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In this section, the hottest scientific articles and commentaries from scientists will be displayed monthly:
Bridging academia to the private sector: it is always a challenge
by Anja Gaugel, Ph.D.
BIOforum Europe Editor
GIT VERLAG GmbH & Co. KG - A Wiley Company, Darmstadt, Germany
Scientific journals, webcasts, podcasts, personal websites; what is this all about? In today’s world, it is no longer good enough for a scientist to be good in the basic research field. It is also imperative for the scientist to be effective in presenting their work to the larger community outside its field. It is necessary for researchers to translate their findings full of subject-specific terminology and jargon into well-comprehensible words for two main reasons. Firstly, in inter-disciplinary laboratories, Biologists, Chemists and Physicists - each of them an expert in its own field, need to collaborate with each other to explore different possible angles at challenging problems. Since these people work so closely together, they need to be able to communicate their expertise to each other and also have to take a look over the edge of their own work. A chemist may have to understand the basics of cloning, sequencing or a microarray; theories that are already of main knowledge to a biologist. Secondly, if researchers want to bring their findings further down the pipeline, they will need to be able to explain their work to the industry in order to get the attention of business people and companies. Our journal BIOforum Europe does exactly that; it is interdisciplinary and works to connect science and industry. Our authors take up this challenge every day, to clarify and present their research findings in the biotechnology and pharmaceutical sectors to a broader community localized in industry and in laboratories of universities.
Link of interest:
Epigenetics: linking environment to phenotype
by Miriam G. Jasiulionis, Ph.D.
1. Kim JK, Samaranayake M, Pradhan S. Epigenetic mechanisms in mammals. Cell. Mol. Life Sci.66: 596 - 612, 2009.
2. Delcuve GP, Rastegar M, Davie JR. Epigenetic Control. J. Cell. Phisiol. 219: 243–250, 2009.
3. Jirtle RL, Skinner MK. Environmental epigenomics and disease susceptibility. Nat. Rev. Genet. 8: 253-262, 2007.
4.Hatchwell E, Greally JM. The potential role of epigenomic dysregulation in complex human disease. Trends Genet. 23(11):588-595, 2007.
5.Cortez CC, Jones PA. Chromatin, cancer and drug therapies. Mutat. Res. 647(1-2):44-51, 2008.
Links of interest:
Non-coding RNAs - changing paradigms in genomics
by Fabricio F. Costa, Ph.D.
Genomic Enterprise CEO and Founder
The development of new technologies in genomics has been allowing deeper analyses and better coverage of the genetic information expressed in specific cell types. Several genome-wide studies have recently shown that eukaryotic genomes have pervasive transcription and produce many thousands of regulatory non-protein-coding RNAs (ncRNAs), which include microRNAs, small interfering RNAs, PIWI-interacting RNAs and various other classes of long ncRNAs (1). ncRNAs have a variety of different functions and they are defined as transcripts or “genes” with a very low protein-coding potential (2). It has been suggested that they don't produce a protein product but a few exceptions have been described of RNAs that can produce small peptides and also function as an RNA molecule (3). Importantly, these RNAs have critical roles as transcriptional and post-transcriptional regulators and as guides of chromatin-modifying complexes in epigenetic mechanisms in eukaryotes (4). It is becoming clear that eukaryotic genes are divided into two distinct categories of transcripts: protein-coding and non-coding. Moreover, different studies have been showing that the proportion of non-coding transcripts (~70-90%) is much higher than that of protein-coding (~3%). It is still too soon to affirm that all non-coding transcripts produced by eukaryotic genomes are functional, however these new discoveries are clearly changing the "status quo" in genomic science. For example, ncRNAs have been associated to different diseases including cancer suggesting that these new players might be more important than previously thought (5). The association of ncRNAs with diseases is opening new possibilities for drug development and biomarker identification by the academic and private sectors (5). One company, named cuRNA, was recently launched in Florida with the objective of utilizing ncRNAs to develop new therapies for diseases that have no current cure. cuRNA is a promising company that has licensed novel technologies based on the therapeutic potential of ncRNAs. Following this trend, big pharmaceutical and biotechnology companies are now paying more attention to this field since ncRNAs have become more a rule than an exception in genomics. Thus, these new discoveries clearly show the importance of rethinking concepts and ideas in science, especially in a young and constant evolving field such as of genome biology.
1. Wilhelm BT, et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature. 453:1239-1243, 2008.
2. Costa FF. Non-coding RNAs: new players in eukaryotic biology. Gene. 357 (2): 83-94, 2005.
3. Chooniedass-Kothari S, et al. The steroid receptor RNA activator is the first functional RNA encoding a protein. FEBS Lett. 566 (1-3): 43-47, 2004.
4. Costa FF. Non-coding RNAs, epigenetics and complexity. Gene. 410: 9-17, 2008.
5. Costa FF. Non-coding RNAs and new opportunities for the private sector. Drug Discov Today. 14 (9-10): 446-452, 2009.
Links of interest:
Electronic Health Record (EHR) - a big step towards Personalized Medicine
by Remi Lewandowski, Ph.D.
