scholarly journals The proteomic architecture of schizophrenia iPSC-derived cerebral organoids reveals alterations in GWAS and neuronal development factors

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael Notaras ◽  
Aiman Lodhi ◽  
Haoyun Fang ◽  
David Greening ◽  
Dilek Colak
Keyword(s):  
High Throughput ◽  
Molecular Mechanisms ◽  
System Development ◽  
Early Adulthood ◽  
Enrichment Analysis ◽  
Nervous System Development ◽  
Model Systems ◽  
Proteomic Profiling ◽  
Human Brain Tissue ◽  
Brain Disorder

AbstractSchizophrenia (Scz) is a brain disorder that has a typical onset in early adulthood but otherwise maintains unknown disease origins. Unfortunately, little progress has been made in understanding the molecular mechanisms underlying neurodevelopment of Scz due to ethical and technical limitations in accessing developing human brain tissue. To overcome this challenge, we have previously utilized patient-derived Induced Pluripotent Stem Cells (iPSCs) to generate self-developing, self-maturating, and self-organizing 3D brain-like tissue known as cerebral organoids. As a continuation of this prior work, here we provide an architectural map of the developing Scz organoid proteome. Utilizing iPSCs from n = 25 human donors (n = 8 healthy Ctrl donors, and n = 17 Scz patients), we generated 3D cerebral organoids, employed 16-plex isobaric sample-barcoding chemistry, and simultaneously subjected samples to comprehensive high-throughput liquid-chromatography/mass-spectrometry (LC/MS) quantitative proteomics. Of 3,705 proteins identified by high-throughput proteomic profiling, we identified that just ~2.62% of the organoid global proteomic landscape was differentially regulated in Scz organoids. In sum, just 43 proteins were up-regulated and 54 were down-regulated in Scz patient-derived organoids. Notably, a range of neuronal factors were depleted in Scz organoids (e.g., MAP2, TUBB3, SV2A, GAP43, CRABP1, NCAM1 etc.). Based on global enrichment analysis, alterations in key pathways that regulate nervous system development (e.g., axonogenesis, axon development, axon guidance, morphogenesis pathways regulating neuronal differentiation, as well as substantia nigra development) were perturbed in Scz patient-derived organoids. We also identified prominent alterations in two novel GWAS factors, Pleiotrophin (PTN) and Podocalyxin (PODXL), in Scz organoids. In sum, this work serves as both a report and a resource that researchers can leverage to compare, contrast, or orthogonally validate Scz factors and pathways identified in observational clinical studies and other model systems.

scholarly journals The Proteomic Architecture of Schizophrenia Cerebral Organoids Reveals Alterations in GWAS and Neuronal Development Factors

2021 ◽  
Author(s):  
Michael Notaras ◽  
Aiman Lodhi ◽  
Haoyun Fang ◽  
David Greening ◽  
Dilek Colak
Keyword(s):  
High Throughput ◽  
Molecular Mechanisms ◽  
System Development ◽  
Early Adulthood ◽  
Enrichment Analysis ◽  
Nervous System Development ◽  
Model Systems ◽  
Proteomic Profiling ◽  
Human Brain Tissue ◽  
Brain Disorder

Schizophrenia (Scz) is a brain disorder that has a typical onset in early adulthood but otherwise maintains unknown disease origins. Unfortunately, little progress has been made in understanding the molecular mechanisms underlying neurodevelopment of Scz due to ethical and technical limitations in accessing developing human brain tissue. To overcome this challenge, we have previously utilized patient-derived Induced Pluripotent Stem Cells (iPSCs) to generate self-developing, self-maturating, and self-organizing 3D brain-like tissue known as cerebral organoids. As a continuation of this prior work [1], here we provide a molecular architectural map of the developing Scz organoid proteome. Utilizing iPSCs from n = 25 human donors (n = 8 healthy Ctrl donors, and n = 17 Scz patients), we generated 3D human cerebral organoids, employed 16-plex isobaric sample-barcoding chemistry, and simultaneously subjected samples to comprehensive high-throughput liquid-chromatography/mass-spectrometry (LC/MS) quantitative proteomics. Of 3,705 proteins identified by high-throughput proteomic profiling, we identified that just ~2.62% of the organoid global proteomic landscape was differentially regulated in Scz organoids. In sum, just 43 proteins were up-regulated and 54 were down-regulated in Scz patient-derived organoids. Notably, a range of neuronal factors were depleted in Scz organoids (e.g., MAP2, TUBB3, SV2A, GAP43, CRABP1, NCAM1 etc.). Based on global enrichment analysis, alterations in key pathways that regulate nervous system development (e.g., axonogenesis, axon development, axon guidance, morphogenesis pathways regulating neuronal differentiation, as well as substantia nigra development) were perturbed in Scz patient-derived organoids. We also identified prominent alterations in two novel GWAS factors, Pleiotrophin (PTN) and Podocalyxin (PODXL), in Scz organoids. In sum, this work serves as both a report and a resource whereby researchers can leverage human-derived neurodevelopmental data from Scz patients, which can be used to mine, compare, contrast, or orthogonally validate novel factors and pathways related to Scz risk identified in datasets from observational clinical studies and other model systems.

