Biology subjects

Notaras, M.

Publications and source records attributed to Notaras, M..

4 recordsLinked to original sources

bioRxiv2022

The evolution of BDNF is defined by strict purifying selection and prodomain spatial coevolution, but what does it mean for human brain disease?

The mammalian gene Brain-Derived Neurotrophic Factor (BDNF) is an essential mediator of brain assembly, development, and maturation which has been implicated in a variety of brain disorders such as neurodevelopmental disorders (e.g. autism spectrum disorder), neuropsychiatric disorders (e.g. depression, PTSD, schizophrenia), and neurodegenerative disorders (e.g. Parkinsons). Loss of BDNF during early development is embryonic lethal, and depletion of BDNF during adolescence or adulthood can result in disease-related neuropathology across a broad range of model organisms. In order to better understand the role of BDNF in disease, we seek to provide an evolutionary context to BDNFs role within the brain by elucidating the molecular and genetic comparative history of BDNF across species. We conduct sequence alignment and phylogenetic reconstruction of the BDNF gene across a diverse selection of over 160 mammalian species spanning [~]177 million years of evolution. Selective evolutionary change was examined via several independent computational models of codon evolution including FEL, MEME, and BGM. We report strict purifying selection in the main functional domain of BDNF (NGF domain, essentially comprising the mature BDNF protein). Specifically, we discover 6 sites in our homologous alignment which are under episodic selection in the early regulatory region of BDNF (i.e. the prodomain) and 23 pairs of coevolving sites that are a part of complex spatial relationships that are distributed across the entire BDNF gene. Thus, we propose that our discovery of both local and distal sites of co-evolution within the pro- and mature-domains of BDNF that likely reflect the evolutionary fine-tuning of BDNFs unique and complex regulatory capacities whilst also retaining its core yet diverse ontogenic functionality within the central nervous system. This discovery consequently supports the idea that the BDNF prodomain is more prone to change than the mature domain, however the fact that this region has also been subject to negative purifying selection also highlights genetic sensitivity and thus partially explains the prodomains disease relevance (e.g. Val66Met and other variants) to numerous neuropsychiatric disorders. HIGHLIGHTSO_LIWe extracted coding sequences for Brain-Derived Neurotrophic Factor (BDNF) from over 160 mammalian genomes that span approximately [~]177 million years of evolution. C_LIO_LIWe observe strict purifying selection in the main functional domain (NGF) of the BDNF gene in mammals. C_LIO_LIWe observe novel results with 6 sites in our homologous alignment which are under episodic selection in the early regulatory region of BDNF (i.e. the prodomain). C_LIO_LIWe observe 23 pairs of coevolving sites within BDNF. Many of which are a part of complex spatial relationships and are distributed across the entire BDNF gene. C_LIO_LIThese data define exactly how "BDNF is highly conserved" by defining exactly where and how the mammalian BDNF has evolved, confirming the widespread belief that the BDNF prodomain is more prone to change than the mature BDNF protein. C_LI

neuroscience↗

bioRxiv2021

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

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.

neuroscience↗

bioRxiv2021

BRN2 and PTN unveil multiple neurodevelopmental mechanisms in Schizophrenia patient-derived cerebral organoids

Due to an inability to ethically access developing human brain tissue as well as identify prospective cases, early-arising neurodevelopmental and cell-specific signatures of Schizophrenia (Scz) have remained unknown and thus undefined. To overcome these challenges, we utilized Scz patient-derived stem cells to generate 3D cerebral organoids to model neuropathology of Scz during this critical period. We discovered that Scz organoids exhibited ventricular neuropathology resulting in altered progenitor survival and disrupted neurogenesis. This ultimately yielded fewer neurons within developing cortical fields of Scz organoids. Single-cell sequencing revealed that Scz progenitors were specifically depleted of neuronal programming factors leading to a remodeling of cell-lineages, altered differentiation trajectories, and distorted cortical cell-type diversity. While Scz organoids were 99.95% similar in their macromolecular diversity to Ctrls, four GWAS factors (PTN, COMT, PLCL1, and PODXL) and peptide fragments belonging to the POU-domain transcription factor family (e.g. POU3F2/BRN2) were altered. This revealed that Scz organoids principally differed not in their proteomic diversity, but specifically in their total quantity of disease and neurodevelopmental factors at the molecular level. Single-cell sequencing also subsequently identified cell-type specific alterations in neuronal programming factors and growth factors, and specifically replicated the depletion of POU3F2 (BRN2) and PTN in both Scz progenitors and neurons. Consequently, in two mechanistic rescue experiments we identified that the transcription factor POU3F2 (BRN2) and growth factor PTN operate as mechanistic substrates of neurogenesis and cellular survival, respectively, in Scz organoids. This suggests that multiple mechanisms of Scz exist in patient-derived organoids, and that these disparate mechanisms converge upon primordial brain developmental pathways such as neuronal differentiation, survival, and growth factor support, which may amalgamate to elevate intrinsic risk of Scz.

neuroscience↗

bioRxiv2018

Compartmentalized nonsense-mediated mRNA decay regulates synaptic plasticity and cognitive function via GluR1 signaling

Synaptic plasticity relies on new protein synthesis in dendrites that involves the selective translation of specific mRNAs. This requires a tight control of mRNA levels in dendrites. Consistently, RNA translation and degradation pathways have been recently linked to neurodevelopmental and neuropsychiatric diseases, suggesting a role for RNA regulation in synaptic plasticity and cognition. Despite being the only RNA regulatory pathway that is associated with multiple mental illnesses, the Nonsense-Mediated mRNA Decay (NMD) pathway presents an unexplored regulatory mechanism for synaptic function and plasticity. NMD is a highly conserved and selective RNA degradation pathway that exerts its function in a cell- and spatiotemporally-specific manner. Here, we show that neuron-specific disruption of NMD in adulthood attenuates learning, memory, hippocampal LTP, and potentiates perseverative/repetitive behavior. While it is known that local translation of specific mRNAs in dendrites enables synaptic plasticity, the tightly-controlled mechanisms that regulate local quantity of specific mRNAs remains poorly understood. We report that the NMD pathway operates within dendrites to regulate GluR1 surface levels. Specifically, NMD modulates the internalization of GluR1 and promotes its local synthesis in dendrites. We identified AMPK as a mechanistic substrate for NMD that contributes to the NMD-mediated regulation of GluR1 by limiting total GluR1 levels. These data establish that NMD regulates synaptic plasticity, cognition, and local protein synthesis in dendrites, providing fundamental insight into the neuron-specific function of NMD within the brain.

neuroscience↗