Mapping a psychosocial syndemic among methamphetamine-using sexual minority men living with HIV.

INTRODUCTION: While research with sexual minority men (SMM) has focused on disparities related to HIV, substance use and mental health, synergistic psychosocial pathways driving these epidemics remain underexplored. We used syndemic theory to assess how psychosocial factors sustain methamphetamine use and hinder recovery efforts for SMM living with HIV. METHODS: A triangulation of network analyses and constructivist grounded theory approaches is utilised to elucidate pathways through which psychosocial factors influence methamphetamine use among this population. Survey data (N = 129) are used for quantitative analyses and a purposive sub-sample (n = 24) was recruited for semi-structured interviews for qualitative analyses. FINDINGS: The network analysis revealed two statistically significant bivariate associations: between post-traumatic stress disorder and depression symptoms (b = 0.37, SD = 0.07, 95% confidence interval [0.23, 0.49]) and between depression symptoms and negative affect (b = 0.26, SD = 0.07, 95% confidence interval [0.12, 0.38]). Findings from the constructivist grounded theory analysis supplement the network analysis by offering a nuanced take on how negative affect, post-traumatic stress disorder, and depression symptoms operate synergistically to promote methamphetamine use and impede recovery efforts. DISCUSSION AND CONCLUSIONS: Participants relay experiences of using methamphetamine to cope with these psychosocial factors through avoidance, escapism, mood elevation, and numbing of emotions. Findings suggest that centring these psychosocial factors may inform more effective, holistic interventions for this high-priority population.

RAB18 regulates extrahepatic siRNA-mediated gene silencing efficacy.

Small interfering RNAs (siRNAs) hold considerable therapeutic potential to selectively silence previously "undruggable" disease-associated targets, offering new opportunities to fight human diseases. This therapeutic strategy, however, is limited by the inability of naked siRNAs to passively diffuse across cellular membranes due to their large molecular size and negative charge. Delivery of siRNAs to liver through conjugation of siRNA to N-acetylgalactosamine (GalNAc) has been a success, providing robust and durable gene knockdown, specifically in hepatocytes. However, the poor delivery and silencing efficacy of siRNAs in other cell types has hindered their applications outside the liver. We previously reported that a genome-wide pooled knockout screen identified RAB18 as a major modulator of GalNAc-siRNA conjugates. Herein, we demonstrate RAB18 knockout/knockdown efficaciously enhances siRNA-mediated gene silencing in hepatic and extrahepatic cell lines and in vivo. Our results reveal a mechanism by which retrograde Golgi-endoplasmic reticulum (ER) transport and the intracellular lipid droplets (LDs) positively regulate siRNA-mediated gene silencing.

A systematic comparison of additive and interaction approaches to modeling the effects of syndemic problems on HIV outcomes in South Africa.

Much of the research on the effects of syndemics on HIV outcomes has utilized an additive approach. However, interaction effects may better account for syndemic synergy than an additive approach, but it remains difficult to specify interaction effects without empirical guidance. We sought to systematically compare additive and interaction effects approaches to modeling the effects of syndemic problems on antiretroviral therapy (ART) using empirically specified interaction terms. Participants were 194 people with HIV (PWH) who received HIV care in Khayelitsha, South Africa. In a series of linear regression models, we examined ten syndemic problems: depression, alcohol use, intimate partner violence (IPV), post-traumatic stress, social anxiety, substance use, food insecurity, poverty, housing instability, and structural barriers to care. Depression, substance use, and food insecurity were selected for interaction terms based on a prior network analysis, which found these problems to be most central. The additive models did not produce statistically significant findings. However, the interaction effects models yielded significant interaction terms in both the full model and a parsimonious model. There was a statistically significant effect of the interaction between depression and food insecurity on ART adherence (b = 0.04, Robust SE = 0.02, 95%CI [0.001-0.08], p = .012). This pattern of results was replicated in the parsimonious model. Findings suggest that when feasible, interaction effects approaches may be a helpful syndemic modeling technique. Results may inform future intervention targets, such as depression and food insecurity, and the importance of addressing both structural and psychosocial syndemic problems.

A living organoid biobank of patients with Crohn's disease reveals molecular subtypes for personalized therapeutics.

