using the TISIDB database. The prognostic significance of LAMB3 in various cancers and clinical subtypes was investigated using Kaplan-Meier and Cox regression analysis. The relationship between LAMB3 expression, various immune cell infiltration, immune checkpoints, tumor mutational load, microsatellite instability, and DNA methylation was examined using the TCGA database. Clinical samples of four lung cancer cell lines and eight lung cancer cases were collected to confirm the expression of mRNA in lung cancer. In 17 cancers, the mRNA for LAMB3 is expressed differently and has good diagnostic and prognostic value in 22 cancers. Cox regression and Nomogram analysis show that LAMB3 is an independent risk factor for 15 cancers. LAMB3 is implicated in a variety of tumorigenesis and immune-related signaling pathways, according to GO, KEGG, and GSEA results. LAMB3 expression was associated with TMB in 33 cancer types and MSI in 32 cancer types, while in lung cancer LAMB3 expression was strongly associated with immune cell infiltration and negatively correlated with all seven methylated CpG islands. Cellular experiments demonstrated that LAMB3 promotes malignant behavior of tumor cells. Preliminary mechanistic exploration revealed its close association with PD-L1, CTLA4, cell stemness gene CD133 and β-catenin-related signaling pathways. Based on these findings, it appears that LAMB3 could be a potential therapeutic target for immunotherapy and tumor prognosis. Our findings reveal an important role for LAMB3 in different cancer types.

Function and prognostic value of basement membrane -related genes in lung adenocarcinoma

Background: Lung adenocarcinoma (LUAD) has become a common cause of cancer-related death. Many studies have shown that the basement membrane (BM) is associated with the development of cancer. However, BM-related gene expression and its relationship to LUAD prognosis remains unclear. Methods: BM-related genes from previous studies were used. Clinical and mRNA expression information were obtained from TCGA database. Cox, minimum absolute contraction, and selection operator regression were applied to analyze the selected genes affecting LUAD prognosis. A prognostic-risk model was then established. Furthermore, this study applied Kaplan-Meier analysis to assess the outcomes of high- and low-risk groups, then explored their differences in drug sensitivity. The DSigDB database was used to screen for therapeutic small-molecule drugs. Results: Fourteen prognostic models based on BM-related genes were successfully constructed and validated in patients with LUAD. We also found that independence was a prognostic factor in all 14 BM-based models. Functional analysis showed that the enrichment of BM-related genes mainly originated from signaling pathways related to cancer. The BM-based model also suggested that immune cell infiltration is associated with checkpoints. The low-risk patients may benefit from cyclopamine and docetaxel treatments. Conclusion: This study identified a reliable biomarker to predict survival in patients with LUAD and offered new insights into the function of BM-related genes in LUAD.

Prognostic nomogram based on the lymph node metastasis indicators for patients with bladder cancer: A SEER population-based study and external validation

PURPOSE

This study aimed to compare the prognostic value of multiple lymph node metastasis (LNM) indicators and to develop optimal prognostic nomograms for bladder cancer (BC) patients.

METHODS

BC patients were obtained from the Surveillance, Epidemiology, and End Results (SEER) database between 2004 and 2015, and randomly partitioned into training and internal validation cohorts. Genomic and clinical data were collected from The Cancer Genome Atlas (TCGA) as external validation cohort. The predictive efficiency of LNM indicators was compared by constructing multivariate Cox regression models. We constructed nomograms on basis of the optimal models selected for overall survival (OS) and cause-specific survival (CSS). The performance of nomograms was evaluated with calibration plot, time-dependent area under the curve (AUC) and decision curve analysis (DCA) in three cohorts. We subsequently estimated the difference of biological function and tumor immunity between two risk groups stratified by nomograms in TCGA cohort.

RESULTS

Totally, 10,093 and 107 BC patients were screened from the SEER and TCGA databases. N classification, positive lymph nodes (PLNs), lymph node ratio (LNR) and log odds of positive lymph nodes (LODDS) were all independent predictors for OS and CSS. The filtered models containing LODDS had minimal Akaike Information Criterion, maximal concordance indexes and AUCs. Age, LODDS, T and M classification were integrated into nomogram for OS, while nomogram for CSS included gender, tumor grade, LODDS, T and M classification. The nomograms were successfully validated in predictive accuracy and clinical utility in three cohorts. Additionally, the tumor microenvironment was different between two risk groups.

