The evolution of our molecular understanding of colorectal cancer: what we are doing now, what the future holds, and how tumor profiling is just the beginning

Colorectal cancer (CRC) has been extensively molecularly characterized in recent years. In addition to the understanding of biologic hallmarks of the disease, the ultimate goal of these studies was to provide tools that could allow us to differentiate subgroups of CRC with prognostic and predictive implications. So far, subtype classification has been largely driven by well-described features: (1) defective mismatch repair resulting in higher mutation rate; (2) cellular proliferation along with chromosomal instability and copy number aberrations; and (3) an invasive stromal phenotype mainly driven by TGF-β linked to epithelial-mesenchymal transition. Recent studies have outlined the complexity of CRC at the gene expression level, confirming how heterogeneous the disease is beyond currently validated parameters, namely KRAS, BRAF mutations and microsatellite instability. In fact, adopting an extended mutation profile upfront, which includes nonrecurrent KRAS, NRAS, and PIK3CA gene variants, likely improves outcomes. In this article, we review the current trends of translational research in CRC, summarize ongoing genomically driven clinical trials, and describe the challenges for defining a comprehensive, robust, and reproducible disease classification system that links molecular features to personalized medicine. We believe that identification of CRC subtypes based on integrative genomic analyses will provide a better guide for patient stratification and for rational design of drugs targeting specific pathways.

Transcriptomics: advances and approaches

Transcriptomics is one of the most developed fields in the post-genomic era. Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specific physiological condition, including messenger RNA, transfer RNA, ribosomal RNA, and other non-coding RNAs. Transcriptomics focuses on the gene expression at the RNA level and offers the genome-wide information of gene structure and gene function in order to reveal the molecular mechanisms involved in specific biological processes. With the development of next-generation high-throughput sequencing technology, transcriptome analysis has been progressively improving our understanding of RNA-based gene regulatory network. Here, we discuss the concept, history, and especially the recent advances in this inspiring field of study.

Applications of nanotechnology, next generation sequencing and microarrays in biomedical research

Next-generation sequencing technologies, microarrays and advances in bio nanotechnology have had an enormous impact on research within a short time frame. This impact appears certain to increase further as many biomedical institutions are now acquiring these prevailing new technologies. Beyond conventional sampling of genome content, wide-ranging applications are rapidly evolving for next-generation sequencing, microarrays and nanotechnology. To date, these technologies have been applied in a variety of contexts, including whole-genome sequencing, targeted re sequencing and discovery of transcription factor binding sites, noncoding RNA expression profiling and molecular diagnostics. This paper thus discusses current applications of nanotechnology, next-generation sequencing technologies and microarrays in biomedical research and highlights the transforming potential these technologies offer.

Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases

High throughput sequencing technologies have become essential in studies on genomics, epigenomics, and transcriptomics. Although sequencing information has traditionally been elucidated using a low throughput technique called Sanger sequencing, high throughput sequencing technologies are capable of sequencing multiple DNA molecules in parallel, enabling hundreds of millions of DNA molecules to be sequenced at a time. This advantage allows high throughput sequencing to be used to create large data sets, generating more comprehensive insights into the cellular genomic and transcriptomic signatures of various diseases and developmental stages. Within high throughput sequencing technologies, whole exome sequencing can be used to identify novel variants and other mutations that may underlie many genetic cardiac disorders, whereas RNA sequencing can be used to analyze how the transcriptome changes. Chromatin immunoprecipitation sequencing and methylation sequencing can be used to identify epigenetic changes, whereas ribosome sequencing can be used to determine which mRNA transcripts are actively being translated. In this review, we will outline the differences in various sequencing modalities and examine the main sequencing platforms on the market in terms of their relative read depths, speeds, and costs. Finally, we will discuss the development of future sequencing platforms and how these new technologies may improve on current sequencing platforms. Ultimately, these sequencing technologies will be instrumental in further delineating how the cardiovascular system develops and how perturbations in DNA and RNA can lead to cardiovascular disease.

[The place of functional genomics in oncological research]

The 1000 genomes project changed the way how we see the human genome. The rapid development of the deep sequencing technologies is raising several practical questions, and the way how we answer these questions will affect deeply the future of the oncological reseach in Hungary. In our manuscript we give a short overview of the results of the 1000 genomes project and we present the place of the functional genomic investigations between other genomic tools. Based on the recent development in the field we summarize the challenges that have to be addressed in the next couple of years.

