scholarly journals Motor neurons from ALS patients with mutations in C9ORF72 and SOD1 exhibit distinct transcriptional landscapes

2019 ◽  
Vol 28 (16) ◽  
pp. 2799-2810 ◽  
Author(s):  
Ching-On Wong ◽  
Kartik Venkatachalam
Keyword(s):  
Cell Adhesion ◽  
Motor Neurons ◽  
Induced Pluripotent Stem Cell ◽  
Data Sets ◽  
Spinal Motor Neurons ◽  
Expression Of Genes ◽  
Sporadic Als ◽  
Elevated Expression ◽  
Induced Pluripotent ◽  
Als Patients

Abstract Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease that culminates in paralysis and death. Here, we present our analyses of publicly available multiOMIC data sets generated using motor neurons from ALS patients and control cohorts. Functional annotation of differentially expressed genes in induced pluripotent stem cell (iPSC)-derived motor neurons generated from patients with mutations in C9ORF72 (C9-ALS) suggests elevated expression of genes that pertain to extracellular matrix (ECM) and cell adhesion, inflammation and TGFβ targets. On the other end of the continuum, we detected diminished expression of genes repressed by quiescence-promoting E2F4/DREAM complex. Proteins whose abundance was significantly altered in C9-ALS neurons faithfully recapitulated the transcriptional aberrations. Importantly, patterns of gene expression in spinal motor neurons dissected from C9-ALS or sporadic ALS patients were highly concordant with each other and with the C9-ALS iPSC neurons. In contrast, motor neurons from patients with mutations in SOD1 exhibited dramatically different signatures. Elevated expression of gene sets such as ECM and cell adhesion genes occurs in C9 and sporadic ALS but not SOD1-ALS. These analyses indicate that despite the similarities in outward manifestations, transcriptional and proteomic signatures in ALS motor neurons can vary significantly depending on the identity of the causal mutations.

scholarly journals Establishment of a Human Induced Pluripotent Stem Cell-Derived Neuromuscular Co-Culture Under Optogenetic Control

2020 ◽  
Author(s):  
Elliot W. Swartz ◽  
Greg Shintani ◽  
Jijun Wan ◽  
Joseph S. Maffei ◽  
Sarah H. Wang ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Induced Pluripotent Stem Cell ◽  
Cell Types ◽  
Calcium Flux ◽  
Electrode Arrays ◽  
Spinal Motor Neurons ◽  
Culture Model ◽  
Skeletal Myotubes ◽  
Induced Pluripotent

SummaryThe failure of the neuromuscular junction (NMJ) is a key component of degenerative neuromuscular disease, yet how NMJs degenerate in disease is unclear. Human induced pluripotent stem cells (hiPSCs) offer the ability to model disease via differentiation toward affected cell types, however, the re-creation of an in vitro neuromuscular system has proven challenging. Here we present a scalable, all-hiPSC-derived co-culture system composed of independently derived spinal motor neurons (MNs) and skeletal myotubes (sKM). In a model of C9orf72-associated disease, co-cultures form functional NMJs that can be manipulated through optical stimulation, eliciting muscle contraction and measurable calcium flux in innervated sKM. Furthermore, co-cultures grown on multi-electrode arrays (MEAs) permit the pharmacological interrogation of neuromuscular physiology. Utilization of this co-culture model as a tunable, patient-derived system may offer significant insights into NMJ formation, maturation, repair, or pathogenic mechanisms that underlie NMJ dysfunction in disease.

scholarly journals Genome Wide Analysis Points towards Subtype-Specific Diseases in Different Genetic Forms of Amyotrophic Lateral Sclerosis

2020 ◽  
Vol 21 (18) ◽  
pp. 6938
Author(s):  
Banaja P. Dash ◽  
Marcel Naumann ◽  
Jared Sterneckert ◽  
Andreas Hermann
Keyword(s):  
Motor Neurons ◽  
Individualized Medicine ◽  
Induced Pluripotent Stem Cell ◽  
Kegg Pathways ◽  
Amyotropic Lateral Sclerosis ◽  
Sporadic Als ◽  
Apparent Death ◽  
Induced Pluripotent ◽  
Simplex Virus ◽  
Lateral Sclerosis

