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Paweł Krawczyk

@pakraw.bsky.social

120 followers 160 following 29 posts

Bioinformatician, postdoc at Laboratory of RNA Biology @DziembowskiLab @IIMCB_Poland Opinions are my own

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Paweł Krawczyk @pakraw.bsky.social · Apr 17

🎉 Incredibly proud to share my first-author paper in
@nature.com! Heartfelt thanks to my mentor @andrzejdziembowski.bsky.social and the brilliant team at DziembowskiLab at @iimcb.bsky.social. More details in the 🧵below ⬇️

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Reposted by Paweł Krawczyk

iimcb.bsky.social @iimcb.bsky.social · Apr 29

Scientists from the IIMCB described a new mechanism that improves the efficiency of mRNA-based therapies. The research findings will facilitate the development of novel therapeutics against cancers and infectious diseases.

#NaturePublication #mRNA #RNAResearch #IIMCB #FunduszeUE

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Reposted by Paweł Krawczyk

Nature @nature.com · Apr 21

Nature research paper: Re-adenylation by TENT5A enhances efficacy of SARS-CoV-2 mRNA vaccines

https://go.nature.com/4cAPx85

Re-adenylation by TENT5A enhances efficacy of SARS-CoV-2 mRNA vaccines - Nature

Upon intramuscular administration, COVID-19 mRNA vaccines are primarily taken up by macrophages, in which the cellular machinery extends their poly(A) tails, thereby increasing mRNA stability and translation, providing an explanation for the efficacy of these vaccines.

go.nature.com

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Reposted by Paweł Krawczyk

Vanessa Linke @massspecvanili.bsky.social · Apr 18

Super excited to share this as my first post with the 🦋 world! In my first co-correspondent article, we (@Mayra Borrero @Agnieszka Chacińska @IMOL Institute) look at the roles of lipids in mitochondrial protein import complexes (spoiler: there are plenty!) &call for methods (spoiler: there are few!)

Trends in Biochemical Sciences @cp-trendsbiochem.bsky.social · Apr 18

Available online - the Forum "#Lipids: emerging actors in mitochondrial protein import" from Vanessa Linke, Agnieszka Chacinska, et al.

#ProteinLipidInteractions #MembraneComplexes #LipidScrambling

Read it here: authors.elsevier.com/a/1kxPM_M0e4...

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Paweł Krawczyk @pakraw.bsky.social · Apr 17

I would really like to know 🙂 we do not have the exact mechanism which is crucial for better understanding. My guess is that the unfolded protein response (Ed Figure 6 a-b in the manuscript) is somehow connected. But we don't have a definitive answer yet.

Paweł Krawczyk @pakraw.bsky.social · Apr 17

It's about spatial distribution. TENT5A is anchored to the ER membrane, thus being close to the RNAs being translated there. In our previous works we were unable to find any specific sequence motifs in TENT5 mRNA substrates.

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Paweł Krawczyk @pakraw.bsky.social · Apr 17

I'm grateful for this milestone in my career - an experience that’s shaped me both scientifically and personally. Looking ahead with excitement to the next chapter and new opportunities to grow.

Paweł Krawczyk @pakraw.bsky.social · Apr 17

🙏 Huge thanks to everyone involved - our incredible team (DziembowskiLab @iimcb.bsky.social), collaborators (University of #Warsaw #UW, Medical University of Warsaw #WUM, #IBB #PAS), and funding agencies (@erc.europa.eu, @ncn.gov.pl, #FNP, #PORT #Łukasiewicz). (20/n)

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Paweł Krawczyk @pakraw.bsky.social · Apr 17

🇵🇱 Notably, this represents a landmark achievement as likely the first @nature.com article of the 21st century conducted entirely in #Polish laboratories! (19/n) #PolishScience

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Paweł Krawczyk @pakraw.bsky.social · Apr 17

This publication represents the culmination of a long,challenging journey.We initially posted our findings as a #preprint on @biorxivpreprint.bsky.social in December 2022.The rigorous review process demanded additional experiments,which significantly strengthened our final manuscript.(18/n)

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Paweł Krawczyk @pakraw.bsky.social · Apr 17

These findings have immediate implications for therapeutic mRNA design: optimization of ER-targeting signals could enhance TENT5A-mediated re-adenylation, potentially improving vaccine efficacy and reducing dosage requirements. (17/n)

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Paweł Krawczyk @pakraw.bsky.social · Apr 17

Notably, this effect was specific to #mRNA vaccines - #TENT5A deficiency did not impair antibody production in response to the protein-based #vaccine #Nuvaxovid (@novavax.bsky.social). (16/n)

