Cancer genetics

Protective alleles and precision healthcare in crewed spaceflight

Common and rare alleles are now being annotated across millions of human genomes, and omics technologies are increasingly being used to develop health and treatment recommendations. However, these alleles have not yet been systematically characterized relative to aerospace medicine. Here, we review published alleles naturally found in human cohorts that have a likely protective effect, which is linked to decreased cancer risk and improved bone, muscular, and cardiovascular health. Although some technical and ethical challenges remain, research into these protective mechanisms could translate into improved nutrition, exercise, and health recommendations for crew members during deep space missions.

VEGF-2578C/A, -460T/C Polymorphisms and Gastrointestinal Tract Cancer Risk: An Updated Meta-Analysis

Functional polymorphisms in the vascular endothelial growth factor (VEGF) alter the susceptibility toward different gastrointestinal tract (GIT) cancers. In this study, we explored the association of VEGF-2578C/A and VEGF-460T/C polymorphisms with esophageal cancer (EC) risk. In total, 330 patients with EC and 330 controls for VEGF-2578C/A polymorphism and 316 patients with EC and 316 controls for VEGF-460T/C polymorphism were genotyped. AA genotype (p = 0.01) and A allele (p = 0.02) of VEGF-2578C/A and CC genotype (p = 0.04) and C allele (p = 0.04) of VEGF-460T/C polymorphism were significantly associated with an increased risk of EC. VEGF-2578C/A and VEGF-460T/C polymorphisms have been studied in different GIT cancers, but results are inconclusive. Therefore, we performed a meta-analysis to assess the association of these polymorphisms with the risk of GIT cancers. The PubMed, ScienceDirect, and Google Scholar databases were used to search the articles. Twenty-one studies on VEGF-2578C/A and 20 studies on VEGF-460T/C polymorphism were included in this meta-analysis. VEGF-2578C/A polymorphism was associated with the decreased risk of GIT cancer in the overall population under the overdominant model (p = 0.009). A significant association of VEGF-2578C/A polymorphism with GIT cancer risk has been observed in the middle easterners, Caucasians, and Asians under different genetic models. VEGF-460T/C polymorphism was significantly associated with an increased risk of GIT cancers in Caucasians. Stratification of the data on the basis of cancer type showed a significant association of VEGF-2578C/A polymorphism with the risk of gallbladder cancer, whereas VEGF-460T/C polymorphism was associated with the risk of hepatocellular cancer, gastric cancer, and colorectal cancer. Our meta-analysis suggested that VEGF-2578C/A and VEGF-460T/C polymorphisms were associated with GIT cancer risk.

A comprehensive analysis of clinical and polygenic germline influences on somatic mutational burden

Tumor mutational burden (TMB), the total number of somatic mutations in the tumor, and copy number burden (CNB), the corresponding measure of aneuploidy, are established fundamental somatic features and emerging biomarkers for immunotherapy. However, the genetic and non-genetic influences on TMB/CNB and, critically, the manner by which they influence patient outcomes remain poorly understood. Here, we present a large germline-somatic study of TMB/CNB with >23,000 individuals across 17 cancer types, of which 12,000 also have extensive clinical, treatment, and overall survival (OS) measurements available. We report dozens of clinical associations with TMB/CNB, observing older age and male sex to have a strong effect on TMB and weaker impact on CNB. We additionally identified significant germline influences on TMB/CNB, including fine-scale European ancestry and germline polygenic risk scores (PRSs) for smoking, tanning, white blood cell counts, and educational attainment. We quantify the causal effect of exposures on somatic mutational processes using Mendelian randomization. Many of the identified features associated with TMB/CNB were additionally associated with OS for individuals treated at a single tertiary cancer center. For individuals receiving immunotherapy, we observed a complex relationship between PRSs for educational attainment, self-reported college attainment, TMB, and survival, suggesting that the influence of this biomarker may be substantially modified by socioeconomic status. While the accumulation of somatic alterations is a stochastic process, our work demonstrates that it can be shaped by host characteristics including germline genetics.

RNASeq Analysis for Accurate Identification of Fusion Partners in Tumor Specific Translocations Detected by Standard FISH Probes in Hematologic Malignancies

Background

Fluorescence labeled DNA probes and in situ hybridization methods had shorter turn round time for results revolutionized their clinical application. Signals obtained from these probes are highly specific, yet they can produce fusion signals not necessarily representing fusion of actual genes due to other genes included in the probe design. In this study we evaluated discordance between cytogenetic, FISH and RNAseq results in 3 different patients with hematologic malignancies and illustrated the need to perform next generation sequencing (NGS) or RNASeq to accurately interpret FISH results.

Methods

Bone marrow or peripheral blood karyotypes and FISH were performed to detect recurring translocations associated with hematologic malignancies in clinical samples routinely referred to our clinical cytogenetics laboratory. When required, NGS was performed on DNA and RNA libraries to detect somatic alterations and gene fusions in some of these specimens. Discordance in results between these methods is further evaluated.

Results

For a patient with plasma cell leukemia standard FGFR3 / IGH dual fusion FISH assay detected fusion that was interpreted as FGFR3-positive leukemia, whereas NGS/RNASeq detected NSD2::IGH. For a pediatric acute lymphoblastic leukemia patient, a genetic diagnosis of PDGFRB-positive ALL was rendered because the PDGFRB break-apart probe detected clonal rearrangement, whereas NGS detected MEF2D::CSF1R. A MYC-positive B-prolymphocytic leukemia was rendered for another patient with a cytogenetically identified t(8;14) and MYC::IGH by FISH, whereas NGS detected a novel PVT1::RCOR1 not previously reported.

Conclusions

These are 3 cases in a series of several other concordant results, nevertheless, elucidate limitations when interpreting FISH results in clinical applications, particularly when other genes are included in probe design. In addition, when the observed FISH signals are atypical, this study illustrates the necessity to perform complementary laboratory assays, such as NGS and/or RNASeq, to accurately identify fusion genes in tumorigenic translocations.

Unveiling the therapeutic potential of natural-based anticancer compounds inducing non-canonical cell death mechanisms

In the Mid-19th century, Rudolf Virchow considered necrosis to be a prominent form of cell death; since then, pathologists have recognized necrosis as both a cause and a consequence of disease. About a century later, the mechanism of apoptosis, another form of cell death, was discovered, and we now know that this process is regulated by several molecular mechanisms that "programme" the cell to die. However, discoveries on cell death mechanisms are not limited to these, and recent studies have allowed the identification of novel cell death pathways that can be molecularly distinguished from necrotic and apoptotic cell death mechanisms. Moreover, the main goal of current cancer therapy is to discover and develop drugs that target apoptosis. However, resistance to chemotherapeutic agents targeting apoptosis is mainly responsible for the failure of clinical therapy and adverse side effects of the chemotherapeutic agents currently in use pose a major threat to the well-being and lives of patients. Therefore, the development of natural-based anticancer drugs with low cellular and organismal side effects is of great interest. In this comprehensive review, we thoroughly examine and discuss natural anticancer compounds that specifically target non-canonical cell death mechanisms.

