Cancer genomics and precision medicine / 药学学报

It has been noted for decades that cancer is essentially a genomic disease. Benefiting from the latest development of high-throughput sequencing and bioinformatics technologies, a variety of genetic alterations have been identified for their roles in cancer occurrence and development, giving rise to new opportunities for anti-cancer drug discovery. In particular, the rapid advancement of cancer genomics has paved the way for the precision medicine that has gained compelling achievement in the past years and significantly benefited cancer patients. In this review, we summarize the main types of genomic abnormalities in cancer, the application of functional genomics research in cancer research, and in particular the translational application of cancer genomics in clinical diagnosis, drug discovery and cancer precision medicine. With this review, we hope to better understand cancer genomics research and provide future perspectives for its application in precision medicine.

Applications of functional genomics in research of benzo[a]pyrenetoxicity：a review / 预防医学

Abstract@#Benzo [a] pyrene ( B [a] P ) is a well-recognized environmental pollutant. Exposure to B[a]P elicits many adverse biological effects, including tumorigenesis, immunosuppression, teratogenicity, and hormonal effects. In addition to B [a] P exposure-induced genetic damages, a growing number of studies demonstrate that epigenetic changes play an important role in chemically induced carcinogenesis. In order to provide better understanding of epigenetic changes of B [a] P and their potential association with genotoxic endpoints, this review summarizes the advances in the applications of functional genomics in the research of B [a] P toxicity, including functional genomics techniques, regulation of human genome expression, DNA sequence variability, model organisms research, and bioinformatics studies, so as to provide insights into the management of B [a] P exposure-induced health injuries and use of genomics techniques to unravel the mechanisms underlying the toxicity of other environmental pollutants.

Genomics and functional genomics in Leishmania and Trypanosoma cruzi: statuses, challenges and perspectives

The availability of Trypanosomatid genomic data in public databases has opened myriad experimental possibilities that have contributed to a more comprehensive understanding of the biology of these parasites and their interactions with hosts. In this review, after brief remarks on the history of the Trypanosoma cruzi and Leishmania genome initiatives, we present an overview of the relevant contributions of genomics, transcriptomics and functional genomics, discussing the primary obstacles, challenges, relevant achievements and future perspectives of these technologies.

An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants / 基因组蛋白质组与生物信息学报·英文版

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 × Mo17 F2 ears. To better understand the functional genomics of kernel development, we developed a mapping and gene identification pipeline, bulked segregant exome sequencing (BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-specific expression data to narrow down the list of candidate genes/mutations and identified deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identified in mutant 531, which occurs within a ∼200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4 (RdDM4) and AMP-binding protein, respectively. This study demonstrates the efficiency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection, providing a new option in mapping-by-sequencing for maize functional genomics studies.

Efficient regeneration and genetic transformation platform applicable to five Musa varieties

Background: Banana (Musa spp.) is an important staple food, economic crop, and nutritional fruit worldwide. Conventional breeding has been seriously hampered by their long generation time, polyploidy, and sterility of most cultivated varieties. Establishment of an efficient regeneration and transformation system for banana is critical to its genetic improvement and functional genomics. Results: In this study, a vigorous and repeatable transformation system for banana using direct organogenesis was developed. The greatest number of shoots per explant for all five Musa varieties was obtained using Murashige and Skoog medium supplemented with 8.9 µM benzylaminopurine and 9.1 µM thidiazuron. One immature male flower could regenerate 380­456, 310­372, 200­240, 130­156, and 100­130 well-developed shoots in only 240­270 d for Gongjiao, Red banana, Rose banana, Baxi, and Xinglongnaijiao, respectively. Longitudinal sections of buds were transformed through particle bombardment combined with Agrobacterium-mediated transformation using a promoterless ß-glucuronidase (GUS) reporter gene; the highest transformation efficiency was 9.81% in regenerated Gongjiao plantlets in an optimized selection medium. Transgenic plants were confirmed by a histochemical assay of GUS, polymerase chain reaction, and Southern blot. Conclusions: Our robust transformation platform successfully generated hundreds of transgenic plants. Such a platform will facilitate molecular breeding and functional genomics of banana.

