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Sichuan Agricultural University and LC Sciences Uncover the Epigenetics of Obesity

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In a new study published online in Nature Communications, researchers from Sichuan Agricultural University and LC Sciences report the miRNAome in porcine adipose and muscle tissues. The report provides a valuable epigenomic source for obesity prediction and prevention and furthers the development of pig as a model organism for human obesity research1.

Scientists now know that the genetic code alone isn’t responsible for adult phenotype or even the offspring of these adults. Epigenetics refers to changes in gene expression affecting phenotype that don’t involve changes to the DNA nucleotide sequence itself, and yet are heritable. DNA methylation, histone modification and microRNA (miRNA) expression are examples of epigenetic mechanisms that have recently been identified as important regulators of gene expression in many biological systems.

Obesity is a huge problem worldwide. Recently, the World Health Organization reported that obesity levels doubled in every region of the world between 1980 and 2008, spurring rates of non-communicable diseases such as diabetes and cancer that now account for almost two out of three deaths globally. It has become evident that epigenetic factors, such as D N A methylation and miRNA expression, have essential roles in obesity development.

Now, a team led by Researchers at the Institute of Animal Genetics and Breeding, Sichuan Agricultural University, China has used a pig model to investigate the systematic association between epigenetic regulators and obesity. Pigs are an excellent model system to study obesity due to their similar physiology to ours including: metabolic features, cardiovascular systems, and propor­tional organ sizes . The researchers generated a genome-wide D N A methylation map as well as miRNA expression and gene expression maps for adipose and muscle tissues from three pig breeds living within comparable environments but displaying distinct fat levels.

The miRNA expression portion of this project was supported by team members from LC Sciences’ Hangzhou, China lab. LC Sciences is a specialist in miRNA sequencing and expression profiling and has previously collaborated with the group from Sichuan Agricultural University. In 2010 they performed a comprehensive search for porcine miRNAs that extended the repertoire of pig miRNAome to 777 unique miRNAs and enabled an atlas of miRNA regulation functions and networks to be constructed which has laid the groundwork for future miRNA studies in pig models2. Additional collaborations with the group include investigations of miRNA expression in porcine gonads3 and human breast milk4. LC Sciences has worked with other agricultural groups in China as well, including: Huazhong5, Yangzhou & Nanjing6 Universities on their porcine miRNA studies.

In the current study, numerous miRNAs having known or potential roles in obesity were identified. Additionally, the researchers found a differentially methylated region in males compared with females. This region is located in the promoter of a miRNA cluster that includes adjacent miR-99b, let-7e and miR-125a. Although no previous evidence exists for a direct relationship of these three miRNAs to obesity, the key functions and targets of these miRNAs potentially contribute to sexual differences in obesity development.

Dr. Qiulei Lang, Head of LC Sciences operations in Asia commented, ”miRNA has been a focus of LC Sciences’ since 2005. Back then we realized its importance and so have tailored our capabilities to support agricultural customers worldwide in their miRNA research. A proprietary RNA-Seq data analysis pipeline that was developed by LC Sciences enabled us to make sense of the tremendous amount of small RNA sequencing data that we generated in this study.”

That data analysis shows global epigenetic similarity and difference among breeds, sexes and anatomic locations. The epigenetically regulated regions in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of obesity.

Dr. Mingzhou Li from Sichuan Agricultural University , said, “The domestic pig is of enormous agricultural significance and provides valuable models for human obesity research. Recently, epige­netic factors, especially DNA methylation and miRNA regulation have gained a greater appreciation as an alternative perspective on the aetiology of complex diseases. Although little is known about the transcription start site of primary miRNA transcripts, our results suggested that DNA methylation in 5′ upstream of stem-loop precursor could have a role in transcriptional silencing of mature miRNA. ”

In the modern industry, pigs have undergone strong genetic selection in the relatively inbred commercial lines for lean meat production, or in some cases, for adipose production, which has led to remarkable phenotypic changes and genetic adaptation, making these breed lines a perfect model for comparative studies.

Principal Investigator Ruiqiang Li from Peking University, said, “This work will serve as a valuable resource for future functional validation, promoting further development of pig as a model organism for human obesity research, as well as maximizing the economic benefits in producing high quality pork.”

About Sichuan Agricultural University - Sichuan Agricultural University (S IC AU) is a university located in Ya’an city, Sichuan province, China and part of the “Project 211”, specialized in biotechnology and agricultural sciences, and as well as offering degrees in physical science, engineering, economics, management, veterinary medicine, liberal arts, pedagogy and law. For more information, please visit www.sicau.edu.cn.

About LC Sciences – LC Sciences is a leader in miRNA discovery and profiling offering flexible services and delivering high quality results based on our innovative µParaflo® custom microarray platform and the latest next-gen sequencing technologies. We have developed complementary bioinformatics tools necessary for extracting biological and functional information from large microRNA and miRNAome data sets. LC Sciences provides microfluidic made-to-order microarrays and delivers the most up-to-date genomics application tools for advancement in basic science and applied biomedical fields. For more information, please visit www.lcsciences.com.

