Quality and Access of Buprenorphine Treatment for Opioid Use Disorder in Medicaid

The United States is in the midst of a drug overdose epidemic that shows no sign of abating. Studies suggest the rate of overdose deaths among Medicaid enrollees is several times higher than the general population rate. Given the continuing overdose epidemic and the elevated overdose risk among Medicaid beneficiaries, and the importance of Medicaid in financing substance use disorder services, there is a need for research on access and quality of opioid use disorder (OUD) treatment in Medicaid. Treatment with the medications buprenorphine or methadone, known as opioid agonist treatment (OAT), has the strongest evidence of reducing overdose mortality from OUD. Nevertheless, these medications are vastly underutilized in practice. This dissertation consists of three chapters that provide evidence for improving access and quality of buprenorphine treatment for OUD in Medicaid. The first chapter uses national data to examine whether Medicaid expansion under the Affordable Care Act increased use of OAT. Many health policy professionals have pointed to the potential of Medicaid expansion for increasing access to OUD treatment, but studies have yet to demonstrate this. This chapter also examines whether limits in the number of OAT providers in states limited the effect of expansion on OAT use. The second chapter examines whether improvements in buprenorphine treatment access may be coming at the cost of quality using data from North Carolina Medicaid. Many states, including North Carolina, have sought to increase access to OAT by encouraging non-specialist primary care providers (PCPs) to deliver buprenorphine treatment. However, some providers and political leaders have raised concerns that PCPs do not have the training or resources to provide high-quality buprenorphine treatment. This chapter provides the first evidence of whether this is the case. The third chapter combines analyses of North Carolina Medicaid claims and interviews with buprenorphine prescribers to understand factors that drive retention in treatment. Treatment guidelines generally recommend patients receive OAT for at least 6 months, but many patients drop out of treatment sooner. This chapter developed a novel mixed-methods approach to identify provider-level practices that could improve retention in treatment while controlling for differences in patient characteristics between providers.Doctor of Philosoph

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output1, 2, 3, 4, 5, with important functional consequences4, 5. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs1, 2 or proteins5, 6 simultaneously, because genomic profiling methods3 could not be applied to single cells until very recently7, 8, 9, 10. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits.National Institutes of Health (U.S.) (NIH Postdoctoral Fellowship (1F32HD075541-01))Charles H. Hood Foundation (Postdoctoral Fellowship)National Institutes of Health (U.S.) (NIH grant U54 AI057159)National Institutes of Health (U.S.) (NIH New Innovator Award (DP2 OD002230))National Institutes of Health (U.S.) (NIH CEGS Award (1P50HG006193-01))National Institutes of Health (U.S.) (NIH Pioneer Awards (5DP1OD003893-03))National Institutes of Health (U.S.) (NIH Pioneer Awards (DP1OD003958-01))Broad Institute of MIT and HarvardBroad Institute of MIT and Harvard (Klarman Cell Observatory

A scoping review of the use of ethnographic approaches in implementation research and recommendations for reporting

Background: Researchers have argued for the value of ethnographic approaches to implementation science (IS). The contested meanings of ethnography pose challenges and possibilities to its use in IS. The goal of this study was to identify sources of commonality and variation, and to distill a set of recommendations for reporting ethnographic approaches in IS. Methods: We included in our scoping review English-language academic journal articles meeting two criteria: (1) IS articles in the healthcare field and (2) articles that described their approach as ethnographic. In March 2019, we implemented our search criteria in four academic databases and one academic journal. Abstracts were screened for inclusion by at least two authors. We iteratively develop a codebook for full-text analysis and double-coded included articles. We summarized the findings and developed reporting recommendations through discussion. Results: Of the 210 articles whose abstracts were screened, 73 were included in full-text analysis. The number of articles increased in recent years. Ethnographic approaches were used within a wide variety of theoretical approaches and research designs. Articles primarily described using interviews and observational methods as part of their ethnographic approaches, though numerous other methods were also employed. The most cited rationales for using ethnographic approaches were to capture context-specific phenomena, understand insiders? perspective, and study complex interactions. In reporting on ethnographic approaches, we recommend that researchers provide information on researcher training and position, reflect on researchers? positionality, describe observational methods in detail, and report results from all the methods used. Conclusion: The number of IS studies using ethnography has increased in recent years. Ethnography holds great potential for contributing further to IS, particularly to studying implementation strategy mechanisms and understanding complex adaptive systems. Plain language summary: Researchers have proposed that ethnographic methods may be valuable to implementation research and practice. Ethnographic approaches have their roots in the field of anthropology, but they are now used in many fields. These approaches often involve a researcher spending time in 'real-world' settings, conducting interviews and observation to understand a group of people. That said, researchers disagree on the meaning of ethnography, which presents a challenge to its use in implementation science (IS). We searched for articles in the field of IS that described their methods as ethnographic. We then reviewed the articles, looking for similarities and differences in how and why ethnographic approaches were used. Many of these articles said they used ethnographic methods because they were interested in issues like context, research participants? views, and complex interactions. We found a large amount of variation in how ethnographic methods were used. We developed recommendations for describing ethnographic methods in a way that readers can clearly understand. We also made several observations of the value ethnographic approaches can bring to IS. Ethnographic methods may be especially useful to studying unplanned and unexpected changes that take place during implementation. These recommendations and observations could be helpful to implementation researchers wishing to use ethnographic methods

