Differential promoter methylation of kinesin family member 1a in plasma is associated with breast cancer and DNA repair capacity

Research advances of MAL family members in tumorigenesis and tumor progression (Review)

The myelin and lymphocyte protein (MAL) family is a novel gene family first identified and characterized in 2002. This family is comprised of seven members, including MAL, MAL2, plasmolipin, MALL, myeloid differentiation‑associated marker (MYADM), MYADML2 and CMTM8, which are located on different chromosomes. In addition to exhibiting extensive activity during transcytosis, the MAL family plays a vital role in the neurological, digestive, respiratory, genitourinary and other physiological systems. Furthermore, the intimate association between MAL and the pathogenesis, progression and metastasis of malignancies, attributable to several mechanisms such as DNA methylation has also been elucidated. In the present review, an overview of the structural and functional properties of the MAL family and the latest research findings regarding the relationship between several MAL members and various cancers is provided. Furthermore, the potential clinical and scientific significance of MAL is discussed and directions for future research are summarized.

Integrated Multi-omics Analysis of Early Lung Adenocarcinoma Links Tumor Biological Features with Predicted Indolence or Aggressiveness

Lung adenocarcinoma (LUAD) is a heterogeneous group of tumors associated with different survival rates, even when detected at an early stage. Here, we aim to investigate the biological determinants of early LUAD indolence or aggressiveness using radiomics as a surrogate of behavior. We present a set of 92 patients with LUAD with data collected across different methodologies. Patients were risk-stratified using the CT-based Score Indicative of Lung cancer Aggression (SILA) tool (0 = least aggressive, 1 = most aggressive). We grouped the patients as indolent (x ≤ 0.4, n = 14), intermediate (0.4 > x ≤ 0.6, n = 27), and aggressive (0.6 > x ≤ 1, n = 52). Using Cytometry by time of flight (CyTOF), we identified subpopulations with high HLA-DR expression that were associated with indolent behavior. In the RNA sequencing (RNA-seq) dataset, pathways related to immune response were associated with indolent behavior, while pathways associated with cell cycle and proliferation were associated with aggressive behavior. We extracted quantitative radiomics features from the CT scans of the patients. Integrating these datasets, we identified four feature signatures and four patient clusters that were associated with survival. Using single-cell RNA-seq, we found that indolent tumors had significantly more T cells and less B cells than aggressive tumors, and that the latter had a higher abundance of regulatory T cells and Th cells. In conclusion, we were able to uncover a correspondence between radiomics and tumor biology, which could improve the discrimination between indolent and aggressive LUAD tumors, enhance our knowledge in the biology of these tumors, and offer novel and personalized avenues for intervention.

Significance

This study provides a comprehensive profiling of LUAD indolence and aggressiveness at the biological bulk and single-cell levels, as well as at the clinical and radiomics levels. This hypothesis generating study uncovers several potential future research avenues. It also highlights the importance and power of data integration to improve our systemic understanding of LUAD and to help reduce the gap between basic science research and clinical practice.

The MAL Family of Proteins: Normal Function, Expression in Cancer, and Potential Use as Cancer Biomarkers

The MAL family of integral membrane proteins consists of MAL, MAL2, MALL, PLLP, CMTM8, MYADM, and MYADML2. The best characterized members are elements of the machinery that controls specialized pathways of membrane traffic and cell signaling. This review aims to help answer the following questions about the MAL-family genes: (i) is their expression regulated in cancer and, if so, how? (ii) What role do they play in cancer? (iii) Might they have biomedical applications? Analysis of large-scale gene expression datasets indicated altered levels of MAL-family transcripts in specific cancer types. A comprehensive literature search provides evidence of MAL-family gene dysregulation and protein function repurposing in cancer. For MAL, and probably for other genes of the family, dysregulation is primarily a consequence of gene methylation, although copy number alterations also contribute to varying degrees. The scrutiny of the two sources of information, datasets and published studies, reveals potential prognostic applications of MAL-family members as cancer biomarkers-for instance, MAL2 in breast cancer, MAL2 and MALL in pancreatic cancer, and MAL and MYADM in lung cancer-and other biomedical uses. The availability of validated antibodies to some MAL-family proteins sanctions their use as cancer biomarkers in routine clinical practice.

Invention of 3Mint for feature grouping and scoring in multi-omics

Advanced genomic and molecular profiling technologies accelerated the enlightenment of the regulatory mechanisms behind cancer development and progression, and the targeted therapies in patients. Along this line, intense studies with immense amounts of biological information have boosted the discovery of molecular biomarkers. Cancer is one of the leading causes of death around the world in recent years. Elucidation of genomic and epigenetic factors in Breast Cancer (BRCA) can provide a roadmap to uncover the disease mechanisms. Accordingly, unraveling the possible systematic connections between-omics data types and their contribution to BRCA tumor progression is crucial. In this study, we have developed a novel machine learning (ML) based integrative approach for multi-omics data analysis. This integrative approach combines information from gene expression (mRNA), microRNA (miRNA) and methylation data. Due to the complexity of cancer, this integrated data is expected to improve the prediction, diagnosis and treatment of disease through patterns only available from the 3-way interactions between these 3-omics datasets. In addition, the proposed method bridges the interpretation gap between the disease mechanisms that drive onset and progression. Our fundamental contribution is the 3 Multi-omics integrative tool (3Mint). This tool aims to perform grouping and scoring of groups using biological knowledge. Another major goal is improved gene selection via detection of novel groups of cross-omics biomarkers. Performance of 3Mint is assessed using different metrics. Our computational performance evaluations showed that the 3Mint classifies the BRCA molecular subtypes with lower number of genes when compared to the miRcorrNet tool which uses miRNA and mRNA gene expression profiles in terms of similar performance metrics (95% Accuracy). The incorporation of methylation data in 3Mint yields a much more focused analysis. The 3Mint tool and all other supplementary files are available at https://github.com/malikyousef/3Mint/.