    1. Li, M. et al. (2012) An atlas of DNA methylomes in porcine adipose and muscle tissues. Nat Commun [Epub ahead of print]. [ abstract ]
    2. Li, M. et al. (2010) MicroRNAome of porcine pre- and postnatal development. PLoS One 5, e11541. [ article ]
    3. Li, M. et al. (201 1 ) Repertoire of porcine microRNAs in adult ovary and testis by deep sequencing. Int J Biol Sci, 7(7), 1045-1055. [ abstract ]
    4. Zhou, Q. et al. (2012) Immune-related Immune-related microRNAs are abundant in breast milk exosomes. Int J Biol Sci, 8(1), 118-123. [ abstract ]
    5. Luo L. et al. (2010) Microarray-based approach identifies differentially expressed microRNAs in porcine sexually immature and mature testes. PLoS One 5(8), e11744. [ article ]
    6. Zhou B, Liu HL, Shi FX, Wang JY. (2010) MicroRNA expression profiles of porcine skeletal muscle. Anim Genet 41(5), 499-508. [ abstract ]

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Michigan Institute of Urology, P. C. to Perform Clinical Trial Using Cellay, Inc’s Same Day OligoFISH® Probes for Prostate Cancer

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St. Clair Shores, Michigan and Cambridge, Massachusetts – Michigan Institute of Urology, P. C. (MIU) and Cellay, Inc. today announced that MIU will exclusively perform a clinical trial for prostate cancer using Cellay’s Same Day OligoFISH® probe panel. Data from this trial will be included in Cellay’s premarket approval (PMA) application for submission to the U.S. Food and Drug Administration. This novel, non-invasive screening test is designed to detect chromosomal abnormalities in prostate cells obtained in a urine sample after a digital rectal exam. This investigational use test uses fluorescence in situ hybridization (FISH) technology to detect chromosome gains and losses which have been associated with prostate cancer.

Prostate cancer is the most common cancer in males in the United States, and there are approximately 200,000 new cases diagnosed annually and 38,000 deaths per year. However, due to inaccuracies of the current screening method, the PSA blood test, more than 600,000 invasive biopsies are performed annually. The ability to differentiate non-aggressive from aggressive, metast atic prostate cancers has been a continuous clinical and diagnostic challenge. Cellay expects that the clinical trial will demonstrate that its rapid non-invasive, Same Day OligoFISH® panels will improve diagnosis, prognosis, and treatment using a cost effective, patient friendly assay.

Alphonse M. Santino, M.D., CEO and a Founder of MIU, noted, “MIU is pleased to be the exclusive clinical trial site for Cellay’s Same Day OligoFISH® probe panels for prostate cancer for its PMA submittal. Our relationship with Cellay reinforces our commitment to the people of Michigan to provide the most effective diagnosis and treatment for urological disorders and disease. This is an important relationship for us and our community, since African-Americans are 3.5 times more likely to develop prostate cancer than the rest of the male population. Moreover, this group presents with the aggressive type of prostate cancer at an earlier age with higher rates of mortality.”

“Cellay appreciates that MIU has committed to serve as exclusive site for the clinical trial of our Same Day OligoFISH® probe panels for prostate cancer. MIU’s physicians’ group is recognized as one of the nation’s premier urology practices and sets the standard for diagnosis and treatment of urologic disorders. Cellay welcomes MIU’s support and participation in this novel clinical trial,” said Ed O’Lear, President & CEO of Cellay.

About Michigan Institute of Urology
As one of the oldest and largest sub-specialty Urology practices in Michigan, MIU is dedicated to providing its patients the most up to date, state of the art urologic care. Its specialists have joined MIU from the most respected research universities and hospitals in the United States.

About Cellay
Cellay is a privately held, manufacturer of Same Day OligoFISH® probes for high complexity, physician owned laboratories, which contract with Cellay to manufacture and supply individual probes or multiple probes of the laboratories’ choice pursuant to FDA and Clinical Laboratory Improvement Amendments (CLIA) regulations. Cellay is registered with the FDA.

About FISH
FISH is an established cytogenetic technique that is used to detect and localize the presence or absence of specific DNA sequences on chromosomes. FISH uses fluorescent probes that bind to only those parts of the chromosome with which they show a high degree of sequence complementarity. Same Day OligoFISH® probes were introduced in 2007 and hybridize extremely fast with much higher analytical sensitivity and penetrability in cells and tissues than traditional probes.

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Enabling microRNA Discoveries – 250th Peer-Reviewed Publication Made Possible By µparaflo Custom Microarray Technology

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LC Sciences, a life sciences company leading the development of innovative microRNA (miRNA) analysis and discovery technologies, announced today the publication of over 250 peer-reviewed studies using the company’s microarray service for analyzing miRNA expression profiles. These studies, by leading researchers in the field, represent significant steps toward realizing these small regulatory RNA’s potential as biomarkers and therapeutic targets.