Association of JAK/STAT genetic variants with cutaneous melanoma

Background

The Janus-activated kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway regulates cutaneous melanoma (CM) development and progression. The JAK1, JAK2, and STAT3 proteins are encoded by polymorphic genes. This study aimed to verify whether single-nucleotide variants (SNVs) in JAK1 (c.1648+1272G>A, c.991-27C>T), JAK2 (c.-1132G>T, c.-139G>A), and STAT3 (c.*1671T>C, c.-1937C>G) altered the risk, clinicopathological aspects, and survival of CM patients as well as protein activity.

Methods

CM patients (N = 248) and controls (N = 274) were enrolled in this study. Genotyping was performed by real-time polymerase chain reaction (PCR), and JAK1, JAK2, and STAT3 expression was assessed by quantitative PCR (qPCR). STAT3 c.-1937C>G SNV was investigated by luciferase, qPCR, western blot, apoptosis, and cell cycle assays in SKMEL-28 cells with CC or GG genotype.

Results

Individuals with STAT3 c.*1671TT and c.-1937CC genotypes and TC haplotype of both SNVs were under about 2.0-fold increased risk of CM. Specific JAK1, JAK2, and STAT3 combined genotypes were associated with up to 4.0-fold increased risk of CM. Higher luciferase activity [4,013.34 vs. 2,463.32 arbitrary units (AU); p = 0.004], STAT3 expression by qPCR (649.20 vs. 0.03 AU; p = 0.003) and western blot (1.69 vs. 1.16 AU; p = 0.01), and percentage of cells in the S phase of the cell cycle (57.54 vs. 30.73%; p = 0.04) were more frequent in SKMEL-28 with STAT3 c.-1937CC than with GG genotype. CM cell line with CC genotype presented higher STAT3 protein levels than the one with GG genotype (1.93 versus 1.27 AU, p = 0.0027).

Conclusion

Our data present preliminary evidence that inherited abnormalities in the JAK/STAT pathway can be used to identify individuals at a high risk of CM, who deserve additional attention for tumor prevention and early detection.

Clinical and biochemical footprints of inherited metabolic diseases. VIII. Neoplasias

Cancer, caused by multiple cumulative pathogenic variants in tumor suppressor genes and proto-oncogenes, is a leading cause of mortality worldwide. The uncontrolled and rapid cell growth of the tumors requires a reprogramming of the complex cellular metabolic network to favor anabolism. Adequate management and treatment of certain inherited metabolic diseases might prevent the development of certain neoplasias, such as hepatocellular carcinoma in tyrosinemia type 1 or hepatocellular adenomas in glycogen storage disorder type 1a. We reviewed and updated the list of known metabolic etiologies associated with various types of benign and malignant neoplasias, finding 64 relevant inborn errors of metabolism. This is the eighth article of the series attempting to create a comprehensive list of clinical and metabolic differential diagnosis by system involvement.

A truncated nuclear norm and graph-Laplacian regularized low-rank representation method for tumor clustering and gene selection

Background

Clustering and feature selection act major roles in many communities. As a matrix factorization, Low-Rank Representation (LRR) has attracted lots of attentions in clustering and feature selection, but sometimes its performance is frustrated when the data samples are insufficient or contain a lot of noise.

Results

To address this drawback, a novel LRR model named TGLRR is proposed by integrating the truncated nuclear norm with graph-Laplacian. Different from the nuclear norm minimizing all singular values, the truncated nuclear norm only minimizes some smallest singular values, which can dispel the harm of shrinkage of the leading singular values. Finally, an efficient algorithm based on Linearized Alternating Direction with Adaptive Penalty is applied to resolving the optimization problem.

Conclusions

The results show that the TGLRR method exceeds the existing state-of-the-art methods in aspect of tumor clustering and gene selection on integrated gene expression data.

Possible relationship between the somatic mutations and the formation of cancers

Cancer is one of the most life-threatening diseases and has been studied for more than 3 thousand years (earliest records of cancer research is 1500BC). But there are still insufficient number of efficient treatments for cancer. This is a review started with introducing the cancer and somatic mutations by explaining the hallmarks of cancer, followed by, the discussion of few types of mutations, which may be potential targets regarding to the therapeutic treatments. Also, some potential targets related to those mutations are listed, such as, pRb proteins with its two subunits (p130 and p107), reverse transcriptase telomerase (TERT), shelterin complex and so on. The statement “cancer is caused by accumulation of somatic mutations” can be supported by the positive correlation between cancer and age. In addition, some mutations, which have contribution on increasing mutation frequencies, has been proved to be the factors of cancer. For example, xeroderma pigmentosum, mutations on DNA MMR rep air and BRCA1 and BRCA2 mutations. This overview of the relationship between cancer and those somatic mutations, which may provide potentials for further cancer treatments.

An Update on the Effects of Probiotics on Gastrointestinal Cancers

Because of their increasing prevalence, gastrointestinal (GI) cancers are regarded as an important global health challenge. Microorganisms residing in the human GI tract, termed gut microbiota, encompass a large number of living organisms. The role of the gut in the regulation of the gut-mediated immune responses, metabolism, absorption of micro- and macro-nutrients and essential vitamins, and short-chain fatty acid production, and resistance to pathogens has been extensively investigated. In the past few decades, it has been shown that microbiota imbalance is associated with the susceptibility to various chronic disorders, such as obesity, irritable bowel syndrome, inflammatory bowel disease, asthma, rheumatoid arthritis, psychiatric disorders, and various types of cancer. Emerging evidence has shown that oral administration of various strains of probiotics can protect against cancer development. Furthermore, clinical investigations suggest that probiotic administration in cancer patients decreases the incidence of postoperative inflammation. The present review addresses the efficacy and underlying mechanisms of action of probiotics against GI cancers. The safety of the most commercial probiotic strains has been confirmed, and therefore these strains can be used as adjuvant or neo-adjuvant treatments for cancer prevention and improving the efficacy of therapeutic strategies. Nevertheless, well-designed clinical studies are still needed for a better understanding of the properties and mechanisms of action of probiotic strains in mitigating GI cancer development.