Children's Memorial Hospital
At the beginning of this year, President Barack Obama announced that every American needs to get an Electronic Health Record (EHR) by 2014. This goal is part of a broader action to stimulate the development of Health Information Technology. The Obama administration and the Congress made available $19 billions of funds to fulfill Clinical Health Act, HITECH Act and sections of American Recovery and Reinvestment Act (1). Currently, EHR is implemented and utilized by 11 percent of hospitals (2) and less than 5 percent of physicians (3) in the United States. Progress in Health Information Technology is directly associated with the growth of Personalized Medicine - briefly described as “the right treatment for the right person at the right time” (4). Physicians always applied personalized medicine in order to set the right dosage of medications, switch drugs to more efficient ones and utilize diagnostic tests. This traditional approach of personalized medicine is based on illness manifestation and patient’s response to therapy. It is well known that patients can respond differently to the same medicine - for example around 75 percent of the cancer patients respond differently to drugs (5). The novel approach of personalized medicine is focused on genetic, genomic and molecular information. Genetic and other molecular tests can predict many diseases, including several types of cancer. The correct use of those tests will allow the choice of the optimal therapy and avoiding trial periods of patient response to drugs. For example, women with HER2-positive breast cancer do not respond well to standard therapies (6). Women with BRCA1 and BRCA2 genetic mutation have approximately 60 percent of chances to develop breast cancer compared to 12 percent in the general female population (7). Patients with identified BRCA1 or BRCA2 mutation can be more preventive and vigilant. Genetic screening also allows the identification of subtypes of Acute Lymphoblastic Leukemia and indicate optimal treatment (8). Testing for genetic variations in the genome would also prevent patients from having adverse drug reaction due to variation in genes coding for enzymes (e.g. CYP450) (9). This kind of genetic information stored in medical databases according to EHR would be a great opportunity for data-mining to find direct associations between diseases, genes and therapies. This is an important time for academic, governmental and non-profit organizations to conduct this type of research using data stored in EHRs. The implementation of EHR in the US and the application of personalized medicine will improve the quality of healthcare, reduce the time of cure for diseases and decrease costs associated with medical care.
1. Personalized Medicine Coalition. The Case for Personalized Medicine, 2009.
3. Hsiao CJ, et al. Preliminary estimates of electronic medical records use by office-based physicians: United States. Health E-Stat. National Center for Health Statistics, 2008.
5. Spear BB, Heath-Chiozzi M, Huff J. Clinical application of pharmacogenetics. Trends in Molecular Medicine, Vol.7 (5): 201-204, 2001.
6. Menard S, et al. Biologic and therapeutic role of HER2 in cancer. Oncogene. 22: 6570-6578, 2003.
8. Pui CH, Evans WE. Treatment of acute lymphoblastic leukemia. N Engl J Med. 354:166-178, 2006.
9. Phillips KA, et al. Potential role of pharmacogenomics in reducing adverse drug reactions: a systematic review. JAMA. 286: 2270-2279, 2001.
Epigenetics and breast cancer
by Giseli Klassen, Ph.D.
Federal University of Parana (UFPR), Curitiba, Brazil
In 2009, almost 200,000 new cases of breast cancer will be diagnosed in the United States (1). In the same year, 40,170 women are estimated to die of this disease (1). The main focus of scientific research lately has been the understanding of mechanisms regulating tumor progression. Epigenetics is a field that studies changes in gene expression. These changes can lead to the activation of oncogenes and the inactivation of tumor suppressor genes, which are genes implicated in the tumorigenesis process. Epigenetics could be divided in two separated mechanisms: DNA methylation and histone modifications. Loss of DNA methylation or hypomethylation at specific regions of the DNA was one the first epigenetic abnormalities identified in cancer cells (2). These regions become hypomethylated in tumors and nearby genes can be activated. Examples of genes that are affected by hypomethylation include oncogenes such as HRAS (3). The first link between hypermethylation and tumor suppressor genes was made for RB, which is implicated in retinoblastoma (4). Recently, several reports have shown the role of epigenetic changes in breast tumor initiation and progression. Importantly, epigenetic modifications can potentially be reversed with specific drugs. ER-positive cancers can be treated with anti-estrogenic drugs, like Tamoxifen and Fluvestrant, however ER hypermethylated-negative cells are no longer responsive to estrogen, therefore, anti-estrogenic drugs have no effect (5). A therapy that could restore gene expression of estrogen receptors in breast cancer could reestablish cancer cell growth regulation through estrogen. A large number of drugs such as DNA methyltransferase inhibitors have begun to be tested in other types of tumors and could potentially be used for breast cancer. Examples of epigenetic drug treatments currently in clinical use include: 5-Azacytide, Procainamide and Hydralazine. However, these therapies alone may not be enough to reverse ER promoter hypermethylation and more investigation about the mechanism of action of these drugs are needed. Criteria for diagnosis and characterization of breast cancer status currently include abnormal biopsy, tumor size, histological grade, hormone receptor status, and HER2/Neu amplification. Future strategies for breast cancer diagnosis could incorporate the use of DNA methylation as a biomarker for early detection and prevention. Our group has already shown that epigenetic modifications are able to classify tumors that are very similar histologically but have different behavior (6). Some companies have already started to develop epigenetic tests for early detection and for prognosis in different types of cancer, including breast tumors. Taken together, these approaches could be used some day as a powerful tool in early detection and treatment for this deadly cancer.
1. Jemal A, et al. Cancer statistics. CA Cancer J Clin. 59: 225-249, 2009.
2.Feinberg AP and Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature. 301: 89-92, 1983.
3.Feinberg AP and Vogelstein B. Hypomethylation of ras oncogenes in primary human cancers.Biochem Biophys Res Commun, 111: 47-54, 1983.
4.Greger V, et al. Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma. Hum Genet. 83:155-158, 1989.
5.Giacinti L, et al. Epigenetic information and estrogen receptor alpha expression in breast cancer. Oncologist. 11: 1-8, 2006.
6. Seniski GG, et al. ADAM33 gene silencing by promoter hypermethylation as a molecular marker in breast invasive lobular carcinoma. BMC Cancer. 9: 80, 2009.
The Bioinformatics Challenges of the Next Generation Sequencers
by Steven Davis, M.Sc.
CEO - Bio:Neos, Inc.
