Biology subjects

Hoffman, M.

Publications and source records attributed to Hoffman, M..

18 recordsLinked to original sources

bioRxiv2025

NKTR-255, a polymer-conjugated IL-15, synergizes with CAR-T cell therapy to activate endogenous anti-tumor immunity and improve tumor control

CAR-T cells have yet to show widespread efficacy in solid tumors due in part to their poor persistence and loss of function in the tumor microenvironment. Further, heterogenous expression of most CAR target antigens in solid tumors can lead to escape of antigen-null tumors that resist CAR-T killing. Strategies to cooperatively boost both CAR-T and endogenous anti-tumor immunity could curb tumor escape and may be critical for achieving durable efficacy in cancer patients. NKTR-255 is a polymer-conjugated IL-15 with extended half-life that can boost endogenous T and NK cells, as well as CD19 CAR-T activity in B cell malignancies. However, whether NKTR-255 is sufficient to overcome CAR-T dysfunction in the suppressive solid tumor microenvironment, and how NKTR-255 and CAR-Ts together re-shape endogenous anti-tumor immunity, is not known. Using an autochthonous mouse model of ROR1+ lung adenocarcinoma, we show that NKTR-255 significantly boosted accumulation, reduced exhaustion, and improved function of tumor-infiltrating CAR-T cells. Compared with NKTR-255 or CAR-T treatment alone, combination of NKTR-255 and CAR-T therapy synergistically increased tumor-infiltrating CD11b+ cytotoxic NK cells, activated dendritic cells, and endogenous tumor-specific T cells that preserved a PD-1+Tcf1+ stem-like phenotype. Consequently, NKTR-255 and CAR-T combination therapy induced complete elimination of ROR1+ tumor and significantly improved survival, with enhanced tumor control dependent on activity of both CAR-Ts and endogenous T cells. Altogether, our data suggest that combining NKTR-255 with CAR-T therapy is a promising strategy to enhance both CAR-T and endogenous anti-tumor immunity to promote coordinated control of aggressive tumors.

immunology↗

bioRxiv2025

Integration of Alzheimer's GWAS, 3D genomics, and single-cell CRISPRi non-coding screen implicates causal variants in a microglial enhancer regulating TSPAN14.

While GWAS have been successful in providing variant-to-trait associations for human complex diseases, functional dissection of the discovered loci has lagged behind. Here, we describe a variant-to-gene (V2G) mapping effort for Alzheimers disease (AD) to implicate causal variants and effector genes from the most recent AD GWAS meta-analyses (101 loci). We leveraged our genomics datasets comprising high-resolution promoter Capture C, ATAC-seq, and RNA-seq from brain-relevant cell types to fine-map AD GWAS variants, identifying 89 candidate causal SNPs and 69 effector genes. We then designed a single-cell CRISPRi screen to perturb candidate regulatory regions (n=74) and assess the transcriptional response in the human microglial cell line, HMC3. Our screen across [~]97,000 cells identified 19 regulatory regions and 19 effector genes. We then elected to functionally dissect our top hit, the TSPAN14 locus, and we show that an intronic region containing AD-associated SNPs rs7080009, rs1870138, and rs1870137 is a microglia-specific enhancer, with the AD risk haplotype increasing its activity. CRISPR precise genomic deletion of this region decreases TSPAN14 expression, alters specific cellular pathways including cell adhesion, and decreases secreted levels of pro-inflammatory cytokines IL-6 and IL-8, which are known biomarkers of aging and AD. Our work provides a systematic framework to map GWAS signals to their effector genes for AD and other brain-related disorders, and provides robust leads to follow up with in-depth functional investigations.

genetics↗

bioRxiv2025

Pooled CAR-T screening in nonhuman primates identifies designs with enhanced proliferation, trafficking, and persistence

