Altered neuroepithelial morphogenesis and migration defects in iPSC-derived cerebral organoids and 2D neural stem cells in familial bipolar disorder

Bipolar disorder (BD) is a severe mental illness that can result from neurodevelopmental aberrations, particularly in familial BD, which may include causative genetic variants. In the present study, we derived cortical organoids from BD patients and healthy (control) individuals from a clinically dense family in the Indian population. Our data reveal that the patient organoids show neurodevelopmental anomalies, including organisational, proliferation and migration defects. The BD organoids show a reduction in both the number of neuroepithelial buds/cortical rosettes and the ventricular zone size. Additionally, patient organoids show a lower number of SOX2-positive and EdU-positive cycling progenitors, suggesting a progenitor proliferation defect. Further, the patient neurons show abnormal positioning in the ventricular/intermediate zone of the neuroepithelial bud. Transcriptomic analysis of control and patient organoids supports our cellular topology data and reveals dysregulation of genes crucial for progenitor proliferation and neuronal migration. Lastly, time-lapse imaging of neural stem cells in 2D in vitro cultures reveals abnormal cellular migration in BD samples. Overall, our study pinpoints a cellular and molecular deficit in BD patient-derived organoids and neural stem cell cultures.

LSD1 Regulates Neurogenesis in Human Neural Stem Cells Through the Repression of Human-Enriched Extracellular Matrix and Cell Adhesion Genes

Neurogenesis begins with neural stem cells undergoing symmetric proliferative divisions to expand and then switching to asymmetric differentiative divisions to generate neurons in the developing brain. Chromatin regulation plays a critical role in this switch. Histone lysine-specific demethylase LSD1 demethylates H3K4me1/2 and H3K9me1/2 but the mechanisms of its global regulatory functions in human neuronal development remain unclear. We performed genome-wide ChIP-seq of LSD1 occupancy, RNA-seq, and Histone ChIP-seq upon LSD1 inhibition to identify its repressive role in human neural stem cells. Novel downstream effectors of LSD1 were identified, including the Notch signaling pathway genes and human-neural progenitor-enriched extracellular matrix (ECM) pathway/cell adhesion genes, which were upregulated upon LSD1 inhibition. LSD1 inhibition led to decreased neurogenesis, and overexpression of downstream effectors mimicked this effect. Histone ChIP-seq analysis revealed that active and enhancer markers H3K4me2, H3K4me1, and H3K9me1 were upregulated upon LSD1 inhibition, while the repressive H3K9me2 mark remained mostly unchanged. Our work identifies the human-neural progenitor-enriched ECM pathway/cell adhesion genes and Notch signaling pathway genes as novel downstream effectors of LSD1, regulating neuronal differentiation in human neural stem cells.

Regulation of chromatin accessibility and gene expression in the developing hippocampal primordium by LIM-HD transcription factor LHX2

In the mammalian cerebral cortex, the hippocampal primordium (Hcp) occupies a discrete position in the dorsal telencephalic neuroepithelium adjacent to the neocortical primordium (Ncp). We examined transcriptomic and chromatin-level features that distinguish the Hcp from the Ncp in the mouse during the early neurogenic period, embryonic day (E)12.5. ATAC-seq revealed that the Hcp was more accessible than the Ncp at this stage. Motif analysis of the differentially accessible loci in these tissues revealed LHX2 as a candidate transcription factor for modulating gene regulatory networks (GRNs). We analyzed LHX2 occupancy profiles and compared these with transcriptomic data from control and Lhx2 mutant Hcp and Ncp at E12.5. Our results revealed that LHX2 directly regulates distinct genes in the Hcp and Ncp within a set of common pathways that control fundamental aspects of development namely pluripotency, axon pathfinding, Wnt, and Hippo signaling. Loss of Lhx2 caused a decrease in accessibility, specifically in hippocampal chromatin, suggesting that this factor may play a unique role in hippocampal development. We identified 14 genes that were preferentially enriched in the Hcp, for which LHX2 regulates both chromatin accessibility and mRNA expression, which have not thus far been examined in hippocampal development. Together, these results provide mechanistic insight into how LHX2 function in the Hcp may contribute to the process by which the hippocampus acquires features distinct from the neocortex.

