Recent Patents on DNA & Gene Sequences (Discontinued) - Volume 4, Issue 3, 2010

RNA silencing has become the most productive field for understanding and exploiting the fundamental system of gene regulation during the last decade. It has been revealed as a new layer of gene regulation that is conserved across all the eukaryotic kingdoms, making the understanding of the molecular mechanism of any biological process incomplete without considering how it is regulated by small RNAs. Despite still being incomplete, the story of RNA silencing has accumulated enough knowledge to be translated into applied developments, and it is now time for the promise to become reality. This thematic issue entitled “Recent Developments on RNA Silencing” reviews, in three extensive manuscripts, most of the current patents and applications related to animals and plants that are based on RNA silencing. In addition, the issue is complemented with a fourth review covering the bioinformatics aspects of RNA silencing, which has become an essential discipline for developments in the field. The first review, a contribution by Francisco E. Nicolas and Alfonso F. Lopez-Martinez, focused on the miRNA silencing pathway of humans and summarizes all the recent developments related to pathological processes. This manuscript entitled “MiRNAs in Human Diseases” reviews a wide range of patents and applications concerning different aspect of human disease, such as diagnosis, prognosis and treatments associated with many pathologies based on gene misregulation. Among the treatments, the authors specifically focused on miRNA modulators, a new generation of compounds designed to replace and/or inhibit miRNA activity in several human diseases, including cancer and viral infections. The review also includes a section dedicated to the delivery of these new compounds. As regards the plant kingdom, this thematic issue presents two perfectly complemented manuscripts that were necessary to cover the high number of inventions published in this field. The first of these reviews is entitled “Recent Patents in RNA Silencing in Plants: Constructs, Methods and Applications in Plant Biotechnology” and has been written by Sara Lopez- Gomollon and Tamas Dalmay. These authors reviewed several general strategies recently used to exploit RNA silencing as a tool to produce plants with improved properties. The second review related to plants is entitled “Patented Specific Applications of Gene Silencing in Plants” and has been written by Ruben Alvarez-Fernandez. In this review, the author focused on patents that are based on engineered gene silencing and designed to solve specific problems, such as the alteration of lignin, biofactories, alkaloids biosynthesis, flowering time fall and many others. The last review, written by Irina Mohorianu, is entitled “Revealing Biological Information Using Data Structuring and Automated Learning”. This is a bioinformatics review that summarizes patents designed to study gene sequence databases, highlighting the applicability of these methods to the RNA silencing field. The diversity of small RNAs and the complexity of the different pathways identified in the general mechanism of RNA silencing make the use of bioinformatics tools essential in most of the new developments related to the field. In fact, many of the patents described in the other three reviews contain bioinformatics analysis of different databases, which makes this review an indispensable contribution to this special issue. In all, this special issue reviews more than two hundred patents related to small RNAs and their applications, which reveals both the importance of this field and the great effort of the authors to thoroughly review all the new advances made in RNA silencing. Finally, I would like to thank all the authors who have taken part for their invaluable contributions to this special issue.

The discovery of microRNAs (miRNAs), a new class of negative regulator that represses gene expression by pairing with their target messenger RNAs (mRNAs), has revealed a natural pathway for controlling gene expression. There are hundreds of miRNAs encoded in the human genome and thousands of target mRNAs, which illustrates the important regulatory roles of miRNAs in cell developmental, differentiation, proliferation and apoptosis pathways. In this scenario, it is not surprising that deregulated miRNAs have been involved in the pathogenesis of many human diseases. The recent development of technologies and compounds to identify and modulate miRNAs has opened new avenues for diagnosis, prognosis and therapeutic applications. Here, we summarize most of the recent patents related to the detection and profiling of miRNAs from pathological samples and to miRNA modulators used as new therapies for disease, including cancer and viral infections, as well as methods for their delivery.

RNA silencing is a recently discovered mechanism to regulate gene expression at transcriptional and posttranscriptional levels. It is based on the recognition and methylation of target genes or cleavage of target mRNAs by small RNA molecules, with length varying from 21 to 24 nucleotides. RNA silencing plays an important role modulating most of the important cell processes, such as growth, development or stress response. During the past few years, diverse strategies have been applied to exploit RNA silencing as a tool to create plants with enhanced economical properties or able to cope with pathogens or abiotic stress. This review describes the most important patents related to RNA silencing in plants, which disclose vectors designed to induce RNA silencing by hairpin RNAs, amplicons or virus-based plasmids, methods for detection and quantification of silencing as well as general uses in plant biotechnology.