Amyotropic lateral sclerosis (ALS) is a lethally progressive and irreversible neurodegenerative disease marked by apparent death of motor neurons present in the spinal cord, brain stem and motor cortex. While more and more gene mutants being established for genetic ALS, the vast majority suffer from sporadic ALS (>90%). It has been challenging, thus, to model sporadic ALS which is one reason why the underlying pathophysiology remains elusive and has stalled the development of therapeutic strategies of this progressive motor neuron disease. To further unravel these pathological signaling pathways, human induced pluripotent stem cell (hiPSCs)-derived motor neurons (MNs) from FUS- and SOD1 ALS patients and healthy controls were systematically compared to independent published datasets. Here through this study we created a gene profile of ALS by analyzing the DEGs, the Kyoto encyclopedia of Genes and Genomes (KEGG) pathways, the interactome and the transcription factor profiles (TF) that would identify altered molecular/functional signatures and their interactions at both transcriptional (mRNAs) and translational levels (hub proteins and TFs). Our findings suggest that FUS and SOD1 may develop from dysregulation in several unique pathways and herpes simplex virus (HSV) infection was among the topmost predominant cellular pathways connected to FUS and not to SOD1. In contrast, SOD1 is mainly characterized by alterations in the metabolic pathways and alterations in the neuroactive-ligand–receptor interactions. This suggests that different genetic ALS forms are singular diseases rather than part of a common spectrum. This is important for patient stratification clearly pointing towards the need for individualized medicine approaches in ALS.

scholarly journals An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients

2020 ◽  
Author(s):  
◽  
Loren Ornelas ◽  
Emilda Gomez ◽  
Lindsay Panther ◽  
Aaron Frank ◽  
...  
Keyword(s):  
Motor Neuron ◽  
Motor Neurons ◽  
Rna Splicing ◽  
Induced Pluripotent Stem Cell ◽  
Patient Specific ◽  
Data Independent Acquisition ◽  
Induced Pluripotent ◽  
Als Patients ◽  
And Control

SummaryNeurodegenerative diseases present a challenge for systems biology, due to the lack of reliable animal models and the difficulties in obtaining samples from patients at early stages of disease, when interventions might be most effective. Studying induced pluripotent stem cell (iPSC)-derived neurons could overcome these challenges and dramatically accelerate and broaden therapeutic strategies. Here we undertook a network-based multi-omic characterization of iPSC-derived motor neurons from ALS patients carrying genetically dominant hexanucleotide expansions in C9orf72 to gain a deeper understanding of the relationship between DNA, RNA, epigenetics and protein in the same pool of tissue. ALS motor neurons showed the expected C9orf72-related alterations to specific nucleoporins and production of dipeptide repeats. RNA-seq, ATAC-seq and data-independent acquisition mass-spectrometry (DIA-MS) proteomics were then performed on the same motor neuron cultures. Using integrative computational methods that combined all of the omics, we discovered a number of novel dysregulated pathways including biological adhesion and extracellular matrix organization and disruption in other expected pathways such as RNA splicing and nuclear transport. We tested the relevance of these pathways in vivo in a C9orf72 Drosophila model, analyzing the data to determine which pathways were causing disease phenotypes and which were compensatory. We also confirmed that some pathways are altered in late-stage neurodegeneration by analyzing human postmortem C9 cervical spine data. To validate that these key pathways were integral to the C9 signature, we prepared a separate set of C9orf72 and control motor neuron cultures using a different differentiation protocol and applied the same methods. As expected, there were major overall differences between the differentiation protocols, especially at the level of in individual omics data. However, a number of the core dysregulated pathways remained significant using the integrated multiomic analysis. This new method of analyzing patient specific neural cultures allows the generation of disease-related hypotheses with a small number of patient lines which can be tested in larger cohorts of patients.

scholarly journals Distinct responses of neurons and astrocytes to TDP-43 proteinopathy in amyotrophic lateral sclerosis

Brain ◽  
2020 ◽  
Vol 143 (2) ◽  
pp. 430-440 ◽  
Author(s):  
Phillip Smethurst ◽  
Emmanuel Risse ◽  
Giulia E Tyzack ◽  
Jamie S Mitchell ◽  
Doaa M Taha ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Motor Neurons ◽  
Induced Pluripotent Stem Cell ◽  
Pathological Feature ◽  
Cell Type ◽  
Sporadic Als ◽  
Cell Type Specific ◽  
Induced Pluripotent ◽  
Human Ipsc ◽  
Lateral Sclerosis

