LNP spike mRNA induction of changes in proteins related to vasculature formation and maintenance (collagen) in the heart

A new Nature paper provides evidence of specific harms induced by modRNA-LNP-based products

A Nature paper has hit the presses entitled: “Nanocarrier imaging at single-cell resolution across entire mouse bodies with deep learning”.¹ It was published on 14 January 2025 in Nature Biotechnology. It explains in true ‘Nature form’ how the lipid nanoparticles biodistribute and not only that, but that the expression of “off-target” spike protein induces local protein expression changes, immune activation and blood vessel damage.

In the Discussion you will find perhaps one of the most important statements in the paper:

This approach enhances targeting precision and supports toxicity risk assessment by uncovering off-target activity and its implications. Notably, SCP-Nano identified off-targeting even at the lowest doses (Fig. 4d), aiding in risk stratification and informing the selection of alternative vaccine formulations or therapies where necessary.

Before I deconstruct this paper, I would just like to state for the record that there is nothing staggeringly new here. Anyone with a science background (especially an immunology background) could have predicted this (and did) based on the way that things just are and, in fact, have been for a long time based on our current understanding of immunology and human physiology. It’s like Byram Bridle always says: we haven’t changed what we’re doing in this fight against tyranny - we’ve stayed the course as immunologists and virologists and continued to do good science and research.

What has changed is that science has been bastardized and weaponized and turned against the people. The science has NOT changed and the integrity of many researchers and doctors has not been swayed.

The very first sentence of the Abstract summarizes the story of the criminal negligence that surrounds the COVID-19 modRNA-LNP gene-based injectable product roll-out, with respect to the lie we were all told with regard to the needle contents staying at the intramuscular injection site. This was never, ever going to be case, and to anyone involved from a research and development point of view, it would have been as simple as reading about Onpattro development, or studying a bit about fat metabolism, to know this.

Efficient and accurate nanocarrier development for targeted drug delivery is hindered by a lack of methods to analyze its cell-level biodistribution across whole organisms.

What this sentence means is that it’s been hard to make these LNP products designed for nucleic acid delivery because we don’t have good ways to measure where they go and what the physiological effects would be if they showed up in say, the heart.

The authors used something called Single Cell Precision Nanocarrier Identification (SCP-Nano) to identify and quantify nanocarriers (including our infamous COVID LNPs) in mice. They looked at their entire bodies (in 3D!) and at single-cell resolution using an ingenious combination of benchwork and deep learning. They saw various tissue distribution patterns following various and sundry injection routes (including intramuscular, intradermal, oral, intravenous and intranasal) using very low doses of product (0.0005 mg kg⁻¹) and perhaps of more concern to us, they saw that intramuscularly-injected LNPs carrying SARS-CoV-2 spike mRNA reached heart tissue and lead to proteome changes which as they write, suggests immune activation and blood vessel damage at “vaccine dose”.

The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time.²

Deep learning is a subset of machine learning that focuses on utilizing neural networks to perform tasks such as classification, regression, and representation learning.

Figure 1: Extracted from Fig. 3: SCP-Nano reveals differences in LNP biodistribution based on different application routes. Source: https://doi.org/10.1038/s41587-024-02528-1

The above findings concern me, as the “best” lung route distribution technique involved the intranasal exposure (the second of the five images), and I feel quite strongly that this could be used to push gene-based (modRNA, RNA and DNA) products on us via intranasal (breathing) routes as it would “avoid the problems of biodistribution”. Which it wouldn’t. The DEFUSE proposal did mention teaming up with PARC to prototype aerosolization delivery routes.

Figure 2: Drastic screenshot. Source: https://drasticresearch.org/wp-content/uploads/2021/09/main-document-preempt-volume-1-no-ess-hr00118s0017-ecohealth-alliance.pdf.

Another important note in their introduction includes mention of the biomolecular corona that forms when introducing an LNP to a biological entity like a mouse, or a human. This is also known, as these fat bubbles are highly analogous to chylomicrons once injected. It’s important to note that the authors used a variety of LNP formulations in their experiments. They used the LNP used in Onpattro: the so-called “clinically approved” MC3-ionizable lipid. They also used the Moderna ionizable lipid SM-102 when they investigated how and if the LNP ‘recipes’ affect off-targeting to the heart, and the associated proteomic changes that they observed with MC3. They additionally used the Pfizer ionizable lipid ALC-0315 when they checked specific heart targeting among the different LNP formulations.

They did this because, of course, we want to know if their findings apply to the “real thing”, right?

However, upon exposure to the in vivo environment, nanocarriers inevitably acquire a protein corona that can influence their biodistribution and cellular interactions, complicating nanocarrier design and the prediction of target tissue.

