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Pilot Grant Program

Application Information

RNA Bioscience Initiative — Pilot Grant Programs

Fall 2022 

The RNA Bioscience Initiative (RBI) at the University of Colorado Anschutz Medical campus seeks to support RNA biology research to enhance basic science, translational, and clinical studies. Towards that goal, the RBI requests applications for three Pilot Grant Programs available for summer 2022.  Pilot Grant Program descriptions, deadlines, and application guidelines are provided below. We describe new capabilities in the RBI and hope applicants will apply these approaches creatively to address new and exciting questions.

Fall 2022 Pilot Grant Program

1.  Long read RNA sequencing (Oxford Nanopore)*

2.  Ribosome profiling*

3.  mRNA packaging in lipid nanoparticles*

 To apply for this RFA, you must express your interest using this "Letter of Intent" form by August 15,  2022. 

*detailed descriptions can be found at the bottom of this page

Program Deadlines

Letter of Intent Due:                                                                                 August 15, 2022

Application Due:                                                                                      September 19, 2022                      

Decisions/Results Communicated to Applicant:                                  October 15, 2022

Funding of Successful Applicants Begins:                                           November 1, 2022


Principal Investigators (PIs) for awards must have faculty appointments at the University of Colorado Anschutz Medical Campus and hold the rank of Assistant, Associate or Full Professor, Research Professor or Instructor. Postdoctoral trainees are also encouraged to apply, provided that a faculty sponsor includes a Letter of Support for the trainee in the application. 

Proposals may not describe the same specific research that is funded by other sources during the grant period.

Application Requirements and Procedures

Step 1.   All applicants must submit a Letter of Intent using form by August 15, 2022.

Step 2.   Full applications must be submitted no later than September 7, 2022 as a single PDF file. Please label the file as PIname.ProposalTitle.GrantProgramName.pdf and include the following materials:

a.  A brief cover letter from the PI containing the title of the proposal and describing the value of the project and a statement that all collaborators listed on the application agree with the proposal.

b.  A proposal consisting of no more than 1 page in standard NIH grant application format. Recommended, but not required, organization for proposals include: specific aims, background and broader impact, and research plan.

c.  NIH formatted Biosketch for the PI or PIs

An electronic online submission link will be provided to all applicants that have submitted a Letter of Intent.  After your submission is complete, you will receive a confirmation receipt by email.  

Eligibility and appropriate project support will be determined by the RNA Bioscience Informatics Fellows and their faculty supervisors, Jay Hesselberth and Neel Mukherjee. The application must have RNA-related research as its focus and currently not be funded by other sources.  These grants do not provide monetary budgets.

Review Criteria

 A peer review panel composed of faculty with a range of expertise will be responsible for award decisions, evaluating eligible applications competitively. The primary factors in award decisions will be the scientific merit of the proposed research, the likelihood to “seed” eventual R series-level or equivalent extramural funding, and the long-term promise of the proposed research. No critiques will be provided to applicants; applicants will be informed with a review response of “Funded”, “Not funded” or “Not eligible”.

Grant Recipient Requirements 

Those receiving a grant will be expected to become active members of the University of Colorado RNA research community. Both the PIs and those working on funded projects are expected to:

•  For all bioinformatics support, include the RBI fellows as authors on publications that result from the award

•  Acknowledge RBI Support in publications

•  Self-identify as a member of the RBI on all publications emanating from the work supported by this grant

•  Use awarded funds solely to support the RNA research described in their proposal

•  Provide a progress report 30 days after the end of funding year

•  Contribute a presentation on research accomplishments at a future symposium hosted by the RBI

•  Participate in the “An Evening with RNA” series held alternatively at the Anschutz and Boulder Campuses

•  Provide follow-up information regarding the long-term impact of the award(s) on your overall research program and funding

Technology Descriptions

1.     Long read RNA sequencing.

Nanopore sequencing on Oxford Nanopore Technology MinION and PromethION platforms enables high throughput sequencing of RNAs and can be used to define full length mRNA splicing isoforms, estimate their polyA tail length, and catalog RNA modifications (e.g., m6A, pseudouridine) with single-base precision (PMID 34750572, 34559589). In addition, advances enable analysis of tRNA populations, providing new insight into metabolic states and translational status. A typical experiment consists of RNA isolation from replicate conditions (done by the investigator), followed by a library preparation and direct RNA analysis by nanopore sequencing (PMID 29334379). Alternatively, the RNA can be converted to cDNA, which provides better performance for analysis of splicing isoforms. cDNA generated via the 10X Genomics Chromium platform can also be nanopore sequenced, enabling the analysis of long read single cell transcriptomic data.

2.     Ribosome profiling.

Ribosome profiling (or “Ribo-seq”) enables precise positioning of ribosomes on mRNAs in cells, and can be used to ask questions about ongoing translation. A typical Ribo-seq experiment enables positioning of ribosomes along mRNA transcripts, providing a measure of translation efficiency per transcript and revealing fundamental aspects of mRNA translation regulation (PMID: 30037969). Moreover, Ribo-seq is a powerful approach to discover non-canonical (unannotated) peptides and antigens that are potential targets for immunotherapy (PMID: 34663921, 34663921).

A typical experiment involves cell culture and flash-freezing the samples (done by the investigator), followed by cell lysis, collecting an aliquot for RNA-seq, isolation of ribosome-mRNA footprints, library preparation, and sequencing (done by the RBI). A minimum of 2 million cells are required and the experiment will need to be planned in advance with RBI consultation.

3.     mRNA packaging in lipid nanoparticles.

mRNA packaging in lipid nanoparticles (LNPs) enables in vivo delivery and translation of mRNA and were used effectively in the COVID-19 mRNA vaccines from Pfizer/BioNTech and Moderna. The RBI has established a pipeline for mRNA design, synthesis, and packaging of mRNA into LNPs, enabling new approaches for vaccination or therapeutic mRNA delivery. The RBI is particularly interested in projects involving delivery of therapeutic antibodies via mRNA-LNPs or use of mRNA-LNPs to generate immune responses to traditionally challenging antigens (e.g., membrane proteins). Typical experiments involve mRNA design and synthesis, and LNP packaging yielding material sufficient for injection of ~15 mice, depending on delivery route, enabling pilot experiments involving a few treatment / control groups with replicates. Investigators will be responsible for measuring in vivo functionality of the mRNA LNPs, involving e.g. flow cytometric detection of encoded antigens in a tissue of interest, or functional assays confirming the effect of the delivered mRNA. Alternatively, the RBI can provide support for single-cell mRNA analysis to identify e.g. cell types impacted by mRNA delivery.