Bioinformatics analysis links type 1 diabetes to vaccines contaminated with animal proteins and autoreactive T cells express skin homing receptors consistent with injected vaccines as causal agent
Vinu Arumugham
Sep 2017
vinucubeacc@gmail.com
Vaccines are contaminated with GAD65 (glutamic acid decarboxylase 65 KDa) and AQP4 (aquaporin- 4) protein containing chick embryo cell cultures. The role of such contamination in the etiology of type 1 diabetes (T1D) and neuromyelitis optica spectrum disorders (NMOSD), was previously described.1,2
Origin of autoreactive T cells
Thymocytes with T cell receptors (TCR) that have high affinity for self peptides are usually negatively selected and destroyed in the thymus.3 T cells with TCR that recognize peptides that differ by as little as one amino acid from a self peptide, can be positively selected and migrate to the periphery.4 These low affinity self reactive (LASR) T cells can become autoreactive when they are activated by a peptide that exactly matches a self peptide except for this one amino acid difference (cognate peptide). LASR T cells have the highest possible affinity to self peptides that still qualifies for positive selection in the thymus. This arrangement seems to have worked very well over millions of years of evolution, until human ingenuity intervened …
Vertebrate animal proteins are very similar to human proteins. Animal protein sequences exactly match human proteins except for occasional amino acid differences.1,2 So animal proteins are an ideal source of peptides to activate such LASR T cells described above. Ingested animal proteins are immunologically processed to produce a tolerogenic response.5 Injected animal proteins are however
another matter. Animal cells and proteins are used as growth media for the culture of viruses and bacteria, and as excipients in the manufacture of vaccines. Such vaccines are contaminated with numerous animal proteins. When animal proteins are injected with vaccines that either contain live viruses or adjuvants that provoke an immune response, LASR T cells can be activated by peptides derived from these animal proteins thus resulting in autoimmunity.
Immunotoxic effects of injected proteins have been known for over a hundred years. But ignorant vaccine regulators have placed no controls on the proteins that contaminate vaccines.6–8 The outcome was predictable. The Pandemrix vaccine was contaminated with influenza virus nucleoproteins which resulted in narcolepsy.9 Rabbit and duck embryo neural tissue contaminated rabies vaccines cause “neuroparalytic accidents”.10 Bovine casein and casamino acids used in vaccines are derived from cow’s milk.11 Therefore cow’s milk proteins contaminate numerous vaccines, contributing to various disorders.7,12
Normally, LASR T cells do not encounter their cognate peptides. Also, due to the lack of innate immune system-derived costimulation, LASR T cells will not be activated if they encounter self peptides complexed with major histocompatibility complex (MHC) molecules on the surface of antigen-presenting cells (APC).13 Following vaccine administration however, innate immune system
costimulation exists. Both live virus vaccines and aluminum adjuvanted subunit vaccines activate the innate immune system.14 Animal protein derived peptides from the vaccines are complexed with MHC on the surface of APCs and presented to LASR T cells. This combination of innate immune system costimulation and LASR T cells encountering their cognate peptides on the surface of APCs, can result in LASR T cell activation and abrogation of peripheral tolerance.
During evolution, animal protein injection into humans was a rare event. Therefore our immune systems did not have an opportunity to evolve a defense for this mode of abuse.
Determining animal proteins responsible for activation of autoreactive T cells Various vaccines are contaminated with cow, pig, African green monkey, guinea pig and chick embryo proteins.5
Homology of these animal antigens to epitopes associated with T1D are shown in the table below.
GAD65115–127
15 is IAFTSEHSHFSLK, GAD65 274–286
15
is MNILLQYVVKSFD, GAD65555–567
16
is
NFFRMVISNPAAT, IA-2805-820
17 is VIVMLTPLVEDGVKQC and B9-23
18
is SHLVEALYLVCGERG.
Organism Common name Contaminated
vaccines
GAD65115–127 GAD65 274–286 IA-2805-820 B9-23 GAD65555–567
Bos taurus Cow Tetanus,
Diphtheria,
Pertussis, Hep
A, Polio,
Rabies,
MMR,
Varicella,
Zoster etc.
100% 92% 100% 100% 100%
Sus scrofa Pig Zoster 100% 92% 100% 100% 100%
Chlorocebus
sabaeus
African Green
Monkey
Polio, Small
pox
100% 100% 100% 100% 100%
Cavia porcellus Guinea Pig Varicella 92% 85% 94% 73% 100%
Gallus gallus Chick MMR, TBE,
Rabies
85% 92% 88% 100% 100%
100% homology is less likely to result in autoimmunity as T cells recognizing those peptides would
have been negatively selected in the thymus. Therefore guinea pigs and chick are likely to be the
biggest contributor to autoimmunity, followed by cow, pig or monkey proteins.
Since the Varicella vaccine is relatively new compared to the measles, mumps and rubella vaccine,
chick proteins are likely the biggest contributor to T1D autoimmunity.
T1D epitope alignment to regions of near identity
Examining the GAD65115–127 and GAD65 274–286 epitopes associated with type 1 diabetes15, it is clear that the epitopes are from locations where the chick GAD65 residues differ slightly from the human GAD65 protein (highlighted in figure below). This is exactly what we would expect in LASR T cell mediated autoimmunity. Such chick GAD65 epitopes can activate LASR T cells. Such activated LASR T cells can cross react with human GAD65 and destroy beta cells. Such autoreactive T cells are functional even with low affinity or very low affinity binding.18,19 Peptides from locations where the homology between chick and human proteins is 100% are less likely to activate T cells because such T cells are likely to have been negatively selected in the thymus.