Abstract Amyotrophic lateral sclerosis (ALS) is a fatal and incurable neurodegenerative disease caused by motor neuron loss, resulting in muscle wasting, paralysis and eventual death. A key pathological feature of ALS is cytoplasmically mislocalized and aggregated TDP-43 protein in >95% of cases, which is considered to have prion-like properties. Historical studies have predominantly focused on genetic forms of ALS, which represent ∼10% of cases, leaving the remaining 90% of sporadic ALS relatively understudied. Additionally, the role of astrocytes in ALS and their relationship with TDP-43 pathology is also not currently well understood. We have therefore used highly enriched human induced pluripotent stem cell (iPSC)-derived motor neurons and astrocytes to model early cell type-specific features of sporadic ALS. We first demonstrate seeded aggregation of TDP-43 by exposing human iPSC-derived motor neurons to serially passaged sporadic ALS post-mortem tissue (spALS) extracts. Next, we show that human iPSC-derived motor neurons are more vulnerable to TDP-43 aggregation and toxicity compared with their astrocyte counterparts. We demonstrate that these TDP-43 aggregates can more readily propagate from motor neurons into astrocytes in co-culture paradigms. We next found that astrocytes are neuroprotective to seeded aggregation within motor neurons by reducing (mislocalized) cytoplasmic TDP-43, TDP-43 aggregation and cell toxicity. Furthermore, we detected TDP-43 oligomers in these spALS spinal cord extracts, and as such demonstrated that highly purified recombinant TDP-43 oligomers can reproduce this observed cell-type specific toxicity, providing further support to a protein oligomer-mediated toxicity hypothesis in ALS. In summary, we have developed a human, clinically relevant, and cell-type specific modelling platform that recapitulates key aspects of sporadic ALS and uncovers both an initial neuroprotective role for astrocytes and the cell type-specific toxic effect of TDP-43 oligomers.

scholarly journals Single-cell RNA-seq analysis of human iPSC-derived motor neurons resolves early and predictive ALS signatures

2020 ◽  
Author(s):  
Ritchie Ho ◽  
Michael J. Workman ◽  
Pranav Mathkar ◽  
Kathryn Wu ◽  
Kevin J. Kim ◽  
...  
Keyword(s):  
Single Cell ◽  
Motor Neurons ◽  
Developmental Stages ◽  
Single Cell Analysis ◽  
Induced Pluripotent Stem Cell ◽  
Sequencing Analysis ◽  
Developmental Gene Expression ◽  
Differentiated Cells ◽  
Sporadic Als ◽  
Induced Pluripotent

SummaryInduced pluripotent stem cell (iPSC) derived neural cultures from amyotrophic lateral sclerosis (ALS) patients can reflect disease phenotypes targetable by treatments. However, widely used differentiation protocols produce mixtures of progenitors, neurons, glia, and other cells at various developmental stages and rostrocaudal neural tube segments. Here we present a methodology using single-cell RNA sequencing analysis to distinguish cell type expression in C9orf72 ALS, sporadic ALS, control, and genome-edited cultures across multiple subjects, experiments, and commercial platforms. Combinations of HOX and developmental gene expression with global clustering classified rostrocaudal, progenitor, and mantle zone fates. This demonstrated that iPSC-differentiated cells recapitulate fetal hindbrain and spinal cord development and resolved early, reproducible, and motor neuron-specific signatures of familial and sporadic ALS. This includes downregulated ELAVL3 expression, which persists into disease endstages. Single-cell analysis thus yielded predictive ALS markers in other human and mouse models which were otherwise undiscovered through bulk omics assays.

