NIH – BRAIN Initiative: Development of Novel Tools to Probe Cell-Specific and Circuit-Specific Processes in Human and Non-Human Primate Brain (UG3/UH3 Clinical Trial Optional)

August 6, 2018 by School of Medicine Webmaster

The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative® is aimed at revolutionizing our understanding of the human brain. By accelerating the development and application of innovative technologies, researchers will be able to produce a new dynamic picture of the brain that, for the first time, will show how individual cells and complex neural circuits interact in both time and space. It is expected that the application of these new tools and technologies will ultimately lead to new ways to treat and prevent brain disorders.

NIH is one of several federal agencies involved in the BRAIN Initiative. Planning for the NIH component of the BRAIN initiative is guided by the long-term scientific plan, “BRAIN 2025: A Scientific Vision,” which details seven high-priority research areas and calls for a sustained federal commitment of $4.5 billion over 12 years. This funding opportunity announcement (FOA) and other FOAs issued as part of the BRAIN initiative are based on careful consideration by the NIH of the recommendations of the BRAIN 2025 Report, and input from the NIH BRAIN Multi-Council Working Group. Videocasts of the NIH BRAIN Multi-council Working Group are available at

To enable rapid progress in development of new technologies as well as in theory and data analysis, the BRAIN Initiative encourages collaborations between neurobiologists and scientists from statistics, physics, mathematics, engineering, and computer and information sciences; NIH welcomes applications from investigators in these disciplines.

Milestones and success criteria will be established to help determine if the tool/method development effort funded by this award should be continued or discontinued. If justified, future year milestones may be revised based on data and information obtained in the current year. In addition to milestones, the decision regarding continued funding will also be based on the robustness of the entire data package that adequately allows an interpretation of the results, overall progress, NIH BRAIN Initiative portfolio balance, program priorities, competitive landscape, and availability of funds. Therefore, continuation is based upon all available evidence at annual review that there remains a reasonable expectation that the project will achieve the goal initially judged to be meritorious by peer review.

NIH encourages BRAIN Initiative applications from investigators that are underrepresented in the biomedical, behavioral, or clinical research workforce (see data at and the most recent report on Women, Minorities, and Persons with Disabilities in Science and Engineering). Such individuals include those from underrepresented racial and ethnic groups, those with disabilities, and those from disadvantaged backgrounds.

NIH also encourages businesses to participate in the BRAIN Initiative. It is possible for companies to submit applications directly to BRAIN Initiative program announcements or to collaborate with academic researchers in joint submissions. Small businesses should consider applying to one of the BRAIN Initiative small business FOAs (

In addition to the National BRAIN initiative, the NIH continues to have a substantial annual investment in neuroscience research. The Institutes and Centers contributing to the NIH BRAIN Initiative ( ) support those research efforts through investigator-initiated applications as well as through specific FOAs. Potential applicants to this FOA are strongly encouraged to contact Scientific/Program staff if they have any questions about the best FOA for their research.

The BRAIN Initiative will require a high level of coordination and sharing between investigators to achieve its goals.

This FOA is related to the Recommendations in Section III.1 and 2 of the Final Report ( of the BRAIN working group. Specifically, this FOA solicits applications that will address the recommendations on “Discovering Diversity” and “Maps at Multiple Scales”, (Section III).

Research Objectives

This FOA is designed to support development and validation of novel tools to facilitate the detailed analysis and/or manipulation of cells and circuits and provide insights into the neural circuitry and structure underlying complex behaviors in humans and non-human primates and other mammalian brains (e.g., sheep, pig). The human brain consists of an estimated one hundred billion neurons and similar number of supporting glial cells that are uniquely organized to confer the extraordinary computational activities of the brain. Considerable progress has been made in defining the cytology and signal transduction processes in the CNS, but circuit-level function and the neural mechanisms of cognition and behavior remain poorly understood. Cell-type and circuit-specific manipulation strategies are key technical factors in addressing these important areas and represent attractive strategies to treat brain disorders. This initiative is focused on developing tools (or vastly improving existing tools) that will ultimately enable access to individual cells and defined groups of cells within neuronal circuits of the human brain. In order to achieve these goals, it is acknowledged that the use of large brains such as non-human primates, sheep and pig will be instrumental in this process. Development of tools that are applicable to human or non-human primate brains should focus on overcoming barriers to use of such tools (i.e., opto/chemo and magnetogenetic acutators). The tools sought through this FOA can include novel genetic or non-genetic methods for targeted delivery of genes, proteins, and chemicals to specific cells or tightly defined cell types and circuits.

