The hallmarks of cancer

High-throughput long noncoding RNA profiling for diagnostic and prognostic markers in cancer: opportunities and challenges.

Pan-cancer analysis of non-coding transcripts reveals the prognostic onco-lncRNA HOXA10-AS in gliomas.

Colorectal cancer (CRC) is the fourth most common cause of death worldwide. Surgery is usually the first line of treatment for patients with CRC but many tumors with similar histopathological features show significantly different clinical outcomes. The discovery of robust prognostic biomarkers in patients with CRC is imperative to achieve more effective treatment strategies and improve patient's care. Recent progress in next generation sequencing methods and transcriptome analysis has revealed that a much larger part of the genome is transcribed into RNA than previously assumed. Collectively referred to as non-coding RNAs (ncRNAs), some of these RNA molecules such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been shown to be altered and to play critical roles in tumor biology. This discovery leads to exciting possibilities for personalized cancer diagnosis, and therapy. Many lncRNAs are tissue and cancer-type specific and have already revealed to be useful as prognostic markers. In this review, we focus on recent findings concerning aberrant expression of lncRNAs in CRC tumors and emphasize their prognostic potential in CRC. Further studies focused on the mechanisms of action of lncRNAs will contribute to the development of novel biomarkers for diagnosis and disease progression.

RNA‐seq‐driven expression analysis to investigate cardiovascular disease genes with associated phenotypes among atrial fibrillation patients

I come from a family in which there have been no scientists or doctors. I was interested, however, in biology at school and started my scientific career by training in medicine at Oxford University and Guys Hospital, London. Practising as a doctor reinforced my curiosity about the biological processes underlying human disease. As a consequence, I pursued a clinical vocation in histopathology, a discipline that couples exposure to the sights and smells of the autopsy room with a daily journey into the often beautiful, sometimes ugly world of healthy and diseased human tissues under the microscope. After an introduction to general histopathology in Nick Wright's department at the Hammersmith Hospital, London, I completed my postgraduate medical training in neuropathology with Peter Lantos at the Maudsley Hospital, London.Peering at the nuclei of cancer cells under the microscope, for me it was a matter of fascination that hidden within them were the key events converting normal cells into cancer cells, and frustration because they were out of reach. Many of the tissue samples examined by pathologists are from cancers. The clonal theory of cancer development and the general role of DNA mutations in generating cancer cell clones had been established by 1986 when I was working as a junior pathologist. Indeed, the first mutated cancer gene, HRAS , had recently been identified through application of the, then new, technologies of recombinant DNA technology. Peering at the nuclei of cancer cells under the microscope, for me it was a matter of fascination that hidden within them were the key events converting normal cells into cancer cells, and frustration because they were out of reach. So, I took 3 years break from medicine to study for a PhD, learning the methods and thinking of molecular oncology in Colin Cooper's laboratory at the Institute …

Alzheimer's disease (AD) is a neurodegenerative disorder with progressive damage to brain cells. It is the leading cause of dementia worldwide that is characterized by impairment of memory and eventually by reasoning and perception disturbances. No curative treatment for dementia is currently available. With the progress of RNA sequencing and transcriptome analysis, the discovery of non-protein coding RNAs expands our knowledge about the genome. Long non-coding RNAs (lncRNAs) which are involved in a wide variety of biological processes as regulatory molecule, have been the focus of much recent research. In this review, we focus on the emerging roles of these lncRNAs in the pathology of Alzheimer's disease. Their expressions are brain-specific and dysregulated in the patient and animal model. Here, we will summarize the pathological features influenced by lncRNAs and therefore provide an lncRNA point-of-view on AD. This should stimulate new research directions and therapeutic options considering lncRNAs as novel prognostic markers and therapeutic targets.