CONCLUSIONS

LODDS demonstrated superior prognostic performance over N classification, PLN and LNR for OS and CSS of BC patients. The nomograms incorporating LODDS provided appropriate prediction of BC, which could contribute to the tumor assessment and clinical decision-making.

hsa-mir-133a-2 promotes the proliferation and invasion of cervical cancer cells by targeting the LAMB3-mediated PI3K/ATK pathway

OBJECTIVE

Cervical cancer, one of the common types of malignant tumors progressed in women, is on the rise in developing countries. Numerous previous studies have demonstrated that hsa-mir-133a-2 miRNA is abnormally expressed in cervical cancer cells. However, its fundamental mechanism in cervical cancer needs to be further clarified. Our study set out to investigate the effect of hsa-mir-133a-2 on the phenotypes of cervical cancer cells as well as any potential molecular processes involved in the proliferation and invasion of cervical cancer cells.

METHODS

The Cancer Genome Atlas-cervical squamous cell carcinoma and endocervical adenocarcinoma(TCGA-CESC) was adopted in order to verify the expression of hsa-mir-133a-2 in cervical cancer tissues and to identify its potential targets. The interaction between Laminin subunit beta-3(LAMB3) and hsa-mir-133a-2 was verified by TargetScan database as well as Luciferase reporter assay. The Cell Counting Kit-8 (CCK8) and transwell methods were utilized to assess the influence of hsa-mir-133a-2 on the proliferation and invasion characteristics of cervical cancer cells. We studied the role that hsa-mir-133a-2 plays in cervical cancer progression through Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis as well as Western Blot (WB) experiment.

RESULTS

Down-regulation of hsa-mir-133a-2 was detected in cervical cancer tissues. It directly targeted LAMB3 and negatively regulated LAMB3 expression. The overexpression of hsa-mir-133a-2 has a significant inhibiting effect on cervical cancer cell proliferation and invasion. The overexpression of hsa-mir-133a-2 significantly inhibits the proliferation and invasion of cervical cancer cells. Moreover, the LAMB3 was able to up-regulate the phosphorylation levels of AKT and phosphatidylinositol 3-kinase (PI3K) protein in cervical cancer cells. hsa-mir-133a-2 could also modulate the PI3K/AKT signaling pathway by targeting LAMB3.

CONCLUSION

hsa-mir-133a-2 inhibits cervical cancer cell proliferation and invasion by indirectly regulating the PI3K/AKT signaling pathway, providing us with a new clinical treatment strategy for cervical cancer.

The potential of Lycium barbarum miR166a in kidney cancer treatment

Predator species of animal can absorb plant microRNA that can regulate target gene expression and physiological function across species. The herb Lycium barbarum, a traditional Chinese medicine, has a wide range of antitumor effects. However, there are no reports on the effects of microRNA derived from it on the cross-border regulation of renal cell carcinoma (RCC). We performed in vitro and in vivo experiments to explore the role and mechanism of the L. barbarum-derived microRNA miR166a (Lb-miR166a) in cross-border regulation of RCC. Our mRNA sequencing analysis showed that Lb-miR166a regulates the expression of various genes in tumor cells, including 1232 upregulated genes and 581 downregulated genes, which were enriched to 1094 Gene Ontology entries and 43 Kyoto Encyclopedia of Genes and Genomes pathways. In vitro cell experiments confirmed that Lb-miR166a can inhibit the proliferation of RCC cells, promote the apoptosis of tumor cells, and inhibit the invasion and metastasis of tumor cells by regulating the expression of related genes. Furthermore, our in vivo tumor-bearing experiment showed that subcutaneous tumor formation volume decreased in Lb-miR166a mice, along with the number of liver metastases. This study elucidates the role and mechanism of Lb-miR166a in RCC treatment (Fig. 1). Our results further mechanistically confirm the antitumor properties of L. barbarum. Our study may contribute to the clinical development of a targeted drug for RCC treatment.