The creation of the field of bioinformatics was principally due to the discovery of the Sanger sequencing method that resulted in abundant sources of genomic data; managing and analyzing this amount of data quickly became impossible without advanced computational techniques. Recently, new technologies have emerged that promise to further transform the fields of bioinformatics and genomics research. Second generation sequencing technologies are currently generating enormous amounts of data (1) and third generation technologies will increase this data throughput even farther (2). The ability to rapidly generate sequence data at speeds 100 to 1000 times previously possible for costs 10 to 100 times cheaper has allowed even the smallest research groups to generate enormous amounts of genomic data. This has enabled more of the research community to perform assays that were previously cost or time prohibitive, especially many types of intra-species assays. Fortunately, advances in computational hardware and storage are meeting the requirements of these new sequencing machines (1). Additionally, these new sequencing technologies have created a wave of new computational analysis techniques (3). especially in the areas of alignment and assembly. However, there is still much work to be done. The inception of the field of bioinformatics originally revolved around not only the need for advanced data analysis techniques, but for efficient data management techniques as well. The increase in data throughput brought on by the new sequencers has begun to force advances in data analysis algorithms, but data management techniques have remained relatively stagnant. Some projects, such as Genologics, GenomeQuest, or WikiLIMS, have introduced support for next generation sequencing data to existing tools or created entirely new data management systems specifically for next-gen data, although many of these projects do not meet the needs of most research groups in either functionality or usability. For example, many tools organize sequence data by runs, with only one human defined identifier per run. For the researchers who want to look at a single read or a small number of reads, they must deal with cryptic computer generated identifiers. In addition, these tools do not provide comprehensive quality assurance features tailored specifically towards next-gen data. Despite the reliability claims of the manufacturers of these sequencers, in practice, errors can be seen frequently especially for certain genomic regions. Additionally, failures in these machines manifest differently then they would with traditional Sanger sequencers. Improved error recognition and handling could be achieved with improved software. In all, these new sequencing technologies have begun an exciting era for genomics research, but the computational requirements needed to handle the enormous amount of data generated by these technologies are intense. The current advances in data analysis are a step in the right direction, but to truly utilize this data to the full extent, new software advances are needed especially in the areas of data management and quality control.
1. Van Etten, William. Managing Data from Next-Gen Sequencing.Genetic Engineering & Biotechnology News. Vol. 28, No. 8, 2008.
2. Check, Heyden E. Genome Sequencing: The Third Generation. Nature.457(7231):768-769, 2009.
Links of interest:
Cracking the Noncoding Fraction of the Human Genome
by Marcelo A. Nobrega, MD, Ph.D.
Dept. of Human Genetics, University of Chicago
With the sequencing of the human and other mammalian genomes, annotating the approximately 98% of these genomes that do not encode for proteins has become one of the main challenges in genomics. It quickly became apparent that at least a sizable fraction of these noncoding sequences have biological functions, since at least 5% of the human and mouse genomes seem to be evolving under purifying selection. This is most likely a gross underestimate of the amount of functional sequences in the human genome, given that many functional sequences are not evolutionarily conserved or shared among distant phylogenies (1). Recent studies have also demonstrated that noncoding sequences serve as the substrate for evolutionary innovation (2) as well as harbor variations that confer risk to a host of common human diseases, evidenced by a number of Genome-wide Association Studies implicating mapping disease loci to non-coding sequences (3). Therefore, identifying functional non-coding sequences and characterizing their biological roles has become one of the main priorities in genomics, a concerted effort spearheaded by the NIH’s ENCODE Consortium.
One of the main functions associated with these noncoding sequences is to serve as regulators of where, when, and how much each gene in the genome is activated. Ultimately, it is the orchestration of which genes are on and which are off which determine the uniqueness or relatedness among cells, again underscoring the critical importance of these noncoding regulatory elements in the human genome. We now know that these regulatory elements can be far away from the genes they regulate (4). Several technologies and strategies have been recently devised to facilitate the identification of these distant elements. We are gradually more able to scan vast amounts of otherwise anonymous sequences (the 98% fraction of noncoding genome) and predict small elements within these sequences that are likely functional. These strategies are now being used to identify noncoding mutations that increase the risk to various diseases, uncovering novel pathways that may potentially become novel therapeutic targets (5). Annotating the noncoding fraction of the genome will also lead to a better understanding of the genetic circuitry defining cellular identity. This knowledge can be used, in turn, to reprogram cells, with important implications to regenerative medicine.
1.Lunyak VV, et al. Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science. 317(5835): 248-251, 2007.
2.Miller CT, Beleza S, Pollen AA, Schluter D, Kittles RA, Shriver MD, Kingsley DM. cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans. Cell.131(6):1179-1189, 2007.
3.Haiman CA, et al. Multiple regions within 8q24 independently affect risk for prostate cancer.Nat Genet. 39(5): 638-644, 2007.
4.Nobrega MA, Ovcharenko I, Afzal V, Rubin EM. Scanning human gene deserts for long-range enhancers. Science. 302(5644):413, 2003.
Emison ES, et al. A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk. Nature. 14;434 (7035): 857-863, 2005.
Links of interest:
Tumor exosomes as blood based biomarkers
Exosomes are 30-100 nm in diameter and shed from many different cell types under both normal and pathological conditions. They can form through inward budding of endosomal membranes giving rise to intracellular multivesicular bodies that later fuse with the plasma membrane releasing the exosomes to the exterior (1). In addition, they can be directly released from cells, for example, the Jurkat T lymphocyte-derived cell line sheds exosomes by outward budding of the plasma membrane. The content of exosomes and their biological function varies depending on the cell of origin. It was recently shown that exosomes contain both mRNAs and microRNAs and that the RNA can be transferred to surrounding cells and be translated into functional proteins (2,3,4). It has been shown that exosomes released from tumor cells can suppress the immune response, stimulate angiogenesis and accelerate tumor growth (4,5,6,7). The effects are likely due to a combination of the transferred proteins and the nucleic acid in the exosomes.
The exosomes are clearly beneficial for the tumor, but can also be used by the physician to tailor treatment against the tumor. Since the tumor exosomes are released into the blood and contain the genetic information from the tumor, the exosomes can be used to assess the mutational and transcriptional profile of the tumor through a blood sample (4). This new platform facilitates mutational profiling over time which is not practical with biopsies. Tumors often contain mutations that are linked to treatment response (i.e. KRAS and EGFR mutations in colon and lung cancer) and it is becoming increasingly important to profile the individual tumors before initiation of treatment. Exosome derived RNA has the potential to improve the diagnosis of cancers and may become an important addition to personalized medicine.