KLF5 promotes KIF1A expression through transcriptional repression of microRNA-338 in the development of pediatric neuroblastoma

BACKGROUND

Neuroblastoma (NB) comprises about 8-10% of pediatric cancers, and microRNA (miR)-338 downregulation has been implicated in NB. However, the underlying molecular mechanism remains largely unclear. The main goal of this study is to probe the regulatory role of miR-338 and the upstream and downstream biomolecules involved in NB.

METHODS

The differentially expressed miRNAs were screened by analyzing the NB gene expression microarray GSE121513 from the GEO database, and the differences in expression of the screened miRNAs were verified in clinically collected NB tissues versus dorsal root ganglions. Subsequently, the relationship between the miR-338 expression and NB cell growth was validated in vitro and in vivo, and the upstream and downstream regulatory mechanisms of miR-338 were further analyzed by bioinformatics. Functional rescue experiments were used to verify their effects on NB cell growth.

RESULTS

miR-338 expressed poorly in NB tissues, and overexpression of miR-338 significantly inhibited NB cell growth in vitro and in vivo. The prediction results showed that miR-338 could target KIF1A, and miR-338 expression was negatively correlated with the expression of KIF1A. We further found that miR-338 was transcriptionally regulated by the transcription factor KLF5. Overexpression of KLF5 or KIF1A significantly attenuated the inhibitory effect of miR-338 mimic on NB cell growth. Finally, miR-338 blocked the Hedgehog signaling pathway by inhibiting the expression of KIF1A.

CONCLUSION

Overexpression of KLF5 reduced expression of miR-338, which in turn increased the expression of KIF1A and activated the Hedgehog signaling pathway, leading to the progression of NB.

Combined Liquid Biopsy Methylation Analysis of CADM1 and MAL in Cervical Cancer Patients

Cervical cancer is the fourth most common cancer in women, which is associated in >95% with a high-risk human papillomavirus (HPV) infection. Methylation of specific genes has been closely associated with the progress of cervical high-grade dysplastic lesions to invasive carcinomas. Therefore, DNA methylation has been proposed as a triage for women infected with high-risk HPV. Methylation analyses of cervical cancer tissue have shown that cell adhesion molecule 1 (CADM1) and myelin and lymphocyte protein (MAL) methylation are present in over 90% of all cervical high-grade neoplasias and invasive cervical cancers. Here, we established a liquid biopsy-based assay to detect MAL and CADM1 methylation in cell free (cf)DNA of cervical cancer. Methylation of the target gene was validated on bisulfite converted smear-DNA from cervical dysplasia patients and afterward applied to cfDNA using quantitative real-time PCR. In 52 smears, a combined analysis of CADM1 and/or MAL (CADM1/MAL) showed methylation in 86.5% of the cases. In cfDNA samples of 24 cervical cancer patients, CADM1/MAL methylation was detected in 83.3% of the cases. CADM1/MAL methylation was detected already in 81.8% of stage I-II patients showing the high sensitivity of this liquid biopsy assay. In combination with a specificity of 95.5% towards healthy donors (HD) and an area under the curve (AUC) of 0.872 in the receiver operating characteristic (ROC) analysis, CADM1/MAL cfDNA methylation detection might represent a novel and promising liquid biopsy marker in cervical cancer.

REC8 inhibits proliferation, migration and invasion of breast cancer cells by targeting CDC20

Breast cancer is one of the most types of common malignant tumor in women. REC8 is a known tumor suppressor in several types of cancer; however, the role of REC8 in breast cancer remains unknown. The purpose of the present study was to investigate the effects and underlying mechanism of REC8 on the proliferation, migration and invasion of breast cancer cells. The expression of REC8 in normal and breast cancer cells was detected by reverse transcription‑quantitative PCR and western blotting. Stable REC8‑overexpressing breast cancer cells were constructed to modify the expression of REC8. The expression of cell division cycle 20 (CDC20) in breast cancer cells was altered using the CDC20 inhibitor apcin. Cell viability, proliferation, migration, invasion and apoptosis were determined by Cell Counting Kit‑8, colony formation, wound healing, Transwell and TUNEL assays, respectively. Western blotting was performed to measure the expression of matrix metalloproteinase‑2/9 and apoptosis‑associated proteins [Bcl‑2, caspase‑3, cleaved caspase‑3 and cleaved poly (ADP‑ribose) polymerase]. Compared with normal breast cells, the expression of REC8 was lower in breast cancer cells. Search Tool for the Retrieval of Interacting Genes/Proteins online database was used to predict the interaction between REC8 and CDC20. Overexpression of REC8 significantly inhibited the proliferation, migration and invasion of breast cancer cells in vitro; these changes were reversed by CDC20 overexpression. In conclusion, the present study demonstrated that REC8 decreased proliferation, migration and invasion of breast cancer cells by inhibiting CDC20.

Myelin and Lymphocyte Protein (MAL): A Novel Biomarker for Uterine Corpus Endometrial Carcinoma

Purpose

Myelin and lymphocyte protein (MAL) plays an essential role in esophageal cancer, classic Hodgkin's lymphoma and breast cancer. However, its role in uterine corpus endometrial carcinoma (UCEC) has not been explored. Therefore, the current study sought to explore the role of MAL in UCEC.

Patients and Methods

Differentially expressed genes (DEGs) were identified by using Limma package in R based on TCGA-UCEC data. Kaplan-Meier plotter analysis was performed to explore the prognostic value of MAL. Function enrichment analyses were performed using GSVA. Further, roles of MAL in UCEC were validated using clinical cohort, which included 120 tumor and adjacent tissues. qRT-PCR and immunohistochemistry analyze the samples. Chi-square tests were performed to explore the associations between MAL expressions and clinicopathological features.

