Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin.

Histone lysine acylation, including acetylation and crotonylation, plays a pivotal role in gene transcription in health and diseases. However, our understanding of histone lysine acylation has been limited to gene transcriptional activation. Here, we report that histone H3 lysine 27 crotonylation (H3K27cr) directs gene transcriptional repression rather than activation. Specifically, H3K27cr in chromatin is selectively recognized by the YEATS domain of GAS41 in complex with SIN3A-HDAC1 co-repressors. Proto-oncogenic transcription factor MYC recruits GAS41/SIN3A-HDAC1 complex to repress genes in chromatin, including cell-cycle inhibitor p21. GAS41 knockout or H3K27cr-binding depletion results in p21 de-repression, cell-cycle arrest, and tumor growth inhibition in mice, explaining a causal relationship between GAS41 and MYC gene amplification and p21 downregulation in colorectal cancer. Our study suggests that H3K27 crotonylation signifies a previously unrecognized, distinct chromatin state for gene transcriptional repression in contrast to H3K27 trimethylation for transcriptional silencing and H3K27 acetylation for transcriptional activation.

A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex.

Identification of structural connections between neurons is a prerequisite to understanding brain function. Here we developed a pipeline to systematically map brain-wide monosynaptic input connections to genetically defined neuronal populations using an optimized rabies tracing system. We used mouse visual cortex as the exemplar system and revealed quantitative target-specific, layer-specific and cell-class-specific differences in its presynaptic connectomes. The retrograde connectivity indicates the presence of ventral and dorsal visual streams and further reveals topographically organized and continuously varying subnetworks mediated by different higher visual areas. The visual cortex hierarchy can be derived from intracortical feedforward and feedback pathways mediated by upper-layer and lower-layer input neurons. We also identify a new role for layer 6 neurons in mediating reciprocal interhemispheric connections. This study expands our knowledge of the visual system connectomes and demonstrates that the pipeline can be scaled up to dissect connectivity of different cell populations across the mouse brain.

Large-scale phenotyping and characterization of age-related hearing loss in outbred CFW mice.

Age-related hearing loss (ARHL), or presbycusis, is one of the most prevalent conditions affecting the global population. A substantial fraction of patients with ARHL have no identifiable mutation despite over a hundred having been discovered, suggesting unidentified monogenic or polygenic causes. In this study, we investigated the hearing function of the aging outbred CFW mice through auditory brainstem response (ABR) thresholds. Through the characterization of 1,132 ABRs, we observed significant variation in both absolute thresholds and the effect of aging. We identify eight distinct patterns of hearing loss and were able to categorize nearly all data within these eight categories. Proportions within each category varied immensely between aging timepoints. We observe a small but consistent hearing deficit in female CFW mice. The resulting phenotypic data are a necessity for ARHL association mapping at a higher resolution than has previously been achieved and provides a new resource for studying ARHL.

Calculating power for the Finkelstein and Schoenfeld test statistic for a composite endpoint with two components.

The Finkelstein and Schoenfeld (FS) test is a popular generalized pairwise comparison approach to analyze prioritized composite endpoints (eg, components are assessed in order of clinical importance). Power and sample size estimation for the FS test, however, are generally done via simulation studies. This simulation approach can be extremely computationally burdensome, compounded by increasing number of composite endpoints and with increasing sample size. Here we propose an analytical solution to calculate power and sample size for commonly encountered two-component hierarchical composite endpoints. The power formulas are derived assuming underlying distributions in each of the component outcomes on the population level, which provide a computationally efficient and practical alternative to the standard simulation approach. Monte Carlo simulation results demonstrate that performance of the proposed power formulas are consistent with that of the simulation approach, and have generally desirable objective properties including robustness to mis-specified distributional assumptions. We demonstrate the application of the proposed formulas by calculating power and sample size for the Transthyretin Amyloidosis Cardiomyopathy Clinical Trial.

Starch Capped Atomically Thin CuS Nanocrystals for Efficient Photothermal Therapy.