Genome-wide CRISPR/Cas9 library screen identifies PCMT1 as a critical driver of ovarian cancer metastasis

Background

The development of lethal cancer metastasis depends on the dynamic interactions between cancer cells and the tumor microenvironment, both of which are embedded in the extracellular matrix (ECM). The acquisition of resistance to detachment-induced apoptosis, also known as anoikis, is a critical step in the metastatic cascade. Thus, a more in-depth and systematic analysis is needed to identify the key drivers of anoikis resistance.

Methods

Genome-wide CRISPR/Cas9 knockout screen was used to identify critical drivers of anoikis resistance using SKOV3 cell line and found protein-L-isoaspartate (D-aspartate) O-methyltransferase (PCMT1) as a candidate. Quantitative real-time PCR (qRT-PCR) and immune-histochemistry (IHC) were used to measure differentially expressed PCMT1 in primary tissues and metastatic cancer tissues. PCMT1 knockdown/knockout and overexpression were performed to investigate the functional role of PCMT1 in vitro and in vivo. The expression and regulation of PCMT1 and integrin-FAK-Src pathway were evaluated using immunoprecipitation followed by mass spectrometry (IP-MS), western blot analysis and live cell imaging.

Results

We found that PCMT1 enhanced cell migration, adhesion, and spheroid formation in vitro. Interestingly, PCMT1 was released from ovarian cancer cells, and interacted with the ECM protein LAMB3, which binds to integrin and activates FAK-Src signaling to promote cancer progression. Strikingly, treatment with an antibody against extracellular PCMT1 effectively reduced ovarian cancer cell invasion and adhesion. Our in vivo results indicated that overexpression of PCMT1 led to increased ascites formation and distant metastasis, whereas knockout of PCMT1 had the opposite effect. Importantly, PCMT1 was highly expressed in late-stage metastatic tumors compared to early-stage primary tumors.

Conclusions

Through systematically identifying the drivers of anoikis resistance, we uncovered the contribution of PCMT1 to focal adhesion (FA) dynamics as well as cancer metastasis. Our study suggested that PCMT1 has the potential to be a therapeutic target in metastatic ovarian cancer.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13046-022-02242-3.

The prognostic and clinical significance of IFI44L aberrant downregulation in patients with oral squamous cell carcinoma

Background

It is a basic task in high-throughput gene expression profiling studies to identify differentially expressed genes (DEGs) between two phenotypes. RankComp, an algorithm, could analyze the highly stable within-sample relative expression orderings (REOs) of gene pairs in a particular type of human normal tissue that are widely reversed in the cancer condition, thereby detecting DEGs for individual disease samples measured by a particular platform.

Methods

In the present study, Gene Expression Omnibus (GEO) Series (GSE) GSE75540, GSE138206 were downloaded from GEO, by analyzing DEGs in oral squamous cell carcinoma based on online datasets using the RankComp algorithm, using the Kaplan-Meier survival analysis and Cox regression analysis to survival analysis, Gene Set Enrichment Analysis (GSEA) to explore the potential molecular mechanisms underlying.

Results

We identified 6 reverse gene pairs with stable REOs. All the 12 genes in these 6 reverse gene pairs have been reported to be associated with cancers. Notably, lower Interferon Induced Protein 44 Like (IFI44L) expression was associated with poorer overall survival (OS) and Disease-free survival (DFS) in oral squamous cell carcinoma patients, and IFI44L expression showed satisfactory predictive efficiency by receiver operating characteristic (ROC) curve. Moreover, low IFI44L expression was identified as risk factors for oral squamous cell carcinoma patients’ OS. IFI44L downregulation would lead to the activation of the FRS-mediated FGFR1, FGFR3, and downstream signaling pathways, and might play a role in the PI3K-FGFR cascades.

Conclusions

Collectively, we identified 6 reverse gene pairs with stable REOs in oral squamous cell carcinoma, which might serve as gene signatures playing a role in the diagnosis in oral squamous cell carcinoma. Moreover, high expression of IFI44L, one of the DEGs in the 6 reverse gene pairs, might be associated with favorable prognosis in oral squamous cell carcinoma patients and serve as a tumor suppressor by acting on the FRS-mediated FGFR signaling.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-09058-y.