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript’s level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a ‘core’ module of antiviral genes is expressed very early by a few ‘precocious’ cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced ‘peaked’ inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses.National Human Genome Research Institute (U.S.). Centers of Excellence in Genomic Science (1P50HG006193-01)National Institutes of Health (U.S.). Pioneer Award (DP1OD003958-01)Howard Hughes Medical InstituteBroad Institute of MIT and Harvard. Klarman Cell Observator

Single cell RNA Seq reveals dynamic paracrine control of cellular variation

High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis, and function of gene expression variation between seemingly identical cells. Here, we sequence single-cell RNA-Seq libraries prepared from over 1,700 primary mouse bone marrow derived dendritic cells (DCs) spanning several experimental conditions. We find substantial variation between identically stimulated DCs, in both the fraction of cells detectably expressing a given mRNA and the transcript’s level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a “core” module of antiviral genes is expressed very early by a few “precocious” cells, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analyzing DCs from knockout mice, and modulating secretion and extracellular signaling, we show that this response is coordinated via interferon-mediated paracrine signaling. Surprisingly, preventing cell-to-cell communication also substantially reduces variability in the expression of an early-induced “peaked” inflammatory module, suggesting that paracrine signaling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations use to establish complex dynamic responses

Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells

A generalized platform for introducing a diverse range of biomolecules into living cells in high-throughput could transform how complex cellular processes are probed and analyzed. Here, we demonstrate spatially localized, efficient, and universal delivery of biomolecules into immortalized and primary mammalian cells using surface-modified vertical silicon nanowires. The method relies on the ability of the silicon nanowires to penetrate a cell’s membrane and subsequently release surface-bound molecules directly into the cell’s cytosol, thus allowing highly efficient delivery of biomolecules without chemical modification or viral packaging. This modality enables one to assess the phenotypic consequences of introducing a broad range of biological effectors (DNAs, RNAs, peptides, proteins, and small molecules) into almost any cell type. We show that this platform can be used to guide neuronal progenitor growth with small molecules, knock down transcript levels by delivering siRNAs, inhibit apoptosis using peptides, and introduce targeted proteins to specific organelles. We further demonstrate codelivery of siRNAs and proteins on a single substrate in a microarray format, highlighting this technology’s potential as a robust, monolithic platform for high-throughput, miniaturized bioassays

Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia

A circuit level understanding of immune cells and hematological cancers has been severely impeded by a lack of techniques that enable intracellular perturbation without significantly altering cell viability and function. Here, we demonstrate that vertical silicon nanowires (NWs) enable gene-specific manipulation of diverse murine and human immune cells with negligible toxicity. To illustrate the power of the technique, we then apply NW-mediated gene silencing to investigate the role of the Wnt signaling pathway in chronic lymphocytic leukemia (CLL). Remarkably, CLL-B cells from different patients exhibit tremendous heterogeneity in their response to the knockdown of a single gene, LEF1. This functional heterogeneity defines three distinct patient groups not discernible by conventional CLL cytogenetic markers and provides a prognostic indicator for patients’ time to first therapy. Analyses of gene expression signatures associated with these functional patient subgroups reveal unique insights into the underlying molecular basis for disease heterogeneity. Overall, our findings suggest a functional classification that can potentially guide the selection of patient-specific therapies in CLL and highlight the opportunities for nanotechnology to drive biological inquiry.National Institutes of Health (U.S.). Pioneer AwardNational Institutes of Health (U.S.) (CEGS Award 1P50HG006193-01)Howard Hughes Medical InstituteMerkin Family Foundation for Stem Cell Researc