Photothermal therapy requires efficient plasmonic nanomaterials with small size, good water dispersibility, and biocompatibility. This work reports a one-pot, 2-min synthesis strategy for ultrathin CuS nanocrystals (NCs) with precisely tunable size and localized surface plasmon resonance (LSPR), where a single-starch-layer coating leads to a high LSPR absorption at the near-IR wavelength 980 nm. The CuS NC diameter increases from 4.7 (1 nm height along [101]) to 28.6 nm (4.9 nm height along [001]) accompanied by LSPR redshift from 978 to 1200 nm, as the precursor ratio decreases from 1 to 0.125. Photothermal temperature increases by 38.6 °C in 50 mg L-1 CuS NC solution under laser illumination (980 nm, 1.44 W cm-2 ). Notably, 98.4% of human prostate cancer PC-3/Luc+ cells are killed by as little as 5 mg L-1 starch-coated CuS NCs with 3-min laser treatment, whereas CuS NCs without starch cause insignificant cell death. LSPR modeling discloses that the starch layer enhances the photothermal effect by significantly increasing the free carrier density and blue-shifting the LSPR toward 980 nm. This study not only presents a new type of photothermally highly efficient ultrathin CuS NCs, but also offers in-depth LSPR modeling investigations useful for other photothermal nanomaterial designs.

Methods of assessing categorical agreement between correlated screening tests in clinical studies.

Advances in breast imaging and other screening tests have prompted studies to evaluate and compare the consistency between experts' ratings of existing with new screening tests. In clinical settings, medical experts make subjective assessments of screening test results such as mammograms. Consistency between experts' ratings is evaluated by measures of inter-rater agreement or association. However, conventional measures, such as Cohen's and Fleiss' kappas, are unable to be applied or may perform poorly when studies consist of many experts, unbalanced data, or dependencies between experts' ratings exist. Here we assess the performance of existing approaches including recently developed summary measures for assessing the agreement between experts' binary and ordinal ratings when patients undergo two screening procedures. Methods to assess consistency between repeated measurements by the same experts are also described. We present applications to three large-scale clinical screening studies. Properties of these agreement measures are illustrated via simulation studies. Generally, a model-based approach provides several advantages over alternative methods including the ability to flexibly incorporate various measurement scales (i.e. binary or ordinal), large numbers of experts and patients, sparse data, and robustness to prevalence of underlying disease.

Enhancer viruses for combinatorial cell-subclass-specific labeling.

Rapid cell type identification by new genomic single-cell analysis methods has not been met with efficient experimental access to these cell types. To facilitate access to specific neural populations in mouse cortex, we collected chromatin accessibility data from individual cells and identified enhancers specific for cell subclasses and types. When cloned into recombinant adeno-associated viruses (AAVs) and delivered to the brain, these enhancers drive transgene expression in specific cortical cell subclasses. We extensively characterized several enhancer AAVs to show that they label different projection neuron subclasses as well as a homologous neuron subclass in human cortical slices. We also show how coupling enhancer viruses expressing recombinases to a newly generated transgenic mouse, Ai213, enables strong labeling of three different neuronal classes/subclasses in the brain of a single transgenic animal. This approach combines unprecedented flexibility with specificity for investigation of cell types in the mouse brain and beyond.

Predictors of Loss to Follow-Up among Men with Tuberculosis in Puducherry and Tamil Nadu, India.

Identifying predictors of loss to follow-up (LTFU; treatment lapse ≥ 2 months) among people with tuberculosis (TB) may assist programmatic efforts in controlling the spread of TB. Newly diagnosed smear-positive TB patients were enrolled in the Regional Prospective Observational Research for TB study in Puducherry and Tamil Nadu, India. Treatment records were used to identify LTFU of those who were enrolled from May 2014 through December 2017. This nested case-control study evaluated male TB patients. Predictors were assessed using multivariable logistic regression. Of 425 men with TB, 82 (19%) were LTFU. In the adjusted analyses of males, divorced/separated marital status (adjusted odds ratio [aOR] 3.80; 95% CI: 1.39-10.38) and at-risk alcohol use (aOR 1.92; 95% CI: 1.12-3.27) were significant predictors for increased risk of LTFU, and diabetes was a significant predictor for decreased risk of LTFU (aOR 0.52; 95% CI: 0.29-0.92). Of 53 men with recorded date of last treatment visit, 23 (43%) and 43 (81%) had LTFU within the first 2 and first 4 months of treatment, respectively. Addressing at-risk alcohol use and providing more intensive follow-up could lead to improved treatment completion.

