Understanding oral cancer in the genome era

Completion of the human genome project approximately 15 years ago was followed closely by advancements in array technology. Investigators quickly applied this new powerful tool to the genomic and proteomic study of oral squamous cell carcinoma (OSCC). Resultant publications documented chromosome, gene, mRNA, and protein alterations that characterize oral cancer. In this review, we summarize how the genomic, proteomic, and epigenetic array studies have provided insight into the process of oral carcinogenesis. We discuss the significant limitations and requirement for validation of these array studies. We also review the manner in which state‐of‐the‐art, high‐throughput approaches are being used to search for salivary and serum oral cancer biomarkers. © 2010 Wiley Periodicals, Inc. Head Neck, 2010     

Current topics in mutations in the cancer genome

Several oncogenes and tumor suppressor genes are involved in the multistep process of carcinogenesis in many cancer types. Recently, global mutational analyses have revealed that the cancer genome has far greater numbers of mutations than previously thought. Furthermore, the next-generation sequencing method, which has a different principle from conventional Sanger sequencing, has provided more information on the cancer genome such as new cancer-related genes and the existence of many rearrangements in solid cancers. Somatic mutations occurring in cancer cells are divided into "driver" and "passenger" mutations. Driver mutations confer a growth advantage upon the neoplastic clone and are crucial for carcinogenesis. The remaining large majority of mutations are passengers, which, by definition, do not confer a growth advantage. Driver genes with low-frequency mutation rates (less than 10%) are also involved in carcinogenesis along with well-known drivers with high-frequency mutations. There are now several celebrated examples of anticancer drugs of which the efficacy in cancer patients can be predicted based on the genotype of several driver genes, such as EGFR, KRAS, and BRAF on the EGFR signaling pathway. The complete catalogs of somatic mutations provided by the sequencing of the cancer genome are expected to prompt new approaches to diagnosis, therapy, and potentially prevention.     

Impact of the human genome project on medical practice

Background: The Human Genome Project is a coordinated effort to define the human genetic blueprint. The goals include construction of a variety of maps of the human genome, including the identification and localization of all genes. The discovery of genes responsible for human diseases has had a significant impact on the practice of medicine. Methods: Methods for defining the human genome include cytogenetic, physical, and genetic mapping techniques. A variety of strategies have been used to identify human genes, especially those genes that are responsible for disease. Once a disease gene has been identified, this information can be used to develop new diagnostic and therapeutic procedures. Results: A number of disease genes have already been identified, leading to improved diagnosis and novel approaches to therapy. A new type of mutation, trinucleotide repeat expansion, has been found to be responsible for at least seven diseases with an unusual inheritance pattern. Conclusions: Materials and technology generated by the Human Genome Project and related research have provided important tools for the diagnosis and treatment of patients afflicted with genetic diseases.     

胚胎基因组的形成和激活

早期胚胎缺乏转录活性,由母源性的转录产物所调控,随着胚胎的发育,胚胎的基因组逐渐形成并被激活。胚胎基因组的形成和激活在早期胚胎的发育中起关键作用,主要包括胚胎细胞核的形成和胚胎细胞质由转录抑制状态向激活状态转变。本文对胚胎基因组的形成和激活的基本特点和分子机制进行综述。     

The paternal genome and the health of the assisted reproductive technology child

As a number of children born by assisted reproductive technology (ART) are increasing each year across the developed world, the health of such offspring is a matter of public concern. Does the integrity of the paternal genome impact on offspring health? In societal terms, as birth rates fall, and the Western population become unsustainable, do the benefits outweigh the costs of creating and providing for this ART conceived subpopulation? There are little data to date to answer these questions. The long-term health of such children has largely been ignored, and success measured only by early (prebirth) outcomes such as embryo quality or pregnancy. However, there are powerful paradigms such as ageing and smoking that give vital clues as to the potential impact of unhealthy spermatozoa on disease risk, mental and physical health, fertility and mortality of these offspring.     

