Non-invasive tools to control and profile gene expression

Objective

This funding opportunity supports research into non-invasive methods for reading and controlling gene expression in living cells and tissues. We are seeking proposals that develop, validate, or improve light-, sound-, magnetic-, chemical-, or thermally responsive systems for switching genes on and off, as well as sequencing and transcript-readout approaches that minimize tissue damage, biopsy requirements, or perturbation of the underlying biology.

Direct electroporation, viral integration, and invasive sampling have driven much of the progress in functional genomics, but they limit how often, how widely, and in which tissues experiments can be performed. Optogenetic, chemogenetic, focused-ultrasound, and magnetogenetic systems, together with cell-free DNA, exosomal RNA, live-cell extraction (e.g., Live-seq), and in vivo spatial transcriptomics, and in situ sequencing methods, point toward a more flexible toolkit. This RFP supports work that improves the specificity, kinetics, dynamic range, and safety of such systems, and that produces clean datasets the broader community can build on.

Eligible projects should be scientifically grounded, with clear hypotheses and well-designed experimental approaches drawing on molecular biology, biophysics, neuroscience, bioengineering, and computational analysis. The goal is to generate proof-of-concept results that move non-invasive control or profiling of gene expression closer to routine experimental and translational use.

Suggested Proposal Topics

Applicants are not limited to these topics, but should demonstrate how their proposal advances non-invasive control or readout of gene activity in living systems.

Optogenetic, chemogenetic, magnetogenetic, or focused-ultrasound systems for spatially and temporally precise control of gene expression in defined cell populations
Light-, sound-, or chemically inducible CRISPRa, CRISPRi, base-editing, or transcription-factor systems with quantified leakiness, dynamic range, and reversibility
Non-viral, transient delivery of switchable transcriptional regulators or RNA-based controllers (e.g., toehold switches, riboswitches, circular RNAs)
Liquid-biopsy approaches (cell-free DNA, cell-free RNA, exosomal transcripts) that report on tissue-specific gene expression without the need for tissue sampling
In situ or in vivo sequencing methods that resolve transcriptional state at single-cell or spatial resolution with minimal tissue disruption
Wearable, implantable, or imaging-based readouts that quantify expression of reporter or endogenous genes longitudinally in the same animal or human
Computational and statistical methods that connect non-invasive readouts to underlying transcriptional or regulatory states with calibrated uncertainty
Reproducibility, benchmarking, and standards work that compares non-invasive control or readout systems on shared tasks and datasets

Funding Details

10,000 USD seed funding will be awarded by the ResearchHub Foundation to fully fund one selected proposal in this initial round. In addition, all eligible proposals will have the opportunity to receive support through community crowdfunding. In previous rounds, additional projects were successfully funded through this mechanism. This initial $10,000 seed award is designed to support focused, high impact pilot studies, while larger scope proposals may be supported through additional donor contributions and community crowdfunding.

See ResearchHub’s funding guide for researchers to learn more about the process.

Eligibility Criteria

Applicants must (1) verify identity and (2) authenticate ORCID on their ResearchHub profile.
There are no restrictions based on the applicant’s country of residence.
PhD students, postdocs, independent researchers, and faculty are eligible.
Collaborative and interdisciplinary teams (e.g., neuroscience + engineering + computer science) are strongly encouraged.
Projects should be feasible within a proposed 6–12 month timeframe using available or obtainable infrastructure.
Proposals involving human tissue or stem cells must demonstrate appropriate ethical oversight and institutional approval.

Disclaimers and Open Science Commitment

Preregistration: All selected applicants must pre-register their study protocol on ResearchHub to be considered for funding.
Fully funded proposals will be eligible to be published as ResearchHub Registered Report (RRR) in the ResearchHub Journal (more info).
Open-Access Data Sharing: By participating, applicants agree to share all data generated through this research in an open-access repository. This ensures transparency and facilitates the scientific community’s engagement with the findings.
Preprint: Researchers are encouraged to upload a preprint of their findings on ResearchHub.
Progress Updates: Researchers are encouraged to share regular updates via the “Updates” tab and may receive RSC tips for updates shared.

Questions

For questions, please post directly in the “Conversation” tab of the funding opportunity on ResearchHub or contact Attila Karsi (attila.editor@researchhub.foundation) or Scott Nelson (scott.editor@researchhub.foundation)

Non-invasive tools to control and profile gene expression

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