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How could we scan DNA for mutations in real-time in vivo?

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jnikola
jnikola May 01, 2022
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Introduction
DNA mutations are changes in a genome caused by DNA replication errors, viral infections, or exposure to mutagens . These changes are the underlying mechanisms of many diseases, disorders, or processes that negatively affect the human lifespan. There are three basic types of mutations: base substitutions, deletions and insertions, which can cause silence, missense, nonsense, frameshift insertion and frameshift deletion changes in the genome sequence.
The ask
Is there a way how we can track these changes in vivo in real-time?
Why?
  • live tracking of errors
  • prevention of diseases
  • better understanding of the DNA repair mechanisms
Some inspirational ideas:
  • track the activity of enzymes involved in DNA replication
  • track the activity of enzymes involved in damage detection
  • track the activity of enzymes involved in DNA damage repair
  • directly track every nucleotide incorporation by non-harmful dies

[1]https://www.genome.gov/genetics-glossary/Mutation#:~:text=Definition,mutagens%20or%20a%20viral%20infection.

dna damage trackingreal time mutation detection
2
Creative contributions

A nanosensing mechanism that stays in the body and scans for mutation related activities

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Subash Chapagain
Subash Chapagain May 03, 2022
Disclaimer: This is all theoretical; works in principle kind of futuristic idea. But not undoable given the tools we have today in biomedical science. In this challenge, I had questioned whether we can design a nanomachine that can sense a specific virus (or any other pathogen) markers in the body, and if we are to design such a nano-sensing method, what could be the things we had to figure out first? Expanding the same idea to mutation detection, would it be possible to develop a nanodevice that circulates in the body and keeps track of mutations? What could be the processes/markers/pathways it could use as proxies for mutation? Like J. Nikola proposed, such a system could be engineered, in theory, to detect the activity of DNA repair proteins, and other enzymes involved in cellular fidelity during replication. However, like Michaela D rightly pointed, to detect these activities in an organismal level might be pretty challenging. However, what if we could engineer some stationary, implantable devices with nano sensing capacity in certain organs of the body that constantly sample the blood cells for markers related to DNA damage? Can we envision a wearable device that we can plug-and-play just for the purpose of detecting possible DNA mutation related activities? What would such a device be like? What processes would it look for? For example, active detection of the level of mRNA transcripts, active detection of ROS levels. What else can we think of?
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jnikola
jnikola2 years ago
Thank you Subash Chapagain for the contribution. We discussed a similar approach in this idea. Although your proposed stationary implantable devices would be great to scan the blood cells for markers, what we need is an overall DNA mutation detection system. It shouldn't be stationary, but applicable to the whole body, since we are interested in mutations in the whole body. It should search exactly mutation events or events that can tell us about the mutation that happened. In that sense, I think detection of mRNA transcripts could be the way, while ROS would probably be more informative of the ongoing stress, not exactly mutations that happened.
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Subash Chapagain
Subash Chapagain2 years ago
J. Nikola To design something that is biocompatible, motile, non-immunogenic and with significantly long half-life that it circulates in the body all the while detecting mutations seems like a herculean task. Rather than depending on one single device, I think the better approach would be to use an array of biomarkers. For instance, try and detect not just mutations in the individual nucleic acid molecules (or chromosomes), but to detect both the causes and effects of mutations: for example ROS and DNA repair enzymes. An overall DNA mutation detection system still seems like too much to ask from one single device for the constraints that we have discussed in this thread. Hence, I propose a combinatorial approach using both direct detection as well as detection via proxies.
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Scanning live cells for the occurring mutations using Live-sec

