Oncogenes and tumor suppressor genes: comparative genomics and network perspectives

Marine algae-derived characterized bioactive compounds as therapy for cancer: A review on their classification, mechanism of action, and future perspectives

In 2022, there were around 20 million new cases and over 9.7 million cancer-related deaths worldwide. An increasing number of metabolites with anticancer activity in algae had been isolated and identified, which were promising candidates for cancer therapy. Red algae are well-known for the production of brominated metabolites, including terpenoids and phenols, which have the capacity to induce cell toxicity. Some non-toxic biological macromolecules, including polysaccharides, are distinct secondary metabolites found in many algae, particularly green algae. They possess anticancer activities by inhibiting tumor angiogenesis, stimulating the immune response, and inducing apoptosis. However, the structure-activity relationship between these components and antitumor activity, as well as certain taxa within the algae, remains relatively unstudied. This work is based on the reports published from 2003 to 2024 in PubMed and ISI Web of Science databases. A comprehensive review of the characterized algal anticancer active compounds, together with their structure and mechanism of action was performed. Also, their structure-activity relationship was preliminarily summarized to better assess their potential properties as a natural, safe bioactive product to be used as an alternative for the treatment of cancers, leading to new opportunities for drug discovery.

Mechanisms of tumor immunosuppressive microenvironment formation in esophageal cancer

As a highly invasive malignancy, esophageal cancer (EC) is a global health issue, and was the eighth most prevalent cancer and the sixth leading cause of cancer-related death worldwide in 2020. Due to its highly immunogenic nature, emer-ging immunotherapy approaches, such as immune checkpoint blockade, have demonstrated promising efficacy in treating EC; however, certain limitations and challenges still exist. In addition, tumors may exhibit primary or acquired resistance to immunotherapy in the tumor immune microenvironment (TIME); thus, understanding the TIME is urgent and crucial, especially given the im-portance of an immunosuppressive microenvironment in tumor progression. The aim of this review was to better elucidate the mechanisms of the suppressive TIME, including cell infiltration, immune cell subsets, cytokines and signaling pathways in the tumor microenvironment of EC patients, as well as the downregulated expression of major histocompatibility complex molecules in tumor cells, to obtain a better understanding of the differences in EC patient responses to immunotherapeutic strategies and accurately predict the efficacy of immunotherapies. Therefore, personalized treatments could be developed to maximize the advantages of immunotherapy.

Melatonin and Its Role in the Epithelial-to-Mesenchymal Transition (EMT) in Cancer

The epithelial-to-mesenchymal transition (EMT) is a cell-biological program that occurs during the progression of several physiological processes and that can also take place during pathological situations such as carcinogenesis. The EMT program consists of the sequential activation of a number of intracellular signaling pathways aimed at driving epithelial cells toward the acquisition of a series of intermediate phenotypic states arrayed along the epithelial-mesenchymal axis. These phenotypic features include changes in the motility, conformation, polarity and functionality of cancer cells, ultimately leading cells to stemness, increased invasiveness, chemo- and radioresistance and the formation of cancer metastasis. Amongst the different existing types of the EMT, type 3 is directly involved in carcinogenesis. A type 3 EMT occurs in neoplastic cells that have previously acquired genetic and epigenetic alterations, specifically affecting genes involved in promoting clonal outgrowth and invasion. Markers such as E-cadherin; N-cadherin; vimentin; and transcription factors (TFs) like Twist, Snail and ZEB are considered key molecules in the transition. The EMT process is also regulated by microRNA expression. Many miRNAs have been reported to repress EMT-TFs. Thus, Snail 1 is repressed by miR-29, miR-30a and miR-34a; miR-200b downregulates Slug; and ZEB1 and ZEB2 are repressed by miR-200 and miR-205, respectively. Occasionally, some microRNA target genes act downstream of the EMT master TFs; thus, Twist1 upregulates the levels of miR-10b. Melatonin is an endogenously produced hormone released mainly by the pineal gland. It is widely accepted that melatonin exerts oncostatic actions in a large variety of tumors, inhibiting the initiation, progression and invasion phases of tumorigenesis. The molecular mechanisms underlying these inhibitory actions are complex and involve a great number of processes. In this review, we will focus our attention on the ability of melatonin to regulate some key EMT-related markers, transcription factors and micro-RNAs, summarizing the multiple ways by which this hormone can regulate the EMT. Since melatonin has no known toxic side effects and is also known to help overcome drug resistance, it is a good candidate to be considered as an adjuvant drug to conventional cancer therapies.

The role of N-acetyltransferases in cancers

Cancer is a major global health problem that disrupts the balance of normal cellular growth and behavior. Mounting evidence has shown that epigenetic modification, specifically N-terminal acetylation, play a crucial role in the regulation of cell growth and function. Acetylation is a co- or post-translational modification to regulate important cellular progresses such as cell proliferation, cell cycle progress, and energy metabolism. Recently, N-acetyltransferases (NATs), enzymes responsible for acetylation, regulate signal transduction pathway in various cancers including hepatocellular carcinoma, breast cancer, lung cancer, colorectal cancer and prostate cancer. In this review, we clarify the regulatory role of NATs in cancer progression, such as cell proliferation, metastasis, cell apoptosis, autophagy, cell cycle arrest and energy metabolism. Furthermore, the mechanism of NATs on cancer remains to be further studied, and few drugs have been developed. This provides us with a new idea that targeting acetylation, especially NAT-mediated acetylation, may be an attractive way for inhibiting cancer progression.