Whole Transcriptome Analysis Revealed a Stress Response to Deep Underground Environment Conditions in Chinese Hamster V79 Lung Fibroblast Cells

Background: Prior studies have shown that the proliferation of V79 lung fibroblast cells could be inhibited by low background radiation (LBR) in deep underground laboratory (DUGL). In the current study, we revealed further molecular changes by performing whole transcriptome analysis on the expression profiles of long non-coding RNA (lncRNA), messenger RNA (mRNA), circular RNA (circRNA) and microRNA (miRNA) in V79 cells cultured for two days in a DUGL.

Methods: Whole transcriptome analysis including lncRNA, mRNAs, circ RNA and miRNA was performed in V79 cells cultured for two days in DUGL and above ground laboratory (AGL), respectively. The differentially expressed (DE) lncRNA, mRNA, circRNA, and miRNA in V79 cells were identified by the comparison between DUGL and AGL groups. Quantitative real-time polymerase chain reaction(qRT-PCR)was conducted to verify the selected RNA sequencings. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was analyzed for the DE mRNAs which enabled to predict target genes of lncRNA and host genes of circRNA.

Results: With |log₂(Fold-change)| ≥ 1.0 and p < 0.05, a total of 1257 mRNAs (353 mRNAs up-regulated, 904 mRNAs down-regulated), 866 lncRNAs (145 lncRNAs up-regulated, 721 lncRNAs down-regulated), and 474 circRNAs (247 circRNAs up-regulated, 227 circRNAs down-regulated) were significantly altered between the two groups. There was no significant difference in miRNA between the two groups. The altered RNA profiles were mainly discovered in lncRNAs, mRNAs and circRNAs. DE RNAs were involved in many pathways including ECM-RI, PI3K-Akt signaling, RNA transport and the cell cycle under the LBR stress of the deep underground environment.

Conclusion: Taken together, these results suggest that the LBR in the DUGL could induce transcriptional repression, thus reducing metabolic process and reprogramming the overall gene expression profile in V79 cells.

Transcriptional alterations of protein coding and noncoding RNAs in triple negative breast cancer in response to DNA methyltransferases inhibition

Background

DNA methylation plays a crucial role in multiple cellular processes such as gene regulation, chromatin stability, and genetic imprinting. In mammals, DNA methylation is achieved by DNA methyltransferases (DNMTs). A number of studies have associated alterations in DNMT activity to tumorigenesis; however, the exact role of DNMTs in shaping the genome in triple negative breast cancer (TNBC) is still being unraveled.

Methods

In the current study, we employed two DNMT inhibitors (Decitabine and 5-Azacytidine), two TNBC models (MDA-MB-231 and BT-549) and whole transcriptome RNA-Seq and characterized the transcriptional alterations associated with DNMT inhibition. Colony forming unit (CFU), flow cytometry, and fluorescent microscopy were used to assess cell proliferation, cell cycle distribution, and cell death, respectively. Ingenuity pathway analysis (IPA) was used for network and pathway analyses.

Results

Remarkably, DNMT inhibition induced the expression of genes involved in endoplasmic reticulum response to stress, response to unfolder protein, as well as cobalamin metabolic processes. In contrast, suppression of cellular processes related to cell cycle and mitosis were hallmarks of DNMT inhibition. Concordantly, DNMT inhibition led to significant inhibition of TNBC cell proliferation, G2-M cell cycle arrest and induction of cell death. Mechanistically, DNMT inhibition activated TP53, NUPR1, and NFkB (complex) networks, while RARA, RABL6, ESR1, FOXM1, and ERBB2 networks were suppressed. Our data also identified the long noncoding RNA (lncRNA) transcriptional portrait associated with DNMT inhibition and identified 25 commonly upregulated and 60 commonly downregulated lncRNAs in response to Decitabine and 5-Azacytidinec treatment in both TNBC models. TPT1-AS1 was the most highly induced (6.3 FC), while MALAT1 was the most highly suppressed (− 7.0 FC) lncRNA in response to DNMT inhibition.

Conclusions

Taken together, our data provides a comprehensive view of transcriptome alterations in the coding and noncoding transcriptome in TNBC in response to DNMT inhibition.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-021-02213-2.