PROTEOMICS in aquaculture: applications and trends

Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.

[Genetic approaches to nutrition personalization]

The paper presents the results of studies conducted in recent years, which show that nutrients and bioactive food components, directly or indirectly regulate the functional activity of genes influencing gene transcriptome, proteome and metabolome. A definition of "nutrigenomics" - the science that emerged at the turn of nutrition and genetics, and studies the relationship of human nutrition with the characteristics of its genome in order to understand how food affects gene expression, and ultimately, on human health. It is shown that the cellular and molecular level, nutrients, first serving as a ligand, the receptors are transcription factors, and secondly, as a substrate or intermediate metabolites are incorporated into metabolic pathways whose products control the expression of genes and, thirdly, positive or negative effect on signaling pathways. We present results of their research, which characterize the rate of prevalence of polymorphisms of genes that are markers of risk for obesity. On the basis of domestic and foreign studies concluded that genetic markers can be used for the diagnosis and prognosis of alimentary-dependent diseases such as obesity, and as well as a predictor for the development of a personalized diet and forecast its performance.

Bringing chemistry to life

Bioorthogonal chemistry allows a wide variety of biomolecules to be specifically labeled and probed in living cells and whole organisms. Here we discuss the history of bioorthogonal reactions and some of the most interesting and important advances in the field.

Development and applications of single-cell transcriptome analysis

Dissecting the relationship between genotype and phenotype is one of the central goals in developmental biology and medicine. Transcriptome analysis is a powerful strategy to connect genotype to phenotype of a cell. Here we review the history, progress, potential applications and future developments of single-cell transcriptome analysis. In combination with live cell imaging and lineage tracing, it will be possible to decipher the full gene expression network underlying physiological functions of individual cells in embryos and adults, and to study diseases.

Genomic approaches with natural fish populations from polluted environments

Transcriptomics and population genomics are two complementary genomic approaches that can be used to gain insight into pollutant effects in natural populations. Transcriptomics identify altered gene expression pathways, and population genomics approaches more directly target the causative genomic polymorphisms. Neither approach is restricted to a predetermined set of genes or loci. Instead, both approaches allow a broad overview of genomic processes. Transcriptomics and population genomic approaches have been used to explore genomic responses in populations of fish from polluted environments and have identified sets of candidate genes and loci that appear biologically important in response to pollution. Often differences in gene expression or loci between polluted and reference populations are not conserved among polluted populations, suggesting a biological complexity that we do not yet fully understand. As genomic approaches become less expensive with the advent of new sequencing and genotyping technologies, they will be more widely used in complementary studies. However, although these genomic approaches are immensely powerful for identifying candidate genes and loci, the challenge of determining biological mechanisms that link genotypes and phenotypes remains.

Targeting microRNAs in cancer: rationale, strategies and challenges

MicroRNAs (miRNAs) are evolutionarily conserved small non-coding RNAs that regulate gene expression. Early studies have shown that miRNA expression is deregulated in cancer and experimental data indicate that cancer phenotypes can be modified by targeting miRNA expression. Based on these observations, miRNA-based anticancer therapies are being developed, either alone or in combination with current targeted therapies, with the goal to improve disease response and increase cure rates. The advantage of using miRNA approaches is based on its ability to concurrently target multiple effectors of pathways involved in cell differentiation, proliferation and survival. In this Review, we describe the role of miRNAs in tumorigenesis and critically discuss the rationale, the strategies and the challenges for the therapeutic targeting of miRNAs in cancer.

Genetics of Parkinson disease and essential tremor

PURPOSE OF REVIEW

Elucidating the genetic background of Parkinson disease and essential tremor is crucial to understand the pathogenesis and improve diagnostic and therapeutic strategies.

RECENT FINDINGS

A number of approaches have been applied including familial and association studies, and studies of gene expression profiles to identify genes involved in susceptibility to Parkinson disease. These studies have nominated a number of candidate Parkinson disease genes and novel loci including Omi/HtrA2, GIGYF2, FGF20, PDXK, EIF4G1 and PARK16. A recent notable finding has been the confirmation for the role of heterozygous mutations in glucocerebrosidase (GBA) as risk factors for Parkinson disease. Finally, association studies have nominated genetic variation in the leucine-rich repeat and Ig containing 1 gene (LINGO1) as a risk for both Parkinson disease and essential tremor, providing the first genetic evidence of a link between the two conditions.