Chimeric antigen receptor T (CAR-T) cell therapy has revolutionized treatment for B-cell malignancies, yet over 60% of patients relapse within one year, often due to insufficient CAR-T persistence. While mouse and primary cell models have been instrumental in advancing CAR-T therapy, they frequently fail to predict clinical outcomes, underscoring the need for more translationally relevant models. To address this limitation, we conducted the first systematic evaluation of CAR structure-function relationships in an immunocompetent nonhuman primate (NHP) model. We engineered an array of 20 CD20-targeted CARs with distinct combinations of hinge, transmembrane, and costimulatory domains. Following ex vivo characterization, we administered pooled autologous CAR-T arrays to three NHPs and tracked CAR abundance longitudinally using a novel digital droplet PCR assay. Ex vivo, CAR-T cells incorporating the MyD88-CD40 costimulatory domain exhibited markedly distinct functional profiles, including increased activation, unique cytokine secretion, tonic signaling, and resistance to exhaustion. In vivo, MyD88-CD40 CARs expanded dramatically, comprising up to 100% of peripheral T cells and significantly outperforming canonical CD28- and 4-1BB-based CARs. This expansion was associated with robust B-cell depletion across all animals. MyD88-CD40 CARs, particularly those with a CD28 hinge and transmembrane domain, demonstrated superior trafficking to secondary lymphoid tissues and persistence through study endpoint, unlike other CARs which waned by day 28. Our findings highlight the value of NHP models for screening CAR designs and identify MyD88-CD40 CARs as candidates with unmatched potency. The unique functional attributes conferred by this domain may provide key insights into features that drive enhanced CAR-T cell activity. Key pointsO_LIWe developed the first pooled CAR-T screening platform in an immunocompetent nonhuman primate model to directly compare CAR designs. C_LIO_LIWe identified MyD88-CD40 costimulatory domain as vastly superior to conventional domains in proliferation, trafficking and persistence. C_LI

immunology↗

bioRxiv2024

Genetic and functional adaptations and alcohol-biased signaling in the mediodorsal thalamus of alcohol dependent mice

Alcohol Use Disorder (AUD) is a significant health concern characterized by cognitive dysfunction and an inability to control alcohol intake leading to severe social and health consequences. It is crucial to uncover neuroadaptations and cellular mechanisms responsible for poor decisions surrounding alcohol drinking. Although the mediodorsal thalamus (MD) is an essential brain region for cognitive function and reward-guided choices, the effects of alcohol dependence on MD neuroadaptations and how dependence alters MD activity during choice behaviors for alcohol over natural rewards (i.e., sucrose) are not well understood. Genetic and physiological adaptations in the MD were assessed in mice treated with the chronic intermittent ethanol (CIE) exposure model of dependence, which increased alcohol intake and preference during choice sessions for water or sucrose. Results indicated that CIE exposure induced changes in transcript expression and excitability of MD neurons. Enrichment analysis of alcohol-sensitive genes revealed dysregulation of genes that control glial function and axonal myelination. Fiber photometry was used to record MD calcium signals in CIE mice during choice drinking sessions for alcohol and either water or sucrose. Results demonstrated that MD activity was elevated at the start of and after licking bouts for alcohol, water, or sucrose, although the signal for alcohol was significantly higher than signal for other solutions and this effect persisted after induction of dependence. These findings demonstrate that CIE exposure causes genetic and physiological neuroadaptations in the MD that coincide with alcohol-biased behaviors, with the MD uniquely responsive to alcohol over other solutions.

neuroscience↗

bioRxiv2024

Real-time activity of dynorphin-expressing neurons in mouse central amygdala during alcohol drinking

Alcohol use disorder (AUD) is a chronic disease that poses significant economic burden and health risks. It is pivotal to better understand brain mechanisms engaged by alcohol that promote misuse. The central amygdala (CeA) has emerged as a key mediator of excessive preclinical alcohol consumption. A dynorphin-expressing subpopulation within the CeA (CeADyn) has been implicated in excessive alcohol drinking, yet how cellular activity of CeADyn neurons relates to ongoing alcohol drinking is not well-understood. The current study interrogated the engagement of CeADyn neurons in male and female mice during voluntary alcohol consumption using fiber photometry and compared this cellular response with that of other solutions having similar motivational and/or taste characteristics. Activity of a calcium sensor, GCaMP7f, expressed in mouse CeADyn neurons was recorded and time-locked to bouts of drinking. Multilevel linear mixed modeling was applied to better resolve focal effects from complex data. These analyses revealed a relatively large increase in CeADyn neuron calcium transients after bouts of alcohol drinking compared to water or sucrose drinking, indicating these neurons are uniquely engaged during alcohol consumption. Drinking behavior unique to alcohol (i.e., longer bout durations) did not fully explain signal differences between alcohol and other solutions nor did the relatively increased alcohol response diminish over time. No other conditions or solutions tested reproduced the pronounced change in CeADyn activity associated with alcohol drinking. These findings, collectively, support the presence of a unique functional signature for alcohol in a cell population known to control excessive alcohol drinking. HighlightsO_LICentral amygdala dynorphin cells (CeADyn) are firmly implicated in alcohol misuse. C_LIO_LICeADyn neuron activity was higher when mice drank alcohol versus other solutions. C_LIO_LINeither how mice drank alcohol nor motivational states could explain this activity. C_LIO_LICeADyn neurons having uniquely high alcohol responses may underlie AUD development. C_LI

neuroscience↗

bioRxiv2023

Prelimbic neuron calcium activity predicts perceived hedonic value across drinking solutions and ethanol dependent states in mice

