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Opioid use disorder (OUD) among pregnant women has become an epidemic in the United States. Pharmacological interventions for maternal OUD most commonly involve methadone, a synthetic opioid analgesic that attenuates withdrawal symptoms and behaviors linked with drug addiction. However, evidence of methadone’s ability to readily accumulate in neural tissue, and cause long-term neurocognitive sequelae, has led to concerns regarding its effect on prenatal brain development. We utilized human cortical organoid (hCO) technology to probe how this drug impacts the earliest mechanisms of cortico-genesis. Bulk mRNA sequencing of 2-month-old hCOs chronically treated with a clinically relevant dose of 1 μM methadone for 50 days revealed a robust transcriptional response to methadone associated with functional components of the synapse, the underlying extracellular matrix (ECM), and cilia. Co-expression network and predictive protein-protein interaction analyses demonstrated that these changes occurred in concert, centered around a regulatory axis of growth factors, developmental signaling pathways, and matricellular proteins (MCPs). TGFβ1 was identified as an upstream regulator of this network and appeared as part of a highly interconnected cluster of MCPs, of which thrombospondin 1 (TSP1) was most prominently downregulated and exhibited dose-dependent reductions in protein levels. These results demonstrate that methadone exposure during early cortical development alters transcriptional programs associated with synaptogenesis, and that these changes arise by functionally modulating extra-synaptic molecular mechanisms in the ECM and cilia. Our findings provide novel insight into the molecular underpinnings of methadone’s putative effect on cognitive and behavioral development and a basis for improving interventions for maternal opioid addiction.

Alzheimer’s disease (AD) manifested before age 65 is commonly referred to as early-onset AD (EOAD) (Reitz et al. Neurol Genet. 2020;6:e512). While the majority (> 90%) of EOAD cases are not caused by autosomal-dominant mutations in PSEN1 , PSEN2 , and APP , they do have a higher heritability (92–100%) than sporadic late-onset AD (LOAD, 70%) (Wingo et al. Arch Neurol. 2012;69:59–64, Fulton-Howard et al. Neurobiol Aging. 2021;99:101.e1–101.e9). Although the endpoint clinicopathological changes, i.e., Aβ plaques, tau tangles, and cognitive decline, are common across EOAD and LOAD, the disease progression is highly heterogeneous (Neff et al. Sci Adv Am Assoc Adv Sci. 2021;7:eabb5398). This heterogeneity, leading to temporally distinct age at onset (AAO) and stages of cognitive decline, may be caused by myriad combinations of distinct disease-associated molecular mechanisms. We and others have used transcriptome profiling in AD patient-derived neuron models of autosomal-dominant EOAD and sporadic LOAD to identify disease endotypes (Caldwell et al. Sci Adv Am Assoc Adv Sci. 2020;6:eaba5933, Mertens et al. Cell Stem Cell. 2021;28:1533–1548.e6, Caldwell et al. Alzheimers Demen. 2022). Further, analyses of large postmortem brain cohorts demonstrate that only one-third of AD patients show hallmark disease endotypes like increased inflammation and decreased synaptic signaling (Neff et al. Sci Adv Am Assoc Adv Sci. 2021;7:eabb5398). Areas of the brain less affected by AD pathology at early disease stages — such as the primary visual cortex — exhibit similar transcriptomic dysregulation as those regions traditionally affected and, therefore, may offer a view into the molecular mechanisms of AD without the associated inflammatory changes and gliosis induced by pathology (Haroutunian et al. Neurobiol Aging. 2009;30:561–73). To this end, we analyzed AD patient samples from the primary visual cortex (19 EOAD, 20 LOAD) using transcriptomic signatures to identify patient clusters and disease endotypes. Interestingly, although the clusters showed distinct combinations and severity of endotypes, each patient cluster contained both EOAD and LOAD cases, suggesting that AAO may not directly correlate with the identity and severity of AD endotypes.

