Biology subjects

Goldman, D.

Publications and source records attributed to Goldman, D..

13 recordsLinked to original sources

bioRxiv2025

Fetal magnetoencephalography based on optically pumped magnetometers

The fetus in the third trimester of gestation has already the remarkable capacity to process external sensory information in utero. So far, investigations of fetal brain responses to sensory information have mostly relied on cryogenic magnetoencephalography (MEG), which is suitable to record fetal brain activity and is not much affected by layers of maternal tissues. Nevertheless, this solution is extremely expensive and limited to a couple of laboratories worldwide. In this work, we took advantage of the next generation cryogenic-free MEG, that is MEG based on optically pumped magnetometers (OPM), to develop a system that could record both fetal and newborn brain responses to auditory stimulation in a longitudinal design. Twenty-one pregnant women in their late third trimester of gestation (35-40 weeks of gestational age) were exposed to sequences of 500 Hz tones. Fetal brain activity was recorded using a wearable belt equipped with OPM sensors arranged on the womens abdomen based on fetal head position. Results revealed that fetal OPM-MEG successfully recorded significant evoked brain responses to auditory stimuli that peaked ~300 ms post-stimulus at the group level. A similar auditory paradigm was performed with on-scalp OPM-MEG in 14 one-month-old infants, with 9 participants common to both timepoints. Infant responses showed a significant latency decrease compared to the fetal ones in terms of magnetometers; a decrease that did not reach significance level for virtual gradiometers. This work demonstrates the ability of OPM-MEG to non-invasively record fetal brain responses to external sensory stimuli. It paves the way for a wider use of fetal MEG to investigate fetal cognition and positions OPM-MEG as the most promising lifespan-compliant solution for monitoring early brain development.

neuroscience↗

bioRxiv2024

Intussusceptive angiogenesis-on-a-chip: Evidence for transluminal vascular bridging by endothelial delamination

Intussusceptive angiogenesis is an increasingly recognized vessel duplication process that generates and reshapes microvascular beds. However, the mechanism by which a vessel splits into two is poorly understood. Particularly vexing is formation of the hallmark transluminal endothelial cell bridge. How an endothelial cell comes to cross a flowing lumen rather than line it is enigmatic. To elucidate this, we used a microvessel-on-a-chip strategy, creating a micro-conduit coherently lined with flow-sensitive endothelial cells but in which transluminal bridges also formed. Bridge morphologies ranged from filamentous strand to multicellular columns with a central core. These bridge architectures were found to recapitulate those in microvessels in embryos, tumours, diseased organs, and the dermis of patients with limb-threatening ischemia. Time-lapse, multi-plane, 3D microscopy of the micro-physiologic conduit revealed that bridges arose from endothelial cells oriented orthogonal to flow that partially released from the wall while retaining attachments at the ends. This delamination process was blocked by hyperactivation of Rho and augmented by interventions that weaken cell-substrate interactions, including inhibiting non-muscle myosin II and blocking 5{beta}1 integrin but, interestingly, not v{beta}3 integrin. Thus, endothelial cells can leave their monolayer and transect a flowing lumen through controlled delamination. This previously unrecognized lumen entry program could explain the launch of intussusceptive angiogenesis and opens a framework for intervening. Significance StatementRapid generation of small blood vessels is vital for embryonic development and many diseases. An efficient means of creating a new microvessel is for an existing vessel to split into two, a process recognized for over 35 years. However, the cellular events underlying vessel splitting remain largely a mystery. The challenge is how to look inside a microvessel and capture transient events. We address this challenge using a microvessel-on-a-chip strategy. We discovered that select endothelial cells lining the wall can partially lift to transect the lumen. This resolves the paradox of an adhesion-dependent cell reaching across a pressurized lumen. It also reframes microvascular therapy considerations, including for diabetics with leg ulcers, a condition we show has hallmarks of microvessel splitting.

physiology↗

bioRxiv2022

The transcriptional and epigenetic reprogramming mediated by chronic IL1β exposure drives self-renewal ability and myeloid priming in TET2 deficient stem and progenitor cells.