1. Thery, C., Zitvogel, L. & Amigorena, S. Exosomes: composition, biogenesis and function. Nature Rev. Immunol. 2, 569–579, 2002.
2. Valadi, H., et al. Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nature Cell Biol. 9, 654–659, 2007.
3. Baj-Krzyworzeka, M., et al. Tumour-derived microvesicles carry several surface determinants and mRNA of tumour cells and transfer some of these determinants to monocytes. Cancer Immunol. Immunother. 55, 808–818, 2006.
4. Skog, J., et al. Glioblastoma microvesicles transport RNA and protein that promote tumor growth and provide diagnostic biomarkers.Nature Cell Biology.1470-1476, 2008.
5. Clayton, A., Mitchell, J. P., Court, J., Mason, M. D. & Tabi, Z. Human tumor-derived exosomes selectively impair lymphocyte responses to interleukin-2. Cancer Res. 67, 7458–7466, 2007.
6. Chaput, N., Taieb, J., Andre, F. & Zitvogel, L. The potential of exosomes in immunotherapy. Exp. Opin. Biol. Ther. 5, 737–747, 2005.
7. Wieckowski, E. & Whiteside, T. L. Human tumor-derived vs dendritic cell-derived exosomes have distinct biologic roles and molecular profiles. Immunol. Res. 36, 247–254, 2006.
Special article by the well-known geneticist in South America, Dr Sergio D. Pena:
An anthropophagical model for science and technology in developing countries
by Sergio D. Pena, MD, Ph.D., FRCP (C)
Full Professor, Biochemistry and Immunology Department
Federal University of Minas Gerais, Belo Horizonte, Brazil
GENE Founder - Nucleo de Genetica Medica
Brazil and many other developing nations are in a conundrum. Knowing well that the control of technological information will be the foremost criterion in the competitive arena of the 21st century, they have to find means to obtain such technology. Should they continue importing from developed countries expensive and often outdated techniques and processes? Or should they innovate with endogenous, original technology?
In the mid 16th Century several books appeared in Europe divulging the legend that Brazilian cannibals ate their brave enemies in the hope of assimilating their good qualities. Inspired by these stories, the Brazilian poet Oswald de Andrade (1890-1954) published in 1928 the Anthropophagic Manifesto (1). Basically, the manifesto proposed that Brazilians should devour the foreign culture and ideas, subjecting them to a critical digestion and transforming them into a rich, creative and new artistic production.
Applied to science and technology, the spirit of the Anthropophagic Manifesto goes beyond merely denouncing the technical colonialism which afflicts developing countries - it offers a way out. The proposed solution is anthropophagy: eating and metabolizing foreign scientific knowledge in order to create a new brand of tropical technology. Thus, let us open our frontiers, let us send our students for training abroad and let us equip our laboratories with the best equipment available. We should thus ingest and digest the best science that the developed world has to offer.
But at the same time let us prioritize our own technologies.Let us create what we veritably need, instead of importing technical “black boxes” under the guise of “technology transfer”.The great Brazilian anthropologist Gilberto Freyre (1900-1987) said that "Brazilian problems need Brazilian solutions". Maybe today, in the globalized world of the 21st Century, such isolationist prescription is no longer possible. However, we should keep his words in mind and create our own technology whenever possible!
Links of interest:
Alternative splicing, proteome diversity and diseases
by Fabio Passetti, Ph.D.
Head of the Laboratory of Bioinformatics and Computational Biology
National Cancer Institute (INCA), RJ - Brazil
The development and commercialization of new technologies is allowing the elucidation of important molecular mechanisms in normal and pathological states. Technologies such as DNA microarrays and second generation DNA sequencers is facilitating our understanding of the impact of alternative splicing in proteome diversity. In that regard, recent studies were able to map that 86% of known human genes produce at least one alternative mRNA showing that our transcriptome (all the genes transcribed by a genome) is more complex than anticipated (1). These findings have a direct impact in proteome diversity, since most of the alternative splicing events can occur within protein-coding regions of mRNAs. The impact of alternative splicing in cancer has been discussed in studies of well known cancer-related genes. For example, the p53 protein is not the only product of translation of the TP53 human gene, since at least 10 splice variants with different functions have already been described (2). Another important cancer-related gene is the vascular endothelial growth factor A (VEGF-A). VEGF-A is an important gene target for cancer treatment since it was directly associated to angiogenesis and metastasis. However, new data about splice variants of VEGF-A have changed the way we understand and develop innovative approaches for better cancer treatments (3). Since alternative splicing can directly affect the cancer proteome, it could be assumed that the resistance to chemotherapy can be related to these events (4). Imatinib mesylate (Gleevec) is a common drug used to treat chronic myelogenous leukemia (CML) patients having the BCR-ABL fused gene. However, a BCR-ABL alternative splice variant was found in some patients who have developed resistance to Imatinib treatment. In order to study the molecular mechanism of Gleevec resistance in these patients a 3D protein model was constructed (5) and new approaches need to be developed to complement the current treatment to CML. In all of the above mentioned cases, extra work will be needed in order to understand the role of alternative splicing in the mechanisms of acquired drug resistance and its importance in treatment and management of diseases.
1. Wang ET, et al. Alternative isoform regulation in human tissue transcriptomes. Nature. 456(7221): 470-6, 2008.
2. Marcel V, Hainaut P. p53 - isoforms - a conspiracy to kidnap p53 tumor suppressor activity? Cell Mol Life Sci. 66(3): 391-406, 2009.
3. Harper SJ, Bates DO. VEGF-A splicing: the key to anti-angiogenic therapeutics? Nat Rev Cancer. 8(11): 880-7, 2008.
4. Passetti F, Ferreira CG, Costa FF. The impact of microRNAs and alternative splicing in pharmacogenomics. Pharmacogenomics J. 9(1): 1-13, 2009.