AO_SCPLOWBSTRACTC_SCPLOWThe medial prefrontal cortex integrates information about salience and valence of stimuli, including rewarding solutions like alcohol and sucrose, and regulates aspects of alcohol seeking and consumption. However, our understanding of how cortical outputs encode alcohol consumption is limited. Using fiber photometry to measure calcium activity in putative prelimbic (PrL) glutamatergic projection neurons, we show similar but distinct patterns of activity during the peri-consummatory phase in response to consumption of water (non-deprived conditions), ethanol (20% v/v), or sucrose (1% w/v). PrL population activity appears to track hedonic value, as GCaMP6f signals ramped immediately preceding bouts for water, ethanol, and sucrose, and the signal scaled with presumed hedonic value, i.e., water<ethanol<sucrose. Further, using machine learning, population activity of PrL neurons prior to consumption was sufficient to predict both consumption of and distinguish between these different solutions. To assess valence encoding, we adulterated the ethanol solution with quinine, a bitter tastant. In non-dependent mice, calcium activity surrounding drinking bouts was reduced, paralleling the decreased consumption of quinine-adulterated ethanol. This effect was not present in ethanol dependent mice, suggesting altered hedonic value of the adulterated solution either due to reduced sensitivity to the aversiveness of quinine or increased sensitivity to the reinforcing value of ethanol. The global population of PrL glutamatergic neurons also display sustained GCaMP6f "up-states" that last tens to hundreds of seconds, which were longer and larger when consummatory bouts occurred. Overall, our results demonstrate a functional signature in PrL neurons that differs across solutions and is disrupted by ethanol dependence.

neuroscience↗

bioRxiv2023

Single-molecule acceptor rise time (smART) FRET for nanoscale distance sensitivity

The structure, dynamics, and binding of individual biomolecules have been extensively investigated using single-molecule Forster resonance energy transfer (smFRET) as a spectroscopic ruler. The FRET efficiency between a fluorophore pair is used to measure distances in the several nanometer range. Existing approaches to detect closer distances come at the expense of sensitivity to longer distances. Here, we introduce single-molecule acceptor rise-time (smART) FRET that spans closer and longer distances. The acceptor rise time encodes the FRET rate, which scales polynomially with distance and thus has a steep dependence that expands the working range by 50%. High precision and accuracy is achieved through the spectroscopic separation between the rise time and the photophysical fluctuations that obfuscate other FRET readouts. Using the nanoscale sensitivity, we resolved the architectures of DNA bound to the single-stranded binding protein from E. coli, demonstrating the ability of smART FRET to elucidate the complex behaviors of biomolecules.

biophysics↗

bioRxiv2022

PLANAtools - an interactive gene expression repository for the planarian Schmidtea mediterranea

MotivationPlanarians are a widespread model for studying regeneration. Major efforts for studying gene function in planarian regeneration produced massive datasets, including transcriptome-wide gene expression analyses from hundreds of conditions. However, the accessibility of gene expression datasets to investigators is limited because of the need for expertise in gene expression analysis in this model, the requirement for computational resources, and the lack of a curated planarian gene expression metadata resource associating samples and their controls. ResultsWe implemented a computational resource, PLANAtools, that is available online and provides a portal to the analysis of over 160 gene expression analyses. Planarian gene expression datasets from the last decade were processed using a standardized pipeline based on curated planarian metadata. PLANAtools generates plots, annotations, and analyses of gene expression data, based on user parameters. AvailabilityPLANAtools is implemented using the R/Shiny framework and is accessible from https://wurtzellab.org/planatools

developmental biology↗

bioRxiv2022

Evolutionarily conserved effects of Notch signaling drive intestinal graft-versus-host disease in mice and non-human primates

