High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells.

Enteroendocrine cells (EECs) sense intestinal content and release hormones to regulate gastrointestinal activity, systemic metabolism, and food intake. Little is known about the molecular make-up of human EEC subtypes and the regulated secretion of individual hormones. Here, we describe an organoid-based platform for functional studies of human EECs. EEC formation is induced in vitro by transient expression of NEUROG3. A set of gut organoids was engineered in which the major hormones are fluorescently tagged. A single-cell mRNA atlas was generated for the different EEC subtypes, and their secreted products were recorded by mass-spectrometry. We note key differences to murine EECs, including hormones, sensory receptors, and transcription factors. Notably, several hormone-like molecules were identified. Inter-EEC communication is exemplified by secretin-induced GLP-1 secretion. Indeed, individual EEC subtypes carry receptors for various EEC hormones. This study provides a rich resource to study human EEC development and function.

Patient-derived organoid biobank identifies epigenetic dysregulation of intestinal epithelial MHC-I as a novel mechanism in severe Crohn's Disease.

OBJECTIVE: Epigenetic mechanisms, including DNA methylation (DNAm), have been proposed to play a key role in Crohn's disease (CD) pathogenesis. However, the specific cell types and pathways affected as well as their potential impact on disease phenotype and outcome remain unknown. We set out to investigate the role of intestinal epithelial DNAm in CD pathogenesis. DESIGN: We generated 312 intestinal epithelial organoids (IEOs) from mucosal biopsies of 168 patients with CD (n=72), UC (n=23) and healthy controls (n=73). We performed genome-wide molecular profiling including DNAm, bulk as well as single-cell RNA sequencing. Organoids were subjected to gene editing and the functional consequences of DNAm changes evaluated using an organoid-lymphocyte coculture and a nucleotide-binding oligomerisation domain, leucine-rich repeat and CARD domain containing 5 (NLRC5) dextran sulphate sodium (DSS) colitis knock-out mouse model. RESULTS: We identified highly stable, CD-associated loss of DNAm at major histocompatibility complex (MHC) class 1 loci including NLRC5 and cognate gene upregulation. Single-cell RNA sequencing of primary mucosal tissue and IEOs confirmed the role of NLRC5 as transcriptional transactivator in the intestinal epithelium. Increased mucosal MHC-I and NLRC5 expression in adult and paediatric patients with CD was validated in additional cohorts and the functional role of MHC-I highlighted by demonstrating a relative protection from DSS-mediated mucosal inflammation in NLRC5-deficient mice. MHC-I DNAm in IEOs showed a significant correlation with CD disease phenotype and outcomes. Application of machine learning approaches enabled the development of a disease prognostic epigenetic molecular signature. CONCLUSIONS: Our study has identified epigenetically regulated intestinal epithelial MHC-I as a novel mechanism in CD pathogenesis.

Transcription and DNA Methylation Patterns of Blood-Derived CD8+ T Cells Are Associated With Age and Inflammatory Bowel Disease But Do Not Predict Prognosis.

BACKGROUND & AIMS: Gene expression patterns of CD8+ T cells have been reported to correlate with clinical outcomes of adults with inflammatory bowel diseases (IBD). We aimed to validate these findings in independent patient cohorts. METHODS: We obtained peripheral blood samples from 112 children with a new diagnosis of IBD (71 with Crohn's disease and 41 with ulcerative colitis) and 19 children without IBD (controls) and recorded medical information on disease activity and outcomes. CD8+ T cells were isolated from blood samples by magnetic bead sorting at the point of diagnosis and during the course of disease. Genome-wide transcription (n = 192) and DNA methylation (n = 66) profiles were generated using Affymetrix and Illumina arrays, respectively. Publicly available transcriptomes and DNA methylomes of CD8+ T cells from 3 adult patient cohorts with and without IBD were included in data analyses. RESULTS: Previously reported CD8+ T-cell prognostic expression and exhaustion signatures were only found in the original adult IBD patient cohort. These signatures could not be detected in either a pediatric or a second adult IBD cohort. In contrast, an association between CD8+ T-cell gene expression with age and sex was detected across all 3 cohorts. CD8+ gene transcription was clearly associated with IBD in the 2 cohorts that included non-IBD controls. Lastly, DNA methylation profiles of CD8+ T cells from children with Crohn's disease correlated with age but not with disease outcome. CONCLUSIONS: We were unable to validate previously reported findings of an association between CD8+ T-cell gene transcription and disease outcome in IBD. Our findings reveal the challenges of developing prognostic biomarkers for patients with IBD and the importance of their validation in large, independent cohorts before clinical application.