A Pipelined Tracer-Aware Approach for Lesion Segmentation in Breast DCE-MRI

The recent spread of Deep Learning (DL) in medical imaging is pushing researchers to explore its suitability for lesion segmentation in Dynamic Contrast-Enhanced Magnetic-Resonance Imaging (DCE-MRI), a complementary imaging procedure increasingly used in breast-cancer analysis. Despite some promising proposed solutions, we argue that a "naive" use of DL may have limited effectiveness as the presence of a contrast agent results in the acquisition of multimodal 4D images requiring thorough processing before training a DL model. We thus propose a pipelined approach where each stage is intended to deal with or to leverage a peculiar characteristic of breast DCE-MRI data: the use of a breast-masking pre-processing to remove non-breast tissues; the use of Three-Time-Points (3TP) slices to effectively highlight contrast agent time course; the application of a motion-correction technique to deal with patient involuntary movements; the leverage of a modified U-Net architecture tailored on the problem; and the introduction of a new "Eras/Epochs" training strategy to handle the unbalanced dataset while performing a strong data augmentation. We compared our pipelined solution against some literature works. The results show that our approach outperforms the competitors by a large margin (+9.13% over our previous solution) while also showing a higher generalization ability.

Identification of key genes in cutaneous squamous cell carcinoma: a transcriptome sequencing and bioinformatics profiling study

Background

Long-term exposure to ultraviolet (UV) radiation can cause cutaneous squamous cell carcinoma (cSCC), which is one of the most common malignant cancers worldwide. Actinic keratosis (AK) is generally considered a precancerous lesion of cSCC. However, the pathogenesis and oncogenic processes of AK and cSCC remain elusive, especially in the context of photodamage.

Methods

In this study, transcriptome sequencing was performed on AK, cSCC, normal sun-exposed skin (NES) tissues, and normal non-sun-exposed skin (NNS) from 24 individuals. Bioinformatics analysis to identify the differentially expressed genes (DEGs) of 4 groups, and potential key genes of cSCC were validated by real-time quantitative reverse transcription PCR (qRT-PCR).

Results

A total of 46,930 genes were differentially expressed in the 4 groups, including 127 genes that were differentially expressed between NES and NNS, 420 DEGs in AK compared to NES, 1,658 DEGs in cSCC compared to NES, and 1,389 DEGs in cSCC compared to AK. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis suggested that the DEGs are involved in multiple pathways, including extracellular matrix (ECM)-receptor interaction, immune, inflammatory, microbial infection, and other related pathways. Finally, 5 new genes (HEPHL1, FBN2, SULF1, SULF2, and TCN1) were confirmed significantly upregulated in cSCC.

Conclusions

Using transcriptome sequencing and integrated bioinformatical analysis, we have identified key DEGs and pathways in cSCC, which could improve our understanding of the cause and underlying molecular events of AK and cSCC. HEPHL1, FBN2, SULF1, SULF2, and TCN1 may be novel potential biomarkers and therapeutic targets of cSCC.

Correntropy-Based Hypergraph Regularized NMF for Clustering and Feature Selection on Multi-Cancer Integrated Data

Non-negative matrix factorization (NMF) has become one of the most powerful methods for clustering and feature selection. However, the performance of the traditional NMF method severely degrades when the data contain noises and outliers or the manifold structure of the data is not taken into account. In this article, a novel method called correntropy-based hypergraph regularized NMF (CHNMF) is proposed to solve the above problem. Specifically, we use the correntropy instead of the Euclidean norm in the loss term of CHNMF, which will improve the robustness of the algorithm. And the hypergraph regularization term is also applied to the objective function, which can explore the high-order geometric information in more sample points. Then, the half-quadratic (HQ) optimization technique is adopted to solve the complex optimization problem of CHNMF. Finally, extensive experimental results on multi-cancer integrated data indicate that the proposed CHNMF method is superior to other state-of-the-art methods for clustering and feature selection.

3D analysis of facial morphology in Dutch children with cancer

Background and Objective; Genetic risk factors for childhood cancer may also influence facial morphology. 3D photography can be used in the recognition of differences in face shape among individuals. In previous research, 3D facial photography was used to identify increased facial asymmetry and greater deviation from normal facial morphology in a group of individuals with distinct morphological features who had childhood cancer compared to healthy controls. In this study, we aim to determine whether there is a difference in facial morphology between children with cancer without previously selected morphological features and healthy controls, detected with 3D facial photography.

METHODS

Facial 3D photographic images were obtained of children with a newly diagnosed malignancy. The resulting sample comprised 13 different cancer types. Patients were excluded if they had a known genetic cause of the cancer. Patients were compared to healthy controls, matched for sex, age and ethnic background. The degree of asymmetry and overall deviation of an individual's face from an age and sex typical control face were measured.

RESULTS

A total of 163 patients of European descent were included. No significant difference in asymmetry between patients and controls could be identified. On average, patients deviated more from an age and sex typical face than the controls.

CONCLUSION

This study shows that children with cancer deviate more than controls, possibly suggesting a higher prevalence of genetic anomalies within this group. The results suggest that this is not sufficient to discriminate patients from controls. Further research is necessary to explore the patterns of individual variation among the overall deviation of patients and controls.

Electromagnetic radiation: a new charming actor in hematopoiesis?

INTRODUCTION

Electromagnetic waves play indispensable roles in life. Many studies addressed the outcomes of Electromagnetic field (EMF) on various biological functions such as cell proliferation, gene expression, epigenetic alterations, genotoxic, and carcinogenic effects, and its therapeutic applications in medicine. The impact of EMF on bone marrow (BM) is of high importance; however, EMF effects on BM hematopoiesis are not well understood.

AREAS COVERED

Publications in English were searched in ISI Web of Knowledge and Google Scholar with no restriction on publication date. A literature review has been conducted on the consequences of EMF exposure on BM non-hematopoietic stem cells, mesenchymal stem cells, and the application of these waves in regenerative medicine. Human blood cells such as lymphocytes, red blood cells and their precursors are altered qualitatively and quantitatively following electromagnetic radiation. Therefore, studying the impact of EMF on related signaling pathways in hematopoiesis and hematopoietic stem cell (HSC) differentiation could give a better insight into its efficacy on hematopoiesis and its potential therapeutic usage.

EXPERT OPINION

In this review, authors evaluated the possible biologic consequences of EMF on the hematopoiesis process in addition to its probable application in the treatment of hematologic disorders.

Genetic control of tumor development in malformation syndromes

One of the questions that arises frequently when caring for an individual with a malformation syndrome, is whether some form of tumor surveillance is indicated. In some syndromes there is a highly variable increased risk to develop tumors, while in others this is not the case. The risks can be hard to predict and difficult to explain to affected individuals and their families, and often also to caregivers. The queries arise especially if syndrome causing mutations are also known to occur in tumors. It needs insight in the mechanisms to understand and explain differences of tumor occurrence, and to offer optimal care to individuals with syndromes. Here we provide a short overview of the major mechanisms of the control for tumor occurrences in malformation syndromes.

LncRNA PLAC2 upregulates miR-663 to downregulate TGF-β1 and suppress bladder cancer cell migration and invasion

BACKGROUND

The roles of lncRNA PLAC2 in bladder cancer (BC) were explored.

