Sequencing technologies – the next generation.

Exellent review about sequencing technologies, from commmercial to open source and future directions. Details about chemistry and technology illustrated by exellent figures. Tables summarizing and comparing each platform. Disadvantages and advantages of each technology, including cost figures. A must!

Nat Rev Genet. 2010 Jan;11(1):31-46. Epub 2009 Dec 8.
Sequencing technologies – the next generation.

Metzker ML.

Human Genome Sequencing Center and Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA. mmetzker@bcm.edu

Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.

PMID: 19997069

Reactome array: forging a link between metabolome and genome.

New technology for profiling metabolic profiles. Technical details and a proof of principle. Mapping to KEGG. Another layer of information, when combined with others, will provide better understanding.

Science. 2009 Oct 9;326(5950):252-7.
Reactome array: forging a link between metabolome and genome.

Beloqui A, Guazzaroni ME, Pazos F, Vieites JM, Godoy M, Golyshina OV, Chernikova TN, Waliczek A, Silva-Rocha R, Al-Ramahi Y, La Cono V, Mendez C, Salas JA, Solano R, Yakimov MM, Timmis KN, Golyshin PN, Ferrer M.

CSIC, Institute of Catalysis, 28049 Madrid, Spain.

We describe a sensitive metabolite array for genome sequence-independent functional analysis of metabolic phenotypes and networks, the reactomes, of cell populations and communities. The array includes 1676 dye-linked substrate compounds collectively representing central metabolic pathways of all forms of life. Application of cell extracts to the array leads to specific binding of enzymes to cognate substrates, transformation to products, and concomitant activation of the dye signals. Proof of principle was shown by reconstruction of the metabolic maps of model bacteria. Utility of the array for unsequenced organisms was demonstrated by reconstruction of the global metabolisms of three microbial communities derived from acidic volcanic pool, deep-sea brine lake, and hydrocarbon-polluted seawater. Enzymes of interest are captured on nanoparticles coated with cognate metabolites, sequenced, and their functions unequivocally established.

PMID: 19815770

A census of amplified and overexpressed human cancer genes.

Very elegant summary of proven cancer genes. Initially containing 6 genes, this list has grown to a few hundreds. That’s all about how “beacons” were identified, and the more we look, the finer picture we see. Table 1 summarizes cancer genes by organ. A must overview and reference.

http://www.nature.com/nrc/journal/v10/n1/full/nrc2771.html

Nat Rev Cancer. 2010 Jan;10(1):59-64.

A census of amplified and overexpressed human cancer genes.

Santarius T, Shipley J, Brewer D, Stratton MR, Cooper CS.

The Wellcome Trust Sanger Centre, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA, UK.

Integrated genome-wide screens of DNA copy number and gene expression in human cancers have accelerated the rate of discovery of amplified and overexpressed genes. However, the biological importance of most of the genes identified in such studies remains unclear. In this Analysis, we propose a weight-of-evidence based classification system for identifying individual genes in amplified regions that are selected for during tumour development. In a census of the published literature we have identified 77 genes for which there is good evidence of involvement in the development of human cancer.

PMID: 20029424

A census of amplified and overexpressed human cancer genes

Exellent summary of genes overepxpressed in different cancers and appeared in multiple studies. 6 pages, one table, a quick-start guide to observe gene expression peaks in cancer.

http://www.nature.com/nrc/journal/v10/n1/abs/nrc2771.html?lang=en

Nature Reviews Cancer 10, 59-64 (January 2010) | doi:10.1038/nrc2771 

Thomas Santarius¹, Janet Shipley², Daniel Brewer², Michael R. Stratton¹ & Colin S. Cooper  About the authors

Abstract

Integrated genome-wide screens of DNA copy number and gene expression in human cancers have accelerated the rate of discovery of amplified and overexpressed genes. However, the biological importance of most of the genes identified in such studies remains unclear. In this Analysis, we propose a weight-of-evidence based classification system for identifying individual genes in amplified regions that are selected for during tumour development. In a census of the published literature we have identified 77 genes for which there is good evidence of involvement in the development of human cancer.

MicroRNAs

Exellent collection of short letters, articles and reviews about miRNAs. Free access, and everything valuable discovered during 2009 is there.

http://www.nature.com/nature/supplements/collections/micrornas/

Structural variation in the human genome

May not be the latest review, but very good description of types of variations in the genome, methods for their detection, drawbacks and challenges we’re facing now. Figures nicely complement the story.