At high altitude Andean region, hypoxia-induced excessive erythrocytosis (EE) is the defining feature of Monge’s disease or chronic mountain sickness (CMS). At the same altitude, resides a population that has developed adaptive mechanism(s) to constrain this hypoxic response (non-CMS). In this study, we utilized an in vitro induced pluripotent stem cell model system to study both populations using genomic and molecular approaches. Our whole genome analysis of the two groups identified differential SNPs between the CMS and non-CMS subjects in the ARID1B region. Under hypoxia, the expression levels of ARID1B significantly increased in the non-CMS cells but decreased in the CMS cells. At the molecular level, ARID1B knockdown (KD) in non-CMS cells increased the levels of the transcriptional regulator GATA1 by 3-fold and RBC levels by 100-fold under hypoxia. ARID1B KD in non-CMS cells led to increased proliferation and EPO sensitivity by lowering p53 levels and decreasing apoptosis through GATA1 mediation. Interestingly, under hypoxia ARID1B showed an epigenetic role, altering the chromatin states of erythroid genes. Indeed, combined Real-time PCR and ATAC-Seq results showed that ARID1B modulates the expression of GATA1 and p53 and chromatin accessibility at GATA1 / p53 target genes. We conclude that ARID1B is a novel erythroid regulator under hypoxia that controls various aspects of erythropoiesis in high-altitude dwellers. Red blood cell: Regulating production under low oxygen conditions Insights into a disorder associated with excess red blood cell production in high-altitude dwellers could have broader relevance to certain cancers and blood diseases. Some people living in the Andes will eventually develop Monge’s disease, in which excessive red cell proliferation induced by low oxygen conditions leads to thickening of the blood and increased risk of heart attack or stroke. Researchers led by Gabriel Haddad of the University of California, San Diego, USA, have shown that a protein called ARID1B normally manages red blood cell levels under low oxygen conditions by regulating other genes that govern cell proliferation and survival. These same ARID1B-modulated gene networks may also contribute to various blood disorders as well as the uncontrolled growth seen in some tumor types in which cells must thrive in very oxygen-poor environments.

Non-familial Alzheimer’s disease (AD) occurring before 65 years of age is commonly referred to as early-onset Alzheimer’s disease (EOAD) and constitutes ~ 5–6% of all AD cases (Mendez et al. in Continuum 25:34–51, 2019). While EOAD exhibits the same clinicopathological changes such as amyloid plaques, neurofibrillary tangles (NFTs), brain atrophy, and cognitive decline (Sirkis et al. in Mol Psychiatry 27:2674–88, 2022; Caldwell et al. in Mol Brain 15:83, 2022) as observed in the more prevalent late-onset AD (LOAD), EOAD patients tend to have more severe cognitive deficits, including visuospatial, language, and executive dysfunction (Sirkis et al. in Mol Psychiatry 27:2674–88, 2022). Patient-derived induced pluripotent stem cells (iPSCs) have been used to model and study penetrative, familial AD (FAD) mutations in APP , PSEN1 , and PSEN2 (Valdes et al. in Research Square 1–30, 2022; Caldwell et al. in Sci Adv 6:1–16, 2020) but have been seldom used for sporadic forms of AD that display more heterogeneous disease mechanisms. In this study, we sought to characterize iPSC-derived neurons from EOAD patients via RNA sequencing. A modest difference in expression profiles between EOAD patients and non-demented control (NDC) subjects resulted in a limited number of differentially expressed genes (DEGs). Based on this analysis, we provide evidence that iPSC-derived neuron model systems, likely due to the loss of EOAD-associated epigenetic signatures arising from iPSC reprogramming, may not be ideal models for studying sporadic AD.

Monge's disease, or Chronic Mountain Sickness (CMS), is a chronic high-altitude disorder characterized by hypoxia-induced excessive erythrocytosis (EE), elevating the risk of stroke and myocardial infarction. Using RNA-seq and ATAC-seq, we profiled iPSC-derived erythroid cells from CMS and non-CMS subjects under normoxia and hypoxia to identify statistically significant, disease-associated transcriptional and chromatin accessibility changes. RNA-seq revealed induction of inflammatory, stress, and erythropoiesis programs in CMS even under normoxia, including robust activation of JAK/STAT signaling, upregulation of heme metabolism and VEGF, and accelerated erythrocyte lineage commitment alongside repression of Notch and WNT/β-catenin. Hypoxia amplified this dysregulated state, and critically, activated NFκB-driven inflammatory signaling together with canonical HIF targets. ATAC-seq revealed pronounced hypoxia-induced changes, with increased accessibility within inflammatory and erythrocyte lineage genes occurring concomitantly with decreased accessibility within pluripotency and ectodermal lineage genes. Pharmacological NFκB inhibition in CMS cells significantly reduced EE ( -value <0.0001), whereas NFκB activation in non-CMS cells was sufficient to drive EE ( -value <0.01), confirming the causal role inferred by our multiomics analyses. Collectively, our multiomics and functional experiments substantiate a coordinated chromatin-transcription paradigm favoring an inflammatory axis that, through hypoxia-driven NFκB activation, accelerates stress-induced erythroid commitment and underlies EE in CMS.