scholarly journals Zebrafish Models of Autosomal Recessive Ataxias

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 836
Author(s):  
Ana Quelle-Regaldie ◽  
Daniel Sobrido-Cameán ◽  
Antón Barreiro-Iglesias ◽  
María Jesús Sobrido ◽  
Laura Sánchez
Keyword(s):  
Animal Models ◽  
Autosomal Recessive ◽  
Molecular Mechanisms ◽  
System Development ◽  
Rapid Development ◽  
Nervous System Development ◽  
Central Nervous System Development ◽  
Cellular Processes ◽  
Recessive Disorders

Autosomal recessive ataxias are much less well studied than autosomal dominant ataxias and there are no clearly defined systems to classify them. Autosomal recessive ataxias, which are characterized by neuronal and multisystemic features, have significant overlapping symptoms with other complex multisystemic recessive disorders. The generation of animal models of neurodegenerative disorders increases our knowledge of their cellular and molecular mechanisms and helps in the search for new therapies. Among animal models, the zebrafish, which shares 70% of its genome with humans, offer the advantages of being small in size and demonstrating rapid development, making them optimal for high throughput drug and genetic screening. Furthermore, embryo and larval transparency allows to visualize cellular processes and central nervous system development in vivo. In this review, we discuss the contributions of zebrafish models to the study of autosomal recessive ataxias characteristic phenotypes, behavior, and gene function, in addition to commenting on possible treatments found in these models. Most of the zebrafish models generated to date recapitulate the main features of recessive ataxias.

scholarly journals Growing Glia: Cultivating Human Stem Cell Models of Gliogenesis in Health and Disease

2021 ◽  
Vol 9 ◽  
Author(s):  
Samantha N. Lanjewar ◽  
Steven A. Sloan
Keyword(s):  
Nervous System ◽  
Stem Cell ◽  
System Development ◽  
Stem Cell Differentiation ◽  
Nervous System Development ◽  
Model Systems ◽  
Human Stem Cell ◽  
Human Stem Cells ◽  
Health And Disease ◽  
Species Specific

Glia are present in all organisms with a central nervous system but considerably differ in their diversity, functions, and numbers. Coordinated efforts across many model systems have contributed to our understanding of glial-glial and neuron-glial interactions during nervous system development and disease, but human glia exhibit prominent species-specific attributes. Limited access to primary samples at critical developmental timepoints constrains our ability to assess glial contributions in human tissues. This challenge has been addressed throughout the past decade via advancements in human stem cell differentiation protocols that now offer the ability to model human astrocytes, oligodendrocytes, and microglia. Here, we review the use of novel 2D cell culture protocols, 3D organoid models, and bioengineered systems derived from human stem cells to study human glial development and the role of glia in neurodevelopmental disorders.

scholarly journals Integrating High-Throughput Approaches and in vitro Human Trophoblast Models to Decipher Mechanisms Underlying Early Human Placenta Development

2021 ◽  
Vol 9 ◽  
Author(s):  
Bum-Kyu Lee ◽  
Jonghwan Kim
Keyword(s):  
High Throughput ◽  
Human Placenta ◽  
Molecular Mechanisms ◽  
Molecular Level ◽  
Cell Types ◽  
Model Systems ◽  
Extravillous Trophoblast ◽  
Human Trophoblast ◽  
Early Human

The placenta is a temporary but pivotal organ for human pregnancy. It consists of multiple specialized trophoblast cell types originating from the trophectoderm of the blastocyst stage of the embryo. While impaired trophoblast differentiation results in pregnancy disorders affecting both mother and fetus, the molecular mechanisms underlying early human placenta development have been poorly understood, partially due to the limited access to developing human placentas and the lack of suitable human in vitro trophoblast models. Recent success in establishing human trophoblast stem cells and other human in vitro trophoblast models with their differentiation protocols into more specialized cell types, such as syncytiotrophoblast and extravillous trophoblast, has provided a tremendous opportunity to understand early human placenta development. Unfortunately, while high-throughput research methods and omics tools have addressed numerous molecular-level questions in various research fields, these tools have not been widely applied to the above-mentioned human trophoblast models. This review aims to provide an overview of various omics approaches that can be utilized in the study of human in vitro placenta models by exemplifying some important lessons obtained from omics studies of mouse model systems and introducing recently available human in vitro trophoblast model systems. We also highlight some key unknown questions that might be addressed by such techniques. Integrating high-throughput omics approaches and human in vitro model systems will facilitate our understanding of molecular-level regulatory mechanisms underlying early human placenta development as well as placenta-associated complications.

