Recent Patents on DNA & Gene Sequences (Discontinued) - Volume 6, Issue 1, 2012

It is a great honor for me to thank all the authors, reviewers, past and present Editorial Board Members of Recent Patents in DNA and Gene Sequences and the Bentham staff involved in the task to make this journal an outstanding one. Recent Patents in DNA and Gene Sequences is really a highly attractive and interesting journal, because it covers patents coming from DNA research which is one of the most active areas in biotechnology. Gene synthesis (review in this issue) is one example that now facilitates research and well as the development of new therapeutic tools for gene therapy (article in this review). An emerging, but also very active and attractive, is the developing of miRNA as therapeutic agents (article in this issue). I expect in the next few years a dramatic increase in the number of new patents concerning DNA and genes, including the epigenetic aspects, considering that recently new modifications of DNA have been discovered, i.e., hydroxymethylcytosine, formylcytosine and carboxylcytosine. These new modifications have been reported to play key roles in gene expression regulation. I am deeply convinced that all these new developments will contribute to generate for Recent Patents in DNA and Gene Sequences, a huge impact in the near future for the scientific community throughout the world. Finally, I would like to thank Bentham Science Publishers for its confidence in my position and its help to assist me as Editor-in-Chief of the journal. I also acknowledge the kind assistance of Ms. Humera Sharif, who has helped me since two years in managing the journal.

Gene therapy concept has been being overcome massive challenges from 1972 in ethical, socio-economical and developmental issues. In this review, we have attempted to go through almost all the arenas and described in a methodical way that reflects not only the initial ethical and scientific thoughts but also adorned a solid depiction of gene therapy related physico-chemical barriers, approaches and strategies till to date.

Gene synthesis is an emerging field which has widespread implications in synthetic biology and molecular biology. The field is constantly evolving which has led to key advances in oligonucleotide synthesis and gene synthesis technologies, with simplicity, cost effectiveness and high throughput. The miniaturization, multiplexing, microfluidic processing and the integrated microchip engineering will drive down cost and increase productivity without compromising DNA synthesis fidelity, whereas the gigantic amount of genome information provides infinite source of DNA elements and genes as raw material for synthetic biology. This article describes some of the recent patents on oligonucleotide synthesis and gene synthesis.

Histopathological diagnosis using Formalin-Fixed Paraffin Embedded (FFPE) tissues is essential for the prognostic and therapeutic management of cancer patients. Pathologists are being confronted with increasing demands, from both clinicians and patients, to provide immunophenotypic and gene expression data from FFPE tissues to allow the planning of personalized therapeutic regimens. Recent improvements in the protocols for pre-analysis processing of pathological tissues aim to better preserve cellular details and to conserve antigens and nucleic acid sequences. These developments have been recently patented. The international protocol for the transporting of surgical specimens from the surgical theatre to the pathology department is to immerse the specimen in formalin. The alternative method of sealing the specimens into bags under a vacuum and then cooling is a well-accepted and environmentally safe procedure that overcomes the many drawbacks linked to transfer in formalin. Importantly, RNA is notoriously poorly preserved in FFPE tissue. Due to this, successful procedures for the extraction of genetic information from archival tissues have been the object of several studies and patents. Novel molecular approaches for RT-qPCR and gene array analysis on FFPE tissues are presented here. Moreover, a major advance is reported in this study, the observation that tissue fixation in cold conditions allows a much better preservation of nucleic acid sequences.

Adjuvant endocrine therapy as well as other forms of targeted therapy such as HER2 inhibitors and antiangiogenic agents reduce the risk of recurrence and improve survival among women with hormone receptor positive breast cancer. However, a significant percentage of women who receive targeted therapy as adjuvant or metastatic treatment do not benefit from this therapy, while a number of women who initially respond will eventually develop disease progression and relapse while on therapy. The observed variability in treatment response to targeted breast cancer treatment could be partly explained by pharmacogenomics. This paper reviews evidence on the role of pharmacogenomics of breast targeted therapy focusing on the clinical relevance of genetic variation. In particular, this article reviews the role of pharmacogenomics of tamoxifen, aromatase inhibitors, HER-2 inhibitors and anti-angiogenic agents. In addition, recent patents in the field are presented that provide promising steps in the field of personalized treatment of breast cancer, although future studies are needed for determining the clinical benefit of the proposed inventions. Finally, we present a testable hypothesis to aide the search for biologically meaningful genetic variation Specifically, we suggest the publication of negative results in the field of pharmacogenomics and pharmacoproteomics, will benefit future research in the field.