Next generation sequencing analysis of lung cancer datasets: A functional genomics perspective.

Cigarette smoking leads to serious epidemics in humans, creating torsion of infection in epithelial cells lining the respiratory tracts. Several researchers in the recent past have theorized that the next generation sequencing (NGS), especially transcriptome sequencing has enhanced understanding lung cancers and other epithelial epidemics. Conversely, pathogenesis specific to lung cancer with respect to molecular fraction of genomic ribonucleic acid has some mutant effect in various populations like smokers with lung cancer, healthy never smokers and vice versa. We review the impending impact of NGS data while providing insights into the biology of lung cancer affecting various populations, which we believe would be an add‑on service for predictive biology approaches. Furthermore, we conclude what would be the outcome of such analysis for Indian population. Bioinformatics analysis was performed using various tools. We identified five genes namely epidermal growth factor receptor, Kirsten rat sarcoma, adenomatosis polyposis down regulated‑1, N‑ethylmaleimide‑sensitive factor attachment protein, gamma and Piezo type mechanosensitive ion channel component 2 whose role was implicated in lung cancer and further analysis has to be performed to check whether or not the genes are indeed completely involved in causing lung cancer.

Effect of aspect ratio on the uptake and toxicity of hydroxylated-multi walled carbon nanotubes in the nematode, Caenorhabditis elegans

OBJECTIVES: In this study, the effect of tube length and outer diameter (OD) size of hydroxylated-multi walled carbon nanotubes (OH-MWCNTs) on their uptake and toxicity was investigated in the nematode Caenorhabditis elegans using a functional mutant analysis. METHODS: The physicochemical properties of three different OH-MWCNTs were characterized. Uptake and toxicity were subsequently investigated on C. elegans exposed to MWCNTs with different ODs and tube lengths. RESULTS: The results of mutant analysis suggest that ingestion is the main route of MWCNTs uptake. We found that OH-MWCNTs with smaller ODs were more toxic than those with larger ODs, and OH-MWCNTs with shorter tube lengths were more toxic than longer counterparts to C. elegans. CONCLUSIONS: Overall the results suggest the aspect ratio affects the toxicity of MWCNTs in C. elegans. Further thorough study on the relationship between physicochemical properties and toxicity needs to be conducted for more comprehensive understanding of the uptake and toxicity of MWCNTs.

Effect of aspect ratio on the uptake and toxicity of hydroxylated-multi walled carbon nanotubes in the nematode, Caenorhabditis elegans

OBJECTIVES: In this study, the effect of tube length and outer diameter (OD) size of hydroxylated-multi walled carbon nanotubes (OH-MWCNTs) on their uptake and toxicity was investigated in the nematode Caenorhabditis elegans using a functional mutant analysis. METHODS: The physicochemical properties of three different OH-MWCNTs were characterized. Uptake and toxicity were subsequently investigated on C. elegans exposed to MWCNTs with different ODs and tube lengths. RESULTS: The results of mutant analysis suggest that ingestion is the main route of MWCNTs uptake. We found that OH-MWCNTs with smaller ODs were more toxic than those with larger ODs, and OH-MWCNTs with shorter tube lengths were more toxic than longer counterparts to C. elegans. CONCLUSIONS: Overall the results suggest the aspect ratio affects the toxicity of MWCNTs in C. elegans. Further thorough study on the relationship between physicochemical properties and toxicity needs to be conducted for more comprehensive understanding of the uptake and toxicity of MWCNTs.

Functional and Evolutionary Genomics of Protein Disulphide Isomerase (PDI) Geneb Family in Wheat and Its Wild relatives: A Review.