Introduction: Decades of efforts have been made to have a better understanding about the human genome, which encodes ~20,000 protein-coding genes as well as an astounding number of transcriptionally active noncoding RNAs. Among these noncoding RNAs, long-noncoding RNAs (lncRNAs) have been increasingly recognized to play essential roles in tumorigenesis, representing a new focus in cancer research. Analogous to the identification of protein-coding cancer driver genes, it is a crucial task in cancer research to identify lncRNA drivers and elucidate their functions in various cancer types. Methods: We first downloaded TCGA RNA-seq BAM files (>60TB) across 20 cancer types from the UCSC Cancer Genomic Hub (CGHub) and quantified the lncRNA expression based on GENCODE lncRNA annotation. To identify lncRNA drivers, we focused on identifying the functional relevant lncRNA-protein pairs through their expression profiling data. To prevent acquiring more false positives from conventional correlation analysis, we applied the context likelihood of relatedness (CLR) algorithm on evaluating co-expressed lncRNA and protein pairs based on RNA-seq and reverse-phase protein array (RPPA) data. In addition, to further increase the clinical relevance of the potential lncRNA drivers, we conducted survival analysis and tumor/normal differential analysis to boost the prediction power of our systematic computational approach. Results: In this study, we integrated lncRNA expression, protein expression and patient survival data to nominate lncRNA drivers in 20 cancers. Among ~4 million lncRNA-protein pairs, we have identified 9 lncRNA drivers and 16 potential lncRNA-protein interaction pairs linked with them. To validate our findings, we selected 3 lncRNAs with high confidence and performed knockdown experiments in multiple cell lines, in which 2 lncRNAs (TMPO-AS1 and HCP5) showed functional relevance with protein-coding genes MSH6 and LCK respectively. Both of the pairs have the same direction of correlations (positive or negative) as we predicted. Our results indicate that the identified lncRNAs may functionally interact with their protein partners identified by our network-based approach, which will further provide the molecular foundation for investigating cancer mechanisms, identifying prognostic lncRNA markers and characterizing additional therapeutic targets. Citation Format: Jun Li, Zhicheng Zhou, Han Liang. A systematic network-based approach to prioritizing lncRNA drivers in cancers. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A36.

Breast cancer (BC) is one of the frequent tumors that seriously endanger the physical and mental well-being in women with strong heterogeneity, and its pathogenesis involves multiple risk factors. Depending on the type of BC, hormonal therapy, targeted therapy, and immunotherapy are the current systemic treatment options along with conventional chemotherapy. Despite significant progress in understanding BC pathogenesis and therapeutic options, there is still a need to identify new therapeutic targets and develop more effective treatments. According to recent sequencing and profiling studies, non-coding (nc) RNAs genes are deregulated in human cancers via deletion, amplification, abnormal epigenetic, or transcriptional regulation, and similarly, the expression of many ncRNAs is altered in breast cancer cell lines and tissues. The ability of single ncRNAs to regulate the expression of multiple downstream gene targets and related pathways provides a theoretical basis for studying them for cancer therapeutic drug development and targeted delivery. Therefore, it is far-reaching to explore the role of ncRNAs in tumor development and their potential as therapeutic targets. Here, our review outlines the potential of two major ncRNAs, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) as diagnostic and prognostic biomarkers as well as targets for new therapeutic strategies in breast cancer.

The lncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression.

This study aims to dissect the complex molecular landscape of glioblastoma multiforme (GBM), focusing on identifying key regulatory non-coding RNAs and protein-coding genes that could serve as therapeutic targets and prognostic biomarkers. GBM is an aggressive form of brain cancer characterized by poor prognosis and limited treatment options. Recent advances in high-throughput genomic technologies have opened new avenues for understanding the molecular underpinnings of GBM, with a particular focus on the roles of ncRNAs. We utilized multiple datasets from the NCBI Gene Expression Omnibus (GEO) to analyze mRNA, miRNA, lncRNA, and circRNA expression profiles in GBM versus normal brain tissues. Differential expression analysis was conducted using GEO2R, followed by pathway enrichment and protein–protein interaction (PPI) network analyses using DAVID and STRING databases, respectively. Hub genes were identified and validated through GEPIA2, and a competing endogenous RNA (ceRNA) network was constructed to elucidate the interactions between non-coding RNAs (ncRNAs) and protein-coding genes. The study identified several differentially expressed genes and ncRNAs, highlighting complex interactions within the PPI network and significant pathway enrichments implicated in GBM progression. The ceRNA network analysis revealed potential regulatory axes mediated by ncRNAs. Validation of hub genes confirmed their differential expression and prognostic value. Additionally, correlations between gene expression, drug sensitivity, and immune cell infiltration were analyzed, offering insights into personalized therapeutic approaches. Our findings underscore the intricate molecular networks in GBM, emphasizing the role of ncRNAs in tumor biology and their potential as therapeutic targets. The study highlights the necessity for further experimental validation of bioinformatics predictions to bridge the gap between genomic insights and clinical application, ultimately aiming to enhance the prognosis and treatment strategies for GBM patients.