Notch signaling promotes T-cell pathogenicity and graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (allo-HCT) in mice, with a dominant role for the Delta-like ligand DLL4. To assess if Notchs effects are evolutionarily conserved and identify key mechanisms, we studied antibody-mediated DLL4 blockade in a non-human primate model similar to human allo-HCT. Short-term DLL4 blockade improved post-transplant survival with striking, durable protection from gastrointestinal GVHD, out of proportion to other disease sites. Unlike prior immunosuppressive strategies, anti-DLL4 interfered with a T-cell transcriptional program associated with intestinal infiltration. In cross-species investigations, Notch inhibition decreased surface abundance of the gut-homing integrin a4b7 in conventional T-cells via b1 competition for a4 binding, while preserving a4b7 in regulatory T-cells. Thereby, DLL4/Notch blockade decreased effector T-cell infiltration into the gut, with increased regulatory to conventional T-cell ratios early after allo-HCT. Our results identify a conserved, biologically unique and targetable role of DLL4/Notch signaling in GVHD. One Sentence SummaryNotch signaling promotes pathogenic effector T cell infiltration of the intestine during acute graft-versus-host disease.

immunology↗

bioRxiv2021

The universal language network: A cross-linguistic investigation spanning 45 languages and 11 language families.

To understand the architecture of human language, it is critical to examine diverse languages; yet most cognitive neuroscience research has focused on a handful of primarily Indo-European languages. Here, we report an investigation of the fronto-temporo-parietal language network across 45 languages and establish the robustness to cross-linguistic variation of its topography and key functional properties, including left-lateralization, strong functional integration among its brain regions, and functional selectivity for language processing.

neuroscience↗

bioRxiv2021

Divergent sex differences in functional brain connectivity networks in excessively drinking C57BL/6J mice

Individuals with alcohol use disorder continue to drink in excess despite the health and societal consequences, and the rate of problematic drinking and alcohol-related harms is increased in women. Clinical imaging studies report widespread adaptations in brain structure after chronic, heavy drinking, and alcohol-related cues enhance brain reactivity in reward-related regions. In rodents, alcohol drinking induces expression of the immediate early gene c-Fos, which can be a marker of cellular activity, across multiple brain regions. Recent evidence also suggests that abstinence from chronic intermittent alcohol exposure can produce mesoscale changes in c-Fos expression. However, there is a substantial gap in our understanding of how excessive drinking affects functional connectivity networks to influence alcohol-seeking behaviors. For this study, male and female C57BL/6J mice were given access to either water or a choice between water and ethanol in the intermittent access drinking model for 4 weeks. After a short-access drinking session, whole brains from high alcohol drinking male and female mice and water drinking controls were then subjected to c-Fos immunolabeling, iDISCO+ clearing, light sheet imaging, and whole-brain c-Fos mapping. Correlation matrices were then generated and graph theoretical statistical approaches were used to determine changes in functional connectivity across sex and drinking condition. We observed robust sex differences in the network of c-Fos+ cells in water drinking mice, and excessive alcohol drinking produce divergent and robust changes in functional network connectivity in male and female mice. In addition, these analyses identified novel hub regions in excessively drinking mice that were unique for each sex. In conclusion, the whole-brain c-Fos mapping analysis identified sex difference in functional network connectivity and unique and understudied regions that may play a critical role in controlling excessive ethanol drinking in male and female mice.

neuroscience↗

bioRxiv2021

Plagl1 is part of the mammalian retinal injury response and a critical regulator of Muller glial cell quiescence

Retinal damage triggers reactive gliosis in Muller glia across vertebrate species, but only in regenerative animals, such as teleost fish, do Muller glia initiate repair; proliferating and undergoing neurogenesis to replace lost cells. By mining scRNA-seq and bulk RNA-seq datasets, we found that Plagl1, a maternally imprinted gene, is dynamically regulated in reactive Muller glia post-insult, with transcript levels transiently increasing before stably declining. To study Plagl1 retinal function, we examined Plagl1+/-pat null mutants postnatally, revealing defects in retinal architecture, visual signal processing and a reactive gliotic phenotype. Plagl1+/-pat Muller glia proliferate ectopically and give rise to inner retinal neurons and photoreceptors. Transcriptomic and ATAC-seq profiles revealed similarities between Plagl1+/-pat retinas and neurodegenerative and injury models, including an upregulation of pro-gliogenic and pro-proliferative pathways, such as Notch, not observed in wild-type retinas Plagl1 is thus an essential component of the transcriptional regulatory networks that retain mammalian Muller glia in quiescence.

neuroscience↗

bioRxiv2020

Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states.