Mature wheat grain contain 8-20% proteins. The storage proteins of wheat determine the characteristics and unique properties of its flour in the process of pasta and bread-making and eventually the quality of the finished products obtained. The storage proteins play an integral role in determining the visco-elastic properties of wheat dough, a feature of high quality wheat. The genes, encoding storage proteins as well as factors that may affect their deposition, such as molecular chaperones and foldase enzymes, are of particular interest to wheat industry. Genomic, cDNA and promoter sequences of the three homoeologous gene encoding the “typical” PDI has been already cloned and characterized. Recently, eight new non-homoeologous wheat genes were cloned and characterized in bread wheat. Study characterizing the variability in a 700 bp region comprising 600 bp of 5’ upstream putative promoter region and 100 bp of the first exon of the typical PDI gene in 15 accessions of Triticum urartu (AA), Aegilops speltoides (BB) and Aegilops taushcii (DD), from diverse origin and Triticum aestivum cv Chinese Spring (AABBDD) has also been completed recently. This review explains how functional and evolutionary genomics tools aid in the study of a gene family and its promoter.

Ionoma de plantas: cenário atual e perspectivas / Ionomics: current scenario and prospects

Os sistemas biológicos são governados pela soma de todos os genes expressos, proteínas, metabólitos e elementos de um organismo. A análise do ionoma de um tecido auxilia a identificar, entre outros aspectos, genes que contribuam para maior ou menor acúmulo de elementos essenciais e metais pesados, bem como a interação entre processos metabólicos. O conhecimento do ionoma, aliado ao uso de técnicas de biologia molecular, formam um sistema muito eficiente para mapeamento gênico, para estudos de genômica funcional e para caracterização geral do estado fisiológico das plantas em uma determinada condição. Além disso, o estudo do ionoma permite avaliar as interações existentes entre os mais diversos íons das plantas e como a disponibilidade de um íon afeta a absorção e uso de outros. O objetivo desta revisão é apresentar e discutir o ionoma como uma ferramenta importante na elucidação dos mais diversos mecanismos envolvidos na absorção, translocação e acúmulo de elementos essenciais e não-essenciais em plantas e sua relação com o metabolismo delas.

Biological systems are governed by the sum of all expressed genes, proteins, metabolites and components of an organism. The analysis of a tissue ionome helps to identify, among others, genes that contribute to a greater or lesser accumulation of essential elements and heavy metals, as well as interaction between metabolic processes. The ionome knowledge, coupled with the use of molecular biology techniques, form a very efficient system for gene mapping, and functional genomic studies, and general characterization of plants physiological status in a given condition. Another interesting process that the ionome study allows to analyse is the interactions among plants' ions and how such ion availability can affect the absorption and use of others. The aim of this review is to present and discuss the ionome as an important tool in the elucidation of several mechanisms involved in absorption, translocation and accumulation of essential and nonessential elements in plant and its relation with their metabolism.

ANÁLISIS DE ESTs DE YUCA (Manihot esculenta): UNA HERRAMIENTA PARA EL DESCUBRIMIENTO DE GENES / Analysis of Cassava (Manihot esculenta) ESTs: A Tool for the Discovery of Genes

La yuca (Manihot esculenta) constituye la base de la alimentación para más de 1.000 millones de personas en el mundo, consolidándose como el cuarto cultivo más importante en el mundo después del arroz, el maíz y el trigo. La yuca es considerada como un cultivo relativamente tolerante a condiciones de estrés abiótico y biótico; sin embargo estas características se encuentran principalmente en variedades no comerciales. Las estrategias de mejoramiento genético convencional o mediadas por transformación genética representan una alternativa para introducir las características deseadas dentro de las variedades comerciales. Un paso fundamental con miras a acelerar los procesos de mejoramiento genético en yuca requiere el descubrimiento de los respectivos genes relacionados con las características buscadas, para lo cual los ESTs (del inglés Expressed Sequence Tags) son una vía rápida para este fin. En este estudio se realizó un análisis de la colección completa de ESTs disponibles en yuca, representada por 80.459 secuencias, los cuales fueron ensamblados en un conjunto de 29.231 genes únicos (unigen), representado por 10.945 contigs y 18.286 singletones. Estos 29.231 genes únicos pueden representar cerca del 80% de los genes del genoma de yuca. Entre el 5 y 10% de los unigenes de yuca no presentaron similitud con las secuencias presentes en las bases de datos de NCBI y pueden constituir genes específicos de yuca. A un grupo de secuencias del set unigen (29%) fue posible asignarles una categoría funcional de acuerdo al vocabulario Gene Ontology. El componente función molecular es el mejor representado con 43% de las secuencias, seguido por el componente proceso biológico (38%) y finalmente el componente celular (19%). Dentro de la colección de ESTs de yuca se identificaron 3.709 microsatélites que podrán ser empleados como marcadores moleculares. Este estudio representa una contribución importante al conocimiento de la estructura genómica funcional de la yuca y se constituye en una herramienta para la identificación de genes asociados a características de interés agrícola para posteriores programas de mejoramiento genético.