Regional Differences in Human Biliary Tissues and Corresponding In Vitro-Derived Organoids.

BACKGROUND AND AIMS: Organoids provide a powerful system to study epithelia in vitro. Recently, this approach was applied successfully to the biliary tree, a series of ductular tissues responsible for the drainage of bile and pancreatic secretions. More precisely, organoids have been derived from ductal tissue located outside (extrahepatic bile ducts; EHBDs) or inside the liver (intrahepatic bile ducts; IHBDs). These organoids share many characteristics, including expression of cholangiocyte markers such as keratin (KRT) 19. However, the relationship between these organoids and their tissues of origin, and to each other, is largely unknown. APPROACH AND RESULTS: Organoids were derived from human gallbladder, common bile duct, pancreatic duct, and IHBDs using culture conditions promoting WNT signaling. The resulting IHBD and EHBD organoids expressed stem/progenitor markers leucine-rich repeat-containing G-protein-coupled receptor 5/prominin 1 and ductal markers KRT19/KRT7. However, RNA sequencing revealed that organoids conserve only a limited number of regional-specific markers corresponding to their location of origin. Of particular interest, down-regulation of biliary markers and up-regulation of cell-cycle genes were observed in organoids. IHBD and EHBD organoids diverged in their response to WNT signaling, and only IHBDs were able to express a low level of hepatocyte markers under differentiation conditions. CONCLUSIONS: Taken together, our results demonstrate that differences exist not only between extrahepatic biliary organoids and their tissue of origin, but also between IHBD and EHBD organoids. This information may help to understand the tissue specificity of cholangiopathies and also to identify targets for therapeutic development.

Similar zooplankton responses to low pH and calcium may impair long-term recovery from acidification.

Throughout much of the 20th century, unprecedented industrial emissions have led to widespread acidification of regions in North America and Europe and, as lake water pH dropped, aquatic ecosystems have experienced dramatic declines in biodiversity. International emission-control agreements have led to sweeping increases in lake pH, however acid-structured zooplankton communities still persist in many lakes. Concomitantly, calcium concentrations have been declining as a legacy of acidification and are approaching or have reached concentrations that could represent a barrier to the re-establishment of zooplankton communities similar to those in non-acidified or circumneutral reference lakes. To understand how declining calcium may influence the re-establishment of zooplankton in acid-damaged lakes we manipulated calcium and pH using a factorial in-lake mesocosm experiment and assessed their individual and combined effects on a regionally diverse zooplankton assemblage. We found that the impacts of low calcium on zooplankton species were similar to those of acidification and, consequently, may prevent the recovery of acid-structured communities. Abundance of the larger bodied and acid-sensitive Daphnia pulex/pulicaria increased in high pH treatments, albeit nonsignificantly yet, by the end of our experiment, only two individuals were sampled among our 10 low calcium enclosures. In contrast, small acid-tolerant cladocerans, such as Daphnia catawba, Daphnia ambigua, and eubosminids maintained significantly higher abundances in low calcium treatments relative to all other treatment combinations. Although we did not detect an effect of calcium on mean body size, the disproportionately high abundance of small cladocerans in low calcium treatments resulted in low calcium communities with higher overall abundance and lower cladoceran evenness. Our results, along with a landscape comparison demonstrating parallel changes in zooplankton relative abundance from 34 historically acidified lakes, suggests that declining calcium will be an important, on-going factor that may limit the recovery of zooplankton, despite regional improvements in lake pH.

