Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity.

AIMS/HYPOTHESIS: Beta cells within the pancreatic islet represent a heterogenous population wherein individual sub-groups of cells make distinct contributions to the overall control of insulin secretion. These include a subpopulation of highly connected 'hub' cells, important for the propagation of intercellular Ca2+ waves. Functional subpopulations have also been demonstrated in human beta cells, with an altered subtype distribution apparent in type 2 diabetes. At present, the molecular mechanisms through which beta cell hierarchy is established are poorly understood. Changes at the level of the epigenome provide one such possibility, which we explore here by focusing on the imprinted gene Nnat (encoding neuronatin [NNAT]), which is required for normal insulin synthesis and secretion. METHODS: Single-cell RNA-seq datasets were examined using Seurat 4.0 and ClusterProfiler running under R. Transgenic mice expressing enhanced GFP under the control of the Nnat enhancer/promoter regions were generated for FACS of beta cells and downstream analysis of CpG methylation by bisulphite sequencing and RNA-seq, respectively. Animals deleted for the de novo methyltransferase DNA methyltransferase 3 alpha (DNMT3A) from the pancreatic progenitor stage were used to explore control of promoter methylation. Proteomics was performed using affinity purification mass spectrometry and Ca2+ dynamics explored by rapid confocal imaging of Cal-520 AM and Cal-590 AM. Insulin secretion was measured using homogeneous time-resolved fluorescence imaging. RESULTS: Nnat mRNA was differentially expressed in a discrete beta cell population in a developmental stage- and DNA methylation (DNMT3A)-dependent manner. Thus, pseudo-time analysis of embryonic datasets demonstrated the early establishment of Nnat-positive and -negative subpopulations during embryogenesis. NNAT expression is also restricted to a subset of beta cells across the human islet that is maintained throughout adult life. NNAT+ beta cells also displayed a discrete transcriptome at adult stages, representing a subpopulation specialised for insulin production, and were diminished in db/db mice. 'Hub' cells were less abundant in the NNAT+ population, consistent with epigenetic control of this functional specialisation. CONCLUSIONS/INTERPRETATION: These findings demonstrate that differential DNA methylation at Nnat represents a novel means through which beta cell heterogeneity is established during development. We therefore hypothesise that changes in methylation at this locus may contribute to a loss of beta cell hierarchy and connectivity, potentially contributing to defective insulin secretion in some forms of diabetes. DATA AVAILABILITY: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD048465.

The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex.

G-quadruplex (G4), a four-stranded DNA or RNA structure containing stacks of guanine tetrads, plays regulatory roles in many cellular functions. So far, conventional G4s containing loops of 1-7 nucleotides have been widely studied. Increasing experimental evidence suggests that unconventional G4s, such as G4s containing long loops (long-loop G4s), play a regulatory role in the genome by forming a stable structure. Other secondary structures such as hairpins in the loop might thus contribute to the stability of long-loop G4s. Therefore, investigation of the effect of the hairpin-loops on the structure and function of G4s is required. In this study, we performed a systematic biochemical investigation of model G4s containing long loops with various sizes and structures. We found that the long-loop G4s are less stable than conventional G4s, but their stability increased when the loop forms a hairpin (hairpin-G4). We also verified the biological significance of hairpin-G4s by showing that hairpin-G4s present in the genome also form stable G4s and regulate gene expression as confirmed by in cellulo reporter assays. This study contributes to expanding the scope and diversity of G4s, thus facilitating future studies on the role of G4s in the human genome.

AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation.

I-motif or C4 is a four-stranded DNA structure with a protonated cytosine:cytosine base pair (C+:C) found in cytosine-rich sequences. We have found that oligodeoxynucleotides containing adenine and cytosine repeats form a stable secondary structure at a physiological pH with magnesium ion, which is similar to i-motif structure, and have named this structure 'adenine:cytosine-motif (AC-motif)'. AC-motif contains C+:C base pairs intercalated with putative A+:C base pairs between protonated adenine and cytosine. By investigation of the AC-motif present in the CDKL3 promoter (AC-motifCDKL3), one of AC-motifs found in the genome, we confirmed that AC-motifCDKL3 has a key role in regulating CDKL3 gene expression in response to magnesium. This is further supported by confirming that genome-edited mutant cell lines, lacking the AC-motif formation, lost this regulation effect. Our results verify that adenine-cytosine repeats commonly present in the genome can form a stable non-canonical secondary structure with a non-Watson-Crick base pair and have regulatory roles in cells, which expand non-canonical DNA repertoires.