Development of novel tools that will delineate anatomical connections between cells and expand our knowledge of circuit architecture and function is an area well poised for additional investment. Several efforts are currently underway to study large-scale, long-range connections, such as the NIH Human Connectome Project, as well as large scale rodent connectional studies. Recent development of innovative technologies (e.g., CLARITY, expansion microscopy, MERFISH, and several other imaging breakthroughs) allows an unprecedented three-dimensional view into the post-mortem brain. While still at an early stage, these exciting technologies hold promise for mapping short- and long-range connections throughout the brain. Coupled with improved activity monitoring technologies in awake, behaving animals, these new tools promise an understanding of circuitry in action. Further development of these technologies is crucial to push the envelope beyond our current capabilities. To this end, applicants from the biological sciences are encouraged to establish collaborations with engineers, chemists, material scientists, nanobiologists, and colleagues in other disciplines to develop groundbreaking approaches to study brain activity.

This FOA solicits applications to develop next-generation, innovative technologies to define and target specific cell types in the large mammalian and non-human primate brain. Of high importance are first-in-class and/or cross-cutting non-invasive or minimally invasive techniques that permit repeated measurements from and manipulations of cells over time in a non-destructive manner.

Tools/technologies relevant for this initiative are expected to be transformative, either through the development of novel tools that may be high-risk or through major advances in current approaches that break through technical barriers and will significantly improve current capabilities. While an emphasis of the BRAIN initiative is the development of novel tools to study the brain, here we highlight the need for innovative approaches to bridge experimental scales. Studies that can explore molecular and cellular mechanisms of neural activity permitting improved precision and sensitivity in the analysis of micro-and macro-circuits are strongly encouraged. Progress in understanding how the activity of the brain translates to complex behaviors will be facilitated by non-invasive approaches for both monitoring and manipulating neural activity in awake, behaving mammals. The ultimate practical goal of this FOA is to move these tools in to practice. The phased award will be dependent on milestones proposed by applicants and agreed upon at time of award. Validation of methods or tools in other organisms will only be considered responsive during the UG3 phase of the award and should focus on feasibility measures to move into human or non-human primate models during the UH3 phase. Milestones must be proposed that will demonstrate feasibility for moving into large brains during Year 3 of the award. The new tools and technologies should inform and/or exploit cell-type and/or circuit-level specificity. Plans for validating the utility of the tool/technology will be an essential feature of a successful application and applicants are expected to address issues related to safety, stability, reliability etc. The development of new genetic and non-genetic tools for delivering genes, proteins and chemicals to cells of interest or approaches that are expected to target specific cell types and/or circuits in the nervous system with greater precision and sensitivity than currently established methods are encouraged. Methods to track and monitor exogenously delivered constructs for brain targeting and circuit manipulation are also desired goals. Applications that provide approaches that break through existing technical barriers to substantially improve current capabilities are highly encouraged.

Applications using invasive devices for recording or stimulating neural activity in the human brain should consider one of the following BRAIN Initiative FOAs, and should contact the listed research contact to discuss the appropriateness of the project:

  • RFA-NS-18-021: BRAIN Initiative:  Next-Generation Invasive Devices for Recording and Modulation in the Human Central Nervous System (UG3/UH3 Clinical Trial Required)
  • RFA-NS-18-023: BRAIN Initiative:  Clinical Studies to Advance Next-Generation Invasive Devices for Recording and Modulation in the Human Central Nervous System (UH3 Clinical Trial Required)
  • RFA-NS-18-022, BRAIN Initiative: Next-Generation Invasive Devices for Recording and Modulation in the Human Central Nervous System (U44 Clinical Trial Required)

Research Scope

This FOA will support the phased development and validation of novel tools to facilitate the detailed analysis and/or manipulation of cells and circuits and provide insights into the neural circuitry and structure underlying complex behaviors in humans and non-human primates. Support will be provided for the initial development phase and can be continued through the validation and application phase if a rigorous set of milestones are achieved. For all tools and methods proposed, applicants should address issues related to safety stability, reliability and/or other relevant topics that may be barriers to adaptation in human or non-human primate brains.