Whole-heart, ungated, free-breathing, cardiac-phase-resolved myocardial perfusion MRI by using Continuous Radial Interleaved simultaneous Multi-slice acquisitions at sPoiled steady-state (CRIMP).

PURPOSE: To develop a whole-heart, free-breathing, non-electrocardiograph (ECG)-gated, cardiac-phase-resolved myocardial perfusion MRI framework (CRIMP; Continuous Radial Interleaved simultaneous Multi-slice acquisitions at sPoiled steady-state) and test its quantification feasibility. METHODS: CRIMP used interleaved radial simultaneous multi-slice (SMS) slice groups to cover the whole heart in 9 or 12 short-axis slices. The sequence continuously acquired data without magnetization preparation, ECG gating or breath-holding, and captured multiple cardiac phases. Images were reconstructed by a motion-compensated patch-based locally low-rank reconstruction. Bloch simulations were performed to study the signal-to-noise ratio/contrast-to-noise ratio (SNR/CNR) for CRIMP and to study the steady-state signal under motion. Seven patients were scanned with CRIMP at stress and rest to develop the sequence. One human and two dogs were scanned at rest with a dual-bolus method to test the quantification feasibility of CRIMP. The dual-bolus scans were performed using both CRIMP and an ungated radial SMS saturation recovery (SMS-SR) sequence with injection dose = 0.075 mmol/kg to compare the sequences in terms of SNR, cardiac phase resolution and quantitative myocardial blood flow (MBF). RESULTS: Perfusion images with multiple cardiac phases in all image slices with a temporal resolution of 72 ms/frame were obtained. Simulations and in-vivo acquisitions showed CRIMP kept the inner slices in steady-state regardless of motion. CRIMP outperformed SMS-SR in slice coverage (9 over 6), SNR (mean 20% improvement), and provided cardiac phase resolution. CRIMP and SMS-SR sequences provided comparable MBF values (rest systolic CRIMP = 0.58 ± 0.07, SMS-SR = 0.61 ± 0.16). CONCLUSION: CRIMP allows for whole-heart, cardiac-phase-resolved myocardial perfusion images without ECG-gating or breath-holding. The sequence can provide MBF if an accurate arterial input function is obtained separately.

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.

OBJECTIVE: Human intestinal epithelial organoids (IEOs) are increasingly being recognised as a highly promising translational research tool. However, our understanding of their epigenetic molecular characteristics and behaviour in culture remains limited. DESIGN: We performed genome-wide DNA methylation and transcriptomic profiling of human IEOs derived from paediatric/adult and fetal small and large bowel as well as matching purified human gut epithelium. Furthermore, organoids were subjected to in vitro differentiation and genome editing using CRISPR/Cas9 technology. RESULTS: We discovered stable epigenetic signatures which define regional differences in gut epithelial function, including induction of segment-specific genes during cellular differentiation. Established DNA methylation profiles were independent of cellular environment since organoids retained their regional DNA methylation over prolonged culture periods. In contrast to paediatric and adult organoids, fetal gut-derived organoids showed distinct dynamic changes of DNA methylation and gene expression in culture, indicative of an in vitro maturation. By applying CRISPR/Cas9 genome editing to fetal organoids, we demonstrate that this process is partly regulated by TET1, an enzyme involved in the DNA demethylation process. Lastly, generating IEOs from a child diagnosed with gastric heterotopia revealed persistent and distinct disease-associated DNA methylation differences, highlighting the use of organoids as disease-specific research models. CONCLUSIONS: Our study demonstrates striking similarities of epigenetic signatures in mucosa-derived IEOs with matching primary epithelium. Moreover, these results suggest that intestinal stem cell-intrinsic DNA methylation patterns establish and maintain regional gut specification and are involved in early epithelial development and disease.

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.

