Increased expression of mitotic checkpoint genes in breast cancer cells with chromosomal instability

BUB1 regulates non-homologous end joining pathway to mediate radioresistance in triple-negative breast cancer

BACKGROUND

Triple-negative breast cancer (TNBC) is a highly aggressive form of breast cancer subtype often treated with radiotherapy (RT). Due to its intrinsic heterogeneity and lack of effective targets, it is crucial to identify novel molecular targets that would increase RT efficacy. Here we demonstrate the role of BUB1 (cell cycle Ser/Thr kinase) in TNBC radioresistance and offer a novel strategy to improve TNBC treatment.

METHODS

Gene expression analysis was performed to look at genes upregulated in TNBC patient samples compared to other subtypes. Cell proliferation and clonogenic survivals assays determined the IC50 of BUB1 inhibitor (BAY1816032) and radiation enhancement ratio (rER) with pharmacologic and genomic BUB1 inhibition. Mammary fat pad xenografts experiments were performed in CB17/SCID. The mechanism through which BUB1 inhibitor sensitizes TNBC cells to radiotherapy was delineated by γ-H2AX foci assays, BLRR, Immunoblotting, qPCR, CHX chase, and cell fractionation assays.

RESULTS

BUB1 is overexpressed in BC and its expression is considerably elevated in TNBC with poor survival outcomes. Pharmacological or genomic ablation of BUB1 sensitized multiple TNBC cell lines to cell killing by radiation, although breast epithelial cells showed no radiosensitization with BUB1 inhibition. Kinase function of BUB1 is mainly accountable for this radiosensitization phenotype. BUB1 ablation also led to radiosensitization in TNBC tumor xenografts with significantly increased tumor growth delay and overall survival. Mechanistically, BUB1 ablation inhibited the repair of radiation-induced DNA double strand breaks (DSBs). BUB1 ablation stabilized phospho-DNAPKcs (S2056) following RT such that half-lives could not be estimated. In contrast, RT alone caused BUB1 stabilization, but pre-treatment with BUB1 inhibitor prevented stabilization (t1/2, ~8 h). Nuclear and chromatin-enriched fractionations illustrated an increase in recruitment of phospho- and total-DNAPK, and KAP1 to chromatin indicating that BUB1 is indispensable in the activation and recruitment of non-homologous end joining (NHEJ) proteins to DSBs. Additionally, BUB1 staining of TNBC tissue microarrays demonstrated significant correlation of BUB1 protein expression with tumor grade.

CONCLUSIONS

BUB1 ablation sensitizes TNBC cell lines and xenografts to RT and BUB1 mediated radiosensitization may occur through NHEJ. Together, these results highlight BUB1 as a novel molecular target for radiosensitization in women with TNBC.

BUB1 regulates non-homologous end joining pathway to mediate radioresistance in triple-negative breast cancer

Background

Triple-negative breast cancer (TNBC) is a highly aggressive form of breast cancer subtype often treated with radiotherapy (RT). Due to its intrinsic heterogeneity and lack of effective targets, it is crucial to identify novel molecular targets that would increase RT efficacy. Here we demonstrate the role of BUB1 (cell cycle Ser/Thr kinase) in TNBC radioresistance and offer a novel strategy to improve TNBC treatment.

Methods

Gene expression analysis was performed to look at genes upregulated in TNBC patient samples compared to other subtypes. Cell proliferation and clonogenic survivals assays determined the IC 50 of BUB1 inhibitor (BAY1816032) and radiation enhancement ratio (rER) with pharmacologic and genomic BUB1 inhibition. Mammary fat pad xenografts experiments were performed in CB17/SCID. The mechanism through which BUB1 inhibitor sensitizes TNBC cells to radiotherapy was delineated by γ-H2AX foci assays, BLRR, Immunoblotting, qPCR, CHX chase, and cell fractionation assays.

Results

BUB1 is overexpressed in BC and its expression is considerably elevated in TNBC with poor survival outcomes. Pharmacological or genomic ablation of BUB1 sensitized multiple TNBC cell lines to cell killing by radiation, although breast epithelial cells showed no radiosensitization with BUB1 inhibition. Kinase function of BUB1 is mainly accountable for this radiosensitization phenotype. BUB1 ablation also led to radiosensitization in TNBC tumor xenografts with significantly increased tumor growth delay and overall survival. Mechanistically, BUB1 ablation inhibited the repair of radiation-induced DNA double strand breaks (DSBs). BUB1 ablation stabilized phospho-DNAPKcs (S2056) following RT such that half-lives could not be estimated. In contrast, RT alone caused BUB1 stabilization, but pre-treatment with BUB1 inhibitor prevented stabilization (t 1/2 , ∼8 h). Nuclear and chromatin-enriched fractionations illustrated an increase in recruitment of phospho- and total-DNAPK, and KAP1 to chromatin indicating that BUB1 is indispensable in the activation and recruitment of non-homologous end joining (NHEJ) proteins to DSBs. Additionally, BUB1 staining of TNBC tissue microarrays demonstrated significant correlation of BUB1 protein expression with tumor grade.

Conclusions

BUB1 ablation sensitizes TNBC cell lines and xenografts to RT and BUB1 mediated radiosensitization may occur through NHEJ. Together, these results highlight BUB1 as a novel molecular target for radiosensitization in women with TNBC.

Discovery of a potent and selective covalent threonine tyrosine kinase (TTK) inhibitor

Threonine tyrosine kinase (TTK) is a critical component of the spindle assembly checkpoint and plays a pivotal role in mitosis. TTK has been identified as a potential therapeutic target for human cancers. Here, we describe our design, synthesis and evaluation of a class of covalent TTK inhibitors, exemplified by 16 (SYL1073). Compound 16 potently inhibits TTK kinase with an IC50 of 0.016 μM and displays improved selectivity in a panel of kinases. Mass spectrometry analysis reveals that 16 covalently binds to the C604 cysteine residue in the hinge region of the TTK kinase domain. Furthermore, 16 achieves strong potency in inhibiting the growth of various human cancer cell lines, outperforming its relative reversible inhibitor, and eliciting robust downstream effects. Taken together, compound 16 provides a valuable lead compound for further optimization toward the development of drug for treatment of human cancers.

Anoikis-related mRNA-lncRNA and DNA methylation profiles for overall survival prediction in breast cancer patients

As a type of programmed cell death, anoikis resistance plays an essential role in tumor metastasis, allowing cancer cells to survive in the systemic circulation and as a key pathway for regulating critical biological processes. We conducted an exploratory analysis to improve risk stratification and optimize adjuvant treatment choices for patients with breast cancer, and identify multigene features in mRNA and lncRNA transcriptome profiles associated with anoikis. First, the variance selection method filters low information content genes in RNA sequence and then extracts the mRNA and lncRNA expression data base on annotation files. Then, the top ten key mRNAs are screened out through the PPI network. Pearson analysis has been employed to identify lncRNAs related to anoikis, and the prognosis-related lncRNAs are selected using Univariate Cox regression and machine learning. Finally, we identified a group of RNAs (including ten mRNAs and six lncRNAs) and integrated the expression data of 16 genes to construct a risk-scoring system for BRCA prognosis and drug sensitivity analysis. The risk score's validity has been evaluated with the ROC curve, Kaplan-Meier survival curve analysis and decision curve analysis (DCA). For the methylation data, we have obtained 169 anoikis-related prognostic methylation sites, integrated these sites with 16 RNA features and further used the deep learning model to evaluate and predict the survival risk of patients. The developed anoikis feature is demonstrated a consistency index (C-index) of 0.778, indicating its potential to predict the survival probability of breast cancer patients using deep learning methods.

FOXM1 is critical for the fitness recovery of chromosomally unstable cells

Tumor progression and evolution are frequently associated with chromosomal instability (CIN). Tumor cells often express high levels of the mitotic checkpoint protein MAD2, leading to mitotic arrest and cell death. However, some tumor cells are capable of exiting mitosis and consequently increasing CIN. How cells escape the mitotic arrest induced by MAD2 and proliferate with CIN is not well understood. Here, we explored loss-of-function screens and drug sensitivity tests associated with MAD2 levels in aneuploid cells and identified that aneuploid cells with high MAD2 levels are more sensitive to FOXM1 depletion. Inhibition of FOXM1 promotes MAD2-mediated mitotic arrest and exacerbates CIN. Conversely, elevating FOXM1 expression in MAD2-overexpressing human cell lines reverts prolonged mitosis and rescues mitotic errors, cell death and proliferative disadvantages. Mechanistically, we found that FOXM1 facilitates mitotic exit by inhibiting the spindle assembly checkpoint (SAC) and the expression of Cyclin B. Notably, we observed that FOXM1 is upregulated upon aneuploid induction in cells with dysfunctional SAC and error-prone mitosis, and these cells are sensitive to FOXM1 knockdown, indicating a novel vulnerability of aneuploid cells.

Genetic deviation associated with photodynamic therapy in HeLa cell

Photodynamic therapy (PDT) is a method that is used in cancer treatment. The main therapeutic effect is the production of singlet oxygen (1O2). Phthalocyanines for PDT produce high singlet oxygen with absorbers of about 600-700 nm.