AUF1 Promotes Proliferation and Invasion of Thyroid Cancer via Downregulation of ZBTB2 and Subsequent TRIM58

The pathogenesis of papillary thyroid cancer (PTC), the most common type of thyroid cancer, is not yet fully understood. This limits the therapeutic options for approximately 7% of invasive PTC patients. The critical role of AUF1 in the progression of thyroid cancer was first reported in 2009, however, its molecular mechanism remained unclear. Our study used CRISPR/Cas 9 system to knockdown AUF1 in IHH4 and TPC1 cells. We noticed that the expression of TRIM58 and ZBTB2 were increased in the AUF1 knockdown IHH4 and TPC1 cells. When TRIM58 and ZBTB2 were inhibited by small hairpin RNAs (shRNAs) against TRIM58 (shTRIM58) and ZBTB2 (shZBTB2), respectively, the proliferation, migration, and invasion ability of the AUF1-knockdown IHH4 and TPC1 cells were increased. In addition, two ZBTB2 binding sites (-719~-709 and -677~-668) on TRIM58 promoter and two AUF1 binding sites (1250-1256 and 1258-1265) on ZBTB2 3’-UTR were identified. These results suggested that AUF1 affecting thyroid cancer cells via regulating the expression of ZBTB2 and TRIM58.

Association of the Epithelial-Mesenchymal Transition (EMT) with Cisplatin Resistance

Therapy resistance is a characteristic of cancer cells that significantly reduces the effectiveness of drugs. Despite the popularity of cisplatin (CP) as a chemotherapeutic agent, which is widely used in the treatment of various types of cancer, resistance of cancer cells to CP chemotherapy has been extensively observed. Among various reported mechanism(s), the epithelial-mesenchymal transition (EMT) process can significantly contribute to chemoresistance by converting the motionless epithelial cells into mobile mesenchymal cells and altering cell-cell adhesion as well as the cellular extracellular matrix, leading to invasion of tumor cells. By analyzing the impact of the different molecular pathways such as microRNAs, long non-coding RNAs, nuclear factor-κB (NF-ĸB), phosphoinositide 3-kinase-related protein kinase (PI3K)/Akt, mammalian target rapamycin (mTOR), and Wnt, which play an important role in resistance exhibited to CP therapy, we first give an introduction about the EMT mechanism and its role in drug resistance. We then focus specifically on the molecular pathways involved in drug resistance and the pharmacological strategies that can be used to mitigate this resistance. Overall, we highlight the various targeted signaling pathways that could be considered in future studies to pave the way for the inhibition of EMT-mediated resistance displayed by tumor cells in response to CP exposure.

Identification of Candidate Genes Associated with Breast Cancer Prognosis

Breast cancer (BC) is the most malignant tumor in women. The molecular mechanisms underlying tumorigenesis still need to be further elucidated. It is necessary to investigate novel candidate genes involved in breast cancer progression and prognosis. In this study, we commit to explore candidate genes that associate with prognosis and therapy in BC by a comprehensive bioinformatic analysis. Four GEO datasets (GSE5764, GSE7904, GSE20711, and GSE29431) and the BC-related transcriptome data in TCGA database were downloaded and used to identify the differently expressed genes (DEGs). The function of DEGs was analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis. The protein-protein interaction (PPI) network of DEGs was constructed to identify hub genes. Prognostic candidate genes were identified through survival analysis. In addition, potential therapeutic targets were identified by constructed gene-drug interaction network through Comparative Toxicogenomics Database. A total of 547 DEGs (302 up and 245 down) were identified. Three core-subnetwork and 25 hub genes were identified in PPI network. Seven genes (namely COL12A1, QPRT, MRPL13, KRT14, KRT15, LAMB3, and MYBPC1) were identified as crucial prognostic candidate genes, which significantly associated with breast cancer overall survival. Furthermore, two representative candidate genes (COL12A1 and LAMB3) were optionally chosen for verification by reverse transcription and quantitative real-time polymerase chain reaction (RT-PCR). What's more, the gene-drugs interaction analysis indicates several antitumor drugs that could affect the expression of these prognostic markers, such as doxorubicin, cisplatin, and tamoxifen. These results identified seven crucial candidate genes that may serve as prognosis biomarkers and novel therapeutic targets of breast cancer, which may facilitate further understanding the molecular pathogenesis and providing potential therapeutic strategies for BC.