Measuring intrarater association between correlated ordinal ratings.

Variability between raters' ordinal scores is commonly observed in imaging tests, leading to uncertainty in the diagnostic process. In breast cancer screening, a radiologist visually interprets mammograms and MRIs, while skin diseases, Alzheimer's disease, and psychiatric conditions are graded based on clinical judgment. Consequently, studies are often conducted in clinical settings to investigate whether a new training tool can improve the interpretive performance of raters. In such studies, a large group of experts each classify a set of patients' test results on two separate occasions, before and after some form of training with the goal of assessing the impact of training on experts' paired ratings. However, due to the correlated nature of the ordinal ratings, few statistical approaches are available to measure association between raters' paired scores. Existing measures are restricted to assessing association at just one time point for a single screening test. We propose here a novel paired kappa to provide a summary measure of association between many raters' paired ordinal assessments of patients' test results before versus after rater training. Intrarater association also provides valuable insight into the consistency of ratings when raters view a patient's test results on two occasions with no intervention undertaken between viewings. In contrast to existing correlated measures, the proposed kappa is a measure that provides an overall evaluation of the association among multiple raters' scores from two time points and is robust to the underlying disease prevalence. We implement our proposed approach in two recent breast-imaging studies and conduct extensive simulation studies to evaluate properties and performance of our summary measure of association.

RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations.

Brain circuits comprise vast numbers of interconnected neurons with diverse molecular, anatomical and physiological properties. To allow targeting of individual neurons for structural and functional studies, we created light-inducible site-specific DNA recombinases based on Cre, Dre and Flp (RecVs). RecVs can induce genomic modifications by one-photon or two-photon light induction in vivo. They can produce targeted, sparse and strong labeling of individual neurons by modifying multiple loci within mouse and zebrafish genomes. In combination with other genetic strategies, they allow intersectional targeting of different neuronal classes. In the mouse cortex they enable sparse labeling and whole-brain morphological reconstructions of individual neurons. Furthermore, these enzymes allow single-cell two-photon targeted genetic modifications and can be used in combination with functional optical indicators with minimal interference. In summary, RecVs enable spatiotemporally precise optogenomic modifications that can facilitate detailed single-cell analysis of neural circuits by linking genetic identity, morphology, connectivity and function.

Heightened brain response to pain anticipation in high-functioning adults with autism spectrum disorder.

Autism spectrum disorder (ASD) is marked by both socio-communicative difficulties and abnormalities in sensory processing. Much of the work on sensory deficits in ASD has focused on tactile sensations and the perceptual aspects of somatosensation, such as encoding of stimulus intensity and location. Although aberrant pain processing has often been noted in clinical observations of patients with ASD, it remains largely uninvestigated. Importantly, the neural mechanism underlying higher order cognitive aspects of pain processing such as pain anticipation also remains unknown. Here we examined both pain perception and anticipation in high-functioning adults with ASD and matched healthy controls (HC) using an anticipatory pain paradigm in combination with functional magnetic resonance imaging (fMRI) and concurrent skin conductance response (SCR) recording. Participants were asked to choose a level of electrical stimulation that would feel moderately painful to them. Compared to HC group, ASD group chose a lower level of stimulation prior to fMRI. However, ASD participants showed greater activation in both rostral and dorsal anterior cingulate cortex during the anticipation of stimulation, but not during stimulation delivery. There was no significant group difference in insular activation during either pain anticipation or perception. However, activity in the left anterior insula correlated with SCR during pain anticipation. Taken together, these results suggest that ASD is marked with aberrantly higher level of sensitivity to upcoming aversive stimuli, which may reflect abnormal attentional orientation to nociceptive signals and a failure in interoceptive inference.