SUMMARY

Although undoubtedly genes remain to be identified, considerable progress has been achieved in the understanding of the genetic basis of Parkinson disease. This same effort is now required for essential tremor. The use of next-generation high-throughput sequencing and genotyping technologies will help pave the way for future insight leading to advances in diagnosis, prevention and cure.

Transcript profiling towards personalised medicine in rheumatoid arthritis

Rheumatoid arthritis (RA ) is a chronic inflammatory joint disease that is heterogeneous in nature. The heterogeneity is reflected by the variation in responsiveness to virtually any treatment modality. Since our understanding of the molecular complexity is incomplete and criteria for categorisation are limited, we mainly consider the disease RA as group average. A powerful way to gain insight into the complexity of RA has arisen from DNA microarray technology, which allows an open-ended survey to comprehensively identify the genes and biological pathways that are associated with clinically defined conditions. During the last decade encouraging results have been generated towards the molecular description of complex diseases in general. Here, I describe developments in genomics research that provide a framework to increase our understanding of the pathogenesis and the identification of biomarkers for early diagnosis, prognosis and stratification, aimed at a personal medicine approach in RA .

Gene Expression Profiling of Vascular Endothelial Cells Exposed to Fluid Mechanical Forces: Relevance for Focal Susceptibility to Atherosclerosis

Gene expression profiling has revealed that cultured vascular endothelial cells (EC) respond to fluid mechanical forces by modulating the mRNA level of a large number of genes. However, differences between the gene arrays and the experimental conditions employed by different researchers make comparison between data sets difficult, and limit the interpretation of the results. Despite these problems, analysis of recent data indicates that the transcriptional response of cultured EC to low-shear disturbed flow conditions similar to those at atherosclerosis-prone areas is distinct from that elicited by atheroprotective high shear laminar flow, providing a molecular basis for the focal nature of atherosclerosis. Many of the genes altered by disturbed flow are involved in key biological processes relevant to atherosclerosis such as inflammation, cell cycle control, apoptosis, thrombosis and oxidative stress. Overall, the gene expression profiling data are consistent with the hypothesis of the hemodynamic etiology of atherosclerotic predilection, viz that at predilected areas in vivo the presence of low shear, non-laminar flow is sufficient to induce a gene expression profile that pre-disposes the endothelium to the initiation and development of atherosclerotic lesions.

From bench to bedside: current and future applications of molecular profiling in renal cell carcinoma

Among the adult population, renal cell carcinoma (RCC) constitutes the most prevalent form of kidney neoplasm. Unfortunately, RCC is relatively asymptomatic and there are no tumor markers available for diagnostic, prognostic or predictive purposes. Molecular profiling, the global analysis of gene and protein expression profiles, is an emerging promising tool for new biomarker identification in RCC. In this review, we summarize the existing knowledge on RCC regarding clinical presentation, treatment options, and tumor marker status. We present a general overview of the more commonly used approaches for molecular profiling at the genomic, transcriptomic and proteomic levels. We also highlight the emerging role of molecular profiling as not only revolutionizing the process of new tumor marker discovery, but also for providing a better understanding of the pathogenesis of RCC that will pave the way towards new targeted therapy discovery. Furthermore, we discuss the spectrum of clinical applications of molecular profiling in RCC in the current literature. Finally, we highlight some of the potential challenging that faces the era of molecular profiling and its transition into clinical practice, and provide an insight about the future perspectives of molecular profiling in RCC.

Global metabolic profiling and its role in systems biology to advance personalized medicine in the 21st century

Systems biology attempts to elucidate the complex interaction between genes, proteins and metabolites to provide a mechanistic understanding of cellular function and how this function is affected by disease processes, drug toxicity or drug efficacy effects. Global metabolic profiling is an important component of systems biology that can be applied in both preclinical and clinical settings for drug discovery and development, and to study disease mechanisms. The metabolic profile encodes the phenotype, which is composed of the genotype and environmental factors. The phenotypic profile can be used to make decisions about the best course of treatment for an individual patient. Understanding the combined effects of genetics and environment through a systems biology framework will enable the advancement of personalized medicine.