An evaluation of KIF20A as a prognostic factor and therapeutic target for lung adenocarcinoma using integrated bioinformatics analysis

The identification of prognostic and therapeutic biomarkers is essential to reduce morbidity and mortality from lung adenocarcinoma (LUAD). This study aimed to identify a reliable prognostic and therapeutic biomarker for LUAD using integrated bioinformatics. Based on the cancer genome atlas (TCGA) and genome-tissue expression (GTEx) analyses, KIF20A has been identified as the hub gene. Following validation using a series of cohorts, survival analysis, meta-analysis, and univariate Cox analysis was conducted. ESTIMATE and CIBERSORT algorithms were then used to study the association of KIF20A with the tumor microenvironment (TME) and the percentage of tumor-infiltrating immune cells (TICs). In vitro experiments were conducted to determine the function of KIF20A. Finally, there was a negative association between the expression of the KIF20A and overall survival, progression-free survival, and disease-free survival, which was confirmed by meta-analysis and COX analysis. Furthermore, KIF20A also had a potential role of altering the TME and TICs proportions in LUAD. Validations in vitro were performed on A549 and PC-9 cell lines, and we found that the knockdown of KIF20A exhibited inhibitory effects on cell proliferation, resulted in cell cycle arrest during the G2/M phase, and induced cellular apoptosis. Our study demonstrated that KIF20A could be utilized as a reliable prognostic marker and treatment target for LUAD. However, further studies are required to validate these findings.

Multi-omics research strategies in ischemic stroke: A multidimensional perspective

Ischemic stroke (IS) is a multifactorial and heterogeneous neurological disorder with high rate of death and long-term impairment. Despite years of studies, there are still no stroke biomarkers for clinical practice, and the molecular mechanisms of stroke remain largely unclear. The high-throughput omics approach provides new avenues for discovering biomarkers of IS and explaining its pathological mechanisms. However, single-omics approaches only provide a limited understanding of the biological pathways of diseases. The integration of multiple omics data means the simultaneous analysis of thousands of genes, RNAs, proteins and metabolites, revealing networks of interactions between multiple molecular levels. Integrated analysis of multi-omics approaches will provide helpful insights into stroke pathogenesis, therapeutic target identification and biomarker discovery. Here, we consider advances in genomics, transcriptomics, proteomics and metabolomics and outline their use in discovering the biomarkers and pathological mechanisms of IS. We then delineate strategies for achieving integration at the multi-omics level and discuss how integrative omics and systems biology can contribute to our understanding and management of IS.

Metabolite-derived protein modifications modulating oncogenic signaling

Malignant growth is defined by multiple aberrant cellular features, including metabolic rewiring, inactivation of tumor suppressors and the activation of oncogenes. Even though these features have been described as separate hallmarks, many studies have shown an extensive mutual regulatory relationship amongst them. On one hand, the change in expression or activity of tumor suppressors and oncogenes has extensive direct and indirect effects on cellular metabolism, activating metabolic pathways required for malignant growth. On the other hand, the tumor microenvironment and tumor intrinsic metabolic alterations result in changes in intracellular metabolite levels, which directly modulate the protein modification of oncogenes and tumor suppressors at both epigenetic and post-translational levels. In this mini-review, we summarize the crosstalk between tumor suppressors/oncogenes and metabolism-induced protein modifications at both levels and explore the impact of metabolic (micro)environments in shaping these.

CircRNA-Associated CeRNAs Regulatory Axes in Retinoblastoma: A Systematic Scoping Review

Retinoblastoma (RB) is one of the most common childhood cancers caused by RB gene mutations (tumor suppressor gene in various patients). A better understanding of molecular pathways and the development of new diagnostic approaches may lead to better treatment for RB patients. The number of studies on ceRNA axes is increasing, emphasizing the significance of these axes in RB. Circular RNAs (circRNAs) play a vital role in competing endogenous RNA (ceRNA) regulatory axes by sponging microRNAs and regulating gene expression. Because of the broadness of ceRNA interaction networks, they may assist in investigating treatment targets in RB. This study conducted a systematic scoping review to evaluate verified loops of ceRNA in RB, focusing on the ceRNA axis and its relationship to circRNAs. This scoping review was carried out using a six-step strategy and the Prisma guideline, and it involved systematically searching the publications of seven databases. Out of 363 records, sixteen articles were entirely consistent with the defined inclusion criteria and were summarized in the relevant table. The majority of the studies focused on the circRNAs circ_0000527, circ_0000034, and circTET1, with approximately two-fifths of the studies focusing on a single circRNA. Understanding the many features of this regulatory structure may help elucidate RB’s unknown causative factors and provide novel molecular potential therapeutic targets and medical fields.

Predicting Differences in Treatment Response and Survival Time of Lung Adenocarcinoma Patients Based on a Prognostic Risk Model of Glycolysis-Related Genes

Background: Multiple factors influence the survival of patients with lung adenocarcinoma (LUAD). Specifically, the therapeutic outcomes of treatments and the probability of recurrence of the disease differ among patients with the same stage of LUAD. Therefore, effective prognostic predictors need to be identified.