FokI-dCas9 mediates high-fidelity genome editing in pigs

Gene editing using clustered regularly interspaced short palindromic repeats/Cas9 has great potential for improving the compatibility of porcine organs with human recipients. However, the risk of detrimental off-target mutations in gene-edited pigs remains largely undefined. We have previously generated GGTA1 knock-in pigs for xenotransplantation using FokI-dCas9, a variant of Cas9 that is reported to reduce the frequency of off-target mutagenesis. In this study, we used whole genome sequencing (WGS) and optimized bioinformatic analysis to assess the fidelity of FokI-dCas9 editing in the generation of these pigs. Genomic DNA was isolated from porcine cells before and after gene editing and sequenced by WGS. The genomic sequences were analyzed using GRIDSS variant-calling software to detect putative structural variations (SVs), which were validated by PCR of DNA from knock-in and wild-type pigs. Platypus variant-calling software was used to detect single-nucleotide variations (SNVs) and small insertions/deletions (indels). GRIDSS analysis confirmed the precise integration of one copy of the knock-in construct in the gene-edited cells. Three additional SVs were detected by GRIDSS: deletions in intergenic regions in chromosome 6 and the X chromosome and a duplication of part of the CALD1 gene on chromosome 18. These mutations were not associated with plausible off-target sites, and were not detected in a second line of knock-in pigs generated using the same pair of guide RNAs, suggesting that they were the result of background mutation rather than off-target activity. Platypus identified 1375 SNVs/indels after quality filtering, but none of these were located in proximity to potential off-target sites, indicating that they were probably also spontaneous mutations. This is the first WGS analysis of pigs generated from FokI-dCas9-edited cells. Our results demonstrate that FokI-dCas9 is capable of high-fidelity gene editing with negligible off-target or undesired on-target mutagenesis.     

Expression of the cytomegalovirus genome in kidney allografts during active and latent infection

Abstract Cytomegalovirus (CMV) infection is suggested to be a risk factor for chronic rejection. Here we investigated whether CMV can persist in renal allografts, and in which structures the viral genome is found during an acute infection and a latent period after an active infection. CMV infection was diagnosed in 72/157 patients by CMV antigenemia tests and by viral cultures. CMV antigens were demonstrated in 38 available biopsies by immunohistochemistry, and CMV genome by DNA hybridization in situ. Standard histology was also performed. CMV antigens were detected in 7/15 biopsies obtained during acute infection, in three with acute rejection, and chronic changes in the other biopsies. CMV genome was located in inflammatory cells, in tubuli and in the capillary endothelium. During a latent period without a positive finding in blood or urine, CMV antigens were still found in 6/31 biopsies. CMV DNA was found in inflammatory cells, tubular and glomerular structures and in the endothelium of the arterioles. During the latent period with persistent CMV in the graft, in most cases (10/12) mild to moderate chronic changes were recorded.     

Genetic modification of mammalian genome at chromosome level

The review is concerned with a progress in genetic modification of a mammalian genome in vitro and in vivo at chromosomal level. Recently three new approaches for the chromosome biotechnology have been developed: Using Cre/loxP-system a researcher is able to produce targeted rearrangements of whole chromosomes or their segments or particular genes within the genome, and therefore to modify the set, position and copy number of the endogenous elements of the genome. Mammalian artificial chromosomes (MACs) provide a possibility to introduce into genome relatively large segments of alien chromosome material, either artificially constructed or derived from the genome of different species. Using ES-somatic cell hybrids allows to transfer whole chromosomes or their fragments between different genomes within and between species. Advantages and limitations of these approaches are discussed.     

The human genome and gene expression profiling.

The mapping and sequencing of the human genome has generated a large resource for answering questions about human disease. This achievement is akin in scientific importance to developing the periodic table of elements. Plastic surgery has always been at the frontier medical research. This resource will help us to improve our understanding on the many unknown physiological and pathogical conditions we deal with daily, such as wound healing keloid scar formation, Dupuytren's disease, rheumatoid arthritis, vascular malformation and carcinogenesis. We are primed in obtaining both disease and normal tissues to use this resource and applying it to clinical use. This review is about the human genome, the basis of gene expression profiling and how it will affect our clinical and research practices in the future and for those embarking on the use of this new technology as a research tool, we provide a brief insight on its limitations and pitfalls.     

Sequence alterations of the whole mitochondrial genome in primary and recurrent ovarian carcinomas

Objectives:To investigate mitochondrial DNA(mtDNA)alterations in primary and recurrent ovarian carcinomas to illuminate the impact of chemotherapy on mtDNA.Methods:Complete mtDNA genomes of tumor tissue from 7 primary ovarian carcinoma patients without treatment and 9 recurrent ones with prior chemotherapies were sequenced as well as their matched normal tissue.MtDNA alterations,including somatic mutations and new polymorphisms and consequent amino-acid alterations were compared between the two groups.Results:A large number of mtDNA new polymorphisms(69)and somatic mutations(17)were found in 16 ovarian carcinoma samples.Chemotherapy might not lead to more,heteroplasmic mutations and consequent amino-acid alterations(P>0.05)in the recurrent ovarian carcinoma patients than in the untreated ones.Conclusions:MtDNA damage was not so certainly made by chemotherapies and some of the mtDNA defects might be part of the disease process rather than a consequence of treatment.