Results

The findings showed that overexpression level of MAL in tumor was correlated with worse survival (p = 0.000424). MAL exhibited predictive power for survival time of UCEC patients (3 years: AUC = 0.635; 5 years: AUC = 0.635). Notably, high expression level of MAL was correlated with advanced stage of UCEC. MAL overexpression was significant in UCEC with microsatellite instability (MSI). Enrichment analysis showed that MAL was enriched mainly in MYC targets, epithelial mesenchymal transition and KRAS signaling. Furthermore, MAL was associated with infiltration of immune cells in the tumor micro-environment and immune checkpoint. Analysis showed a positive association between MAL and T cell (CD4+ memory resting). Correlation analysis showed that MAL was significantly positively correlated with several immune checkpoint, including CD274 (R = 0.3389, p = 0.0081), LAG3 (R = 0.2913, p = 0.0229), PDCD1LG2 (R = 0.5345, p < 0.0001). The prognosis value of MAL was confirmed through the experiment.

Conclusion

The findings of the current study indicated that MAL is an effective prognostic biomarker and potential therapeutic target for UCEC patients. These results indicated that MAL functions as a diagnosis and therapeutic marker in UCEC treatment.

Identification of m6A-Related Biomarkers Associated with Prognosis of Colorectal Cancer

Background

Colorectal cancer (CRC) is the second most deadly cancer in the world according to GLOBOCAN 2020 data. Accumulating evidence suggests that RNA methylation modification is also misregulated in human cancers and may be a potential ideal target for cancer treatment.

Material/Methods

m6A-related differentially expressed genes (DEGs) were identified from colon adenocarcinoma and rectum adenocarcinoma esophageal carcinoma patients with different pathological stages. The protein-protein interaction (PPI) network construction, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs were conducted. Cox regression analysis was applied to the screening of m6A-related DEGs significantly associated with the overall survival (OS), and those selected genes were used for LASSO regression analysis to construct prognostic signature and calculate patients’ risk scores.

Results

We identified 673 m6A-related DEGs from CRC patients in different pathologic stages, and 146 of them were associated with OS. CTNNB1, TRIM37, RAB7A, CASC5/KNL1, CENPE, CCNB1, UBE2H, HSPA8, KIF1A, and FBXW4 were hub genes of the PPI network. Nine m6A-related genes were screened out to build the prognostic risk model. TNM stage, vascular invasion, and the risk score were independently related to the OS of CRC patients.

Conclusions

Nine candidate m6A-related mRNA biomarkers (LRRC17, NFKB1, NOS2, PCDHB2, RAB7A, RPS6KA1, RRNAD1, TLE6, and UBE2H) were found to be closely related to the clinicopathology and prognosis of colorectal cancer, indicating that they could be potential prognostic biomarkers for patients with colorectal cancer.

LINE-1 methylation mediates the inverse association between body mass index and breast cancer risk: A pilot study in the Lebanese population

INTRODUCTION

Lebanon is among the top countries worldwide in combined incidence and mortality of breast cancer, which raises concern about risk factors peculiar to this country. The underlying molecular mechanisms of breast cancer require elucidation, particularly epigenetics, which is recognized as a molecular sensor to environmental exposures.

PURPOSE

We aim to explore whether DNA methylation levels of AHRR (marker of cigarette smoking), SLC1A5 and TXLNA (markers of alcohol consumption), and LINE-1 (a genome-wide repetitive retrotransposon) can act as molecular mediators underlying putative associations between breast cancer risk and pertinent extrinsic (tobacco smoking and alcohol consumption) and intrinsic factors [age and body mass index (BMI)].

METHODS

This is a cross-sectional pilot study which includes breast cancer cases (N = 65) and controls (N = 54). DNA methylation levels were measured using bisulfite pyrosequencing on available peripheral blood samples (N = 119), and Multivariate Imputation by Chained Equations (MICE) was used to impute missing DNA methylation values in remaining samples. Multiple mediation analysis was performed to assess direct and indirect (via DNA methylation) effects of intrinsic and extrinsic factors on breast cancer risk.

RESULTS

In relation to exposure, AHRR hypo-methylation was associated with cigarette but not waterpipe smoking, suggesting potentially different biomarkers of these two forms of tobacco use; SLC1A5 and TXLNA methylation were not associated with alcohol consumption; LINE-1 methylation was inversely associated with BMI (β-value [95% confidence interval (CI)] = -0.04 [-0.07, -0.02]), which remained significant after adjustment for age, smoking and alcohol consumption. In relation to breast cancer, there was no detectable association between AHRR, SLC1A5 or TXLNA methylation and cancer risk, but LINE-1 methylation was significantly higher in breast cancer cases when compared to controls (mean ± SD: 72.00 ± 0.66 versus 70.89 ± 0.73, P = 4.67 × 10-14). This difference remained significant after adjustment for confounders (odds ratio (OR) [95% CI] = 9.75[3.74, 25.39]). Moreover, LINE-1 hypo-methylation mediated 83% of the inverse effect of BMI on breast cancer risk.

CONCLUSION

This pilot study demonstrates that alterations in blood LINE-1 methylation mediate the inverse effect of BMI on breast cancer risk. This warrants large scale studies and stratification based on clinic-pathological types of breast cancer.

Downregulation of DUSP9 Promotes Tumor Progression and Contributes to Poor Prognosis in Human Colorectal Cancer

Background

Dual-specificity phosphatase 9 (DUSP9) belongs to the dual-specificity protein phosphatase subfamily. Recently, increasing attention has been paid on the role of DUSP9 in a variety of cancers. However, its functional role in tumor development is still unclear, especially in colorectal cancer (CRC).