Metastatic propagation of thyroid cancer; organ tropism and major modulators

Thyroid cancer, as the most prevalent endocrine malignancy, comprises nearly 1% of all cancers in the world. The metastatic propagation of thyroid cancer is under the control of a number of modulating processes and factors such as signaling pathways and their components, cell division regulators, metabolic reprogramming factors, extracellular matrix remodelers, epithelial to mesenchymal transition modulators, epigenetic mechanisms, hypoxia and cytokines. Identifying the exact molecular mechanisms of these dysregulated processes could help to discover the key targets for therapeutic purposes and utilizing them as diagnostic, prognostic and predictors of the clinical course of patients. In this review article, we describe different aspects of thyroid cancer metastasis by focusing on defective genes and pathways involved in its metastatic spread.

An Integrated Microarray Analysis Reveals Significant Diagnostic and Prognostic Biomarkers in Pancreatic Cancer

Background

Pancreatic cancer (PAC) is a lethal cancer and it is essential to develop accurate diagnostic and prognostic biomarkers for PAC.

Material/Methods

An integrated microarray analysis of PAC was conducted to identify differentially expressed genes (DEGs) between PAC and non-tumor controls. Expression of DEGs were further confirmed by The Cancer Genome Atlas and the Genotype-Tissue Expression. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and protein–protein integration network construction were performed to further research the biological functions of DEGs. Receiver-operating characteristic analysis and survival analysis were used to evaluate the diagnostic and prognostic value of DEGs for PAC.

Results

Seventeen microarray datasets were downloaded from Gene Expression Omnibus to conduct the integrated microarray analysis. A total of 1136 DEGs (596 upregulated and 540 downregulated DEGs) in PAC tissues compared with non-tumor controls were identified. Pancreatic secretion (Kegg: 04972), insulin signaling pathway (Kegg: 04910), and several cancer-related pathways including pathways in cancer (Kegg: 05200), MAPK signaling pathway (Kegg: 04010), and pancreatic cancer (Kegg: 05212) were enriched for DEGs in PAC. Seven DEGs (AHNAK2, CDH3, IFI27, ITGA2, LAMB3, SLC6A14, and TMPRSS4) were found to have both great diagnostic and prognostic value for PAC. High expression of these 7 DEGs were significantly associated with poor prognosis of patients with PAC.

Conclusions

These 7 DEGs might be potential diagnostic and prognostic biomarkers for PAC and help uncovering the mechanism of PAC.

MiR-24-3p Inhibits the Progression of Pancreatic Ductal Adenocarcinoma Through LAMB3 Downregulation

Pancreatic ductal adenocarcinoma (PDAC) is associated with several genetic syndromes. However, the molecular mechanism underlying PDAC progression is still unknown. In this study, we showed that Laminin Subunit Beta 3 (LAMB3) was aberrantly overexpressed in PDAC and was closely associated with the overall survival rate of patients with PDAC. Functional studies demonstrated that LAMB3 played important roles in cell proliferation, the cell cycle, and invasion capacity. Using bioinformatics analysis, we determined that miR-24-3p was an upstream miRNA of LAMB3, and further experiments verified that miR-24-3p regulated LAMB3 expression in PDAC cells. A dual-luciferase reporter system demonstrated that miR-24-3p directly targeted the LAMB3 3'UTR, and FISH assay confirmed that miR-24-3p and LAMB3 mRNA mostly resided in cytoplasm, accounting for their post-translational regulation. Rescue assay demonstrated that miR-24-3p exerted its anti-cancer role by suppressing LAMB3 expression. Finally, by using a subcutaneous xenotransplanted tumor model, we demonstrated that miR-24-3p overexpression inhibited the proliferation of PDAC by suppressing LAMB3 expression in vivo. Collectively, our results provide evidence that the miR-24-3p/LAMB3 axis plays a vital role in the progression of PDAC and indicate that the miR-24-3p/LAMB3 axis may represent a novel therapeutic target for PDAC.

microRNA-329 suppresses epithelial-to-mesenchymal transition and lymph node metastasis in bile duct cancer by inhibiting laminin subunit beta 3