5. Lee TS, et al. BCR-ABL alternative splicing as a common mechanism for imatinib resistance: evidence from molecular dynamics simulations. Mol Cancer Ther. 7(12): 3834-41, 2008.
Links of interest:
Mobile elements and brain complexity
by Alysson R. Muotri, Ph.D.
Assistant Professor, UCSD
The complexity of the human brain, with thousands of neuronal types, permits the development of sophisticated behavior, such as language, tool use, self-awareness, symbolic thought, cultural learning and consciousness. Understanding what produces neuronal diversification during brain development is a fascinating subject in neuroscience. Brain formation is an incredibly wasteful process and natural selection likely decides cell life or death. In this competition, variation and selection sculpt each brain, creating individuality. But what exactly is the source of variation in those unique neurons? Protein-coding genes appeared to be an answer until the sequencing of the human genome showed that "genes" represent less than 2% of our genome. There is simply not enough genetic information to give rise to all neuronal types in the brain. Variation must be generated elsewhere. The lack of obvious function for non-coding genetic sequences inspired the concept of junk DNA, suggesting that these sequences are merely evolutionary remnants. This "junk" includes mobile elements, thought to be intracellular parasites (1). Mobile elements multiply by a copy-and-paste mechanism, inserting copies in new genomic locations, occasionally changing the expression of nearby genes (1). There are several examples of mobile elements shaping the genome during evolution, but their somatic effects have been overlooked; after all, selfish elements moving outside germ cells miss the next generation. Only a few insertions of mobile elements cause human diseases, such as cancer, as a consequence of a somatic dysfunction. A lot of excitement came when we first showed that a human L1 element was active during stem cell differentiation, leading to neuronal mosaicism in an individual brain (2,3). The discovery that L1 elements can impact neuronal genomes challenges the dogma that neurons are genetically homogeneous. L1 elements can change the genetic information in single neurons, allowing neuronal networks to develop in distinct different ways. Such activity expands the number of cell types that can be produced from a given genetic pool. This variety and flexibility may contribute to the uniqueness of individual brains, observed even between genetically identical twins. The confirmation that this hypothesis is correct will transform our understanding of brain development, in a similar way to the finding of V (D) J recombination in the immune system. Both are regulated, tissue-specific somatic genetic variations that exist to adapt the individual to the ever-changing environment (4). The study of retroelements in the nervous system may lead to new and unexplored possibilities for therapeutic interventions for neuropsychiatric diseases.
1. Muotri, A. R., Marchetto, M. C. N., Coufal, N. & Gage, F. H. The necessary junk - new functions for transposable elements. Hum Mol Genet. 16, 159-67, 2007.
2. Muotri, A. R., Chu, V. T., Marchetto, M. C. N., Deng, W., Moran, J. V. & Gage, F. H. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition.Nature. 435, 903-10, 2005.
3. Muotri, A. R. & Gage, F. H. Generation of neuronal variability and complexity. Nature. 441, 1087-93, 2006.
4. Muotri, A. R., Zhao, C., Marchetto, M. C. N. & Gage, F. H. Environmental influence on L1 retrotransposons in the adult hippocampus. Hippocampus (accepted, 2009).
Links of interest:
Faroe Islands - the First Nationwide Genome Project?
by Bogi Eliasen, MsC in Political Sciences
Bitland Consulting Group
The Faroe Islands are known in the scientific community for its big potential in genetic research. This tiny country is located in the middle of the North Atlantic Ocean between Scotland, Norway and Iceland. It has a population of around 50.000 and it is seen as one of the most isolated populations for genetic research based on the population homogeneity and a good centralized health system with data storage. A powerful way to identify genes associated to diseases are to find them in small populations, where the variation is not too big and the ancestors can be traced. One of these populations is the Faroese. The islands are isolated in the middle of North Atlantic and that qualifies them as a good research source as the interaction with foreigners has been limited. The Faroes also have the benefit of a good parish register, where all births and weddings have been registered thus providing a good structure to track back in time all genetic data. Some research projects are already in progress and in 2005 the Genetic Resource Center of the Faroe Islands was established facilitating more practical and legal frames for genetic projects to be implemented. The Faroe Islands have a very good historic record of genealogy and centralized diagnostic health information for the past 100 years. In addition to collecting fresh tissue samples from subjects enrolled in specific projects, there are archival tissues available from an estimated 25,000 Faroese in the form of Guthrie cards and 200.000 samples embedded in paraffin blocks from an estimated 30,000 people and 12.000 cryopreserved samples. Numerous genetic projects are based on Faroese material, and to name a few, panic anxiety, studies on multiple sclerosis, schizophrenia, bipolar diseases and metabolism.The Human Genome Project was a milestone. An ongoing project is the 1000 Genome Project which will look deeper into human genetic variation.The next milestones will be to sequence genomes on a whole nation. The Faroe Islands might just be the perfect place for such a project. The distinct nature of the Faroe Islands being isolated in the North Atlantic Ocean and having stored data from all populations will be useful for a Nationwide Genome Project. With just around 50.000 people and with the cost of DNA sequencing falling very fast, it could be possible to start a Nationwide Genome Project in about three years and this could be one of the first steps that will reveal the benefits of genetic knowledge of a whole nation.
Links of interest:
Human genomic ancestry, genealogy, history and cultural identity
by Fabricio R. Santos, Ph.D.