METHODS

The expression of PLAC2 in two types of tissue of BC patients was detected by RT-qPCR and the expression data were compared by paired t test. The 56 patients were staged according to the AJCC criteria, and 12, 15, 15 and 14 cases were classified into stage I-IV, respectively. The expression of TGF-β1 and miR-663 in BC tissues were also detected by RT-qPCR experiments.

RESULTS

Our data showed that the expression levels of PLAC2 were significantly lower in BC tissues than that in non-cancer tissues. The expression of PLAC2 was not affect by clinical stages and low expression levels of PLAC2 predicted lower survival rate. The expression of PLAC2 was positively correlated with miR-663 and inversely correlated with TGF-β1 in BC tissues. In BC cells, downregulated TGF-β1 and upregulated miR-663 were observed after the overexpression of PLAC2. Overexpression of PLAC2 also resulted in suppressed invasion and migration of BC cells. Overexpression of miR-663 resulted in downregulated TGF-β1 but did not affect the expression of PLAC2. Overexpression of TGF-β1 reduced the inhibitory effects of overexpression of PLAC2 and miR-663 on cell migration and invasion.

CONCLUSION

PLAC2 can upregulate miR-663 to downregulate TGF-β1 and suppress BC cell migration and invasion.

Immuno-Surgical Management of Pancreatic Cancer with Analysis of Cancer Exosomes

Exosomes (EXs), a type of extracellular vesicles secreted from various cells and especially cancer cells, mesenchymal cells, macrophages and other cells in the tumor microenvironment (TME), are involved in biologically malignant behaviors of cancers. Recent studies have revealed that EXs contain microRNAs on their inside and express proteins and glycolipids on their outsides, every component of which plays a role in the transmission of genetic and/or epigenetic information in cell-to-cell communications. It is also known that miRNAs are involved in the signal transduction. Thus, EXs may be useful for monitoring the TME of tumor tissues and the invasion and metastasis, processes that are associated with patient survival. Because several solid tumors secrete immune checkpoint proteins, including programmed cell death-ligand 1, the EX-mediated mechanisms are suggested to be potent targets for monitoring patients. Therefore, a companion therapeutic approach against cancer metastasis to distant organs is proposed when surgical removal of the primary tumor is performed. However, EXs and immune checkpoint mechanisms in pancreatic cancer are not fully understood, we provide an update on the recent advances in this field and evidence that EXs will be useful for maximizing patient benefit in precision medicine.

Fisetin effects on cell proliferation and apoptosis in glioma cells

This research investigated the antiproliferative effects of 1-500 μM fisetin in T98G and BEAS-2B cells by MTT assay. The IC50 of fisetin in T98G cells for 24 and 48 h were 93 and 75 μM, respectively. Apoptotic alterations of fisetin-treated T98G cells were observed by transmission electron microscopy. BEAS-2B was then used in comparison to T98G cells to determine the cytotoxic effects of fisetin. The IC50 of fisetin for 24 and 48 h were recorded as 270 and 90 μM in BEAS-2B cells, respectively. Different concentrations of fisetin were selected to determine the apoptotic and necrotic effects. Consequently, fisetin was determined to have more apoptotic effects in T98G than BEAS-2B cells, dose- and time-dependently. Moreover, fisetin was found to have cytotoxicity at lower doses in T98G cells compared to carmustine, as positive control. CASPASE 3, CASPASE 9, CASPASE 8, and BAX expressions were increased by the selected fisetin doses of 25 and 50 μM, while that of BCL-2 and survivin was reduced in T98G cells. These results will serve as an essential basis of future in vitro and in vivo studies, in the continuous search for alternative treatment agents for gliomas.

GWAS in cancer: progress and challenges

The genome-wide association study (GWAS) is an effective method to detect single-nucleotide polymorphisms (SNPs) of multiple individual genes based on linkage disequilibrium (LD). GWAS examines genotypes and distinguishing gene characteristics that are exhibited in diseases. In the past few decades, more and more literature has reported the results of applying GWAS to study tumors. Although many pleiotropic loci associated with complex phenotypes have been identified by GWAS, the biological functions of many genetic variation loci remain unclear, and the genetic mechanisms of most complex phenotypes cannot be systematically explained. In this article, we will review the new findings of several tumor types, and categorize the new sites and mechanisms that have recently been discovered. We linked the mechanisms of action of various tumors and searched for links to related gene expression pathways. We found that susceptible sites can be divided into hub genes and peripheral genes; the two interact to link gene expression in a variety of diseases.

Robust hypergraph regularized non-negative matrix factorization for sample clustering and feature selection in multi-view gene expression data

Background

As one of the most popular data representation methods, non-negative matrix decomposition (NMF) has been widely concerned in the tasks of clustering and feature selection. However, most of the previously proposed NMF-based methods do not adequately explore the hidden geometrical structure in the data. At the same time, noise and outliers are inevitably present in the data.

Results

To alleviate these problems, we present a novel NMF framework named robust hypergraph regularized non-negative matrix factorization (RHNMF). In particular, the hypergraph Laplacian regularization is imposed to capture the geometric information of original data. Unlike graph Laplacian regularization which captures the relationship between pairwise sample points, it captures the high-order relationship among more sample points. Moreover, the robustness of the RHNMF is enhanced by using the L_2,1-norm constraint when estimating the residual. This is because the L_2,1-norm is insensitive to noise and outliers.

Conclusions

Clustering and common abnormal expression gene (com-abnormal expression gene) selection are conducted to test the validity of the RHNMF model. Extensive experimental results on multi-view datasets reveal that our proposed model outperforms other state-of-the-art methods.

Geo-clustered chronic affinity: pathways from socio-economic disadvantages to health disparities

Objective

Our objective was to develop and test a new concept (affinity) analogous to multimorbidity of chronic conditions for individuals at census tract level in Memphis, TN. The use of affinity will improve the surveillance of multiple chronic conditions and facilitate the design of effective interventions.

Methods

We used publicly available chronic condition data (Center for Disease Control and Prevention 500 Cities project), socio-demographic data (US Census Bureau), and demographics data (Environmental Systems Research Institute). We examined the geographic pattern of the affinity of chronic conditions using global Moran’s I and Getis-Ord Gi* statistics and its association with socio-economic disadvantage (poverty, unemployment, and crime) using robust regression models. We also used the most common behavioral factor, smoking, and other demographic factors (percent of the male population, percent of the population 67 years, and over and total population size) as control variables in the model.

Results

A geo-distinctive pattern of clustered chronic affinity associated with socio-economic deprivation was observed. Statistical results confirmed that neighborhoods with higher rates of crime, poverty, and unemployment were associated with an increased likelihood of having a higher affinity among major chronic conditions. With the inclusion of smoking in the model, however, only the crime prevalence was statistically significantly associated with the chronic affinity.