MiRNAs have proven to be an extremely important part of the gene expression regulation mechanism of a wide variety of cellular processes. This is evident in the amount of relevant findings by LC Sciences’ customers being translated into published reports and the diverse range of study areas that these publications encompass: cancer research, neuroscience, cardiovascular research, reproductive biology, plant science, microbiology, immunology and stem cell research. LC Sciences’ miRNA profiling service, powered by its µParaflo® custom microarray technology, provides quick, reliable, fully analyzed datasets enabling researchers to immediately move forward with groundbreaking research.

The miRNA field is still nascent, and it is advancing rapidly. The race to discovery has produced a continuous stream of new miRNA sequences as well as routine revisions of inaccurate or incomplete sequences. This fluidity has caused many microarrays with static content to fall away and has fueled reports of the wholesale replacement of microarrays by new methods such as RNA-Seq. But the nimble, customizable format of the µParaflo® array has given it staying power, not only by enabling it to keep current with all known miRNAs, but also by making use of data generated by RNA-Seq. These custom arrays have benefited from RNA-sequencing generating novel content that other arrays are unable to capture and take advantage of.

The 250th study, entitled “Wolbachia uses host microRNAs to manipulate host gene expression and facilitate colonization of the dengue vector Aedes aegypti.” appeared in the May 31st issue of PNAS and was one of a group of articles published recently by LC Sciences’ customers describing microarray expression analysis of miRNAs recently discovered through RNA Sequencing.

Researchers at the University of Queensland, Australia studied the underlying mechanisms of host manipulation by a widespread endosymbiont. Using microarrays, they show that the miRNA profile of the mosquito, Aedes aegypti, is significantly altered by a life-shortening strain of W. pipientis bacteria. This is extremely important work as introduction of Wolbachia into mosquitoes has been proposed as a method for malaria control. They found that a host miRNA (aae-miR-2940) is induced after W. pipientis infection in both mosquitoes and cell lines.

This study illustrates the versatility of µParaflo® from a couple of perspectives. First, mosquito, an important though non-model species was the target of interest here and mosquito arrays, as well as arrays from any of the 153 species listed in the miRBase public sequence database, are readily available from LC Sciences. Second, custom content (novel miRNA sequences from an earlier sequencing study on the same species) was quickly integrated into the content of the insect array providing an even richer expression dataset. Though all the previously described, known insect miRNAs were also present on the arrays, several custom sequences were significantly differentially expressed in infected mosquitoes and a custom sequence turned out to be one that became a focus of the investigation. Dr. Sassan Asgari, lead researcher for the study, commented that microarrays “…provided an affordable approach to the study of differential expression of small RNAs and miRNAs in particular.”

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MicroTissues, Inc. Announces New Product Launch for the 3D Petri Dishâ„¢

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MicroTissues, Inc. announced today the launch of its 3D Petri Dishâ„¢ line of products. The 3D Petri Dishâ„¢ is a new tool for the world wide industry of life sciences research and drug discovery. Invented at Brown University, the 3D Petri Dishâ„¢ grows living human cells in three dimensions (3D) where they replicate the function of natural tissues and organs. There are important applications for these human 3D microtissues in cancer and stem cell research as well as toxicity testing, drug discovery and cell therapy.

“The scientific community has recognized the need for a reliable 3D cell culture technology that accurately produces natural cell-to-cell interactions and is easy to use” said Brian Morgan, Marketing Manager of MicroTissues, Inc. “Not only does our 3D Petri Dish™ line of products create 3D microtissues without artificial scaffolds, the microtissues are uniform in size, easy to harvest and accessible to the standard biochemical and microscopy methods that cutting edge labs demand. No other 3D cell product has all these technical advantages. And, we have the only reusable product.”

MicroTissues, Inc offers eight products that are precision micro-molds used to cast 3D Petri Dishesâ„¢ that fit in standard multi-well plates. The micro-molds are autoclavable and reusable. In a single pippetting step, the 3D Petri Dishâ„¢ forms hundreds of spheroids (hepatospheres, cardiospheres, mammospheres, neurospheres, and embryoid bodies), and microtissues with more complex shapes and geometries. Over thirty different cell types, including primary human cells, have been shown to form 3D microtissues in the 3D Petri Dishâ„¢.

MicroTissues, Inc. a privately held company with an exclusive worldwide license to US and international patent applications on the 3D Petri Dish™, is advancing technologies and applications of 3D cell culture.

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MicroTissues, Inc.’s 3D Petri Dishâ„¢ Is Helping to Reduce Animal Use in Research

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MicroTissues, Inc. announced today that its 3D Petri Dish™ is targeted towards helping to reduce the numbers of animals used in research. The 3D Petri Dish™ is a new tool for the world wide industry of life sciences research and drug discovery that grows living cells in three dimensions (3D). These 3D microtissues replicate the function of natural tissues and organs better than conventional 2D methods and are increasingly being used in toxicity testing of new drugs and cosmetics.

“Worldwide, efforts are underway to reduce the use of animals in research and we’re excited to be offering a new technology for toxicity testing” said Brian Morgan, Marketing Manager of MicroTissues, Inc. “The 3D Petri Dish™ is a reliable 3D cell culture technology that accurately produces natural cell-to-cell interactions and is easy to use. And, it forms 3D microtissues from human cells, so toxicity testing data is more relevant.”

