Cell Data Recorders Using NapDNAbp for Stimulus History

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Solution Overview

Problem

Current technologies lack effective methods to record a cell's history, including the strength and duration of endogenous or exogenous stimuli, in a multiplexable, durable, and minimally perturbative manner, which is crucial for understanding cellular aging, disease emergence, and cellular state transitions.

Innovation Solution

The development of a cell data recording system using nucleic acid programmable DNA binding proteins (napDNAbp) or fusion proteins with nucelic acid editing domains, which induce recordable changes in cellular DNA in response to stimuli, allowing for the simultaneous recording of multiple cell states and the measurement of stimulus strength and duration using sequencing technologies.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If digital memory devices are used to store cellular information, then information storage is achieved in distinct binary states, but the ability to record stimulus strength and duration is lost

Engineering Contradiction:

Improvestimulus strength and duration recordingVSAvoidrecording capability

Core Design Contradiction:

Measurement precisionVSAdaptability or versatility

Solution Approach 1:

The patent transforms the recording system from binary digital states to analog continuous states by changing the measurement parameter from discrete on/off signals to continuous DNA methylation levels. The epigenetic marks on DNA can exist in varying degrees of methylation, allowing the system to encode stimulus strength (amplitude) and duration as continuous parameters rather than discrete binary values, thereby achieving precise measurement of stimulus characteristics while maintaining recording versatility

Inventive Principle:

Principle #35Parameter changes

2Measurement precision

If sequencing technologies are used to measure cellular DNA changes, then single-cell resolution is achieved, but dependence on large cell populations is eliminated

Engineering Contradiction:

Improvesingle-cell resolutionVSAvoidcell population requirement

Core Design Contradiction:

Measurement precisionVSQuantity of substance

Solution Approach 1:

The patent uses DNA as a stable copy or record of cellular history that can be extracted and sequenced without requiring large populations of live cells. The epigenetic marks serve as permanent copies of stimulus exposure history that can be analyzed through DNA sequencing techniques, allowing single-cell resolution studies with minimal cell numbers since the information is preserved in the genetic material itself rather than requiring ongoing cellular activity

Inventive Principle:

Principle #26Copying

3Duration of action of stationary object

If napDNAbp or fusion proteins are used to induce DNA changes, then permanent cellular marks are created, but cellular perturbation is minimized

Engineering Contradiction:

Improvemark durabilityVSAvoidcellular perturbation

Core Design Contradiction:

Duration of action of stationary objectVSObject-affected harmful factors

Solution Approach 1:

The patent uses epigenetic modification enzymes (such as DNA methyltransferases or demethylases) as intermediaries that create stable marks on DNA without permanently altering the genetic sequence. These enzymes act as mediators that can be recruited to specific genomic loci through guide RNAs, where they catalyze reversible epigenetic changes that serve as durable records of stimulus exposure. The intermediaries enable permanent marking through epigenetic inheritance while minimizing cellular perturbation because the underlying DNA sequence remains unchanged and the modifications can be reversed if needed

Inventive Principle:

Principle #24Intermediary (Mediator)

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

This system enables the recording of cellular history with high fidelity, allowing for the analysis of cellular states over time and the detection of stress exposures, which can provide insights into aging and disease processes without significantly perturbing the cell.

Implementation Method 1

a nucleic acid programmable DNA binding protein (napDNAbp) (e.g., a Cas9 domain) or a fusion protein comprising a nucleic acid programmable DNA binding protein and a nucelic acid editing domain

Methodology Applied

Scientific EffectNucleic acid base pairing:

Implementation Method 2

induce changes in cellular DNA (e.g., double-strand breaks, nucleobase editing) in response to a stimulus or change in cell

Methodology Applied

Scientific EffectDNA double-strand break:

Implementation Method 3

induce changes in cellular DNA (e.g., double-strand breaks, nucleobase editing) in response to a stimulus or change in cell

Methodology Applied

Scientific EffectNucleobase editing:

Implementation Method 4

Certain embodiments of these cell data recorders employ sequencing technologies (e.g., high-throughput sequencing) to measure readout (e.g., changes in cellular DNA)

Methodology Applied

Scientific EffectDNA sequencing:

Data Source

PatentUS20250136960A1Cell data recorders and uses thereof

Publication Date: 2025.05.01 THE BROAD INST INC

AI summary

Described herein are compositions, vectors, cells, methods, and kits that provide cell data recorder systems for recording cell states. The cell data recorder systems allow for the recording of both the presence and duration of one or more stimuli in a programmable, reproducible, and multiplexable manner. These cell data recorder systems employ a nucleic acid programmable DNA binding protein, such as a Cas9 nuclease, or a fusion protein comprising a nucleic acid programmable DNA binding domain and a nucleic acid editing domain to introduce recordable changes in the genome of a cell or in a plasmid within the cell.