Chromatin remodelling complexes in cerebral cortex development and neurodevelopmental disorders

The diverse number of neurons in the cerebral cortex are generated during development by neural stem cells lining the ventricle, and they continue maturing postnatally. Dynamic chromatin regulation in these neural stem cells is a fundamental determinant of the emerging property of the functional neural network, and the chromatin remodellers are critical determinants of this process. Chromatin remodellers participate in several steps of this process from proliferation, differentiation, migration leading to complex network formation which forms the basis of higher-order functions of cognition and behaviour. Here we review the role of these ATP-dependent chromatin remodellers in cortical development in health and disease and highlight several key mouse mutants of the subunits of the complexes which have revealed how the remodelling mechanisms control the cortical stem cell chromatin landscape for expression of stage-specific transcripts. Consistent with their role in cortical development, several putative risk variants in the subunits of the remodelling complexes have been identified as the underlying causes of several neurodevelopmental disorders. A basic understanding of the detailed molecular mechanism of their action is key to understating how mutations in the same networks lead to disease pathologies and perhaps pave the way for therapeutic development for these complex multifactorial disorders.

An evolutionarily conserved Lhx2-Ldb1 interaction regulates the acquisition of hippocampal cell fate and regional identity

The protein co-factor Ldb1 regulates cell fate specification by interacting with LIM-homeodomain (LIM-HD) proteins in a tetrameric complex consisting of an LDB:LDB dimer that bridges two LIM-HD molecules, a mechanism first demonstrated in the Drosophila wing disc. Here, we demonstrate conservation of this interaction in the regulation of mammalian hippocampal development, which is profoundly defective upon loss of either Lhx2 or Ldb1 Electroporation of a chimeric construct that encodes the Lhx2-HD and Ldb1-DD (dimerization domain) in a single transcript cell-autonomously rescues a comprehensive range of hippocampal deficits in the mouse Ldb1 mutant, including the acquisition of field-specific molecular identity and the regulation of the neuron-glia cell fate switch. This demonstrates that the LHX:LDB complex is an evolutionarily conserved molecular regulatory device that controls complex aspects of regional cell identity in the developing brain.

Understanding brain development - Indian researchers' past, present and growing contribution

The brain is the seat of all higher-order functions in the body. Brain development and the vast array of neurons and glia it produces is a baffling mystery to be studied. Neuroscientists using a vast number of model systems have been able to crack many of the nitty-gritty details using various model systems. One way has been to size down the problem by utilizing the power of genetics using simple model systems such as Drosophila to create a fundamental framework in order to unravel the basic principles of brain development. Scientists have used simpler organisms to uncover the fundamental principles of brain development and also to study the evo-devo angle to brain development. Complex circuitry has been unraveled in complex model systems, such as the mouse, to reveal the intricacies and regional specialization of brain function. This is an ever-growing field, and with newer genetic and molecular tools, together with several new centers of excellence, India's contribution to this fascinating field of study is continually rising. Here, I review the pioneering work done by Indian developmental neurobiologists in the past and their mounting contribution in the present.

Relax, Don't RAN Translate It

The (GGGGCC)n repeat expansion in C9orf72, which is the most common cause of frontotemporal dementia and amyotrophic lateral sclerosis, is translated through repeat-associated non-AUG (RAN) translation. In this issue of Neuron, Cheng et al. (2019) report that the helicase DDX3X, which unwinds (or relaxes) RNA, suppresses RAN translation and toxicity.

Frontotemporal dementia causative CHMP2B impairs neuronal endolysosomal traffic-rescue by TMEM106B knockdown

Mutations in the endosome-associated protein CHMP2B cause frontotemporal dementia and lead to lysosomal storage pathology in neurons. We here report that physiological levels of mutant CHMP2B causes reduced numbers and significantly impaired trafficking of endolysosomes within neuronal dendrites, accompanied by increased dendritic branching. Mechanistically, this is due to the stable incorporation of mutant CHMP2B onto neuronal endolysosomes, which we show renders them unable to traffic within dendrites. This defect is due to the inability of mutant CHMP2B to recruit the ATPase VPS4, which is required for release of CHMP2B from endosomal membranes. Strikingly, both impaired trafficking and the increased dendritic branching were rescued by treatment with antisense oligonucleotides targeting the well validated frontotemporal dementia risk factor TMEM106B, which encodes an endolysosomal protein. This indicates that reducing TMEM106B levels can restore endosomal health in frontotemporal dementia. As TMEM106B is a risk factor for frontotemporal dementia caused by both C9orf72 and progranulin mutations, and antisense oligonucleotides are showing promise as therapeutics for neurodegenerative diseases, our data suggests a potential new strategy for treating the wide range of frontotemporal dementias associated with endolysosomal dysfunction.