Methods

The functional role of DUSP9 in inhibiting the progression of CRC was verified using colony formation assay, wound healing assay, nude mice xenograft model, etc. RNA-seq was performed to assess the gene expression profiling in SW480 cells with DUSP9 stable knockdown and shControl cells. Bisulfite sequencing (BSE) was performed to reveal the methylation status of CpG island in the promoter of DUSP9.

Results

DUSP9 was significantly downregulated in tumor tissues compared with peritumor tissues. Mechanistically, the high methylation status of CpG island in the promoter of DUSP9 may lead to the downregulation of DUSP9 in CRC. Clinically, low DUSP9 expression in CRC was closely associated with depth of invasion, metastasis (TNM) stage, and poor survival, indicating that DUSP9 may be involved in the progression of CRC. Functional study revealed that DUSP9 inhibited proliferation, migration, invasion, and epithelial–mesenchymal transition of CRC cells both in vitro and in vivo. Transcriptome profiling studies revealed that Erk signaling was involved in the tumor progression mediated by DUSP9 silencing, which is confirmed by cell experiments and clinical tissue sample staining analysis.

Conclusion

Our findings demonstrate that DUSP9 plays a critical role in the progression of CRC, and therapeutic intervention to increase the expression or activity of DUSP9 may be a potential target for CRC treatment in the future.

Silencing KIF18B enhances radiosensitivity: identification of a promising therapeutic target in sarcoma

Background

Sarcomas are rare heterogeneous tumours, derived from primitive mesenchymal stem cells, with more than 100 distinct subtypes. Radioresistance remains a major clinical challenge for sarcomas, demanding urgent for effective biomarkers of radiosensitivity.

Methods

The radiosensitive gene Kinesin family member 18B (KIF18B) was mined through bioinformatics with integrating of 15 Gene Expression Omnibus (GEO) datasets and The Cancer Genome Atlas (TCGA) database. We used radiotherapy-sh-KIF18B combination to observe the anti-tumour effect in sarcoma cells and subcutaneous or orthotopic xenograft models. The KIF18B-sensitive drug T0901317 (T09) was further mined to act as radiosensitizer using the Genomics of Drug Sensitivity in Cancer (GDSC) database.

Findings

KIF18B mRNA was significantly up-regulated in most of the subtypes of bone and soft tissue sarcoma. Multivariate Cox regression analysis showed that KIF18B high expression was an independent risk factor for prognosis in sarcoma patients with radiotherapy. Silencing KIF18B or using T09 significantly improved the radiosensitivity of sarcoma cells, delayed tumour growth in subcutaneous and orthotopic xenograft model, and elongated mice survival time. Furthermore, we predicted that T09 might bind to the structural region of KIF18B to exert radiosensitization.

Interpretation

These results indicated that sarcomas with low expression of KIF18B may benefit from radiotherapy. Moreover, the radiosensitivity of sarcomas with overexpressed KIF18B could be effectively improved by silencing KIF18B or using T09, which may provide promising strategies for radiotherapy treatment of sarcoma.

Fundings

A full list of funding can be found in the Funding Sources section.

Discovery of rare coding variants in OGDHL and BRCA2 in relation to breast cancer risk in Chinese women

The missing heritability of breast cancer could be partially attributed to rare variants (MAF < 0.5%). To identify breast cancer-associated rare coding variants, we conducted whole-exome sequencing (~50×) in genomic DNA samples obtained from 831 breast cancer cases and 839 controls of Chinese females. Using burden tests for each gene that included rare missense or predicted deleterious variants, we identified 29 genes showing promising associations with breast cancer risk. We replicated the association for two genes, OGDHL and BRCA2, at a Bonferroni-corrected p < 0.05, by genotyping an independent set of samples from 1,628 breast cancer cases and 1,943 controls. The association for OGDHL was primarily driven by three predicted deleterious variants (p.Val827Met, p.Pro839Leu, p.Phe836Ser; p < 0.01 for all). For BRCA2, we characterized a total of 27 disruptive variants, including 18 nonsense, six frameshift and three splicing variants, whereas they were only detected in cases, but none of the controls. All of these variants were either very rare (AF < 0.1%) or not detected in >4,500 East Asian women from the genome Aggregation database (gnomAD), providing additional support to our findings. Our study revealed a potential novel gene and multiple disruptive variants of BRCA2 for breast cancer risk, which may identify high-risk women in Chinese populations.

OGDHL Expression as a Prognostic Biomarker for Liver Cancer Patients

Background and Objective

Liver cancer is a highly malignant tumor, and patients typically have poor prognoses. Metabolic reprogramming is a hallmark of cancer, and downregulation of oxoglutarate dehydrogenase-like (OGDHL) contributes to the onset and progression of several cancers. We examined the role of altered OGDHL expression in liver cancer and determined its value as a diagnostic and prognostic indicator for patients.

Material and Methods

R (version 3.5.1) and several R extensions were used for data mining of The Cancer Genome Atlas (TCGA) dataset (including RNAseq and clinical information) and statistical analysis. Receiver operating characteristic analysis was used to determine the diagnostic value of OGDHL. The chi-squared test was used to identify the clinical correlates of OGDHL downregulation. Survival analysis (with the log-rank test) and univariate and multivariate Cox analysis were used to evaluate the effect of OGDHL expression on overall survival (OS) and relapse-free survival. TCGA was used for analysis of gene set enrichment.

Results

OGDHL had lower expression in cancerous liver tissues than noncancerous adjacent tissues, and low expression correlated with more advanced patient age, histologic grade, stage, T classification, and poor survival. Patients with lower OGDHL expression had shorter OS and relapse-free survival. Multivariate Cox regression indicated that low OGDHL expression was an independent risk factor for poor prognosis. Gene set enrichment analysis indicated enrichment of the mitotic spindle, G2M checkpoint, and E2F targets in the OGDHL low expression phenotype.