The sequencing of the human genome, the identification of common single-nucleotide polymorphisms (SNPs) and haplotype blocks, and advances in microarray technology have enabled the study of complex diseases at a level of detail not previously imaginable. These have aided in the design and analyses of association and linkage studies of many complex diseases including cardiovascular disease. Recent technological advances have enabled the undertaking of large-scale genome-wide association studies (GWAS) that can assay hundreds of thousands of polymorphic sites on hundreds to thousands of individuals to find genomic regions associated with disease. Although results from these experiments enable the identification of smaller regions of association compared with previous studies, as with all linkage and association studies, there is the need for the further investigation of regions of interest for the causal genes or variants. The purpose of this review is to present a detailed demonstration as to how publicly available resources can be used to easily guide more detailed research into genomic regions of interest identified in linkage and association study data. Large-scale projects, such as the Human Genome Sequencing project,1,2 have generated large volumes and varieties of annotated genomic data necessitating the development of Internet-based tools to organize and make practically available these public data. One important tool in human disease research is the web-based graphical genome browsers that use the human genome sequence as the framework on which to organize genomic annotations, providing various ways for researchers to view and extract important information. Currently, there are 3 human genome browsers that have been developed for public use: (1) the National Center for Biotechnology Information (NCBI) Map Viewer3; (2) the University of California Santa Cruz (UCSC) Genome Browser4; and (3) the European Bioinformatics Institute’s Ensembl system.5 Although these genome browsers share common features and …

Non-coding RNAs in hepatitis B or C-associated hepatocellular carcinoma: Potential diagnostic and prognostic markers and therapeutic targets

B-cell chronic lymphocytic leukemia (CLL) is characterized accumulation in bone marrow, peripheral blood and secondary lymphoid tissues of neoplastic, mature small B lymphocytes. It is the most common adult leukemia in the western countries but much rarer in Asian countries with an incidence of 3.9/100,000/year in the United States and about 0.45/100,000/year in Hong Kong. Despite being an indolent illness in the majority, it remains an incurable disease with some patients pursuing an aggressive clinical course. Therefore, to optimize treatment outcome, identification of new prognostic markers, and hence better risk-stratification is needed.
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\nIn the human genome, apart from protein-coding genes (PCGs), with the development of high-throughput RNA sequencing, non-coding RNAs (ncRNAs) with little or no protein-coding capacity were discovered. Based on transcript size, ncRNAs are generally grouped into two major classes: small ncRNAs and lncRNAs. miRNAs, being single-stranded non-coding RNAs measuring 19-25 nucleotides (nt), is an important type of small ncRNAs, which serve as post-transcriptional regulators of gene expression via mRNA cleavage or translational repression of their corresponding target PCGs. lncRNAs, mRNA-like transcripts ranging from 200 nt to ~100 kilobases, have been shown to regulate the expression of their target genes through epigenetic, transcriptional or post-transcriptional mechanisms. Indeed, dysregulation of miRNAs and lncRNAs have been implicated in human cancers, suggesting a potential oncogenic or tumor suppressive role for ncRNAs. Apart from histone modification, DNA methylation is another important epigenetic modification leading to gene silencing without altering DNA sequence, and hence impacting cellular signaling and biological processes. In this thesis, the hypothesis that aberrant promoter methylation of tumor suppressor miRNAs or lncRNAs might contribute to CLL leukemogenesis is tested.
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\nBy the candidate gene approach, the role of DNA methylation of tumor suppressor miRNAs, such as miR-34 family, miR-9 family and miR-3151, together with the lncRNA BM742401 was investigated in CLL. The tumor suppressor role of miR-34b/c, miR-9-3, miR-3151 and BM742401 were demonstrated in CLL cell lines. Remarkably, restoration of miR-9 in CLL cells led to downregulation of NFκB1, which is a known target of miR-9, thereby testifying a role of miR-9-3 methylation in the constitutive activation of NFκB signaling pathway in CLL. Moreover, miR-3151 methylation protected CLL cells from apoptosis through over-expression of both of its direct PCG targets MADD and PIK3R2, leading to constitutive activation of MEK/ERK and PI3K/AKT signaling respectively, and consequently upregulation of MCL1. Furthermore, despite infrequent inactivating TP53 mutation in CLL at diagnosis, methylation of miR-34b/c, which are direct transcriptional targets of TP53, is implicated in the perturbation of the TP53-regulated tumor suppressor network. Finally, in primary CLL samples at diagnosis, frequent methylation of miR-3151 and BM742401 and modest methylation of miR-34b/c and miR-9-3 were demonstrated. Of note, miR-9-3 methylation was shown associated with advanced Rai stage (≥ stage 2) in CLL patients, suggesting miR-9-3 methylation as a potential poor risk factor for survival.
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\nIn conclusion, hypermethylation of tumor suppressor ncRNAs including miR-34b/c, miR-9-3, miR-3151 and lncRNA BM742401 is associated with constitutive activation of NFκB, MEK/ERK and PI3K/AKT signaling, and hence implicated in CLL pathogenesis.