Cassava (Manihot esculenta) is the main source of calories for more than 1,000 millions of people around the world and has been consolidated as the fourth most important crop after rice, corn and wheat. Cassava is considered tolerant to abiotic and biotic stress conditions; nevertheless these characteristics are mainly present in non-commercial varieties. Genetic breeding strategies represent an alternative to introduce the desirable characteristics into commercial varieties. A fundamental step for accelerating the genetic breeding process in cassava requires the identification of genes associated to these characteristics. One rapid strategy for the identification of genes is the possibility to have a large collection of ESTs (Expressed Sequence Tag). In this study, a complete analysis of cassava ESTs was done. The cassava ESTs represent 80,459 sequences which were assembled in a set of 29,231 unique genes (unigen), comprising 10,945 contigs and 18,286 singletones. These 29,231 unique genes represent about 80% of the genes of the cassava’s genome. Between 5% and 10% of the unigenes of cassava not show similarity to any sequences present in the NCBI database and could be consider as cassava specific genes. A functional category was assigned to a group of sequences of the unigen set (29%) following the Gene Ontology vocabulary. The molecular function component was the best represented with 43% of the sequences, followed by the biological process component (38%) and finally the cellular component with 19%. In the cassava ESTs collection, 3,709 microsatellites were identified and they could be use as molecular markers. This study represents an important contribution to the knowledge of the functional genomic structure of cassava and constitutes an important tool for the identification of genes associated to agricultural characteristics of interest that could be employed in cassava breeding programs.

Sequenciamento de DNA de nova geração e suas aplicações na genômica de plantas / Next generation DNA sequencing and its applications in plant genomics

As plataformas de sequenciamento de nova geração são uma alternativa poderosa para estudos de genômica estrutural e funcional. Na genômica de plantas, os trabalhos com as novas plataformas têm sido destinados ao sequenciamento de transcritos, ressequenciamento ou sequenciamento de novo de genomas plastidiais. Neste trabalho, são detalhadas as tecnologias das plataformas mais utilizadas atualmente, bem como é revisada a aplicação dessas tecnologias na genômica estrutural e funcional de plantas.

The next-generation DNA sequencing technologies are a powerful alternative to studies in structural and functional genomics. In plant genomics studies, the work with these new platforms has been used for the sequencing of transcripts, re-sequencing, and the de novo sequencing of plastid genomes. This research details the technological principles of the next-generation DNA sequencing platforms most used and reviews its application in structural and functional plant genomics.

Bioinformatic prediction of the relationship between PPP4RI gene with tumor and its preliminary application in gastric cancer / 第二军医大学学报