Effective 2009, the European Union banned the use of animal testing for cosmetic products and many believe the trend to reduce the use of animals in research will continue worldwide. MicroTissues, Inc. is helping to address this issue by offering eight products that are precision micro-molds used to cast 3D Petri Dishesâ„¢ that fit in standard multi-well plates. The 3D Petri Dishâ„¢ forms hundreds of multi-cellular 3D spheroids from cells useful for toxicity testing including hepatospheres, cardiospheres, mammospheres, neurospheres, and embryoid bodies. The 3D Petri Dishâ„¢ technology also forms microtissues with complex shapes having geometries that mimic natural organs. Over thirty different cell types, including primary human cells, have been shown to form 3D microtissues in the 3D Petri Dishâ„¢.

MicroTissues, Inc. a privately held company with an exclusive worldwide license to US and international patent applications on the 3D Petri Dish™, is advancing technologies and applications of 3D cell culture. The company’s products stand above the rest because they are designed to create more natural and more reliable 3D cell culture environments based on cell-to-cell interactions in convenient and consistent formats that generate high content information. The company’s lead line of products, the 3D Petri Dish™, is serving the needs of researchers in a wide range of areas including cancer research, stem cell biology, toxicity testing, developmental biology, drug discovery, regenerative medicine and tissue engineering. In addition to products for basic research, MicroTissues, Inc. is using its platform technology to pursue applications in drug discovery and cell therapy. For more information, please visit www.microtissues.com.

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MicroTissues, Inc.’s 3D Petri Dishâ„¢ Used in Time Magazine’s Medical Breakthrough of 2010

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MicroTissues, Inc. announced today that its 3D Petri Dish™ was used in one of Time magazine’s medical breakthroughs of 2010. Researchers at Brown University and Women and Infants Hospital used the 3D Petri Dish™ to invent the first artificial human ovary, a discovery important for fertility research and a possible infertility treatment for cancer patients. In lab studies, the investigators used the 3D Petri Dish™ to assemble three different cell types into a 3D structure resembling an ovary where they functioned for all intents and purposes like a real ovary, even successfully maturing a human egg from its earliest stages in the follicle to a fully developed form.

“This is an exciting medical breakthrough and an significant validation of the importance of the 3D Petri Dish™ technology” said Brian Morgan, Marketing Manager of MicroTissues, Inc. “Cell-to-cell interactions are critical for the function of the ovary and the 3D Petri Dish™ is designed to promote these interactions. The honeycomb shaped 3D microtissue used in these studies is a great example of the kinds of complex shaped microtissues that can only be produced with the 3D Petri Dish™.”

MicroTissues, Inc offers eight products that are precision micro-molds used to cast 3D Petri Dishes™ that fit in standard multi-well plates. The micro-molds are autoclavable and reusable. The 3D Petri Dish™ is used to form 3D spheroids and microtissues with more complex shapes and geometries such as toroids and honeycombs. Over thirty different cell types, including primary human cells, have been shown to form 3D microtissues in the 3D Petri Dish™.

MicroTissues, Inc. a privately held company with an exclusive worldwide license to US and international patent applications on the 3D Petri Dish™, is advancing technologies and applications of 3D cell culture. The company’s products stand above the rest because they are designed to create more natural and more reliable 3D cell culture environments based on cell-to-cell interactions in convenient and consistent formats that generate high content information. The company’s lead line of products, the 3D Petri Dish™, is serving the needs of researchers in a wide range of areas including cancer research, stem cell biology, toxicity testing, developmental biology, drug discovery, regenerative medicine and tissue engineering. In addition to products for basic research, MicroTissues, Inc. is using its platform technology to pursue applications in drug discovery and cell therapy. For more information, please visit www.microtissues.com.

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The Porcine microRNAome is Revealed

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Researchers from LC Sciences LLC and a collaboration of Universities1 have established a porcine microRNAome, a complete catalog of all microRNAs expressed in the species Sus scrofa2. MicroRNAs (miRNAs) are small regulatory RNA molecules known to control a wide array of cellular functions such as growth and development and whose dysregulation has been associated with disease. The findings of this study lay the groundwork for a greater understanding of the species through further mapping of tissue- and stage-specific miRNAs.

The domestic pig is an important species from various standpoints. First, it is a major protein source in the human diet world-wide. Additionally, its anatomy, physiology, and genome size are very similar to the human species, and there has been increasing molecular genetic evidence showing the comparability of human and pig, making it a suitable model system for human biology. Pigs are now model animals for biomedical research of cardiovascular, immunological, cancer, diabetes, and a range of other diseases. Finally, the pig has become an important source of organs and tissue for transplantation into humans.

Prior to this study, miRbase3, the primary public repository for miRNA sequence data, listed only 73 unique pig miRNAs, this out of a total of 10,883 database entries encompassing over 100 species. The number of miRNAs for pig was significantly lower than for other species with similar size genomes (such as Human with 894 miRNAs) suggesting the existence of far more pig miRNAs.