Clonal hematopoiesis (CH) increases the risk for the development of hematological malignancy and cardiovascular disease. IL1{beta} is elevated in patients with CH and its inhibition mitigates cardiovascular risk in murine models with Tet2 loss-of-function. How IL1{beta} alters population dynamics of hematopoietic cells upon Tet2 deletion (Tet2-KO) is not well understood. We demonstrated IL1{beta} expands Tet2-KO monocytes/macrophages, and long-term hematopoietic stem cells. IL1{beta} promoted myeloid bias over other lineages of Tet2-KO HSPCs coinciding with the failure to demethylate lineage-associated enhancer and transcription factor binding sites. IL1{beta} enhanced the self-renewal ability of Tet2-KO HSPCs by upregulating genes associated with self-renewal and by resisting the demethylation of binding sites of transcription factors promoting terminal differentiation. The IL1{beta}-mediated premalignant phenotype is suppressed by the IL1{beta} antagonist or deletion of the IL1 receptor-1, in vivo in aged mice. Our results demonstrate that targeting IL1 signaling could be an efficient early intervention strategy in preleukemic disorders. STATEMENT OF SIGNIFICANCEIL1{beta} promoted myeloid expansion and self-renewal capacity of TET2-null pre-leukemic cells. Lineage bias occurred early within progenitors towards pro-inflammatory macrophages. Genes specific to aging and with roles in promoting self-renewal capacity, and myeloid bias were upregulated. Hypermethylation occurred within lymphoid and erythroid lineage-specific regulatory elements. Targeting IL1R1 reduced aberrant myeloid bias and premalignant phenotype.

cancer biology↗

bioRxiv2022

Molecular and spatial profiling of the paraventricular nucleus of the thalamus

The paraventricular nucleus of the thalamus (PVT) is known to regulate various cognitive and behavioral processes. However, while functional diversity among PVT circuits has often been linked to cellular differences, the molecular identity and spatial distribution of PVT cell types remains unclear. To address this gap, here we used single nucleus RNA sequencing (snRNA-seq) and identified five molecularly distinct PVT neuronal subtypes. Additionally, multiplex fluorescent in situ hybridization of top marker genes revealed that PVT subtypes are organized by a combination of previously unidentified molecular gradients. Lastly, comparing our dataset with a recently published single-cell sequencing atlas of thalamus yielded novel insight into the PVTs connectivity with cortex, including unexpected innervation of auditory and visual areas. This comparison also revealed that our data contains a largely non-overlapping transcriptomic map of multiple midline thalamic nuclei. Collectively, our findings uncover previously unknown features of the molecular diversity and anatomical organization of the PVT and provide a valuable resource for future investigations.

neuroscience↗

bioRxiv2021

Maternal Obesity Dysregulates Fetal Hematopoietic Stem and Progenitor Cell Development in Rhesus Macaques

BackgroundMaternal obesity adversely impacts the in utero metabolic environment and offsprings health, but its effect on fetal hematopoiesis and immune cell development remains incompletely understood, particularly in models that resemble human development. MethodsWe studied gestational day 130-135 fetuses derived from rhesus macaque dams chronically exposed to a high-fat Western-style diet (WSD) or a low-fat control diet. Fetal immune cell phenotypes and fetal bone marrow architecture and hematopoietic stem and progenitor cell (FBM HSPC) function were examined using bone computed tomography, histology, flow cytometry, single-cell RNA-sequencing, and HSPC transplantation assays. FindingsMaternal WSD induced premature FBM cavity opening and a codominant increase in the number of FBM adipocytes. Furthermore, a maternal WSD induced a proinflammatory transcriptional response in FBM HSPCs. FBM macrophages from the WSD group exhibited heightened proinflammatory responses to toll-like receptor agonist stimulation. Maternal WSD exposure suppressed the expression of genes required for B-cell development and decreased the frequencies of FBM B-cells. Finally, maternal WSD led to poor engraftment of FBM HSPCs in nonlethally irradiated immunodeficient NOD/SCID/IL2r{gamma}-/- mice. InterpretationsMaternal WSD impairs FBM development, drives a hyperinflammatory phenotype, and induces functional and differentiation impairment in FBM HSPCs in a translationally relevant nonhuman primate model. FundingNational Institute of Health RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSMaternal obesity is associated with increased risk of infections and proinflammatory disease in offspring. The translationally-relevant rhesus macaque model was utilized to address the effects of maternal obesogenic diet on fetal hematopoietic and immune cell development. Added value of this studyWe assessed changes in fetal immune cell phenotypes and fetal hematopoietic stem and progenitor cell function using immunohistochemistry, flow cytometry, single-cell RNA sequencing, and transplantation assays. We determined that chronic consumption of a maternal obesogenic diet induced the development of adipogenic and proinflammatory environments in the fetal bone marrow. Additionally, we detected the impairment in B-cell differentiation program in fetal hematopoietic stem and progenitor cells. Implications of all the available evidenceThese data demonstrate that maternal obesogenic diet modulates fetal hematopoietic development and could impact the offsprings immune system, including proinflammatory phenotype and a decline in B-cell function.