Methods: Based on the tumor mutation burden (TMB) data obtained from The Cancer Genome Atlas (TCGA) database, LUAD patients were divided into high and low TMB groups, and differentially expressed glycolysis-related genes between the two groups were screened. The least absolute shrinkage and selection operator (LASSO) and Cox regression were used to obtain a prognostic model. A receiver operating characteristic (ROC) curve and a calibration curve were generated to evaluate the nomogram that was constructed based on clinicopathological characteristics and the risk score. Two data sets (GSE68465 and GSE11969) from the Gene Expression Omnibus (GEO) were used to verify the prognostic performance of the gene. Furthermore, differences in immune cell distribution, immune-related molecules, and drug susceptibility were assessed for their relationship with the risk score.

Results: We constructed a 5-gene signature (FKBP4, HMMR, B4GALT1, SLC2A1, STC1) capable of dividing patients into two risk groups. There was a significant difference in overall survival (OS) times between the high-risk group and the low-risk group (p < 0.001), with the low-risk group having a better survival outcome. Through multivariate Cox analysis, the risk score was confirmed to be an independent prognostic factor (HR = 2.709, 95% CI = 1.981–3.705, p < 0.001), and the ROC curve and nomogram exhibited accurate prediction performance. Validation of the data obtained in the GEO database yielded similar results. Furthermore, there were significant differences in sensitivity to immunotherapy, cisplatin, paclitaxel, gemcitabine, docetaxel, gefitinib, and erlotinib between the low-risk and high-risk groups.

Conclusion: Our results reveal that glycolysis-related genes are feasible predictors of survival and the treatment response of patients with LUAD.

The MicroRNA-Based Strategies to Combat Cancer Chemoresistance via Regulating Autophagy

Chemoresistance frequently occurs in cancer treatment, which results in chemotherapy failure and is one of the most leading causes of cancer-related death worldwide. Understanding the mechanism of chemoresistance and exploring strategies to overcome chemoresistance have become an urgent need. Autophagy is a highly conserved self-degraded process in cells. The dual roles of autophagy (pro-death or pro-survival) have been implicated in cancers and chemotherapy. MicroRNA (miRNA) is a class of small non-coding molecules that regulate autophagy at the post-transcriptional level in cancer cells. The association between miRNAs and autophagy in cancer chemoresistance has been emphasized. In this review, we focus on the dual roles of miRNA-mediated autophagy in facilitating or combating chemoresistance, aiming to shed lights on the potential role of miRNAs as targets to overcome chemoresistance.

Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure

Background

Numerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging.

Results

In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants.

Conclusions

Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-021-01021-x.

Stress Granules Involved in Formation, Progression and Metastasis of Cancer: A Scoping Review

The assembly of stress granules (SGs) is a well-known cellular strategy for reducing stress-related damage and promoting cell survival. SGs have become important players in human health, in addition to their fundamental role in the stress response. The critical role of SGs in cancer cells in formation, progression, and metastasis makes sense. Recent researchers have found that several SG components play a role in tumorigenesis and cancer metastasis via tumor-associated signaling pathways and other mechanisms. Gene-ontology analysis revealed the role of these protein components in the structure of SGs. Involvement in the translation process, regulation of mRNA stability, and action in both the cytoplasm and nucleus are among the main features of SG proteins. The present scoping review aimed to consider all studies on the effect of SGs on cancer formation, proliferation, and metastasis and performed based on a six-stage methodology structure and the PRISMA guideline. A systematic search of seven databases for qualified articles was conducted before July 2021. Publications were screened, and quantitative and qualitative analysis was performed on the extracted data. Go analysis was performed on seventy-one SGs protein components. Remarkably G3BP1, TIA1, TIAR, and YB1 have the largest share among the proteins considered in the studies. Altogether, this scoping review tries to demonstrate and provide a comprehensive summary of the role of SGs in the formation, progression, and metastasis of cancer by reviewing all studies.

HOPX Exhibits Oncogenic Activity during Squamous Skin Carcinogenesis

Cutaneous squamous cell carcinomas (SCCs) are frequent heterogeneous tumors arising from sun-exposed regions of the skin and characterized by complex pathogenesis. HOPX is a member of the homeodomain-containing superfamily of proteins holding an atypical homeodomain unable to bind to DNA. First discovered in the heart as a regulator of cardiac development, in the skin, HOPX modulates the terminal differentiation of keratinocytes. There is a particular interest in studying HOPX in squamous skin carcinogenesis because it has the atypical structure and the functional duality as an oncogene and a tumor suppressor gene, reported in different malignancies. In this study, we analyzed the effects of HOPX knockdown and overexpression on SCC tumorigenicity in vitro and in vivo. Our data show that HOPX knockdown in SCC cells inhibits their proliferative and invasive activity through the acceleration of apoptosis. We established that methylation of two alternative HOPX promoters leads to differential expression of HOPX transcripts in normal keratinocytes and SCC cells. Importantly, we report that HOPX acts as an oncogene in the pathogenesis of SCC probably through the activation of the second alternative promoter and the modulation of apoptosis.

Branched evolution and genomic intratumor heterogeneity in the pathogenesis of cutaneous T-cell lymphoma

Mycosis fungoides (MF) is a slowly progressive cutaneous T-cell lymphoma (CTCL) for which there is no cure. In the early plaque stage, the disease is indolent, but development of tumors heralds an increased risk of metastasis and death. Previous research into the genomic landscape of CTCL revealed a complex pattern of >50 driver mutations implicated in more than a dozen signaling pathways. However, the genomic mechanisms governing disease progression and treatment resistance remain unknown. Building on our previous discovery of the clonotypic heterogeneity of MF, we hypothesized that this lymphoma does not progress in a linear fashion as currently thought but comprises heterogeneous mutational subclones. We sequenced exomes of 49 cases of MF and identified 28 previously unreported putative driver genes. MF exhibited extensive intratumoral heterogeneity (ITH) of a median of 6 subclones showing a branched phylogenetic relationship pattern. Stage progression was correlated with an increase in ITH and redistribution of mutations from stem to clades. The pattern of clonal driver mutations was highly variable, with no consistent mutations among patients. Similar intratumoral heterogeneity was detected in leukemic CTCL (Sézary syndrome). Based on these findings, we propose a model of MF pathogenesis comprising divergent evolution of cancer subclones and discuss how ITH affects the efficacy of targeted drug therapies and immunotherapies for CTCL.