scholarly journals Decoding molecular markers and transcriptional circuitry of naive and primed states of human pluripotency

2020 ◽  
Author(s):  
Arindam Ghosh ◽  
Anup Som
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
System Development ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
List Type ◽  
Metabolic Processes ◽  
Primed State

ABSTRACTPluripotent stem cells (PSCs) have been observed to occur in two distinct states — naive and primed. Both naive and primed state PSCs can give rise to tissues of all the three germ layers in vitro but differ in their potential to generate germline chimera in vivo. Understanding the molecular mechanisms that govern these two states of pluripotency in human can open up a plethora of opportunities for studying early embryonic development and in biomedical applications. In this work, we use weighted gene co-expression network (WGCN) approach to identify the key molecular makers and their interactions that define the two distinct pluripotency states. Signed-hybrid WGCN was reconstructed from transcriptomic data (RNA-seq) of naive and primed state pluripotent samples. Our analysis revealed two sets of genes that are involved in establishment and maintenance of naive (4791 genes) and primed (5066 genes) states. The naive state genes were found to be enriched for biological processes and pathways related to metabolic processes while primed state genes were associated with system development. Further, we identified the top 10% genes by intra-modular connectivity as hubs and the hub transcription factors for each group, thus providing a three-tier list of genes associated with naive and primed states of pluripotency in human.HIGHLIGHTSWeighted gene co-expression network analysis (WGCNA) identified 4791 and 5066 genes to be involved in naive and primed states of human pluripotency respectively.Functional and pathway enrichment analysis revealed the naive genes were mostly related to metabolic processes and primed genes to system development.The top 10% genes based on intra-modular connectivity from each group were defined as hubs.Identified 52 and 33 transcription factors among the naive and primed module hubs respectively.The transcription factors might play a switch on-off mechanism in induction of the two pluripotent states.

scholarly journals Systems pathology analysis identifies neurodegenerative nature of age-related retinal diseases

2018 ◽  
Author(s):  
Tiina Öhman ◽  
Fitsum Tamene ◽  
Helka Göös ◽  
Sirpa Loukovaara ◽  
Markku Varjosalo
Keyword(s):  
Molecular Mechanisms ◽  
System Development ◽  
Fibrous Tissue ◽  
Nervous System Development ◽  
Public Health Issue ◽  
Retinal Diseases ◽  
Label Free ◽  
Systems Pathology ◽  
Age Related ◽  
Vitreoretinal Diseases

AbstractAging is a phenomenon associated with profound medical implications. Idiopathic epiretinal membrane (iEMR) and macular hole (MH) are the major vision-threatening vitreoretinal diseases affecting millions of aging people globally, making these conditions an important public health issue. The iERM is characterized by fibrous tissue developing on the surface of the macula, leading to biomechanical and biochemical macular damage. MH is a small breakage in the macula associated with many ocular conditions. Although several individual factors and pathways are suggested, a systems pathology level understanding of the molecular mechanisms underlying these disorders is lacking. Therefore, we performed mass spectrometry based label-free quantitative proteomics analysis of the vitreous proteomes from patients with iERM (n=26) and MH (n=21) to identify the key proteins as well as the multiple interconnected biochemical pathways contributing to the development of these diseases. We identified a total of 1014 unique proteins, of which many were linked to inflammation and complement cascade, revealing the inflammational processes in retinal diseases. Additionally, we detected a profound difference in proteomes of the iEMR and MH compared to the non-proliferative diabetic retinopathy. A large number of neuronal proteins were present at higher levels in iERM and MH vitreous, including neuronal adhesion molecules, nervous system development proteins and signalling molecules. This points toward the important role of neurodegeneration component in the pathogenesis of age-related vitreoretinal diseases. Despite of marked similarities, several unique vitreous proteins were identified in both iERM and MH conditions, providing a candidate targets for diagnostic and new therapeutic approaches. Identification of previously reported and novel proteins in human vitreous humor from patient with iERM and MH provide renewed understanding of the pathogenesis of age-related vitreoretinal diseases.

