Keywords
peptide sharing - cross-reactivity - autoimmunity - nonhuman primates - preclinical
tests
Introduction
Molecular mimicry and the consequent potential cross-reactivity following infections
have been repeatedly described in humans.[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12] Such cross-reactivity is not evident in experimental infections of primates.[13] Actually, following preclinical studies performed in primates[14]
[15]
[16]
[17]
[18] as recommended by the Food and Drug Administration,[19] the reports declare that primate active immunization by pathogen vaccine administration
is well tolerated and exempt of relevant events. Hence, the questions: why the potential
cross-reactivity and the consequent potential autoimmune sequelae do not occur in
primates following experimental infections or during preclinical tests? What are the
genetic/phenetic determinants behind the different responses of humans and primates?
It was reasoned that, if it is true that molecular mimicry between infectious agents
and human proteins contributes to or causes cross-reactions and postinfection autoimmune
pathologies, then the human proteome should be characterized by different levels/patterns
of molecular mimicry versus pathogens when compared with the proteomes of nonhuman
primates. According to this rationale, this study comparatively analyzed primate and
human proteomes for peptide sharing with pathogens by using heptapeptides as immunobiological
units.[20]
[21]
[22] Analyses were also expanded to other mammalian species that are used in research
laboratories (i.e., mice, rats, rabbits) and domestic animals such as dogs and cats.
Results suggest that mice represent more suitable animal models for exploring potential
autoimmune cross-reactions following pathogen administration and highlight new evolutionary
scenarios in the origins of Homo sapiens.
Materials and Methods
Peptide sharing analyses have been described elsewhere.[9]
[10]
[11]
[12] Briefly, pathogen proteomes (or proteins) were dissected into heptapeptides offset
by one residue, and then each pathogen heptapeptide was analyzed for occurrences within
proteomes from the following organisms (with National Center for Biotechnology Information
[NCBI] TaxId in parentheses): Homo sapiens (9606); gorilla, Gorilla gorilla gorilla (9595); chimpanzee, Pan troglodytes (9598); and rhesus macaque, Macaca mulatta (9544). In addition, proteomes from the following mammalian organisms were analyzed
as controls: cow, Bos taurus (9913); dog, Canis lupus familiaris (9615); cat, Felis catus (9685); rabbit, Oryctolagus cuniculus (9986); mouse, Mus musculus (10090); rat, Rattus norvegicus (10116); pig, Sus scrofa (9823); and bat, Pteropus alecto (9402).
The analyzed pathogen proteomes (or proteins) are (with NCBI TaxId in parentheses):
poliovirus (12081); measles virus (70149); dengue virus (11059); severe acute respiratory
syndrome-related coronavirus 2 (SARS-CoV-2) (2697049); hemagglutinin from influenza
A virus, H1N1 (641809); major capsid protein L1 from human papillomavirus type 16
(333760); and protective antigen from Bacillus anthracis (1392).
Peptide matching analyses were conducted by using the PIR Peptide Matching program.[23]
Results
The heptapeptide sharing between the pathogen proteomes/proteins and the 12 mammalian
proteomes is analytically detailed in [Supplementary Tables S1–S7] (online only), and is graphically illustrated in [Figs. 1] and [2].
Fig. 1 Heptapeptide sharing between mammalian proteomes and proteomes from: (A) poliovirus, (B) measles virus, (C) dengue virus, and (D) severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2).
Fig. 2 Heptapeptide sharing between mammalian proteomes and (A) hemagglutinin from influenza A virus, H1N1, (B) L1 from human papillomavirus type 16, and (C) protective antigen from Bacillus anthracis.
Specifically, [Fig. 1] shows that:
-
A massive heptapeptide sharing exists between the human proteome and poliovirus, measles
virus, dengue virus, and SARS-CoV-2 proteomes.
-
The viral heptapeptide sharing is likewise high with the murine proteome and, at a
relatively lesser extent, with the rat proteome.
-
In contrast, cat, dog, cow, pig, rabbit, and the three primates analyzed here have
no or a low number of heptapeptides (see, for instance, cow) in common with the analyzed
pathogens.