Background Early‐onset Alzheimer’s disease (EOAD) is a complex disease that occurs at an early age at onset (AAO) before 65 years, constituting 5‐6% of all AD cases and remains poorly understood. Patient‐derived induced pluripotent stem cells (iPSCs) have been used to model different forms of EOAD that display heterogeneous disease mechanisms. Method We examined iPSC‐derived neurons from both familial EOAD harboring mutations in PSEN1A79V , PSEN2N141I, and APPV717I and non‐familial EOAD patients at an early AAO. RNA‐seq for familial and non‐familial EOAD patients as well as ATAC‐seq for familial EOAD patients were carried out to characterize the gene expression and chromatin accessibility changes, respectively. Differential expression and enrichment analysis, TF activity identification, and co‐expression module detection were performed for familial EOAD RNA‐seq. Clustering and surrogate neuron marker classification were performed for non‐familial EOAD RNA‐seq. Differential peak analysis, TF motif footprinting and peak functional enrichment were performed for familial EOAD ATAC‐seq. Result Our approach allowed us to identify the correlation between gene expression and chromatin accessibility associated with key disease familial EOAD endotypes. We identified limitations with our non‐familial EOAD neuron model to study sporadic AD, providing evidence that these neurons present variation of differentiation across patient clones, patient variability and an immature culture state. Common endotypes were identified across three familial EOAD mutations such as dedifferentiation of a mature neuron to a less differentiated quasi‐neuron state and repression of mitochondrial function and metabolism. Integrative analysis allowed us to ascertain the master transcriptional regulators associated with these endotypes, including REST, ASCL1, and ZIC family members (activation), as well as NRF1 (repression). Our non‐familial EOAD study showed a modest difference in expression profiling and a limited number of differentially expressed genes (DEGs) between diseased and control subjects. Conclusion iPSC‐derived neurons demonstrated that familial EOAD mutations share common regulatory changes within endotypes with varying severity, leading to reversion to a less‐differentiated neuron state. Extending the usage of these neurons to non‐familial EOAD may not serve as ideal to study sporadic AD. Overall, we have demonstrated that human neuron modeling can be applied to different forms of EOAD to understand the disease etiology better.

Background PSEN1, PSEN2, and APP mutations cause Alzheimer’s disease (AD) with an early age at onset (AAO) and progressive cognitive decline. PSEN1 mutations are more common and generally have an earlier AAO; however, certain PSEN1 mutations cause a later AAO, similar to those observed in PSEN2 and APP . Methods We examined whether common disease endotypes exist across these mutations with a later AAO (~ 55 years) using hiPSC-derived neurons from familial Alzheimer’s disease (FAD) patients harboring mutations in PSEN1 A79V , PSEN2 N141I , and APP V717I and mechanistically characterized by integrating RNA-seq and ATAC-seq. Results We identified common disease endotypes, such as dedifferentiation, dysregulation of synaptic signaling, repression of mitochondrial function and metabolism, and inflammation. We ascertained the master transcriptional regulators associated with these endotypes, including REST, ASCL1, and ZIC family members (activation), and NRF1 (repression). Conclusions FAD mutations share common regulatory changes within endotypes with varying severity, resulting in reversion to a less-differentiated state. The regulatory mechanisms described offer potential targets for therapeutic interventions.

Opioid use disorder (OUD) among pregnant women has become an epidemic in the United States. Pharmacological interventions for OUD involve methadone, a synthetic opioid analgesic that attenuates withdrawal symptoms and behaviors linked with maternal drug addiction. However, methadone's ability to readily accumulate in neural tissue, and cause long-term neurocognitive sequelae, has led to concerns regarding its effect on prenatal brain development. We took advantage of human cortical organoid (hCO) technology to probe how this drug impacts the earliest mechanisms giving rise to the cerebral cortex. To this end, we conducted bulk mRNA sequencing of 2-month-old hCOs derived from two cell lines that were chronically treated with a clinically relevant dose of 1μM methadone for 50 days. Differential expression and gene ontology analyses revealed a robust transcriptional response to methadone associated with functional components of the synapse, the underlying extracellular matrix (ECM), and cilia. Further unsupervised co-expression network and predictive protein-protein interaction analyses demonstrated that these changes occurred in concert, centered around a regulatory axis consisting of growth factors, developmental signaling pathways, and matricellular proteins. Our results demonstrate that exposure to methadone during early cortico-genesis fundamentally alters transcriptional programs associated with synapse formation, and that these changes arise by modulating extra-synaptic molecular mechanisms in the ECM and cilia. These findings provide novel insight into methadone's putative effect on cognitive and behavioral development and a basis for improving interventions for maternal opioid addiction.Competing Interest StatementThe authors have declared no competing interest.

