Research

The mission of the lab is to follow a network-based approach to understand the pathogenesis of neurodegenerative diseases, with the ultimate aim being to utilize this strategy to develop combination treatments. This strategy distinguishes our lab from a decades-long tradition in the field of zeroing in on specific genes and focusing on the development of monotherapies for the treatment of neurodegenerative diseases.

Simultaneously, the lab aspires to remain at the cutting edge in terms of cellular and molecular biology techniques and to advance the neurodegeneration field by developing innovative tools and technologies that we will share with the research community.

The building blocks - key publications

  • A High Throughput Screen to understand the networks involved in the cell-to-cell transfer of a-synuclein

    We published the first genome wide, high throughput screen on a-synuclein propagation, which identified 38 genes that regulate this process. The innovative aspect of this study was the genetic screen for a specific disease mechanism, which lead to the identification of several biologically and genetically plausible genes that integrate into gene expression and protein networks alongside known Mendelian and risk genes for Parkinson’s disease. This was a “proof of concept” study that established a framework for gene discovery in complex diseases and a strategy to overcome sample size and power limitations of conventional Mendelian and genome wide association studies.

    Kara et al, Cell Rep, 2021

  • Novel Forster Resonance Energy Transfer (FRET) assays to study the conformation of secreted Apolipoprotein E (ApoE)

    ApoE4 is a major risk factor for the development of Alzheimer’s disease, whereas E2 is protective and E3 has a neutral effect. We showed that the conformation of intracellular apoE within HEK cells and astrocytes adopts a directional pattern; in other words, E4 adopts the most closed conformation, E2 adopts the most open conformation, and E3 adopts an intermediate conformation. Intermolecular interactions between apoE molecules were isoform-specific, indicating a great diversity in the structure of apoE lipoparticles. Finally, we showed that secreted E4 is the most lipidated isoform in astrocytes, suggesting that increased lipidation acts as a folding chaperone enabling E4 to adopt a closed conformation.

    Kara et al, J Biol Chem, 2017

  • Using Next Generation Sequencing to understand the genetic basis of spastic paraplegias

    The hereditary spastic paraplegias are a genetically heterogeneous group of degenerative disorders. We investigated a series of 97 index cases with complex spastic paraplegia. The SPG11 gene was first analyzed, revealing homozygous or compound heterozygous mutations in 31% of probands, the largest SPG11 series reported to date. We studied the autophagic response to starvation in eight affected SPG11 cases and control fibroblast cell lines, but in our restricted study we did not observe correlations between disease status and autophagic or lysosomal markers. In the remaining cases, next generation sequencing revealed variants in a number of known complex spastic paraplegia genes, including SPG7, FA2H and ZFYVE26/SPG15. Variants were also identified in the Parkinson's disease-associated gene ATP13A2, neuronal ceroid lipofuscinosis gene TPP1 and the hereditary motor and sensory neuropathy DNMT1 gene, highlighting the genetic heterogeneity of spastic paraplegia. No plausible genetic cause was identified in 51% of probands, likely indicating the existence of as yet unidentified genes.

    Kara et al, Brain, 2016

Research projects pursued in the lab

We will be pursuing the following research questions, building on our proven expertise in high throughput screens, genomics, neuropathology and development of genetically encoded fluorescent tools.

  • Follow up studies on the genes identified through our recently published high throughput screen on a-synuclein propagation to identify their mechanism of action.

  • Study the role of and genetic networks underlying selective vulnerability in the pathogenesis of neurodegenerative diseases.

  • Elucidate the pathways that lead to the formation of a-synuclein inclusions.

  • Development of novel genetically encoded tools to study specific disease mechanisms.

There is emphasis on understanding genetic networks in every project, consistently with the overall mission of the lab; therefore, all projects incorporate one or more of high throughput screens or -omics at either the discovery phase or to dissect the function and interactors of a specific target.

Model systems
We are currently using mammalian cell lines (including stable cell lines), induced pluripotent stem cells (iPSc) and human brain tissue. In the future, and as our research program advances, we will expand our toolkit to also include mouse work.

Diseases
We are mainly interested in Parkinson’s disease, but we also have projects on Alzheimer’s disease and Multiple System Atrophy.

Techniques
Standard cell and molecular biology techniques, flow cytometry, microscopy (standard imaging and FRET, FLIM, FRAP), iPSc, high throughput genetic and chemical screens, single cell and spatial transcriptomics, proteomics, lipidomics, genomics, optogenetics, histology.

Core facilities available at Rutgers
Rutgers has extensive core facilities, most of which are located at the Piscataway campus at which the lab is based, and include proteomics, lipidomics, histology, Zeiss and Leica confocals, GE InCell Analyzer 6000, spectral flow cytometers, and many more. Additional facilities can be found at the Newark campus, including the Amnis ImageStream X MarkII flow cytometer, BD flow cytometry analyzers and 10x genomics Visium. A searchable website listing the core facilities can be found here.

Collaborations
We have an extensive network of collaborators from within Rutgers and other institutions including UCL, Harvard, Yale, Boston University, the University of Manchester and through the International Parkinson’s disease Genomics Consortium (IPDGC). Our collaborators facilitate access to human tissue, model systems, patient materials and genetic data. We also have joint research projects and exchange expertise on experimental and analysis techniques, which enables us to pursue innovative and ambitious research projects.

We are always open to new collaborations that address exciting research questions and fit in with the overall research theme of our lab.