An integrated deep learning and dynamic programming method for predicting tumor suppressor genes, oncogenes, and fusion from PDB structures

Mutations in proto-oncogenes (ONGO) and the loss of regulatory function of tumor suppression genes (TSG) are the common underlying mechanism for uncontrolled tumor growth. While cancer is a heterogeneous complex of distinct diseases, finding the potentiality of the genes related functionality to ONGO or TSG through computational studies can help develop drugs that target the disease. This paper proposes a classification method that starts with a preprocessing stage to extract the feature map sets from the input 3D protein structural information. The next stage is a deep convolutional neural network stage (DCNN) that outputs the probability of functional classification of genes. We explored and tested two approaches: in Approach 1, all filtered and cleaned 3D-protein-structures (PDB) are pooled together, whereas in Approach 2, the primary structures and their corresponding PDBs are separated according to the genes' primary structural information. Following the DCNN stage, a dynamic programming-based method is used to determine the final prediction of the primary structures' functionality. We validated our proposed method using the COSMIC online database. For the ONGO vs TSG classification problem the AUROC of the DCNN stage for Approach 1 and Approach 2 DCNN are 0.978 and 0.765, respectively. The AUROCs of the final genes' primary structure functionality classification for Approach 1 and Approach 2 are 0.989, and 0.879, respectively. For comparison, the current state-of-the-art reported AUROC is 0.924. Our results warrant further study to apply the deep learning models to humans' (GRCh38) genes, for predicting their corresponding probabilities of functionality in the cancer drivers.

Current paradigms in epigenetic anticancer therapeutics and future challenges

Any alteration at the genetic or epigenetic level, may result in multiplex of diseases including tumorigenesis which ultimately results in the cancer development. Restoration of the normal epigenome by reversing the epigenetic alterations have been reported in tumors paving the way for development of an effective epigenetic treatment in cancer. However, delineating various epigenetic events has been a challenging task so far despite substantial progress in understanding DNA methylation and histone modifications during transcription of genes. Many inhibitors in the form of epigenetic drugs mostly targeting chromatin and histone modifying enzymes including DNA methyltransferase (DNMT) enzyme inhibitors and a histone deacetylases (HDACs) inhibitor, have been in use subsequent to the approval by FDA for cancer treatment. Similarly, other inhibitory drugs, such as FK228, suberoylanilide hydroxamic acid (SAHA) and MS-275, have been successfully tested in clinical studies. Despite all these advancements, still we see a hazy view as far as a promising epigenetic anticancer therapy is concerned. The challenges are to have more specific and effective inhibitors with negligible side effects. Moreover, the alterations seen in tumors are not well understood for which one has to gain deeper insight into the tumor pathology as well. Current review focusses on such epigenetic alterations occurring in cancer and the effective strategies to utilize such alterations for potential therapeutic use and treatment in cancer.

Cancer vs. SARS-CoV-2 induced inflammation, overlapping functions, and pharmacological targeting

Inflammation is an intrinsic defence mechanism triggered by the immune system against infection or injury. Chronic inflammation allows the host to recover or adapt through cellular and humoral responses, whereas acute inflammation leads to cytokine storms resulting in tissue damage. In this review, we present the overlapping outcomes of cancer inflammation with virus-induced inflammation. The study emphasises how anti-inflammatory drugs that work against cancer inflammation may work against the inflammation caused by the viral infection. It is established that the cytokine storm induced in response to SARS-CoV-2 infection contributes to disease-associated mortality. While cancer remains the second among the diseases associated with mortality worldwide, cancer patients' mortality rates are often observed upon extended periods after illness, usually ranging from months to years. However, the mortality rates associated with COVID-19 disease are robust. The cytokine storm induced by SARS-CoV-2 infection appeared to be responsible for the multi-organ failure and increased mortality rates. Since both cancer and COVID-19 disease share overlapping inflammatory mechanisms, repurposing some anticancer and anti-inflammatory drugs for COVID-19 may lower mortality rates. Here, we review some of these inflammatory mechanisms and propose some potential chemotherapeutic agents to intervene in them. We also discuss the repercussions of anti-inflammatory drugs such as glucocorticoids and hydroxychloroquine with zinc or antiviral drugs such as ivermectin and remdesivir against SARS-CoV-2 induced cytokine storm. In this review, we emphasise on various possibilities to reduce SARS-CoV-2 induced cytokine storm.