The researchers used advanced deep sequencing and developed bioinformatics technologies to analyze all the small RNA molecules that are transcribed from all the genes in the pig genome. After filtering, mapping, alignment and classification of all the reads, they had shown that the pig miRNAome has 777 unique miRNA sequences. The sequencing results will not only greatly enhance the utility of the pig microRNAome as the blueprint of advanced pathway network studies of miRNA and their target mRNAs, but also provide information on time-dependent variations of the microRNAome as to sequence lengths, counts, composition, genomic location, and the relative expression of conserved versus pig-specific miRNAs.

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LC Sciences Pairs Deep Sequencing with Customized Microarrays to Offer New Seq-Array Service for Discovery & Profiling Applications

LC Sciences today announced the launch of its new Seq-Array(SM) services designed to take full advantage of both the latest deep sequencing capabilities and the proven genomics tool – microarray. This combination of technologies advances microRNA research to the next level of depth and understanding that was not possible before with either of the technologies alone. LC Sciences has been a leading provider of microRNA discovery and profiling services since 2005.

LC Sciences Pairs Deep Sequencing with Customized Microarrays to Offer New Seq-Array Service for Discovery & Profiling Applications

microRNA is a young, dynamic field of study and though significant discoveries are being made every day, the very complex regulatory mechanisms of these small RNAs are still not fully understood. Continued advancement requires adaptable, even customizable research tools that can keep pace with the rapidly advancing research in this field. While deep sequencing yields results that broadly cover genome-wide miRNAs from samples of various origins, the relatively high cost and low throughput nature of sample handling, makes the systematic follow through of the sequencing discoveries for validation and/or profiling in a reproducible manner time consuming and expensive. Microarrays have achieved wide acceptance as the preferred tool to systematically profile and compare the gene expression of large numbers of samples rapidly, reproducibly, and cost effectively; however they are dependent on previously known sequence information. Seq-ArraySM is a combination of these technologies that maximizes the effectiveness of each method while overcoming the limitations of the other.

Seq-ArraySM for microRNA starts with exploratory small RNA deep sequencing of a single or mix of RNA samples to perform a broad search and generate a comprehensive atlas of all microRNAs within a given research study. Next, bioinformatics are employed to map the raw sequencing reads to a custom generated sequence database, classify and align all sequences and sequence variants, as well as to predict novel microRNAs. A custom SeqArrayâ„¢ microarray is designed based on the mapped novel microRNAs, the predicted novel microRNAs, and any previously described publicly available microRNA sequences. Finally, expression profiling of large numbers of samples on the custom array design together with additional bioinformatics work completes an efficient pathway to focused biological insights including: revealing regulatory target genes, defining gene expression pathways, and discovering biomarkers.

“We feel like this is a productive match of the two technologies,” says Dr. Christoph Eicken, Head of Technical Services at LC Sciences. “It’s something we have really already been doing for a while and thought it made sense to package together as a single service. Often times researchers come to us who are studying a non-typical species with very limited or no prior knowledge of microRNA sequences or function in their model system. By the end of the complete Seq-ArraySM project they have become the world authority on microRNA in their area of research. It’s been very exciting to be part of this.”

About microRNA – microRNAs are small non-protein-coding RNA molecules that function as negative regulators of gene expression by targeting specific mRNAs. This either inhibits translation or promotes mRNA degradation.

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LC Sciences First miRNA Microarray Service Provider to Offer Plant MicroRNA Database (PMRD) Probe Content

Taking full advantage of its flexible µParaflo® Biochip Technology, Houston based LC Sciences today announced immediate availability of probe content from the newly created Plant MicroRNA Database (PMRD) for their microRNA (miRNA) microarray customers . This announcement comes immediately following a publication in Nucleic Acids Researchintroducing the public database 1 . The PMRD integrates available plant miRNA data deposited in other public databases, gleaned from the recent literature, and data generated by the database organizers. It is freely available at http://bioinformatics.cau.edu.cn/PMRD.

LC Sciences miRNA microarrays make use of a microfluidics on-chip synthesis platform, termed µParaflo®, versus a traditional spotted array based on pre-synthesized oligonucleotides. This on-chip synthesis platform means made-to-order microarrays can be produced, delivering the most up-to-date research tools to researchers; in this case, the PMRD content.

In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, the possible target genes for each miRNA with a predicted interaction site are included in the database. This represents a significant increase in content vs plant miRNA microarrays based solely on the miRBase content.

The public miRBase sequence database 2 serves as the primary probe content for many commercially available miRNA profiling microarrays (http://microrna.sanger.ac.uk/sequences/). Detection of miRNAs using a microarray offers the opportunity for genome-wide miRNA expression profiling by examining all known miRNA transcripts in a single experiment. However, in a rapidly evolving field such as miRNA research, it is important to have a flexible system that can keep up with all the newly discovered and predicted sequences. Pre-spotted glass slide arrays immediately go out of date whenever new miRNA database versions are released. LC Sciences’ microarrays ensure scientists have the most complete picture of miRNAs expressed in their experimental samples.