-
Quantitatively, the highest number of peptide commonalities (namely, 281, see [Supplementary Table S1], online only) occurs between SARS-CoV-2 and Homo sapiens proteomes, while the bat Pteropus alecto was found to have no heptapeptide sequences in common with any of the analyzed pathogen
proteomes/proteins.
Results similar to those reported in [Fig. 1] are obtained when pathogen protein antigens (namely, influenza A HINI hemagglutinin,
HPV16 L1, and B. anthracis protective antigen) are analyzed for peptide sharing with the 12 mammalian organisms
([Fig. 2]). It can be seen that the shared heptapeptides occur in human, mouse, and rat proteomes,
while primates and the other mammalian species remain almost completely excluded from
the sharing or share a low number of heptapeptides.
Discussion
Translational research requires animal models that allow researchers and clinicians
to predict human responses. Nonhuman primates have long been fundamental research
models for testing new therapies in clinical trials. Actually, this study documents
that, when analyzing molecular mimicry, a highest number of pathogen heptapeptides
occur in the human proteome but not in primate proteomes. As a logical consequence,
this implies that the potential cross-reactive autoimmune effects of the pathogen
versus human peptide overlapping cannot be evaluated in primates. In this regard,
[Figs. 1] and [2] indicate that only mice and rats and, at a minor extent, cows should be utilized
in preclinical tests.
Our data are widely supported by clinical findings monitored during experimental infections.
In summary:
-
as reviewed by Wachtman and Mansfield,[13] natural poliovirus infection has not been diagnosed in rhesus macaques. Rhesus macaques
are experimentally susceptible to poliovirus infection and develop encephalomyelitis
if inoculated with poliovirus parenterally (usually intracranially). However, in many
cases, no clinical signs are evident;
-
likewise, measles disease is usually mild or asymptomatic in macaques, unless animals
are stressed or immunosuppressed[23];
-
experimental dengue infection of macaques and other monkeys produces viremia and antibody
response but has been associated with only minimal clinical signs[24]; and
-
experimental SARS-CoV infections in primates do not reach the level of severity observed
in human patients succumbing to respiratory failure. Indeed, SARS-CoV administered
intranasally and intratracheally to rhesus, cynomolgus, and African green monkeys
replicated in the respiratory tract but did not induce illness.[25]
Then, the data illustrated in [Figs. 1] and [2] appear of indisputable medical importance since scientifically substantiate what
Hogan[26] clinically remarked, that is, the fact that the rhesus macaque model is of limited
utility in preclinical tests, while only mice might represent a correct animal model
for testing and evaluating immunotherapies to be used in humans.[27]
[28]
Moreover, besides the medical relevance in the current experimental clinical context,
the present study opens a new research perspective in the comparative study of humans
and apes. Indeed, although the nucleotide difference between, for example, humans
and chimpanzees is surprisingly small and amounts to a nucleotide difference of only
1 to 2%, on the other hand 80% of the proteins are different between the two species.[29] Understanding how the small nucleotide difference led to such a massive phenetic
difference might be a key for understanding not only the fascinating evolutionary
history of the origins of humans and apes, but also for investigating the basis of
the autoimmune diseases that afflict humans, but not primates.
Conclusion
Viruses appear to have played crucial roles in the viral eukaryogenesis process[30]
[31] as well as in the split between humans and apes million years ago. Indeed, the striking
difference between primates and humans in the peptide sharing with pathogens not only
indicates that primates are unreliable animal models for preclinical tests, but also
highlights different phenotypic profiles that evolved along different evolutionary
pathways. Such evolutionary pathways warrant further studies to understand primates'
resistance to infections that are instead lethal in humans. Then, it seems that the
role of the viruses in the cellular evolution of the human being has to be analyzed
in a wider evolutionary and temporal context, where specific pathogen sequences were
selectively incorporated into (or deleted from) the human and ape genomes. A comparative
and multidisciplinary research approach appears to be mandatory to understand and
fight the new and (re)emerging pathogens that violently threaten the human being,
especially in the light of the massive peptide overlap between viral and human proteomes.[32]
[33]