Crohn's disease (CD) is a complex and heterogeneous condition with no perfect preclinical model or cure. To address this, we explore adult stem cell-derived organoids that retain their tissue identity and disease-driving traits. We prospectively create a biobank of CD patient-derived organoid cultures (PDOs) from colonic biopsies of 53 subjects across all clinical subtypes and healthy subjects. Gene expression analyses enabled benchmarking of PDOs as tools for modeling the colonic epithelium in active disease and identified two major molecular subtypes: immune-deficient infectious CD (IDICD) and stress and senescence-induced fibrostenotic CD (S2FCD). Each subtype shows internal consistency in the transcriptome, genome, and phenome. The spectrum of morphometric, phenotypic, and functional changes within the "living biobank" reveals distinct differences between the molecular subtypes. Drug screens reverse subtype-specific phenotypes, suggesting phenotyped-genotyped CD PDOs can bridge basic biology and patient trials by enabling preclinical phase "0" human trials for personalized therapeutics.

A network analysis of positive psychosocial factors and indication of suboptimal HIV care outcomes among Black women living with HIV.

Black women living with HIV (BWLWH) face barriers that impact health outcomes. However, positive psychosocial indicators may influence HIV care outcomes. Among this cross-sectional study of 119 BWLWH, a network analysis was utilized to examine relationships between positive psychosocial factors and HIV-related health outcomes. A preliminary polychoric analysis was conducted to examine correlations between the variables, and the network analyzed connections between resilience, self-efficacy, self-esteem, perceived social support, religious coping, post-traumatic growth, and an indicator variable for suboptimal HIV care outcomes (low medication adherence, detectable viral load, and missed HIV-related health visits) and determined the centrality measures within the network. Seven significant associations were found among the factors: self-efficacy and self-esteem, post-traumatic growth and resilience, post-traumatic growth and self-efficacy, post-traumatic growth and religious coping, perceived social support and resilience, self-esteem and resilience, self-esteem and perceived social support (bootstrapped 95% CI did not contain zero). Self-efficacy was the strongest indicator associated with the other factors. Although not statistically significant, the indicator for suboptimal HIV care outcomes was negatively associated with perceived social support and religious coping. Future interventions incorporating self-efficacy may be beneficial to the overall well-being of Black women.

Leveraging A Digital Pill System to Understand Prevention-Effective Adherence to Oral Hiv Pre-Exposure Prophylaxis Among Men Who Have Sex with Men with Substance Use.

Daily oral pre-exposure prophylaxis (PrEP) is highly effective for HIV prevention, though efficacy depends on adherence. Digital pill systems (DPS) can enable direct, real-time adherence measurement. HIV-negative men who have sex with men (MSM) with substance use (excluding alcohol) utilized a DPS over 90 days and completed weekly surveys reporting sexual activity, condom use, and substance use. Responses indicating (1) any sexual activity and substance use or (2) condomless anal intercourse (CAI) in the prior week were categorized as high risk for HIV acquisition. PrEP adherence data for the 7-day period preceding each response was dichotomized as ≤ 3 and ≥ 4 doses/week, indicating prevention-effective adherence, and compared by HIV risk level. Thirteen MSM were analyzed (median age: 32). Of 113 surveys, 48.7% indicated high HIV risk, with 12.4% reporting CAI alone, 16.8% any sexual activity and substance use, and 19.5% both CAI and substance use. Weekly mean PrEP adherence was 90.3% (6.3 of 7 doses/week), with ≥ 4 doses/week recorded during 92.0% of weeks. The proportion of participants with ≥ 4 recorded doses/week was 88.9% during weeks with CAI alone, 89.5% during weeks with any sexual activity and substance use, 92.0% during weeks with both CAI and substance use, and 92.8% during lower risk weeks. Participants ingested ≥ 4 doses/week during 89.1% of all high-risk weeks and 94.8% of low-risk weeks. Overall, participants maintained high levels of PrEP adherence while engaging in HIV risk behaviors. DPS can be deployed concurrently with data collection tools to assess ingestion patterns during periods of elevated risk.

HPTN 083-02: factors influencing adherence to injectable PrEP and retention in an injectable PrEP study.