Nat Rev Genet. 2006 Feb;7(2):85-97.
Structural variation in the human genome.

Feuk L, Carson AR, Scherer SW.

The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada.

The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of what we term ’structural variation’ in the human genome. This comprises microscopic and, more commonly, submicroscopic variants, which include deletions, duplications and large-scale copy-number variants – collectively termed copy-number variants or copy-number polymorphisms – as well as insertions, inversions and translocations. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.

PMID: 16418744

Stem cell bioprocessing: fundamentals and principles

Exellent review about types of stem cells (embryonic, mesenchymal), culturing conditions (including feeder-free), ECM composition and cell adhesion, artificial scaffolds for 3D culture, bioreactors, design of experiments (including Plackett-Burman), analysis and characterization of stem cells. It’s not just about stem cells, but all aspects mentioned above are well summarized and referenced.

J R Soc Interface. 2009 Mar 6;6(32):209-32.

Stem cell bioprocessing: fundamentals and principles.

Placzek MR, Chung IM, Macedo HM, Ismail S, Mortera Blanco T, Lim M, Cha JM, Fauzi I, Kang Y, Yeo DC, Ma CY, Polak JM, Panoskaltsis N, Mantalaris A.

Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.

In recent years, the potential of stem cell research for tissue engineering-based therapies and regenerative medicine clinical applications has become well established. In 2006, Chung pioneered the first entire organ transplant using adult stem cells and a scaffold for clinical evaluation. With this a new milestone was achieved, with seven patients with myelomeningocele receiving stem cell-derived bladder transplants resulting in substantial improvements in their quality of life. While a bladder is a relatively simple organ, the breakthrough highlights the incredible benefits that can be gained from the cross-disciplinary nature of tissue engineering and regenerative medicine (TERM) that encompasses stem cell research and stem cell bioprocessing. Unquestionably, the development of bioprocess technologies for the transfer of the current laboratory-based practice of stem cell tissue culture to the clinic as therapeutics necessitates the application of engineering principles and practices to achieve control, reproducibility, automation, validation and safety of the process and the product. The successful translation will require contributions from fundamental research (from developmental biology to the ‘omics’ technologies and advances in immunology) and from existing industrial practice (biologics), especially on automation, quality assurance and regulation. The timely development, integration and execution of various components will be critical-failures of the past (such as in the commercialization of skin equivalents) on marketing, pricing, production and advertising should not be repeated. This review aims to address the principles required for successful stem cell bioprocessing so that they can be applied deftly to clinical applications.

PMID: 19033137 [PubMed - indexed for MEDLINE]

Use of microRNA sponges to explore tissue-specific microRNA functions in vivo.

Preview of an elegant idea of sequestering miRNAs. Make a gene that will produce sequences complimentary to an miRNA, and it will bind and deactivate an miRNA.

Nat Methods. 2009 Dec;6(12):873-874.

Use of microRNA sponges to explore tissue-specific microRNA functions in vivo.

Cohen SM.

Stephen M. Cohen is in the Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, Singapore.

MicroRNA depletion by sequestration produces flexible hypomorphs that mimic mutants obtained by microRNA gene targeting.

PMID: 19935840

Tools for gene- and protein lists analysis

One approach (algorithm) nicely encompass several tools fitted for different analyses, be in gene- or protein lists, or compounds.

 