Federal University of Minas Gerais
Belo Horizonte, Brazil
The sequencing of the human genome allowed the development of new tools for assessing the past of our species, Homo sapiens. The genealogical path of humanity is a current theme of research for the history-tellers who use DNA. In the recent past, only data from archaeology, palaeoanthropology, cultural anthropology, etc could be used to investigate the ancestral roots of human populations. Now, genetics nourished by the boom of genomics is bringing a new view of the human past revealed by the DNA inherited from our ancestors (1). At the individual perspective, many genealogical companies are currently offering DNA testing service that is promising to survey your private genomic ancestry to establish hidden links with your direct ancestors. However, this service can only be provided because several bioanthropologists and geneticists have studied thousands of individuals from indigenous populations worldwide. Indigenous, in this case, mean living populations who represent native groups from a particular place in the world, descendants of natives who were also living in that same place at least 500 years ago. This new discipline, the historical genetics, aims to reveal all migration paths of ancestors who colonized all corners of the continents before the large and well documented transoceanic migrations starting in the end of the XV century.Several approaches have been used to depict the genealogical history of humanity, some describing lineages of ancestry inherited directly from deep ancestors (2), others trusting in admixture studies to survey the apportionment of genomic sequences inherited from all possible ancestors (3). This information, as for every science, is subjected to relative uncertainties, but anyway provides many factual clues about the human past. For example, genetic studies of paternal (Y chromosome) and maternal (mitochondrial DNA) lineages have clearly pointed out to a genealogical origin of Native Americans coming from the Siberian heartland, between 15,000 and 21,000 years ago (4). The migration path through the Bering Strait is not a doubt, neither the Asian origin of the migrants, but new studies are needed to resolve the date of the entry into Americas, as well as to map the routes taken by the first migrants to reach South America (5). Thus, although genetics have also contributed to the history of many ancestral migrations, other studies are requested to fulfill details of this World Heritage, the history of humanity. For example, recent detailed studies have contributed to the history of Phoenicians in Europe (6) and to the genealogy of Semitic people in the Iberian Peninsula (7).To increase the information about the pre-history of humanity, a project is being executed by different research institutions worldwide, and is called the Genographic Project. This project is under financial support of National Geographic Society, IBM and Waitt Family Foundation, and includes, besides the scientific research, a genealogical service and a fund (Legacy Fund) to sponsor new projects of cultural preservation. The focus of the scientific project is to unveil the historical genetics of indigenous populations worldwide, and to communicate to the world society (usually cosmopolite and considered non-indigenous) about the importance of these indigenous communities to the human history. Many indigenous societies are currently under serious threats, losing their language, music, religion etc. The important message is that we should celebrate our diversity, recognizing that different cultures emerged during their peculiar history, inherited from ancestors that built all human societies today. This project is a historical rescue of the indigenous past, which dominant societies tried to erase, for example, the conquerors in America built many Spanish towns above ancient Inca cities such as Cusco in Peru. The ultimate goal of the Genographic Project is to make freely available a detailed Virtual Map of the Human History. New insights on the history of African past (8) and the legacy of the Crusaders into current Lebanon population (9) are examples of historical details investigated by the Genographic Consortium.The knowledge of an individual´s genealogy is a legitimate right for every person, many times seen as a quest for his own identity. Although our past is an important legacy from our ancestors, the modern culture represented today by many cosmopolite cities worldwide is usually a complex melting point of many indigenous (native) cultures, developed under relative isolation until the XV century. However, there are nowadays many cultural identities that can be directly traced back to the original inhabitants of many places on earth, which are under a serious menace due to the globalization. Their history is one of the most precious values, not only to them but to all humanity, which can now be assessed by genomic tools.
1.Santos FR & Tyler-Smith C. Human Migrations - McGraw-Hill Yearbook of Science and Technology. New York, E.U.A.: McGraw-Hill Book Co, 2001.
2. Carvalho-Silva DR et al. The phylogeography of Brazilian Y chromosome lineages. Am J Hum Genet. 68: 281-286, 2001.
3. Parra FC et al. Color and genomic ancestry in Brazilians. PNAS 100: 177-182, 2003.
4. Gonzalez-Jose et al. The Peopling of America: Craniofacial Shape Variation on a Continental Scale and its Interpretation from an Interdisciplinary View. Am J Phys Anthr. 137: 175-187, 2008.
5. Tarazona-Santos E & Santos FR. The Peopling of the Americas: A Second Major Migration? Am J Hum Genet. 70: 1377-1380, 2002.
6.Zalloua P et al. Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean. Am J Hum Genet. 83: 633-642, 2008.
7. Adams SM et al. The genetic legacy of religious diversity and intolerance: paternal lineages of christians, jews, and muslims in the Iberian peninsula. Am J Hum Genet. 83: 725-736, 2008.
8. Behar DM et al. The Dawn of Human Matrilineal Diversity. Am J Hum Genet. 82: 1130-1140, 2008.
9. Zalloua P et al. Y-chromosomal diversity in Lebanon is structured by recent historical events. Am J Hum Genet. 82: 873-882, 2008.
Links of interest:
Pseudogenes in the genome: functional or not?
by Elio F. Vanin, Ph.D.
Director, Cancer Virology Core
Children’s Memorial Research Center
Processed pseudogenes, which are part of a larger group of mobile nucleic acids termed “retroposons”, were first described in 1980 (1). They are present in the genome of mammals but seem to be unique for each species, implying that their presence happened after mammalian radiation. They generally have the following distinct characteristics: 1) they are homologous (to various degrees) to a functional gene but lack the intervening sequences (introns); 2) the homology between the processed pseudogene and the functional gene begins at the point of transcriptional initiation; 3) they have a stretch of A residues at the 3’ end, in a position that the poly A sequence would be in the mRNA; 4) direct repeats are present 5’ to the position corresponding to the transcriptional start site and 3’ to the stretch of A residues and 5) they lack any promoter elements 5’ to the position corresponding to the transcriptional start site. As a result of these characteristics it was postulated that they are derived from the functional gene via an RNA intermediate and that they were randomly integrated into the genome. Also, as most of them lack 5’ promoter elements they are not transcribed and therefore not “functional” although exceptions have been described (2,3). For reviews on this topic see Vanin (4) and Mighell et al. (2) while a database has also been established (www.pseudogene.org) .One of the major questions that is still to be answered for the majority of the processed pseudogenes is whether they have or had, at some time, a function. A small number of processed pseudogenes have been found which code for proteins while one has been shown to control the expression of the gene which codes for the protein (2). This still leaves the majority without any discernable function. I would like to suggest that the processed pseudogenes that are no longer transcribed did have a function at one time but no longer do and that this function may also be attributed to retroposons in general. This function is to serve as “glues” to repair double stranded breaks which occur in certain regions of the genome during replication and are potentially deleterious. An example of such a region is the DNA which resulted in β-thalassemia-1(5). During evolution, this segment of DNA underwent three separate non-homologous breakage and reunion events. These were 1) the insertion of a processed pseudogene (a retroposon); 2) the insertion of an Alu family sequence (a retroposon) and 3) the breakage and reunion event that led to the thalassemia. Therefore this segment of DNA has undergone three separate non-homologous breakage and reunion events and on one of these occasions a mRNA present in the nucleus was used to repair the break and on a second occasion an Alu family transcript was used for the repair. In conclusion, although the majority of processed pseudogenes could not possibly code for a protein or serve as a regulatory RNA, at present, their formation was the result of repair mechanisms within the nucleus. Without this repair of potentially deleterious double-stranded breaks which occur during replication of the nuclear DNA the cell would potentially die.