Conclusion

Chronic affinity disadvantages were disproportionately accumulated in socially disadvantaged areas. We showed links between commonly co-observed chronic diseases at the population level and systematically explored the complexity of affinity and socio-economic disparities. Our affinity score, based on publicly available datasets, served as a surrogate for multimorbidity at the population level, which may assist policymakers and public health planners to identify urgent hot spots for chronic disease and allocate clinical, medical and healthcare resources efficiently.

Dietary protein sources and tumoral overexpression of RhoA, VEGF-A and VEGFR2 genes among breast cancer patients

BACKGROUND

High protein intake may promote angiogenesis giving support to the development of metastasis according to the experimental data. However, nutritional epidemiologic evidence is inconsistent with metastasis. Therefore, we aimed to study the association between dietary intake of protein and tumoral expression levels of Ras homologous gene family member A (RhoA), vascular endothelial growth factor-A (VEGF-A), and VEGF receptor-2 (VEGFR2) in primary breast cancer (BC) patients.

METHODS

Over this consecutive case series, 177 women primary diagnosed with histopathologically confirmed BC in Tabriz (Iran) were enrolled between May 2011 and November 2016. A validated food frequency questionnaire was completed for eligible participants. Fold change in gene expression was measured using quantitative real-time PCR. Principal component factor analysis (PCA) was used to express dietary groups of proteins.

RESULTS

Total protein intake was associated with the expression level of VEGF-A in progesterone receptor-positive (PR+: β = 0.296, p < 0.01) and VEGFR2 in patients with involvement of axillary lymph node metastasis (ALNM+: β = 0.295, p < 0.01) when covariates were adjusted. High animal protein intake was correlated with overexpression of RhoA in tumors with estrogen receptor-positive (ER+: β = 0.230, p < 0.05), ALNM+ (β = 0.238, p < 0.05), and vascular invasion (VI+: β = 0.313, p < 0.01). Animal protein intake was correlated with the overexpression of VEGFR2 when tumors were positive for hormonal receptors (ER+: β = 0.299, p < 0.01; PR+: β = 0.296, p < 0.01). Based on the PCA outputs, protein provided by whole meat (white and red meat) was associated inversely with RhoA expression in ALNM+ (β = - 0.253, p < 0.05) and premenopausal women (β = - 0.285, p < 0.01) in adjusted models. Whole meat was correlated with VEGFR2 overexpression in VI+ (β = 0.288, p < 0.05) and premenopausal status (β = 0.300, p < 0.05) in adjusted models. A group composed of dairy products and legumes was correlated with the overexpression of RhoA (β = 0.249, p < 0.05) and VEGF-A (β = 0.297, p < 0.05) in VI+.

CONCLUSIONS

Based on the multivariate findings, the dietary protein could associate with the overexpression of RhoA and VEGF-VEGFR2 in favor of lymphatic and vascular metastasis in BC patients.

Transcriptome profiling revealed multiple genes and ECM-receptor interaction pathways that may be associated with breast cancer

Background

Exploration of the genes with abnormal expression during the development of breast cancer is essential to provide a deeper understanding of the mechanisms involved. Transcriptome sequencing and bioinformatics analysis of invasive ductal carcinoma and paracancerous tissues from the same patient were performed to identify the key genes and signaling pathways related to breast cancer development.

Methods

Samples of breast tumor tissue and paracancerous breast tissue were obtained from 6 patients. Sequencing used the Illumina HiSeq platform. All. Only perfectly matched clean reads were mapped to the reference genome database, further analyzed and annotated based on the reference genome information. Differentially expressed genes (DEGs) were identified using the DESeq R package (1.10.1) and DEGSeq R package (1.12.0). Using KOBAS software to execute the KEGG bioinformatics analyses, enriched signaling pathways of DEGs involved in the occurrence of breast cancer were determined. Subsequently, quantitative real time PCR was used to verify the accuracy of the expression profile of key DEGs from the RNA-seq result and to explore the expression patterns of novel cancer-related genes on 8 different clinical individuals.

Results

The transcriptomic sequencing results showed 937 DEGs, including 487 upregulated and 450 downregulated genes in the breast cancer specimens. Further quantitative gene expression analysis was performed and captured 252 DEGs (201 downregulated and 51 upregulated) that showed the same differential expression pattern in all libraries. Finally, 6 upregulated DEGs (CST2, DRP2, CLEC5A, SCD, KIAA1211, DTL) and 6 downregulated DEGs (STAC2, BTNL9, CA4, CD300LG, GPIHBP1 and PIGR), were confirmed in a quantitative real time PCR comparison of breast cancer and paracancerous breast tissues from 8 clinical specimens. KEGG analysis revealed various pathway changes, including 20 upregulated and 21 downregulated gene enrichment pathways. The extracellular matrix–receptor (ECM-receptor) interaction pathway was the most enriched pathway: all genes in this pathway were DEGs, including the THBS family, collagen and fibronectin. These DEGs and the ECM-receptor interaction pathway may perform important roles in breast cancer.

Conclusion

Several potential breast cancer-related genes and pathways were captured, including 7 novel upregulated genes and 76 novel downregulated genes that were not found in other studies. These genes are related to cell proliferation, movement and adhesion. They may be important for research into breast cancer mechanisms, particularly CST2 and CA4. A key signaling pathway, the ECM-receptor interaction signal pathway, was also identified as possibly involved in the development of breast cancer.

Electronic supplementary material

The online version of this article (10.1186/s11658-019-0162-0) contains supplementary material, which is available to authorized users.

Overcoming Resistance to Natural Killer Cell Based Immunotherapies for Solid Tumors

Despite advances in the diagnostic and therapeutic modalities, the prognosis of several solid tumor malignancies remains poor. Different factors associated with solid tumors including a varied genetic signature, complex molecular signaling pathways, defective cross talk between the tumor cells and immune cells, hypoxic and immunosuppressive effects of tumor microenvironment result in a treatment resistant and metastatic phenotype. Over the past several years, immunotherapy has emerged as an attractive therapeutic option against multiple malignancies. The unique ability of natural killer (NK) cells to target cancer cells without antigen specificity makes them an ideal candidate for use against solid tumors. However, the outcomes of adoptive NK cell infusions into patients with solid tumors have been disappointing. Extensive studies have been done to investigate different strategies to improve the NK cell function, trafficking and tumor targeting. Use of cytokines and cytokine analogs has been well described and utilized to enhance the proliferation, stimulation and persistence of NK cells. Other techniques like blocking the human leukocyte antigen-killer cell receptors (KIR) interactions with anti-KIR monoclonal antibodies, preventing CD16 receptor shedding, increasing the expression of activating NK cell receptors like NKG2D, and use of immunocytokines and immune checkpoint inhibitors can enhance NK cell mediated cytotoxicity. Using genetically modified NK cells with chimeric antigen receptors and bispecific and trispecific NK cell engagers, NK cells can be effectively redirected to the tumor cells improving their cytotoxic potential. In this review, we have described these strategies and highlighted the need to further optimize these strategies to improve the clinical outcome of NK cell based immunotherapy against solid tumors.