One of the central challenges in the field of allo-immunity is deciphering the mechanisms driving T cells to infiltrate and subsequently occupy target organs to cause disease. The act of CD8-dominated T cell infiltration is critical to acute graft-versus-host disease (aGVHD), wherein donor T cells become activated, tissue-infiltrating and highly cytotoxic, causing wide-spread tissue damage after allogeneic hematopoietic stem cell transplant (allo-HCT). However, in human and non-human primate studies, deconvolving the transcriptional programs of newly recruited relative to resident memory T cells in the gastrointestinal (GI) tract has remained a challenge. In this study, we combined the novel technique of Serial Intravascular Staining (SIVS) with single-cell RNA-Seq (scRNA-seq) to enable detailed dissection of the tightly connected processes by which T cells first infiltrate tissues and then establish a pathogenic tissue residency program after allo-HCT in non-human primates. Our results have enabled the creation of a spatiotemporal map of the transcriptional drivers of CD8 T cell infiltration into the primary aGVHD target-organ, the GI tract. We identify the large and small intestines as the only two sites demonstrating allo-specific, rather than lymphdepletion-driven T cell infiltration. The donor CD8 T cells that infiltrate the GI tract demonstrate a highly activated, cytotoxic phenotype while simultaneously rapidly developing canonical tissue-resident memory (TRM) protein expression and transcriptional signatures, driven by IL-15/IL-21 signaling. Moreover, by combining SIVS and transcriptomic analysis, we have been able to work backwards from this pathogenic TRM programing, and, for the first time, identify a cluster of genes directly associated with tissue invasiveness, prominently including specific chemokines and adhesion molecules and their receptors, as well as a central cytoskeletal transcriptional node. The clinical relevance of this new tissue invasion signature was validated by its ability to discriminate the CD8 T cell transcriptome of patients with GI aGVHD. These results provide new insights into the mechanisms controlling tissue infiltration and pathogenic CD8 TRM transcriptional programing, uncovering critical transitions in allo-immune tissue invasion and destruction. One sentence summaryFlow cytometric and transcriptomic analysis reveals coordinated tissue-infiltration and tissue-residency programs driving gastrointestinal aGVHD.

immunology↗

bioRxiv2019

Motif elucidation in ChIP-seq datasets with a knockout control

Chromatin immunoprecipitation-sequencing (ChIP-seq) is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout experiments can generate improved motifs but require optimal differential analysis. We introduce peaKO--a computational method to automatically optimize motif analyses with knockout controls, which we compare to two other methods. PeaKO often improves elucidation of the target factor and highlights the benefits of knockout controls, which far outperform input controls. It is freely available at https://peako.hoffmanlab.org.

bioinformatics↗

bioRxiv2018

Monitoring Neural Activity During Exposure to Drugs of Abuse With In Vivo Fiber Photometry

Drugs of abuse are known to alter activity in areas of brain associated with reward, cognition and decision making. Changes in neural activity in these regions that follow repeated exposures to abused substances may underlie the development of addictive behaviors and contribute to the high rates of relapse associated with drug use. Measuring real-time changes in neural activity during drug seeking and taking is important for correlating changes in behavior with alterations in neuronal signaling typically measured using ex vivo electrophysiological recordings. In this study, C57BL/6J mice or Sprague-Dawley rats were injected in different brain areas with adeno-associated viruses (AAV) encoding the calcium sensor GCaMP6f along with an optical fiber. Calcium-dependent fluorescence was monitored in the nucleus accumbens core or mPFC during and following exposure to toluene vapor and in the medial prefrontal cortex (mPFC) and orbitofrontal cortex (OFC) during ethanol drinking. Toluene vapor, at concentrations previously shown to induce conditioned place preference, produced a rapid decrease in the frequency of calcium transients in the NAc core of rats that recovered following washout of the toluene vapor. In a probabilistic risk task, GCaMP6 signals in rat mPFC increased just prior to lever pressing and showed decreases during the reward phase that were proportional to reward size. Toluene pretreatment elevated the signal during the decision-making period while post-lever responses were independent of reward size. Using the drinking in the dark (DID) protocol in mice, we observed a consistent increase in GCaMP6 fluorescence during the period leading up to an ethanol drinking bout, a decrease during consumption and a rebound increase following the bout. The initial increase in signal prior to consumption was greater for ethanol and sucrose than water. GCaMP6 signals in the lateral OFC also decreased during ethanol consumption and increased following bout completion while no increase in activity was noted prior to bout initiation. Following repeated cycles of chronic intermittent ethanol (CIE) exposure that enhanced ethanol consumption, OFC calcium signals during and after ethanol drinking were similar to those in air-treated animals. Addition of quinine to the ethanol solution augmented the decrease in signal during consumption in both air and CIE mice while having no effect on the magnitude of the rebound in activity. Conversely, when sucrose was added to the ethanol solution, air exposed mice showed blunted changes in GCaMP6 signals while those in CIE mice were enhanced. Overall, the results from these experiments complement and extend data from prior behavioral and electrophysiological studies and support the use of in vivo fiber photometry in the study of effects of abused substances on brain function.