KEGGspider PMID: 19094223 KEGG spider is a web-based tool for interpretation of experimentally derived gene lists in order to gain an understanding of metabolism variations at a genomic level. KEGG spider implements a “pathway-free” framework, which overcomes a major bottleneck of exisiting enrichment analyses: it provides global models uniting genes from different metabolic pathways. By analyzing a number of experimentally derived gene lists, we demonstrate that KEGG spider provides deeper insights into metabolism variations in comparison to existing methods. http://mips.helmholtz-muenchen.de/proj/keggspider/ PPI spider PMID: 19405022 PPI spider implements a robust statistical framework for the interpretation of protein lists in the context of a global PPI network. The input list is translated into a network model according to the topology of the PPI network. Our approach takes into account that the input list may have missing proteins and automatically includes in the network model the most relevant proteins that seem to be missing. As output, our procedure provides a model of protein interactions that represent the most probable scenario of how proteins within the list are connected. Statistical significance of the model is computed by a Monte Carlo simulation procedure. http://mips.helmholtz-muenchen.de/proj/ppispider/ PLIPS PMID: 19216535 The ultimate result of a proteomics study is a list of proteins found to be present (or differentially present) at various cell physiological conditions. Normally the results are presented in a publication in one or several tables. The bulk of his type of information remains dispersed in hundreds of proteomics related publications. We have developed a web mining tool which allows collecting this information by searching through full text papers and automatically selecting tables, which report a list of protein identifiers. By searching through major proteomics journals, we have collected approximately 800 independent studies published recently, which reported about 1000 different protein lists. Based on this data, we developed a computational tool PLIPS (Protein Lists Identified in Proteomics Studies). PLIPS accepts as input a list of protein/gene identifiers. Using statistical analyses PLIPS identifies recently published proteomics studies, which report protein lists that significantly intersects with a query list. http://mips.helmholtz-muenchen.de/proj/plips/ ProfCom PMID: 18460543 ProfCom is a web-based tool for the interpretation of genes that were identified to be functionally linked by experiment. http://webclu.bio.wzw.tum.de/profcom/ TICL PMID: 19292876 TICL is a web Tool for automatic Interpretation of Gompound list. The inferred models by TICL represent a set of linked metabolic reactions that unite compounds from the list. TICL also provides a robust statistical treatment of the inferred models. http://mips.helmholtz-muenchen.de/proj/cmp/

.

 

Inferring cellular networks–a review

Exellent review about types of network analysis algorithms, advantages and disadvantages of each. You need to know the notation, but it’s still perfectly conscise review. Figure summarizing features of each analysis – a must!

BMC Bioinformatics. 2007 Sep 27;8 Suppl 6:S5. 

Inferring cellular networks–a review.

Markowetz F, Spang R.

Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany. florian@genomics.princeton.edu

In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most currently used methods can be organized by a few key concepts. The first part of the review deals with conditional independence models including Gaussian graphical models and Bayesian networks. The second part discusses probabilistic and graph-based methods for data from experimental interventions and perturbations.

PMID: 17903286 [PubMed - indexed for MEDLINE]

miRecords: an integrated resource for microRNA-target interactions

At last! Out of many avaliable algorithms for miRNA target prediction comes this tool, integrating the data not only from majority of them, but also experimentally validated data. Great help for anyone doing miRNA studies.

http://miRecords.umn.edu/miRecords

Nucleic Acids Res. 2009 Jan;37(Database issue):D105-10. Epub 2008 Nov 7.  

miRecords: an integrated resource for microRNA-target interactions.

Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T.

Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA.

MicroRNAs (miRNAs) are an important class of small noncoding RNAs capable of regulating other genes’ expression. Much progress has been made in computational target prediction of miRNAs in recent years. More than 10 miRNA target prediction programs have been established, yet, the prediction of animal miRNA targets remains a challenging task. We have developed miRecords, an integrated resource for animal miRNA-target interactions. The Validated Targets component of this resource hosts a large, high-quality manually curated database of experimentally validated miRNA-target interactions with systematic documentation of experimental support for each interaction. The current release of this database includes 1135 records of validated miRNA-target interactions between 301 miRNAs and 902 target genes in seven animal species. The Predicted Targets component of miRecords stores predicted miRNA targets produced by 11 established miRNA target prediction programs. miRecords is expected to serve as a useful resource not only for experimental miRNA researchers, but also for informatics scientists developing the next-generation miRNA target prediction programs. The miRecords is available at http://miRecords.umn.edu/miRecords.

PMID: 18996891 [PubMed - indexed for MEDLINE]

Cooperative action on miRNAs during senescence

miRNA abundance decreases with age. Combined, but not individual, action of four miRNAs responsible for regulating of MKK4 porotein level. Four miRNAs decrease during replicative senescence, and MKK4 protein level increases and inhibits cell proliferation. Elegant proof of principle of close interactions among different genome products.

Sci Signal. 2009 Oct 27;2(94):ra69.  

Increased MKK4 abundance with replicative senescence is linked to the joint reduction of multiple microRNAs.

Marasa BS, Srikantan S, Masuda K, Abdelmohsen K, Kuwano Y, Yang X, Martindale JL, Rinker-Schaeffer CW, Gorospe M.

Laboratory of Cellular and Molecular Biology, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.