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Enabling microRNA Discoveries – LC Sciences Tops 100th Customer Publication

LC Sciences announced today the publication of the 100th peer-reviewed study by one of its customers using the company’s microarray service for analyzing microRNA (miRNA) expression profiles and for discovery of novel small RNAs. These studies, by leading researchers in the field, contribute to a fast growing body of knowledge defining this recently discovered class of regulatory RNAs.

To date, miRNAs have proven to be extremely important part of the gene expression regulation mechanism. Expression profiling and functional studies conducted so far indicate that miRNAs participate in the regulation of almost every cellular process investigated and this is evident in the amount of relevant findings being translating into published reports.

The publications to date by LC Sciences’ customers span a diverse range of study areas, including cancer research, neuroscience, cardiovascular research, MicroRNA Publications reproductive biology, plant science, virology, stem cell research, immunology, and small RNA discovery. Their miRNA profiling service has provided a tool for many researchers to explore and examine a wide assortment of miRNA cellular networks and the resulting publications are often the first description of miRNA activity in these systems.

LC Sciences’ miRNA profiling service, powered by its µParaflo® microfluidic technology, provides quick, reliable, fully analyzed data enabling researchers to immediately move forward with innovative research, and publish their results faster. Microarray results require extensive validation prior to publication. The speed with which researchers using this miRNA profiling service have published their discoveries demonstrates the high-quality and reliability of these results.

The 100th study, entitled “MicroRNA-146a feedback inhibits RIG-I-dependent Type I IFN production in macrophages by targeting TRAF6, IRAK1, and IRAK2” appeared in the September issue of The Journal of Immunology and was one of a group of articles published recently by LC Sciences’ customers describing miRNA involvement in the immune system. Researchers at the National Key Laboratory of Medical Immunology, China studied the fine tuning effect that miRNA has on inflammatory response to viral infection and even propose a new mechanism for the evasion of innate immune control by viruses. MiRNA microarray data revealed, and real-time quantitative PCR confirmed, many up-regulated miRNAs in vesicular stomatitis virus (VSV) infected mouse macrophages. Specifically miR-146a expression was significantly up-regulated. Further studies revealed that miR-146a negatively regulated VSV-triggered interferon production (which is necessary to exert feedback control over inflammation) promoting VSV replication in macrophages. The identification of miRNAs and a better understanding of their expression in response to various stimuli/pathogens may reveal that miRNAs offer multiple new therapeutic targets/strategies for fine tuning the immune response to treat and prevent of a number of inflammatory diseases.

“We are very excited about the announcement of the 100th peer-viewed publication by one of our customers,” says Chris Hebel, VP of Business Development at LC Sciences. “MiRNA has become a very hot area of research and many scientists would like to be the first to describe the mechanism of miRNA as it relates to their field of study. We are happy to provide a first look into this exciting new field for them and are proud that our technology has been a part of such groundbreaking work”.

About µParaflo® Technology – The µParaflo® technology is a microfluidic platform for in situ parallel synthesis of biomolecular chips and miniaturization of bioassays including binding and enzymatic reactions. This unique platform technology is based on a new class of three-dimensional pico-liter microfluidic reaction devices, and a digital light controlled synthesis method that employs conventional oligonucleotide or peptide synthesis chemistry; a completely programmable process. The seamless integration of these multidisciplinary technologies enables a significant advance in parallelization, miniaturization, customization, and automation.

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LC Sciences’ Versatile Microfluidics Chip Technology Extended to Target Selection Applications

LC Sciences has announced the availability of a custom target enrichment service for next-generation sequencing applications. LC Sciences now provides a service for Target-Specific Selection of a defined genomic region (such as Mbp region at a specific location, suspected cancer regions, SNP regions, regions for genomic comparisons) or RNA sequences (such as sets of transcriptome sequences known f r o m previous screening experiments, mRNAs, and miRNAs). This new service enables researchers to take full advantage of new “next-generation” high throughput sequencing technologies.

It is clear that these new sequencing technologies can be more effectively utilized for systematic studies of genetic variation by targeting certain specific regions (subsets) of complex genomes. Essentially, our service achieves more coverage and deeper sequencing by reducing sample complexity and focusing reads on the areas of interest.

LC Sciences µParaflo® technology’s unique combination of advanced microfluidics and innovative synthesis chemistry provides a robust synthesis process which is necessary to achieve high quality selection and the flexibility to handle almost any target selection project. This technology has been used to produce custom sequence microarrays [Nucleic Acids Res. 2004,32,5409] and custom designed oligonucleotide mixture libraries (OligoMix®) [Nature. 2004,432,1050] since 2003 and is now particularly well suited to providing target selection solutions. The versatility of the technology makes it a good fit for the diverse needs of researchers embarking on new high-throughput sequencing projects.