An Efficient System for Gene Perturbation in Embryonic Hippocampal Progenitors Using Ex Vivo Electroporation Followed by In Vitro Dissociated Cell Culture

We established an efficient cell culture assay that permits combinatorial genetic perturbations in hippocampal progenitors to examine cell-autonomous mechanisms of fate specification. The procedure begins with ex vivo electroporation of isolated, intact embryonic brains, in a manner similar to in utero electroporation but with greatly improved access and targeting. The electroporated region is then dissected and transiently maintained in organotypic explant culture, followed by dissociation and plating of cells on coverslips for in vitro culture. This assay recapitulates data obtained in vivo with respect to the neuron-glia cell fate switch and can be effectively used to test intrinsic or extrinsic factors that regulate this process. The advantages of this ex vivo procedure over in utero electroporation include the fact that distinct combinations of perturbative reagents can be introduced in different embryos from a single litter, and issues related to embryonic lethality of transgenic animals can be circumvented.

Quantitative ethnomedicinal study of plants used in the Nelliyampathy hills of Kerala, India

ETHNOPHARMACOLOGICAL RELEVANCE

Inspite of tremendous advances made in allopathic medical practices, medicinal plants have played an important role throughout the world in treating and preventing a variety of diseases and hence there is urgency in recording such data. This is the first ethnobotanical study in which statistical calculations about plants are done by the Pearson correlation coefficient (PCC) method. The present study was aimed to identify plants collected for medicinal purposes by the traditional healers of Nelliyampathy hills, located in Palakkad district of Kerala, India and to document the traditional names, preparation and uses of these plants.

METHODS

The field study was carried out over a period of 2 years (2011-2013) using semi-structured interviews with 66 informants (most of the informants belonged to an age between 50 and 70 years) in six remote locations in the hills. Ethnomedicinal data was analyzed using frequency citation (FC), relative frequency of citation (RFC) and use value (UV) along with a Pearson correlation coefficient (PCC). Demographic characteristics of participants, ethnobotanical inventory of plants and data on medicinal application and administration were recorded.

RESULTS

A total of 85 medicinal plants belonging to 49 families were reported to be used against 19 different ailments in the hills. The maximum reported medicinal plant families were Cucurbitaceae with 6 species followed by Acanthaceae, Malvaceae and Fabaceae (each 5 species), Asteraceae, Lamiaceae, Moraceae and Myrtaceae (each 3 species), the most dominant life form of the species includes herbs (42) followed by tree (20), climber (15) and shrub (8), the most frequent used part was leaves (40%) followed by root (14%), seed and flowers (each12%), fruit (9%), bark (7%), stem (2%), latex (2%), rhizome and whole plant (each 1%), the most common preparation and administration methods were paste (32%), powder (22%), decoction and juice (each 20%) and raw (4%), infusion and inhalation (each1% ). The Pearson correlation coefficient between RFC and UV was 0.638 showing highly positive significant association.

CONCLUSIONS

In this study, we have documented considerable indigenous knowledge about the native medicinal plants in Nelliyampathy hills for treating common ailments. The plants such as further investigated phytochemically and pharmacologically which leads to natural drug discovery development may be based on the present study. The study has various socioeconomic dimensions which are associated with the local communities.