Assessment of different carrier materials for the preparation of microbial formulations to enhance the shelf life and its efficacy on the growth of spinach (Spinacia oleracea L.).

The current study was undertaken to determine the ability of different carrier materials for sustaining the viability of microbial consortium during storage. Different bioformulations consisting of carrier material and microbial consortium were prepared and examined for viability and stability for one year stored at 4 °C and ambient temperature. Total 8 bio-formulations were prepared consisting five economically viable carriers (gluten, talc, charcoal, bentonite, broth medium) and a microbial consortium. In present study, maximum enhanced shelf-life of consortium based on colony forming unit count were recorded for talc + gluten based (B4) bioformulation (9.03 log10 cfu/g) over other bio-formulations stored for 360 days. Furthermore, the pot experiments was conducted to evaluate the efficacy of B4 formulation on growth of spinach in comparison with recommended dose of chemical fertilizer, uninoculated and no amendment control. The results depicted that B4 formulation increased biomass (176-666%), leaf area (33-123%), chlorophyll content (131-789%) and protein content (68.4-94.4%) of spinach over controls. Further B4 application significantly increased the nutrients like available nitrogen (131-475%), phosphorus (75-178%) and potassium (31-191%) of pot soil along with noteworthy improvement in root colonization as evident from scanning electron microscope analysis in comparison to controls at 60 days after sowing. Therefore, exploiting B4 formulation can serve as the environmentally sound approach to enhance the productivity, biomass and nutritional value of spinach. Thus, Plant growth promoting microbes-based formulation can be the novel paradigm to improve the soil health and eventually the crop productivity in economical and sustainable manner.

Attenuation of Hg(II)-induced cellular and DNA damage in human blood cells by uric acid.

Mercury (Hg) is a widespread environmental pollutant and toxicant that induces multiple organ damage in humans and animals. Hg toxicity is mediated by the induction of oxidative stress in the target cells. We used uric acid (UA), a potent antioxidant found in biological fluids, to protect human red blood cells (RBC) and lymphocytes against Hg-mediated cell, organelle, and genotoxicity. RBCs were incubated with mercuric chloride (HgCl2), an Hg(II) compound, either alone or in the presence of UA. Incubation of RBCs with only HgCl2 increased the production of nitrogen and oxygen radical species, enhanced methemoglobin levels, heme degradation, free ferrous iron, oxidation of proteins and membrane lipids, and reduced the antioxidant capacity of cells. UA enhanced the antioxidant capacity of RBCs and restored metabolic, plasma membrane-bound, and antioxidant enzyme activities. Scanning electron microscopy showed that UA prevented HgCl2-mediated morphological changes in RBCs. HgCl2 dissipated the mitochondrial membrane potential and increased lysosomal membrane damage in lymphocytes, but UA pre-treatment attenuated these effects. Genotoxicity analysis by comet assay showed that UA protected lymphocyte DNA from HgCl2-induced damage. Importantly, UA itself did not exhibit any deleterious effects on RBCs or lymphocytes. Thus, UA protects human blood cells from Hg(II)-mediated oxidative damage, reducing the harmful effects of this extremely toxic metal. We suggest that UA has a similar protective role in plasma against heavy metal toxicity.

Targeted epigenetic modulation using a DNA-based histone deacetylase inhibitor enhances cardiomyogenesis in mouse embryonic stem cells.

The epigenome has an essential role in orchestrating transcriptional activation and modulating key developmental processes. Previously, we developed a library of pyrrole-imidazole polyamides (PIPs) conjugated with suberoylanilide hydroxamic acid (SAHA), a histone deacetylase (HDAC) inhibitor, for the purpose of sequence-specific modification of epigenetics. Based on the gene expression profile of SAHA-PIPs and screening studies using the α-myosin heavy chain promoter-driven reporter and SAHA-PIP library, we identified that SAHA-PIP G activates cardiac-related genes. Studies in mouse ES cells showed that SAHA-PIP G could enhance the generation of spontaneous beating cells, which is consistent with upregulation of several cardiac-related genes. Moreover, ChIP-seq results confirmed that the upregulation of cardiac-related genes is highly correlated with epigenetic activation, relevant to the sequence-specific binding of SAHA-PIP G. This proof-of-concept study demonstrating the applicability of SAHA-PIP not only improves our understanding of epigenetic alterations involved in cardiomyogenesis but also provides a novel chemical-based strategy for stem cell differentiation.