AIM

It is aimed to analyze cancer cell pathways by flow cytometry analysis and cancer-related genes with q-PCR device by applying phthalocyanine L1ZnPC, which we use as photosensitizer in photodynamic therapy, in HELA cell line. In this study, we investigate the molecular basis of L1ZnPC's anti-cancer activity.

MATERIAL METHOD

The cytotoxic effects of L1ZnPC, a phthalocyanine obtained from our previous study, in HELA cells were evaluated and it was determined that it led to a high rate of death as a result. The result of photodynamic therapy was analyzed using q-PCR. From the data received at the conclusion of this investigation, gene expression values were calculated, and expression levels were assessed using the 2-∆∆Ct method to examine the relative changes in these values. Cell death pathways were interpreted with the FLOW cytometer device. One-Way Analysis of Variance (ANOVA) and the Tukey-Kramer Multiple Comparison Test with Post-hoc Test were used for the statistical analysis.

CONCLUSION

In our study, it was observed that HELA cancer cells underwent apoptosis at a rate of 80% with drug application plus photodynamic therapy by flow cytometry method. According to q-PCR results, CT values ​​of eight out of eighty-four genes were found to be significant and their association with cancer was evaluated. L1ZnPC is a new phthalocyanine used in this study and our findings should be supported by further studies. For this reason, different analyses are needed to be performed with this drug in different cancer cell lines. In conclusion, according to our results, this drug looks promising but still needs to be analyzed through new studies. It is necessary to examine in detail which signaling pathways they use and their mechanism of action. For this, additional experiments are required.

Comprehensive analysis of the expression and prognosis for RAI2: A promising biomarker in breast cancer

Introduction

Retinoic acid-induced 2 (RAI2) was initially related to cell differentiation and induced by retinoic acid. RAI2 has been identified as an emerging tumor suppressor in breast cancer and colorectal cancer.

Methods

In this study, we performed systematic analyses of RAI2 in breast cancer. Meta-analysis and Kaplan-Meier survival curves were applied to identify the survival prediction potential of RAI2. Moreover, the association between RAI2 expression and the abundance of six tumor-infiltrating immune cells was investigated by TIMER, including B cells, CD8+ T cells, CD4+ T cells, B cells, dendritic cells, neutrophils, and macrophages. The expression profiles of high and low RAI2 mRNA levels in GSE7390 were compared to identify differentially expressed genes (DEGs) and the biological function of these DEGs was analyzed by R software, which was further proved in GSE7390.

Results

Our results showed that the normal tissues had more RAI2 expression than breast cancer tissues. Patients with high RAI2 expression were related to a favorable prognosis and more immune infiltrates. A total of 209 DEGs and 182 DEGs were identified between the expression profiles of high and low RAI2 mRNA levels in the GSE7390 and GSE21653 databases, respectively. Furthermore, Gene Ontology (GO) enrichment indicated that these DEGs from two datasets were both mainly distributed in “biological processes” (BP), including “organelle fission” and “nuclear division”. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis demonstrated that these DEGs from two datasets were both significantly enriched in the “cell cycle”. Common hub genes between the DEGs in GSE7390 and GSE21653 were negatively associated with RAI2 expression, including CCNA2, MAD2L1, MELK, CDC20, and CCNB2.

Discussions

These results above suggested that RAI2 might play a pivotal role in preventing the initiation and progression of breast cancer. The present study may contribute to understanding the molecular mechanisms of RAI2 and enriching biomarkers to predict patient prognosis in breast cancer.

Demystifying the Role of Prognostic Biomarkers in Breast Cancer through Integrated Transcriptome and Pathway Enrichment Analyses

Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of death in women. Researchers have discovered an increasing number of molecular targets for BC prognosis and therapy. However, it is still urgent to identify new biomarkers. Therefore, we evaluated biomarkers that may contribute to the diagnosis and treatment of BC. We searched TCGA datasets and identified differentially expressed genes (DEGs) by comparing tumor (100 samples) and non-tumor (100 samples) tissues using the Deseq2 package. Pathway and functional enrichment analysis of the DEGs was performed using the DAVID (Database for Annotation, Visualization, and Integrated Discovery) database. The protein–protein interaction (PPI) network was identified using the STRING database and visualized through Cytoscape software. Hub gene analysis of the PPI network was completed using cytohubba plugins. The associations between the identified genes and overall survival (OS) were analyzed using a Kaplan–Meier plot. Finally, we have identified hub genes at the transcriptome level. A total of 824 DEGs were identified, which were mostly enriched in cell proliferation, signal transduction, and cell division. The PPI network comprised 822 nodes and 12,145 edges. Elevated expression of the five hub genes AURKA, BUB1B, CCNA2, CCNB2, and PBK are related to poor OS in breast cancer patients. A promoter methylation study showed these genes to be hypomethylated. Validation through genetic alteration and missense mutations resulted in chromosomal instability, leading to improper chromosome segregation causing aneuploidy. The enriched functions and pathways included the cell cycle, oocyte meiosis, and the p53 signaling pathway. The identified five hub genes in breast cancer have the potential to become useful targets for the diagnosis and treatment of breast cancer.

Targeting the anaphase-promoting complex/cyclosome (APC/C) enhanced antiproliferative and apoptotic response in bladder cancer

Improving the chemotherapy sensitivity of bladder cancer is a current clinical challenge. It is critical to seek out effective combination therapies that include low doses of cisplatin due to its dose-limiting toxicity. This study aims to investigate the cytotoxic effects of the combination therapy including proTAME, a small molecule inhibitor, targeting Cdc-20 and to determine the expression levels of several APC/C pathway-related genes that may play a role in the chemotherapy response of RT-4 (bladder cancer) and ARPE-19 (normal epithelial) cells. The IC20 and IC50 values were determined by MTS assay. The expression levels of apoptosis-associated (Bax and Bcl-2) and APC/C-associated (Cdc-20, Cyclin-B1, Securin, and Cdh-1) genes were assessed by qRT-PCR. Cell colonization ability and apoptosis were examined by clonogenic survival experiment and Annexin V/PI staining, respectively. Low-dose combination therapy showed a superior inhibition effect on RT-4 cells by increasing cell death and inhibiting colony formation. Triple-agent combination therapy further increased the percentage of late apoptotic and necrotic cells compared to the doublet-therapy with gemcitabine and cisplatin. ProTAME-containing combination therapies resulted in an elevation in Bax/Bcl-2 ratio in RT-4 cells, while a significant decrease was observed in proTAME-treated ARPE-19 cells. Cdc-20 expression in proTAME combined treatment groups were found to be decreased compared to their control groups. Low-dose triple-agent combination induced cytotoxicity and apoptosis in RT-4 cells effectively. It is essential to evaluate the role of APC/C pathway-associated potential biomarkers as therapeutic targets and define new combination therapy regimens to achieve improved tolerability in bladder cancer patients in the future.

Current Progress and Perspectives of CDC20 in Female Reproductive Cancers

The cancers of the cervix, endometrium, ovary, and breast are great threats to women's health. Cancer is characterized by the uncontrolled proliferation of cells and deregulated cell cycle progression is one of the main causes of malignancy. Agents targeting cell cycle regulators may have potential anti-tumor effects. CDC20 (cell division cycle 20 homologue) is a co-activator of the anaphase-promoting complex/cyclosome (APC/C) and thus acts as a mitotic regulator. In addition, CDC20 serves as a subunit of the mitotic checkpoint complex (MCC) whose function is to inhibit APC/C. Recently, higher expression of CDC20 has been reported in these cancers and was closely associated with their clinicopathological parameters, indicating CDC20 a potential target for cancer treatment that is worth further study. In the present review, we summarized current progress and put forward perspectives of CDC20 in female reproductive cancers.

Ethnic and racial-specific differences in levels of centrosome-associated mitotic kinases, proliferative and epithelial-to-mesenchymal markers in breast cancers

Molecular epidemiology evidence indicates racial and ethnic differences in the aggressiveness and survival of breast cancer. Hispanics/Latinas (H/Ls) and non-Hispanic Black women (NHB) are at higher risk of breast cancer (BC)-related death relative to non-Hispanic white (NHW) women in part because they are diagnosed with hormone receptor-negative (HR) subtype and at higher stages. Since the cell cycle is one of the most commonly deregulated cellular processes in cancer, we propose that the mitotic kinases TTK (or Mps1), TBK1, and Nek2 could be novel targets to prevent breast cancer progression among NHBs and H/Ls. In this study, we calculated levels of TTK, p-TBK1, epithelial (E-cadherin), mesenchymal (Vimentin), and proliferation (Ki67) markers through immunohistochemical (IHC) staining of breast cancer tissue microarrays (TMAs) that includes samples from 6 regions in the Southeast of the United States and Puerto Rico -regions enriched with NHB and H/L breast cancer patients. IHC analysis showed that TTK, Ki67, and Vimentin were significantly expressed in triple-negative (TNBC) tumors relative to other subtypes, while E-cadherin showed decreased expression. TTK correlated with all of the clinical variables but p-TBK1 did not correlate with any of them. TCGA analysis revealed that the mRNA levels of multiple mitotic kinases, including TTK, Nek2, Plk1, Bub1, and Aurora kinases A and B, and transcription factors that are known to control the expression of these kinases (e.g. FoxM1 and E2F1-3) were upregulated in NHBs versus NHWs and correlated with higher aneuploidy indexes in NHB, suggesting that these mitotic kinases may be future novel targets for breast cancer treatment in NHB women.