Overview of the genetic basis toward early detection of breast cancer

Cancer is a socioeconomical burden in any nation. Out of that, breast cancer is identified as the most common malignancy worldwide among women irrespective of age. As women are an important segment in a community, the weakening of their strength toward the development of a nation is a critical problem in each nation. In this review, it was aimed to discuss the characteristics of cancer genome, cancer genetics, and cancer epigenetics in general and then focus on discussing both genetic and nongenetic factors responsible for the predisposition of breast cancer in humans. More emphasis was placed on genes responsible for the early onset of the disease and which can be used as genetic tools in the identification of the disease at an early stage. Then the context of genetic involvement toward the breast cancer occurrence before age of 40 years was highlighted accordingly. In addition to genetic testing, the review paid adequate attention to mention novel liquid biopsy techniques and other clinical, laboratory, and radiologic assessments. These techniques can be used in early detection and recurrence as well as the surveillance of the patients after primary therapies.

Brief Description of Inheritance Patterns

Increasing data about the human genome and associations between certain genetic regions with various conditions and diseases positioned human genetics at the top of the most emerging fields in medicine. Many diagnostics algorithms and therapeutical approaches used in everyday practice are based on genetic data. Molecular genetic diagnostics covered by this book uses genetic data obtained using germline DNA. In this book, the role of somatic mutation testing will be not covered; however, in many chapters, i.e., on hereditary tumor syndromes, the role of somatic mutations as the second hit for tumorigenesis will be mentioned. Genetic variants (genotypes) identified in germline DNA are responsible for transmission of diseases (phenotypes). This chapter will briefly summarize classical inheritance patterns. Most of the heritable human diseases are transmitted in an autosomal recessive way, but others, i.e., inherited tumor syndromes, follow the autosomal dominant pattern. Nomenclature used for pedigree analysis as well as the main features of inheritance patterns are also briefly reviewed.

Co-differential Gene Selection and Clustering Based on Graph Regularized Multi-View NMF in Cancer Genomic Data

Cancer genomic data contain views from different sources that provide complementary information about genetic activity. This provides a new way for cancer research. Feature selection and multi-view clustering are hot topics in bioinformatics, and they can make full use of complementary information to improve the effect. In this paper, a novel integrated model called Multi-view Non-negative Matrix Factorization (MvNMF) is proposed for the selection of common differential genes (co-differential genes) and multi-view clustering. In order to encode the geometric information in the multi-view genomic data, graph regularized MvNMF (GMvNMF) is further proposed by applying the graph regularization constraint in the objective function. GMvNMF can not only obtain the potential shared feature structure and shared cluster group structure, but also capture the manifold structure of multi-view data. The validity of the proposed GMvNMF method was tested in four multi-view genomic data. Experimental results showed that the GMvNMF method has better performance than other representative methods.

The associations between MDM4 gene polymorphisms and cancer risk

Considerable studies have investigated the associations between MDM4 gene polymorphisms and cancer risk recently, but with contradictory results. The aim of this meta-analysis was to evaluate the associations between MDM4 gene polymorphisms and cancer risk. Relevant studies were identified by a systematic search of PubMed, Embase, and CNKI databases. Crude odds ratios (ORs) and 95% confidence intervals (CIs) were used to describe the strength of the associations. Fifty-six studies published in 11 publications involving 18,910 cases and 51,609 controls were included in this meta-analysis. Five MDM4 gene polymorphisms were evaluated: rs4245739, rs1563828, rs11801299, rs10900598, and rs1380576. Our analyses suggested that the rs4245739 polymorphism was significantly associated with overall cancer risk. Furthermore, stratification analyses of ethnicity indicated that rs4245739 decreased the risk of cancer among the Asian population, and stratification analyses of smoking status indicated that rs4245739 decreased the risk of cancer among nonsmokers. However, stratification analyses of cancer type and sex suggested that rs4245739 was not related to cancer risk. There were no associations of rs1563828, rs11801299, rs10900598, or rs1380576 with overall cancer risk. In conclusion, our analyses indicated that rs4245739 polymorphism in the MDM4 gene may play an important role in the etiology of cancer.

Zinc finger protein 91 (ZFP91) activates HIF-1α via NF-κB/p65 to promote proliferation and tumorigenesis of colon cancer

Zinc finger protein 91 (ZFP91) has been reported to be involved in various biological processes. However, the clinical significance and biological role of ZFP91 in colon cancer remains unknown. Here, we show that ZFP91 expression is upregulated in patients with colon cancer. We found that ZFP91 upregulated HIF-1α at the levels of promoter and protein in colon cancer cells. Using chromatin immunoprecipitation, electrophoretic mobility shift assay and luciferase reporter gene assay, we found that NF-κB/p65 is required for the binding of ZFP91 to the HIF-1α promoter at -197/-188 base pairs and for the transcriptional activation of HIF-1α gene mediated by ZFP91. Flow cytometry, 5-ethynyl-2'-deoxyuridine (EdU) incorporation and tumor xenograft assay demonstrated that ZFP91 enhanced cell proliferation of colon cancer through upregulating HIF-1α in vitro and in vivo. Furthermore, ZFP91 is positively associated with HIF-1α in human colon cancer. Thus, we concluded that ZFP91 activates transcriptional coregulatory protein HIF-1α through transcription factor NF-κB/p65 in the promotion of proliferation and tumorigenesis in colon cancer cell. ZFP91 may serve as a driver gene to activate HIF-1α transcription in the development of cancer.

The associations between CYP24A1 polymorphisms and cancer susceptibility: A meta-analysis and trial sequential analysis

PURPOSE

Published data have shown that vitamin D may have a protective effect on cancer development. CYP24A1, the main enzyme responsible for the degradation of active vitamin D, plays an important role in many cancer related cellular processes. Up to now, relationships between CYP24A1 polymorphisms and cancer susceptibility have been widely investigated, whereas the results are inconsistent. The aim of present meta-analysis was to explore the associations between CYP24A1 polymorphisms and cancer susceptibility.

METHODS

We searched on EMBASE, Web of Science, PubMed and China National Knowledge Infrastructure (CNKI) electronic databases (up to July 1, 2017) for relevant studies. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to make the evaluation clear.

RESULTS

Twenty-nine studies published in eight publications involving 20,593 cases and 25,458 controls were included. Five CYP24A1 gene polymorphisms were evaluated: rs2181874, rs2585428, rs4809960, rs6022999, and rs6068816. Our analyses suggested that rs2585428 and rs4809960 polymorphisms were significantly associated with overall cancer risk. Stratification analyses of ethnicity indicated that rs2585428 and rs4809960 polymorphisms decreased the risk of cancer among Caucasians. When studies were stratified by cancer type, our results indicated that rs2585428 significantly decreased the risk of pancreas cancer, while rs4809960 significantly decreased the risk of breast cancer. There were no associations of rs2181874, rs6022999, or rs6068816 with overall cancer risks.