INTRODUCTION: HPTN 083 demonstrated the superiority of long-acting cabotegravir (CAB-LA) versus daily oral emtricitabine/tenofovir disoproxil fumarate (TDF/FTC) as pre-exposure prophylaxis (PrEP) among cisgender men and transgender women who have sex with men (MSM/TGW). HPTN 083 provided the first opportunity to understand experiences with injectable PrEP in a clinical trial. METHODS: Participants from two US sites (Chicago, IL and Atlanta, GA) and one international site (Rio de Janeiro, Brazil) were purposively sampled for individual qualitative interviews (N = 40), between November 2019 and March 2020, to explore trial experiences, barriers to adherence and other factors that may have impacted study implementation or outcomes. The blinded phase ended early due to efficacy; this analysis includes interviews conducted prior to unblinding with three groups defined by adherence (i.e. injection visit attendance): adherent (n = 27), non-adherent (n = 12) and early discontinuers (n = 1). Data were organized using NVivo software and analysed using content analysis. RESULTS: Participants (mean age: 27) were primarily cisgender MSM (90%) and Black/African American (60%). Reasons for trial enrolment and PrEP use included a preference for using HIV prevention medication versus treatment in the event of HIV acquisition; the ability to enhance health via study-related education and services; access to a novel, convenient HIV prevention product at no cost; and contributing to MSM/TGW communities through research. Participants contrasted positive experiences with study staff with their routine clinical care, and emphasized increased scheduling flexibility, thorough communication, non-judgemental counselling and open, affirming environments (e.g. compassion, less stigma) as adherence facilitators. Injection experiences were positive overall; some described early injection-related anxiety, which abated with time and when given some measure of control (e.g. pre-injection countdown), and minimal injection site discomfort. Some concerns and misperceptions about injectable PrEP were reported. Barriers to adherence, across all adherence categories, included structural factors (e.g. financial constraints, travel) and competing demands (e.g. work schedules). CONCLUSIONS: Respondents viewed injectable PrEP trial participation as a positive experience and a means of enhancing wellbeing. Study site flexibility and affirming clinic environments, inclusive of non-judgemental counselling, were key facilitators of adherence. To support injection persistence, interventions that address structural barriers and promote flexible means of injection delivery may be most effective.

Identification and characterization of recent retrovirus in Rhinolophus ferrumequinum bats.

An investigation into retrovirus was conducted in six species of bats (Myotis aurascens, Myotis petax, Myotis macrodactylus, Miniopterus fuliginosus, Rhinolophus ferrumequinum, and Pipistrellus abramus) inhabiting South Korea. Exogenous retroviruses (XRVs) were detected in the tissue samples of R. ferrumequinum individuals by PCR assay. Proviruses were identified in all tissue samples through viral quantification using a digital PCR assay per organ (lung, intestine, heart, brain, wing, kidney, and liver), with viral loads varying greatly between each organ. In phylogenetic analysis based on the whole genome, the Korean bat retroviruses and the R. ferrumequinum retrovirus (RfRV) strain formed a new clade distinct from the Gammaretrovirus clade. The phylogenetic results determined these viruses to be RfRV-like viruses. In the Simplot comparison, Korean RfRV-like viruses exhibited relatively strong fluctuated patterns in the latter part of the envelope gene area compared to other gene areas. Several point mutations within this region (6,878-7,774 bp) of these viruses were observed compared to the RfRV sequence. One Korean RfRV-like virus (named Y4b strain) was successfully recovered in the Raw 264.7 cell line, and virus particles replicated in the cells were confirmed by transmission electron microscopy. RfRVs (or RfRV-like viruses) have been spreading since their first discovery in 2012, and the Korean RfRV-like viruses were assumed to be XRVs that evolved from RfRV.IMPORTANCER. ferrumequinum retrovirus (RfRV)-like viruses were identified in greater horseshoe bats in South Korea. These RfRV-like viruses were considered exogenous retroviruses (XRVs) that emerged from RfRV. Varying amounts of provirus detected in different organs suggest ongoing viral activity, replication, and de novo integration in certain organs. Additionally, the successful recovery of the virus in the Raw 264.7 cell line provides strong evidence supporting their status as XRVs. These viruses have now been identified in South Korea and, more recently, in Kenya since RfRV was discovered in China in 2012, indicating that RfRVs (or RfRV-like viruses) have spread worldwide.

Smartphone and Wearable Device-Based Digital Phenotyping to Understand Substance use and its Syndemics.