What this means is that it was entirely predictable, based on what we know about specific LNPs and biomolecular corona formation, that these things would traffic … wherever. They can also be made to be specific by embedding specific proteins like APOE to traffic the cargo to the liver.

The truth is that the LNPs traffic their contents (to include RNA and DNA) anywhere and everywhere in the body. They always knew this. They had to know this. So they lied. They didn’t make a mistake.

Back to the paper. The SCP-Nano technique which is a robust deep-learning pipeline, is quite amazing since it can be used to map introduced particles at the single-cell level for visualization in 3D. This approach involves using whole body imaging data, and analyzing it using deep learning. So it’s a combination of human bench and AI in silico to yield very “illuminating” results.

Deep learning is a subset of machine learning that focuses on utilizing neural networks to perform tasks such as classification, regression, and representation learning.

In the image below, you can see the visualization of LNP distribution by organ.

Figure 3: Extracted from Fig. 2: SCP-Nano—a deep-learning-based pipeline to segment and analyze all targeted cells. Source: https://doi.org/10.1038/s41587-024-02528-1

For the deep-learning model nerds out there, the highest-performing model the authors employed was “a 3D U-Net architecture with six encoding and five decoding layers with a leaky rectified linear unit (ReLU) activation function”.

What’s worth repeating here, is that they detected these particles following introduction of a 0.0005 mg kg⁻¹ dose which is equivalent to a “vaccine” dose. They confirmed their findings with histology as well for the pathologists out there.

We demonstrate the utility of SCP-Nano for studying LNP-based mRNA delivery, quantifying biodistribution at doses as low as 0.0005 mg kg⁻¹ (as commonly used in vaccines, which is 100–1,000 times lower than those typically used in conventional imaging studies for nanoparticles), uncovering application-route-dependent tissue tropism.

They refer to where they found an accumulation of LNPs as “off-target” locations, meaning that they found these things in places where they weren’t expected or meant to go like the lungs, liver and the spleen. Another place they found these accumulations was in the heart.

So what did this accumulation do to the hearts of these mice? Remember, these guys did way more than just visualize where the LNPs went, they looked at the effects of expressed mRNA, and spike mRNA!, at the protein level. In the following Figure, the authors highlight the locations of accumulation of both mRNA and spike protein. As you can see, they found both in the liver, spleen and heart as indicated by the blown-up regions of the whole body image of the mouse.

Figure 4: Extracted from Fig. 4: SCP-Nano reveals protein expression from LNP-delivered mRNA and LNP off-targeting. Source: https://doi.org/10.1038/s41587-024-02528-1

As the authors correctly point out, this is concerning because we have injected LNPs encasing foreign spike-based nucleotides into billions of people, and millions of people have experienced, or are experiencing, cardiac adverse events. This is very well documented and evidenced especially with regard to myocarditis.

Given that MC3-based LNPs are used in RNA therapeutics and drug development in mice, non-human primates and humans^{23,38,39,40,41} and that there are reports of cardiac complications after vaccination using another LNP formulation^{42,43,44,45,46}, we further explored potential effects of the LNP-driven mRNA expressions in the heart.

To further investigate the “issue of LNP-driven mRNA expression in the heart”, the authors raised the injected dose, re-injected the mice and quantified. They found LNP-mRNA-derived spike protein in both immune cells and non-immune cells throughout the body, and this means that the spike RNA is being brought to these essential cells, tissues and organs via the LNPs, and that the spike protein is made on-site. We knew this too. More specifically, they found spike in endothelial cells and not in cardiomyocytes, immune cells or arteries in the heart.

Hmm.

Figure 5: Slide from presentation to D4CE on September 7, 2023. Source: https://rumble.com/v3gs4pw-damages-from-the-modified-mrna-containing-lnps-from-vessels-to-brain-a-numb.html?e9s=src_v1_upp

The study continues. To determine the impact of off-target localized mRNA expression, they sampled mice with and without mRNA expression and they found distinct changes “related to cell metabolism and signaling and immune system in mRNA-expressing groups”.

They also looked at proteomic changes induced by LNPs alone and also found distinct changes and more specifically, they found “375 differentially expressed proteins (DEPs) (240 upregulated and 135 downregulated in no-cargo LNP compared to PBS)” and not surprisingly, these factors are associated with metabolic processes, including ribosome activity, translation and RNA metabolism. We would expect these changes seeing as how we’re talking about hi-jacking cells to abuse them to mass-produce foreign proteins.

When they further looked at the impact of spike mRNA expression on proteomic changes, they found “578 upregulated and 201 downregulated proteins in the LNP spike mRNA compared to no-cargo LNP samples”. If you read on, it gets a bit scary. These up-regulated proteins include … you guessed it: collagen.