BACKGROUND & AIMS: We analyzed DNA methylation patterns and transcriptomes of primary intestinal epithelial cells (IEC) of children newly diagnosed with inflammatory bowel diseases (IBD) to learn more about pathogenesis. METHODS: We obtained mucosal biopsies (N = 236) collected from terminal ileum and ascending and sigmoid colons of children (median age 13 years) newly diagnosed with IBD (43 with Crohn's disease [CD], 23 with ulcerative colitis [UC]), and 30 children without IBD (controls). Patients were recruited and managed at a hospital in the United Kingdom from 2013 through 2016. We also obtained biopsies collected at later stages from a subset of patients. IECs were purified and analyzed for genome-wide DNA methylation patterns and gene expression profiles. Adjacent microbiota were isolated from biopsies and analyzed by 16S gene sequencing. We generated intestinal organoid cultures from a subset of samples and genome-wide DNA methylation analysis was performed. RESULTS: We found gut segment-specific differences in DNA methylation and transcription profiles of IECs from children with IBD vs controls; some were independent of mucosal inflammation. Changes in gut microbiota between IBD and control groups were not as large and were difficult to assess because of large amounts of intra-individual variation. Only IECs from patients with CD had changes in DNA methylation and transcription patterns in terminal ileum epithelium, compared with controls. Colon epithelium from patients with CD and from patients with ulcerative colitis had distinct changes in DNA methylation and transcription patterns, compared with controls. In IECs from patients with IBD, changes in DNA methylation, compared with controls, were stable over time and were partially retained in ex-vivo organoid cultures. Statistical analyses of epithelial cell profiles allowed us to distinguish children with CD or UC from controls; profiles correlated with disease outcome parameters, such as the requirement for treatment with biologic agents. CONCLUSIONS: We identified specific changes in DNA methylation and transcriptome patterns in IECs from pediatric patients with IBD compared with controls. These data indicate that IECs undergo changes during IBD development and could be involved in pathogenesis. Further analyses of primary IECs from patients with IBD could improve our understanding of the large variations in disease progression and outcomes.

Co-Occurring Symptoms Contribute to Persistent Fatigue in Prostate Cancer.

PURPOSE: Cancer-related fatigue is one of the most debilitating side effects of cancer and cancer therapy. We aimed to investigate co-occurring symptoms associated with persistent fatigue in men receiving external beam radiation therapy (EBRT) for nonmetastatic prostate cancer. METHODS: A sample of 47 men with prostate cancer scheduled to receive radiotherapy (RT) were followed at baseline and 1 year after RT. Clinical and demographic data were obtained from chart review. Symptom measurements included urinary dysfunction (American Urological Association symptoms score), fatigue (Functional Assessment of Cancer Therapy - Fatigue questionnaire), sleep disturbance (Patient-Reported Outcomes Measurement Information System - Sleep Disturbance form), pain (physical well-being domain pain item of the Functional Assessment of Cancer Therapy - General), and depressive symptoms (Hamilton Depression Rating Scale). Paired t tests, correlations, general linear models, and logistic regressions were used to determine associations between fatigue and other symptom scores. RESULTS: At 1 year after RT, 34% of subjects continued to experience fatigue. Urinary dysfunction was the best clinical predictor of persistent fatigue. Pain and depressive symptoms further improved the predictive power of the model. A multivariate linear regression model containing all these three clinical variables (urinary dysfunction, pain, and depressive symptoms) explained 74% of total variance associated with persistent fatigue after RT. CONCLUSIONS: Persistent fatigue at 1 year after EBRT in prostate cancer survivors is likely related to a cluster of symptoms elicited by chronic inflammation. Therapies that target each of these symptoms will likely reduce fatigue in this patient population.

Size-growth asymmetry is not consistently related to productivity across an eastern US temperate forest network.