Uniprot20 and BLASTP21 are used to perform protein sequence alignment analysis.
Human GAD65 vs. chick GAD65
PREDICTED: glutamate decarboxylase 2 [Gallus gallus]
Homing marker provides evidence of T cell activation site. Hedman et al.22 write:
“No significant differences were seen in any of the Th1-associated receptors, and only the percentages of CD8+ cells expressing the Th2-associated receptor CCR4 was higher in the diabetic group in comparison with healthy individuals (Fig. 2a,b), but not observed on CD4+ cells.”
As Berin et al.23 describe, the CCR4 receptor indicates skin homing and the site of initial priming. Skin homing would be expected since the animal antigen containing vaccines were administered via the subcutaneous or intramuscular route. Such CD8 T cells expressing CCR4 are involved in the
destruction of beta cells.24
Vaccines disable at least one layer of natural protection against autoimmunity T cells with high affinity to self peptides being negatively selected in the thymus is one major layer of natural defense against autoimmunity. T cells in the periphery need to be activated with a self peptide. This is another major layer of natural defense against autoimmunity.
Vaccines are contaminated with numerous animal proteins. Animal proteins contain numerous peptides identical to self peptides. Upon administration of such vaccines, with innate immune system-derived costimulation active, these animal protein derived peptides activate T cells that have escaped thymic negative selection. So this layer of defense is disabled.
Protein sequence alignment
Here we analyze protein sequence alignment between T1D autoantigens and various viral, bacterial,
fungal proteins that contaminate vaccines along with animal proteins. Chick and Coxsackievirus
protein sequence alignment scores are also included for comparison. Natural infection with
Coxsackievirus has been linked to T1D.25
Method
BLASTP methodology was used for protein sequence alignment. As shown before26, a BLASTP
sequence alignment score of 19.3 was obtained comparing human hypocretin receptor and H1N1
nucleoprotein contained in the Pandemrix vaccine. This level of sequence alignment was sufficient to
cause autoimmunity that resulted in hypocretin dysregulation and narcolepsy.9 Therefore any score
equal to or higher than 19.3 suggests high probability of autoimmunity.
While vaccines target one or a few particular viral, bacterial proteins, most vaccines are contaminated
with all proteins from that virus or bacteria. Example: the Pandemrix vaccine contained both H1N1
hemagglutinin (target) and H1N1 nucleoproteins (contaminant). The exceptions are recombinant
vaccines. In recombinant vaccines, the vaccine contains only the target protein from the target
organism. The target protein is produced usually by genetically modifying yeast (Saccharomyces
cerevisiae). Hepatitis B27,28 and HPV vaccines29 are produced using this technique. Such vaccines are however, contaminated with all Saccharomyces cerevisiae proteins.
Autoantigen Insulin B
10-18
PPI
15–24
ALWGPDPAAA
IGRP
265–273
VLFGLGFAI
IA-2
797–805
WQMVWESGCTV
GAD65
115–127
IAFTSEHSHFSLK
GAD65
274–286
MNILLQYVVKSFD
Organism
Gallus Gallus 32 21.8 22.7 38.8 38 39.7
Haemophilus Influenzae 25.2 21 21 20.2 20.6 23.5
Streptococcus pneumoniae 23.1 23.5 24.4 23.1 23.1 26.1
Corynebacterium diphtheriae 21.8 21 22.7 21 20.2 20.6
Bordetella Pertussis 20.2 24.8 24.4 21 19.3 20.6
Clostridium tetani 21.8 18.5 20.6 19.7 19.3 22.7
Neisseria meningitidis 21.4 21 18.9 21.8 21 24
Hepatitis B virus 18.9 21* 21.4 16.8 19.7 21*
Coxsackievirus 20.6 16.3 18.9
Influenza A virus 18.5 17.6 19.7 19.7 18.9
Saccharomyces cerevisiae 21.8 26.5 21.4 21.8 23.5 24
Rubella virus 18.5
Mumps virus 18.5
* Hepatitis core protein match. Applicable to Hepatitis B infection, but not recombinant vaccines, as
they do not contain core proteins.
As we can see above, there are numerous scores above the 19.3 baseline that corresponds to the level of sequence alignment in Pandemrix vaccine induced narcolepsy. So these contaminants can contribute to autoimmune diseases.
Most epidemiological studies are invalid
Most epidemiological studies investigating the role of vaccines in autoimmune diseases, ignore the
mechanism of causation. Hypothesizing a mechanism allows for a study design that accounts for
appropriate controls. By ignoring the mechanism, these studies have the wrong controls and the results are invalidated due to confounding factors. Relying on such invalid epidemiological studies have lead researchers down blind alleys for decades. Researchers must determine root cause by focusing on mechanisms of causation.
Conclusion
The above findings add to the growing evidence of vaccines inducing autoimmune diseases.
While the analysis above focused on T1D, the mechanisms described are obviously likely to be active
in any number of autoimmune diseases.2
It is quite obvious that there are fundamental problems with vaccine design and safety. Vaccine
designers need to go back to the drawing board. We need vaccines that are safe by design. 8,30
Detailed BLASTP Results
Sequence alignment between human GAD65 epitopes and various animal species GAD65 proteins that contaminate vaccines.
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