Systems Biology-based Approaches Research Articles

Systems biology of the autophagy-lysosomal pathway

The mechanisms of the control and activity of the autophagy-lysosomal protein degradation machinery are emerging as an important theme for neurodevelopment and neurodegeneration. However, the underlying regulatory and functional networks of known genes controlling autophagy and lysosomal function and their role in disease are relatively unexplored. We performed a systems biology-based integrative computational analysis to study the interactions between molecular components and to develop models for regulation and function of genes involved in autophagy and lysosomal function. Specifically, we analyzed transcriptional and microRNA-based post-transcriptional regulation of these genes and performed functional enrichment analyses to understand their involvement in nervous system-related diseases and phenotypes. Transcriptional regulatory network analysis showed that binding sites for transcription factors, SREBP1, USF, AP-1 and NFE2, are common among autophagy and lysosomal genes. MicroRNA enrichment analysis revealed miR-130, 98, 124, 204 and 142 as the putative post-transcriptional regulators of the autophagy-lysosomal pathway genes. Pathway enrichment analyses revealed that the mTOR and insulin signaling pathways are important in the regulation of genes involved in autophagy. In addition, we found that glycosaminoglycan and glycosphingolipid pathways also make a major contribution to lysosomal gene regulation. The analysis confirmed the known contribution of the autophagy-lysosomal genes to Alzheimer and Parkinson diseases and also revealed potential involvement in tuberous sclerosis, neuronal ceroidlipofuscinoses, sepsis and lung, liver and prostatic neoplasms. To further probe the impact of autophagy-lysosomal gene deficits on neurologically-linked phenotypes, we also mined the mouse knockout phenotype data for the autophagylysosomal genes and found them to be highly predictive of nervous system dysfunction. Overall this study demonstrates the utility of systems biology-based approaches for understanding the autophagy-lysosomal pathways and gaining additional insights into the potential impact of defects in these complex biological processes.

Health technology assessment in the era of personalized health care

This article examines the challenges for health technology assessment (HTA) in the light of new developments of personalized health care, focusing on European HTA perspectives. Using the example of the Integrated Genome Research Network - Mutanom (IG Mutanom) project, with focus on personalized cancer diagnostics and treatment, we assess the scope of current HTA and examine it prospectively in the context of the translation of basic and clinical research into public health genomics and personalized health care. The approaches developed within the IG-Mutanom project are based on innovative technology potentially providing targeted therapies for cancer; making translation into clinical practice requires a novel course of action, however. New models of HTA are needed that can account for the unique types of evidence inherent to individualized targeted therapies. Using constructive health technology assessment (CTA) models is an option, but further suitable models should be developed. Integrative, systems biology-based approaches toward personalized medicine call for novel assessment methods. The translation of their highly innovative technologies into the practice of health care requires the development of new HTA concepts.

Linking biological activity with herbal constituents by systems biology-based approaches: effects of Panax ginseng in type 2 diabetic Goto-Kakizaki rats

Although a number of animal experiments and clinical trials have investigated the effects of ginseng roots on diabetes, the relationship between their therapeutic effects on diabetes and the quality and the growth age of this herb have not yet been reported. This study systematically investigated the effects of 3- to 6-year-old ginseng roots on glycemic and plasma lipid control in a rat model of type 2 diabetes. Six groups of male Goto-Kakizaki (GK) rats received either metformin, 3- to 6-year-old ginseng roots, or no treatment. The treatments were administered twice daily for 9 weeks. A combined approach was used that involved applying liquid chromatography-mass spectrometry-based lipidomics, measuring biochemical parameters and profiling the components of ginseng roots of different ages. Compared to the untreated controls, treatment with 4- and 6-year-old ginseng roots significantly improved glucose disposal, and 5-year-old ginseng treatment significantly increased high density lipoprotein cholesterol. Treatment with 6-year-old ginseng significantly decreased total plasma triacylglyceride (TG) and very-low-density lipoprotein cholesterol and improved plasma glycated hemoglobin (HbA1c). In addition, treatment with 4- to 6-year-old ginseng influenced plasma lipidomics in diabetic GK rats by reducing TG lipid species. Metformin significantly reduced fasting blood glucose by 41% and reduced HbA1c by 11%, but showed no effects on the plasma lipid parameters. The present study demonstrates that ginseng roots show growth age-dependent therapeutic effects on hyperlipidemia and hyperglycemia in diabetic GK rats. These age-dependent effects may be linked with the variation in both the ratios and concentrations of specific bioactive ginsenosides in ginseng roots of different growth ages. This study introduced novel systems biology-based approaches for linking biological activities with potential active components in herbal mixtures.