This FOA seeks applications in areas including, but not limited to:

  • Improving the stability, reliability, or safety of circuit therapeutic tools for use in large animal brains (including sheep, pig, and primate models).
  • Novel methods with high safety profiles to deliver actuators (non-genetic and genetic) that are cell- and circuit-specific in human and non-human primates.
  • Novel conditional intersectional tools that are both activity- and cell-specific.
  • Novel methods for tagging individual neurons such that cellular components of a functional circuit can be explored.
  • Adaptation, refinement and validation of gene delivery systems for targets in large brains (e.g., human and non-human primate).
  • Chemical or genetic engineering of blood brain barrier-crossing carrier agents (such as tagged antibodies or other tools) to allow delivery of specific cargoes (e.g., neuronal actuators, effectors, tracers or sensors) to specific cells or circuits.
  • Novel methods for non-invasive targeted access to, or manipulation of, distinct cell types in defined circuits with spatio-temporal control.
  • Novel trans-synaptic tracers that can work in retrograde and anterograde direction or deliver cargoes to cells in the nervous system.
  • New methods to trace cell lineage to understand how circuits develop.
  • Enhanced temporal and spatial resolution techniques for noninvasive molecular imaging of neuronal cells for in situ brain studies.
  • Unique combinations of tools for multiplex analysis and/or manipulation of single cells in situ to maximize data content over many parameters (e.g., RNAs, proteins, metabolites, organelles, electrochemical dynamics, signal secretion/reception/transduction, cytoarchitecture or migratory changes).
  • Innovative tools that provide significant advances in sensitivity, selectivity or spatiotemporal resolution of molecules/structures/activities within single cells in the brain and between ostensibly similar cells in situ (e.g., high resolution imaging of molecular interactions within single cells).
  • Novel automated and scalable assays for high-throughput analysis of single cells in situ in the brain, including scalability of measured parameters in parallel, cell numbers and/or speed of processing.
  • New tools and approaches that minimize tissue and cell perturbations so that cell viability is maintained, allowing for multiple repeated measures in the same cell over time.
  • Novel methods for visualizing or manipulating epigenomic marks or gene expression in neural cells.
  • Innovative approaches to bridge scales of experimental approach. Studies that can explore molecular and cellular mechanisms of neural activity in broader contexts are encouraged.
  • Innovative molecular complementation methods to identify synaptic connections and determine their phenotypes.
  • Development of cell type-specific molecular sensors and additional tools and approaches to address circuit-specific manipulation and monitoring. Validation could include behavioral measures.
  • Generation of genetic modifications that express cell type-specific labels such as fluorescent indicators or other markers.

Applications will be considered non-responsive and will not be reviewed if they propose:

  • To develop tools or approaches that use organisms other than large brain mammals or non-human primates, except in the UG3 phase where some feasibility studies may be warranted.
  • Studies to develop transgenic models of disease.
  • Projects whose main goal is to address a scientific question(s).

The UG3/UH3 is a two-phased award. The UG3 phase should be focused on the development of the tool, method, or approach, including demonstrating feasibility for use in humans. Each phase will be milestone driven and only those projects attaining the UG3 milestones have potential to progress to the UH3 phase. The UG3 phase supports feasibility, safety, biocompatibility testing and optimization of tools in large brains (e.g., sheep, pig) as well as non-human primates and humans if possible. The initial UG3 phase could support non-clinical testing toward filing of an IND/IDE for a significant risk (SR) study or to obtain IRB approval for a non-significant risk (NSR) clinical trial. Only those UG3 projects that have met specific criteria (see below) will transition to the subsequent UH3 phase after NIH administrative review. The UH3 phase could support a small clinical trial. The UH3 phase supports testing/validation of the tools in efforts to evaluate the performance, sensitivity, and selectivity of the tool(s) in humans or non-human primates.

