Center for Genomics of Neurodegenerative Disease – Phatnani Lab

The Center for Genomics of Neurodegenerative Disease (CGND) is dedicated to the study of neurodegenerative diseases such as ALS, dementia, Alzheimer’s disease, frontotemporal dementia, Parkinson’s disease, and Huntington’s disease. CGND’s vision is to establish a center for applying state of the art genetics, genomics and bioinformatics to the study of neurodegenerative disease mechanisms.

CGND’s goals are to use whole genome sequencing to identify mutations that cause neurodegenerative disease. To gain insights into the relationship between mutations, gene expression and disease mechanisms, whole genome sequencing data will ultimately be integrated with other genomic-scale data such as RNA-SEQ, RNA-protein interactions, and DNA methylation patterns.

CGND is helping to create a uniform system of collecting clinical annotation to better enable the integration of genomic data with clinical profiles. This information will be freely available to the research community in a data warehouse for whole genome sequencing and RNA-SEQ analyses.

Approach

Projects

Autophagy and ALS

Group Lead: James Gregory

ALS is a complex neurodegenerative disorder that involves the interaction of many genes and multiple cell types. Our long-term goal is to investigate how mutations that affect autophagy impact ALS disease risk, progression, and potential therapeutic interventions. Here, the short-term objective is to use human induced pluripotent stem cell (hiPSC)-derived motor neurons (MNs) and glia to investigate cell autonomous and non-autonomous effects of autophagic dysfunction. The central hypothesis is that ALS mutations differentially impact MN and glia function with respect to cellular stress, autophagy, and protein aggregation, and that this is reflected in the unique gene expression signatures of each cell type. A major component of this proposal is to build the tools necessary for efficient genome engineering and the methods with which to empirically query cell-type specific gene expression and cellular function within complex neuron/glia co-cultures. Altogether, our studies will elucidate the intra- and intercellular impact of autophagy dysfunction and provide a rigorous and systematic framework with which to evaluate the complex interactions of the growing list genetic variants and cell types linked to ALS.

Functional Genetics in ALS

Group Lead: Delphine Fagegaltier

CGND has engaged several collaborations to leverage the NYGC ALS Consortium datasets which are the largest collection of multi-tissue, multi-subject data in ALS. The working group uses these datasets to identify genes, pathways and regulatory elements contributing to human ALS disease and its associated variations with the aim to stratify ALS patients into molecular subtypes.

The Functional Genetics working group explores regulatory elements, eQTLs, sQTLs, splicing defects and alterations of gene expression in the cohort to stratify ALS patients subtypes and characterize the molecular function of genetic variants and candidate genes in ALS. By identifying novel regulatory mechanisms leading to ALS, the multi-level analyses will enable a mechanistic interpretation of gene expression networks and the genetic basis of ALS disease. Integrative and comparative analyses to other neurodegenerative diseases aim to identify shared and specific dysregulations in neurological disease.

Consortium data are also used for other studies. For example, in a study led by Jim Manley at Columbia University, the analysis of RNASeq data from about 60 ALS-FTD cases linked hnRNPH and TDP43 insolubility to the severity of splicing defects across the ALS and FTD spectrum at large, including sporadic ALS cases, thereby implying that hnRNPH sequestration away from its target genes was not restricted to patients carrying C9orf72 repeat expansions. In fact, splicing defects found in ALS and FTD appear when any of several RNA-binding proteins becomes insoluble, despite consistent TDP43 aggregate pathology. Changes in the concentration and the solubility of any of these proteins, even when introduced through subtle mutations, creates imbalanced RBP availability, leading in turn to various defects in RNA processing.