Paweł Krawczyk @pakraw.bsky.social · Apr 17

🐭 In vivo studies showed that TENT5A-deficient mice produced significantly less antigen-specific #antibodies following #mRNA #vaccination. This highlights the essential role of #TENT5A in mounting an effective immune response to mRNA-based vaccines. (15/n)

Paweł Krawczyk @pakraw.bsky.social · Apr 17

Our findings reveal a mechanistic principle: spatial proximity to ER-resident #TENT5A governs re-adenylation efficiency. This positions the #endoplasmic #reticulum as a central hub not only for #mRNA translation, but also for post-transcriptional regulation. (14/n)

Paweł Krawczyk @pakraw.bsky.social · Apr 17

Surprisingly, comparative analysis revealed differential re-adenylation efficiency between vaccine formulations:
@biontech.bsky.social #Pfizer #BNT162b2 demonstrated reduced re-adenylation compared to mRNA-1273, correlating with diminished #ER membrane association. (13/n)

Paweł Krawczyk @pakraw.bsky.social · Apr 17

The re-adenylation phenomenon exhibits substrate specificity - consistently observed in synthetic mRNAs encoding proteins targeted to the #endoplasmic #reticulum (ER), including #spike #glycoprotein, #Zika virus antigens, and #malaria parasitic proteins. (12/n)

Paweł Krawczyk @pakraw.bsky.social · Apr 17

We found that #macrophages—not dendritic cells—are the primary cells that take up mRNA vaccine #LNPs and express #TENT5A, positioning them as key players in regulating mRNA stability via re-adenylation. (11/n)

Paweł Krawczyk @pakraw.bsky.social · Apr 17

Of note, recent work from our lab showed that TENT5A incorporates non-adenosines into poly(A) tails of mRNA-1273, further underscoring its role in shaping the fate of therapeutic mRNAs. 👉 nature.com/articles/s41... (10/n)

Direct profiling of non-adenosines in poly(A) tails of endogenous and therapeutic mRNAs with Ninetails - Nature Communications

Ninetails, a neural network that uses Nanopore Direct RNA sequencing data to identify non-A residues in mRNA poly(A) tails is presented. Particularly non-A of therapeutic, mitochondrial, and TENT5A/C ...

nature.com

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Paweł Krawczyk @pakraw.bsky.social · Apr 17

We identified #TENT5A -a polyA polymerase our lab has studied extensively - as responsible for this effect. Its expression is induced by vaccine delivery, most likely through innate immune signaling (please compare our previous paper: doi.org/10.1126/scia...).
#InnateImmunity(9/n)

Paweł Krawczyk @pakraw.bsky.social · Apr 17

We then detected the same #polyA elongation pattern in #macrophages - both those sorted from muscles surrounding injection sites and in the in vitro models (mouse bone marrow-derived macrophages (mBMDMs) and human monocyte-derived macrophages (hMDMs)). (8/n)

Paweł Krawczyk @pakraw.bsky.social · Apr 17

Crucially, when examining #mRNA #vaccines at injection sites in #mice, we discovered an unexpected phenomenon: #polyA tails were extended from ~100 to ~200 nucleotides - contradicting the expected degradation pattern observed in standard cell lines. (7/n) #mRNAStability

Paweł Krawczyk @pakraw.bsky.social · Apr 17

In typical cellular models (HEK293T), we observed that mRNA-1273 degradation is initiated via removal of the terminal pentamer (mΨCmΨAG), followed by #CCR4-NOT-mediated #deadenylation—the canonical #mRNA #decay pathway. (6/n) #RNAMetabolism

Paweł Krawczyk @pakraw.bsky.social · Apr 17

The #Moderna #mRNA-1273 vaccine possesses a ~100 nucleotide #polyA tail terminated with a distinctive pentamer (mΨCmΨAG), which served as a critical molecular marker, facilitating differentiation between processed and unprocessed tails. (5/n)

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Paweł Krawczyk @pakraw.bsky.social · Apr 17

To overcome this obstacle, I developed a Dynamic Time Warping approach to detect and analyze vaccine molecules using #DRS with high fidelity, enabling precise characterization of #polyA tails from #therapeutic #mRNAs. (4/n)

Paweł Krawczyk @pakraw.bsky.social · Apr 17

We employed @nanoporetech.com
#direct #RNA #sequencing (DRS) to characterize individual therapeutic mRNA molecules - specifically focusing on #polyA #tail dynamics. However, #methylpseudouridine (mΨ) modifications in therapeutic mRNAs create significant analytical challenges. (3/n)

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Paweł Krawczyk @pakraw.bsky.social · Apr 17

Our research elucidates a critical post-transcriptional modification enhancing #mRNA #vaccine efficacy. We've identified #TENT5A-mediated re-adenylation as a key determinant of therapeutic mRNA stability and immunogenicity in #SARS_CoV_2 #vaccines. (2/n) #mRNABiology

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