Digital phenotyping is a process that allows researchers to leverage smartphone and wearable data to explore how technology use relates to behavioral health outcomes. In this Research Concepts article, we provide background on prior research that has employed digital phenotyping; the fundamentals of how digital phenotyping works, using examples from participant data; the application of digital phenotyping in the context of substance use and its syndemics; and the ethical, legal and social implications of digital phenotyping. We discuss applications for digital phenotyping in medical toxicology, as well as potential uses for digital phenotyping in future research. We also highlight the importance of obtaining ground truth annotation in order to identify and establish digital phenotypes of key behaviors of interest. Finally, there are many potential roles for medical toxicologists to leverage digital phenotyping both in research and in the future as a clinical tool to better understand the contextual features associated with drug poisoning and overdose. This article demonstrates how medical toxicologists and researchers can progress through phases of a research trajectory using digital phenotyping to better understand behavior and its association with smartphone usage.

A Panoramic View of Cell Population Dynamics in Mammalian Aging.

To elucidate the aging-associated cellular population dynamics throughout the body, here we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissue samples, encompassing a range of organs across different life stages, sexes, and genotypes. This comprehensive dataset allowed us to identify more than 3,000 unique cellular states and catalog over 200 distinct aging-associated cell populations experiencing significant depletion or expansion. Our panoramic analysis uncovered temporally structured, organ- and lineage-specific shifts of cellular dynamics during lifespan progression. Moreover, we investigated aging-associated alterations in immune cell populations, revealing both widespread shifts and organ-specific changes. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte-dependent. The breadth and depth of our 'cell-omics' methodology not only enhance our comprehension of cellular aging but also lay the groundwork for exploring the complex regulatory networks among varied cell types in the context of aging and aging-associated diseases.

The salience of structural barriers and behavioral health problems to ART adherence in people receiving HIV primary care in South Africa.

Multilevel factors (individual and structural) influence adherence to antiretroviral therapy, particularly in high HIV prevalence areas such as South Africa. The present study examined the relative importance of structural barriers to HIV care and behavioral health factors, depression and alcohol use, in Khayelitsha, Cape Town, South Africa. People receiving HIV care in six primary care clinics in Khayelitsha (N = 194) completed the Center for Epidemiologic Studies Depression Scale, the Alcohol Use Disorders Identification Test, the Structural Barriers to Medication Taking questionnaire, and a qualitative rating of past-two-week adherence. Correlations were employed to examine associations among these variables, and hierarchical regression analysis was used to examine the unique effects of structural barriers over and above depression and alcohol use as predictors of adherence. Participants were primarily Black South African (99%) women (83%), and 41 years old on average. All four variables were significantly correlated. The hierarchical regression analysis showed that among behavioral health predictors, alcohol use alone significantly predicted ART adherence (b = -.032, p = .002). When structural barriers was added to the model, it was the only significant unique predictor of ART adherence (b = -1.58, p < .001). Findings highlight the need to consider structural vulnerabilities in HIV care in South Africa when developing behavioral health interventions.

Acceptance of digital phenotyping linked to a digital pill system to measure PrEP adherence among men who have sex with men with substance use.

Once-daily oral HIV pre-exposure prophylaxis (PrEP) is an effective strategy to prevent HIV, but is highly dependent on adherence. Men who have sex with men (MSM) who use substances face unique challenges maintaining PrEP adherence. Digital pill systems (DPS) allow for real-time adherence measurement through ingestible sensors. Integration of DPS technology with other digital health tools, such as digital phenotyping, may improve understanding of nonadherence triggers and development of personalized adherence interventions based on ingestion behavior. This study explored the willingness of MSM with substance use to share digital phenotypic data and interact with ancillary systems in the context of DPS-measured PrEP adherence. Adult MSM on PrEP with substance use were recruited through a social networking app. Participants were introduced to DPS technology and completed an assessment to measure willingness to participate in DPS-based PrEP adherence research, contribute digital phenotyping data, and interact with ancillary systems in the context of DPS-based research. Medical mistrust, daily worry about PrEP adherence, and substance use were also assessed. Participants who identified as cisgender male and were willing to participate in DPS-based research (N = 131) were included in this subsample analysis. Most were White (76.3%) and non-Hispanic (77.9%). Participants who reported daily PrEP adherence worry had 3.7 times greater odds (95% CI: 1.03, 13.4) of willingness to share biometric data via a wearable device paired to the DPS. Participants with daily PrEP adherence worry were more likely to be willing to share smartphone data (p = 0.006) and receive text messages surrounding their daily activities (p = 0.003), compared to those with less worry. MSM with substance use disorder, who worried about PrEP adherence, were willing to use DPS technology and share data required for digital phenotyping in the context of PrEP adherence measurement. Efforts to address medical mistrust can increase advantages of this technology for HIV prevention.