Adapted from Conlon et al. Elife (2018)

Pathologic features and associated changes in gene expression in post mortem spinal cord and cortex from patients with ALS

Group Lead: Joana Petrescu

Amyotrophic lateral sclerosis (ALS) is a clinically heterogeneous disorder with respect to a) the site of onset of motor symptoms, b) whether or not motor symptoms are accompanied by cognitive impairment, c) the type of pathology observed in the brain and spinal cord, and d) which cell types are affected by this pathology. The sources of this heterogeneity are presently not well understood. Our aim is to identify pathological signatures which correlate with regional involvement and disease progression in ALS. Furthermore, we aim to identify the perturbations in cellular function and intercellular interactions which accompany pathological features in brain and spinal cord tissues from patients with ALS. In order to accomplish these aims, we are using highly multiplexed protein imaging to deeply phenotype pathological changes in tissues from patients with ALS and spatially resolved transcriptomic profiling to discover changes in gene expression profiles relative to these pathological features.

 

Multiomic analysis of pathological features in post mortem tissues from patients with ALS-FTD.

Fluidics and imaging setup for automated highly multiplexed immunofluorescence imaging.

Subcellular RNA localization in ALS

Group Lead: Güney Akbalik

The selective vulnerability of motor neurons (MNs) in ALS is poorly understood, particularly because many genes associated with ALS are ubiquitously expressed and involved in fundamental pathways that are essential across cell types. We hypothesize that the highly branched morphology of MNs and astrocytes compared to other cell types makes them more susceptible to RNA mislocalization, which may disrupt local protein synthesis at the distal spots (e.g. neuromuscular junctions) that is essential for normal cellular and synaptic function. Mislocalization of RNA may also disrupt intercellular communication between MNs, astrocytes, oligodendrocytes, etc. and contribute to ALS pathology. Indeed, human astrocytes can have up to several million protrusions with connections to neurons in the CNS. We aim to identify the subcellular transcriptome alterations in hiPSC-derived MNs and astrocytes from ALS patients with known mutations (TDP43, FUS, C9orf72, SOD1) compared to controls. The results will also elucidate whether RNA mislocalization is a common feature of ALS and could identify new avenues for drug targets.

Astrocytes differentiated from human stem cells. Green and purple: markers specific for astrocytes. Blue: nucleus.

Motor neurons differentiated from human stem cells. Axons: in magenta, dendrites: in green, nucleus: in blue

Motor neurons (on the left compartment) projecting their axons to the right compartment of a microfluidic chamber through microchannels between two compartments. Axons: in green, dendrites: in red, nucleus: in blue. This system enables us to isolate axons separately to analyze axonal RNAs.

Transforming Growth Factor Beta Project Summary

Project Lead: Cat Braine

ALS is a genetically complex disease; diverse mutations cause motor neuron death by disrupting various interrelated pathways. To date no therapy targeting a single factor can rescue motor neuron loss. Transforming Growth Factor Beta (TGF-b) is upstream of many of the pathways changed in disease and has been shown to be dysregulated in multiple ALS models. Upregulation of TGF-b signaling has been identified as neuroprotective in many neurodegenerative disease models; however, there is evidence that endogenous TGF-b signaling is disrupted in ALS. The goal of this research is to understand how TGF-b signaling directly affects motor neuron survival and gene expression in the SOD1G93A model of ALS. This project’s central hypothesis is that disease related disruption of TGF-b signaling in motor neurons contributes to their death. This hypothesis will be tested using viral therapies in a transgenic ALS animal model followed by gene expression profiling. These studies will define the role of TGF-b signaling in diseased and healthy motor neurons and begin to unravel how this pathway antagonizes pro-inflammatory pathological processes in motor neurons that are vulnerable to this disease.

Particle analysis of TGF-BRII accumulations (red) in motor neurons. Processed image for quantification on the right.

GFAP (green), a marker of astrocytes, and IL-1B (red) an inflammatory cytokine co-localize in the ventral horn of a spinal cord where TGF-BRII has been conditionally knocked out of microglia.

P62 accumulations in motor neurons in the ventral horn of the spinal cord of a diseased animal.

TGF-BRII accumulations (magenta) in MMP9 (green) positive motor neurons. Nuclei are marked by DAPI (yellow).

This work was partially supported by a gift from the Simons Foundation