Systems Biology-Based Approaches to Understand HIV-Exposed Uninfected Women

Worldwide HIV infects women more frequently than men, and it is clear that not all exposed to HIV become infected. Several populations of HIV-exposed uninfected (EU) women have been identified, including discordant couples and sex workers. Understanding what provides natural protection in EU women is critical in vaccine or microbicide development. However, correlates of protection in these women are still unclear. Most studies have used classical methods, examining single genes or cellular factors, a mainstay for traditional immunobiology. This reductionist approach may be limited in the information it can provide. Novel technologies are now available that allow us to take a "systems biology" approach, which allows the study of a complex biological system and identifies factors that may provide protection against HIV infection. Herein we report developments in discovery-based systems biology approaches in EU women and how this broadens our understanding of natural protection against HIV-1.

Enhancement of Soluble Transcription Factor (TAT-HOXB4 and TAT-NUP98HOXA10HD) - Mediated Human Hematopoietic Stem Cell Self-Renewal by Minimizing Inhibitory Endogenous Signalling.

Abstract 1493Poster Board I-516Predictive control of human hematopoietic stem cell (HSC) self-renewal would enable more effective strategies to treat hematologic disease. Although evidence suggests that both cell autonomous (stem cell-associated transcription factors) and cell non-autonomous (the stem cell niche) mechanisms regulate stem cell fate, the dynamic interplay between these regulatory axis are poorly understood. Using a defined synthetic stem cell niche, we have been investigating the role of the transcription factors HOXB4 and the engineered fusion gene between NUP98 and the homeodomain of HOXA10 (NUP98A10HD), provided as soluble membrane-permeable proteins, as clinically relevant reagents to enhance in vitro HSC self-renewal. To aid our understanding of interactions between these complex processes, we have developed systems biology-based approaches to describe and predict cell supportive and non-supportive cell-cell interaction networks. Using a controlled and automated system to achieve semi-continuous protein delivery, and an accompanying model to predict dynamic intracellular protein concentrations, we have optimized strategies for the addition of the TAT-HOXB4 and TAT-NUP98A10HD fusion proteins to umbilical cord blood cultures. Our results demonstrate that an optimized delivery scheme of 1.5nM (from day 0-4) and 6nM (from day 4-8) every 30min, produces stable intracellular levels of TAT-HOXB4, and results in a increase of primitive progenitor cells, as measured by colony counts from bulk long term culture-initiating cell (LTC-IC) assays, of 1.9x greater than the classic, non-optimized TAT-HOXB4 delivery scheme (40nM every 4h) and 3.1x greater than untreated control cells. Ongoing studies are extending these significantly enhanced primitive progenitor outputs to HSC self-renewal using the NOD/SCID repopulating cell assay. Our results thus far demonstrate that the nuclear concentrations of HSC-associated transcription factors can significantly impact stem cell self-renewal. In these studies we also observed, for the first time, that endogenously produced secreted factors limit HSC output, and that TAT-HOXB4 acts to desensitize the primitive blood progenitor cells to negative feedback regulation by secreted factors. As a means of prospectively regulating the levels of endogenously produced factors in culture, we have implemented a media delivery approach, in which cell culture media volume is adjusted throughout the culture period, to counteract increasing negative inhibitors by endogenously produced secreted factors. Using this “fed-batch” delivery approach, we have achieved significant (p<0.05) improvement in the total cell number (TNC), colony forming cells (CFCs), and LTC-ICs, of 4.6x, 4.9x, and 4.1x respectively, above the blood stem and progenitor numbers obtained from untreated control cells. Furthermore, data suggests that this non-autonomous regulation promotes HSC self-renewal for a more prolonged period in vitro, with total expansions after 12 days of culture reaching 80x for CFCs and 22x for LTC-ICs. Media dilution strategies have been optimized to further limit negative feedback from mature cell types by monitoring and counteracting rising concentrations of specific critical factors, such as TGF-β1. Collectively, these studies shed new insight into the complexity of strict HSC regulation to predictively enhance in vitro HSC self-renewal, and provide evidence that overcoming cell non-autonomous control of HSC self-renewal should enable novel strategies to enhance endogenous stem cell growth. Disclosures:No relevant conflicts of interest to declare.