Conclusion

OGDHL has potential as a diagnostic and prognostic biomarker for liver cancer.

On The Role of Myelin and Lymphocyte Protein (MAL) In Cancer: A Puzzle With Two Faces

Myelin and lymphocyte protein (MAL) is an integral membrane protein constituent of lipid rafts, and it is implicated in apical transport of proteins in polarized epithelial cells. However, beyond the involvement of MAL in apical sorting and as its function as a raft stabilizer, it is still not totally clear how MAL participates in cell proliferating processes. More controversial and interesting is the fact that MAL has been implicated in carcinogenesis in two opposite ways. First, this protein is overexpressed in ovarian cancer and some kinds of lymphomas where it seems to favor cancer progression. Conversely, it has been reported that downregulation of the MAL gene by promoter hypermethylation is a hallmark of several adenocarcinomas. So far, there is not enough experimental evidence to help us understand this phenomenon, and no MAL mutations or MAL isoforms have been associated with these opposite functions. This review provides an updated summary of the structure and functions of MAL, and we will discuss the possible mechanisms underlying its roles as a tumor suppressor and a tumor progression factor.

Microarray-based analysis of whole-genome DNA methylation profiling in early detection of breast cancer

Emerging evidence indicated that changes in DNA methylation early in breast cancer (BC) development might be clinically relevant for therapeutic decisions. Through analysis of whole-genome gene expression microarray and DNA methylation microarray, we explored genes with abnormal DNA methylation in BC for early detection. Firstly, human BC tissues and adjacent non-cancerous tissues were collected from nine BC patients. Gene expression microarray sequencing was conducted for identifying differentially expressed genes and DNA methylation microarray sequencing for differentially methylated genes in BC. Differentially expressed genes and methylated genes in BC were further explored using the Cancer Genome Atlas database. The correlation between DNA methylation and gene expression was illustrated by multiple comparisons. In other 60 clinical samples, methylation specific polymerase chain reaction (PCR) and reverse transcription quantitative PCR were applied for the methylation of HOXA4 and IGF1 genes in BC and adjacent non-cancerous tissues. In total, 1680 upregulated genes and 1249 downregulated genes were determined in BC. Chromosome 16 and 17 showed more differentially methylated genes, and DNA methylation level was increased in BC tissues in each gene region. Chromosome 19 showed more differentially methylated genes, and DNA methylation level was increased in BC tissues in the exoniensis 1, untranslated region-5 and transcriptional start site 200 gene regions. In other 60 clinical samples, HOXA4 and IGF1 in BC tissues presented increased DNA methylation and decreased gene expression in BC. MCF7 cells treated with RG108 showed decreased HOXA4 and IGF1 expressions. It was estimated that HOXA4 and IGF1 were identified with increased DNA methylation and decreased gene expression in BC, which may serve as biomarkers in early BC detection.

Identification of the copy number variant biomarkers for breast cancer subtypes

Breast cancer is a common and threatening malignant disease with multiple biological and clinical subtypes. It can be categorized into subtypes of luminal A, luminal B, Her2 positive, and basal-like. Copy number variants (CNVs) have been reported to be a potential and even better biomarker for cancer diagnosis than mRNA biomarkers, because it is considerably more stable and robust than gene expression. Thus, it is meaningful to detect CNVs of different cancers. To identify the CNV biomarker for breast cancer subtypes, we integrated the CNV data of more than 2000 samples from two large breast cancer databases, METABRIC and The Cancer Genome Atlas (TCGA). A Monte Carlo feature selection-based and incremental feature selection-based computational method was proposed and tested to identify the distinctive core CNVs in different breast cancer subtypes. We identified the CNV genes that may contribute to breast cancer tumorigenesis as well as built a set of quantitative distinctive rules for recognition of the breast cancer subtypes. The tenfold cross-validation Matthew's correlation coefficient (MCC) on METABRIC training set and the independent test on TCGA dataset were 0.515 and 0.492, respectively. The CNVs of PGAP3, GRB7, MIR4728, PNMT, STARD3, TCAP and ERBB2 were important for the accurate diagnosis of breast cancer subtypes. The findings reported in this study may further uncover the difference between different breast cancer subtypes and improve the diagnosis accuracy.

Nuclear microtubule filaments mediate non-linear directional motion of chromatin and promote DNA repair

Damaged DNA shows increased mobility, which can promote interactions with repair-conducive nuclear pore complexes (NPCs). This apparently random mobility is paradoxically abrogated upon disruption of microtubules or kinesins, factors that typically cooperate to mediate the directional movement of macromolecules. Here, we resolve this paradox by uncovering DNA damage-inducible intranuclear microtubule filaments (DIMs) that mobilize damaged DNA and promote repair. Upon DNA damage, relief of centromeric constraint induces DIMs that cooperate with the Rad9 DNA damage response mediator and Kar3 kinesin motor to capture DNA lesions, which then linearly move along dynamic DIMs. Decreasing and hyper-inducing DIMs respectively abrogates and hyper-activates repair. Accounting for DIM dynamics across cell populations by measuring directional changes of damaged DNA reveals that it exhibits increased non-linear directional behavior in nuclear space. Abrogation of DIM-dependent processes or repair-promoting factors decreases directional behavior. Thus, inducible and dynamic nuclear microtubule filaments directionally mobilize damaged DNA and promote repair.

Following DNA damage, different processes come to action to aid repair. The authors here find that microtubule filaments within the cell nucleus capture and non-randomly mobilize damaged chromatin to mediate DNA repair.