MicroRNAs (miRNAs, miRs) are a class of non-coding single-stranded RNAs, which can negatively regulate gene expression at posttranscriptional levels by miRNA-mRNA interaction. It has been demonstrated that miRNAs play important roles in a variety of biological process, including cell proliferation, differentiation, apoptosis, and tumorigenesis. Recent studies have shown crucial roles of specific miRNAs in controlling oligodendrocyte (OL) differentiation and myelination. Dysregulation of miRNAs is a vital event in the pathogenesis of demyelinating diseases. Furthermore, new patents of miRNAs also provide new strategies for gene therapy and miR-drug development for demyelinating diseases, especially multiple sclerosis. In this review, we briefly introduce the roles of miRNAs in OL differentiation and in the pathogenesis of demyelinating diseases, with emphasis on the implication of miRNAs patents in disease diagnostic and therapeutic perspective and its related technologies and challenges in clinical application.

Breast cancer afflicts more than 1.3 million people worldwide and is the main cause of cancer-related deaths among women. Many efforts are underway to develop new therapeutic and biomarker strategies for the management of this disease. Hormone receptors and human epidermal growth factor receptor 2 (HER2) are currently the most important molecular tools in this regard. Moreover, targeted therapies including trastuzumab in particular are the primary treatment in both the adjuvant and recurrent settings. However, many studies reported that selected patients may present with resistance to trastuzumab due to the presence of p95HER2 fragments. To address this challenge, drugs such as lapatinib and others described in recent patents promise alternative therapeutic options. We discuss the most recent patents related to HER2 and p95HER2 fragments for breast cancer treatment.

Bacillus thuringiensis (Bt) is the most widely used microbial control agent. The broad spectrum of susceptible hosts, production on artificial media and ease of application has caused the widespread use of this bacterium against several pests in agriculture, forest and vectors of human diseases. B.thuringiensis toxins are highly species specific which provide economic, environmental benefits, potential for future control and spread of the technology worldwide. This makes the B. thuringiensis crystal proteins an interesting tool for the implementation in integrated pest management programs. It has gained importance over the last 100 years for its biocontrol properties which is used in this review as a case study and analysis of the patents granted on B. thuringiensis was carried out. This study categorizes a number of patents related to B.thuringiensis insecticidal crystal proteins, application of B.thuringiensis insecticidal crystal proteins and the development of patentable technologies. The analyses were done using various criteria like patenting trends over the years, assignees playing a major role, comparison of the technology used in different patents and the patenting activity across the insect orders. Patent documents related to bacterium B.thuringiensis contain a trove of technical and commercial information and thus, patent analysis is considered as a useful tool for R&D management and techno economical development. Patent analysis also helps identifying and evaluating new and alternate technologies, keeping abreast with latest technologies for business interests, finding solutions to technical problems and ideas for new innovative trends.

To determine if there is a gene variant of protein serine-threonine phosphatase with EF hand (PPEF-1) in T-cell lymphoblastic lymphoma SUP-T1 cell line, both in silico and in vitro approaches were conducted. In silico, a cDNA clone showing similar sequence to PPEF-1 was isolated from the SUP-T1 cDNA library and named PPEF-1V. The full-length of the PPEF-1V cDNA clone is a 2135bp containing a 1503bp open reading frame extending from 188bp to 1690bp, which corresponds to an encoded protein of 501 amino acid residues with a predicted molecular mass of 57.8 kDa. Alignment on both PPEF-1V and PPEF-1 sequences showed that PPEF-1V is a 350bp deletion in the nucleotide sequence of PPEF-1 from 128-477bp and a 152-amino-acid N-terminal deletion in the amino acid sequence of PPEF-1. In vitro, PPEF-1V transcript fragment was only highly expressed in T-cell lymphoblastic lymphoma cell line. In conclusion, the present patent showed that PPEF-1V could be a potential target for diagnosis or treatment of T-cell lymphoblastic lymphoma.

The patents annotated in this section have been selected from various patent data bases. These recent patents are relevant to the articles published in this journal issue, categorized by different biotechnology methods, processes and techniques involved.