MKK4 (mitogen-activated protein kinase kinase 4) is a pivotal upstream activator of c-Jun N-terminal kinase and p38. Here, we report that the abundance of MKK4 increases in senescent human diploid fibroblasts through enhanced translation. We identified four microRNAs (miR-15b, miR-24, miR-25, and miR-141) that target the MKK4 messenger RNA (mRNA); the abundance of these microRNAs decreased during replicative senescence. Individually modulating the amount of each microRNA did not modify MKK4 abundance, but their concomitant overexpression decreased and their joint reduction increased MKK4 abundance. Reporter analyses indicated that these microRNAs acted through the MKK4 5′ and 3′ untranslated regions. Elevated MKK4 abundance inhibited cell proliferation and increased the phosphorylation and activity of p38 and PRAK (p38-regulated/activated protein kinase). Thus, multiple microRNAs acting on a single target, the MKK4 mRNA, collectively influence MKK4 abundance during replicative senescence.

PMID: 19861690 [PubMed - in process]

 

Cancer resistance

Exellent work on cancer resistance in a small rodent, naked mole-rat. Indeed, this animal is outstanding from its lifespan (28 years) to its apparent invincibility to cancer. That’s extremely useful property, so, as authors said,

Cancer-prone mouse models are valuable for development of cancer treatments. However, to find ways to prevent cancer before it occurs it would be extremely useful to study cancer resistant models such as the naked mole-rat.

The New York Times: The Life Span of a Rodent May Aid Human Health

 

Proc Natl Acad Sci U S A. 2009 Oct 26. [Epub ahead of print] 

Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat.

Seluanov A, Hine C, Azpurua J, Feigenson M, Bozzella M, Mao Z, Catania KC, Gorbunova V.

Department of Biology, University of Rochester, Rochester, NY 14627.

The naked mole-rat is the longest living rodent with a maximum lifespan exceeding 28 years. In addition to its longevity, naked mole-rats have an extraordinary resistance to cancer as tumors have never been observed in these rodents. Furthermore, we show that a combination of activated Ras and SV40 LT fails to induce robust anchorage-independent growth in naked mole-rat cells, while it readily transforms mouse fibroblasts. The mechanisms responsible for the cancer resistance of naked mole-rats were unknown. Here we show that naked mole-rat fibroblasts display hypersensitivity to contact inhibition, a phenomenon we termed “early contact inhibition.” Contact inhibition is a key anticancer mechanism that arrests cell division when cells reach a high density. In cell culture, naked mole-rat fibroblasts arrest at a much lower density than those from a mouse. We demonstrate that early contact inhibition requires the activity of p53 and pRb tumor suppressor pathways. Inactivation of both p53 and pRb attenuates early contact inhibition. Contact inhibition in human and mouse is triggered by the induction of p27(Kip1). In contrast, early contact inhibition in naked mole-rat is associated with the induction of p16(Ink4a). Furthermore, we show that the roles of p16(Ink4a) and p27(Kip1) in the control of contact inhibition became temporally separated in this species: the early contact inhibition is controlled by p16(Ink4a), and regular contact inhibition is controlled by p27(Kip1). We propose that the additional layer of protection conferred by two-tiered contact inhibition contributes to the remarkable tumor resistance of the naked mole-rat.

PMID: 19858485

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

Very troughout review about how 95% of genes are alternatively spliced. Splicing and spliceosome assembly figure, description of participating proteins. Good figures help to comprehend the current picture.

Nat Rev Mol Cell Biol. 2009 Nov;10(11):741-54. Epub 2009 Sep 23.  

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

Chen M, Manley JL.

Department of Biological Sciences, Columbia University, New York, New York 10027, USA.

Alternative splicing of mRNA precursors provides an important means of genetic control and is a crucial step in the expression of most genes. Alternative splicing markedly affects human development, and its misregulation underlies many human diseases. Although the mechanisms of alternative splicing have been studied extensively, until the past few years we had not begun to realize fully the diversity and complexity of alternative splicing regulation by an intricate protein-RNA network. Great progress has been made by studying individual transcripts and through genome-wide approaches, which together provide a better picture of the mechanistic regulation of alternative pre-mRNA splicing.

