Systems-level Approach Research Articles

Scaled traumatic brain injury results in unique metabolomic signatures between gray matter, white matter, and serum in a piglet model.

Traumatic brain injury (TBI) is a leading cause of death and long-term disability in the United States. The heterogeneity of the disease coupled with the lack of comprehensive, standardized scales to adequately characterize multiple types of TBI remain to be major challenges facing effective therapeutic development. A systems level approach to TBI diagnosis through the use of metabolomics could lead to a better understanding of cellular changes post-TBI and potential therapeutic targets. In the current study, we utilize a GC-MS untargeted metabolomics approach to demonstrate altered metabolism in response to TBI in a translational pig model, which possesses many neuroanatomical and pathophysiologic similarities to humans. TBI was produced by controlled cortical impact (CCI) in Landrace piglets with impact velocity and depth of depression set to 2m/s;6mm, 4m/s;6mm, 4m/s;12mm, or 4m/s;15mm resulting in graded neural injury. Serum samples were collected pre-TBI, 24 hours post-TBI, and 7 days post-TBI. Partial least squares discriminant analysis (PLS-DA) revealed that each impact parameter uniquely influenced the metabolomic profile after TBI, and gray and white matter responds differently to TBI on the biochemical level with evidence of white matter displaying greater metabolic change. Furthermore, pathway analysis revealed unique metabolic signatures that were dependent on injury severity and brain tissue type. Metabolomic signatures were also detected in serum samples which potentially captures both time after injury and injury severity. These findings provide a platform for the development of a more accurate TBI classification scale based unique metabolomic signatures.

The Perfect Pitch: Attaining Institutional Buy-In for Well-Being Initiatives

By the end of the Workshop, participants will be able to do as follows: 1) discuss 2 to 3 salient points about the trends in the well-being of child and adolescent psychiatrist, business benefits of well-being initiatives, and system benefits when well-being is promoted and sustained; and 2) use “pitch” skills to effectively communicate around promoting awareness of burnout and well-being, financial and business benefits of institutional support for well-being, and enacting systems-level approaches for well-being.

Closing Thoughts: On the Power of Youth and System Change

Change is happening in the Cooperative Extension System as the organization focuses its efforts on the overall goal of creating a culture of health in the United States. Well Connected Communities is a Cooperative Extension and National 4-H Council initiative supported by the Robert Wood Johnson Foundation that involves modeling a systems-level approach to community efforts versus an individual prevention model. The initiative also engages the power of youth to catalyze progress for communities to achieve their best health and well-being.

Neurotransmitter identity and electrophysiological phenotype are genetically coupled in midbrain dopaminergic neurons

Most neuronal types have a well-identified electrical phenotype. It is now admitted that a same phenotype can be produced using multiple biophysical solutions defined by ion channel expression levels. This argues that systems-level approaches are necessary to understand electrical phenotype genesis and stability. Midbrain dopaminergic (DA) neurons, although quite heterogeneous, exhibit a characteristic electrical phenotype. However, the quantitative genetic principles underlying this conserved phenotype remain unknown. Here we investigated the quantitative relationships between ion channels’ gene expression levels in midbrain DA neurons using single-cell microfluidic qPCR. Using multivariate mutual information analysis to decipher high-dimensional statistical dependences, we unravel co-varying gene modules that link neurotransmitter identity and electrical phenotype. We also identify new segregating gene modules underlying the diversity of this neuronal population. We propose that the newly identified genetic coupling between neurotransmitter identity and ion channels may play a homeostatic role in maintaining the electrophysiological phenotype of midbrain DA neurons.

Multidisciplinary approaches for studying rhizobium-legume symbioses.

The rhizobium-legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.

PKCε contributes to lipid-induced insulin resistance through cross talk with p70S6K and through previously unknown regulators of insulin signaling