Discussion of the applicability of microarrays: profiling of leukemias

Leukemias are classified according to clinical, morphologic, and immunologic phenotypes, caused by specific genetic aberrations in association to distinct prognostic profiles. Usually the subtypes are defined using complementary laboratory methods, such as multiparameter flow cytometry, cytogenetics in combination with fluorescence in situ hybridization, and molecular methods such as the polymerase chain reaction. The genetic variations of the different subtypes lead to distinct changes also in gene expression, which is comprehensively analysed by DNA microarrays. Thus, first gene expression profiling studies showed that analysis with whole-genome DNA microarrays leads to a prediction accuracy of 95.6% with respect to the classical methods, and even allowed a further distinction of subtypes. It is expected that diagnostic strategies can be optimized with this new technology and that the understanding of the molecular pathogenesis of leukemias will be significantly improved. This could also lead to the identification of new targets for future drugs.

Gene expression measurements in the context of epidemiological studies

BACKGROUND

Gene expression measurements became an attractive tool to assess biological responses in epidemiological studies. However, collection of blood samples poses various technical problems. We used gene expression data from two epidemiological studies to evaluate differences between sampling methods, comparability of two methods for measuring RNA levels and stability of RNA samples over time.

METHODS

For the PARSIFAL study, PBLC of 1155 children were collected using EDTA tubes in two countries. In the PASTURE study, tubes containing RNA-stabilizing solutions (PAXgene) Blood RNA Tubes; PreAnalytiX) were used to collect cord blood leucocytes of 982 children in five countries. Real-time PCR (conventional single tube assay and high-throughput low density arrays) was used to quantify expression of various innate immunity genes. In 77 PARSIFAL samples, gene expression was measured repeatedly during prolonged storage.

RESULTS

In PARSIFAL (EDTA tubes) the median RNA yield after extraction significantly differed between the two centres (70 and 34 ng/microl). Collecting blood into an RNA-stabilizing solution markedly reduced differences in RNA yield in PASTURE (range of medians 91-107 ng/microl). The agreement [Spearman rank correlation (r)] between repeated measurements of gene expression decreased with increasing storage time [e.g., for CD14: r (first/second measurement) = 0.35; r (first/third measurement) = 0.03]. RNA levels measured with either the conventional method or low-density arrays were comparable (r > 0.9).

CONCLUSION

Collecting blood samples into tubes containing an RNA-stabilizing solution increases RNA yield and reduces its variability. Long-term storage of samples may lead to RNA degradation, requiring special attention in longitudinal studies.

Mass spectrometry in systems biology: an overview

As an emerging field, systems biology is currently the talk of the town, which challenges our philosophy in comprehending biology. Instead of the reduction approach advocated in molecular biology, systems biology aims at systems-level understanding of correlations among molecular components. Such comprehensive investigation requires massive information from the "omics" cascade demanding high-throughput screening techniques. Being one of the most versatile analytical methods, mass spectrometry has already been playing a significant role at this early stage of systems biology. In this review, we documented the advances in modern mass spectrometry technologies as well as nascent inventions. Recent applications of mass spectrometry-based techniques and methodologies in genomics, proteomics, transcriptomics and metabolomics will be further elaborated individually. Undoubtedly, more applications of mass spectrometry in systems biology can be expected in the near future.

Proteomics: A Paradigm Shift

Proteome--the protein complement of a genome--has become the protein renaissance and a key research tool in the post-genomic era. The basic technology involves the routine usage of gel electrophoresis and spectrometry procedures for deciphering the primary protein sequence/structure as well as knowing certain unique post-translational modifications that a particular protein has undergone to perform a specific function in the cell. However, the recent advancements in protein analysis have ushered this science to provide deeper, bigger and more valuable perspectives regarding performance of subtle protein-protein interactions. Applications of this branch of molecular biology are as vast as the subject is and include clinical diagnostics, pharmaceutical and biotechnological industries. The 21st century hails the use of products, procedures and advancements of this science as finer touches required for the grooming of fast-paced technology.

Biotechnology and stem cell research: a glance into the future

The present review addresses the issues related to innovative contributions in biotechnology and their potential role in stem cell research at present and in the future. We can expect that future developments and applications in biotechnological sciences and industry will effect the direction of emerging cellular therapies. The use of these advances may offer a unique opportunity to investigate the mechanisms related to the journey from embryonic cells or bone-marrow derived stem/progenitor cells to cardiomyocytes or endothelial cells and the molecular regulators of cell differentiation.