RNA silencing is the name of a broad family of phenomena including RNA interference (RNAi) in animals and basal eukaryotes, quelling in fungi and posttranscriptional gene silencing (PTGS) in plants. PTGS is a fertile research field and since its discovery many applications have been developed related to plant breeding. This minireview summarizes those patents which apply engineered gene silencing to specific problems. The range of inventions is divided in two main sections: manipulation of traits and resistance to phytopathogens and pests. Subtopics like manipulation of tolerances to abiotic stress, alteration of lignin, biofactories, alkaloids biosynthesis and flowering time fall within the first section, and introduction of resistances to insects, nematodes, bacteria, virus and fungi can be found within the second one.

The intermediary steps between a biological hypothesis, concretized in the input data, and meaningful results, validated using biological experiments, commonly employ bioinformatics tools. Starting with storage of the data and ending with a statistical analysis of the significance of the results, every step in a bioinformatics analysis has been intensively studied and the resulting methods and models patented. This review summarizes the bioinformatics patents that have been developed mainly for the study of genes, and points out the universal applicability of bioinformatics methods to other related studies such as RNA interference. More specifically, we overview the steps undertaken in the majority of bioinformatics analyses, highlighting, for each, various approaches that have been developed to reveal details from different perspectives. First we consider data warehousing, the first task that has to be performed efficiently, optimizing the structure of the database, in order to facilitate both the subsequent steps and the retrieval of information. Next, we review data mining, which occupies the central part of most bioinformatics analyses, presenting patents concerning differential expression, unsupervised and supervised learning. Last, we discuss how networks of interactions of genes or other players in the cell may be created, which help draw biological conclusions and have been described in several patents.

DNA sequencing techniques witnessed fast development in the last decades, primarily driven by the Human Genome Project. Among the proposed new techniques, Nanopore was considered as a suitable candidate for the single DNA sequencing with ultrahigh speed and very low cost. Several fabrication and modification techniques have been developed to produce robust and well-defined nanopore devices. Many efforts have also been done to apply nanopore to analyze the properties of DNA molecules. By comparing with traditional sequencing techniques, nanopore has demonstrated its distinctive superiorities in main practical issues, such as sample preparation, sequencing speed, cost-effective and read-length. Although challenges still remain, recent researches in improving the capabilities of nanopore have shed a light to achieve its ultimate goal: Sequence individual DNA strand at single nucleotide level. This patent review briefly highlights recent developments and technological achievements for DNA analysis and sequencing at single molecule level, focusing on nanopore based methods.

Gastrointestinal malignancies are among the most common malignancies worldwide. Advances in technology and treatment have improved diagnosis and monitoring of these tumors. As a consequence, identification of new biomarkers that can be applied at different levels of disease is urgently needed. DNA methylation is a process in which cytosines acquire a methyl group in 5' position only if they are followed by a guanine. An emerging catalog of specific genes inactivated by DNA methylation in gastrointestinal tumors has been established. In this review we will give a brief overview of the main sources of DNA used to investigate methylation biomarkers and several related patents. One of these is related to multiple genes that predict the risk of development of esophageal adenocarcinoma. Another evaluated methylation status of 24 genes to find one frequently methylated in primary tumors as well as plasma samples from gastric cancer patients. Others patented the epigenetic silencing of miR-342 as a promissory biomarker for colorectal carcinoma. Thus, the new field of DNA methylation biomarkers holds the promise of better methods for screening, early detection, disease progression and outcome predictor of therapy response in gastrointestinal oncology.

The invention of microarray technology has empowered scientists to quickly transition from single gene studies to massively parallel experiments investigating thousands of genes. The use of DNA microarrays relies on accurate design for probes that are immobilized on a surface and bind specifically to complementary targets in a complex solution. The quality of a set of DNA probes heavily relies on DNA hybridization - the process of joining two single-strands of DNA to form a double-stranded molecule, and is traditionally ensured by using specific design criteria. The design of DNA probes for microarrays requires very stringent criteria, due to the necessity of choosing unique sequences that perfectly complement specific regions from large genomic data sets, while avoiding hybridization with every other region of the same genome. Patents and research publications presenting various probe design methods are reviewed in this manuscript and future potential extensions of current technologies are suggested.

The patents annotated in this section have been selected from various patent databases. These recent patents are relevant to the articles published in this journal issue, categorized by significant fields of gene therapy methods, process and techniques involved.