Insulin resistance drives the development of type 2 diabetes (T2D). In liver, diacylglycerol (DAG) is a key mediator of lipid-induced insulin resistance. DAG activates protein kinase C ε (PKCε), which phosphorylates and inhibits the insulin receptor. In rats, a 3-day high-fat diet produces hepatic insulin resistance through this mechanism, and knockdown of hepatic PKCε protects against high-fat diet-induced hepatic insulin resistance. Here, we employed a systems-level approach to uncover additional signaling pathways involved in high-fat diet-induced hepatic insulin resistance. We used quantitative phosphoproteomics to map global in vivo changes in hepatic protein phosphorylation in chow-fed, high-fat-fed, and high-fat-fed with PKCε knockdown rats to distinguish the impact of lipid- and PKCε-induced protein phosphorylation. This was followed by a functional siRNA-based screen to determine which dynamically regulated phosphoproteins may be involved in canonical insulin signaling. Direct PKCε substrates were identified by motif analysis of phosphoproteomics data and validated using a large-scale in vitro kinase assay. These substrates included the p70S6K substrates RPS6 and IRS1, which suggested cross talk between PKCε and p70S6K in high-fat diet-induced hepatic insulin resistance. These results identify an expanded set of proteins through which PKCε may drive high-fat diet-induced hepatic insulin resistance that may direct new therapeutic approaches for T2D.

Achieving Health System Wide 90 Minute Door-to-balloon Times for STEMI Transfers

Introduction Most patients experiencing STEMI present to facilities that lack interventional cardiology services, thus requiring transport to a tertiary center. The national D2B goal time for patients requiring interfacility transfer is 120 minutes or less; our previous work achieved that goal by implementing an STEMI autolaunch process. To further improve D2B times for transfer patients we took a systems level approach to develop a high reliability STEMI transfer system. The primary interventions, system changes, and results are presented. Methods This was a quality improvement project that entailed a collaboration between the Emergency Services Institute, Heart and Vascular Institute, Critical Care Transport, health system community hospitals and local emergency medical services throughout our region. Over 18 months, system changes were developed by the interdisciplinary team (Table 1), implemented, and evaluated with feedback provided to all involved on a monthly basis. Results Patients presenting to community hospital ED's experienced a 16 minute reduction in door-in-door-out time (now 44 minutes versus 60 minutes). Additionally the mean D2B times for all patients requiring transfer in the health system reduced to and remained at 90 minutes for 12 consecutive months in 2017. Reported mortality at the project start was below the 50th percentile and now exceeds the 90th percentile nationally. Conclusion Our results show that improving and maintaining D2B times for patients needing interfacility transfer requires a systems level approach that must encompass the entire healthcare system from initial patient activation through to discharge. The interventions developed can be adapted and applied in other settings.

Modeling patient access to therapeutic oxytocin in Zanzibar, Tanzania

BackgroundOur objective is to estimate the effects of therapeutic oxytocin supply chain factors and social determinants of health on patient access to oxytocin in low-income settings using system dynamics modeling. Postpartum hemorrhage (PPH), a major cause of maternal mortality disproportionately affects women in low and middle income countries (LMICs). The World Health Organization recommends therapeutic oxytocin as the frontline uterotonic for PPH management and prevention. However, lack of access to quality therapeutic oxytocin in Tanzania, and throughout Sub-Saharan Africa, continues to result in a high number of preventable maternal deaths.MethodsWe used publicly available data from Zanzibar and Sub-Saharan Africa, literature review, oxytocin degradation kinetics and previously developed systems dynamics models to understand the barriers in patient access to quality therapeutic oxytocin.ResultsThe model makes four basic predictions. First, there is a major gap between therapeutic oxytocin procurement and availability. Second, it predicts that at current population increase rates, oxytocin supply will have to be doubled in the next 30 years. Third, supply and storage temperature until 30 °C has minimal effect on oxytocin quality and finally distance of 5 km or less to birthing facility has a small effect on overall access to oxytocin.ConclusionsThe model provides a systems level approach to therapeutic oxytocin access, incorporating supply and procurement, socio-economic factors, as well as storage conditions to understand how women’s access to oxytocin over time can be sustained for better health outcomes.

Evolving wastewater infrastructure paradigm to enhance harmony with nature.

Restoring and improving harmony between human activities and nature are essential to human well-being and survival. The role of wastewater infrastructure is evolving toward resource recovery to address this challenge. Yet, existing design approaches for wastewater systems focus merely on technological aspects of these systems. If system design could take advantage of natural ecological processes, it could ensure infrastructure development within ecological constraints and maximize other benefits. To test this hypothesis, we illustrate a data-driven, systems-level approach that couples natural ecosystems and the services they deliver to explore how sustainability principles could be embedded into the life phases of wastewater systems. We show that our design could produce outcomes vastly superior to those of conventional paradigms that focus on technologies alone, by enabling high-level recovery of both energy and materials and providing substantial benefits to offset a host of unintended environmental effects. This integrative study advances our understanding and suggests approaches for regaining a balance between satisfying human demands and maintaining ecosystems.