Signaling, metabolism, and cancer: An important relationship for therapeutic intervention

In cancerous cells, significant changes occur in the activity of signaling pathways affecting a wide range of cellular activities ranging from growth and proliferation to apoptosis, invasiveness, and metastasis. Extensive changes also happen with respect to the metabolism of a cancerous cell encompassing a wide range of functions that include: nutrient acquisition, biosynthesis of macromolecules, and energy generation. These changes are important and some therapeutic approaches for treating cancers have focused on targeting the metabolism of cancerous cells. Oncogenes and tumor suppressor genes have a significant effect on the metabolism of cells. There appears to be a close interaction between metabolism and the signaling pathways in a cancerous cell, in which the interaction provides the metabolic needs of a cancerous cell for uncontrolled proliferation, resistance to apoptosis, and metastasis. In this review, we have reviewed the latest findings in this regard and briefly review the most recent research findings regarding targeting the metabolism of cancer cells as a therapeutic approach for treatment of cancer.

Functional genomics of AP-2α and AP-2γ in cancers: in silico study

BACKGROUND

Among all causes of death, cancer is the most prevalent and is only outpaced by cardiovascular diseases. Molecular theory of carcinogenesis states that apoptosis and proliferation are regulated by groups of tumor suppressors or oncogenes. Transcription factors are example of proteins comprising representatives of both cancer-related groups. Exemplary family of transcription factors which exhibits dualism of function is Activating enhancer-binding Protein 2 (AP-2). Scientific reports concerning their function in carcinogenesis depend on particular family member and/or tumor type which proves the issue to be unsolved. Therefore, the present study examines role of the best-described AP-2 representatives, AP-2α and AP-2γ, through ontological analysis of their target genes and investigation what processes are differentially regulated in 21 cancers using samples deposited in Genomic Data Analysis Center (GDAC) Firehose.

METHODS

Expression data with clinical annotation was collected from TCGA-dedicated repository GDAC Firehose. Transcription factor targets were obtained from Gene Transcription Regulation Database (GTRD), TRANScription FACtor database (TRANSFAC) and Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining (TRRUST). Monocle3 R package was used for global samples profiling while Protein ANalysis THrough Evolutionary Relationships (PANTHER) tool was used to perform gene ontology analysis.

RESULTS

With RNA-seq data and Monocle3 or PANTHER tools we outlined differences in many processes and signaling pathways, separating tumor from normal tissues or tumors from each other. Unexpectedly, a number of alterations in basal-like breast cancer were identified that distinguished it from other subtypes, which could bring future clinical benefits.

CONCLUSIONS

Our findings indicate that while the AP-2α/γ role remains ambiguous, their activity is based on processes that underlie the cancer hallmarks and their expression could have potential in diagnosis of selected tumors.

Autophagy-mediating microRNAs in cancer chemoresistance

Chemoresistance is a complex phenomenon responsible for failure in response to chemotherapy agents and more than 90% of deaths in cancer patients. MicroRNAs (miRNAs), as a subgroup of non-coding RNAs with lengths between 21 and 25 nucleotides, are involved in various cancer processes like chemoresistance via interacting with their target mRNAs and suppressing their expression. Autophagy is a greatly conserved procedure involving the lysosomal degradation of cytoplasmic contents and organelles to deal with environmental stresses like hypoxia and starvation. Autophagy contributes to response to chemotherapy agents: autophagy can act as a protective mechanism for mediating the resistance in response to chemotherapy or can induce autophagic cell death and mediate the sensitivity to chemotherapy. On the other hand, one of the processes targeted by microRNAs in the regulation of chemoresistance is autophagy. Hence, we studied the literatures on chemoresistance mechanisms, the miRNAs' role in cancer, and the miRNAs' role in chemoresistance by modulating autophagy. Graphical Abstract.

Mutant FOXL2C134W Hijacks SMAD4 and SMAD2/3 to Drive Adult Granulosa Cell Tumors

The mutant protein FOXL2^C134W is expressed in at least 95% of adult-type ovarian granulosa cell tumors (AGCT) and is considered to be a driver of oncogenesis in this disease. However, the molecular mechanism by which FOXL2^C134W contributes to tumorigenesis is not known. Here, we show that mutant FOXL2^C134W acquires the ability to bind SMAD4, forming a FOXL2^C134W/SMAD4/SMAD2/3 complex that binds a novel hybrid DNA motif AGHCAHAA, unique to the FOXL2^C134W mutant. This binding induced an enhancer-like chromatin state, leading to transcription of nearby genes, many of which are characteristic of epithelial-to-mesenchymal transition. FOXL2^C134W also bound hybrid loci in primary AGCT. Ablation of SMAD4 or SMAD2/3 resulted in strong reduction of FOXL2^C134W binding at hybrid sites and decreased expression of associated genes. Accordingly, inhibition of TGFβ mitigated the transcriptional effect of FOXL2^C134W. Our results provide mechanistic insight into AGCT pathogenesis, identifying FOXL2^C134W and its interaction with SMAD4 as potential therapeutic targets to this condition. SIGNIFICANCE: FOXL2^C134W hijacks SMAD4 and leads to the expression of genes involved in EMT, stemness, and oncogenesis in AGCT, making FOXL2^C134W and the TGFβ pathway therapeutic targets in this condition. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/17/3466/F1.large.jpg.