Modeling and forecasting forests as carbon sinks require that we understand the primary factors affecting productivity. One factor thought to be positively related to stand productivity is the degree of asymmetry, or the slope of the relationship between tree size and biomass growth. Steeper slopes indicate disproportionate productivity of big trees relative to small trees. Theoretically, big trees outcompete smaller trees during favorable growth conditions because they maintain better access to light. For this reason, high productivity forests are expected to have asymmetric growth. However, empirical studies do not consistently support this expectation, and those that do are limited in spatial or temporal scope. Here, we analyze size-growth relationships from 1970 to 2011 across a diverse network of forest sites in the eastern United States (n = 16) to test whether asymmetry is consistently related to productivity. To investigate this relationship, we analyze asymmetry-productivity relationships between our 16 forests at non-overlapping annual, 2-, 5-, 10-, and 20-year sampling intervals and find that asymmetry is negatively related to productivity, but the strength depends on the specific interval considered. Within-site temporal variability in asymmetry and productivity are generally positively correlated over time, except at the 5-year remeasurement interval. Rather than confirming or failing to support a positive relationship between asymmetry and productivity, our findings suggest caution interpreting these metrics since the relationship varies across forest types and temporal scales.

Clinical course and outcomes of diagnosing Inflammatory Bowel Disease in children 10 years and under: retrospective cohort study from two tertiary centres in the United Kingdom and in Italy.

BACKGROUND: Most children with Inflammatory Bowel Disease (IBD) are diagnosed between 11 and 16 years of age, commonly presenting with features of typical IBD. Children with onset of gut inflammation under 5 years of age often have a different underlying pathophysiology, one that is genetically and phenotypically distinct from other children with IBD. We therefore set out to assess whether children diagnosed after the age of 5 years, but before the age of 11, have a different clinical presentation and outcome when compared to those presenting later. METHODS: Retrospective cohort study conducted at two European Paediatric Gastroenterology Units. Two cohorts of children with IBD (total number = 160) were compared: 80 children diagnosed between 5 and 10 years (Group A), versus 80 children diagnosed between 11 and 16 (Group B). Statistical analysis included multiple logistic regression. RESULTS: Group A presented with a greater disease activity (p = 0.05 for Crohn's disease (CD), p = 0.03 for Ulcerative Colitis (UC); Odds Ratio 1.09, 95 % Confidence Interval: 1.02-1.1), and disease extent (L2 location more frequent amongst Group A children with CD (p = 0.05)). No significant differences were observed between age groups in terms of gastro-intestinal and extra-intestinal signs and symptoms at disease presentation, nor was there a difference in the number of hospitalisations due to relapsing IBD during follow-up. However, children in Group A were treated earlier with immunosuppressants and had more frequent endoscopic assessments. CONCLUSION: While clinicians feel children between 5 and 10 years of age have a more severe disease course than adolescents, our analysis also suggests a greater disease burden in this age group. Nevertheless, randomized trials to document longer-term clinical outcomes are urgently needed, in order to address the question whether a younger age at disease onset should prompt per se a more "aggressive" treatment. We speculate that non-clinical factors (e.g. genetics, epigenetics) may have more potential to predict longer term outcome than simple clinical measures such as age at diagnosis.

Coeliac disease in children with type 1 diabetes: are current guidelines proving difficult to implement in practice?

Updated European guidelines for the diagnosis of coeliac disease (CD) in the paediatric population (the European Society for Gastroenterology, Hepatology, and Nutrition, January 2012) outlined distinct diagnostic algorithms for patients with type 1 diabetes mellitus (T1DM). In this short report we demonstrate a period prevalence of CD in the T1DM population of 5.8% at a large tertiary centre. In addition to this, using a questionnaire circulated to paediatricians, we assessed present practice in the diagnosis of CD in T1DM 16 months following the European Society for Gastroenterology, Hepatology, and Nutrition guideline publication. Our results indicate that present practice and adherence to guidelines varies substantially. Further dissemination and perhaps simplification of guidelines may be required.

Resident gut microbiota community determines the efficacy of soluble fiber in reducing adiposity.