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jnikola
jnikola Sep 20, 2022
How would it work?
  1. Collection of cells from the tissue of interest
  2. Preregistering individual cells using genetic "barcodes"
  3. Extraction of the cellular component of interest (cytoplasmic mRNA) of single or multiple cells using an established single-cell extraction protocol
  4. Sequencing of the mRNA
  5. Repeating the process after specific stimuli (treatment, radiation, differentiation)
IMPORTANT NOTE:
*This method can be used to analyze live cells without serious perturbations, but still requires cell collection and extraction using microscopy. In order to make it applicable as wearable technology for everyday mutation scanning, we need to work out how to apply it directly to in-body cells.
*Different barcodes should be used in wearable mutation scanner so we don't introduce errors in the live cell genome.
Background
Typical single-cell sequencing requires cell collection, cell lysis, extraction of the DNA or RNA and sequencing. In other words, you must sacrifice the cells to see what's happening inside. However, a recent paper published in Nature showed that cells do not necessarily need to be killed in order to find out what's happening on a gene level. They introduced a single-cell transcriptome profiling based on fluidic force microscopy (fluidic FM).
They managed to stratify different cell types and states without major cellular perturbations. They also profiled transcriptomes of individual macrophages before and after lipopolysaccharide stimulation. Although you probably thought they did it on a cell-wide level, no, they preregistered transcriptomes of individual macrophages that were subsequently monitored by time-lapse imaging after LPS exposure and in that way - recorded the transcriptome change of an individual cell before and after treatment!
Read this interesting paper for more details!

[1]Guillaume-Gentil O, Grindberg RV, Kooger R, Dorwling-Carter L, Martinez V, Ossola D, Pilhofer M, Zambelli T, Vorholt JA. Tunable Single-Cell Extraction for Molecular Analyses. Cell. 2016 Jul 14;166(2):506-516. doi: 10.1016/j.cell.2016.06.025. PMID: 27419874.

[2]Chen, W., Guillaume-Gentil, O., Rainer, P.Y. et al. Live-seq enables temporal transcriptomic recording of single cells. Nature 608, 733–740 (2022). https://doi.org/10.1038/s41586-022-05046-9

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General comments

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Shubhankar Kulkarni
Shubhankar Kulkarni2 years ago
It would be great when we would be able to do that. I initially thought of using a dye or a molecule that targets specific locations and then using some kind of illumination device to visualize it. The current problem is visualization, I think. Even if your marker reaches the mutation, the DNA is wrapped with multiple layers. If you want the method to be non-invasive, the layers start from the skin, other tissues, desired cells, their membranes, and finally, the nucleus. Even if you reach the DNA, finding the mutations is a daunting task. This is because DNA is a lot to search into and secondly, everything is constantly moving in terms of both, 3D rotation of molecules and change in their location across the nucleus. Also, the cells may shift a bit. If you are looking into blood cells, they are moving constantly and very fast.
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Subash Chapagain
Subash Chapagain2 years ago
Shubhankar Kulkarni This was what I was thinking about as well. Even if detecting a mutation could be possible, but how do we deal with the problem of detecting the detection itself (say META-DETECTION)? Most of the signal transduction that we use in laboratory uses dyes and reagents that are potentially toxic to the cells. If we are to develop a mutation-detection system, what kind of dye/reporters would we be using? How do we deal with the issues of biocompatibility? What about the half-life/stability? There are so many questions to figure out.
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Michaela D
Michaela D2 years ago
Subash Chapagain and Shubhankar Kulkarni another important factor to take into account is what we would consider a harmful mutation vs a SNP (Single Nucleotide Polymorphism), which is a neutral variation. Even if we managed to visualize every change in the DNA in every cell (different cells will have different changes), most of the signal we would get would be SNPs. All this information would have to be processed to evaluate what is dangerous.
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Subash Chapagain
Subash Chapagain2 years ago
Michaela D Indeed. The challenge beyond detection itself is to address the overwhelmingly higher ratio of signal to noise due to SNPs. Some SNPs might cause severe defects (if they cause frameshifts, for eg) whereas most of them might be simply silent. This presents altogether a different challenge. However, one particular instance where such a detection system could be extremely useful, as far as I can think, is to determine the intra-host evolution of pathogens (mostly viruses). What if we could detect not the mutations of the host cells, but mutations that a viral pathogen is undergoing within the host?
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Michaela D
Michaela D2 years ago
Are you referring to live mutation detection in a human? As far as I know, the closest you can get to that is isolating cells from different tissues and then analyzing their DNA. However, it would not be possible to analyze the DNA of billions of cells in vivo, and, I do not think you can analyze the DNA of any number of cells without killing them first.
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