Early-Onset Familial Alzheimer's Disease (EOFAD) is a dominantly inherited neurodegenerative disorder elicited by mutations in the PSEN1, PSEN2, and APP genes. Hallmark pathological changes and symptoms observed, namely the accumulation of misfolded Amyloid-β (Aβ) in plaques and Tau aggregates in neurofibrillary tangles associated with memory loss and cognitive decline, are understood to be temporally accelerated manifestations of the more common sporadic Late-Onset Alzheimer's Disease. The complete penetrance of EOFAD-causing mutations has allowed for experimental models which have proven integral to the overall understanding of AD. However, the failure of pathology-targeting therapeutic development suggests that the formation of plaques and tangles may be symptomatic and not describe the etiology of the disease. Here, we use an integrative, multi-omics approach and systems-level analysis in hiPSC-derived neurons to generate a mechanistic disease model for EOFAD. Using patient-specific cells from donors harboring mutations in PSEN1 differentiated into neurons, we characterize the disease-related gene expression and chromatin accessibility changes by RNA-Seq, ATAC-Seq, and histone methylation ChIP-Seq. Here, we show that the defining disease-causing mechanism of EOFAD is dedifferentiation, causing neurons to traverse the lineage-defining chromatin landscape along an alternative axis to a mixed-lineage cell state with gene signature profiles indicative of less-defined ectoderm as well as non-ectoderm lineages via REST-mediated repression of neuronal lineage specification gene programs and the activation of non-specific germ layer precursor gene programs concomitant with modifications in chromatin accessibility. Further, a reanalysis of existing transcriptomic data from PSEN1 patient brain samples demonstrates that the mechanisms identified in our experimental system recapitulate EOFAD in the human brain. Our results comprise a disease model which describes the mechanisms culminating in dedifferentiation that contribute to neurodegeneration. Footnotes * This updated manuscript includes additional analysis and ChIP-Seq data in support of the conclusions presented.

INTRODUCTION The molecular mechanisms that contribute to sex differences, in particular female predominance, in Alzheimer's disease (AD) prevalence, symptomology, and pathology, are incompletely understood. METHODS To address this problem, we investigated cellular metabolism and immune responses (“immunometabolism endophenotype”) across AD individuals as a function of sex with diverse clinical diagnosis of cognitive status at death (cogdx), Braak staging, and Consortium to Establish a Registry for AD (CERAD) scores using human cortex metabolomics and transcriptomics data from the Religious Orders Study / Memory and Aging Project (ROSMAP) cohort. RESULTS We identified sex‐specific metabolites, immune and metabolic genes, and pathways associated with the AD diagnosis and progression. We identified female‐specific elevation in glycerophosphorylcholine and N‐acetylglutamate, which are AD inflammatory metabolites involved in interleukin (IL)‐17 signaling, C‐type lectin receptor, interferon signaling, and Toll‐like receptor pathways. We pinpointed distinct microglia‐specific immunometabolism endophenotypes (i.e., lipid‐ and amino acid‐specific IL‐10 and IL‐17 signaling pathways) between female and male AD subjects. In addition, female AD subjects showed evidence of diminished excitatory neuron and microglia communications via glutamate‐mediated immunometabolism. DISCUSSION Our results point to new understanding of the molecular basis for female predominance in AD, and warrant future independent validations with ethnically diverse patient cohorts to establish a likely causal relationship of microglial immunometabolism in the sex differences in AD. Highlights Sex‐specific immune metabolites, gene networks and pathways, are associated with Alzheimer's disease pathogenesis and disease progression. Female AD subjects exhibit microglial immunometabolism endophenotypes characterized by decreased glutamate metabolism and elevated interleukin‐10 pathway activity. Female AD subjects showed a shift in glutamate‐mediated cell‐cell communications between excitatory neurons to microglia and astrocyte.