scholarly journals New data on dinophilid neurogenesis: a variation of a common pattern

2020 ◽  
Author(s):  
Elizaveta Fofanova ◽  
Tatiana Mayorova ◽  
Elena Voronezhskaya
Keyword(s):  
Nervous System ◽  
Developmental Stages ◽  
System Development ◽  
Nervous System Development ◽  
Model Systems ◽  
Common Pattern ◽  
Acetylated Tubulin ◽  
Reported Study ◽  
Pioneer Neurons ◽  
Tubulin Antibodies

Abstract BackgroundThe structure and development of the nervous system in Lophotrochozoa species is of the most important questions for comparative neurobiology. During the last decade the number of comprehensive studies on the development of serotonergic and FMRFamidergic systems has been skyrocketing. However, the detailed research of the earliest events of Polychaeta neurogenesis is still sparce. Polychaeta is a huge taxon within Lophotrochozoa. Its representatives are widely used as model systems in developmental and physiological investigations. Dinophilidae is a unique Polychaeta group. Its representatives combine morphological traits of different lophotrochozoan taxa. Moreover, adult dinophilids demonstrate morphological similarity to a trochophore larva. This similarity may be associated with either archaic origin of this group or neoteny. The main goal of our study is to provide a detailed description of the earliest events in Dinophilus neurogenesis. These data might improve our understanding of Polychaeta development and evolution.ResultsWe have studied the earliest events in nervous system development in two relative species D. gyrociliatus and D. taeniatus using immunochemical labelling of serotonin, FMRF-amide related peptides, and acetylated tubulin. We used external ciliation as marker for staging. Both species go through the same developmental stages: prototroch, ventral ciliary field and ciliary bands. In both species the first neurons differenciate revealed by anti alpha-acetylated tubulin antibodies only and show no reaction with 5-HT or FMRFa antibodies. These neurons located at the anterior and posterior parts of the embryo in both species. In D. taeniatus embryons the anterior cell is transient and disappear just after head neuropil is constructed. On the contrary, in D. gyrociliatus embryos the anterior cell is not transient and remains at the same position during the whole life span of the specimen. Caudal cell is present during the whole embryogenesis in both species. Neurites of these early neurons surround the stomadeum and constitute anlagen of paired ventro-lateral longitudinal bundles. During the development the number of neurites increases and they form compact head neuropil, paired ventro-lateral and lateral longitudinal bundles, unpaired medial longitudinal bundle and transverse commissures in ventral hyposphere. Serotonin- and FMRFamide-immunoreactive neurons differentiate adjacent to ventro-lateral bundles and head neuropil, respectively, after the establishment of main structures of the nervous system at the ventral ciliary field and ciliary bands stages. Processes of serotonin-, FMRFamide- immunopositive neurons constitute the small portion of tubulin immunopositive neuropil at all described stages.ConclusionsWe announce a detailed data on the earliest events in D. gyrociliatus and D. taeniatus neurodevelopment based on anti-acetylated tubulin, serotonin, and FMRFamide-like immuno labeling. The first nerve elements demonstrate no 5-HT-IR and no FMRFa-IR, which differs from the most Polychaetes and even Lophotrochozoans, investigated so far. Moreover, these animals do not have a typical apical organ (or perhaps do not have it at all) and the pioneer neurons of D.gyrociliatus are also peculiar in that they join the definitive nervous system unlike other lophotrochozoans where pioneer nerons are transient. Thus, Dinophilus neurogenesis demonstrates a variation of common scheme. The reported study was funded by RFBR, project number 19-3460040.

31 Gametic Incompatibility: Improving the Success of Mate Allocation in Dairy Cattle

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 16-17
Author(s):  
Audrey A A Martin ◽  
Samir Id-Lahoucine ◽  
Dan Tulpan ◽  
Stephen J Leblanc ◽  
Angela Cánovas ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
System Development ◽  
Enrichment Analysis ◽  
Mendelian Inheritance ◽  
Nervous System Development ◽  
Transmission Ratio Distortion ◽  
Reproductive Capacity ◽  
Pathway Enrichment Analysis ◽  
Inbreeding Coefficients ◽  
Offspring Genotype