Genomic features of human limb specific enhancers.

To elucidate important cellular and molecular interactions that regulate patterning and skeletal development, vertebrate limbs served as a model organ. A growing body of evidence from detailed studies on a subset of limb regulators like the HOXD cluster or SHH, reveals the importance of enhancers in limb related developmental and disease processes. Exploiting the recent genome-wide availability of functionally confirmed enhancer dataset, this study establishes regulatory interactions for dozens of human limb developmental genes. From these data, it appears that the long-range regulatory interactions are fairly common during limb development. This observation highlights the significance of chromosomal breaks/translocations in human limb deformities. Transcriptional factor (TF) analysis predicts that the differentiation of early nascent limb-bud into future territories entail distinct TF interaction networks. Conclusively, an important motivation for annotating the human limb specific regulatory networks is to pave way for the systematic exploration of their role in disease and evolution.

The ESAT-6 protein of Mycobacterium tuberculosis interacts with beta-2-microglobulin (ß2M) affecting antigen presentation function of macrophage.

ESAT-6, an abundantly secreted protein of Mycobacterium tuberculosis (M. tuberculosis) is an important virulence factor, inactivation of which leads to reduced virulence of M. tuberculosis. ESAT-6 alone, or in complex with its chaperone CFP-10 (ESAT-6:CFP-10), is known to modulate host immune responses; however, the detailed mechanisms are not well understood. The structure of ESAT-6 or ESAT-6:CFP-10 complex does not suggest presence of enzymatic or DNA-binding activities. Therefore, we hypothesized that the crucial role played by ESAT-6 in the virulence of mycobacteria could be due to its interaction with some host cellular factors. Using a yeast two-hybrid screening, we identified that ESAT-6 interacts with the host protein beta-2-microglobulin (ß2M), which was further confirmed by other assays, like GST pull down, co-immunoprecipitation and surface plasmon resonance. The C-terminal six amino acid residues (90-95) of ESAT-6 were found to be essential for this interaction. ESAT-6, in complex with CFP-10, also interacts with ß2M. We found that ESAT-6/ESAT-6:CFP-10 can enter into the endoplasmic reticulum where it sequesters ß2M to inhibit cell surface expression of MHC-I-ß2M complexes, resulting in downregulation of class I-mediated antigen presentation. Interestingly, the ESAT-6:ß2M complex could be detected in pleural biopsies of individuals suffering from pleural tuberculosis. Our data highlight a novel mechanism by which M. tuberculosis may undermine the host adaptive immune responses to establish a successful infection. Identification of such novel interactions may help us in designing small molecule inhibitors as well as effective vaccine design against tuberculosis.

Is home delivery really preferred? a mixed-methods national study in Pakistan.

BACKGROUND: Pakistan has a high maternal mortality ratio and a low rate of skilled birth attendants (SBAs). To address these two important issues, the Pakistan Maternal Newborn and Child Health (MNCH) programme launched the community midwives (CMW) initiative in 2007. CMWs are supposed to conduct deliveries at community level outside health facilities. The purpose of the current study is to document perceptions about CMWs and preferences for birthing place. METHODS: A mixed-methods study was conducted covering four provinces. For the quantitative survey, households were selected through a multistage sampling technique from rural districts. In 1,450 rural households, preferences of respondents about CMW-conducted deliveries were recorded. Qualitative data were obtained through focus group discussions (FGDs) and in-depth interviews (IDIs) with women, community elders, CMWs, and MNCH programme personnel in the same areas where the quantitative study was carried out. In both studies, preferences and the reasons behind particular respondent preferences were recorded. Frequencies of responses were analysed for the quantitative study. Narration and quotes from various types of participants were used to present findings from FGDs and IDIs. RESULTS: In the quantitative study, 42% of respondents expressed a preference for birthing stations, i.e. a place where CMWs conduct deliveries; 22% preferred home deliveries. Birthing stations were favoured because of the availability of space and equipment and the proximity to women's homes. These findings were largely supported by the qualitative component, although a range of views about where a CMW should conduct deliveries were expressed. CONCLUSION: Insights into where CMWs might provide delivery services were obtained through this study. Birthing stations may be an option as a preferred location for delivery care and should be considered as part of Pakistan's national CMW programme.

