Can mRNAs modify our DNA (publication misunderstanding)?

Question

I am a bit confused about a publication (few month old) which seems to say that RNA can modify our DNA. The publication is the following one.

Unfortunately, I am not a medical expert (and even more in english :D) so I'd like opinions for more expert persons ;). From my understanding, in some cases, the SARS-COV-2 RNA can modify our DNA :

We show here that SARS-CoV-2 RNA can be reverse-transcribed and integrated into the genome of the infected cell and be expressed as chimeric transcripts fusing viral with cellular sequences.

All three methods provided evidence that SARS-CoV-2 sequences can be integrated into the genome of the host cell.

If my understanding is true, why is there a consensus saying that mRNA cannot go into the DNA ?

Thanks in advance,

Nicolas

Answer 1

The short answer is maybe, but rarely, and the whole Covid virus has never been seen to integrate into the cell's DNA intact. Any integration requires "helper" molecules not found in the Covid virus, and only very rarely found in a normal cell.

It's been known for many decades that RNA in a cell can be converted into DNA and integrated into the cell's genomic DNA. This is extremely rare except under certain conditions. For example, a class of viruses (including HIV) called "retroviruses" carries an enzyme called reverse transcriptase or RT that the viruses use to convert their RNA genome into DNA and "hide" by splicing that into the cell's own DNA. Covid does NOT have such an enzyme.

However, during evolution, our cells have picked up many small DNA elements ("jumping genes" or transposons), many of which "hop" by reverse-transcribing their transcript and inserting that new DNA somewhere in the cell's DNA. They continue to "hop" to this day, rarely. Occasionally, they make an error and convert some of the other mRNA in the cell into DNA and insert it into the genome. LINE1 elements in particular make up almost 20% of our cellular DNA, so the paper's authors tried to see if any LINE1 elements were able to (rarely) incorporate Covid fragments into a cell's DNA.

Greatly simplified, the authors tried to answer the following questions:

1. Can laboratory cells which have been engineered to make lots of the LINE1 transposase, then infected with Covid, end up with fragments of Covid virus in their DNA?

2. Can "normal", non-engineered laboratory cells infected with Covid, end up with fragments of Covid virus in their DNA?

3. Do any patient samples from Covid-infected patients show any fragments of Covid virus in their cellular DNA?

The method the authors used to check this was to massively sequence mRNAs from cells, and look for any that had normal cellular gene sequences spliced onto Covid sequences. Their reasoning was that such chimeric transcripts must represent genes with reverse-transcribed Covid DNA spliced into the genomic DNA of the gene, and so appearing in the gene's RNA transcript. It turned out there was a big technical problem with this (hence the wishy washy conclusions of the paper) - the sequencing sample preparation process will also rarely splice two mRNA sequences together even if they were not spliced in the cell. However, that artificial process tends to almost always only splice two "antisense" strands, while the LINE1 process should have no preference between sense and antisense. Thus, the authors reasoned that if they were finding only antisense/antisense that could be an artifact, while significant amounts of antisense/sense splices would indicate real splices from the genomic DNA.

The answers they inferred were roughly:

1. Yes, artifcially expressing lots of LINE1 tranposase resulted in detectable integration of partial Covid virus sequences in the cellular DNA.
2. With more normal laboratory cells, they found many fewer integrated Covid virus fragments, but still found some.
3. With patient samples, there were many additional technical problems; they think they found some Covid fragments integrated in cells from 1 patient, but are not nearly as confident with that result as for (1) and (2).

In any case, the integrated Covid sequences they found seem to be only fragments of the virus (although their techniques could not be fully sure on this); they never found a whole virus integrated into any cell.

As a practical matter, the "consensus" is correct, but given billions of people and quadrillions of Covid viruses, there might be a few outliers.

Paper ref: Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues PNAS May 25, 2021 118 (21) e2105968118; https://doi.org/10.1073/pnas.2105968118

LINE1 review: "LINE-1 Elements in Structural Variation and Disease" Annu Rev Genomics Hum Genet. 2011; 12: 187–215. doi: 10.1146/annurev-genom-082509-141802 Author's manuscript freely downloadable from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124830/pdf/nihms606127.pdf

Related Question explaining why another paper is NOT reliable: " Intracellular Reverse Transcription of Pfizer BioNTech COVID-19 mRNA Vaccine BNT162b2 In Vitro in Human Liver Cell Line by Alden et al. ( Curr. Issues Mol. Biol. 2022, 44(3), 1115-1126; "

Update Apr 2022: Here are two additional papers comments that are highly relevant:

journals.asm.org/doi/10.1128/JVI.00294-21"Host-Virus Chimeric Events in SARS-CoV-2-Infected Cells Are Infrequent and Artifactual"

https://doi.org/10.1073/pnas.2109066118"No evidence of SARS-CoV-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues"

Answer 2

Answering on

"If my understanding is true, why is there a consensus saying that mRNA cannot go into the DNA ?"

I highlighted several quotes from the paper's references that may answer your question:

Akira Shimizu, Characterisation of cytoplasmic DNA complementary to non-retroviral RNA viruses in human cells, 2014: "...Thus, the genetic information of the non-retroviral RNA virus genome can flow into the DNA of mammalian cells expressing LINE-1-like elements." That study was on "infection of various human cell lines and primary fibroblasts with the vesicular stomatitis virus (VSV)".

Geuking et al., Recombination of Retrotransposon and Exogenous RNA Virus Results in Nonretroviral cDNA Integration, 2009: "We found that illegitimate recombination between an exogenous nonretroviral RNA virus, lymphocytic choriomeningitis virus, and the endogenous intracisternal A-type particle (IAP) retrotransposon occurred and led to reverse transcription of exogenous viral RNA."

Weiss/Kellam, Illicit viral DNA,, Nature volume 390, pages235–236 (1997):

"More than 20 years ago, the late Victor Zhdanov (...) claiming that complementary DNA copies of RNA viruses such as measles and polio occurred in retrovirus-infected cells. The observations raised eyebrows at the time, because promiscuous cDNA synthesis seemed to run counter to everything known about viral replication. But the data were neither confirmed nor refuted, and were soon forgotten."

These quotes show that Crick's dogma - from DNA to RNA, with the exception of retro-viruses - still holds. The fact that the study you refer to was severely scrutinized and its validity questioned by peer review seems to lay proof that the dogma you speak of is valid even today.

To sum up: Crick's dogma still holds (and will), and the study in question contradicts that rule in its results.

Note: See Geuking et al. in the context of the quote about distinguishing between retro-transcription and integration into the genome. These authors speak of, in particular, "recombination" between non-retro-virus and retro-transcriptional elements termed endogenous virus (virus-viral recombination). Crick's rule, in a restricted sense, may not cover integration of DNA into the genome, and, conversely, it may play down the role of non-genome DNA, external or episomal.