Bile duct cancer (BDC), also known as cholangiocarcinoma, is a highly desmoplastic cancer with a growth pattern characterized by periductal extension and infiltration. Studies have suggested that microRNAs (miRNAs) play an important role in BDC progression. Here we aim at investigating the effects of miR-329 on BDC development, focusing especially on epithelial-to-mesenchymal transition (EMT) in vitro and lymph node metastasis in vivo. Expression microarrays associated with BDC tissues were collected and differentially expressed genes were analyzed, followed by miRNA target prediction and verification. The role miR-329 played in BDC was examined using gain-of-function and loss-of-function methods. The expressions of miR-329, laminin subunit beta 3 (LAMB3), and EMT markers, in addition to cell proliferation, migration, and invasion were evaluated. Furthermore, nude mice models of BDC were established to observe tumor growth and metastatic lymph nodes. The LAMB3 was identified as an upregulated gene based on the GSE77984 and GSE45001 microarray analysis. LAMB3 was also predicted and confirmed to be a target gene of miR-329 by dual-luciferase reporter assay. Through further cell experiments, the EMT process was reversed, cell proliferation, invasion, and migration were suppressed, when miR-329 was upregulated. Furthermore, in vivo experiments exhibited that the overexpression of miR-329 inhibited tumor growth and the number of metastatic lymph nodes. This study provides in vivo and in vitro evidence that miR-329 inhibits BDC progression through translational repression of LAMB3. Therefore, the obtained results may aid as an experimental basis for improving prognosis of BDC.

In-Depth Proteomics Analysis to Identify Biomarkers of Papillary Thyroid Cancer Patients Older Than 45 Years with Different Degrees of Lymph Node Metastases

PURPOSE

Investigations of the molecular mechanisms underlying the metastatic phenotype of papillary thyroid cancer (PTC) and identification of novel candidate biomarkers to better predict PTC metastasis are urgently required.

EXPERIMENTAL DESIGN

Tandem mass tag-based quantitative proteomics approach is used to identify differentially expressed proteins (DEPs) in PTC tumorous tissues with different degrees of lymph node metastases (LNMs). Furthermore, DEPs and their clinical significance are analyzed in another independent Cancer Genome Atlas dataset.

RESULTS

The protein profiles among tumorous tissues with different degrees of LNMs are clearly distinguished, while the protein profiles in normal tissues are remarkably similar. DEPs in tumorous tissues are mostly enriched in the categories associated with pathological hallmarks of cancer, including extracellular matrix, metabolism, and cell growth. The expression patterns of six DEPs (LAMC2, LAMB3, ATP5A1, MYO1G, S100A4, and FAS) are confirmed by the Cancer Genome Atlas dataset. Additionally, the elevated expression of LAMC2 and MYO1G mRNA levels in tumorous tissues show a positive relationship with unfavorable variables, including larger tumor size, LNMs, high AJCC staging, BRAF^V600E mutation, and poor prognosis.

CONCLUSIONS AND CLINICAL RELEVANCE

LAMC2 and MYO1G are identified as potential candidate biomarkers for the prediction of PTC metastasis and prognosis.

LAMB3 mediates apoptotic, proliferative, invasive, and metastatic behaviors in pancreatic cancer by regulating the PI3K/Akt signaling pathway

The poor prognosis of patients with pancreatic ductal adenocarcinoma (PDAC) is partially attributed to the invasive and metastatic behavior of this disease. Laminin subunit beta-3 (LAMB3) encodes one of the three subunits of LM-332, an extracellular matrix protein secreted by cultured human keratinocytes. In addition, LAMB3 is involved in the invasive and metastatic abilities of some types of cancer, including colon, pancreas, lung, cervix, stomach, and prostate cancer, but the role and mechanism of LAMB3 in PDAC have not been previously determined. Herein, we tentatively investigated the role of LAMB3 in the malignant biological behavior of PDAC. In this study, we demonstrated that LAMB3 is upregulated in PDAC. Inhibition of LAMB3 abrogated the tumorigenic outcomes of PI3K/Akt signaling pathway activation, including those involving cell cycle arrest, cell apoptosis, proliferation, invasion and migration in vitro, and tumor growth and liver metastasis in vivo. Our results showed that LAMB3 could mediate cell cycle arrest and apoptosis in PDAC cells and alter the proliferative, invasive, and metastatic behaviors of PDAC by regulating the PI3K/Akt signaling pathway. LAMB3 may be a novel therapeutic target for the treatment of PDAC in the future.