多组学技术及其在生命科学研究中应用概述

随着新一代测序技术、高分辨质谱技术、多组学整合分析方法及数据库的发展,组学技术正从传统的单一组学向多组学技术发展。以多组学驱动的系统生物学研究将带来生命科学研究的新范式。本文简要概述了基因组学、表观基因组学、转录组学,蛋白质组学及代谢组学的进展,重点介绍多组学技术平台的组成和功能,多组学技术的应用现状及在合成生物学及生物医学等领域的应用前景。     

Post‐genomic behavioral genetics: From revolution to routine

What was once expensive and revolutionary—full‐genome sequence—is now affordable and routine. Costs will continue to drop, opening up new frontiers in behavioral genetics. This shift in costs from the genome to the phenome is most notable in large clinical studies of behavior and associated diseases in cohorts that exceed hundreds of thousands of subjects. Examples include the Women's Health Initiative ( www.whi.org ), the Million Veterans Program ( www.research.va.gov/MVP ), the 100 000 Genomes Project ( genomicsengland.co.uk ) and commercial efforts such as those by deCode ( www.decode.com ) and 23andme ( www.23andme.com ). The same transition is happening in experimental neuro‐ and behavioral genetics, and sample sizes of many hundreds of cases are becoming routine ( www.genenetwork.org , www.mousephenotyping.org ). There are two major consequences of this new affordability of massive omics datasets: (1) it is now far more practical to explore genetic modulation of behavioral differences and the key role of gene‐by‐environment interactions. Researchers are already doing the hard part—the quantitative analysis of behavior. Adding the omics component can provide powerful links to molecules, cells, circuits and even better treatment. (2) There is an acute need to highlight and train behavioral scientists in how best to exploit new omics approaches. This review addresses this second issue and highlights several new trends and opportunities that will be of interest to experts in animal and human behaviors.     

Beyond the Sterility of a Distinct African Bioethics: Addressing the Conceptual Bioethics Lag in Africa

In the current debate on the future of bioethics in Africa, several authors have argued for a distinct communitarian African bioethics that can counter the dominancy of Western atomistic principlism in contemporary bioethics. In this article I examine this rather contentious argument and evaluate its validity and viability. Firstly, I trace the contextual origins of contemporary bioethics and highlight the rise and dominance of principlism. I particularly note that principlism was premised on a content‐thin notion of the common morality that is in need of enrichment. I also contend that bioethics is essentially two‐dimensional, being both conceptual and empirical, and indicate the lag in Africa with regard to conceptual bioethics. I then appeal for authentic engagement by 1) African health care professionals, 2) African health care training institutions, 3) Africa's bioethics development partners, and 4) African bioethicists and philosophers, towards addressing this critical lag. I underline the need to maintain the essential universality of bioethics as a discipline. I particularly argue against the pursuit of a distinct African bioethics, as it appears to be rooted in sterile African ethno‐philosophy. Rather, African bioethicists and philosophers would do well to elucidate the universalisability of insights from traditional African thought, for the benefit of bioethics as a whole. Thus we must engage beyond the sterility of a distinct African bioethics ‐ authentically reflecting on the essentially universal contemporary bioethical concerns ‐ to effectively articulate a viable trajectory for bioethics in Africa.     

Ovarian stem cells: From basic to clinical applications

The field of reproductive biology has undergone significant developments in the last decade. The notion that there is a fixed reserve pool of oocytes before birth was established by Zuckerman in 1951. However, in 2004, an article published in nature challenged this central dogma of mammalian reproductive biology. Tilly’s group reported the existence of ovarian germline stem cells (GSCs) in postnatal ovaries of mice and suggested that the bone marrow could be an extragonadal source of ovarian GSCs. These findings were strongly criticized; however, several independent groups have since successfully isolated and characterized ovarian GSCs in postnatal mice. The ovarian GSCs are located in the ovarian surface epithelium and express markers of undifferentiated GSCs. When transplanted into mouse ovaries, mouse ovarian GSCs could differentiate and produce embryos and offspring. Similarly, in a recent study, ovarian GSCs were found to be present in the ovaries of women of reproductive age. Conversely, there is increasing evidence that stem cells responsible for maintaining a healthy state in normal tissue may be a source of some cancers, including ovarian cancer. Cancer stem cells (CSCs) have been found in many tissues, including ovaries. Some researchers have suggested that ovarian cancer may be a result of the transformation and dysfunction of ovarian GSCs with self-renewal properties. Drug resistant and metastasis-generating CSCs are responsible for many important problems affecting ovarian cancer patients. Therefore, the identification of CSCs will provide opportunities for the development of new therapeutic strategies for treatments for infertility and ovarian cancer. In this article, we summarize the current understanding of ovarian GSCs in adult mammals, and we also discuss whether there is a relationship between GSCs and CSCs.     