IL-6 induces tumor suppressor protein tyrosine phosphatase receptor type D by inhibiting miR-34a to prevent IL-6 signaling overactivation

Protein tyrosine phosphatase receptor type D (PTPRD) is a tumor suppressor gene that is epigenetically silenced and mutated in several cancers, including breast cancer. Since IL-6/STAT3 signaling is often hyperactivated in breast cancer and STAT3 is a direct PTPRD substrate, we investigated the role of PTPRD in breast cancer and the association between PTPRD and IL-6/STAT3 signaling. We found that PTPRD acts as a tumor suppressor in breast cancer tissues and that high PTPRD expression is positively associated with tumor size, lymph node metastasis, PCNA expression, and patient survival. Moreover, breast cancers with high PTPRD expression tend to exhibit high IL-6 and low phosphorylated-STAT3 expression. IL-6 was found to inhibit miR-34a transcription and induce PTPRD expression in breast cancer and breast epithelial cells, whereas PTPRD was shown to mediate activated STAT3 dephosphorylation and to be a conserved, direct target of miR-34a. IL-6-induced PTPRD upregulation was blocked by miR-34a mimics, whereas experimental PTPRD overexpression suppressed MDA-MB-231 cell migration, invasion, and epithelial to mesenchymal transition, decreased STAT3 phosphorylation, and increased miR-34a transcription. Our findings suggest that PTPRD mediates activated STAT3 dephosphorylation and is induced by the IL-6/STAT3-mediated transcriptional inhibition of miR-34a, thereby establishing a negative feedback loop that inhibits IL-6/STAT3 signaling overactivation.

DNA methylation-based classification and identification of bladder cancer prognosis-associated subgroups

BACKGROUND

Bladder cancer (BCA) is the most common urinary tumor, but its pathogenesis is unclear, and the associated treatment strategy has rarely been updated. In recent years, a deeper understanding of tumor epigenetics has been gained, providing new opportunities for cancer detection and treatment.

METHODS

We identified prognostic methylation sites based on DNA methylation profiles of BCA in the TCGA database and constructed a specific prognostic subgroup.

RESULTS

Based on the consistent clustering of 402 CpGs, we identified seven subgroups that had a significant association with survival. The difference in DNA methylation levels was related to T stage, N stage, M stage, grade, sex, age, stage and prognosis. Finally, the prediction model was constructed using a Cox regression model and verified using the test dataset; the prognosis was consistent with that of the training set.

CONCLUSIONS

The classification based on DNA methylation is closely related to the clinicopathological characteristics of BCA and determines the prognostic value of each epigenetic subtype. Therefore, our findings provide a basis for the development of DNA methylation subtype-specific therapeutic strategies for human bladder cancer.

Regulating tumor suppressor genes: post-translational modifications

Tumor suppressor genes cooperate with each other in tumors. Three important tumor suppressor proteins, retinoblastoma (Rb), p53, phosphatase, and tensin homolog deleted on chromosome ten (PTEN) are functionally associated and they regulated by post-translational modification (PTMs) as well. PTMs include phosphorylation, SUMOylation, acetylation, and other novel modifications becoming growing appreciated. Because most of PTMs are reversible, normal cells use them as a switch to control the state of cells being the resting or proliferating, and PTMs also involve in cell survival and cell cycle, which may lead to abnormal proliferation and tumorigenesis. Although a lot of studies focus on the importance of each kind of PTM, further discoveries shows that tumor suppressor genes (TSGs) form a complex “network” by the interaction of modification. Recently, there are several promising strategies for TSGs for they change more frequently than carcinogenic genes in cancers. We here review the necessity, characteristics, and mechanisms of each kind of post-translational modification on Rb, p53, PTEN, and its influence on the precise and selective function. We also discuss the current antitumoral therapies of Rb, p53 and PTEN as predictive, prognostic, and therapeutic target in cancer.

Network Properties of Cancer Prognostic Gene Signatures in the Human Protein Interactome

Prognostic gene signatures are critical in cancer prognosis assessments and their pinpoint treatments. However, their network properties remain unclear. Here, we obtained nine prognostic gene sets including 1439 prognostic genes of different cancers from related publications. Four network centralities were used to examine the network properties of prognostic genes (PG) compared with other gene sets based on the Human Protein Reference Database (HPRD) and String networks. We also proposed three novel network measures for further investigating the network properties of prognostic gene sets (PGS) besides clustering coefficient. The results showed that PG did not occupy key positions in the human protein interaction network and were more similar to essential genes rather than cancer genes. However, PGS had significantly smaller intra-set distance (IAD) and inter-set distance (IED) in comparison with random sets (p-value < 0.001). Moreover, we also found that PGS tended to be distributed within network modules rather than between modules (p-value < 0.01), and the functional intersection of the modules enriched with PGS was closely related to cancer development and progression. Our research reveals the common network properties of cancer prognostic gene signatures in the human protein interactome. We argue that these are biologically meaningful and useful for understanding their molecular mechanism.

Effects of ordered mutations on dynamics in signaling networks

BACKGROUND

Many previous clinical studies have found that accumulated sequential mutations are statistically related to tumorigenesis. However, they are limited in fully elucidating the significance of the ordered-mutation because they did not focus on the network dynamics. Therefore, there is a pressing need to investigate the dynamics characteristics induced by ordered-mutations.

METHODS

To quantify the ordered-mutation-inducing dynamics, we defined the mutation-sensitivity and the order-specificity that represent if the network is sensitive against a double knockout mutation and if mutation-sensitivity is specific to the mutation order, respectively, using a Boolean network model.

RESULTS

Through intensive investigations, we found that a signaling network is more sensitive when a double-mutation occurs in the direction order inducing a longer path and a smaller number of paths than in the reverse order. In addition, feedback loops involving a gene pair decreased both the mutation-sensitivity and the order-specificity. Next, we investigated relationships of functionally important genes with ordered-mutation-inducing dynamics. The network is more sensitive to mutations subject to drug-targets, whereas it is less specific to the mutation order. Both the sensitivity and specificity are increased when different-drug-targeted genes are mutated. Further, we found that tumor suppressors can efficiently suppress the amplification of oncogenes when the former are mutated earlier than the latter.