Elevated FKBP52 expression indicates a poor outcome in patients with breast cancer

The 52-kDa FK506-binding protein (FKBP52), a regulator of steroid hormone receptor signaling, is potentially involved in a variety of hormone-dependent cancer types. The present study investigated the expression and clinical implications of FKBP52 in breast cancer. Immunohistochemistry was performed on samples from 145 breast cancer patients and on 66 unmatched breast non-cancerous tissues (as controls) to determine the expression level of FKBP52. Publicly available microarray and RNA-seq datasets used in the present study were downloaded from the European Bioinformatics Institute ArrayExpress. Kaplan-Meier survival analysis was also performed. FKBP52 expression was moderately higher in the tumors than that in the non-cancerous tissues, but this difference was not statistically significant (P=0.176). However, available microarray datasets exhibited a significant difference in FKBP52 mRNA levels between breast tumors and controls. In the 145 breast cancer patients, elevated FKBP52 expression was significantly associated with advanced Tumor-Node-Metastasis (TNM) stage (P=0.015), lymph node metastasis (P=0.015) and tumors with poor histological differentiation (P=0.047). FKBP52 expression was negatively associated with estrogen receptor expression (P=0.033), but positively associated with human epidermal growth factor receptor 2 expression (P=0.033). However, there was no association between FKBP52 and progesterone receptor expression. Survival analyses demonstrated that FKBP52 was indicative of a poor overall survival rate (P=0.026), which was consistent with the result of Kaplan-Meier analysis, exhibiting a negative association between the mRNA of FKBP52 and overall survival (OS) (P=0.044). Other than for FKBP52 [hazard ratio (HR), 2.315; 95% confidence interval (CI), 1.077-4.975; P=0.032], univariate analysis revealed that clinical stage exhibited a significant influence on the prognosis of the breast cancer patients (HR, 2.148; 95% CI, 1.011-4.566; P=0.047). However, multivariate analysis revealed that only clinical stage, not FKBP52, was an independent prognostic factor (HR, 2.721; 95% CI, 1.169-6.335; P=0.020). Patients were further classified according to their OS. Compared with the controls (3.94±2.992), FKBP52 expression in breast cancer patients with OS of ≤3 years (5.39±3.409; P=0.042) or OS of ≤5 years (5.88±3.473; P=0.005) was significantly increased, respectively. However, no significant difference in FKBP52 expression was observed between controls and individuals with an OS time of >3 years (4.84±3.769; P=0.109) or >5 years (5.32±3.372; P=0.090). Elevated FKBP52 expression may be involved in tumor progression and invasion, given its positive association with TNM stage and lymph node metastasis. Although it is not an independent predictor, FKBP52 has promise as a biological marker for estimating the progression of breast cancer.

Kinesin superfamily: roles in breast cancer, patient prognosis and therapeutics

Breast cancer pathobiology is known to be influenced by the differential expression of a group of proteins called the kinesin superfamily (KIFs), which is instrumental in the intracellular transport of chromosomes along microtubules during mitosis. During cellular division, kinesins are strictly regulated through temporal synthesis so that they are present only when needed. However, their misregulation may contribute to uncontrolled cell growth owing to premature sister chromatid separation, highlighting their importance in cancer. This review covers the functions of kinesins in normal and breast cancer cells, the use of kinesins for breast cancer patient prognosis, and the targeting of these molecules for therapeutics. A better understanding of KIF proteins may be pivotal to improved disease outcomes for breast cancer patients.

Identification of altered pathways in breast cancer based on individualized pathway aberrance score

The objective of the present study was to identify altered pathways in breast cancer based on the individualized pathway aberrance score (iPAS) method combined with the normal reference (nRef). There were 4 steps to identify altered pathways using the iPAS method: Data preprocessing conducted by the robust multi-array average (RMA) algorithm; gene-level statistics based on average Z; pathway-level statistics according to iPAS; and a significance test dependent on 1 sample Wilcoxon test. The altered pathways were validated by calculating the changed percentage of each pathway in tumor samples and comparing them with pathways from differentially expressed genes (DEGs). A total of 688 altered pathways with P<0.01 were identified, including kinesin (KIF)- and polo-like kinase (PLK)-mediated events. When the percentage of change reached 50%, 310 pathways were involved in the total 688 altered pathways, which may validate the present results. In addition, there were 324 DEGs and 155 common genes between DEGs and pathway genes. DEGs and common genes were enriched in the same 9 significant terms, which also were members of altered pathways. The iPAS method was suitable for identifying altered pathways in breast cancer. Altered pathways (such as KIF and PLK mediated events) were important for understanding breast cancer mechanisms and for the future application of customized therapeutic decisions.

Detection of Methylated Circulating DNA as Noninvasive Biomarkers for Breast Cancer Diagnosis

Internationally, breast cancer is the most common female cancer, and is induced by a combination of environmental, genetic, and epigenetic risk factors. Despite the advancement of imaging techniques, invasive sampling of breast epithelial cells is the only definitive diagnostic procedure for patients with breast cancer. To date, molecular biomarkers with high sensitivity and specificity for the screening and early detection of breast cancer are lacking. Recent evidence suggests that the detection of methylated circulating cell-free DNA in the peripheral blood of patients with cancer may be a promising quantitative and noninvasive method for cancer diagnosis. Methylation detection based on a multi-gene panel, rather than on the methylation status of a single gene, may be used to increase the sensitivity and specificity of breast cancer screening. In this review, the results of 14 relevant studies, investigating the efficacy of cell-free DNA methylation screening for breast cancer diagnosis, have been summarized. The genetic risk factors for breast cancer, the methods used for breast cancer detection, and the techniques and limitations related to the detection of cell-free DNA methylation status, have also been reviewed and discussed. From this review, we conclude that the analysis of peripheral blood or other samples to detect differentially methylated cell-free DNA is a promising technique for use in clinical settings, and may improve the sensitivity of screening for both, early detection and disease relapse, and thus improve the future prognosis of patients with breast cancer.

