The Big Tent

CTSI 2016 NIH Renewal Proposal Launchpad

National Repository for Stem Cell Derived Neurons

Primary Author: Bruce Miller
Proposal Status: 

The failure of large clinical trials for Alzheimer’s disease (AD), frontotemporal dementia (FTD), amyotrophic lateral sclerosis and Parkinson’s disease (PD) are forcing the field to consider more targeted treatments for genetically homogeneous cohorts. Precision medicine approaches to the diagnosis and treatment of patients offer huge opportunities to advance the dementia field. New trials for AD patients with presenilin-1 mutations and FTD patients with progranulin and tau mutations have already been started or are being considered.  

Dr. Shinya Yamanaka brought a revolution to stem cell technology by delineating a method to convert skin cells to induced pluripotent stem cells (iPSCs).  This approach has facilitated development of new models of neurodegeneration for patients with FTD-related mutations of progranulin (1,2) or C9orf72 (3). Similarly, iPSC-based modeling of the detrimental effects of apolipoprotein E4 and the tau polymorphism A152T (Yadong Huang, personal, communication) is facilitating a precision medicine approach to the determination of disease effects of specific genes. Via iPSC technology, large quantities of neurons can be produced allowing exploration of the pathological consequences of genetic polymorphisms while simultaneously allowing drug screening of neurons from patients with genetically caused forms of dementia. (4)

We propose to create through UCSF’s CTSI a national core of neurons from patients with both sporadic and genetic forms of Alzheimer’s disease, frontotemporal dementia, amyotrophic lateral sclerosis, Parkinson’s disease and other rare forms of dementia. Selected investigators will study and manipulate these neurons in order to develop model systems for the major mutations that cause AD, FTD, ALS and PD. Simultaneously, age-matched control neuronal lines would also be generated for comparison studies. Large numbers of these neurons would be created for and distributed to other CTSI sites investigators and scientists across the world, requesting the use of these valuable cells.  

Comprehensive clinical phenotyping would be performed on the participants in this project that would include clinical characterization (demographics, cognitive, motor and imaging data), and family history.  Whole genome sequencing of the cells would be performed at UCLA and transciptome analysis would be done at UCSB. The resulting multidimensional data would be incorporated into the UCSF Precision Medicine Knowledgebase, linking it with related neuroscientific datasets and analytic resources to maximize its value for the larger research community. The project would be led by UCSF’s Memory and Aging Center (Bruce Miller, Kate Rankin, Aimee Kao), the Gladstone Institute (Yadong Huang), the Broad Institute (Steve Haggarty), UCSD (Irene Litvan), and UCLA (Dan Geschwind and Giovanni Coppola). Partial support for the study will be supplied by three private foundations, the UCSF NIA supported by an Alzheimer Disease Research Center (Miller), and a grant supported by the NINDS (Huang).

 

References:

1. Almeida S, Gascon E, Tran H, Chou HJ, Gendron TF, Degroot S, Tapper AR, Sellier C, Charlet-Berguerand N, Karydas A, Seeley WW, Boxer AL, Petrucelli L, Miller BL, Gao FB. Modeling key pathological features of frontotemporal dementia with C9ORF72 repeat expansion in iPSC-derived human neurons. Acta Neuropathol. 2013 Jul 9.

2. Almeida S, Zhang Z, Coppola G, Mao W, Futai K, Karydas A, Geschwind MD, Tartaglia MC, Gao F, Gianni D, Sena-Esteves M, Geschwind DH, Miller BL, Farese RV Jr, Gao FB.

3. Induced pluripotent stem cell models of progranulin-deficient frontotemporal dementia uncover specific reversible neuronal defects. Cell Rep. 2012 Oct 25;2(4):789-98.

4. Cenik B, Sephton CF, Dewey CM, Xian X, Wei S, Yu K, Niu W, Coppola G, Coughlin SE, Lee SE, Dries DR, Almeida S, Geschwind D, Gao FB, Miller BL, Farese RV Jr, Posner BA, Yu G, Herz J. Suberoylanilide hydroxamic acid (vorinostat) up-regulates progranulin transcription: rational therapeutic approach to frontotemporal dementia. J Biol Chem. 2011 May 6;286(18):16101-8.

5. Zhao WN, Cheng C, Theriault KM, Sheridan SD, Tsai LH, Haggarty SJ.  A high-throughput screen for Wnt/β-catenin signaling pathway modulators in human iPSC-derived neural progenitors. J Biomol Screen. 2012 Oct;17(9):1252-63.