immunology↗

bioRxiv2021

Notch signaling via Hey1 and Id2b regulates Müller glia's regenerative response to retinal injury

Zebrafish Muller glia (MG) respond to retinal injury by suppressing Notch signaling and producing progenitors for retinal repair. A certain threshold of injury-derived signal must be exceeded in order to engage MG in a regenerative response (MGs injury-response threshold). Pan-retinal Notch inhibition expands the zone of injury-responsive MG at the site of focal injury, suggesting that Notch signaling regulates MGs injury-response threshold. We found that Notch signaling enhanced chromatin accessibility and gene expression at a subset of regeneration-associated genes in the uninjured retina. Two Notch effector genes, hey1 and id2b, were identified that reflect bifurcation of the Notch signaling pathway, and differentially regulate MGs injury-response threshold and proliferation of MG-derived progenitors. Furthermore, Notch signaling component gene repression in the injured retina suggests a role for Dll4, Dlb, and Notch3 in regulating Notch signaling in MG and epistasis experiments confirm that the Dll4/Dlb-Notch3-Hey1/Id2b signaling pathway regulates MGs injury-response threshold and proliferation.

developmental biology↗

bioRxiv2021

Using a Human Circulation Mathematical Model to Simulate the Effects of Hemodialysis and Therapeutic Hypothermia.

BackgroundThe human blood circulation is an intricate process regulated by multiple biophysical factors. Our patients often suffer from renal disease and atrial fibrillation, and are given treatments such as therapeutic hypothermia, exercise, and hemodialysis. In this work, a hemodynamic mathematical model of human circulation coupled to a representative dialysis machine is developed and used to explore causal mechanisms of our recent clinical observations. MethodsAn ordinary differential equation model consisting of human whole body circulation, baroreflex control, and a hemodialysis machine was implemented. Experimentally informed parameter alterations were used to implement hemodialysis and therapeutic hypothermia. By means of parameter perturbation, four model populations encompassing baseline, dialysed, hypothermia treated, and simultaneous dialysed with hypothermia were generated. In model populations, multiple conditions including atrial fibrillation, exercise, and renal failure were simulated. The effects of all conditions on clinically relevant non-invasive measurables such as heart rate and blood pressure were quantified. A parameter sensitivity analysis was implemented to rank model output influencing parameters in the presented model. ResultsResults were interpreted as alterations of the respective populations mean values and standard deviations of the clinical measurables, both in relation to the baseline population. A clinical measurables smaller standard deviation (in comparison to baseline population) was interpreted as a stronger association between a given clinical measure and the corresponding underlying process, which may permit the use of deducing one by observation of the other. The modelled dialysis was observed to increase systolic blood pressure, vessel shear, and heart rate. Therapeutic hypothermia was observed to reduce blood pressure as well as the intra-population standard deviation (heterogeneity) of blood flow in the large (aorta) and small (kidney) vasculature. Therapeutic hypothermia reduced shear in vessels, suggesting a potential benefit with respect to endothelial dysfunction and maintenance of microcirculatory blood flow. The action of therapeutic hypothermia under conditions such as atrial fibrillation, exercise, and renal failure was to reduce total blood flow, which was applicable in all simulated populations. Therapeutic hypothermia did not affect the dialysis function, but exercise improved the efficacy of dialysis by facilitating water removal. ConclusionsThis study illuminates some mechanisms of action for therapeutic hypothermia. It also suggests clinical measurables that may be used as surrogates to diagnose underlying diseases such as atrial fibrillation.