CONCLUSION

Associations between CYP24A1 polymorphisms and cancer risks were examined, and additional multi-center studies with large samples are necessary to validate our results.

CLPTM1L gene rs402710 (C > T) and rs401681 (C > T) polymorphisms associate with decreased cancer risk: a meta-analysis

Cleft lip and palate transmembrane 1-like (CLPTM1L) gene rs402710 (C > T) and rs401681 (C > T) polymorphisms have been widely studied for their potential relation to cancer risk, but studies have produced conflicting results. To systematically evaluate the association between these two polymorphisms and overall cancer risk, we conducted a comprehensive meta-analysis on all relevant articles found in the PubMed and EMBASE databases published prior to May 1, 2017. There were 26 articles with 28 studies, including 30,770 cases and 34,089 controls, for the rs402710 polymorphism and 38 articles with 48 studies, including 67,849 cases and 328,226 controls, for the rs401681 polymorphism. The pooled results indicated that both rs402710 and rs401681 polymorphisms are significantly associated with decreased overall cancer risk. In our stratification analysis, a significant association of the rs402710 polymorphism with lung and bladder cancers was identified among Asian and Caucasian populations in both hospital-based and population-based studies. The rs401681 polymorphism was significantly associated with a decreased risk of lung cancer, bladder cancer, and basal cell carcinoma in Asians and in hospital-based studies. CLPTM1L gene rs402710 and rs401681 polymorphisms thus have a protective association with various types of cancer, especially lung cancer among Asians.

The Effect of Reproductive Factors on Breast Cancer Presentation in Women Who Are BRCA Mutation Carrier

PURPOSE

Germline mutations in the BRCA1 and BRCA2 genes confer increased risks for breast cancers. However, the clinical presentation of breast cancer among women who are carriers of the BRCA1 or BRCA2 (BRCA1/2 carriers) mutations is heterogenous. We aimed to identify the effects of the reproductive histories of women with the BRCA1/2 mutations on the clinical presentation of breast cancer.

METHODS

We retrospectively analyzed clinical data on women with proven BRCA1 and BRCA2 mutations who were recruited to the Korean Hereditary Breast Cancer study, from 2007 to 2014.

RESULTS

Among the 736 women who were BRCA1/2 mutation carriers, a total of 483 women had breast cancers. Breast cancer diagnosis occurred at significantly younger ages in women who experienced menarche at ≤14 years of age, compared to those who experienced menarche at >14 years of age (37.38±7.60 and 43.30±10.11, respectively, p<0.001). Additionally, the number of full-term pregnancies was significantly associated with the age of diagnosis, especially in women with the BRCA2 mutation. The prevalence of advanced stages (stage II or III vs. stage I) of disease in parous women was higher than in nulliparous women (68.5% vs. 55.2%, p=0.043). This association was more pronounced in women with the BRCA2 mutation (hazard ratio, 2.67; p=0.014).

CONCLUSION

Our results suggest that reproductive factors, such as the age of onset of menarche and the presence of parity, are associated with the clinical presentation patterns of breast cancer in BRCA1/2 mutation carriers.

The oncogenic Golgi phosphoprotein 3 like overexpression is associated with cisplatin resistance in ovarian carcinoma and activating the NF-κB signaling pathway

Background

Chemo-resistance is a leading cause of tumor relapse and treatment failure in patients with ovarian cancer. The identification of effective strategies to overcome drug resistance will have a significant clinical impact on the disease.

Methods

The protein and mRNA expression of GOLPH3L in ovarian cancer cell lines and patient tissues were determined using Real-time PCR and Western blot, respectively. 177 human ovarian cancer tissue samples were analyzed by IHC to investigate the association between GOLPH3L expression and the clinicopathological characteristics of ovarian cancer patients. Functional assays, such as MTT, FACS, and Tunel assay used to determine the oncogenic role of GOLPH3L in human ovarian cancer progression. Furthermore, western blotting and luciferase assay were used to determine the mechanism of GOLPH3L promotes chemoresistance in ovarian cancer cells.

Results

The expression of GOLPH3L was markedly upregulated in ovarian cancer cell lines and tissues, and high GOLPH3L expression was associated with an aggressive phenotype and poor prognosis with ovarian cancer patients. GOLPH3L overexpression confers CDDP resistance on ovarian cancer cells; however, inhibition of GOLPH3L sensitized ovarian cancer cell lines to CDDP cytotoxicity both in vitro and in vivo. Additionally, GOLPH3L upregulated the levels of nuclear p65 and phosphorylated inhibitor of nuclear factor Kappa-B kinase-β and IκBα, thereby activating canonical nuclear factor-κB (NF-κB) signaling.

Conclusions

Our findings suggest that GOLPH3L is a potential therapeutic target for the treatment of ovarian cancer: targeting GOLPH3L signaling may represent a promising strategy to enhance platinum response in patients with chemoresistant ovarian cancer.

Electronic supplementary material

The online version of this article (10.1186/s13046-017-0607-0) contains supplementary material, which is available to authorized users.

Overexpression of NSUN2 by DNA hypomethylation is associated with metastatic progression in human breast cancer

NSUN2 is a RNA methyltransferase that has been shown to be implicated in development of human cancer. However, the functional role of NSUN2, mechanism of NSUN2 overexpression and its association with clinicopathologic features in breast cancer remain unclear. To investigate alterations in the expression and functional role of NSUN2 in breast cancer, NSUN2 expression was assessed in breast cancer cells and tissues obtained from cancers at different American Joint Committee on Cancer (AJCC) stages, and its functions were investigated using breast cancer cells. NSUN2 expression was shown to be significantly higher in breast cancer cells and tissues than in normal breast epithelial cells and tissues, at both mRNA and protein levels. Overexpression of NSUN2 was shown to promote cell proliferation, migration, and invasion while NSUN2 knockdown inhibited these processes in vitro and in vivo. NSUN2 expression level was associated with the methylation level of its promoter. Our results demonstrated that the overall expression of NSUN2 significantly correlated with clinical stage (P=0.027), tumor classification (P=0.012), pathological differentiation (P=0.023), as well as with the expression levels of estrogen receptor (P<0.001), progesterone receptor (P=0.001), and Ki-67 (P<0.001). Our findings provide a unique insight into the roles and effects of NSUN2 overexpression in breast cancer cells, and highlight the necessity of the investigation of novel therapeutic targets, such as NSUN2, for the improvement of breast cancer treatments.

The Association Between XPG Gene Polymorphism and Gastric Cancer Risk

PURPOSE

Studies exploring the association between the Xeroderma pigmentosum group G (XPG) gene polymorphisms and gastric cancer (GC) risk provide conflicting findings. Thus, this meta-analysis was performed.