DUSP1 promoter methylation in peripheral blood leukocyte is associated with triple-negative breast cancer risk

DNA methylation is one of the most common epigenetic alterations, providing important information regarding cancer risk and prognosis. A case-control study (423 breast cancer cases, 509 controls) and a case-only study (326 cases) were conducted to evaluate the association of DUSP1 promoter methylation with breast cancer risk and clinicopathological characteristics. No significant association between DUSP1 methylation in peripheral blood leukocyte (PBL) DNA and breast cancer risk was observed. DUSP1 methylation was significantly associated with ER/PR-negative status; in particular, triple-negative breast cancer patients showed the highest frequency of DUSP1 methylation in both tumour DNA and PBL DNA. Soybean intake was significantly correlated with methylated DUSP1 only in ER-negative (OR 2.978; 95% CI 1.245-7.124) and PR negative (OR 2.735; 95% CI 1.315-5.692) patients. Irregular menstruation was significantly associated with methylated DUSP1 only in ER-positive (OR 3.564; 95% CI 1.691-7.511) and PR-positive (OR 3.902, 95% CI 1.656-9.194) patients. Thus, DUSP1 methylation is a cancer-associated hypermethylation event that is closely linked with triple-negative status. Further investigations are warranted to confirm the association of environmental factors, including fruit and soybean intake, irregular menstruation, and ER/PR status, with DUSP1 methylation in breast tumour DNA.

Cell-free DNA as a diagnostic marker for cancer: current insights

The increasing knowledge of the molecular pathogenesis of cancer and the rapid development of new molecular techniques are promoting the study of early molecular alterations involved in cancer development in body fluids. Specific genetic and epigenetic alterations could be found in plasma, serum, and urine cell-free DNA (cfDNA) and could potentially be used as diagnostic biomarkers for several types of cancers. This review focuses on the role of cfDNA in diagnosis: a PubMed search was performed by selecting papers according to journal impact factor and robustness of statistical analysis. A comprehensive evaluation of “liquid biopsy”, including cfDNA analysis, will be one of the critical challenges to better understand the early mechanisms of cancer development.

Methylation analysis of plasma cell-free DNA for breast cancer early detection using bisulfite next-generation sequencing

Circulating cell-free DNA (cfDNA) has been considered as a potential biomarker for non-invasive cancer detection. To evaluate the methylation levels of six candidate genes (EGFR, GREM1, PDGFRB, PPM1E, SOX17, and WRN) in plasma cfDNA as biomarkers for breast cancer early detection, quantitative analysis of the promoter methylation of these genes from 86 breast cancer patients and 67 healthy controls was performed by using microfluidic-PCR-based target enrichment and next-generation bisulfite sequencing technology. The predictive performance of different logistic models based on methylation status of candidate genes was investigated by means of the area under the ROC curve (AUC) and odds ratio (OR) analysis. Results revealed that EGFR, PPM1E, and 8 gene-specific CpG sites showed significantly hypermethylation in cancer patients' plasma and significantly associated with breast cancer (OR ranging from 2.51 to 9.88). The AUC values for these biomarkers were ranging from 0.66 to 0.75. Combinations of multiple hypermethylated genes or CpG sites substantially improved the predictive performance for breast cancer detection. Our study demonstrated the feasibility of quantitative measurement of candidate gene methylation in cfDNA by using microfluidic-PCR-based target enrichment and bisulfite next-generation sequencing, which is worthy of further validation and potentially benefits a broad range of applications in clinical oncology practice. Quantitative analysis of methylation pattern of plasma cfDNA by next-generation sequencing might be a valuable non-invasive tool for early detection of breast cancer.

Epigenetic Biomarkers of Breast Cancer Risk: Across the Breast Cancer Prevention Continuum

Epigenetic biomarkers, such as DNA methylation, can increase cancer risk through altering gene expression. The Cancer Genome Atlas (TCGA) Network has demonstrated breast cancer-specific DNA methylation signatures. DNA methylation signatures measured at the time of diagnosis may prove important for treatment options and in predicting disease-free and overall survival (tertiary prevention). DNA methylation measurement in cell free DNA may also be useful in improving early detection by measuring tumor DNA released into the blood (secondary prevention). Most evidence evaluating the use of DNA methylation markers in tertiary and secondary prevention efforts for breast cancer comes from studies that are cross-sectional or retrospective with limited corresponding epidemiologic data, raising concerns about temporality. Few prospective studies exist that are large enough to address whether DNA methylation markers add to the prediction of tertiary and secondary outcomes over and beyond standard clinical measures. Determining the role of epigenetic biomarkers in primary prevention can help in identifying modifiable pathways for targeting interventions and reducing disease incidence. The potential is great for DNA methylation markers to improve cancer outcomes across the prevention continuum. Large, prospective epidemiological studies will provide essential evidence of the overall utility of adding these markers to primary prevention efforts, screening, and clinical care.

Circulating DNA as biomarker in breast cancer

As the release of tumor-associated DNA into blood circulation is a common event in patients with cancer, screening of plasma or serum DNA may provide information on genetic and epigenetic profiles associated with breast cancer development, progression, and response to therapy. Quantitative testing of circulating DNA can reflect tumor burden, and molecular characterization of circulating DNA can reveal important tumor characteristics relevant to the choice of targeted therapies in individual patients. Contrary to circulating DNA from blood that presents molecular changes in tumor DNA in real time, tissue biopsies can deliver only a spatially and temporally limited snapshot of the heterogeneous tumor. Analyses of circulating DNA might provide prognostic and predictive information and therefore advance personalized medicine. However, standardization of different technical platforms as well as the control of pre-analytical and analytical factors is mandatory before its introduction into clinical practice. In the present review, we discussed technical aspects and clinical relevance of the analyses of circulating plasma/serum DNA in patients with breast cancer.