A stepped care approach to clinical suicide prevention.

Despite the enormous humanitarian and economic toll of suicide, mental health systems of care are largely underprepared to work effectively with suicidal individuals and suicide is a leading "Sentinel Event" in U.S. health care settings (The Joint Commission, 2016). In response to these concerns, a recent policy initiative called "Zero Suicide" has advocated a systems-level response to the suicidal risk within health care and this policy initiative is yielding positive results (Hogan & Goldstein Grumet, 2016). Along these lines, a "stepped care" approach developed by Jobes (2016) has been adapted and used within the Zero Suicide curriculum as a model for systems-level care that is suicide-specific, evidence-based, least-restrictive, and cost-effective. The Collaborative Assessment and Management of Suicidality (CAMS) is an example of one suicide-specific evidence-based clinical intervention that can be adapted and used across the full range of stepped care service settings (Jobes, 2016). This article describes various applications and uses of CAMS at all service levels and highlights CAMS-related innovations. It is argued that psychological services are uniquely poised to make a major difference in clinical suicide prevention through a systems-level approach using evidence-based care such as CAMS. (PsycINFO Database Record

Enhancing Family Engagement in Schoolwide Positive Behavioral Interventions and Supports

Schoolwide positive behavioral interventions and supports (PBIS) is a systems-level approach to promote appropriate behavior, increase academic achievement, and improve school climate. The PBIS infrastructure engages families as partners in school systems and extends evidence-based positive behavior support to the home. The article discusses a pilot investigation and describes objectives, associated activities, and implementation guidance to engage families as partners in PBIS.

Abstract 281: Identifying genetic variation and cellular heterogeneity with a comprehensive cancer analysis toolkit

Abstract Understanding disease development, progression and response to treatment remains elusive for most types of cancer. This is due both to the genetic complexity seen in tumors as well as differences in how the surrounding cells and immune system respond to the developing tumor. To fully understand all aspects of disease progression and response to treatment, a systems level approach is needed. We have developed a platform that allows for high resolution multi-omics analysis of the tumor and its microenvironment. This platform is built upon a microfluidic system that enables the production of hundreds of thousands to millions of partitioned barcoded reactions. On this platform we generate Linked-Reads that allow for the detailed resolution of complex structural variant events. To obtain more detailed information about tumor heterogeneity and clonal structure, we also perform single cell DNA analysis that allows for the detection of sub-megabase copy number variants at the single cell level.The platform also provides detailed resolution of the cells occupying the microenvironment surrounding the tumor. Using a combination of single cell gene expression and enriched V(D)J B and T cell repertoire analysis, we identify cells constituting a tumor, as well as the immune and nonimmune cells surrounding the tumor. We also provide single cell profiling of the paired antigen receptor chains for both B and T cells. As a demonstration, we have performed this analysis on three types of tumor samples: metastatic melanoma (MM), primary colorectal cancer (CRC) and primary clear cell renal carcinoma (CCRC). We are able to identify a clonal expansion in the CCRC sample and determine there is no expansion in the CRC sample. The combination of these approaches allows for unparalleled characterization of disease development, progression and response. Citation Format: Sarah Garcia, Rajiv Bharadwaj, Stéphane Boutet, Claudia Catalanotti, Valeria Giangerra, Josephine Lee, Jessica Terry, Stephen Williams, Grace X. Zheng, Tarjei Mikkelsen, Michael Schnall-Levin, Ben Hindson, Deanna M. Church. Identifying genetic variation and cellular heterogeneity with a comprehensive cancer analysis toolkit [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 281.

Abstract 1322: A systems-level approach identifies novel links between iron and fatty acid metabolism in high-grade serous ovarian cancer