“It’s really the flexibility of the technology that sets it apart f r o m others”, says Dr. Christoph Eicken, Head of Technical Services, Microarrays. “First, this is a completely custom synthesis technology, meaning almost any selected genomic region of any species and all known RNA transcripts can be targeted. Second, target selection may be achieved by hybridization using complementary capture probes immobilized on surface or by in-solution hybridization. By altering the target selection approach we take, we can address the widely varied needs of each individual sequencing project. With our help, researchers can tailor design the target selection process based on the specificity, coverage, selection resolution and throughput requirements of their particular project.”

LC Sciences’ microarray based approach utilizes thousands of custom oligonucleotide sequences which are synthesized in situ on a programmable high density microfluidics chip as capture probes designed to target specific regions of interest in any genome (or transcriptome). Samples are hybridized to the chip, undesired sequences are washed off and the captured target sequences are recovered by eluting them f r o m the chip. The selected target sequences are ready for high-throughput sequencing or further processing.

When target selection in-solution makes sense, this flexible chemistry can directly synthesize biotinylated or phosphorylated oligonucleotides (capture probes) that are designed to target specific genomic/sequence regions of interest. After hybridization with a sample, magnetic beads are added and the capture probes are affinity linked to the beads. The captured target sequences are separated f r o m other sequences by washing the beads after which the target sequences can be recovered. Alternatively, the oligonucleotides (OligoMix®) may be immobilized on beads prior to target selection, again depending on the needs of the particular project.

LC Sciences currently offers its Target-Specific Selection application as a service, as it has successfully done with other applications of the µParaflo® technology such as miRNA profiling, small RNA discovery, kinase profiling and epitope mapping with peptide arrays, and others.

“We find that researchers would prefer to spend their valuable time focusing on their research, not figuring out how to make successful use of someone else’s new technology”, says Chris Hebel, Director of Business Development. “We offer a comprehensive solution: customers tell us their experiment goals, send us their samples and we provide the material ready for sequencing. There is no reason they need to become target selection experts to keep their research moving forward. We have already developed methods to design optimized hybridization probes and suitable experimental procedures and conditions for different sample types, such as miRNA, small RNA, or genomic DNA samples, on different sequencing platforms. We can even perform the high-throughput sequencing and deliver the results, as not all labs have access to next-generation sequencers yet.”

More information about LC Sciences’ Targeted Sequencing Sample Enrichment Service and the µParaflo® technology is available at:http://www.lcsciences.com/targeted_sequencing.html.

About LC Sciences – LC Sciences is a genomics and proteomics products company offering a comprehensive line of DNA, RNA, and peptide microarrays for nucleic acid/protein profiling and functional analysis, biomarker-discovery, novel drug screening, and the custom development of miniaturized assay devices for diagnostics and biosensing applications. Based on the µParaflo® microfluidics technology, LC Sciences’ innovative products and services offer significant flexibility and customization capability for rapidly evolving, diverse customer needs. In an era of rapid technological advancement, LC Sciences offers service products which enable efficient one-stop solution for assays of DNA, RNA, protein, enzymes, antibodies, or small molecules. LC Sciences also provides unique synthetic DNA and RNA products such as OligoMix®, generated using their microfluidic biochip synthesizer. These innovative products drive synthetic biology, systems biology and sequencing applications by reducing the cost and increasing the speed of highly multiplexing large-scale nucleic acid and protein engineering experiments.

More information about LC Sciences is available at www.lcsciences.com.

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Biochemicals, Biopharmaceutical, Biotech, Biotech Products, Biotech Services, Biotechnology, Gene, Genetics, Microarrays, Pharmaceuticals, Science

LC Sciences announced the availability of probe content miRBase 10.0 for their microRNA (miRNA) microarray customers

Taking advantage of its flexible µParaflo™ Chip Technology, Houston based LC Sciences today announced immediate availability of probe content miRBase 10.0 for their microRNA (miRNA) microarray customers. This announcement comes less than a week after Sanger Institute’s update of their sequence database for known miRNAs (miRBase) 1 to version 10.0 (http://microrna.sanger.ac.uk/sequences). As the jump in

version numbers from 9.2 to 10.0 suggests, this update marks a major milestone and features significant changes: 489 new hairpin sequences and 971 novel mature miR and miR* experimentally verified products have been added.

These numbers represent an increase of unique miRNA sequences by 42%. “This exciting increase in data means that researchers using pre-spotted glass arrays with probe content based on versions as recent as 9.1 are missing 49% of mouse, and more than 50% of human sequences, just to give two examples. The other important point is that these sequences are experimentally verified and publicly available data. Unlike with proprietary probe content the researcher has full access and control over the results.” said Chris Hebel, Director of Business Development at LC Sciences.

The importance of this update is emphasized by another aspect of the release: many human, mouse and rat mature miRNAs were renamed and the sequence boundaries changed to reflect the predominant forms identified in recent large-scale cloning studies. The public miRBase sequence database serves as the primary probe content for many commercially available miRNA profiling microarrays. Detection of miRNAs using a microarray offers the opportunity for genome-wide miRNA expression profiling by examining all known miRNA transcripts in a single experiment. However, the continued updating of the database can be problematic for researchers using pre-spotted glass slide arrays as the probe content of the arrays immediately goes out of date whenever a new miRBase version is released. Especially, in a rapidly evolving field as miRNA research it is important to scientists to have the most complete picture of miRNAs expressed in their experimental samples.