Consumption of dietary fiber has been linked to several health benefits. Among these, dietary fiber breakdown through the process of anaerobic fermentation by the colonic microbiota leads to the production of beneficial metabolites, mainly short-chain fatty acids (acetate, propionate, and butyrate), which have been implicated in reduced calorie intake. Nevertheless, the link between gut microbiota and obesity remains unclear. We investigated the effects of dietary fibers on food intake and body weight gain in two independent but similarly designed studies in rats. In the first study, the inclusion of 10% w/w pectin, fructooligosaccharides or beta-glucan (n = 10/group) in the diets each significantly reduced body weight gain ('responders') compared to the cellulose control whereas, in a closely matched, but not fully identical study (n = 8/group), no effect of dietary fiber on body weight ('non-responders') was observed. The aim of this work was to explore the basis of this differential response between the two similarly designed and comparable studies, with a focus on the potential role of the gut microbiota in the control of food intake and body weight.

Family Wellbeing and Sexual Health of Patients Receiving Treatment for Prostate Cancer.

Purpose: Prostate cancer and its treatment may affect patients' sexual function and social wellbeing. This study investigated the relationship between social/family wellbeing and sexual health in patients with prostate cancer. Additionally, the moderating effect of clinical characteristics on this relationship was also explored. Patients and Methods: This is a descriptive correlational study using baseline data of a longitudinal study enrolling 137 patients with prostate cancer. Sexual Function (SF) and Sexual Function Distress (SFD) data were collected using the Symptom Index questionnaire. Demographic data were obtained during study intake and clinical data were obtained from chart review. Bivariate correlation determined the correlations among continuous demographic/clinical data, social/family wellbeing, and sexual health. Moderated regression analysis determined the moderating effects of clinical characteristics on the relationship of social/family wellbeing and sexual health. Results: Moderate positive correlation was found between social/family wellbeing and SF, whereas a weak negative correlation was noted between social/family wellbeing and SFD. Depression was significantly correlated with social/family wellbeing and SFD. Both sexual health domains were significantly correlated with Gleason score. A significant difference was noted in the social/family wellbeing and both SF and SFD in participants receiving androgen deprivation therapy (ADT) compared to those not receiving ADT. Concomitant ADT use was the only clinical characteristic found to be a significant moderator of the relationship between social/family wellbeing and SFD, but none of the clinical characteristics was found to have a moderating effect on the relationship of social/family wellbeing and SF. Among patients who were not receiving ADT, high social/family wellbeing was associated with low SFD. Patients who were receiving ADT reported slightly higher SFD despite having higher social/family wellbeing. Conclusion: Ensuring sexual health in patients with prostate cancer requires a comprehensive approach to address factors contributing to sexual health such as side effects of treatment and family wellbeing.

Erratum: Author Correction: A single-cell comparison of adult and fetal human epicardium defines the age-associated changes in epicardial activity.

[This corrects the article DOI: 10.1038/s44161-022-00183-w.].

A Roadmap for the Human Gut Cell Atlas.

The number of studies investigating the human gastrointestinal tract using various single-cell profiling methods has increased substantially in the past few years. Although this increase provides a unique opportunity for the generation of the first comprehensive Human Gut Cell Atlas (HGCA), there remains a range of major challenges ahead. Above all, the ultimate success will largely depend on a structured and coordinated approach that aligns global efforts undertaken by a large number of research groups. In this Roadmap, we discuss a comprehensive forward-thinking direction for the generation of the HGCA on behalf of the Gut Biological Network of the Human Cell Atlas. Based on the consensus opinion of experts from across the globe, we outline the main requirements for the first complete HGCA by summarizing existing data sets and highlighting anatomical regions and/or tissues with limited coverage. We provide recommendations for future studies and discuss key methodologies and the importance of integrating the healthy gut atlas with related diseases and gut organoids. Importantly, we critically overview the computational tools available and provide recommendations to overcome key challenges.

Photoperiodic expression of two RALDH enzymes and the regulation of cell proliferation by retinoic acid in the rat hypothalamus.