CFI-402257, a TTK inhibitor, effectively suppresses hepatocellular carcinoma

Deregulation of cell cycle is a typical feature of cancer cells. Normal cells rely on the strictly coordinated spindle assembly checkpoint (SAC) to maintain the genome integrity and survive. However, cancer cells could bypass this checkpoint mechanism. In this study, we showed the clinical relevance of threonine tyrosine kinase (TTK) protein kinase, a central regulator of the SAC, in hepatocellular carcinoma (HCC) and its potential as therapeutic target. Here, we reported that a newly developed, orally active small molecule inhibitor targeting TTK (CFI-402257) effectively suppressed HCC growth and induced highly aneuploid HCC cells, DNA damage, and micronuclei formation. We identified that CFI-402257 also induced cytosolic DNA, senescence-like response, and activated DDX41-STING cytosolic DNA sensing pathway to produce senescence-associated secretory phenotypes (SASPs) in HCC cells. These SASPs subsequently led to recruitment of different subsets of immune cells (natural killer cells, CD4⁺ T cells, and CD8⁺ T cells) for tumor clearance. Our mass cytometry data illustrated the dynamic changes in the tumor-infiltrating immune populations after treatment with CFI-402257. Further, CFI-402257 improved survival in HCC-bearing mice treated with anti-PD-1, suggesting the possibility of combination treatment with immune checkpoint inhibitors in HCC patients. In summary, our study characterized CFI-402257 as a potential therapeutic for HCC, both used as a single agent and in combination therapy.

Chronic carbon black nanoparticles exposure increases lung cancer risk by affecting the cell cycle via circulatory inflammation

As a widely used pure elemental carbon in colloidal particles, carbon black was listed as a group 2B carcinogen by IARC in 2010. The most available mechanism information about carbon black and carcinogenesis are from in vivo or in vitro studies. However, few studies concerned the nanoparticle's real-ambient exposure causing systemic change and further affecting the target organ. Herein, we used an ex vivo biosensor assay to investigate the transcriptome change of primary bronchial epithelial cells after treatment with the plasma from workers with long-term occupational carbon black exposure history. Based on ex vivo biosensor assay and transcriptome sequencing, we found the effect of internal systemic environment on epithelial cells after carbon black exposure was an inflammatory response, which mainly activates cell cycle-related pathways. After exposure to carbon black, the internal systemic environment could activate cancer-related pathways like epithelial-mesenchymal transition, hypoxia, TNF-α signaling via NF-κB. The hub genes in the carbon black group (CDC20 and PLK1) and their correlation with the systemic environment were uncovered by constructing the protein-protein interaction network. Inflammatory cytokines, especially CRP, were strongly correlated with the expression of CDC20 and PLK1. Besides, we also find a strong correlation between CDC20 and cytokinesis-block micronucleus endpoints in peripheral blood (rho = 0.591, P < 0.001). Our results show that long-term carbon black exposure might activate cell cycle-related pathways through circulating inflammation and increase the risk of cancer, while the oxidative stress caused by diesel exhaust particles are mainly related to PAHs exposure. After exposure to carbon black, the systemic environment could activate cancer-related pathways like diesel exhaust particles, increasing the risk of lung cancer. These attempts might provide a further understanding of the indirect effect of chronic occupational inhaled carbon black exposure on pulmonary carcinogenesis.

BUB3, beyond the Simple Role of Partner

The BUB3 protein plays a key role in the activation of the spindle assembly checkpoint (SAC), a ubiquitous surveillance mechanism that ensures the fidelity of chromosome segregation in mitosis and, consequently, prevents chromosome mis-segregation and aneuploidy. Besides its role in SAC signaling, BUB3 regulates chromosome attachment to the spindle microtubules. It is also involved in telomere replication and maintenance. Deficiency of the BUB3 gene has been closely linked to premature aging. Upregulation of the BUB3 gene has been found in a variety of human cancers and is associated with poor prognoses. Here, we review the structure and functions of BUB3 in mitosis, its expression in cancer and association with survival prognoses, and its potential as an anticancer target.

Identification of Key Prognostic Genes of Triple Negative Breast Cancer by LASSO-Based Machine Learning and Bioinformatics Analysis

Improved insight into the molecular mechanisms of triple negative breast cancer (TNBC) is required to predict prognosis and develop a new therapeutic strategy for targeted genes. The aim of this study is to identify key genes which may affect the prognosis of TNBC patients by bioinformatic analysis. In our study, the RNA sequencing (RNA-seq) expression data of 116 breast cancer lacking ER, PR, and HER2 expression and 113 normal tissues were downloaded from The Cancer Genome Atlas (TCGA). We screened out 147 differentially co-expressed genes in TNBC compared to non-cancerous tissue samples by using weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were constructed, revealing that 147 genes were mainly enriched in nuclear division, chromosomal region, ATPase activity, and cell cycle signaling. After using Cytoscape software for protein-protein interaction (PPI) network analysis and LASSO feature selection, a total of fifteen key genes were identified. Among them, BUB1 and CENPF were significantly correlated with the overall survival rate (OS) difference of TNBC patients (p value < 0.05). In addition, BUB1, CCNA2, and PACC1 showed significant poor disease-free survival (DFS) in TNBC patients (p value < 0.05), and may serve as candidate biomarkers in TNBC diagnosis. Thus, our results collectively suggest that BUB1, CCNA2, and PACC1 genes could play important roles in the progression of TNBC and provide attractive therapeutic targets.

CDC20 in and out of mitosis: a prognostic factor and therapeutic target in hematological malignancies

Cell division cycle 20 homologue (CDC20) is a well-known regulator of cell cycle, as it controls the correct segregation of chromosomes during mitosis. Many studies have focused on the biological role of CDC20 in cancer development, as alterations of its functionality have been linked to genomic instability and evidence demonstrated that high CDC20 expression levels are associated with poor overall survival in solid cancers. More recently, novel CDC20 functions have been demonstrated or suggested, including the regulation of apoptosis and stemness properties and a correlation with immune cell infiltration. Here, we here summarize and discuss the role of CDC20 inside and outside mitosis, starting from its network of interacting proteins. In the last years, CDC20 has also attracted more interest in the blood cancer field, being overexpressed and showing an association with prognosis both in myeloid and lymphoid malignancies. Preclinical findings showed that selective CDC20 and APC/C^CDC20/APC/C^CDH1 inhibitors, namely Apcin and proTAME, are effective against lymphoma and multiple myeloma cells, resulting in mitotic arrest and apoptosis and synergizing with clinically-relevant drugs. The evidence and hypothesis presented in this review provide the input for further biological and chemical studies aiming to dissect novel potential CDC20 roles and targeting strategies in hematological malignancies.

BUBs Are New Biomarkers of Promoting Tumorigenesis and Affecting Prognosis in Breast Cancer

Background

A tumor occurs because of abnormal cell multiplication caused by many variables like a significant disturbance in the regulation of cell growth and the instability of chromosome mitosis. Budding uninhibited by benzimidazoles 1 (BUB1), BUB1 mitotic checkpoint serine/threonine kinase B (BUB1B), and budding uninhibited by benzimidazoles 3 (BUB3) are key regulators of mitosis, and their abnormal expression is highly correlated with breast cancer (BrCa), sarcoma, hepatic carcinoma, and other malignant tumors. However, the occurrence of BUBs (BUB1, BUB1B, and BUB3) and the development of BrCa have not been systematically explained.

Methods

Find out the target gene by looking up literature on PubMed and CNKI. Using the R software, TCGA, GEO, Kaplan-Meier Plotter, TIMER, and other databases, we studied the level of transcription, genetic changes, and physiological functions of BUBs in BrCa patients and their relationship with the origin, development, prognosis, immunity, and drug resistance of BrCa patients. Findings. We found that the high expression level of BUBs in BrCa tissues proposed a poor prognosis. The multivariate Cox regression analysis suggested that BUB1B and BUB3 might be independent prognostic factors of BrCa. In addition, the Metascape functional enrichment analysis showed that BUBs may be involved in the composition of the spindle, chromosome, and other structures and play a role in mitosis, sister chromatid separation, and other processes. Pathway enrichment suggests that BUBs may affect the cell cycle and lead to abnormal proliferation. Meanwhile, we also found that BUB3 can negatively regulate B lymphocytes, and BUB1 and BUB1B inhibit immune responses by promoting the secretion level of checkpoint molecules of the immune system, leading to immune escape of tumor cells.

Conclusion

We speculate that BUB1, BUB1B, and BUB3 may be therapeutic targets for BrCa patients and also provide new therapeutic strategies for BrCa treatment.