The resolution of the genetics of gene expression

Understanding the influence of genetics on the molecular mechanisms underpinning human phenotypic diversity is fundamental to being able to predict health outcomes and treat disease. To interrogate the role of genetics on cellular state and function, gene expression has been extensively used. Past and present studies have highlighted important patterns of heritability, population differentiation and tissue-specificity in gene expression. Current and future studies are taking advantage of systems biology-based approaches and advances in sequencing technology: new methodology aims to translate regulatory networks to enrich pathways responsible for disease etiology and 2nd generation sequencing now offers single-molecular resolution of the transcriptome providing unprecedented information on the structural and genetic characteristics of gene expression. Such advances are leading to a future where rich cellular phenotypes will facilitate understanding of the transmission of genetic effect from the gene to organism.

Approaches to Biomarkers in Human Colorectal Cancer: Looking Back, to go Forward

Like all human cancers, colorectal cancer is a complicated disease. While a mature body of research involving colorectal cancer has implicated the putative sequence of genetic alterations that trigger the disease and sustain its progression, there is a surprising paucity of well-validated, clinically useful diagnostic markers of this disease. For prognosis or guiding therapy, single gene-based markers of colorectal cancer often have limited specificity and sensitivity. Genome-wide analyses (microarrays) have been used to propose candidate patterns of gene expression that are prognostic of outcome or predict the tumor's response to a therapy regimen; however, these patterns frequently do not overlap, and this has raised questions concerning their use as biomarkers. The limitation of gene-expression approaches to marker discovery occurs because the change in mRNA expression across tumors is highly variable and, alone, accounts for a limited variability of the phenotype, such as with cancer. More robust and accurate markers of cancer will result from integrating all the information we have about the cell: genomics, proteomics and interactomics. This article will discuss traditional markers in colorectal cancer, both genomic and proteomic, including their respective approaches and limitations, then conclude with examples of systems biology-based approaches for candidate marker discovery, and discuss how this approach is reshaping our view of a biomarker.

Evaluating Disorders with a Complex Genetics Basis. The Future Roles of Meta-analysis and Systems Biology

Growing evidence suggests that complex gene and environment interactions underlie a number of diseases including chronic inflammatory diseases of the digestive system. The rapid advances in information and technology provide opportunities to discover the risks or etiology for a variety of disorders within individual patients. However, the availability of new data and new technology has outstripped the conceptual framework of simple disorders and challenges current statistical approaches. Here we address the issues surrounding study design and sample size for complex genetic traits, with special attention to meta-analysis and systems biology. We conclude that meta-analysis should play a limited role in evaluating studies of complex genetic diseases. Instead, systems biology-based approaches should be developed to integrate multiple, focused, and mechanistic association studies with the goal of assisting in the risk assessment of patients on a person-by-person basis.

Proteomics and systems biology approaches to signal transduction in sepsis.

Sepsis and resulting multiple system organ failure are the leading causes of mortality in intensive care units. Although it is generally appreciated that rampant, deregulated inflammatory pathways play a major role in sepsis, a comprehensive understanding based on the integrated response of multiple signal transduction pathways has remained elusive. Here we review the main signal transduction pathways involved in the progression from inflammation to sepsis and discuss emerging genomic, proteomic, and systems biology approaches to decipher how these signaling pathways converge to cause the septic state. We propose that an integrative approach involving functional proteomics will provide a quantitative and mechanistic description that unifies inflammatory signaling networks in sepsis and will identify critical regulatory nodes for therapeutic manipulation. These types of systems biology-based approaches may lead to more effective therapies than those currently available.