PMID: 19773805

TGF-beta helps cells fly solo

Preview to a paper describing the role of TGFB in cell motility. Increased TGFB signaling makes cells more self-standing and self-migratory. Cells that have suppressed TGFB signalling migrate collectively. Features of single and collective cell motility summarized in Table 1, as well as in Figure 1.

Nat Cell Biol. 2009 Nov;11(11):1281-1284. Epub 2009 Oct 18.

Matise LA, Pickup MW, Moses HL.

Lauren Matise, Michael Pickup and Harold Moses are at the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232-6838, USA. hal.moses@vanderbilt.edu.

Intravital imaging demonstrates that TGF-beta signalling regulates the mode of cancer cell motility. Cells with active TGF-beta signalling migrate as single cells and are capable of hematogenous and lymphatic spread, whereas cells lacking TGF-beta signalling invade lymphatics collectively.

PMID: 19838176

Comparative assessment of siRNA and shRNA off target effects: what is slowing clinical development.

Short RNAs are good for silencing, but what do they silence? Here’s an idea about multiple targets of short RNAs. shRNA produce less off-target effect. But still one should watch out what exactly is affected.

Cancer Gene Ther. 2009 Nov;16(11):807-9. Epub 2009 Aug 28. Links

Rao DD, Senzer N, Cleary MA, Nemunaitis J.

Gradalis Inc., Dallas, TX, USA.

This review considers comparisons of the off-target effects of siRNA to shRNA and their potential impact on the efficacy and toxicity of RNAi based therapeutics.

PMID: 19713999

Rethinking how DNA methylation patterns are maintained

Methylation regulates which genes are transcribed, when, and how fast. This mini-review tells about  methylation patterns of the DNA, how it is maintained and transferred to daughter cells during replications, and how responsible enzymes interact. But still we don’t know how methylation patterns are created at the first place.

Nat Rev Genet. 2009 Nov;10(11):805-11. Epub 2009 Sep 30. Links

Jones PA, Liang G.

Peter A. Jones and Gangning Liang are at the Department of Urology, Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-9181, USA. jones_p@ccnt.usc.edu

DNA methylation patterns are set up early in mammalian development and are then copied during the division of somatic cells. A long-established model for the maintenance of these patterns explains some, but not all, of the data that are now available. We propose a new model that suggests that the maintenance of DNA methylation relies not only on the recognition of hemimethylated DNA by DNA methyltransferase 1 (DNMT1) but also on the localization of the DNMT3A and DNMT3B enzymes to specific chromatin regions that contain methylated DNA.

PMID: 19789556

The pervasive and interleaved transcriptome

Exellent poster about complex nature of transcription. Start site organization, bidirectional transcription, miRNA transcription from introns – just to name a few features. Zoom in and read.

The diversity of types and functions of RNAs that transcriptomic studies has now uncovered points to a more elegant, complex and richer reservoir of genetic information being stored and processed from eukaryotic genomes than could previously have been imagined.

The first 30 years of p53: growing ever more complex.

Exellent summary of how p53 was discovered and its wide roles unfolded. This is a perfect example how complex may be a single gene, which gives not less than 9 alternatively spliced isoforms. Firstly discoveres as an oncogene, than p53 become tumor suppressor, and implications in nearly all biological processes followed. Trerapeutic approaches of targeting p53 and its co-players. And challenges that are just beginning to unfold when interactions of p53 with other proteins come to light.

Nat Rev Cancer. 2009 Oct;9(10):749-58. Links

Levine AJ, Oren M.

Arnold J. Levine is at the Institute for Advanced Study, School of Natural Sciences, Einstein Drive, Princeton, New Jersey 08540, USA. alevine@ias.edu

Thirty years ago p53 was discovered as a cellular partner of simian virus 40 large T-antigen, the oncoprotein of this tumour virus. The first decade of p53 research saw the cloning of p53 DNA and the realization that p53 is not an oncogene but a tumour suppressor that is very frequently mutated in human cancer. In the second decade of research, the function of p53 was uncovered: it is a transcription factor induced by stress, which can promote cell cycle arrest, apoptosis and senescence. In the third decade after its discovery new functions of this protein were revealed, including the regulation of metabolic pathways and cytokines that are required for embryo implantation. The fourth decade of research may see new p53-based drugs to treat cancer. What is next is anybody’s guess.

PMID: 19776744

THE YEAST TWO-HYBRID ASSAY

Exellent description of the technique. For more details Wikipedia may help, but this technical essay is a perfect place to start.