Abstract The low survival rate for high-grade serous ovarian cancer (HGSOC) motivates novel approaches to identify causative and therapeutically targetable factors involved in HGSOC initiation and progression. Cancer cells are known to sequester iron, which can potentiate cancer progression via mechanisms that have not yet been completely elucidated. In order to uncover novel, and potentially therapeutically tractable links, between iron and HGSOC, we developed an algorithm to identify perturbed regulatory pathways containing differentially expressed iron-related genes in microarray data from clinical sources and an experimental model of HGSOC. Used in tandem with over-representation analysis for iron-related genes, the algorithm led us to uncover an iron dependence of fatty acid import and synthesis pathways, which are upregulated in HGSOC and other cancers, and to develop a network synthesizing the relationship between iron, fatty acid metabolism, and HGSOC. We use the network to derive specific hypotheses of mechanisms by which iron impacts fatty acid metabolic pathways to promote tumorigenesis. We have thus shown that a systems-level approach to identifying novel regulatory links between iron and HGSOC has yielded a previously unappreciated association between iron and fatty acid metabolism that may be exploited for therapeutic potential. This work has been supported in part by NIH grants F32CA214030 to AK, R01CA188025 to SVT, and RO1CA171101 to FMT. Citation Format: Anna Konstorum, Miranda L. Lynch, Suzy V. Torti, Frank M. Torti, Reinhard C. Laubenbacher. A systems-level approach identifies novel links between iron and fatty acid metabolism in high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1322.

Abstract 3298: High-content phenotyping of somatic cancer mutations by functional variomics

Abstract Cancer genomes are highly complex with numerous somatic mutations identified across patient populations. Previous studies on genomic mutations have shed light on new means for cancer therapeutic interventions. With rapid advances in next-generation sequencing, accumulating genotypic information in the absence of efficient and systematic functional analyses of genomic aberrations will create a bottleneck in understanding genotype-phenotype relationships in cancer. To address these challenges, here we report a systems-level functional variomics approach integrating high-throughput phenotyping with robust computational analyses to investigate mutation-specific effects. This systematic functional platform consists of massively parallel mutagenesis, sensitive survival assays using growth factor-dependent cell models, and functional network perturbation profiling of mutations on signaling effects. We profile several thousands of genomic aberrations, including point mutations, gene fusions and indels, and significantly expand the repertoire of characterized actionable mutations. This study represents a valuable resource and provides insights in prioritizing cancer-causing mutations, and uncovering patient-specific disease mechanisms at a high resolution, a critical step towards personalized precision medicine. Citation Format: Nidhi Sahni, Patrick Kwok-Shing Ng, Kang Jin Jeong, Gordon B. Mills. High-content phenotyping of somatic cancer mutations by functional variomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3298.

DNA methylation and inflammation marker profiles associated with a history of depression

Depression is a common and disabling disorder, representing a major social and economic health issue. Moreover, depression is associated with the progression of diseases with an inflammatory etiology including many inflammatory-related disorders. At the molecular level, the mechanisms by which depression might promote the onset of these diseases and associated immune-dysfunction are not well understood. In this study we assessed genome-wide patterns of DNA methylation in whole blood-derived DNA obtained from individuals with a self-reported history of depression (n = 100) and individuals without a history of depression (n = 100) using the Illumina 450K microarray. Our analysis identified six significant (Šidák corrected P < 0.05) depression-associated differentially methylated regions (DMRs); the top-ranked DMR was located in exon 1 of the LTB4R2 gene (Šidák corrected P = 1.27 × 10-14). Polygenic risk scores (PRS) for depression were generated and known biological markers of inflammation, telomere length (TL) and IL-6, were measured in DNA and serum samples, respectively. Next, we employed a systems-level approach to identify networks of co-methylated loci associated with a history of depression, in addition to depression PRS, TL and IL-6 levels. Our analysis identified one depression-associated co-methylation module (P = 0.04). Interestingly, the depression-associated module was highly enriched for pathways related to immune function and was also associated with TL and IL-6 cytokine levels. In summary, our genome-wide DNA methylation analysis of individuals with and without a self-reported history of depression identified several candidate DMRs of potential relevance to the pathogenesis of depression and its associated immune-dysfunction phenotype.

Defective Replication Stress Response Is Inherently Linked to the Cancer Stem Cell Phenotype

Extensive spontaneous DNA damage from oncogene-induced replication stress is ubiquitous in precancerous lesions. While this damage induces differentiation, senescence, or apoptosis in normal cells, defects in DNA replication stress response (RSR) allow cells to continue proliferating, ultimately leading to early tumorigenesis. Using systems-level approaches, we developed a replication stress response defect gene signature that predicted riskof cancer development from hyperplastic lesions. Intriguingly, we found that replication stress response defects rewire non-malignant cells into a cancer stem cell (CSC)-like state, and analysis of CSCs indicated that they inherently harbor replication stress response defects. High-throughput drug screening to elucidate molecules required for survival of replication stress response defective cells identified a dependence on MEK/ERK signaling. Inhibition of this signaling cascade restored oncogene-induced senescence through a p53-independent MDM2/p21 axis. Moreover, MEK/ERK inhibition also depleted CSC populations. Together, these findings provide insights into the role of replication stress response defects in CSCs and an actionable pathway for therapeutic targeting.