1. Vanin et al. A mouse globin-related pseudogene (ψα30.5) lacking intervening sequences. Nature, 286, 222, 1980.
2. Mighell et al. Vertebrate Pseudogenes. FEBS. Lett., 468,109, 2000.
3. Hirotsune et al. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature, 423, 91, 2003.
4. Vanin, E.F. Processed Pseudogenes. Ann. Rev. Genet., 19, 253, 1985.
5. Vanin et al. Unexpected relationships between four large deletions in the human β-globin gene cluster. Cell, 35, 701, 1983.
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The evolving field of phosphoproteomics
After the completion of the human genome sequencing in 2001, different “omics” projects have been launched by the scientific community. Among these, the proteome was one of the first project in the post-genomic era in the field of systems biology. The main aim of this project is to analyze the complete set of proteins produced by a genome and how they interact. However, the identification and annotation of proteins showed far more difficult than previously anticipated. Proteins are differentially expressed in distinct cell types, not all mRNAs are translated into proteins, and if they are, the amount of protein produced may also vary depending on the gene and the physiological state of the cell. Moreover, processes such as alternative splicing can generate different types of proteins from the same gene. In addition, proteins can have post-translational modifications that affect their structure, interactions with other proteins and function. It’s already known that over 300 different post-translational modifications can occur in proteins (1). In particular, phosphorylation has been widely studied due to the association between deregulated phosphorylation and several human pathologies including cancer (2) and autoimmune diseases (3). It is estimated that up to 30% of all proteins can be phosphorylated (4) and due to the reversible nature of phosphorylation, its addition in proteins can produce fast and precise changes in cellular processes such as protein interactions, cell signaling, cytoskeleton remodeling, cell cycle events and cell-cell interactions. Protein phosphorylation analysis is still very challenging due to its complexity, range, temporal dynamics and other features compared to the unphosphorylated forms. With recent technical advances, especially the development of high-throughput mass spectrometers and new computer algorithms the field of phosphoproteomics is evolving in the identification and characterization of proteins containing a phosphate group. This field has advanced quickly enabling the identification, quantification and analysis of hundreds to thousands of phosphorylation sites in a given biological sample. Despite the generation of massive amounts of data, phosphoproteomics alone provides minimal insights into biology. It remains critical for researchers to determine and characterize the function of the identified phosphorylation changes. The rapid advance in the field of phosphoproteomics in recent years has facilitated the correlation of phosphorylation dynamics with a specific signaling network and across different networks. However, continued efforts in the development of more precise and accurate equipments are needed to generate reliable results and link this complex and massive amount of data with a specific biological function. This will provide a more comprehensive view of the proteome and move us closer towards fulfilling the goal of functional characterization of human cells.
1. Witze ES, et al. Mapping protein post-translational modifications with mass spectrometry. Nature Methods (4) 10, 798-806, 2007.
2. Blume-Jensen P, Hunter T. Oncogenic kinase signalling. Nature. 411(6835): 355-365, 2001.
3. Gatzka M, Walsh CM. Apoptotic signal transduction and T cell tolerance. Autoimmunity. 40(6): 442-452, 2007
4. Cohen P. The origins of protein phosphorylation. Nat Cell Biol. 4, E127-130, 2002.
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Mosaic genomes in the era of PersonalOMICS
by Rinaldo W. Pereira, Msc, Ph.D.
Catholic University of Brasilia
It is now widely accepted that modern humans have their origin from somewhere around 200,000 years ago in the north of Africa (1,2). From this group, 100 to 10,000 of our ancestors started their journey to inhabit Europe, Asia, Oceania, and the Americas (2). The last ancient wave of migration was settled around 13,000 to 15,000 years ago (2). During this amazing journey of modern human populations, DNA variability was shaped mainly by demographic (migration and drift) and genomic effects (basically natural selection) (1). Based on DNA variability, continental groups differentiate from each other and show different risk to some common diseases and complex phenotypes (i.e. Africans have more bone mineral density than Europeans and Asians). Five hundred years ago, Europeans, Africans and Native American Indians started in the Americas a marvelous process of mixing up nearly 200,000 years of complex evolution. Since the admixture pattern was not the same along North, Central and South America or even the same in countries inside each of the continents, miscegenation of populations in Brazil and South America is of special interest. Brazilians are in general, in spite of skin or physical features, a mixture of very complex genotypes (3). Consequently, most Brazilians represent mosaics of European, African and Amerindian genomes bringing together different DNA landscapes not present in the world before the year of 1,500 A.D. (3). It is not yet completely understood how this relatively recent mosaic nature impacts in protein expression and other genomic features, such as DNA sequence, structural variability and epigenetic modifications. Studies using genomes of the Brazilian population are providing evidence that recent miscegenation of human populations represent a natural experiment (3,4). The advent of high throughput technologies in the coming era of second and third generation DNA sequencers that have been recently launched by different companies will facilitate the understanding of these mosaic genomes. This will allow a deeper evaluation of complex genotypes and phenotypes, something that was not possible with the old technologies. The integration of this data with those from the ancestral groups that originated admixed populations will be of importance for the future of the personalOMIC era (newly conceived term represented by individual genomes, epigenomes, transcriptomes and proteomes) (4,5). Population geneticists will clearly face a new horizon full of interesting discoveries and changes in current paradigms based in “mosaic” genomes.