Comments

OVERVIEW FOR CTSI RETREAT DISCUSSION:


Summarize the problem being addressed. Please make sure this is NOT disease-specific.

Given the paucity of effective therapies for clinically heterogeneous diseases such as neurodegeneration and psychiatric disorders, precision medicine approaches to the diagnosis and treatment of such disorders holds immense promise.  However, obtaining well-characterized neurons from patients with multigenic causes for these disorders is time consuming, expensive and requires a large infrastructure of clinical, laboratory and informatics expertise.


Summarize the solution being proposed.  Please make sure this is NOT disease-specific, although you can provide examples of specific test cases

We propose to create a National Repository for iPSC-derived neurons in neurodegenerative and psychiatric diseases. Induced pluripotent stem cells (iPSC) technology revolutionized medicine by allowing the development of new cellular models of disease and facilitating a precision medicine approach to the determination of effects of specific genetic variants. Via iPSC technology, large quantities of human neurons can be produced to explore the pathological consequences of genetic polymorphisms and allow drug screening using disease-specific neurons.


What partners are involved in the solution?

The project would be led by UCSF’s Memory and Aging Center (Bruce Miller, Kate Rankin, Aimee Kao), the Gladstone Institute (Yadong Huang), the Broad Institute (Steve Haggarty), UCSD (Irene Litvan), UCSB (Kenneth Kosik), and UCLA (Dan Geschwind and Giovanni Coppola). Partial support for the study will be supplied by three private foundations, the UCSF Alzheimer Disease Research Center supported by NIA (Miller), and a consortium grant supported by the NINDS (Huang).


What is the potential impact?

Comprehensive clinical phenotyping (ie history, exam, imaging, cog testing) would be performed on the subjects in this project. Whole genome sequencing of the cells would be performed at UCLA and transciptome analysis would be done at UCSB. The resulting multidimensional data would be incorporated into the UCSF Precision Medicine Knowledgebase, linking it with related medical datasets and analytic resources to maximize its value for the larger research community. Selected investigators will study and manipulate the iPSC-derived neurons to develop model systems for the major mutations that cause neurodegenerative and psychiatric diseases. These invaluable neurons would then be distributed to other CTSI sites investigators and scientists across the world.

The Big Tent:  CTSI 2016 NIH Renewal Proposal Launchpad

Notes

 

1.      How do we maximize impact and broad applicability of the proposal?

 

  • Though it makes sense to “start with what we know”, i.e., developing neural progenitor cells (NPC’s), we will more explicitly build into the proposal the ways we are setting up the process/infrastructure to make this a “use case” for development/archiving of other types of cells derived from iPSCs (e.g., cardiac muscle, etc.).

 

  • We will be more clear about how the creation of the multilevel (i.e. iPSC/NPCs plus phenotype, genotype, genomic) dataset will facilitate/accelerate scientific discovery, vis-à-vis the knowledge network; be clearer about broader scientific applications (i.e., how is this scientific infrastructure)

 

  • We will also identify mechanisms for data linking across levels – should propose to have a data/bioinformatics core involved in building, quality control, and maintenance of the datasets

 

  • We will be more clear about how the currently diverse methodological approaches to development of NPCs will be managed, vis-à-vis validation (e.g., use 2-3 methods in parallel and compare?)

 

2.      What foundation exists on campus already that will ensure success of the initiative?

 

The team will leverage campus initiatives that are geared to foster efforts just like this

  • CTSI’s expertise and leadership in bioinformatics (from policy to tools, e.g. RedCap); wide array of consultation services
  • UCSF Precision Medicine Knowledgebase, linking it with related neuroscientific datasets and analytic resources to maximize its value for the larger research community.

 

3.      What creative and/or innovative partnerships could be leveraged to ensure success?

 

We will seek to leverage the many UC system-wide efforts that exist and poise this effort as a “use case” for the following initiatives:

  • UC BRAID including
    • UC ReX
    • IRB harmonization including use of the UC IRB MOU for multicenter studies and its effort to streamline processes and create a central system for SCRO
    • Engage UC and their work on global informed consent for biobanking including their robust effort in engaging the community
    • Biobanking and work on governance and operations of system-wide biorepositories
  • UC Share
    • we have already consulted with Laura Vant t’veer about this initiative and will leverage their work to create a system-wide resource for clinical genomics infrastructure

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