Aurora kinase A inhibition induces synthetic lethality in SMAD4-deficient colorectal cancer cells via spindle assembly checkpoint activation

SMAD4 loss-of-function mutations have been frequently observed in colorectal cancer (CRC) and are recognized as a drug target for therapeutic exploitation. In this study, we performed a synthetic lethal drug screening with SMAD4-isogenic CRC cells and found that aurora kinase A (AURKA) inhibition is synthetic lethal with SMAD4 loss. Inhibition of AURKA selectively inhibited the growth of SMAD4^-/- CRC in vitro and in vivo. Mechanistically, SMAD4 negatively regulated AURKA level, resulting in the significant elevation of AURKA in SMAD4^-/- CRC cells. Inhibition of AURKA induced G₂/M cell cycle delay in SMAD4^+/+ CRC cells, but induced apoptosis in SMAD4^-/- CRC cells. We further observed that a high level of AURKA in SMAD4^-/- CRC cells led to abnormal mitotic spindles, leading to cellular aneuploidy. Moreover, SMAD4^-/- CRC cells expressed high levels of spindle assembly checkpoint (SAC) proteins, suggesting the hyperactivation of SAC. The silencing of key SAC proteins significantly rescued the AURKA inhibition-induced cell death in SMAD4^-/- cells, suggesting that SMAD4^-/- CRC cells are hyper-dependent on AURKA activity for mitotic exit and survival during SAC hyperactivation. This study presents a unique synthetic lethal interaction between SMAD4 and AURKA and suggests that AURKA could be a potential drug target in SMAD4-deficient CRC.

CYCLOBUTANES IN SMALL MOLECULE DRUG CANDIDATES

Cyclobutanes are increasingly used in medicinal chemistry in the search for relevant biological properties. Important characteristics of the cyclobutane ring include its unique puckered structure, longer C−C bond lengths, increased C−C π‐character and relative chemical inertness for a highly strained carbocycle. This review will focus on contributions of cyclobutane rings in drug candidates to arrive at favorable properties. Cyclobutanes have been employed for improving multiple factors such as preventing cis/trans‐isomerization by replacing alkenes, replacing larger cyclic systems, increasing metabolic stability, directing key pharmacophore groups, inducing conformational restriction, reducing planarity, as aryl isostere and filling hydrophobic pockets.

Upregulation of REV7 correlates with progression of malignant melanoma

REV7 is a multifunctional protein implicated in DNA damage tolerance, cell cycle control, and gene expression, and is involved in the carcinogenesis of various human tumors. It has been reported that REV7 expression is associated with ultraviolet-induced mutagenesis; however, the role of REV7 expression in skin cancers, including malignant melanomas, remains unclear. In the present study, we investigated the clinical and biological significance of REV7 in malignant melanoma. Levels of REV7 expression in human skin cancers were evaluated immunohistochemically. Positive expression of REV7 was frequently observed in malignant melanomas, as well as in squamous cell carcinomas and basal cell carcinomas. Enhanced immunoreactivity to REV7 was closely linked with cell proliferation assessed by Ki-67 labeling indexes in the three skin cancers, and was related with tumor thickness in malignant melanomas. REV7 depletion in malignant melanoma cells MEWO and G361 suppressed cell proliferation, migration, and invasion abilities. REV7 depletion also affected the expression of intracellular signaling molecules AKT and ERK in MEWO cells, resulting in downregulation of ERK signal activation. In addition, REV7 depletion facilitated sensitivity to cisplatin, but not to dacarbazine, in MEWO cells. Our results suggest that REV7 expression correlates with disease progression of malignant melanoma.

Cell cycle control in cancer

Cancer is a group of diseases in which cells divide continuously and excessively. Cell division is tightly regulated by multiple evolutionarily conserved cell cycle control mechanisms, to ensure the production of two genetically identical cells. Cell cycle checkpoints operate as DNA surveillance mechanisms that prevent the accumulation and propagation of genetic errors during cell division. Checkpoints can delay cell cycle progression or, in response to irreparable DNA damage, induce cell cycle exit or cell death. Cancer-associated mutations that perturb cell cycle control allow continuous cell division chiefly by compromising the ability of cells to exit the cell cycle. Continuous rounds of division, however, create increased reliance on other cell cycle control mechanisms to prevent catastrophic levels of damage and maintain cell viability. New detailed insights into cell cycle control mechanisms and their role in cancer reveal how these dependencies can be best exploited in cancer treatment.

Research progress of Bub3 gene in malignant tumors

The spindle assembly checkpoint (SAC) is a highly conserved monitoring system that ensures a fidelity of chromosome segregation during mitosis. Bub3, a mitotic Checkpoint Protein, is a member of the Bub protein family, and an important factor in the SAC. Abnormal expression of Bub3 results in mitotic defects, defective spindle gate function, chromosomal instability and the development of aneuploidy cells. Aneuploidy is a state of abnormal karyotype that has long been considered as a marker of tumorigenesis. Karyotypic heterogeneity in tumor cells, known as "chromosomal instability" (CIN), can be used to distinguish cancerous cells from their normal tissue counterpart. In this review, we summarize the expression and clinical significance of Bub3 in a variety of tumors and suggest that it has potential in the treatment of cancer. This article is protected by copyright. All rights reserved.

Comprehensive Analysis of Regulatory Factors and Immune-Associated Patterns to Decipher Common and BRCA1/2 Mutation-Type-Specific Critical Regulation in Breast Cancer

Background: BRCA1/2 mutations are closely related to high lifetime risk of breast cancer (BC). The objective of this study was to identify the genes, regulators, and immune-associated patterns underlying disease pathology in BC with BRCA1/2 somatic mutations and their associations with clinical traits. Methods: RNA sequencing data and clinical information from The Cancer Genome Atlas (TCGA; N = 36 BRCA1-mutant BC; N = 49 BRCA2-mutant BC; and N = 117 BRCA1/2-wild-type BC samples) were used for discovery, which included consensus network analysis, function enrichment, and analysis of hub genes; other TCGA data (N = 117 triple-negative BC) and two Gene Expression Omnibus database expression profiles were used as validation cohorts. Results: Consensus network analysis helped to identify specific co-expressed modules that showed positive correlations with tumor stage, number of positive lymph nodes, and margin status in BRCA1/2-mutant BC but lacking correlations in BRCA1/2-wild-type BC. Functional enrichment suggested potential mechanisms in BRCA1/2 carriers that could regulate the cell cycle, immune response, cellular metabolic processes, and cell migration, via enriched pathways including p53 and JAK-STAT signaling. Consensus network analysis identified the specific and common carcinogenic mechanisms involving BRCA mutations. Regulators cross-linking these modules include E2F or IRF transcription factor family, associated with cell cycle or immune response regulation module, respectively. Eight hub genes, including ISG15, BUB1, and TTK, were upregulated in several BRCA1/2-mutant BC datasets and showed prognostic value in BC. Furthermore, their genetic expression was related to higher levels of immune infiltration in BRCA1/2-mutant BC, which manifested as recruitment of T helper cells (Th1 cells), follicular helper T cells, and regulatory T cells, and T cell exhaustion. Moreover, important indicators for evaluation of BC immunotherapy, tumor mutational burden and neoantigen load also positively correlated with expression of some hub genes. Conclusion: We constructed a BRCA1/2 mutation-type-specific co-expressed gene network with related transcription factors and immune-associated patterns that could regulate and influence tumor metastasis and immune microenvironment, providing novel insights into the pathological process of this disease and the corresponding BRCA mutations.

Frequent expression of a novel cancer testis antigen, protein kinase human monopolar spindle 1 (hMps1/TTK) in human urinary bladder transitional cell carcinoma

Urothelial bladder cancer (UBC) is a frequently occurring malignancy of the urinary tract. The present study was undertaken to evaluate the mRNA and immunohistochemical (IHC) expression of protein kinase human monopolar spindle 1 (hMps1/TTK) gene in transitional cell carcinoma (TCC) of the bladder and correlate its expression with the clinicopathological characteristics of patients. In the present study, quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR) was used to evaluate TTK mRNA expression in TCC. IHC analysis of TTK was also evaluated. Independent Student's t, ANOVA and chi-square (χ²) tests were used to analyze the data statistically. The frequency of TTK mRNA over expression was detected in 50% of UBC (38/76) by qRT-PCR. Relative mean fold expression of TTK mRNA was found significantly (p < 0.05) higher in muscle-invasive bladder cancer (MIBC) as compared to non-muscle-invasive bladder cancer (NMIBC) patients (8.96 ± 4.51 vs. 5.64 ± 3.53, p = 0.03). Moreover, IHC reveals heterogenous immunostaining pattern of TTK in TCC tissues. The frequency of TTK protein over expression was detected in 56.9% (37 of 65) UBC patients. No significant IHC expression of TTK was detected among adjacent noncancerous tissues (ANCTs) and benign prostatic hyperplasia (BPH) used as control. Collectively our study observations conclude that TTK is a novel cancer/testis antigen (CTA) as a diagnostic marker for early diagnosis of UBC.

Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

The prognosis of malignant gliomas such as glioblastoma multiforme (GBM) has remained poor due to limited therapeutic strategies. Thus, it is pivotal to determine prognostic factors for gliomas. Thyroid Receptor Interacting Protein 13 (TRIP13) was found to be overexpressed in several solid tumors, but its role and clinical significance in gliomas is still unclear. Here, we conducted a comprehensive expression analysis of TRIP13 to determine the prognostic values. Gene expression profiles of the Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA) and GSE16011 dataset showed increased TRIP13 expression in advanced stage and worse prognosis in IDH-wild type lower-grade glioma. We performed RT-PCR and Western blot to validate TRIP13 mRNA expression and protein levels in GBM cell lines. TRIP13 co-expressed genes via database screening were regulated by essential cancer-related upstream regulators (such as TP53 and FOXM1). Then, TCGA analysis revealed that more TRIP13 promoter hypomethylation was observed in GBM than in low-grade glioma. We also inferred that the upregulated TRIP13 levels in gliomas could be regulated by dysfunction of miR-29 in gliomas patient cohorts. Moreover, TRIP13-expressing tumors not only had higher aneuploidy but also tended to reduce the ratio of CD8⁺/Treg, which led to a worse survival outcome. Overall, these findings demonstrate that TRIP13 has with multiple functions in gliomas, and they may be crucial for therapeutic potential.

Cell division cycle proteinising prognostic biomarker of breast cancer

Cell division cycle protein (CDC20) has been observed to be expressed higher in various kinds of human cancers and was associated with poor prognosis. However, studies on role of CDC20 in breast cancer are seldom reported till now, most of which are not systematic and conclusive. The present study was performed to analyze the expression pattern, potential function, and distinct prognostic effect of CDC20 in breast cancer using several online databases including Oncomine, bc-GenExMiner, PrognoScan, and UCSC Xena. To verify the results from databases, we compared the mRNA CDC20 expression in breast cancer tissues and adjacent normal tissues of patients by real-time PCR. We found that CDC20 was expressed higher in different types of breast cancer, comparing with normal tissues. Moreover, the patients with a more advanced stage of breast cancer tended to express higher level CDC20. CDC20 was expressed higher in breast cancer tissues than normal tissues from patients in our hospital, consistent with the results from databases. Estrogen receptor (ER) and progesterone receptor (PR) status were negatively correlated with CDC20 level. Conversely, Scarff–Bloom–Richardson (SBR) grade, Nottingham prognostic index (NPI), epidermal growth factor receptor-2 (HER-2) status, basal-like status, and triple-negative status were positively related to CDC20 expression in breast cancer patients with respect to normal individuals. Higher CDC20 expression correlated with worse survival. Finally, a positive correlation between CDC20 and Targeting protein for Xenopus kinesin-like protein 2 (TPX2) expression was revealed. CDC20 could be considered as a potential predictive indicator for prognosis of breast cancer with co-expressed TPX2 gene.

CRISPR-cas9 Screening Identified Lethal Genes Enriched in Cell Cycle Pathway and of Prognosis Significance in Breast Cancer

Background

Lethal genes have not been systematically analyzed in breast cancer which may have significant prognostic value. The current study aims to investigate vital genes related to cell viability by analyzing the CRISPR-cas9 screening data, which may provide novel therapeutic target for patients.

Methods

Genes differentially expressed between tumor and normal tissue from the Cancer Genome Atlas (TCGA) and genes related to cell viability by CRISPR-cas9 screening from Depmap (Cancer Dependency Map) were overlapped. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis was conducted to identify which pathways of overlapped genes were enriched. GSE21653 set was randomized into training and internal validation dataset at a ratio of 3:1, and external validation was performed in GSE20685 set. The least absolute shrinkage and selection operator (LASSO) regression was used to construct a signature to predict recurrence-free survival (RFS) of breast cancer patients. Univariate and multivariate Cox regression were used to evaluate the prognostic value of this signature. Differentially expressed genes (DEGs) between high-risk and low-risk patients were then analyzed to identify the main pathways regulated by this signature. Weighted correlation network analysis (WGCNA) was conducted to recognize modules correlated with high risk. Enrichment analysis was then used to identify pathways regulated by genes shared in the overlapped genes, DEGs, and WGCNA.

Results

A total of 86 oncogenes were upregulated in TCGA database and overlapped with lethal genes in Depmap database, which were enriched in cell cycle pathway. A total of 51 genes were included in the gene signature based on LASSO regression, and the median risk score of 2.36 was used as cut-off to separate low-risk patients from high-risk patients. High-risk patients showed worse RFS compared with low-risk patients in internal training, internal validation, and external validation dataset. Time-dependent receiver operating characteristic curves of 3 and 5 years indicated that risk score was superior to tumor stage, age, and PAM50 in both entire and external validation datasets. Cell cycle was the main different pathway between the high-risk and low-risk groups. Meanwhile, cell cycle was also the main pathway enriched in the 25 genes which were shared among 86 genes, DEGs, and WGCNA.

Conclusion

Cell cycle pathway, identified by CRISPR-cas9 screening, was a key pathway regulating cell viability, which has significant prognostic values and can serve as a new target for breast cancer patient treatment.

Long non-coding RNA NORAD upregulation induced by airborne particulate matter (PM10) exposure leads to aneuploidy in A549 lung cells

Air pollution is a worldwide problem that affects human health predominantly in the largest cities. Particulate matter of 10 μm or less in diameter (PM₁₀) is considered a risk factor for multiple diseases, including lung cancer. The long non-coding RNA NORAD and the components of the spindle assembly checkpoint (SAC) ensure proper chromosomal segregation. Alterations in the SAC cause aneuploidy, a feature associated with carcinogenesis. In this study, we demonstrated that PM₁₀ treatment increased the expression levels of NORAD as well as those of SAC components mitotic arrest deficient 1 (MAD1L1), mitotic arrest deficient 2 (MAD2L1), BubR1 (BUB1B), aurora B (AURKB), and survivin (BIRC5) in the lung A549 cell line. We also demonstrated that MAD1L1, MAD2L1, and BUB1B expression levels were reduced when cells were transfected with small interfering RNAs (siRNAs) against NORAD. Interestingly, the expression levels of AURKB and BIRC5 (survivin) were not affected by transfection with NORAD siRNAs. Cells treated with PM₁₀ exhibited a decrease in mitotic arrest and an increase in micronuclei frequency in synchronized A549 cells. PM₁₀ exposure induced aneuploidy events as a result of SAC deregulation. We also observed a reduction in the protein levels of Pumilio 1 after PM₁₀ treatment. Our results provide novel clues regarding the effect of PM₁₀ in the generation of chromosomal instability, a phenotype observed in lung cancer cells.

BUB1B Overexpression Is an Independent Prognostic Marker and Associated with CD44, p53, and PD-L1 in Renal Cell Carcinoma

INTRODUCTION

BUB1 mitotic checkpoint serine/threonine kinase B encoded by BUB1B gene is a member of the spindle assembly checkpoint family. Several reports have demonstrated that overexpression of BUB1B is associated with cancer progression and prognosis.

OBJECTIVE

This study aims to clarify the expression and function of BUB1B in renal cell carcinoma (RCC).

METHODS

The expression of BUB1B was determined using immunohistochemistry and bioinformatics analysis in RCC. The effects of BUB1B knockdown on cell growth and invasion were evaluated. We analyzed the interaction between BUB1B, cancer stem cell markers, p53, and PD-L1 in RCC.

RESULTS

In 121 cases of RCC, immunohistochemistry showed that 30 (25%) of the RCC cases were positive for BUB1B. High BUB1B expression was significantly correlated with high nuclear grade, T stage, and M stage. A Kaplan-Meier analysis showed that the high expression of BUB1B was associated with poor overall survival after nephrectomy. High BUB1B expression was associated with CD44, p53, and PD-L1 in RCC. Knockdown of BUB1B suppressed cell growth and invasion in RCC cell lines. Knockdown of BUB1B also suppressed the expression of CD44 and increased the expression of phospho-p53 (Ser15). In silico analysis showed that BUB1B was associated with inflamed CD8+, exhausted T-cell signature, IFN-γ signature, and the response to nivolumab.

CONCLUSION

These results suggest that BUB1B plays an oncogenic role and may be a promising predictive biomarker for survival in RCC.

Gene networks and transcriptional regulators associated with liver cancer development and progression

Background

Treatment options for hepatocellular carcinoma (HCC) are limited, and overall survival is poor. Despite the high frequency of this malignoma, its basic disease mechanisms are poorly understood. Therefore, the aim of this study was to use different methodological approaches and combine the results to improve our knowledge on the development and progression of HCC.

Methods

Twenty-three HCC samples were characterized by histological, morphometric and cytogenetic analyses, as well as comparative genomic hybridization (aCGH) and genome-wide gene expression followed by a bioinformatic search for potential transcriptional regulators and master regulatory molecules of gene networks.