Autonomic and brain responses associated with empathy deficits in autism spectrum disorder.

Accumulating evidence suggests that autonomic signals and their cortical representations are closely linked to emotional processes, and that related abnormalities could lead to social deficits. Although socio-emotional impairments are a defining feature of autism spectrum disorder (ASD), empirical evidence directly supporting the link between autonomic, cortical, and socio-emotional abnormalities in ASD is still lacking. In this study, we examined autonomic arousal indexed by skin conductance responses (SCR), concurrent cortical responses measured by functional magnetic resonance imaging, and effective brain connectivity estimated by dynamic causal modeling in seventeen unmedicated high-functioning adults with ASD and seventeen matched controls while they performed an empathy-for-pain task. Compared to controls, adults with ASD showed enhanced SCR related to empathetic pain, along with increased neural activity in the anterior insular cortex, although their behavioral empathetic pain discriminability was reduced and overall SCR was decreased. ASD individuals also showed enhanced correlation between SCR and neural activities in the anterior insular cortex. Importantly, significant group differences in effective brain connectivity were limited to greater reduction in the negative intrinsic connectivity of the anterior insular cortex in the ASD group, indicating a failure in attenuating anterior insular responses to empathetic pain. These results suggest that aberrant interoceptive precision, as indexed by abnormalities in autonomic activity and its central representations, may underlie empathy deficits in ASD.

Structural insights into acetylated-histone H4 recognition by the bromodomain-PHD finger module of human transcriptional coactivator CBP.

Bromodomain functions as the acetyl-lysine binding domains to regulate gene transcription in chromatin. Bromodomains are rapidly emerging as new epigenetic drug targets for human diseases. However, owing to their transient nature and modest affinity, histone-binding selectivity of bromodomains has remained mostly elusive. Here, we report high-resolution crystal structures of the bromodomain-PHD tandem module of human transcriptional coactivator CBP bound to lysine-acetylated histone H4 peptides. The structures reveal that the PHD finger serves a structural role in the tandem module and that the bromodomain prefers lysine-acetylated motifs comprising a hydrophobic or aromatic residue at -2 and a lysine or arginine at -3 or -4 position from the acetylated lysine. Our study further provides structural insights into distinct modes of singly and diacetylated histone H4 recognition by the bromodomains of CBP and BRD4 that function differently as a transcriptional coactivator and chromatin organizer, respectively, explaining their distinct roles in control of gene expression in chromatin.

Multiple effects of ß-amyloid on single excitatory synaptic connections in the PFC.

Prefrontal cortex (PFC) is recognized as an AD-vulnerable region responsible for defects in cognitive functioning. Pyramidal cell (PC) connections are typically facilitating (F) or depressing (D) in PFC. Excitatory post-synaptic potentials (EPSPs) were recorded using patch-clamp from single connections in PFC slices of rats and ferrets in the presence of ß-amyloid (Aß). Synaptic transmission was significantly enhanced or reduced depending on their intrinsic type (facilitating or depressing), Aß species (Aß 40 or Aß 42) and concentration (1-200 nM vs. 0.3-1 µ M). Nanomolar Aß 40 and Aß 42 had opposite effects on F-connections, resulting in fewer or increased EPSP failure rates, strengthening or weakening EPSPs and enhancing or inhibiting short-term potentiation [STP: synaptic augmentation (SA) and post-tetanic potentiation (PTP)], respectively. High Aß 40 concentrations induced inhibition regardless of synaptic type. D-connections were inhibited regardless of Aß species or concentration. The inhibition induced with bath application was hard to recover by washout, but a complete recovery was obtained with brief local application and prompt washout. Our data suggests that Aß 40 acts on the prefrontal neuronal network by modulating facilitating and depressing synapses. At higher levels, both Aß 40 and Aß 42 inhibit synaptic activity and cause irreversible toxicity once diffusely accumulated in the synaptic environment.