Pregnancy Associated Plasma Protein-A (PAPP-A) Levels in Acute Coronary Syndrome: A Case Control Study in a Tertiary Care Centre.

In recent years, an important objective of cardiovascular research has been to find new markers that would improve the risk stratification and diagnosis of patients presenting with symptoms of acute coronary syndrome (ACS). Established biomarkers for diagnosis of ACS includes troponins and creatine kinase MB (CK-MB). Pregnancy associated plasma protein A (PAPP-A) is an emerging marker which has been described as a marker of plaque instability. PAPP-A is a large metalloproteinase involved in insulin-like growth factor signaling and has been shown to be involved in pathological processes like atherosclerosis. Many studies have been published regarding release of PAPP-A in circulation during ACS. The objective of this study was to evaluate the role of PAPP-A as an early marker of ACS by comparing levels of PAPP-A in patients with acute myocardial infarction (AMI) and unstable angina (UA) with asymptomatic controls. The association of PAPP-A with markers of myocardial necrosis and the association of PAPP-A levels to the presence of risk factors for coronary artery disease was also studied. We measured PAPP-A levels in patients with AMI (30), UA (23) and asymptomatic controls (45). PAPP-A was estimated using PAPP-A US (ultra sensitive) ELISA manufactured by DRG (Germany). PAPP-A levels were significantly elevated in patients with AMI and in patients with UA (mean levels 64.26 ± 1.05 and 36.23 ± 1.05 ng/ml respectively; p < 0.001). Mean PAPP-A levels in controls were 10.68 ± 1.04 ng/ml. In UA cases PAPP-A levels were elevated when the troponin I and CK-MB levels were within the normal range. No correlation was observed between PAPP-A with markers of myocardial necrosis. PAPP-A can serve as a useful biomarker in the diagnosis of ACS, especially UA, where cardiac troponin levels and CK-MB levels are not elevated and ECG changes are inconclusive.

Endocytosis of Mycobacterium tuberculosis heat shock protein 60 is required to induce interleukin-10 production in macrophages.

Understanding the signaling pathways involved in the regulation of anti-inflammatory and pro-inflammatory responses in tuberculosis is extremely important in tailoring a macrophage innate response to promote anti-tuberculosis immunity in the host. Although the role of toll-like receptors (TLRs) in the regulation of anti-inflammatory and pro-inflammatory responses is known, the detailed molecular mechanisms by which the Mycobacterium tuberculosis bacteria modulate these innate responses are not clearly understood. In this study, we demonstrate that M. tuberculosis heat shock protein 60 (Mtbhsp60, Cpn60.1, and Rv3417c) interacts with both TLR2 and TLR4 receptors, but its interaction with TLR2 leads to clathrin-dependent endocytosis resulting in an increased production of interleukin (IL)-10 and activated p38 MAPK. Blockage of TLR2-mediated endocytosis inhibited IL-10 production but induced production of tumor necrosis factor (TNF)-α and activated ERK1/2. In contrast, upon interaction with TLR4, Mtbhsp60 remained predominantly localized on the cell surface due to poorer endocytosis of the protein that led to decreased IL-10 production and p38 MAPK activation. The Escherichia coli homologue of hsp60 was found to be retained mainly on the macrophage surface upon interaction with either TLR2 or TLR4 that triggered predominantly a pro-inflammatory-type immune response. Our data suggest that cellular localization of Mtbhsp60 upon interaction with TLRs dictates the type of polarization in the innate immune responses in macrophages. This information is likely to help us in tailoring the host protective immune responses against M. tuberculosis.

CO2-Free Ethylene Oxide Production via Liquid-Phase Epoxidation with Fe2O3/MSM Catalyst.