Objective: To investigate the relationship of PPP4R1 gene with the oncogenesis and metastasis of gastric carcinoma by using bioinformatics analysis, and to verify the result by RT-PCR. Methods: IntNetDB was used to search for the neighborhoods of gene PPP4R1 and cliques by CFinder; Chilibot was used to explore the association between the cliques and carcinoma, then the association of PPP4R1 with gastric carcinoma was deduced. Eighteen pairs of primary and metastatic specimens from the same patient and 12 pairs primary carcinoma and the adjacent normal specimens from the same patient were analyzed by RT-PCR for PPP4R1 expression. Results: It was found that the community genes of PPP4R1 included PPP2R5E, MTMR4, PPP3CC, CTDP1, CTDSP1, FLJ22405, PPP1CB, PPP1CC, PPP2R2A, PPP2R5A, PPP2R5C, CTDSP2, and PPP1CA as searched by Cfinder2. 0 when k = 14. Nine of the genes were associated with carcinoma and 2 associated with carcinoma and metastasis. The result of RT-PCR showed that higher expression of PPP4R1 was found in 15 of the 18 primary gastric cancer specimens compared with the paired metastatic specimens (P<0.01); higher expression was also found in 9 of the 12 adjacent normal specimens compared with the paired cancer specimens (P< 0.01). Conclusion: Gene PPP4R1 may be associated with the oncogeriesis and metastasis of gastric carcinoma; bioinformatics is an efficient way to investigate function of new genes.

Application of Bioinformatics and Systems Biology in Medicinal Plant Studies / 中草药·英文版

One important purpose to investigate medicinal plants is to understand genes and enzymes that govern the biological metabolic process to produce bioactive compounds.Genome wide high throughput technologies such as genomics,transcriptomics,proteomics and metabolomics can help reach that goal.Such technologies can produce a vast amount of data which desperately need bioinformatics and systems biology to process,manage,distribute and understand these data.By dealing with theomicsdata,bioinformatics and systems biology can also help improve the quality of traditional medicinal materials,develop new approaches for the classification and authentication of medicinal plants,identify new active compounds,and cultivate medicinal plant species that tolerate harsh environmental conditions.In this review,the application of bioinformatics and systems biology in medicinal plants is briefly introduced.

PCR-microarray analysis of fibrosis-associate gene expression in extensive fibrotic renal tissue resulting from hydronephrosis / 国际外科学杂志

Objective To investigate the fibrosis-associated genes, especially those transforming growth factor-β(TGF-β) associated, expression in the tissue of extensive fibrotic kidney resulting from severe by-dronephrosis. Methods Compared 12 extensive fibrotic kidneys resulting from severe hydronephrosis with 6 normal renal tissues using PCR array. All samples were collected from our hospital from Aug. 2005 to Dec. 2006. The data were treated with △△Ct method. When 2△△Ct≤<0.5 or≥2, the difference was considered sig-nificant. Results A total of 49 differential genes expressed in the fibrotic renal tissues were screened out, of which, 25 were up-regulated and 24 were down-regulated. The differential genes included members and receptors of TGF-β super family and bone morphogenetic protein(BMP) family, target molecule of TGF-β or BMP signal pathway and several regulators. Conclusions Through investigating with PCR array, we certifi-cated the positive effect of Nodal, GSC and IGFI to renal fibrosis. And we suppose that TGF-β play a sec-ondary role in renal fibrosis, while BMP family and Leftyl work in a functional genome in the regulating of renal fibrosis.

Encyclopedia of Autographa californica Nucleopolyhedrovirus Genes / 中国病毒学·英文版

The Autographa californica multiple capsid nucleopolyhedrovirus (AcMNPV) was the first baculovirus for which the complete nucleotide sequence became known. Since then 15 years lapsed and much research has been performed to elucidate putative functions of the annotated open reading frames of this virus and this endeavour is still ongoing. AcMNPV is the most well-known and well-studied baculovirus species, not in the least for its application as a vector for the high-level expression of foreign genes in insect cells. This article is the first monograph of a single baculovirus and gives a current overview of what is known about the 151 AcMNPV ORFs, including (putative) function and temporal and spatial presence of transcripts and protein. To date 60 ORFs have a proven function, another 19 ORFs have homologs for which functions are known in other baculoviruses and 72 ORFs are still enigmatic. This paper should assist the reader in quickly finding the essentials of AcMNPV.