Single cell human genomic analyses: a way to refine the knowledge of cellular heterogeneity origins in individual subject

Single cell genomics performed on individual human subjects' tumors, neural tissues, and sperm samples revealed the existence of genetic heterogeneity arising through either mutations in exomes, deletions, recombinations, and duplications of DNA sequences, as well as aneuploidy. These genetic changes happen during cell cycles followed by cell division. The aim of this review is to strictly focus on single cell human genomics and intends to deliver information that can help to refine fundamental knowledge relating to genetic causes of cellular heterogeneity origins in both healthy and disease states. Allogenic heterogeneity as well as heterogeneity origins of cells possessing the same genome with different gene expression patterns is not the subject of this review. Future research still requires: a) improvement for complete and errorless DNA acquisition and sequencing of not only selected parts of the genome, and b) analyses of more samples that contain millions of cells. These data will deliver a more precise comparative representation of genetic diversity among single cells in an individual human subject. Consequently, we will be able to better distinguish between the role of genetic, versus epigenetic, and stochastic factors in the cellular diversity of over 30 trillion cells present in a human body.     

Variable conceptions of population in community resource genetic projects: a challenge for governance

In recent years, human genetic research has developed rapidly, and the cost of sequencing and computational technology continues to decline. This research has also been pushed forward by a major organizational innovation: the development of large, open-access databases of human gene sequences or biospecimens known as community resource projects. This article describes a challenge for the governance of these projects: conceptions of population vary significantly across organizational contexts. This makes it difficult to manage risk appropriately, as measures intended to address hazards to one kind of population may be inadequate for others. Unstable conceptions of population may also make it difficult to identify the stakeholders interested in the governance of these projects. This argument is developed by examining two cases, the International HapMap Project and 1000 Genomes Project, which make use of at least six distinct conceptions of population in different organizational segments.     

A VIP hybrid antagonist: From developmental neurobiology to clinical applications

Summary 1. The 28 amino acid vasoactive intestinal peptide, VIP, was originally isolated from the intestine, following a bioassay measuring vasodilating properties. Immunocytochemistry, receptor binding assays and in situ hybridizations have demonstrated VIP abundance in the nervous system, suggesting multiple bioactivities.2. A pharmacological approach was chosen to dissect VIP activities and a prototype VIP antagonist (Met-Hybrid) consisting of a carboxyl fragment of VIP_7–28 and a six amino acid fragment of neurotensin, neurotensin_6–11-VIP_7–28 was synthesized.3. This hybrid peptide was designed to maintain the binding capacity of one parent molecule (VIP), while loosing the agonistic properties, representing a classical competitive receptor antagonist. Furthermore, the new molecule exhibited increased specificity to central nervous system VIP receptors.4. The Met-Hybrid was originally discovered as a potent inhibitor of VIP functionin vivo. In the adult rodent, acute administration of the antagonist resulted in blockade of VIP-mediated potentiation of sexual behavior and chronic intracerebroventricular application impaired VIP-associated learning abilities. During ontogeny, chronic injections of the molecule resulted in neuronal damage, disruption of the diurnal rhythmicity of motor behavior, and retardation in the acquisition of neonatal reflexes in the rat.5. During gestation, severe microcephaly was induced by acute administration of the Met-Hybrid to pregnant mice. The hybrid antagonist inhibited VIP-stimulated mitosis in whole embryo cultures and in a variety of cancer cell linesin vitro andin vivo, suggesting therapeutical potential.     

On Abortion: Exploring Psychological Meaning and Attitudes in a Sample of Mexican Gynecologists

Elective abortion has become an issue of ethical and political debate in many countries including Mexico. As gynecologists are directly involved in the practice of abortion, it is important to know the psychological meaning that the term ‘elective abortion’ has for them. This study explores the psychological meaning and attitudes toward elective abortion of one hundred and twenty‐three Mexican gynecologists. We used the semantic networks technique, which analyzed the words the participants associated with the term ‘elective abortion’. The defining words most frequently used by participants implied a negative sanction. There were important differences by gender and religiosity: male gynecologists, as well as those with strong religious beliefs (mainly Catholics), revealed a more negative psychological meaning and more negative attitudes than females or physicians with weak religious beliefs. A contribution of the present study is that it highlights the importance of psychology to enhancing understanding of the issue of elective abortion.     

Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

Speciation, the evolution of reproductive isolation among populations, is continuous, complex, and involves multiple, interacting barriers. Until it is complete, the effects of this process vary along the genome and can lead to a heterogeneous genomic landscape with peaks and troughs of differentiation and divergence. When gene flow occurs during speciation, barriers restricting gene flow locally in the genome lead to patterns of heterogeneity. However, genomic heterogeneity can also be produced or modified by variation in factors such as background selection and selective sweeps, recombination and mutation rate variation, and heterogeneous gene density. Extracting the effects of gene flow, divergent selection and reproductive isolation from such modifying factors presents a major challenge to speciation genomics. We argue one of the principal aims of the field is to identify the barrier loci involved in limiting gene flow. We first summarize the expected signatures of selection at barrier loci, at the genomic regions linked to them and across the entire genome. We then discuss the modifying factors that complicate the interpretation of the observed genomic landscape. Finally, we end with a road map for future speciation research: a proposal for how to account for these modifying factors and to progress towards understanding the nature of barrier loci. Despite the difficulties of interpreting empirical data, we argue that the availability of promising technical and analytical methods will shed further light on the important roles that gene flow and divergent selection have in shaping the genomic landscape of speciation.     

Sites of retroviral DNA integration: From basic research to clinical applications

One of the most crucial steps in the life cycle of a retrovirus is the integration of the viral DNA (vDNA) copy of the RNA genome into the genome of an infected host cell. Integration provides for efficient viral gene expression as well as for the segregation of viral genomes to daughter cells upon cell division. Some integrated viruses are not well expressed, and cells latently infected with human immunodeficiency virus type 1 (HIV-1) can resist the action of potent antiretroviral drugs and remain dormant for decades. Intensive research has been dedicated to understanding the catalytic mechanism of integration, as well as the viral and cellular determinants that influence integration site distribution throughout the host genome. In this review, we summarize the evolution of techniques that have been used to recover and map retroviral integration sites, from the early days that first indicated that integration could occur in multiple cellular DNA locations, to current technologies that map upwards of millions of unique integration sites from single in vitro integration reactions or cell culture infections. We further review important insights gained from the use of such mapping techniques, including the monitoring of cell clonal expansion in patients treated with retrovirus-based gene therapy vectors, or patients with acquired immune deficiency syndrome (AIDS) on suppressive antiretroviral therapy (ART). These insights span from integrase (IN) enzyme sequence preferences within target DNA (tDNA) at the sites of integration, to the roles of host cellular proteins in mediating global integration distribution, to the potential relationship between genomic location of vDNA integration site and retroviral latency.     

The estrogen-regulated 52K-cathepsin-D in breast cancer: From biology to clinical applications

We have studied estrogen-regulated proteins in an attempt to understand the mechanism by which estrogens stimulate cell proliferation and mammary carcinogenesis. In estrogen receptor positive human breast cancer celllines (MCF7, ZR75-1) estrogens specifically increase the production into the culture medium of a 52,000 daltons (52K) glycoprotein. Several high affinity monoclonal antibodies to the partially purified secretory 52K protein have allowed to purify to homogeneity this protein and its cellular processed products. The 52K protein has been identified as the secreted precursor of a cathepsin-D like protease bearing mannose-6-phosphate signals and routed to lysosomes via mannose-6-phosphate receptor. The protease is mitogenic in vitro on estrogen deprived MCF7 cells and is able to degrade basement membrane and proteoglycans following its activation. The cellular related proteins, as detected by immunohistochemistry and immunoassay are more concentrated in proliferative mammary ducts than in resting ducts and their concentration in breast cancer cytosol appears to be more correlated with lymph nodes invasion and disease free survival (with S. Thorpe, Copenhagen) than with the estrogen receptor (RE) level. The protein is also produced constitutively by RE-negative cell lines, while in some antiestrogen resistant variants, it becomes inducible by tamoxifen, contrary to the wild type MCF7 cells. Cloning of its cDNA in λgt11 has allowed to show that the mRNA is rapidly induced by estrogens and to sequence the protein and compare it to that of the normal human kidney cathepsin-D. We conclude that the estrogen-induced cathepsin-D like protease may have important autocrine and/or paracrine functions in stimulating the growth and invasion of hormone-dependent and independent breast cancers and may be useful as a tissue marker to predict high risk mastopathies and breast cancer invasiveness, In addition to other estrogen regulated growth factors, the precursor of lysosomal proteases has the potential to stimulate the proliferation and invasiveness of breast cancer cells as long as they are secreted in excess rather than being routed to lysosomes.     

From genome to proteome: great progress in the domesticated silkworm (Bombyx mori L.)

As the only truly domesticated insect, the silkworm not only has great economic value, but it also has value as a model for genetics and molecular biology research. Genomics and proteomics have recently shown vast potential to be essential tools in domesticated silkworm research, especially after the completion of the Bombyxmori genome sequence. This paper reviews the progress of the domesticated silkworm genome, particularly focusing on its genetic map, physical map and functional genome. This review also presents proteomics, the proteomic technique and its application in silkworm research.     

Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees

The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomic analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood‐decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens and trunk pathogen Porodaedalea pini. Many gene families of lignin‐degrading enzymes were identified from these fungi, reflecting their ability as white rot fungi. Comparing against distant fungi highlighted the expansion of 1,3‐beta‐glucan synthases in P. noxius, which may account for its fast‐growing attribute. We identified 13 linkage groups conserved within Agaricomycetes, suggesting the evolution of stable karyotypes. We determined that P. noxius has a bipolar heterothallic mating system, with unusual highly expanded ~60 kb A locus as a result of accumulating gene transposition. We investigated the population genomics of 60 P. noxius isolates across multiple islands of the Asia Pacific region. Whole‐genome sequencing showed this multinucleate species contains abundant poly‐allelic single nucleotide polymorphisms with atypical allele frequencies. Different patterns of intra‐isolate polymorphism reflect mono‐/heterokaryotic states which are both prevalent in nature. We have shown two genetically separated lineages with one spanning across many islands despite the geographical barriers. Both populations possess extraordinary genetic diversity and show contrasting evolutionary scenarios. These results provide a framework to further investigate the genetic basis underlying the fitness and virulence of white rot fungi.     

CXCL8 in thyroid disease: From basic notions to potential applications in clinical practice

CXCL8 was the first chemokine shown to be secreted by thyrocytes. Experimental data suggest that CXCL8 plays a role in thyroid homeostasis but its role in thyroid diseases remains poorly investigated. Clinical studies measuring the serum levels of CXCL8 in patients with autoimmune-thyroid-diseases reported conflicting results. Solid evidences support a role of CXCL8 as a tumor-promoting agent in several human cancers. Studies in thyroid cancer are still in their initial stage, but promising. Several evidences indicate that thyroid cancer may share with other human malignancies some of the effects of CXCL8 and highlight the possibility of using CXCL8 as a marker of aggressiveness. Basic and clinical evidences in favor or against a role for CXCL8 in thyroid diseases are discussed.     

The Path to Enlightenment： Making Sense of Genomic and Proteomic Information

Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.     

A hot topic: the genetics of adaptation to geothermal vents in Mimulus guttatus

Identifying the individual loci and mutations that underlie adaptation to extreme environments has long been a goal of evolutionary biology. However, finding the genes that underlie adaptive traits is difficult for several reasons. First, because many traits and genes evolve simultaneously as populations diverge, it is difficult to disentangle adaptation from neutral demographic processes. Second, finding the individual loci involved in any trait is challenging given the respective limitations of quantitative and population genetic methods. In this issue of Molecular Ecology, Hendrick et al. (2016) overcome these difficulties and determine the genetic basis of microgeographic adaptation between geothermal vent and nonthermal populations of Mimulus guttatus in Yellowstone National Park. The authors accomplish this by combining population and quantitative genetic techniques, a powerful, but labour‐intensive, strategy for identifying individual causative adaptive loci that few studies have used (Stinchcombe & Hoekstra 2008 ). In a previous common garden experiment (Lekberg et al. 2012), thermal M. guttatus populations were found to differ from their closely related nonthermal neighbours in various adaptive phenotypes including trichome density. Hendrick et al. (2016) combine quantitative trait loci (QTL) mapping, population genomic scans for selection and admixture mapping to identify a single genetic locus underlying differences in trichome density between thermal and nonthermal M. guttatus. The candidate gene, R2R3 MYB, is homologous to genes involved in trichome development across flowering plants. The major trichome QTL, Tr14, is also involved in trichome density differences in an independent M. guttatus population comparison (Holeski et al. 2010) making this an example of parallel genetic evolution.     

MicroRNAs and long non-coding RNAs in pancreatic cancer: From epigenetics to potential clinical applications

MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two relevant classes of non-coding RNAs (ncRNAs) that play a pivotal role in a number of molecular processes through different epigenetic regulatory mechanisms of gene expression. As a matter of fact, the altered expression of these types of RNAs leads to the development and progression of a varied range of multifactorial human diseases. Several recent reports elucidated that miRNA and lncRNAs have been implicated in pancreatic cancer (PC). For instance, dysregulation of such ncRNAs has been found to be associated with chemoresistance, apoptosis, autophagy, cell differentiation, tumor suppression, tumor growth, cancer cell proliferation, migration, and invasion in PC. Moreover, several aberrantly expressed miRNAs and lncRNAs have the potential to be used as biomarkers for accurate PC diagnosis. Additionally, miRNAs and lncRNAs are considered as promising clinical targets for PC. Therefore, in this review, we discuss recent experimental evidence regarding the clinical implications of miRNAs and lncRNAs in the pathophysiology of PC, their future potential, as well as the challenges that have arisen in this field of study in order to drive forward the design of ncRNA-based diagnostics and therapeutics for PC.