Real-World Implementation Challenges Associated with a Digital Pill System to Measure Adherence to HIV Pre-Exposure Prophylaxis from Two Studies of Men Who Have Sex With Men.

Once-daily oral pre-exposure prophylaxis (PrEP) is highly effective for HIV prevention, but its efficacy is dependent on adherence, which can be challenging for men who have sex with men (MSM) with substance use. Digital pill systems (DPS) represent a novel tool for directly measuring adherence through ingestible radiofrequency sensors that confirm ingestions in real-time. We examined operational challenges across two studies involving DPS to measure PrEP adherence. While most participants successfully operated the system, a number of technological and sociobehavioral challenges requiring intervention were identified across both studies. Technological issues were both system- and participant-related, and were primarily addressed with technical updates and participant re-education, while sociobehavioral issues, including health and housing changes and issues with technology access, warranted innovative solutions. Future research leveraging DPS technology should develop robust supportive infrastructure and mitigation procedures to promptly identify and resolve operational issues to optimize the potential benefits of DPS use.

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain.

Cytosine DNA methylation is essential in brain development and is implicated in various neurological disorders. Understanding DNA methylation diversity across the entire brain in a spatial context is fundamental for a complete molecular atlas of brain cell types and their gene regulatory landscapes. Here we used single-nucleus methylome sequencing (snmC-seq3) and multi-omic sequencing (snm3C-seq)1 technologies to generate 301,626 methylomes and 176,003 chromatin conformation-methylome joint profiles from 117 dissected regions throughout the adult mouse brain. Using iterative clustering and integrating with companion whole-brain transcriptome and chromatin accessibility datasets, we constructed a methylation-based cell taxonomy with 4,673 cell groups and 274 cross-modality-annotated subclasses. We identified 2.6 million differentially methylated regions across the genome that represent potential gene regulation elements. Notably, we observed spatial cytosine methylation patterns on both genes and regulatory elements in cell types within and across brain regions. Brain-wide spatial transcriptomics data validated the association of spatial epigenetic diversity with transcription and improved the anatomical mapping of our epigenetic datasets. Furthermore, chromatin conformation diversities occurred in important neuronal genes and were highly associated with DNA methylation and transcription changes. Brain-wide cell-type comparisons enabled the construction of regulatory networks that incorporate transcription factors, regulatory elements and their potential downstream gene targets. Finally, intragenic DNA methylation and chromatin conformation patterns predicted alternative gene isoform expression observed in a whole-brain SMART-seq2 dataset. Our study establishes a brain-wide, single-cell DNA methylome and 3D multi-omic atlas and provides a valuable resource for comprehending the cellular-spatial and regulatory genome diversity of the mouse brain.

Brain-wide correspondence of neuronal epigenomics and distant projections.

Single-cell analyses parse the brain's billions of neurons into thousands of 'cell-type' clusters residing in different brain structures1. Many cell types mediate their functions through targeted long-distance projections allowing interactions between specific cell types. Here we used epi-retro-seq2 to link single-cell epigenomes and cell types to long-distance projections for 33,034 neurons dissected from 32 different regions projecting to 24 different targets (225 source-to-target combinations) across the whole mouse brain. We highlight uses of these data for interrogating principles relating projection types to transcriptomics and epigenomics, and for addressing hypotheses about cell types and connections related to genetics. We provide an overall synthesis with 926 statistical comparisons of discriminability of neurons projecting to each target for every source. We integrate this dataset into the larger BRAIN Initiative Cell Census Network atlas, composed of millions of neurons, to link projection cell types to consensus clusters. Integration with spatial transcriptomics further assigns projection-enriched clusters to smaller source regions than the original dissections. We exemplify this by presenting in-depth analyses of projection neurons from the hypothalamus, thalamus, hindbrain, amygdala and midbrain to provide insights into properties of those cell types, including differentially expressed genes, their associated cis-regulatory elements and transcription-factor-binding motifs, and neurotransmitter use.