The non-cell-autonomous component of ALS: new in vitro models and future challenges

2014 ◽  
Vol 42 (5) ◽  
pp. 1270-1274 ◽  
Author(s):  
Laura Ferraiuolo
Keyword(s):  
Motor Neurons ◽  
Neural Progenitor Cells ◽  
Neurodegenerative Disorder ◽  
Induced Pluripotent Stem Cell ◽  
Cell Types ◽  
In Vitro Models ◽  
Future Challenges ◽  
Induced Pluripotent ◽  
Als Patients

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder affecting the motor nerves. At present, there is no effective therapy for this devastating disease and only one Food and Drug Administration (FDA)-approved drug, riluzole, is known to moderately extend survival. In the last decade, the field of ALS has made a remarkable leap forward in understanding some of the genetic causes of this disease and the role that different cell types play in the degenerative mechanism affecting motor neurons. In particular, astrocytes have been implicated in disease progression, and multiple studies suggest that these cells are valuable therapeutic targets. Recent technological advancements have provided new tools to generate astrocytes from ALS patients either from post-mortem biopsies or from skin fibroblasts through genetic reprogramming. The advent of induced pluripotent stem cell (iPSC) technology and the newly developed induced neural progenitor cells (iNPCs) have created unprecedented exciting opportunities to unravel the mechanisms involved in neurodegeneration and initiate high-throughput drug screenings.

scholarly journals ALS Motor Neurons Exhibit Hallmark Metabolic Defects That Are Rescued by Nicotinamide and SIRT3 Activation

2019 ◽  
Author(s):  
Jin-Hui Hor ◽  
Munirah Mohamad Santosa ◽  
Valerie Jing Wen Lim ◽  
Beatrice Xuan Ho ◽  
Amy Taylor ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Cortical Neurons ◽  
Metabolic Flux ◽  
Metabolic Profiles ◽  
Metabolic Defects ◽  
Sporadic Als ◽  
Altered Metabolism ◽  
Induced Pluripotent ◽  
Als Patients ◽  
Lateral Sclerosis

SUMMARYMotor neurons (MNs) are highly energetic cells and recent studies suggest that altered energy metabolism precede MN loss in Amyotrophic Lateral Sclerosis (ALS), an age-onset neurodegenerative disease. However, clear mechanistic insights linking altered metabolism and MN death are still missing. In this study, induced pluripotent stem cells (iPSCs) from healthy controls, familial ALS and sporadic ALS patients were differentiated towards spinal MNs, cortical neurons and cardiomyocytes. Metabolic flux analyses reveal a MN-specific deficiency in mitochondrial respiration in ALS. Intriguingly, all forms of familial and sporadic ALS MNs tested in our study exhibited similar defective metabolic profiles, which were attributed to hyper-acetylation of mitochondrial proteins. In the mitochondria, SIRT3 functions as a mitochondrial deacetylase to maintain mitochondrial function and integrity. We found that activating SIRT3 using nicotinamide or a small molecule activator reversed the defective metabolic profiles in all our ALS MNs, as well as correct a constellation of ALS-associated phenotypes.

scholarly journals ALS motor neurons exhibit hallmark metabolic defects that are rescued by SIRT3 activation

2020 ◽  
Author(s):  
Jin-Hui Hor ◽  
Munirah Mohamad Santosa ◽  
Valerie Jing Wen Lim ◽  
Beatrice Xuan Ho ◽  
Amy Taylor ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Cortical Neurons ◽  
Metabolic Flux ◽  
Metabolic Profiles ◽  
Metabolic Defects ◽  
Sporadic Als ◽  
Altered Metabolism ◽  
Induced Pluripotent ◽  
Als Patients ◽  
Lateral Sclerosis

Abstract Motor neurons (MNs) are highly energetic cells and recent studies suggest that altered energy metabolism precede MN loss in amyotrophic lateral sclerosis (ALS), an age-onset neurodegenerative disease. However, clear mechanistic insights linking altered metabolism and MN death are still missing. In this study, induced pluripotent stem cells from healthy controls, familial ALS, and sporadic ALS patients were differentiated toward spinal MNs, cortical neurons, and cardiomyocytes. Metabolic flux analyses reveal an MN-specific deficiency in mitochondrial respiration in ALS. Intriguingly, all forms of familial and sporadic ALS MNs tested in our study exhibited similar defective metabolic profiles, which were attributed to hyper-acetylation of mitochondrial proteins. In the mitochondria, Sirtuin-3 (SIRT3) functions as a mitochondrial deacetylase to maintain mitochondrial function and integrity. We found that activating SIRT3 using nicotinamide or a small molecule activator reversed the defective metabolic profiles in all our ALS MNs, as well as correct a constellation of ALS-associated phenotypes.

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