  1. UG3 Tool Development Phase.  The UG3 Phase of this FOA supports milestone-driven tool development. The applicant should describe the specific tool, its potential, and what developments are required to translate the tool to larger animal or human brains. Tools that meet the scientific milestones and feasibility requirements will be eligible for transition to the second UH3 stage pending NIH administrative review, availability of funds, and programmatic balance as described below. For applications wishing to perform human studies in the UH3 phase, a detailed regulatory pathway pre-clinical testing plan with commensurate milestones must be included. Regulatory milestones include pre-submission meetings where pre-clinical testing is discussed with the FDA as well as further pre-IND/IDE meetings. Relationships with industry partners that may be necessary for clinical testing should be described. An IND/IDE will be required for the UH3 transition prior to the start of any clinical trials.
  2. UH3 Tool Evaluation and Validation Phase.  The UH3 Phase of the FOA will support milestone-driven evaluation and validation of tool performance. This phase should evaluate the tool’s capability as well as performance in the context of large brains. Capability can be demonstrated by the ability to target, manipulate, record, or otherwise impact brain circuitry in a measurable fashion. Performance should be evaluated by the tool’s stability, safety, reliability, or other similar metrics tested within a large brain construct. Validation should extend the tool’s use outside of the primary investigators’ lab to assess performance across multiple constructs. Different variants within a species and trans-species testing may be used to demonstrate generalizability. While not required for this FOA, applications that propose independent evaluation of the tool by outside laboratories will be prioritized. For applications proposing clinical studies, detailed milestones focusing on patient recruitment, retention, safety, and performance metrics should be included.

Applicants are strongly encouraged to consult the appropriate Scientific/Research Contact, listed below, to discuss the alignment of their proposed work with BRAIN Initiative Program goals.

Milestones and Go/No-Go Criteria

Because tool/technology development in the UG3 phase is likely to be high risk, it is anticipated that there will be attrition of some projects after the development phase (UG3). Objective milestones of success and go/no-go rules for tool optimization/validation will be required and both should have quantitative criteria associated with them (see Section IV.2 for details). Milestones are defined as annual goals while the Go/No-Go criteria are defined as the major goals to be met to inform the UG3 to UH3 transition.

Specific Go/No-Go criteria should be detailed at the UG3 to UH3 phase transition. Projects that seek to test first-in-human during the UH3 phase should have regulatory approval as their major Go/No-Go criteria. Projects that will focus on animal-model validation in the UH3 should detail specific performance metrics to be obtained in the UG3 phase prior to transition.

NIH program staff will contact the applicant to discuss and negotiate the proposed milestones and any changes recommended prior to funding the application. The final agreed upon and approved milestones will be specified in the Notice of Award (NoA). Progress towards achievement of the final set of milestones will be evaluated by NIH program staff. Program staff may involve independent consultants with relevant expertise. If justified, future milestones may be revised based on data and information obtained during the previous project period. If, based on the progress report, a funded project does not meet the milestones, funding for the project will be discontinued. In addition to milestones, the decision regarding continued funding will also be based on the overall robustness of the entire data package that adequately allows an interpretation of the results (regardless if they have been captured in the milestones), overall progress, portfolio balance and program priorities, competitive landscape, and availability of funds.

NIH encourages increasing the rigor and reproducibility of observed results. In some cases, conducting additional critical experiments will be important for NIH to have confidence in making a funding decision. Therefore, program staff may suggest modification or additional experiments that need to be conducted prior to or during the award as an additional milestone(s). In most cases, these studies will be supported by additional funds.

UG3 phase to UH3 phase transition:

An administrative review will be conducted by program staff, with potential input by independent consultants, to decide whether a UG3 phase project will be transitioned into the UH3 phase based on the:

  • successful achievement of the defined milestones for the UG3 phase of the project;
  • likelihood of success in further pre-clinical/clinical validation testing;
  • competitive landscape;
  • program balance;
  • availability of funds;
  • for significant risk studies, submission of an IND/IDE for the clinical trial with documentation of final or conditional approval of the IDE from the FDA;
  • IRB approval(s), if necessary;
  • for clinical studies, submission of the final clinical protocol and supporting documents to NIH for administrative review, and notification of approval by NIH;
  • feedback on activities involving human subjects obtained from relevant NIH human subject protection bodies;
  • agreement on updated timeline, milestones and budget for the UH3 phase

Appeals of the transition decision will not be accepted.

Deadlines:  October 9, 2018; September 26, 2019 and September 28, 2020 (letters of intent are due 30 days prior to the deadline)


Filed Under: Funding Opportunities