In this study, we present an approach for ethylene oxide (EO) production that addresses environmental concerns by eliminating greenhouse gas emissions. Our catalyst, Fe2O3/MSM, was synthesized using a hydrothermal method, incorporating Fe2O3 nanoparticles into a well-structured mesoporous silica matrix (MSM). We selected peracetic acid as the oxidant, enabling CO2-free EO production while yielding valuable by-products such as acetic acid, monoethylene glycol, and diethylene glycol. X-ray diffraction (XRD), X- ray photoelectron spectroscopy (XPS), and Brunauer-Emmett-Teller (BET) analyses confirmed the heteroatom structure of the catalysts and porosity, while Transmission electron microscopy (TEM) analysis provided insights into its morphology. Then, the synthesized catalyst was used in the liquid-phase epoxidation of ethylene for EO production. Our systematic experiments involved varying critical parameters such as temperature, ethylene to oxidant ratio, catalyst dosage, and solvent to optimize EO selectivity and ethylene conversion. The results of this study demonstrated an 80.2 % ethylene conversion to EO with an EO selectivity of 87.6 %. The production process yielded valuable by-products without CO2 emissions, highlighting its environmental friendliness.

Proline-proline-glutamic acid (PPE) protein Rv1168c of Mycobacterium tuberculosis augments transcription from HIV-1 long terminal repeat promoter.

Cells of the monocyte/macrophage lineage are shown to play a role in the pathogenesis of human immunodeficiency virus (HIV). The occurrence of HIV type 1 (HIV-1) infection is found to be accelerated in people infected with Mycobacterium tuberculosis, but the mechanism by which mycobacterial protein(s) induces HIV-1 LTR trans-activation is not clearly understood. We show here that the M. tuberculosis proline-proline-glutamic acid (PPE) protein Rv1168c (PPE17) can augment transcription from HIV-1 LTR in monocyte/macrophage cells. Rv1168c interacts specifically with Toll-like receptor-2 (TLR2) resulting in downstream activation of nuclear factor-κB (NF-κB) resulting in HIV-1 LTR trans-activation. Another PPE protein, Rv1196 (PPE18), was also found to interact with TLR2 but had no effect on HIV-1 LTR trans-activation because of its inability to activate the NF-κB signaling pathway. In silico docking analyses and mutation experiments have revealed that the N-terminal domain of Rv1168c specifically interacts with LRR motifs 15-20 of TLR2, and this site of interaction is different from that of Rv1196 protein (LRR motifs 11-15), indicating that the site of interaction on TLR2 dictates the downstream signaling events leading to activation of NF-κB. This information may help in understanding the mechanism of pathogenesis of HIV-1 during M. tuberculosis co-infection.

Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers.

BACKGROUND: Human genome is enriched with thousands of conserved non-coding elements (CNEs). Recently, a medium throughput strategy was employed to analyze the ability of human CNEs to drive tissue specific expression during mouse embryogenesis. These data led to the establishment of publicly available genome wide catalog of functionally defined human enhancers. Scattering of enhancers over larger regions in vertebrate genomes seriously impede attempts to pinpoint their precise target genes. Such associations are prerequisite to explore the significance of this in vivo characterized catalog of human enhancers in development, disease and evolution. RESULTS: This study is an attempt to systematically identify the target gene-bodies for functionally defined human CNE-enhancers. For the purpose we adopted the orthology/paralogy mapping approach and compared the CNE induced reporter expression with reported endogenous expression pattern of neighboring genes. This procedure pinpointed specific target gene-bodies for the total of 192 human CNE-enhancers. This enables us to gauge the maximum genomic search space for enhancer hunting: 4 Mb of genomic sequence around the gene of interest (2 Mb on either side). Furthermore, we used human-rodent comparison for a set of 159 orthologous enhancer pairs to infer that the central nervous system (CNS) specific gene expression is closely associated with the cooperative interaction among at least eight distinct transcription factors: SOX5, HFH, SOX17, HNF3ß, c-FOS, Tal1beta-E47S, MEF and FREAC. CONCLUSIONS: In conclusion, the systematic wiring of cis-acting sites and their target gene bodies is an important step to unravel the role of in vivo characterized catalog of human enhancers in development, physiology and medicine.