The Phenotypic Effects of Exosomes Secreted from Distinct Cellular Sources: a Comparative Study Based on miRNA Composition

Exosomes are nano-sized vesicles composed of lipids, proteins, and nucleic acids. Their molecular landscape is diverse, and exosomes derived from different cell types have distinct biological activities. Since exosomes are now being utilized as delivery vehicles for exogenous therapeutic cargoes, their intrinsic properties and biological effects must be understood. We performed miRNA profiling and found substantial differences in the miRNA landscape of prostate cancer (PC3) and human embryonic kidney (HEK) 293 exosomes with little correlation in abundance of common miRNAs (R2 = 0.16). Using a systems-level bioinformatics approach, the most abundant miRNAs in PC3 exosomes but not HEK exosomes were predicted to significantly modulate integrin signaling, with integrin-β3 loss inducing macrophage M2 polarization. PC3 but not HEK exosomes downregulated integrin-β3 expression levels by 70%. There was a dose-dependent polarization of RAW 264.7 macrophages toward an M2 phenotype when treated with PC3-derived exosomes but not HEK-derived exosomes. Conversely, HEK exosomes, widely utilized as delivery vehicles, were predicted to target cadherin signaling, with experimental validation showing a significant increase in the migratory potential of MCF7 breast cancer cells treated with HEK exosomes. Even widely utilized exosomes are unlikely to be inert, and their intrinsic activity ought to be assessed before therapeutic deployment.

The APEX Approaches: A Unified LRR-RK Network Revealed.

Leucine-rich repeat receptor kinases (LRR-RKs) represent a large and functionally diverse family of transmembrane proteins critical for signal recognition and transduction at the plant cell plasma membrane. Here, we discuss a recent report which used a systems-level approach to validate key paradigms by constructing an LRR-RK interaction network model.

Systems Biology Methods for Alzheimer's Disease Research Toward Molecular Signatures, Subtypes, and Stages and Precision Medicine: Application in Cohort Studies and Trials.

Alzheimer's disease (AD) is a complex multifactorial disease, involving a combination of genomic, interactome, and environmental factors, with essential participation of (a) intrinsic genomic susceptibility and (b) a constant dynamic interplay between impaired pathways and central homeostatic networks of nerve cells. The proper investigation of the complexity of AD requires new holistic systems-level approaches, at both the experimental and computational level. Systems biology methods offer the potential to unveil new fundamental insights, basic mechanisms, and networks and their interplay. These may lead to the characterization of mechanism-based molecular signatures, and AD hallmarks at the earliest molecular and cellular levels (and beyond), for characterization of AD subtypes and stages, toward targeted interventions according to the evolving precision medicine paradigm. In this work, an update on advanced systems biology methods and strategies for holistic studies of multifactorial diseases-particularly AD-is presented. This includes next-generation genomics, neuroimaging and multi-omics methods, experimental and computational approaches, relevant disease models, and latest genome editing and single-cell technologies. Their progressive incorporation into basic research, cohort studies, and trials is beginning to provide novel insights into AD essential mechanisms, molecular signatures, and markers toward mechanism-based classification and staging, and tailored interventions. Selected methods which can be applied in cohort studies and trials, with the European Prevention of Alzheimer's Dementia (EPAD) project as a reference example, are presented and discussed.

Barriers to Physical and Mental Health: Understanding the Intersecting Needs of Cambodian and Latino Residents in Urban Communities.

A community needs assessment was conducted to explore barriers and facilitators to good physical and mental health among Cambodian and Latino residents in an urban community in Southern California. Thirty-six Cambodians and 29 Latinos completed the interviewer-facilitated survey administered door-to-door, and another 20 Cambodian and 18 Latino residents participated in focus groups. Crime, limited knowledge of positive health behaviors, lack of access to affordable healthcare, and lack of access to safe spaces for recreational activities were identified as threats to good health. Participant recommendations to support health in the community included increasing police presence to improve safety and reduce violence, and increasing opportunities/locations for physical exercise. While differences between Cambodian and Latino residents exist, the identified threats and suggested improvements were primarily associated with environmental factors, highlighting the need for systems level approaches that recognize the relationship between community context and health.