LC Sciences miRNA microarrays make use of a microfluidics on-chip synthesis platform, termed µParaFlo™, versus a traditional spotted array based on pre-synthesized oligonucleotides. This on-chip synthesis platform solves the issue of out of date microarrays because made-to-order microarrays can be produced, delivering the most up-to-date research tools to researchers.

In addition to providing much more uniform and reproducible features than a spotted array, on-chip synthesis permits the total customization of content on each individual microarray opening up additional applications such as the discovery of new miRNAs and other small non-coding RNAs.

About microRNA (miRNA)
miRNAs are small non-protein-coding RNA molecules that function as negative regulators of gene expression by base pairing with specific mRNAs. This either inhibits translation or promotes mRNA degradation. About miRBase – The miRBase sequence database is a comprehensive database of miRNA sequence data, annotation, and predicted gene targets and is the primary public repository for these data. Release 10.0 of the database contains 5071 entries representing hairpin precursor miRNAs, expressing 4922 maturemiRNA products, in primates, rodents, birds, fish, worms, flies, plants and viruses (miRBase release summary). miRBase also provides a gene-naming service for assigning official miRNA names to novel miRNAs before they are published. It is freely available to all at http://microrna.sanger.ac.uk/.

About LC Sciences
LC Sciences offers specialty microarray services for nucleic acid/protein profiling and functional analysis, biomarker-discovery, and novel drug screening. Our array service products are based on Atactic Technologies’ µParaflo™ platform technologies that encompass advanced digital chemical synthesis, pico-liter scale biochemical assays, and microfluidic reaction devices containing high density individual 3D chambers.

 

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CodeLink business assets have been transferred under the agreement between Applied Microarrays and GE Healthcare

Applied Microarrays, Inc announced today the completion of Applied Microarrays’ purchase of certain assets of GE Healthcare’s CodeLinkâ„¢ Gene Expression Bioarray System. Under the terms of the agreement, Applied Microarrays, Inc acquires certain equipment, inventory, licenses and assigned contracts associated with the CodeLink platform. Financial terms were not disclosed.

The transaction enables Applied Microarrays to provide CodeLink users with continued and uninterrupted access to the industry-leading gene expression platform as Applied Microarrays, Inc continues to develop, market, distribute, sell, and support the existing CodeLink catalogue of whole genome expression arrays, Codelink custom arrays and Codelink inside arrays.

Alastair Malcolm, president and chief executive officer of Applied Microarrays, said, “We’re pleased to now have a unique opportunity to launch our company with a full range of microarray design, development, and manufacturing competencies and at the same time ensure a seamless transition for customers.

Eric Roman, General Manager Genomic Sciences, GE Healthcare, said, “There has been strong demand from CodeLink customers to keep these products in the marketplace. We’re delighted to have found a way for our customers to continue working with one of the best gene expression platforms available.”

“The CodeLink platform is customer-proven over several years, notably demonstrating world-class technical performance in the FDA-led MicroArray Quality Control project,” Malcolm said. Applied Microarrays is immediately opening the CodeLink platform to the microarray community for new applications development, offering customers the opportunity to place their unique custom array content on to a robust, proven platform which can be manufactured in high volume.

Applied Microarrays aims to be a leading contract manufacturer of microarrays, of any type, for any customer, with no limitations on substrate material or spotted fluid. “We are fortunate in this regard to have acquired an intact high-capacity microarray spotting facility, employing Six Sigma techniques since its inception to produce leadership quality products,” Malcolm said.

About Applied Microarrays, Inc.
Applied Microarrays is a new company headquartered in Tempe, Arizona. Using the microarray assets acquired from GE, and staffed with experts who developed the CodeLink platform and manufacturing capabilities, the company will specialize in contract development and manufacturing of custom microarrays of all types. The company will additionally continue to offer the CodeLink family of gene expression arrays, and customer-specified subsets of that content on multi-array formats. Our vision is to be the microarray partner of choice for focused “omics” research, and the leading high-volume contract manufacturer for research and diagnostic arrays.

About GE Healthcare
GE Healthcare provides transformational medical technologies and services that are shaping a new age of patient care. GE Healthcare’s expertise in medical imaging and information technologies, medical diagnostics, patient monitoring systems, performance improvement, drug discovery, and biopharmaceutical manufacturing technologies is helping clinicians around the world re-imagine new ways to predict, diagnose, inform, treat and monitor disease, so patients can live their lives to the fullest.

GE Healthcare’s broad range of products and services enable healthcare providers to better diagnose and treat cancer, heart disease, neurological diseases and other conditions earlier. GE Healthcare’s vision for the future is to enable a new “early health” model of care focused on earlier diagnosis, pre-symptomatic disease detection and disease prevention. Headquartered in the United Kingdom, GE Healthcare is a $17 billion unit of General Electric Company (NYSE: GE). Worldwide, GE Healthcare employs more than 46,000 people committed to serving healthcare professionals and their patients in more than 100 countries.

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