Coordination between ECM and cell-cell adhesion regulates the development of islet aggregation, architecture, and functional maturation.

Pancreatic islets are three-dimensional cell aggregates consisting of unique cellular composition, cell-to-cell contacts, and interactions with blood vessels. Cell aggregation is essential for islet endocrine function; however, it remains unclear how developing islets establish aggregation. By combining genetic animal models, imaging tools, and gene expression profiling, we demonstrate that islet aggregation is regulated by extracellular matrix signaling and cell-cell adhesion. Islet endocrine cell-specific inactivation of extracellular matrix receptor integrin ß1 disrupted blood vessel interactions but promoted cell-cell adhesion and the formation of larger islets. In contrast, ablation of cell-cell adhesion molecule α-catenin promoted blood vessel interactions yet compromised islet clustering. Simultaneous removal of integrin ß1 and α-catenin disrupts islet aggregation and the endocrine cell maturation process, demonstrating that establishment of islet aggregates is essential for functional maturation. Our study provides new insights into understanding the fundamental self-organizing mechanism for islet aggregation, architecture, and functional maturation.

Can home visits for early child development be implemented with sufficient coverage and quality at scale? Evidence from the SPRING program in India and Pakistan.

Introduction: There is limited evidence from low and middle-income settings on the effectiveness of early child development interventions at scale. To bridge this knowledge-gap we implemented the SPRING home visiting program where we tested integrating home visits into an existing government program (Pakistan) and employing a new cadre of intervention workers (India). We report the findings of the process evaluation which aimed to understand implementation. Methods and materials: We collected qualitative data on acceptability and barriers and facilitators for change through 24 in-depth interviews with mothers; eight focus group discussions with mothers, 12 with grandmothers, and 12 with fathers; and 12 focus group discussions and five in-depth interviews with the community-based agents and their supervisors. Results: Implementation was sub-optimal in both settings. In Pakistan issues were low field-supervision coverage and poor visit quality related to issues scheduling supervision, a lack of skill development, high workloads and competing priorities. In India, issues were low visit coverage - in part due to employing new workers and an empowerment approach to visit scheduling. Coaching caregivers to improve their skills was sub-optimal in both sites, and is likely to have contributed to caregiver perceptions that the intervention content was not new and was focused on play activities rather than interaction and responsivity - which was a focus of the coaching. In both sites caregiver time pressures was a key reason for low uptake among families who received visits. Discussion: Programs need feasible strategies to maximize quality, coverage and supervision including identifying and managing problems through monitoring and feedback loops. Where existing community-based agents are overstretched and system strengthening is unlikely, alternative implementation strategies should be considered such as group delivery. Core intervention ingredients such as coaching should be prioritized and supported during training and implementation. Given that time and resource constraints were a key barrier for families a greater focus on communication, responsivity and interaction during daily activities could have improved feasibility.

DNA Methylation-Dependent Restriction of Tyrosine Hydroxylase Contributes to Pancreatic ß-Cell Heterogeneity.

The molecular and functional heterogeneity of pancreatic ß-cells is well recognized, but the underlying mechanisms remain unclear. Pancreatic islets harbor a subset of ß-cells that co-express tyrosine hydroxylase (TH), an enzyme involved in synthesis of catecholamines that repress insulin secretion. Restriction of the TH+ ß-cells within islets is essential for appropriate function in mice, such that a higher proportion of these cells corresponds to reduced insulin secretion. Here, we use these cells as a model to dissect the developmental control of ß-cell heterogeneity. We define the specific molecular and metabolic characteristics of TH+ ß-cells and show differences in their developmental restriction in mice and humans. We show that TH expression in ß-cells is restricted by DNA methylation during ß-cell differentiation. Ablation of de novo DNA methyltransferase Dnmt3a in the embryonic progenitors results in a dramatic increase in the proportion of TH+ ß-cells, whereas ß-cell-specific ablation of Dnmt3a does not. We demonstrate that maintenance of Th promoter methylation is essential for its continued restriction in postnatal ß-cells. Loss of Th promoter methylation in response to chronic overnutrition increases the number of TH+ ß-cells, corresponding to impaired ß-cell function. These results reveal a regulatory role of DNA methylation in determining ß-cell heterogeneity.

Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity.

Aims/hypothesis: Beta cells within the pancreatic islet represent a heterogenous population wherein individual sub-groups of cells make distinct contributions to the overall control of insulin secretion. These include a subpopulation of highly-connected 'hub' cells, important for the propagation of intercellular Ca2+ waves. Functional subpopulations have also been demonstrated in human beta cells, with an altered subtype distribution apparent in type 2 diabetes. At present, the molecular mechanisms through which beta cell hierarchy is established are poorly understood. Changes at the level of the epigenome provide one such possibility which we explore here by focussing on the imprinted gene neuronatin (Nnat), which is required for normal insulin synthesis and secretion. Methods: Single cell RNA-seq datasets were examined using Seurat 4.0 and ClusterProfiler running under R. Transgenic mice expressing eGFP under the control of the Nnat enhancer/promoter regions were generated for fluorescence-activated cell (FAC) sorting of beta cells and downstream analysis of CpG methylation by bisulphite and RNA sequencing, respectively. Animals deleted for the de novo methyltransferase, DNMT3A from the pancreatic progenitor stage were used to explore control of promoter methylation. Proteomics was performed using affinity purification mass spectrometry and Ca2+ dynamics explored by rapid confocal imaging of Cal-520 and Cal-590. Insulin secretion was measured using Homogeneous Time Resolved Fluorescence Imaging. Results: Nnat mRNA was differentially expressed in a discrete beta cell population in a developmental stage- and DNA methylation (DNMT3A)-dependent manner. Thus, pseudo-time analysis of embryonic data sets demonstrated the early establishment of Nnat-positive and negative subpopulations during embryogenesis. NNAT expression is also restricted to a subset of beta cells across the human islet that is maintained throughout adult life. NNAT+ beta cells also displayed a discrete transcriptome at adult stages, representing a sub-population specialised for insulin production, reminiscent of recently-described "ßHI" cells and were diminished in db/db mice. 'Hub' cells were less abundant in the NNAT+ population, consistent with epigenetic control of this functional specialization. Conclusions/interpretation: These findings demonstrate that differential DNA methylation at Nnat represents a novel means through which beta cell heterogeneity is established during development. We therefore hypothesise that changes in methylation at this locus may thus contribute to a loss of beta cell hierarchy and connectivity, potentially contributing to defective insulin secretion in some forms of diabetes.

Comparison and Validation of Multiple Detectors against Monte Carlo Simulation for the Use of Small-Field Dosimetry.

Aim: The aim of this study was to compare the Exradin W2 scintillator, PTW microDiamond, IBA Razor Nano, and IBA Razor chamber detectors for small-field dose measurements and validate the measured data against the EGSnrc user code and observe the variation between daisy-chained and direct measurement methods for the above detectors. Materials and Methods: The W2 scintillator, microDiamond, Razor Nano, and Razor chamber detectors were used to measure the in-plane and cross-plane profiles and the output factors (OFs) at 10 cm depth, and 90 source-to-surface distance for 6MV X-rays (Elekta Versa HD). The field sizes ranged from 0.5 cm × 0.5 cm to 5 cm × 5 cm. The BEAMnrc/DOSXYZnrc user codes (EGSnrc) were used to simulate the reference profiles. Gamma analysis was performed to compare the measured and simulated dose distributions. Results: The OFs measured with the W2 scintillator, microDiamond, Razor Nano chamber, Razor chamber, and the calculated Monte Carlo (MC) showed agreement to within 1% for the 3 cm × 3 cm field size. The uncertainty in the MC simulation was observed to be 0.4%. The percent difference in OFs measured using daisy-chained and direct measurement methods was within 0.15%, 0.4%, 1.4%, and 2.4% for microDiamond, W2 scintillator, Nano, and Razor chamber detectors, respectively. Conclusion: The lateral beam profiles and OFs of W2 scintillator, microDiamond, Razor Nano, and Razor chambers exhibit good agreement with the MC simulation within the nominal field sizes. Our results demonstrate that we can achieve considerable time-saving by directly measuring small-field OFs without daisy-chained methods using microDiamond and W2 scintillator. In terms of ease of use, sensitivity, reproducibility, and from a practical standpoint, we recommend microDiamond for small-field dosimetry.