Results

Histological evaluation revealed low, intermediate and high-grade HCCs, and gene expression analysis split them into two main sets: GE1-HCC and GE2-HCC, with a low and high proliferation gene expression signature, respectively. Array-based comparative genomic hybridization demonstrated a high level of chromosomal instability, with recurrent chromosomal gains of 1q, 6p, 7q, 8q, 11q, 17q, 19p/q and 20q in both HCC groups and losses of 1p, 4q, 6q, 13q and 18q characteristic for GE2-HCC. Gene expression and bioinformatics analyses revealed that different genes and gene regulatory networks underlie the distinct biological features observed in GE1-HCC and GE2-HCC. Besides previously reported dysregulated genes, the current study identified new candidate genes with a putative role in liver cancer, e.g. C1orf35, PAFAH1B3, ZNF219 and others.

Conclusion

Analysis of our findings, in accordance with the available published data, argues in favour of the notion that the activated E2F1 signalling pathway, which can be responsible for both inappropriate cell proliferation and initial chromosomal instability, plays a pivotal role in HCC development and progression. A dedifferentiation switch that manifests in exaggerated gene expression changes might be due to turning on transcriptional co-regulators with broad impact on gene expression, e.g. POU2F1 (OCT1) and NFY, as a response to accumulating cell stress during malignant development. Our findings point towards the necessity of different approaches for the treatment of HCC forms with low and high proliferation signatures and provide new candidates for developing appropriate HCC therapies.

DNA Methylation Based Molecular Subtypes Predict Prognosis in Breast Cancer Patients

BACKGROUND

Epigenetic changes are tightly linked to tumorigenesis development and malignant transformation' However, DNA methylation occurs earlier and is constant during tumorigenesis. It plays an important role in controlling gene expression in cancer cells.

METHODS

In this study, we determining the prognostic value of molecular subtypes based on DNA methylation status in breast cancer samples obtained from The Cancer Genome Atlas database (TCGA).

RESULTS

Seven clusters and 204 corresponding promoter genes were identified based on consensus clustering using 166 CpG sites that significantly influenced survival outcomes. The overall survival (OS) analysis showed a significant prognostic difference among the 7 groups (p<0.05). Finally, a prognostic model was used to estimate the results of patients on the testing set based on the classification findings of a training dataset DNA methylation subgroups.

CONCLUSIONS

The model was found to be important in the identification of novel biomarkers and could be of help to patients with different breast cancer subtypes when predicting prognosis, clinical diagnosis and management.

Identification of CDK1 as a candidate marker in cutaneous squamous cell carcinoma by integrated bioinformatics analysis

BACKGROUND

Cutaneous squamous cell carcinoma (cSCC) is a relatively common cancer that accounts for nearly 50% of non-melanoma skin cancer cases. However, the genotypes that are linked with poor prognosis and/or high relapse rates and pathogenic mechanisms of cSCC are not fully understood. To address these points, three gene expression datasets were analyzed to identify candidate biomarker genes in cSCC.

METHODS

The GSE117247, GSE32979, and GSE98767 datasets comprising a total of 32 cSCC samples and 31 normal skin tissue samples were obtained from the National Center for Biotechnology Information Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified and underwent pathway enrichment analyses with the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG). A putative DEG protein-protein interaction (PPI) network was also established that included hub genes. The expression of CDK1, MAD2L1, BUB1 ans CDC20 were examined in the study.

RESULTS

A total of 335 genes were identified, encompassing 219 found to be upregulated and 116 genes that were downregulated in cSCC, compared to normal tissue. Enriched functions of these DEGs were associated with Ephrin receptor signaling and cell division; cytosol, membrane, and extracellular exosomes; ATP-, poly(A) RNA-, and identical protein binding. We also established a PPI network comprising 332 nodes and identified KIF2C, CDC42, AURKA, MAD2L1, MYC, CDK1, FEN1, H2AFZ, BUB1, BUB1B, CKS2, CDC20, CCT2, ACTR2, ACTB, MAPK14, and HDAC1 as candidate hub genes. The expression of CDK1 are significantly higher in the cSCC tissues than that in normal skin.

CONCLUSIONS

The DEGs identified in this study are potential therapeutic targets and biomarkers for cSCC. CDK1 is a gene closely related to the occurrence and development of cSCC, which may play an important role. Bioinformatics analysis shows that it is involved in the important pathway of the pathogenesis of cSCC, and may be recognized and applied as a new biomarker in the future diagnosis and treatment of cSCC.

MiR-582-5p Inhibits Bladder Cancer-Genesis by Suppressing TTK Expression

BACKGROUND

Bladder cancer (BC) refers to the malignant growth found in the cells and tissues of the urinary bladder. While many studies have researched the progression of BC, scientists are yet to fully understand the mechanism of BC. This research aimed to explore the role of miR-582-5p and its target gene TTK in BC pathogenesis.

METHODS

The evaluation of miR-582-5p and TTK mRNA expression in BC tissues or cells was performed using qRT-PCR. TargetScan was then used to predict the binding site of miR-582-5p on TTK mRNA. Subsequently, dual-luciferase reporter and RNA pull-down assays were employed to validate the binding relationship between miR-582-5p and TTK mRNA. CCK-8, BrdU, flow cytometry, and caspase-3 activity assays were later conducted to evaluate the viability, proliferation, cell cycle, and apoptosis of BC cells.

RESULTS

Investigations revealed that miR-582-5p was downregulated in BC tissues and cells. Meanwhile, miR-582-5p inhibited the viability and proliferation of BC cells while stimulating the apoptosis and cycle arrest of the cells. TTK, the target gene of miR-582-5p, was later found to be over-expressed in BC tissues and cells. TTK, however, was observed to exhibit an opposite effect on miR-582-5p. Simply put, it stimulated BC cell malignant phenotypes, and this stimulation could be directly reversed by miR-582-5p.

CONCLUSION

This research confirmed that miR-582-5p could restrain bladder carcinogenesis by inhibiting TTK expression.

Identification of grade-related genes and construction of a robust genomic-clinicopathologic nomogram for predicting recurrence of bladder cancer

BACKGROUND

Bladder cancer (BC) is a common tumor in the urinary system with a high recurrence rate. The individualized treatment and follow-up after surgery is the key to a successful outcome. Currently, the surveillance strategies are mainly depending on tumor stage and grade. Previous evidence has proved that tumor grade was a significant and independent risk factor of BC recurrence. Exploring the grade-related genes may provide us a new approach to predict prognosis and guide the post-operative treatment in BC patients.

METHODS

In this study, the weighted gene co-expression network analysis was applied to identify the hub gene module correlated with BC grade using GSE71576. After constructing a protein-protein interaction (PPI) network with the hub genes inside the hub gene module, we identified some potential core genes. TCGA and another independent dataset were used for further validation.

RESULTS

The results revealed that the expression of AURKA, CCNA2, CCNB1, KIF11, TTK, BUB1B, BUB1, and CDK1 were significantly higher in high-grade BC, showing a strong ability to distinguish BC grade. The expression levels of the 8 genes in normal, paracancerous, tumorous, and recurrent bladder tissues were progressively increased. By conducting survival analysis, we proved their prognostic value in predicting the recurrence of BC. Eventually, we constructed a prognostic nomogram by combining the 8-core-gene panel with clinicopathologic features, which had shown great performance in predicting the recurrence of BC.

CONCLUSION

We identified 8 core genes that revealed a significant correlation with the tumor grade as well as the recurrence of BC. Finally, we proved the value of a novel prognostic nomogram for predicting the relapse-free survival of BC patients after surgery, which could guide their treatment and follow-up.

Genomic Instability in Circulating Tumor Cells

Simple Summary

In this review, we focus on recent advances in the detection and quantification of tumor cell heterogeneity and genomic instability of CTCs and the contribution of chromosome instability studies to genetic heterogeneity in CTCs at the single-CTC level.

Abstract

Circulating tumor cells (CTCs) can promote distant metastases and can be obtained through minimally invasive liquid biopsy for clinical assessment in cancer patients. Having both genomic heterogeneity and instability as common features, the genetic characterization of CTCs can serve as a powerful tool for a better understanding of the molecular changes occurring at tumor initiation and during tumor progression/metastasis. In this review, we will highlight recent advances in the detection and quantification of tumor cell heterogeneity and genomic instability in CTCs. We will focus on the contribution of chromosome instability studies to genetic heterogeneity in CTCs at the single-CTC level by discussing data from different cancer subtypes and their impact on diagnosis and precision medicine.

A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear

MOTIVATION

DNA methylation is a biological process impacting the gene functions without changing the underlying DNA sequence. The DNA methylation machinery usually attaches methyl groups to some specific cytosine residues, which modify the chromatin architectures. Such modifications in the promoter regions will inactivate some tumor-suppressor genes. DNA methylation within the coding region may significantly reduce the transcription elongation efficiency. The gene function may be tuned through some cytosines are methylated.

METHODS

This study hypothesizes that the overall methylation level across a gene may have a better association with the sample labels like diseases than the methylations of individual cytosines. The gene methylation level is formulated as a regression model using the methylation levels of all the cytosines within this gene. A comprehensive evaluation of various feature selection algorithms and classification algorithms is carried out between the gene-level and residue-level methylation levels.