neuroscience↗

bioRxiv2018

Subclonal architecture, evolutionary trajectories and patterns of inheritance of germline variants in pediatric glioblastoma

Pediatric glioblastoma (pGBM) is a lethal cancer with no effective therapies. Intratumoral genetic heterogeneity and mode of tumor evolution have not been systematically addressed for this cancer. Whole-genome sequencing of germline-tumor pairs showed that pGBM is characterized by intratumoral genetic heterogeneity and consequent subclonal architecture. We found that pGBM undergoes extreme evolutionary trajectories, with primary and recurrent tumors having different subclonal compositions. Analysis of variant allele frequencies supported a model of tumor growth involving slow-cycling cancer stem cells that give rise to fast-proliferating progenitor-like cells and to non-dividing cells. pGBM patients germlines had subclonal structural variants, some of which underwent dynamic frequency fluctuations during tumor evolution. By sequencing germlines of mother-father-patient trios, we found that inheritance of deleterious germline variants from healthy parents cooperate with de novo germline and somatic events to the tumorigenic process. Our studies therefore challenge the current notion that pGBM is a relatively homogeneous molecular entity.

cancer biology↗

bioRxiv2018

Phylogenetic, population genetic, and morphological analyses reveal evidence for one species of Eastern Indigo Snake (Drymarchon couperi)

Accurate species delimitation and description are necessary to guide effective conservation management of imperiled species. The Eastern Indigo Snake (Drymarchon couperi) is a large species in North America that is federally-protected as Threatened under the Endangered Species Act. Recently, two associated studies hypothesized that Drymarchon couperi is two species. Here, we use diverse approaches to test the two-species hypothesis for D. couperi. Our analyses reveal that (1) phylogenetic reconstruction in previous studies was based entirely on variance of mitochondrial DNA sequence data, (2) microsatellite data demonstrate significant population admixture and nuclear gene flow between mitochondrial lineages, and (3) morphological analyses recover a single diagnosable species. Our results are inconsistent with the two-species hypothesis, thus we reject it and formally place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA may be driven by high dispersal of males relative to females. We caution against species delimitation exercises when one or few loci are used without evaluation of contemporary gene flow, particularly species with strong sex-biased dispersal (e.g., squamates) and/or when results have implications for ongoing conservation efforts.

zoology↗

bioRxiv2016

A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types

Semi-automated genome annotation methods such as Segway enable understanding of chromatin activity. Here we present chromatin state annotations of 164 human cell types using 1,615 genomics data sets. To produce these annotations, we developed a fully-automated annotation strategy in which we train separate unsupervised annotation models on each cell type and use a machine learning classifier to automate the state interpretation step. Using these annotations, we developed a measure of the importance of each genomic position called the \"conservation-associated activity score,\" which we use to aggregate information across cell types into a multi-cell type view. The aggregated conservation-associated activity score provides a measure of importance directly attributable to a specific activity in a specific set of cell types. In contrast to evolutionary conservation, this measure is not biased to detect only elements shared with related species. Using the conservation-associated activity score, we combined all our annotations into a single, cell type-agnostic encyclopedia that catalogs all human transcriptional and regulatory elements, enabling easy and intuitive interpretation of the effect of genome variants on phenotype, such as in disease-associated, evolutionarily conserved or positively selected loci. These resources, including cell type-specific annotations, encyclopedia, and a visualization server, are available at http://noble.gs.washington.edu/proj/encyclopedia.\n\nAuthor SummaryGenome annotation algorithms are an effective class of tools for understanding the function of the genome. These algorithms take as input a set of genome-wide measurements about the activity at each base pair in a given tissue, such as where a given protein is binding or how accessible the DNA is to being read by a protein. The genome is then partitioned and each segment is assigned a label such that positions with the same label exhibit similar patterns in the input data. Such annotations are widely used for many applications, such as to understand the mechanism of impact of a given genetic variant. Here we present, to our knowledge, the most comprehensive set of genome annotations created so far, encompassing 164 human cell types and including 1,615 genomics data sets. These comprehensive annotations are made possible by a strategy that automates the previous interpretation step. Furthermore, we present several methodological innovations that make these genome annotations more useful.

genomics↗