biophysics↗

bioRxiv2020

Microglia Stimulate Zebrafish Brain Repair Via a Specific Inflammatory Cascade

The adult zebrafish brain, unlike mammals, has a remarkable regenerative capacity. Although inflammation inhibits regeneration in mammals, it is necessary for zebrafish brain repair. Microglia are resident brain immune cells that regulate the inflammatory response. To explore the microglial role in repair, we used liposomal clodronate, colony stimulating factor-1 receptor (csf1r) inhibition to ablate microglia and two genetic mutants that lacks microglia during brain injury. We found that microglial ablation inhibited injury-induced neurogenesis and regeneration. Microglial suppression specifically attenuated cell proliferation at the progenitor cell amplification stage of neurogenesis. Notably, the loss of microglia impaired phospho-stat3 (signal transducer and activator of transcription 3) and {beta}-catenin signaling by dynamic regulation of tumor necrosis factor-a after injury, and the ectopic activation of stat3 and {beta}-catenin rescued neurogenesis defects caused by microglial loss. Microglial absence leads to neutrophil accumulation, hindering the resolution of inflammation and macrophages are not sufficient for regeneration. These findings reveal specific roles of microglia and inflammatory signaling during zebrafish telencephalic regeneration that should provide strategies to improve mammalian brain repair.

neuroscience↗

bioRxiv2019

A Meta-Analysis of Hippocampal Transcriptional Profiling Studies in a Selectively-Bred Rat Model Provides Converging Evidence with Genetic Sequencing to Implicate Specific Candidate Genes and Pathways in the Liability for Internalizing and Externalizing Psychiatric Disorders

BackgroundFor over 16 years, we have selectively bred rats to show either high or low levels of exploratory activity within a novel environment. These "bred High Responder" (bHR) and "bred Low Responder" (bLR) rats serve as a model for temperamental extremes, exhibiting large differences in many internalizing and externalizing behaviors relevant to mood and substance abuse disorders. MethodsOur study elucidated persistent differences in gene expression related to bHR/bLR phenotype across development and adulthood in the hippocampus, a region critical for emotional regulation. We meta-analyzed eight transcriptional profiling datasets (microarray, RNA-Seq) spanning 43 generations of selective breeding (adult: n=46, P7: n=22, P14: n=49, P21: n=21; all male). We cross-referenced these results with exome sequencing performed on our colony to pinpoint candidates likely to mediate the effect of selective breeding on behavioral phenotype. ResultsGenetic and transcriptional profiling results converged to implicate two genes with previous associations with metabolism and mood: Thyrotropin releasing hormone receptor and Uncoupling protein 2. Our results also highlighted bHR/bLR functional differences in the hippocampus, including a network essential for neurodevelopmental programming, proliferation, and differentiation, containing hub genes Bone morphogenetic protein 4 and Marker of proliferation ki-67. Finally, we observed differential expression related to microglial activation, which is important for synaptic pruning, including two genes within implicated chromosomal regions: Complement C1q A chain and Milk fat globule-EGF factor 8. ConclusionThese candidate genes and functional pathways have the capability to direct bHR/bLR rats along divergent developmental trajectories and promote a widely different reactivity to the environment.

neuroscience↗

bioRxiv2018

Fast, versatile, and quantitative annotation of complex images

We report a generic smartphone app for quantitative annotation of complex images. The app is simple enough to be used by children, and annotation tasks are distributed across app users, contributing to efficient annotation. We demonstrate its flexibility and speed by annotating >30,000 images, including features of rice root growth and structure, stem cell aggregate morphology, and complex worm (C. elegans) postures, for which we show that the speed of annotation is >130-fold faster than state-of-the-art techniques with similar accuracy.

bioengineering↗

bioRxiv2018

Synthetic-evolution reveals that phosphoregulation of the mitotic kinesin-5 Cin8 is constrained

Cdk1 has been found to phosphorylate the majority of its substrates in disordered regions. These phosphorylation sites do not appear to require precise positioning for their function. The mitotic kinesin-5 Cin8 was shown to be phosphoregulated at three Cdk1 sites in disordered loops within its catalytic motor domain. Here, we examined the flexibility of Cin8 phosphoregulation by analyzing the phenotypes of synthetic Cdk1-sites that were systematically generated by single amino-acid substitutions, starting from a phosphodeficient variant of Cin8. Out of 29 synthetic Cdk1 sites that we created, eight were non-functional; 19 were neutral, similar to the phosphodeficient variant; and two gave rise to phosphorylation-dependent spindle phenotypes. Of these two, one site resulted in novel phosphoregulation, and only one site, immediately adjacent to a native Cdk1 site, produced phosphoregulation similar to wild-type. This study shows that, while the gain of a single phosphorylation site can confer regulation and modulate the dynamics of the spindle, to achieve optimal regulation of a mitotic kinesin-5 motor protein, phosphoregulation has to be site-specific and precise.