RESULTS

A comprehensive evaluation was conducted to compare the gene and cytosine methylation levels for their associations with the sample labels and classification performances. The unsupervised clustering was also improved using the gene methylation levels. Some genes demonstrated statistically significant associations with the class label, even when no residue-level methylation features have statistically significant associations with the class label. So in summary, the trained gene methylation levels improved various methylome-based machine learning models. Both methodology development of regression algorithms and experimental validation of the gene-level methylation biomarkers are worth of further investigations in the future studies. The source code, example data files and manual are available at http://www.healthinformaticslab.org/supp/.

Impact of genetic polymorphisms in kinetochore and spindle assembly genes on chromosomal aberration frequency in healthy humans

Genomic instability is a characteristic of a majority of human malignancies. Chromosomal instability is a common form of genomic instability that can be caused by defects in mitotic checkpoint genes. Chromosomal aberrations in peripheral blood are also indicative of genotoxic exposure and potential cancer risk. We evaluated associations between inherited genetic variants in 33 mitotic checkpoint genes and the frequency of chromosomal aberrations (CAs) in the presence and absence of environmental genotoxic exposure. Associations with both chromosome and chromatid type of aberrations were evaluated in two cohorts of healthy individuals, namely an exposed and a reference group consisting of 607 and 866 individuals, respectively. Binary logistic and linear regression analyses were performed for the association studies. Bonferroni-corrected significant p-value was 5 × 10^-4 for 99 tests based on the number of analyzed genes and phenotypes. In the reference group the most prominent associations were found with variants in CCNB1, a master regulator of mitosis, and in genes involved in kinetochore function, including CENPH and TEX14, whereas in the exposed group the main association was found with variants in TTK, also an important gene in kinetochore function. How the identified variants may affect the fidelity of mitotic checkpoint remains to be investigated, however, the present study suggests that genetic variation may partly explain interindividual variation in the formation of CAs.

MAD2B contributes to parietal epithelial cell activation and crescentic glomerulonephritis via Skp2

Mitotic spindle assembly checkpoint protein 2 (MAD2B), a well-known anaphase-promoting complex/cyclosome (APC/C) inhibitor and a small subunit of DNA polymerase-ζ, is critical for mitotic control and DNA repair. Previously, we detected a strong increase of MAD2B in the glomeruli from patients with crescentic glomerulonephritis and anti-glomerular basement membrane (anti-GBM) rats, which predominantly originated from activated parietal epithelial cells (PECs). Consistently, in vitro MAD2B was increased in TNF-α-treated PECs, along with cell activation and proliferation, as well as extracellular matrix accumulation, which could be reversed by MAD2B genetic depletion. Furthermore, we found that expression of S phase kinase-associated protein 2 (Skp2), an APC/C^CDH1 substrate, was increased in the glomeruli of anti-GBM rats, and TNF-α-stimulated PECs and could be suppressed by MAD2B depletion. Additionally, genetic deletion of Skp2 inhibited TNF-α-induced PEC activation and dysfunction. Finally, TNF-α blockade or glucocorticoid therapy administered to anti-GBM rats could ameliorate MAD2B and Skp2 accumulation as well as weaken PEC activation. Collectively, our data suggest that MAD2B has a pivotal role in the pathogenesis of glomerular PEC activation and crescent formation through induction of Skp2 expression.

Identification of a five-gene signature for predicting the progression and prognosis of stage I endometrial carcinoma

Uterine corpus endometrial carcinoma (UCEC) is often diagnosed at an early clinical stage based on abnormal vaginal bleeding. However, the prognosis of UCEC is poor. The present study was conducted to identify novel tumor grade-related genes with the potential to predict the prognosis and progression of UCEC. A total of three gene expression microarray datasets were downloaded from the Gene Expression Omnibus database, and one RNA-sequencing dataset with corresponding clinical information of patients with UCEC was obtained from The Cancer Genome Atlas database. In summary, 1,447 differentially expressed genes (DEGs) were identified between endometrial cancerous tissues and normal endometrial tissues. Weighted gene co-expression network analysis was performed to assess the associations between DEGs and clinical traits. In total, five genes were found to be highly associated with the tumorigenesis and prognosis of UCEC. Among them, BUB1 mitotic checkpoint serine/threonine kinase B, cyclin B1, cell-division cycle protein 20 and non-SMC condensing I complex subunit G were involved in cell cycle regulation pathways, and DLG-associated protein 5 was involved in the Notch receptor 3 signaling pathway based on functional enrichment analyses. Of the five genes, four were highly expressed in endometrial cancerous tissues compared with normal endometrial tissues at the protein level. In addition, the higher expression of these genes predicted a higher tumor grade and worse overall survival. In conclusion, the present study revealed a 5-gene signature that can be used to predict the progression of UCEC.

Screening and Identification of Key Biomarkers in Inflammatory Breast Cancer Through Integrated Bioinformatic Analyses

Background: Inflammatory breast cancer (IBC) is a rare type of breast cancer with poor prognoses, moreover its pathogenesis is not entirely clear. The aim of this study was to identify key genes of IBC, which might serve as diagnostic biomarkers and/or therapeutic targets. Methods: Two microarray datasets, GSE23720 and GSE45581, were obtained from the Gene Expression Omnibus database, and a differential expression analysis was performed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to understand the potential biological functions of the differentially expressed genes (DEGs). Next, a protein-protein interaction (PPI) network was constructed and visualized by Cytoscape. Functional modules and hub genes were screened using MCODE and cytohubba plug-ins, and the Cancer Genome Atlas survival analysis along with quantitative reverse transcriptional polymerase chain reactions of clinical samples was used to validate the effect that the hub genes have on IBC. Results: A total of 215 DEGs were identified, consisting of 105 upregulated and 110 downregulated genes. GO and KEGG analyses showed that the enriched terms and pathways were mainly associated with cell cycle, proliferation, drug metabolism, and oncogenesis. From the PPI network, we identified six hub genes, including Cell Division Cycle 45 (CDC45), Polo Like Kinase 1 (PLK1), BUB1 Mitotic Checkpoint Serine/Threonine Kinase B (BUB1B), Cell Division Cycle 20 (CDC20), Aurora Kinase A (AURKA), and Mitotic Arrest Deficient 2 Like 1 (MAD2L1). The survival analyses and expression validation studies verified the robustness of these hub genes. Conclusion: This study provides new insights into the understanding of the molecular mechanisms of IBC; in addition, the identified hub genes may serve as potential targets for diagnosis and treatment.

Proliferation-associated long noncoding RNA, TMPO-AS1, is a potential therapeutic target for triple-negative breast cancer

Triple‐negative breast cancer (TNBC) is an aggressive subtype of breast cancer compared with luminal or epidermal growth factor receptor 2 subtypes, thus effective therapeutic options for TNBC are yet to be developed. Nowadays, oncogenic long noncoding RNAs (lncRNAs) are applied to cancer management as a new class of therapeutic targets. We previously showed that thymopoietin antisense transcript 1 (TMPO‐AS1) is a proliferation‐associated lncRNA that contributes to hormone‐dependent breast cancer progression by stabilizing estrogen receptor‐α mRNA. We here showed that TMPO‐AS1 is abundantly expressed in basal‐like breast cancer subtype based on the transcriptomic data in The Cancer Genome Atlas as well as in TNBC cell lines and patient‐derived cells. Small interfering RNA‐based loss‐of‐function analyses showed that TMPO‐AS1 knockdown substantially represses the proliferation and migration of TNBC cells. Expression microarray analysis showed that TMPO‐AS1 alters gene signatures related to transforming growth factor‐β signaling in addition to proliferative E2F signaling pathways. TMPO‐AS1‐targeted siRNA treatment through engineered drug delivery systems using cancer‐targeted polyion complex micelle or nanoball technology significantly impaired the in vivo growth of primary and metastatic TNBC xenograft tumors. Our findings suggest that TMPO‐AS1 plays a key role in TNBC pathophysiology and could be a potential therapeutic target for TNBC.

Identification of new candidate genes and signalling pathways associated with the development of neuroendocrine pancreatic tumours based on next generation sequencing data

Despite advances in classification, treatment, and imaging, neuroendocrine tumours remain a clinically complex subject. In this work, we studied the genetic profile of well-differentiated pancreatic neuroendocrine tumours (PanNETs) in a cohort of Caucasian patients and analysed the signalling pathways and candidate genes potentially associated with the development of this oncological disease. Twenty-four formalin-fixed paraffin-embedded (FFPE) samples of well-differentiated PanNETs were subjected to massive parallel sequencing using the targeted gene panel (409 genes) of the Illumina NextSeq 550 platform (San Diego, USA). In 24 patients, 119 variants were identified in 54 genes. The median mutation rate per patient was 5 (2.8-7). The detected genetic changes were dominated by missense mutations (67%) and nonsense mutations (29%). 18% of the mutations were activating, 35% of the variants led to a loss of function of the encoded protein, and 52% were not classified. Twenty-six variants were described as new. Functionally significant changes in the tertiary structure and activity of the protein molecules in an in silico assay were predicted for 5 new genetic variants. The 5 highest priority candidate genes were selected: CREB1, TCF12, PRKAR1A, BCL11A, and BUB1B. Genes carrying the identified mutations participate in signalling pathways known to be involved in PanNETs; in addition, 38% of the cases showed genetic changes in the regulation of the SMAD2/3 signalling pathway. Well-differentiated PanNETs in a Russian cohort demonstrate various molecular genetic features, including new genetic variations and potential driver genes. The highlighted molecular genetic changes in the SMAD2/3 signalling pathway suggest new prospects for targeted therapy.