Identification of 1,531 cSNPs from Full-length Enriched cDNA Libraries of the Korean Native Pig Using in Silico Analysis

Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for functional genomics related studies, genome annotation and SNP discovery. We analyzed 7,392 high-quality chromatograms (Phred value >30) obtained from sequencing the 5' ends of clones derived from full-length enriched cDNA libraries of Korean native pigs including brainstem, liver, cerebellum, neocortex and spleen libraries. In addition, 50,000 EST sequence trace files obtained from GenBank were combined with our sequences to identify cSNPs in silico. The process generated 11,324 contigs, of which 2,895 contigs contained at least one SNP and among them 610 contigs had a minimum of one sequence from Korean native pigs. Of 610 contigs, we randomly selected 262 contigs and performed in silico analysis for the identification of cSNPs. From the results, we identified 1,531 putative coding single nucleotide polymorphisms (cSNPs) and the SNP detection frequency was one SNP per 465 bp. A large-scale sequencing result of clones from full-length enriched cDNA libraries and identified cSNPs will serve as a useful resource to functional genomics related projects such as a pig HapMap project in the near future

Genomic-based discovery and validation of novel anti-filarial drugs.

Background: Lymphatic filariasis is a mosquito-transmitted disease, while onchocerciasis is transmitted by blackflies. There is no vaccine for these infections. New drugs are required for improvement of current therapies. Objective: This article reviews recent advances in filarial parasite genomics and opportunities for new antifilarial drug research. Methods and results: Genomic approach to filarial parasites provides new prospects for target validation. Comparative genomics filters enable us to select filarial parasite-specific gene products of interest. Functional genomics filters allow the selection of gene products essential for pathogen survival. The validated targets could be prioritized and categorized by informatics methods and manual curation. Conclusion: Lymphatic filariasis and onchocerciasis can be eliminated by either sterilizing or killing adult worms. It is most advantageous to target Wolbachia species for developing new drugs. Functional genomic approaches using microarrays, proteomics, and model organisms, have significantly expanded options for researchers. The genomic-based approach is promising for anti-filarial drug discovery in the future.

Genómica funcional en embriones y ovocitos humanos individuales / Functional genomics in single embryo and human oocytes

Durante tres décadas, el análisis de embriones y ovocitos humanos ha consistido principalmente, en su evaluación morfológica o citogenética; paulatinamente se han incorporado técnicas moleculares como FISH y PCR. Sin embargo, el desarrollo de nuevos métodos de amplificación de RNA, usando células individuales, ha permitido analizar la expresión génica en ovocitos, complejos cúmulo-ovocito y embriones de preimplantación. Estas técnicas revolucionarán el estudio de la biología reproductiva humana y la reproducción asistida, permitiendo un análisis objetivo y poderoso de los complejos procesos e interacciones del inicio de la vida, explicando las causas de la infertilidad humana y generando nuevas terapéuticas para ésta.

During three decades human embryo and oocyte analyses have been performed based on morphological or cytogenetical evaluations; molecular techniques, like FISH and PCR, have been gradually incorporated. However, the development of new techniques of individual cell RNA amplification has allowed the analysis of gene expression in oocytes, cumulus-oocyte complex and preimplantation embryos. These techniques will change radically the study of human reproductive biology and assisted reproduction, allowing a powerful and objective analysis of the complex processes and the interactions that may explain the causes of infertility and generate new therapeutics.

Construction of an RNase P Ribozyme Library System for Functional Genomics Applications

An RNase P ribozyme library has been developed as a tool for functional genomics studies. Each clone of this library contains a random 18-mer and the sequence of M1 RNA, the catalytic subunit of RNase P. Repression of target gene expression is thus achieved by the complementary binding of mRNA to the random guide sequence and the successive target cleavage via M1 RNA. Cellular expression of the ribozyme expression was confirmed, and EGFP mRNA was used as a model to demonstrate that the RNase P ribozyme expression system can inhibit the target gene expression. The constructed RNase P ribozyme library has a complexity of 1.4x10(7). This novel library system should become a useful in functional genomics, to identify novel gene functions in mammalian cells.