Notably, we found changes in proteins related to vasculature formation and maintenance (individual differentially expressed markers: Cd34 and several members of the collagen family; vascular function score in Fig. 4l and Supplementary Table 2).

I’ve written a few articles related to collagen/fibrin.

Figure 6: A list of some of my Substack articles pertaining to collagen production associated with SARS-2 and the COVID shots. Source: https://jessicar.substack.com

This suggests that not only spike mRNA but also delivery and expression of any mRNA should be carefully assessed for targeted drug delivery via LNPs.

The authors suggest from these results that it’s this platform is NOT PLUG-N-PLAY. I agree with the authors.

They weren’t sure if their results up to a certain point were the result of the LNP with the selected MC3 ionizable lipid, so they checked out the SM-103 ionizable lipid-based LNP used by Moderna as well. They found that the Moderna LNP recipe induced the same changes in gene dysregulation.

Similar to our observations with MC3-based LNPs, proteins associated with the vasculature were among the most dysregulated genes, including several involved in maintaining vascular structure, which were strongly downregulated (individual proteins in Supplementary Fig. 15d.

Good thing that Moderna stock is dropping.

They went on to compare and contrast various LNP formulations including the one used by Pfizer with ionizable ALC-0315 to investigate this observed ‘heart targeting’ by LNPs from the point of view of biomolecular corona formation. This was important to do because maybe one of the formulations attracts specific biomolecules that traffics the LNPs to the heart, for example. But no. They found that biomolecules such as vitronectin were strongly enriched in all LNP coronas, so no big difference between them.

Using mass spectrometry proteomics, we observed the presence of proteins, such as vitronectin, which can attach to endothelial cells and, thereby, facilitate the LNP targeting to the heart cells.

It’s at this point that I would like to point out that this paper is primarily about their new pipeline for visualization at the single cell level whereby their intention was not to necessarily implicate the potential dangers of the COVID shots, but to demonstrate the broad applicability of SCP-Nano. The paper continues to demonstrate further applications with regard to visualization of DNA origami and adeno-associated virus (AAV) distribution.

But, although I think what they’ve done here is incredible and that the SCP-Nano will become the prototype that will likely be adopted for future research discovery, I only really care about what they found that pertains to the “real world” and its people right now with regard to the COVID shots.

We’ve been screaming from the rooftops that the shots cause heart damage. We knew the LNPs biodistribute from FOIA-requested pharmokokinetic studies, we knew that manufacture of spike protein at so-called “off-target” sites like the heart was never going to turn out to be a good thing for the person who’s heart it was. We knew that the fibrotic lesions on the hearts of injected people was the direct result of the damage induced by the spike protein being manufactured on-site having been trafficked there by the LNPs. We also knew that any cell mounting spike-peptides on MHCs would be targeted for cell destruction, including endothelial cells associated with the heart.

The fact that these authors have demonstrated proteomic changes induced by spike mRNA expression to include 578 upregulated and 201 downregulated proteins is staggering, but sadly, kind of not surprising. It seems logical that the metabolic expenditure of any cell subjected to these COVID LNPs would go toward churning out these foreign proteins and likely, this would be at the expense of the production of other proteins. It’s interesting though how many were downregulated as well. I have so many questions.

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Addendum: On the collagen markers that were differentially-expressed.

Figure 7: Vascular markers from Supplementary Table 2 and differentially expressed collagen names from Supplementary Data 1. Source: https://doi.org/10.1038/s41587-024-02528-1.

Of the markers associated with collagen that were differentially-expressed, many were up-regulated as shown in the above Table from Supplementary Data 1. From cartilage and eye health to angiogenesis, so many uses for collagen. Type XV collagen is known as a tumor suppressor.³

The collagen families: Fibrillar (Type I, II, III, V, XI), Facit (Type IX, XII, XIV), Short chain (Type VIII, X), Basement membrane (Type IV), Other (Type VI, VII, XIII)

Please read this article to find out more about what it might mean for Col1a1 to be Up.

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So why does it take a Nature paper published 3 years out to move the needle on this? Will the needle be moved? Finally?

You can click on the following image to get to the presentation I gave to Doctors for COVID Ethics (Michael Palmer’s group not that other one) about LNPs and potential dangers.

1. Luo, J., Molbay, M., Chen, Y. et al. Nanocarrier imaging at single-cell resolution across entire mouse bodies with deep learning. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-024-02528-1

2. https://en.wikipedia.org/wiki/Proteome

3. https://en.wikipedia.org/wiki/Collagen,_type_XV,_alpha_1