Clinical Implications of Chromosomal Instability (CIN) and Kinetochore Abnormalities in Breast Cancers

Genetic instability is a defining property of cancer cells and is the basis of various lesions including point mutations, copy number alterations and translocations. Chromosomal instability (CIN) is part of the genetic instability of cancer and consists of copy number alterations in whole or parts of cancer cell chromosomes. CIN is observed in differing degrees in most cancers. In breast cancer, CIN is commonly part of the genomic landscape of the disease and has a higher incidence in aggressive sub-types. Tumor suppressors that are commonly mutated or disabled in cancer, such as p53 and pRB, play roles in protection against CIN, and as a result, their dysfunction contributes to the establishment or tolerance of CIN. Several structural and regulatory proteins of the centromeres and kinetochore, the complex structure that is responsible for the correct distribution of genetic material in the daughter cells during mitosis, are direct or, mostly, indirect transcription targets of p53 and pRB. Thus, despite the absence of structural defects in genes encoding for centromere and kinetochore components, dysfunction of these tumor suppressors may have profound implications for the correct function of the mitotic apparatus contributing to CIN. CIN and its prognostic and therapeutic implications in breast cancer are discussed in this article.

Integrative module analysis of HCC gene expression landscapes

Despite hepatocellular carcinoma (HCC) being a common cancer globally, its initiation and progression are not well understood. The present study was designed to investigate the hub genes and biological processes of HCC, which change substantially during its progression. Three gene expression profiles of 480 patients with HCC were obtained from the Gene Expression Omnibus database. Subsequent to performing functional annotations and constructing protein-protein interaction (PPI) networks, 657 differentially expressed genes were identified, which were subsequently used to screen candidate hub genes. PPI networks were modularized using the weighted gene correlation network analysis algorithm, the topological overlapping matrix and the hierarchical cluster tree, which were utilized via STRING. Clinical data obtained from The Cancer Genome Atlas were then analyzed to validate the experiments performed using six hub genes. Additionally, a transcription factor and microRNA-mRNA network were constructed to determine the potential regulatory mechanisms of six hub genes. The results revealed that the oxidation-reduction process and cell cycle associated processes were markedly involved in HCC progression. Six highly expressed genes, including cyclin B2, cell division cycle 20, mitotic arrest deficient 2 like 1, minichromosome maintenance complex component 2, centromere protein F and BUB mitotic checkpoint serine/threonine kinase B, were confirmed as hub genes and validated via experiments associated with cell division. These hub genes are necessary for confirmatory experiments and may be used in clinical gene therapy as biomarkers or drug targets.

The Multi-Modal Effect of the Anti-fibrotic Drug Pirfenidone on NSCLC

Although immune checkpoint and targeted therapies offer remarkable benefits for lung cancer treatment, some patients do not qualify for these regimens or do not exhibit consistent benefit. Provided that lung cancer appears to be driven by transforming growth factor beta signaling, we investigated the single drug potency of Pirfenidone, an approved drug for the treatment of lung fibrosis. Five human lung cancer cell lines and one murine line were investigated for transforming growth factor beta inhibition via Pirfenidone by using flow cytometry, In-Cell western analysis, proliferation assays as well as comprehensive analyses of the transcriptome with subsequent bioinformatics analysis. Overall, Pirfenidone induced cell cycle arrest, down-regulated SMAD expression and reduced proliferation in lung cancer. Furthermore, cell stress pathways and pro-apoptotic signaling may be mediated by reduced expression of Survivin. A murine subcutaneous model was used to assess the in vivo drug efficacy of Pirfenidone and showed reduced tumor growth and increased infiltration of T cells and NK cells. This data warrant further clinical evaluation of Pirfenidone with advanced non-small cell lung cancer. The observed in vitro and in vivo effects point to a substantial benefit for using Pirfenidone to reactivate the local immune response and possible application in conjunction with current immunotherapies.

Identification of potential key genes for HER-2 positive breast cancer based on bioinformatics analysis

BACKGROUNDS

HER-2 positive breast cancer is a subtype of breast cancer with poor clinical outcome. The aim of this study was to identify differentially expressed genes (DEGs) for HER-2 positive breast cancer and elucidate the potential interactions among them.

MATERIAL AND METHODS

Three gene expression profiles (GSE29431, GSE45827, and GSE65194) were derived from the Gene Expression Omnibus (GEO) database. GEO2R tool was applied to obtain DEGs between HER-2 positive breast cancer and normal breast tissues. Gene ontology (GO) annotation analysis and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis was performed by the Database for Annotation, Visualization and Integrated Discovery (David) online tool. Protein-protein interaction (PPI) network, hub gene identification and module analysis was conducted by Cytoscape software. Online Kaplan-Meier plotter survival analysis tool was also used to investigate the prognostic values of hub genes in HER-2 positive breast cancer patients.

RESULTS

A total of 54 upregulated DEGs and 269 downregulated DEGs were identified. Among them, 10 hub genes including CCNB1, RAC1, TOP2A, KIF20A, RRM2, ASPM, NUSAP1, BIRC5, BUB1B, and CEP55 demonstrated by connectivity degree in the PPI network were screened out. In Kaplan-Meier plotter survival analysis, the overexpression of RAC1 and RRM2 were shown to be associated with an unfavorable prognosis in HER-2 positive breast cancer patients.

CONCLUSIONS

This present study identified a number of potential target genes and pathways which might impact the oncogenesis and progression of HER-2 positive breast cancer. These findings could provide new insights into the detection of novel diagnostic and therapeutic biomarkers for this disease.

Identification of key candidate genes and pathways in endometrial cancer: Evidence from bioinformatics analysis

Endometrial cancer (EC) is the fourth most common cancer in women worldwide. Although researchers are exploring the biological processes of tumorigenesis and development of EC, the gene interactions and biological pathways of EC are not accurately verified. In the present study, bioinformatics methods were used to screen for key candidate genes and pathways that were associated with EC and to reveal the possible mechanisms at molecular level. Microarray datasets (GSE63678, GSE17025 and GSE3013) from the Gene Expression Omnibus database were downloaded and 118 differentially expressed genes (DEGs) were selected using a Venn diagram. Functional enrichment analyses were performed on the DEGs. A protein-protein interaction network was constructed, including the module analysis. A total of 11 hub genes were identified from the DEGs, and functional enrichment analyses were performed to clarify their possible biological processes. A total of 118 DEGs were selected from three mRNA datasets. Functional enrichment demonstrated 27 downregulated genes that were primarily involved in the positive regulation of transcription from RNA polymerase II promoter, protein binding and the nucleus. A total of 91 upregulated DEGs were mainly associated with cell division, protein binding and the nucleus. Pathway analysis indicated that the downregulated DEGs were mainly enriched in pathways associated with cancer, and the upregulated DEGs were mainly enriched in the cell cycle. The 11 hub genes were primarily enriched in the cell cycle, oocyte meiosis, progesterone-mediated oocyte maturation, the p53 signaling pathway and viral carcinogenesis. The integrated analysis showed that cyclin B1, ubiquitin conjugating enzyme E2 C and cell division cycle 20 may participate in the tumorigenesis, development and invasion of EC. In conclusion, the hub genes and pathways identified in the present study contributed to the understanding of carcinogenesis and progression of EC at the mechanistic and molecular-biological level. As candidate targets for the diagnosis and treatment of EC, these genes deserve further investigation.

The anaphase-promoting complex: A key mitotic regulator associated with somatic mutations occurring in cancer

The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that helps control chromosome separation and exit from mitosis in many different kinds of organisms, including yeast, flies, worms, and humans. This review represents a new perspective on the connection between APC/C subunit mutations and cancer. The complex nature of APC/C and limited mutation analysis of its subunits has made it difficult to determine the relationship of each subunit to cancer. In this work, cancer genomic data were examined to identify APC/C subunits with a greater than 5% alteration frequency in 11 representative cancers using the cBioPortal database. Using the Genetic Determinants of Cancer Patient Survival database, APC/C subunits were also studied and found to be significantly associated with poor patient prognosis in several cases. In comparing these two kinds of cancer genomics data to published large-scale genomic analyses looking for cancer driver genes, ANAPC1 and ANAPC3/CDC27 stood out as being represented in all three types of analyses. Seven other subunits were found to be associated both with >5% alteration frequency in certain cancers and being associated with an effect on cancer patient prognosis. The aim of this review is to provide new approaches for investigators conducting in vivo studies of APC/C subunits and cancer progression. In turn, a better understanding of these APC/C subunits and their role in different cancers will help scientists design drugs that are more precisely targeted to certain cancers, using APC/C mutation status as a biomarker.