cell biology↗

bioRxiv2018

Computational assessment of blood flow heterogeneity in dialysis patients’ cardiac ventricles

Dialysis prolongs life but augments cardiovascular mortality. Imaging data suggests that dialysis increases myocardial blood flow (BF) heterogeneity, but its causes remain poorly understood. A biophysical model of human coronary vasculature was used to explain the imaging observations, and highlight causes of coronary BF heterogeneity.\n\nPost-dialysis CT images from patients under control, pharmacological stress (adenosine), therapy (cooled dialysate), and adenosine and cooled dialysate conditions were obtained. The data presented disparate phenotypes. To dissect vascular mechanisms, a 3D human coronary vasculature model was implemented. Simulations were performed to investigate the effects of altered aortic pressure and blood vessel diameters on myocardial BF heterogeneity which was quantified using relative dispersion, fractal dimension, and transmural BF distribution.\n\nImaging showed that stress and therapy potentially increased mean and total BF, while reducing heterogeneity. BF histograms of one patient showed multi-modality. Using the model, it was found that total coronary BF increased as coronary perfusion pressure (CPP) was increased. BF heterogeneity was differentially affected by large or small vessel blocking. BF heterogeneity was found to be inversely related to small blood vessel diameters. Simulation of large artery stenosis indicates that BF became heterogeneous (increase relative dispersion) and gave multi-modal histograms. The total transmural BF as well as transmural BF heterogeneity reduced due to large artery stenosis, generating large patches of very low O_SCPCAPBFC_SCPCAP regions downstream. Blocking of arteries at various orders showed that blocking larger arteries results in multi-modal BF histograms and large patches of low BF, whereas smaller artery blocking results in augmented relative dispersion and fractal dimension. Transmural heterogeneity was also affected. Finally, the effects of augmented aortic pressure in the presence of blood vessel blocking shows differential effects on BF heterogeneity as well as transmural BF.\n\nImproved aortic blood pressure may lead to improved BF. Stress and therapy may be effective if they dilate small vessels. A potential cause for the observed complex BF distributions (multi-modal BF histograms) may indicate existing large vessel stenosis.\n\nThe intuitive BF heterogeneity methods used can be readily used in clinical studies. Further development of the model and methods will permit personalised assessment of patient BF status.

biophysics↗

bioRxiv2017

Do Candidate Genes Affect the Brain’s White Matter Microstructure? Large-Scale Evaluation of 6,165 Diffusion MRI Scans

AbstractSusceptibility genes for psychiatric and neurological disorders - including APOE, BDNF, CLU,CNTNAP2, COMT, DISC1, DTNBP1, ErbB4, HFE, NRG1, NTKR3, and ZNF804A - have been reported to affect white matter (WM) microstructure in the healthy human brain, as assessed through diffusion tensor imaging (DTI). However, effects of single nucleotide polymorphisms (SNPs) in these genes explain only a small fraction of the overall variance and are challenging to detect reliably in single cohort studies. To date, few studies have evaluated the reproducibility of these results. As part of the ENIGMA-DTI consortium, we pooled regional fractional anisotropy (FA) measures for 6,165 subjects (CEU ancestry N=4,458) from 11 cohorts worldwide to evaluate effects of 15 candidate SNPs by examining their associations with WM microstructure. Additive association tests were conducted for each SNP. We used several meta-analytic and mega-analytic designs, and we evaluated regions of interest at multiple granularity levels. The ENIGMA-DTI protocol was able to detect single-cohort findings as originally reported. Even so, in this very large sample, no significant associations remained after multiple-testing correction for the 15 SNPs investigated. Suggestive associations (1.3x10-4 < p < 0.05, uncorrected) were found for BDNF, COMT, and ZNF804A in specific tracts. Meta-and mega-analyses revealed similar findings. Regardless of the approach, the previously reported candidate SNPs did not show significant associations with WM microstructure in this largest genetic study of DTI to date; the negative findings are likely not due to insufficient power. Genome-wide studies, involving large-scale meta-analyses, may help to discover SNPs robustly influencing WM microstructure.

neuroscience↗