Glucose-stimulated translation regulation of insulin by the 5' UTR-binding proteins

Insulin is the key regulator of glucose homeostasis in mammals, and glucose-stimulated insulin biosynthesis is essential for maintaining glucose levels in a narrow range in mammals. Glucose specifically promotes the translation of insulin in pancreatic β-islet, and the untranslated regions of insulin mRNA play a role in such regulation. Specific factors in the β-islets bind to the insulin 5' UTR and regulate its translation. In the present study we identify protein-disulfide isomerase (PDI) as a key regulator of glucose-stimulated insulin biosynthesis. We show that both in vitro and in vivo PDI can specifically associate with the 5' UTR of insulin mRNA. Immunodepletion of PDI from the islet extract results in loss of glucose-stimulated translation indicating a critical role for PDI in insulin biosynthesis. Similarly, transient overexpression of PDI resulted in specific translation activation by glucose. We show that the RNA binding activity of PDI is mediated through PABP. PDI catalyzes the reduction of the PABP disulfide bond resulting in specific binding of PABP to the insulin 5' UTR. We also show that glucose stimulation of the islets results in activation of a specific kinase that can phosphorylate PDI. These findings identify PDI and PABP as important players in glucose homeostasis.

Novel splice variant of mouse insulin2 mRNA: implications for insulin expression

Insulin is a secreted peptide that controls glucose homeostasis in mammals, and insulin biosynthesis is regulated by glucose at many levels. Rodent insulin is encoded by two non-allelic genes. We have identified a novel splice variant of the insulin2 gene in mice that constitutes about 75% of total insulin2 mRNA. The alternate splicing does not alter the ORF but reduces the 5'UTR by 12 bases. A reporter gene containing the novel short 5'UTR, is more efficiently expressed in cells, suggesting that alternative splicing of insulin mRNA in mice could result in an additional level of regulation in insulin biosynthesis.

The role of many-particle excitations in Coulomb blockaded transport

We discuss the role of electron-electron and electron-phonon correlations in current flow in the Coulomb blockade regime, focusing specifically on non-trivial signatures arising from the breakdown of mean-field theory. By solving transport equations directly in Fock space, we show that electron-electron interactions manifest as gateable excitations experimentally observed in the current-voltage characteristic. While these excitations might merge into an incoherent sum that allows occasional simplifications, a clear separation of excitations into slow 'traps' and fast 'channels' can lead to further novelties such as negative differential resistance, hysteresis and random telegraph signals. Analogous novelties for electron-phonon correlation include the breakdown of commonly anticipated Stokes-anti-Stokes intensities, and an anomalous decrease in phonon population upon heating due to reabsorption of emitted phonons.

A minimal element in 5'UTR of insulin mRNA mediates its translational regulation by glucose

Glucose induced translation of insulin in pancreatic beta cells is mediated by the 5'UTR of insulin mRNA. We determined the minimal sequence/structure in the 5'UTR of rat insulin gene1 for this regulation. We show that specific factors in the pancreatic islets bind to the 5'UTR of the insulin mRNA upon glucose stimulation. We identified a minimal 29-nucleotide element in the 5'UTR that is sufficient to form the complex, and confer glucose mediated translation activation. Conserved residues in the predicted stem loop region of the un-translated region (UTR) seem to be important for the complex formation and the translation regulation.

A "cleanup procedure" involving periodate oxidation in the enzymatic synthesis of chemically pure alpha-32P and alpha-33P labelled deoxyribonucleotides

Enzymatic synthesis of alpha-(32)P and alpha-(33)P labelled deoxyribonucleotides involves the transfer of radiolabelled phosphorus from either gamma-(32)P adenosine triphosphate (gamma-ATP) or gamma-(32)P guanosine triphosphate (gamma-GTP). Subsequent removal of these ribonucleotides is essential for the preparation of chemically pure deoxyribonucleotides. Agarose-phenyl boronate columns, which bind specifically to cis-diol moieties, have been used for the removal of ribonucleotide contaminants. However, this involves column losses and additional radiation exposure. In the present work we describe a chemical method for the improvement of the chemical purity, based on the preferential oxidation of ribose sugars by periodate. The cis-diol moiety of ribose is specifically oxidised to the dialdehyde. The excess periodate ions were destroyed using ethylene glycol. The phosphate group was then cleaved by beta-elimination using alkali. The product was purified using anion exchange chromatography. The efficiency of the process was validated using tracer gamma-(32)P ATP and alpha-(32)P dATP. Samples at various steps were analysed by TLC, autoradiography and HPLC. During the process ATP is oxidised whereas 2'-deoxyadenosine triphosphate (dATP) remains intact. The alpha-(32)P dATP synthesized by this process was assayed for its incorporation in lambda-DNA by the random priming method and was found to be effectively incorporated. The process developed is an efficient and convenient method for the preparation of chemically pure deoxyribonucleotides.