Retinoic acid (RA) has been found to regulate hypothalamic function, but precisely where it acts is unknown. This study shows expression of retinaldehyde dehydrogenase (RALDH) enzymes in tanycytes that line the third ventricle in an area overlapping with the site of hypothalamic neural stem cells. The influence of RA was examined on the proliferation of progenitors lining the third ventricle using organotypic slice cultures. As has been shown in other regions of neurogenesis, RA was found to inhibit proliferation. Investigations of the dynamics of RALDH1 expression in the rat hypothalamus have shown that this enzyme is in tanycytes under photoperiodic control with highest levels during long versus short days. In parallel to this shift in RA synthesis, cell proliferation in the third ventricle was found to be lowest during long days when RA was highest, implying that RALDH1 synthesized RA may regulate neural stem cell proliferation. A second RA synthesizing enzyme, RALDH2 was also present in tanycytes lining the third ventricle. In contrast to RALDH1, RALDH2 showed little change with photoperiodicity, but surprisingly the protein was present in the apparent absence of mRNA transcript and it is hypothesized that the endocytic tanycytes may take this enzyme up from the cerebrospinal fluid (CSF).

Patterning of retinoic acid signaling and cell proliferation in the hippocampus.

The nuclear receptor ligand retinoic acid (RA) has been identified as an endogenous regulatory factor in the hippocampus, acting on pyramidal neurons and granule neuron progenitors, but almost nothing is known about the distribution of RA itself in the hippocampus. This study describes the source of RA for the rodent hippocampus in the meninges via the key RA synthetic enzyme retinaldehyde dehydrogenase 2 (RALDH2). Diffusion of RA from the meninges potentially creates a gradient of RA across the infrapyramidal and suprapyramidal blades of the dentate gyrus, enhanced by the expression of the RA catabolic enzyme Cyp26B1 between the blades, and an infrapyramidal and suprapyramidal blade difference is evident in RA-regulated transcription. This asymmetry may contribute to some of the physiological and molecular differences between the blades, including a disparity in the rates of cell proliferation in the subgranular zone of the two blades through RA inhibition of cell proliferation. Such differences can be altered by either the application of excess RA, its effect dependent on the relative position along the septotemporal axis, or change in RA signaling through mutation of retinol binding protein, while the capacity of RA to inhibit proliferation of cells in the dentate gyrus is demonstrated using in vitro slice culture. Use of synthetic and catabolic enzymes in the hippocampus to create differing zones of RA concentration parallels the mechanisms used in the developing brain to generate patterns of RA-regulated transcription.

Neural mass model-based study of frontal-temporal theta oscillations in human subjects during the performance of a cognitive control task.

Cognitive control, the ability to rapidly shift one's attention and behavioral strategy in response to environmental changes, is often compromised across psychiatric disorders. One of the well-validated behavioral paradigms for tapping into the cognitive control circuits is a cognitive interference task, where subjects must suppress a natural response to follow a less intuitive rule. Slower response times on these tasks indicate difficulty exerting control to overcome response conflict. Conflict evokes robust electrophysiological signatures, such as theta (4-8 Hz) oscillations in the prefrontal cortex (PFC). However, the underlying neural mechanisms of conflict-evoked theta oscillations in the PFC are not clear. The objective of this work is to use a neural mass model (NMM) to find feasible cortical networks generating theta oscillations during conflict processing in human subjects. We used intracranial EEG (iEEG) recorded from dorsolateral PFC (dIPFC) and lateral temporal lobe (LTL) of human subjects with intractable epilepsy undergoing invasive monitoring, while they performed a multi-source interference task (MSIT). We used a dynamic causal modeling (DCM) framework to simulate dIPFC-LTL theta using a Jansen-Rit NMM. We found significant evidence for an LTL input into the dlPFC during the initial 500 ms of conflict processing compared to a bidirectional connection between the dlPFC and LTL. We conclude that a neural mass modeling framework can be used to elucidate candidate mechanisms of neural oscillations underlying conflict resolution in human subjects. Clinical Relevance- This can be used to find feasible target mechanisms for designing therapy in patients with compromised cognitive control. This framework can also be expanded to serve as an in-silico test bed for designing and testing neuromodulatory interventions such as electrical stimulation for improving cognitive control in mood/anxiety disorders.