CONCLUSION

Taken together, our results help to understand the importance of the order of mutations with respect to the dynamical effects in complex biological systems.

Novel ablation methods for treatment of gliomas

Primary brain tumors are among the deadliest cancers that remain highly incurable. A need exists for new approaches to tumor therapy that can circumvent the blood brain barrier (BBB), target highly resistant tumors and cancer stem-like cells (CSCs) as well create an anti-cancer immunomodulatory environment. Successful treatments may also require a combinatory approach utilizing surgery, chemotherapy, radiation and novel ablation strategies that can both eliminate the bulk tumor and prevent any potential residual CSCs from propagating in the resected tissue. A number of thermal and non-thermal ablation methods have been developed and tested, which have gained much enthusiasm for the treatment of brain tumors. Here we review the most common primary brain tumors and the candidate ablation methods for targeting the tumor and its microenvironment.

Genetic interactions between INPP4B and RAD50 is prognostic of breast cancer survival

RAD50 is commonly depleted in basal-like breast cancer with concomitant absence of INPP4B and several tumor suppressors such as BRCA1 and TP53. Our previous study revealed that INPP4B and RAD50 interact and such an interaction is associated with breast cancer survival at the transcriptional, translational and genomic levels. In the present study, we explored single nucleotide polymorphisms (SNPs) of these two genes that have synergistic effects on breast cancer survival to decipher mechanisms driving their interactions at the genetic level. The Cox's proportional hazards model was used to test whether SNPs of these two genes are interactively associated with breast cancer survival, following expression quantitative trait loci (eQTL) analysis and functional investigations. Our study revealed two disease-associating blocks, each encompassing five and two non-linkage disequilibrium linked SNPs of INPP4B and RAD50, respectively. Concomitant presence of any rare homozygote from each disease-associating block is synergistically prognostic of poor breast cancer survival. Such synergy is mediated via bypassing pathways controlling cell proliferation and DNA damage repair, which are represented by INPP4B and RAD50. Our study provided genetic evidence of interactions between INPP4B and RAD50, and deepened our understandings on the orchestrated genetic machinery governing tumor progression.

Driver gene alterations and activated signaling pathways toward malignant progression of gastrointestinal stromal tumors

Mutually exclusive KIT and PDGFRA mutations are considered to be the earliest events in gastrointestinal stromal tumors (GIST), but insufficient for their malignant progression. Herein, we aimed to identify driver genes and signaling pathways relevant to GIST progression. We investigated genetic profiles of 707 driver genes, including mutations, gene fusions, copy number gain or loss, and gene expression for 65 clinical specimens of surgically dissected GIST, consisting of six metastatic tumors and 59 primary tumors from stomach, small intestine, rectum, and esophagus. Genetic alterations included oncogenic mutations and amplification‐dependent expression enhancement for oncogenes (OG), and loss of heterozygosity (LOH) and expression reduction for tumor suppressor genes (TSG). We assigned activated OG and inactivated TSG to 27 signaling pathways, the activation of which was compared between malignant GIST (metastasis and high‐risk GIST) and less malignant GIST (low‐ and very low‐risk GIST). Integrative molecular profiling indicated that a greater incidence of genetic alterations of driver genes was detected in malignant GIST (96%, 22 of 23) than in less malignant GIST (73%, 24 of 33). Malignant GIST samples groups showed mutations, LOH, and aberrant expression dominantly in driver genes associated with signaling pathways of PI3K (PIK3CA, AKT1, and PTEN) and the cell cycle (RB1, CDK4, and CDKN1B). Additionally, we identified potential PI3K‐related genes, the expression of which was upregulated (SNAI1 and TPX2) or downregulated (BANK1) in malignant GIST. Based on our observations, we propose that inhibition of PI3K pathway signals might potentially be an effective therapeutic strategy against malignant progression of GIST.

The biological characteristics of transcription factors AP-2α and AP-2γ and their importance in various types of cancers

The Activator Protein 2 (AP-2) transcription factor (TF) family is vital for the regulation of gene expression during early development as well as carcinogenesis process. The review focusses on the AP-2α and AP-2γ proteins and their dualistic regulation of gene expression in the process of carcinogenesis. Both AP-2α and AP-2γ influence a wide range of physiological or pathological processes by regulating different pathways and interacting with diverse molecules, i.e. other proteins, long non-coding RNAs (lncRNA) or miRNAs. This review summarizes the newest information about the biology of two, AP-2α and AP-2γ, TFs in the carcinogenesis process. We emphasize that these two proteins could have either oncogenic or suppressive characteristics depending on the type of cancer tissue or their interaction with specific molecules. They have also been found to contribute to resistance and sensitivity to chemotherapy in oncological patients. A better understanding of molecular network of AP-2 factors and other molecules may clarify the atypical molecular mechanisms occurring during carcinogenesis, and may assist in the recognition of new diagnostic biomarkers.