MATERIALS AND METHODS

The PubMed and EMBASE databases were comprehensively searched to identify studies for the inclusion in the meta-analysis. The strength of the association was evaluated by calculating pooled odds ratios and 95% confidence intervals.

RESULTS

Nine case-control studies involving 3540 cases and 3953 controls were included in the meta-analysis, which revealed that the XPG rs751402 polymorphism is positively associated with GC risk and could be viewed as a risk factor of GC in three genetic models.

CONCLUSION

The XPG gene rs751402 polymorphism is associated with an increased risk of GC in Chinese Han populations. This finding should be verified by larger studies that include additional ethnic groups.

Biological determinants of radioresistance and their remediation in pancreatic cancer

Despite recent advances in radiotherapy, a majority of patients diagnosed with pancreatic cancer (PC) do not achieve objective responses due to the existence of intrinsic and acquired radioresistance. Identification of molecular mechanisms that compromise the efficacy of radiation therapy and targeting these pathways is paramount for improving radiation response in PC patients. In this review, we have summarized molecular mechanisms associated with the radio-resistant phenotype of PC. Briefly, we discuss the reversible and irreversible biological consequences of radiotherapy, such as DNA damage and DNA repair, mechanisms of cancer cell survival and radiation-induced apoptosis following radiotherapy. We further describe various small molecule inhibitors and molecular targeting agents currently being tested in preclinical and clinical studies as potential radiosensitizers for PC. Notably, we draw attention towards the confounding effects of cancer stem cells, immune system, and the tumor microenvironment in the context of PC radioresistance and radiosensitization. Finally, we discuss the need for examining selective radioprotectors in light of the emerging evidence on radiation toxicity to non-target tissue associated with PC radiotherapy.

A single nucleotide polymorphism of AIRE gene located in the 21q22.3 increases the risk of rheumatoid arthritis

Several studies addressed the association of autoimmune regulator (AIRE) gene polymorphism with the risk of rheumatoid arthritis (RA); however, their conclusions were inconsistent. For better investigating the effects of this polymorphism on the risk of RA, we conducted this study to evaluate the role of AIRE rs2075786 polymorphism in the risk of RA. Four eligible studies involving 6,755 cases and 7,970 controls were identified by searching the databases of PubMed, CNKI and EMBASE up to February 2017. Our study revealed that AIRE rs2075786 polymorphism was associated with an increased risk of RA under all genetic models. In the subgroup analysis, AIRE rs2075786 polymorphism contributed to RA susceptibility among Asians, but not among Caucasians. To summarize,, this meta-analysis confirms that AIRE rs2075786 polymorphism may play a significant role in increasing the risk of RA. Stratification analysis by ethnicity reveals that AIRE rs2075786 polymorphism is associated with an increased risk of RA among Asians, but not among Caucasians. These findings need further validation in the large multicenter case-control studies.

PCA Based on Graph Laplacian Regularization and P-Norm for Gene Selection and Clustering

In modern molecular biology, the hotspots and difficulties of this field are identifying characteristic genes from gene expression data. Traditional reconstruction-error-minimization model principal component analysis (PCA) as a matrix decomposition method uses quadratic error function, which is known sensitive to outliers and noise. Hence, it is necessary to learn a good PCA method when outliers and noise exist. In this paper, we develop a novel PCA method enforcing P-norm on error function and graph-Laplacian regularization term for matrix decomposition problem, which is called as PgLPCA. The heart of the method designing for reducing outliers and noise is a new error function based on non-convex proximal P-norm. Besides, Laplacian regularization term is used to find the internal geometric structure in the data representation. To solve the minimization problem, we develop an efficient optimization algorithm based on the augmented Lagrange multiplier method. This method is used to select characteristic genes and cluster the samples from explosive biological data, which has higher accuracy than compared methods.

GOLPH3 induces epithelial-mesenchymal transition via Wnt/β-catenin signaling pathway in epithelial ovarian cancer

Golgi phosphoprotein 3 (GOLPH3), a newly recognized oncogene, is associated with tumor growth, metastasis, and poor prognosis in several types of cancer. However, its biological role and underlying mechanism in epithelial ovarian cancer (EOC) remain poorly understood. Here, we found that GOLPH3 was overexpressed in EOC tissues and cell lines. This overexpression promoted the migration and invasion of EOC cells. Moreover, GOLPH3 upregulated the expression of epithelial–mesenchymal transition (EMT) markers, such as N‐cadherin and Snail, and the Wnt/β‐catenin‐related genes cyclin‐D1 and c‐Myc, which were restored via silencing of GOLPH3 expression. Furthermore, the inhibitor and activator of the Wnt/β‐catenin pathway, XAV939 and LiCl, enhanced or decreased, respectively, the effect of GOLPH3 on EMT, which further confirmed that GOLPH3 promoted EMT progression via activation of Wnt/β‐catenin signaling. In addition, we found that EDD, the human hyperplastic discs gene, was consistent with GOLPH3 expression and also promoted the EMT process and activated Wnt/β‐catenin signaling. These findings demonstrate that EDD might be a downstream factor of GOLPH3. Taken together, our findings demonstrate the existence of a GOLPH3–Wnt/β‐catenin–EMT axis in EOC and provide a new therapeutic target to treat EOC.

The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers

BACKGROUND

Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits.

METHODS

The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background.

RESULTS

The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis.

CONCLUSIONS

Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental, and lifestyle-related exposures.

IMPACT

Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.

Use of Magnetic Nanoparticles as Targeted Therapy: Theranostic Approach to Treat and Diagnose Cancer

The metastasis of cancer epitomizes the diagnostic and therapeutic challenge as a result of cancer heterogeneity. To overcome the uncontrolled growth of the proliferating cells, nanosystems have been developed and have undergone many preclinical trials both in vitro and in vivo and many practices have been further applied clinically on human beings. In practice, magnetic nanoparticles- (MNPs-) based systems following the application of Fe3O4 bound antitumor drug have shown an enhanced therapeutic index in comparison with conventional chemotherapy ensuring the significant decline in nanosystems’ toxicity. A number of improved strategies employing nanoparticle engineering have been in practice for upgrading selectivity of metastatic cells and to have direct access to poorly manageable tumor regions. Targeted nanoparticle therapy paving the way towards tumor biomarkers and tissue specific cancer stages provides effective strategies for nonaccessible tumor regions, thus leading to the tangible modification in the history of cancer world. An infinite number of targets have been exploited for surface receptor specificity to distinct types of nanoparticles and are presently enduring clinical practices both in vitro and in vivo. The aim of this review is to take into view current nanotechnology-based research in cancer imaging for diagnosis and treatment. Several commercially available magnetic nanoparticles-based systems applied as contrast agents for metastatic cancer imaging and treatment via hyperthermia have also been focused on.