Tracing diagnosis trajectories over millions of inpatients reveal an unexpected association between schizophrenia and rhabdomyolysis, bioRxiv, 2018-11-20

AbstractWhile it has been technically feasible to create longitudinal representations of individual health at a nationwide scale, the use of these techniques to identify novel disease associations for the risk stratification of patients has had limited success. Here, we created a large-scale US longitudinal disease network of traced readmission patterns (i.e., disease trajectories), merging data from over 10.4 million inpatients from 350 California hospitals through the Healthcare Cost and Utilization Project between 1980 and 2010. We were able to create longitudinal representations of disease progression mapping over 300 common diseases, including the well-known complication of heart failure after acute myocardial infarction. Surprisingly, out of these generated disease trajectories, we discovered an unknown association between schizophrenia, a chronic mental disorder, and rhabdomyolysis, a rare disease of muscle breakdown. It was found that 92 of 3674 patients (2.5%) with schizophrenia were readmitted for rhabdomyolysis (relative risk, 2.21 [1.80–2.71, confidence interval = 0.95] P-value 9.54E-15), which has a general population incidence of 1 in 10,000. We validated this association using independent electronic health records from over 830,000 patients treated over seven years at the University of California, San Francisco (UCSF) medical center. A case review of 29 patients at UCSF who were treated for schizophrenia and who went on to develop rhabdomyolysis demonstrated that the majority of cases (62%) are idiopathic, which suggests a biological connection between these two diseases. Together, these findings demonstrate the power of using public disease registries in combination with electronic medical records to discover novel disease associations.One Sentence SummaryBased on the longitudinal health records from millions of California inpatient discharges, we created a temporal network that enabled us to understand statewide patterns of hospital readmissions, which led to the novel finding that hospitalization for schizophrenia is significantly associated with rehospitalization for rhabdomyolysis.

biorxiv bioinformatics 0-100-users 2018

Disorganization of the histone core promotes organization of heterochromatin into phase-separated droplets, bioRxiv, 2018-11-19

AbstractThe heterochromatin protein HP1 is proposed to enable chromatin compaction via liquid droplet formation. Yet, a connection between phase separation and chromatin compaction has not been experimentally demonstrated. More fundamentally, how HP1 action at the level of a single nucleosome drives chromatin compaction remains poorly understood. Here we directly demonstrate that the S. pombe HP1 protein, Swi6, compacts arrays of multiple nucleosomes into phase-separated droplets. Using hydrogen-deuterium exchange, NMR, and mass-spectrometry, we further find that Swi6 substantially increases the accessibility and dynamics of buried histone residues within a mononucleosome. Restraining these dynamics via site-specific disulfide bonds impairs the compaction of nucleosome arrays into phase-separated droplets. Our results indicate that chromatin compaction and phase separation can be highly coupled processes. Further, we find that such coupling is promoted by a counter-intuitive function of Swi6, namely disorganization of the octamer core. Phase separation is canonically mediated by weak and dynamic multivalent interactions. We propose that dynamic exposure of buried histone residues increases opportunities for multivalent interactions between nucleosomes, thereby coupling chromatin compaction to phase separation. We anticipate that this new model for chromatin organization may more generally explain the formation of highly compacted chromatin assemblies beyond heterochromatin.

biorxiv biophysics 0-100-users 2018

Variability of bacterial behavior in the mammalian gut captured using a growth-linked single-cell synthetic gene oscillator, bioRxiv, 2018-11-17

AbstractThe dynamics of the bacterial population that comprises the gut microbiota plays key roles in overall mammalian health. However, a detailed understanding of bacterial growth within the gut is limited by the inherent complexity and inaccessibility of the gut environment. Here, we deploy an improved synthetic genetic oscillator to investigate dynamics of bacterial colonization and growth in the mammalian gut under both healthy and disease conditions. The synthetic oscillator, when introduced into both Escherichia coli and Salmonella Typhimurium maintains regular oscillations with a constant period in generations across growth conditions. We determine the phase of oscillation from individual bacteria using image analysis of resultant colonies and thereby infer the number of cell divisions elapsed. In doing so, we demonstrate robust functionality and controllability of the oscillator circuit’s activity during bacterial growth in vitro, in a simulated murine gut microfluidic environment, and in vivo within the mouse gut. We determine different dynamics of bacterial colonization and growth in the gut under normal and inflammatory conditions. Our results show that a precise genetic oscillator can function in a complex environment and reveal single cell behavior under diverse conditions where disease may create otherwise impossible-to-quantify variability in growth across the population.

biorxiv synthetic-biology 0-100-users 2018

Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq, bioRxiv, 2018-11-14

AbstractGenome editing using nucleases such as CRISPR-Cas induces programmable DNA damage at a target genomic site but can also affect off-target sites. Here, we develop a powerful, sensitive assay for the unbiased identification of off-target sites that we term DISCOVER-Seq. This approach takes advantage of the recruitment of endogenous DNA repair factors for genome-wide identification of Cas-induced double-strand breaks. One such factor, MRE11, is recruited precisely to double-strand breaks, enabling molecular characterization of nuclease cut sites with single-base resolution. DISCOVER-Seq detects off-targets in cellular models and in vivo upon adenoviral gene editing of mouse livers, paving the way for real-time off-target discovery during therapeutic gene editing. DISCOVER-Seq is furthermore applicable to multiple types of Cas nucleases and provides an unprecedented view of events that precede repair of the affected sites.

biorxiv molecular-biology 0-100-users 2018

Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution, bioRxiv, 2018-11-13

AbstractThe fast development of single particle cryo-EM has made it more feasible to obtain the 3D structure of well-behaved macromolecules with molecular weight higher than 300 kDa at ~3 Å resolution. It remains a challenge to obtain high resolution structure of molecules smaller than 100 kDa using single particle cryo-EM, mainly due to the low contrast of the molecules embedded in vitreous ice. In this work, we applied the Cs-corrector-VPP coupled cryo-EM to study 52 kDa streptavidin (SA) protein supported on a thin layer of graphene film and embedded in vitreous ice. We were able to solve both the apo-SA and biotin-bound SA at near-atomic resolution using single particle cryo-EM. We demonstrated that the method is capable to determine the structure of molecule as small as 39 kDa and potentially even smaller molecules. Furthermore, we found that using the graphene film to avoid the adsorption to the air-water interface is critical to maintain the protein’s high-resolution structural information.

biorxiv biophysics 0-100-users 2018

Target-specific co-transmission of acetylcholine and GABA from a subset of cortical VIP+ interneurons, bioRxiv, 2018-11-13

AbstractThe modulation of cortex by acetylcholine (ACh) is typically thought to originate from long-range projections arising in the basal forebrain. However, a subset of VIP interneurons express ChAT, the synthetic enzyme for ACh, and are a potential local source of cortical ACh. Which neurotransmitters these VIPChAT interneurons (VCINs) release is unclear, and which post-synaptic cell types these transmitters target is not known. Using quantitative molecular analysis of VCIN pre-synaptic terminals, we show expression of the molecular machinery to release both ACh and GABA, with ACh release restricted to a subset of boutons. A systematic survey of potential post-synaptic cell types shows that VCINs release GABA primarily onto other inhibitory interneuron subtypes, while ACh neurotransmission is notably sparse, with most ACh release onto layer 1 interneurons and other VCINs. Therefore, VCINs are an alternative source of cortical ACh signaling that supplement GABA-mediated disinhibition with highly targeted excitation through ACh.

biorxiv neuroscience 0-100-users 2018