Our research focus is the development of technologies to study and solve the causes of neural injury and disease. As part of the W.M. Keck Center for Collaborative Neuroscience and the Rutgers Stem Cell Research Center, we share several collaborative projects with our colleagues.
- Ataxia-telangiectasia Based on previous collaborative projects with the laboratory of Dr. Karl Herrup (Li et al., 2012, Nature Medicine; Li et al., 2013, Nature Neuroscience; Jiang et al., 2015, Brain), we have prepared iPSC from several Ataxia-telangiectasia (A-T) subjects. Source cells for iPSC reprogramming were collected at the Ataxia-telangiectasia Clinical Center at The Johns Hopkins Hospital, under the direction of Dr. Howard Lederman. Among the A-T iPSC produced, we identified a spontaneous ATM gene reversion, providing us with an isogenic pair of iPSC lines (ATM– vs. ATM+; Lin et al., 2015 Stem Cell Reports. Our goal is to model the broad genetic diversity present in A-T patients but lacking in traditional models such as mouse knockouts.
- Risk gene variants in addiction disorders Another set of projects, in collaboration with Dr. Jay Tischfield, build on the large-scale screening for human genetic variants associated with nicotine and alcohol abuse. iPSC lines were prepared from subjects collected by the COGEND project, under the direction of Dr. Laura Bierut, or the COGA project. These projects are all in collaboration with Dr. Zhiping Pang. Our goal is to identify mechanisms in human neurons that predict optimal therapies based on specific genetic variants. A recent article appeared in Scientific Reports on a variant of the CHRNA5 gene (Oni et al., 2016).
- Genetic and toxin risk in Alzheimer’s Together with Dr. Jason Richardson, we have prepared iPSC from Alzheimer’s disease (AD) subjects carrying variants of the APOE gene, which is the greatest genetic risk factor for AD. Dr. Richardson has found that exposure to DDT or its metabolite DDE, particularly in subjects carrying the APOE ε4/ε4 variant, compounds the risk for AD. This is a unique example of a gene x environment interaction for a major neurodegenerative disorder.
We recently joined with RUCDR Infinite Biologics® to form the NIMH Stem Cell Center, a service to bank cells from subjects with mental disorders for use in creating induced pluripotent stem cells (iPSC). The Center will also create iPSC as directed by the scientific advisory board. We participate in many collaborative studies to use specific genetic background sample to prepare iPSC in the study of addiction, schizophrenia, Alzheimer’s disease, autism and more. Find our recent iPSC protocol book here.
Previous work from our laboratory identified 146 new microRNAs in human embryonic stem cells (hESC). We sequenced more than 107 unique small RNA sequences using ultra-deep SOLiD sequencing technology, aligned these with genome in “colorspace” using SHRiMP (Rumble, 2009), and fit results to a model of Microprocessor cleavage (miRDeep, Friedlander, 2008). This produced 818 candidate genomic loci matching the basic structure of a microRNA precursor and aligning with observed RNA sequences. This list was filtered for small RNAs that were immunoprecipitated with anti-Ago2 antibody, reasoning that functional microRNAs should be associated with RISC complexes. 146 of the predicted microRNAs were identified in Ago2 IP samples. Among these new microRNAs, 30% share seed sequences with previously-known microRNAs, suggesting that many are new members of existing microRNA families. Sequence conservation analysis shows that most new microRNAs are conserved across several mammalian species but are not broadly conserved across animals, consistent with a recent evoluationary appearance. These new microRNAs are regulated during hESC differentiation in patterns similar to other microRNAs. This work was published in PLoSOne at this address: http://dx.plos.org/10.1371/journal.pone.0007192. Also read an article in Epigenie covering this work!
Genome data links for Li et al. (2013):
Li, J., R.P. Hart, E.M. Mallimo, M.R. Swerdel, A. Kusnecov & K. Herrup (2013) EZH2-mediated H3K27 trimethylation mediates neurodegeneration in ataxia-telangiectasia. Nature Neuroscience, 16(12):1745-53. Links to NIH SRA and GEO datasets.
Supplemental data for Hannila et al. (2013):
Download supplemental files for “Secretory leukocyte protease inhibitor reverses inhibition by CNS myelin, promotes regeneration in the optic nerve, and suppresses expression of the TGFβ signaling protein Smad2” https://doi.org/10.6084/m9.figshare.6656234
Supplemental links for Goff et al. (2009):
- Complete set of supplemental figures (1.2 Mb PDF, opens in a new window)
- UCSC Genome Browser BED file of 818 computed microRNA-encoding genes (right-click and select “Copy Shortcut” and paste link into Genome Browser’s “add custom tracks” form.)
- UCSC Genome Browser BED file of 146 Ago2-immunoprecipitated microRNA genes (right-click and select “Copy Shortcut” and paste link into Genome Browser’s “add custom tracks” form.)
- GEO dataset for microarrays used in Fig. 1
- SRA dataset for SOLiD results of H1 ESC and NSC listed as experiment 1 in Supplemental Table 1