Preliminary feasibility of a wrist-worn receiver to measure medication adherence via an ingestible radiofrequency sensor.

Adherence to medications is a complex task that requires complex biobehavioral support. To better provide tools to assist with medication adherence, digital pills provide an option to directly measure medication taking behaviors. These systems comprise a gelatin capsule with radiofrequency emitter, a wearable Reader that collects the radio signal and a smartphone app that collects ingestion data displays it for patients and clinicians. These systems are feasible in measuring adherence in the real-world, even in stigmatized diseases like HIV treatment adherence. While the current iteration of the digital pill system utilizes a wearable Reader worn like a necklace, preliminary feedback demonstrated that a miniaturized system that was worn on the wrist could be more functional in the real-world. This paper therefore describes the development and preliminary field testing of a wrist-borne wearable Reader to facilitate acquisition of oral HIV pre-exposure prophylaxis (PrEP) adherence data among individual prescribed PrEP.

A global view of aging and Alzheimer's pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains.

Conventional methods fall short in unraveling the dynamics of rare cell types related to aging and diseases. Here we introduce EasySci, an advanced single-cell combinatorial indexing strategy for exploring age-dependent cellular dynamics in the mammalian brain. Profiling approximately 1.5 million single-cell transcriptomes and 400,000 chromatin accessibility profiles across diverse mouse brains, we identified over 300 cell subtypes, uncovering their molecular characteristics and spatial locations. This comprehensive view elucidates rare cell types expanded or depleted upon aging. We also investigated cell-type-specific responses to genetic alterations linked to Alzheimer's disease, identifying associated rare cell types. Additionally, by profiling 118,240 human brain single-cell transcriptomes, we discerned cell- and region-specific transcriptomic changes tied to Alzheimer's pathogenesis. In conclusion, this research offers a valuable resource for probing cell-type-specific dynamics in both normal and pathological aging.

Sex Differences in the Cognitive Performance of a South African Cohort of People With HIV and Comorbid Major Depressive Disorder.

Women with HIV (WWH) may be more vulnerable to cognitive impairment than men with HIV (MWH), which may be explained by the direct effects of HIV or by sociodemographic and psychiatric characteristics. We recruited 105 people with HIV (PWH; 76 women) with incomplete antiretroviral therapy adherence, comorbid major depressive disorder, and socioeconomically disadvantaged backgrounds. Participants completed neuropsychological testing and measures gathering sociodemographic, medical, and psychiatric information. We compared WWH and MWH cognitive performance using unadjusted and adjusted regressions, and within each respective group, we explored predictors of cognitive performance. Results showed no significant between-sex differences in cognitive performance, both globally and within domains. Fewer years of education (ß = 0.94), illiteracy (ß = 4.55), and greater food insecurity (ß = -0.28) predicted lower cognitive performance in WWH but not MWH. We conclude that sex differences in PWH are likely due to sample characteristics representing broader inequalities, rather than true biological differences.

Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain.

Differential polyadenylation sites (PAs) critically regulate gene expression, but their cell type-specific usage and spatial distribution in the brain have not been systematically characterized. Here, we present Infernape, which infers and quantifies PA usage from single-cell and spatial transcriptomic data and show its application in the mouse brain. Infernape uncovers alternative intronic PAs and 3'-UTR lengthening during cortical neurogenesis. Progenitor-neuron comparisons in the excitatory and inhibitory neuron lineages show overlapping PA changes in embryonic brains, suggesting that the neural proliferation-differentiation axis plays a prominent role. In the adult mouse brain, we uncover cell type-specific PAs and visualize such events using spatial transcriptomic data. Over two dozen neurodevelopmental disorder-associated genes such as Csnk2a1 and Mecp2 show differential PAs during brain development. This study presents Infernape to identify PAs from scRNA-seq and spatial data, and highlights the role of alternative PAs in neuronal gene regulation.

Single-cell DNA methylation and 3D genome architecture in the human brain.

Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517 thousand cells (399 thousand neurons and 118 thousand non-neurons) from 46 regions of three adult male brains. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. We further developed single-cell methylation barcodes that reliably predict brain cell types using the methylation status of select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell-type-specific gene regulation in adult human brains.