Abstract In the dairy industry, mate allocation is mainly based on the parents’ breeding values and inbreeding coefficients aiming to achieve the producer’s breeding goal. With artificial insemination, the portfolio of sires to choose from is large and the quality of the semen doses is standardized. However, not all sire-dam matings are equally likely to produce a successful pregnancy. Among other reproduction issues, the success of a mating could vary due to the incompatibility of gametes coming from the sire and the dam and could influence the fertilization’s success, additionally to the reproductive capacity of the parents. Considering the gametic incompatibility of the potential parents could be a novel option to improve mating plans. Under the hypothesis that gametic incompatibility has a significant effect on reproduction and reduces the odds of fertilization and pregnancy, this study aimed to determine the genetic background of gametic incompatibility. Transmission ratio distortion (TRD), which detects deviations from Mendelian inheritance expectations, is commonly used to identify deleterious mutations. We adapted the TRD model by including an interaction effect between the gametes leading to the offspring genotype to detect regions with TRD effects and gametic incompatibility. Our dataset contained 436,651 genotyped (50K SNP) Canadian Holstein cattle from 283,817 parents-offspring trios. A total of 482 regions with TRD containing 671 positional genes were found. The functional analysis detected biological pathways associated with uterus development, embryonic skeletal system development, and nervous system development. Additionally, gene ontology terms from the topology-based pathway enrichment analysis were mostly related to the steroid hormones signalling pathway. Although difficult, genes specific to gametic incompatibility could be differentiated from genes underlying other reproduction processes by refining the genetic regions with TRD. With further investigation, we will provide new information to improve mate allocation for the dairy cattle industry.

Environment and Brain Plasticity: Towards an Endogenous Pharmacotherapy

2014 ◽  
Vol 94 (1) ◽  
pp. 189-234 ◽  
Author(s):  
Alessandro Sale ◽  
Nicoletta Berardi ◽  
Lamberto Maffei
Keyword(s):  
Environmental Enrichment ◽  
Molecular Mechanisms ◽  
Brain Plasticity ◽  
System Development ◽  
Basic Research ◽  
Nervous System Development ◽  
Adult Brain ◽  
Aging Brain ◽  
Cerebral Neurons ◽  
And Function

Brain plasticity refers to the remarkable property of cerebral neurons to change their structure and function in response to experience, a fundamental theoretical theme in the field of basic research and a major focus for neural rehabilitation following brain disease. While much of the early work on this topic was based on deprivation approaches relying on sensory experience reduction procedures, major advances have been recently obtained using the conceptually opposite paradigm of environmental enrichment, whereby an enhanced stimulation is provided at multiple cognitive, sensory, social, and motor levels. In this survey, we aim to review past and recent work concerning the influence exerted by the environment on brain plasticity processes, with special emphasis on the underlying cellular and molecular mechanisms and starting from experimental work on animal models to move to highly relevant work performed in humans. We will initiate introducing the concept of brain plasticity and describing classic paradigmatic examples to illustrate how changes at the level of neuronal properties can ultimately affect and direct key perceptual and behavioral outputs. Then, we describe the remarkable effects elicited by early stressful conditions, maternal care, and preweaning enrichment on central nervous system development, with a separate section focusing on neurodevelopmental disorders. A specific section is dedicated to the striking ability of environmental enrichment and physical exercise to empower adult brain plasticity. Finally, we analyze in the last section the ever-increasing available knowledge on the effects elicited by enriched living conditions on physiological and pathological aging brain processes.

scholarly journals Regulation of Gliogenesis by lin-32/Atoh1 in Caenorhabditis elegans

2020 ◽  
Vol 10 (9) ◽  
pp. 3271-3278 ◽  
Author(s):  
Albert Zhang ◽  
Kentaro Noma ◽  
Dong Yan
Keyword(s):  
Nervous System ◽  
Caenorhabditis Elegans ◽  
Embryonic Development ◽  
Molecular Mechanisms ◽  
System Development ◽  
Nervous System Development ◽  
Proneural Gene ◽  
C Elegans ◽  
Fundamental Process ◽  
Mutant Phenotypes

Abstract The regulation of gliogenesis is a fundamental process for nervous system development, as the appropriate glial number and identity is required for a functional nervous system. To investigate the molecular mechanisms involved in gliogenesis, we used C. elegans as a model and identified the function of the proneural gene lin-32/Atoh1 in gliogenesis. We found that lin-32 functions during embryonic development to negatively regulate the number of AMsh glia. The ectopic AMsh cells at least partially arise from cells originally fated to become CEPsh glia, suggesting that lin-32 is involved in the specification of specific glial subtypes. Moreover, we show that lin-32 acts in parallel with cnd-1/ NeuroD1 and ngn-1/ Neurog1 in negatively regulating an AMsh glia fate. Furthermore, expression of murine Atoh1 fully rescues lin-32 mutant phenotypes, suggesting lin-32/Atoh1 may have a conserved role in glial specification.

Sign in / Sign up

Export Citation Format

Share Document