1. Pääbo S. The mosaic that is our genome. Nature. 421:409-412, 2003.
2. Excoffier L. Human demographic history: refining the recent African origin model. Current Opinion in Genetics & Development. 12:675–682, 2002.
3. Parra FC, et al. Color and genomic ancestry in Brazilians. Proc Natl Acad Sci U S A. 100: 177-182, 2003.
4. Seldin, MF. Admixture mapping as a tool in gene discovery. Current Opinion in Genetics & Development .17:177–181, 2007.
5. Kussmann et al. OMICS-driven biomarker discovery in nutrition and health. Journal of Biotechnology. 124:758–787, 2006.
The Growing Demands on Bioinformatics
by Jared Bischof, MsC - Bioinformatics expert
Children's Memorial Research Center and Northwestern University - Chicago, IL
This is a very exciting time for bioinformatics research. With the generation of new, high-throughput DNA sequencing technologies a new kind of genetic research will soon become available. A company named Pacific Biosciences is developing a Single-Molecule, Real-Time (SMRT) DNA sequencing technology (1,2). The technology utilizes the observation of phosolinked nucleotides during DNA synthesis to attain long reads in a short run-time at a lower cost than current technologies. A different fluorescent dye molecule is attached to a phosphate chain of each of the four nucleotide bases. When a nucleotide is incorporated into the synthesized DNA, the fluorescent dye is cleaved away as part of the natural process of DNA synthesis. This approach essentially eavesdrops on the cell’s ability to duplicate an entire genome in under an hour and the company claims this technique will one day provide the sequencing of a human genome in minutes for less than $100 (http://www.pacificbiosciences.com). This technology would be an incredible breakthrough and would allow researchers to sequence a cohort of healthy and diseased individuals to isolate the genetic causes of various disorders. However, it is important for the field of bioinformatics to prepare for the amount of data that could be generated by such technologies and the amount of computation they could require. For instance, the hardware requirements just to store and backup this amount data would be orders of magnitude greater than that with which most researchers are currently prepared to handle. Also, an even greater task would be assembling and manipulating the data after it has been obtained. It took researchers a great deal of time and effort to assemble a single reference genome. With the type of data this new technology could generate, the assembly alone would probably take more time than the sequencing. Additionally, recent studies have found that there are a greater number of structural variations in the human genome than initially suspected, making the problem even more complex (3,4). In order for us to fully realize the potential that these new sequencing platforms will provide, computer scientists and biologists will need to work side-by-side to prepare for these new challenges.
1. Lundquist PM, et al. Parallel confocal detection of single molecules in real time. Optics Letters. 33(9): 1026-8, 2008.
2. Korlach J, et al. Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. PNAS. 105(4): 1176-81, 2008.
3. Korbel JO, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science. 318(5849): 420-6, 2007.
4. Chen J, et al. Scanning the human gnome at kilobase resolution. Genome Research. 18(5):751-62, 2008.
Links of interest:
SMALL GENES WITH A BIG IMPACT
by Tom Wurdinger, Ph.D.
Complex networks regulate gene expression in normal cells and disruption of these networks may lead to diseases. In the last 15 years, several studies have revealed the existence of an abundant class of small regulatory genes, known as microRNAs (miRNAs). They were first described in the model organism C.elegans (1) and some of the mechanisms by which microRNAs work was the subject of a Nobel Prize in 2006 (2). Diverse normal biological processes including development, cell proliferation, differentiation and cell death are regulated by miRNAs. Just as miRNAs are involved in the normal functioning of cells, several miRNAs have been associated with pathologies (3). For example, multiple studies already showed that miRNAs can be deregulated in different types of cancer. For other diseases, e.g. viral infections and diabetis, molecular defects in miRNAs have also been described. This has sparked interest in targeting these regulators of gene expression as a means of countering diseases and has led to increased funding opportunities for academic research. Financial incentives for development and commercialization of miRNA-based diagnostics and therapeutics have been an important subject in R&D. By measuring the activity of genes encoding miRNAs, signatures can be determined that enable molecular classification of diseases. Companies such as Rosetta Genomics, Exiqon, and Asuragen currently focus on using miRNAs as cancer biomarkers (4,5). Regulus Therapeutics and Santaris Pharma work on the development of miRNA inhibitors as a novel class of RNA-based drugs, which have shown promising therapeutic effects in pre-clinical models (6,7). Thus, besides using miRNAs as a potential novel class of biomarkers, interfering with miRNA function using miRNA modulators offers a new therapeutic opportunity that might be applicable to several multigenic diseases. This is an emerging field that will have a big impact on the design of molecular therapies to treat diseases in the future.
1. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–854, 1993.
2. Melino G, Nicotera P, Macino G. In the beginning there was RNA, then came transcription regulation: the Nobel Prize Lectures 2006. Cell Death Differ. 14(12): 1975-1976, 2007.
3. Czech MP. MicroRNAs as therapeutic targets. N Engl J Med. 354 (11):1194-1195, 2006.
4. Rosenfeld N, et al. microRNAs accurately identify cancer tissue origin. Nat Biotechnol. 26(4): 462-469, 2008.
5. Szafranska AE, et al. MicroRNA expression alterations are linked to tumorigenesis and non-neoplastic processes in pancreatic ductal adenocarcinoma. Oncogene. 26(30): 4442-4452, 2007.
6. Esau CC. Inhibition of microRNA with antisense oligonucleotides. Methods. (1): 55-60, 2008.
7. Elmén J, et al. LNA-mediated microRNA silencing in non-human primates. Nature. 452(7189): 896-899, 2008.
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