Improvements in technology and sequencing of the human genome have provided a template for polymerase chain reaction primers to amplify and sequence coding exons of large protein-coding genes. This has lead to genome-wide analyses of human cancers and sequencing of all protein-encoding genes in more than 80 human cancers. Medulloblastomas (MBs) are the most common malignant brain tumor in children and are diagnosed in approximately 1 in 200 000 children less than 15 years old each year.1 Prior research has identified 2 subgroups of MBs associated with either alterations in genes of the Hedgehog pathway and those mutated in the Wnt pathway.2,3 Alterations in TP53 (8), MYC, and OTX2 have also been uncovered.4,5 Although these alterations have helped define genetic subtypes of MDs, most patients do not have these mutations. In a recent study by Parsons et al, copy alterations were assessed using microarrays and all known protein-coding genes microRNA genes were sequenced.6 The authors found that each tumor had 11 gene alterations, 5 to 10 times fewer than that of other solid tumors sequenced to date. Mutations in known pathways of medulloblastoma were confirmed including Wnt and Hedgehog pathways. Additionally, a number of new mutations were uncovered including histone-lysine N-methyltransferase genes MLL2 or MLL3 in 16% of MB patients. These involved genes were found to be tumor suppressor genes, being responsible for chromatin remodeling and transcriptional regulation. In contrast to germline mutations present in the fertilized egg from which individuals develop, somatic mutations occur in normal cells as tissues progress during postnatal life. Somatic mutations in tumors either have no effect on tumor growth (passenger mutations) or confer an advantage allowing it to expand, invade local tissue, and/or metastasize (driver mutation). Passenger mutations provide a record of the number of divisions a cell has undergone during both normal development and tumor progression. Although most adult cancers such as breast, ovary, colorectal, and pancreas, and glioma7,8 have 1000 to 10 000 somatic mutations, some cancers particularly prone to environmental carcinogens such as melanoma and lung cancer may have more than 100 000.7,9-11 The low number of mutations in medulloblastomas, along with key mutations in developmental pathways, may be key differences differentiating adult from childhood cancers. An improved genetic classification for MB could be beneficial both in terms of defining prognosis as well as developing specific therapies. Currently, large cell/anaplastic MBs associated with MYC amplification have a worse prognosis than desmoplastic MBs that are often associated with PTCH1 or other Hedgehog pathway alterations.3,12,13 The classic MB subtype does not have a defining molecular alterations, and the MLL2/MLL3 mutations do not fit into a definable subtype.6 Furthermore, some cases show no mutations in cancer genes or only one alteration of any gene. Clearly, there are far more alterations to identify. As our understanding of malignant brain tumor biology has progressed, so too has the goal to develop more effective, less toxic, rationally conceived therapeutics. The standard of care for adjuvant therapies are relatively uniform, consisting of a combination of radiation and cytotoxic chemotherapy. As molecular profiling continues to evolve, however, the opportunities for more targeted, individualized intervention are rapidly increasing. Moving forward, under the International Cancer Genome Consortium, large-scale sequencing of each major cancer subtype is underway.14 With improvement in technology and declines in cost, it is likely that whole genome sequencing will be the methodology of the future rather than limiting exploration to sequencing the DNA of exons of protein-coding genes or analysis of transcriptomes. Complete sequencing will have a role on detection, diagnosis, treatment, and prevention, while further defining pathogenesis, progression, and mechanisms of drug resistance. Although each cancer type is likely defined by overlapping sets of mutated genes, a single genomic screening test may become an integral element of treatment planning of newly diagnosed patients and the design of clinical trials. To this end, initial stratification of brain tumors patients into molecularly determined treatment groups has already begun. The 2 best examples are promoter methylation and transcriptional silencing of O-6-methlylguanine-DNA methyltransferase (MGMT), which leads to improved GMB chemosensitivity, and eGFR vIII mutation, which may allow response to the eGFR inhibitor erlotinib. These findings represent a paradigm shift—one that stratifies patients by molecular determinants into treatment groups, thereby guiding personalized, biologically grounded therapies.Figure 1: Axial MRI with and without contrast depicting a classic medulloblastoma.Ricardo J. Komotar Robert M. Starke E. Sander Connolly Michael B. Sisti

Chapter 9 - Crosstalk Between Non-Coding RNAs and the Epigenome in Development