Targeting epigenetics for cancer therapy

Cancer can be identified as a chaotic cell state, which breaks the rules that govern growth and reproduction, with main characteristics such as uncontrolled division, invading other tissues, usurping resources, and eventually killing its host. It was once believed that cancer is caused by a progressive series of genetic aberrations, and certain mutations of genes, including oncogenes and tumor suppressor genes, have been identified as the cause of cancer. However, piling evidence suggests that epigenetic modifications working in concert with genetic mechanisms to regulate transcriptional activity are dysregulated in many diseases, including cancer. Cancer epigenetics explain a wide range of heritable changes in gene expression, which do not come from any alteration in DNA sequences. Aberrant DNA methylation, histone modifications, and expression of long non-coding RNAs (lncRNAs) are key epigenetic mechanisms associated with tumor initiation, cancer progression, and metastasis. Within the past decade, cancer epigenetics have enabled us to develop novel biomarkers and therapeutic target for many types of cancers. In this review, we will summarize the major epigenetic changes involved in cancer biology along with clinical and preclinical results developed as novel cancer therapeutics.

Tracing the path of cancer initiation: the AA protein-based model for cancer genesis

Background

Cancer is a defiant disease which cure is still far from being attained besides the colossal efforts and financial means deployed towards that end. The continuing setbacks encountered with today’s arsenal of anti-cancer drugs and cancer therapy modalities; show the need for a radical approach in order to get to the root of the problem. And getting to the root of cancer initiation and development leads us to challenge the present dogmas surrounding the pathogenesis of this disease.

Results

This comprehensive analysis brings to light the following points: (i) Cancer with its plethora of genetic and cellular symptoms could originate from one major event switching a cell from normalcy-to-malignancy; (ii) The switching event is postulated to involve a pathological breakup of a non-mutated protein, called here AA protein, resulting in the acquisition of new cellular functions present only in cancer cells; (iii) Following this event, DNA mutations begin to accumulate as secondary events to ensure perpetuity of cancer. Supporting arguments for this protein-based model come mainly from these observations: (i) The AA protein-based model reconciles together the clonal-and-stem cell theories into one inclusive model; (ii) The breakup of a normal protein could be behind the cancer-linked inflammation symptom; (iii) Cancer hallmarks are but adaptive traits, earned as a result of the switch from normalcy-to-malignancy.

Conclusions

Adaptation of cancer cells to their microenvironment and to different anti-cancer drugs is deemed here as the ultimate cancer hallmark, that needs to be understood and controlled. This adaptive power of cancer cells parallels that of bacteria also known with their resistance to a large range of substances in nature and in the laboratory. Consequently, cancer development could be viewed as a backward walk on the line of Evolution. Finally this unprecedented analysis demystifies cancer and puts the finger on the core problem of malignancy while offering ideas for its control with the ultimate goal of leading to its cure.

Natural products targeting the p53-MDM2 pathway and mutant p53: Recent advances and implications in cancer medicine

The p53 tumor suppressor plays a major role in controlling the initiation and development of cancer by regulating cell cycle arrest, apoptosis, senescence, and DNA repair. The MDM2 oncogene is a major negative regulator of p53 that inhibits the activity of p53 and reduces its protein stability. MDM2, p53, and the p53-MDM2 pathway represent well-documented targets for preventing and/or treating cancer. Natural products, especially those from medicinal and food plants, are a rich source for the discovery and development of novel therapeutic and preventive agents against human cancers. Many natural product-derived MDM2 inhibitors have shown potent efficacy against various human cancers. In contrast to synthetic small-molecule MDM2 inhibitors, the majority of which have been designed to inhibit MDM2-p53 binding and activate p53, many natural product inhibitors directly decrease MDM2 expression and/or MDM2 stability, exerting their anticancer activity in both p53-dependent and p53-independent manners. More recently, several natural products have been reported to target mutant p53 in cancer. Therefore, identification of natural products targeting MDM2, mutant p53, and the p53-MDM2 pathway can provide a promising strategy for the development of novel cancer chemopreventive and chemotherapeutic agents. In this review, we focus our discussion on the recent advances in the discovery and development of anticancer natural products that target the p53-MDM2 pathway, emphasizing several emerging issues, such as the efficacy, mechanism of action, and specificity of these natural products.

Role of micro-RNAs in drug resistance of multiple myeloma

While novel therapeutic approaches have profoundly improved survival of multiple myeloma (MM) patients, drug resistance and treatment refractoriness still persists. This obstacle highly demands thorough investigation into the root and underlying molecular mechanisms to develop more effective strategies. The advent of micro-RNAs (miRNAs) in the study of cancer biology and pathogenesis in recent years has revolutionized therapy in this field and particularly opened new windows to further understanding of tumor drug resistance. However; in spite of the fact that miRNAs involvement in MM pathogenesis and progression has been substantially evidenced, miRNA investigation in MM drug resistance is still in its infancy. Our knowledge of the potential role of miRNAs in MM drug resistance comes from few recent reports confirming that some miRNAs including miR-137/197, miR-21 and miR-221/222 could negatively modulate drug sensitivity of MM cells. Further continuous researches are required to exploit miRNAs to elucidate the critical mechanisms controlling drug resistance in MM. In this review, we will highlight the most recent observations on the role of miRNAs in MM drug resistance. Moreover, approaches and insights into clinical application of miRNAs to overcome MM drug resistance will be discussed.

Education, collaboration, and innovation: intelligent biology and medicine in the era of big data

Here we present a summary of the 2014 International Conference on Intelligent Biology and Medicine (ICIBM 2014) and the editorial report of the supplement to BMC Genomics and BMC Systems Biology that includes 20 research articles selected from ICIBM 2014. The conference was held on December 4-6, 2014 at San Antonio, Texas, USA, and included six scientific sessions, four tutorials, four keynote presentations, nine highlight talks, and a poster session that covered cutting-edge research in bioinformatics, systems biology, and computational medicine.