Wnt/β-catenin pathway is required for epithelial to mesenchymal transition in CXCL12 over expressed breast cancer cells

CXCL12 is positively associated with the metastasis and prognosis of various human malignancies. Cancer-associated fibroblasts (CAFs), the main cells secreting CXCL12, are capable of inducing epithelial to mesenchymal transition (EMT) of breast cancer cells. However, it has not been completely understood whether CXCL12 is involved in EMT of breast cancer cells and the underlying mechanisms. The present study aimed to investigate the effects of CXCL12 on the EMT and cancer stem cell (CSC)-like phenotypes formation by transfecting pEGFP-N1-CXCL12 plasmid into MCF-7 cells. Real time-PCR and Western blot analysis demonstrated the successful over expression of CXCL12 in MCF-7 cells. Cell counting kit-8 assay, wound healing assay and Transwell invasion analysis confirmed that over expression of CXCL12 significantly promoted the proliferation, migration and invasion in MCF-7 cells (P<0.05). In addition, ALDH activity was dramatically enhanced compared with parental (P<0.001), accompanied by the notably elevated mRNA and protein levels of OCT-4, Nanog, and SOX2 in CXCL12 overexpressed-MCF-7 cells (P<0.001). Furthermore, we observed the down regulation of E-cadherin and up regulation of vimentin, N-cadherin, and α-SMA in CXCL12 overexpressed-MCF-7 cells (P<0.01). Meanwhile, western blot and immunofluorescence assay showed that over expression of CXCL12 activated Wnt/β-catenin pathway to induce EMT of MCF-7 cells, as evidenced by the increased expression of E-cadherin after silencing β-catenin by siRNA interference (P<0.001). Collectively, our findings suggested that over expression of CXCL12 could trigger EMT by activating Wnt/β-catenin pathway and induce CSC-like phenotypes formation to promote the proliferation and metastasis in MCF-7. Hence, CXCL12 may become a promising candidate for breast cancer therapy.

Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential

BACKGROUND

Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as DNA copy-number alteration, mRNA and miRNA expression, can clarify biological functions and pathways deregulated in cancer. The integrative methods that are used to investigate these data involve different fields, including biology, bioinformatics, and statistics.

RESULTS

These methodologies are presented in this review, and their implementation in breast cancer is discussed with a focus on integration strategies. We report current applications, recent studies and interesting results leading to the identification of candidate biomarkers for diagnosis, prognosis, and therapy in breast cancer by using both individual and combined analyses.

CONCLUSION

This review presents a state of art of the role of different technologies in breast cancer based on the integration of genetics and epigenetics, and shares some issues related to the new opportunities and challenges offered by the application of such integrative approaches.

Hitting the brakes: targeting microtubule motors in cancer

Despite the growing number of therapies that target cancer-specific pathways, cytotoxic treatments remain important clinical tools. The rationale for targeting cell proliferation by chemotherapeutic agents stems from the assumption that tumours harbour a greater fraction of actively dividing cells than normal tissues. One such group of cytotoxic drugs impair microtubule polymers, which are cytoskeletal components of cells essential for many processes including mitosis. However, in addition to their antimitotic action, these agents cause debilitating and dose-limiting neurotoxicity because of the essential functions of microtubules in neurons. To overcome this limitation, drugs against mitosis-specific targets have been developed over the past decade, albeit with variable clinical success. Here we review the key lessons learnt from antimitotic therapies with a focus on inhibitors of microtubule motor proteins. Furthermore, based on the cancer genome data, we describe a number of motor proteins with tumour type-specific alterations, which warrant further investigation in the quest for cytotoxic targets with increased cancer specificity.

Epigenetic mechanisms of breast cancer: an update of the current knowledge

Epigenetic alterations are heritable changes in gene expression that occur without causing any change in DNA sequence. They are important key factors for cancer development and prognosis. Breast cancer is induced by the accumulation of altered gene regulation. Besides genetic mutations, epigenetics mechanisms have an important role in breast cancer tumorigenesis. Investigations related with aberrant epigenetic regulations in breast cancer focus on initiating molecular mechanisms in cancer development, identification of new biomarkers to predict breast cancer aggressiveness and the potential of epigenetic therapy. In this review, we will summarize the recent knowledge about the role of epigenetic alterations related with DNA methylation and histone modification in breast cancer. In addition, altered regulation of breast cancer specific genes and the potential of epigenetic therapy will be discussed according to epigenetic mechanisms.

Methylation of cell-free circulating DNA in the diagnosis of cancer

A range of molecular alterations found in tumor cells, such as DNA mutations and DNA methylation, is reflected in cell-free circulating DNA (circDNA) released from the tumor into the blood, thereby making circDNA an ideal candidate for the basis of a blood-based cancer diagnosis test. In many cancer types, mutations driving tumor development and progression are present in a wide range of oncogenes and tumor suppressor genes. However, even when a gene is consistently mutated in a particular cancer, the mutations can be spread over very large regions of its sequence, making evaluation difficult. This diversity of sequence changes in tumor DNA presents a challenge for the development of blood tests based on DNA mutations for cancer diagnosis. Unlike mutations, DNA methylation that can be consistently measured, as it tends to occur in specific regions of the DNA called CpG islands. Since DNA methylation is reflected within circDNA, detection of tumor-specific DNA methylation in patient plasma is a feasible approach for the development of a blood-based test. Aberrant circDNA methylation has been described in most cancer types and is actively being investigated for clinical applications. A commercial blood test for colorectal cancer based on the methylation of the SEPT9 promoter region in circDNA is under review for approval by the Federal Drug Administration (FDA) for clinical use. In this paper, we review the state of research in circDNA methylation as an application for blood-based diagnostic tests in colorectal, breast, lung, pancreatic and ovarian cancers, and we consider some of the future directions and challenges in this field. There are a number of potential circDNA biomarkers currently under investigation, and experience with SEPT9 shows that the time to clinical translation can be relatively rapid, supporting the promise of circDNA as a biomarker.