The evolutionary history of oncogenic and non-oncogenic papillomaviruses

Project Information

ONCOGENEVOL

Grant agreement ID: 750180

DOI

10.3030/750180

Project closed

EC signature date 30 March 2017

Start date 1 June 2017

End date 31 July 2019

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 185 076,00

EU contribution

€ 185 076,00

Coordinated by

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France

Periodic Reporting for period 1 - ONCOGENEVOL (The evolutionary history of oncogenic and non-oncogenic papillomaviruses)

Reporting period: 2017-06-01 to 2019-05-31

Summary of the context and overall objectives of the project

Papillomaviruses (PVs) have a wide host range, infecting mammals, birds, turtles, snakes and fish. Certain PVs are a major public health concern as in humans they are responsible for virtually all cases of cervical cancer, and for a fraction of cancers on the anus, penis, vagina, vulva and oropharynx. But oncogenic PVs are actually an unfortunate exception, as most PVs cause asymptomatic infections, and a few cause benign, wart-like lesions. Despite the efforts directed towards the understanding of the different clinical manifestations of infection, our knowledge on PV evolution remains fragmentary. A better understanding of the evolutionary history of PVs will expand our current knowledge on the origin of these viruses and on the evolutionary changes that make these viruses oncogenic.
The main aim of this project was to better understand the factors that differentiate between oncogenic and non-oncogenic PVs. To investigate this, we have combined computational and experimental methods to study specific events that occurred during PV genome evolution. In WP1 the goal was to resurrect the ancestral oncogenes and experimentally test hypotheses about the function of the ancestral proteins in different environmental contexts. In WP2 the goal was to computationally generate comprehensive scenario of all the events that led to the PV genomes that we observe today, such as the emergence of the viral oncogenes. We further investigated how the presence of these oncogenes is linked to the phenotype we observe. In WP3 the goal was to explore the evolutionary origin of PVs and test whether they share a common ancestor with other closely related viruses.
Here, we conclude that ancestral PVs existed already 430 million years ago. Moreover, we inferred that the ancestral PV genome did not contain any of the oncogenes (E5, E6 and E7) and thus these were acquired later during PV evolution. The E6 and E7 oncogenes, that are present in most PV genomes we observe today, appear to have evolved from a common ancestor. The E5 oncogene, that is present in only a few PV genomes, does not appear to have evolved from a common ancestor, and thus evolved independently multiple times. The mechanism that best explains the independent origin is de novo gene evolution in a long non-coding region in the PV genome. As little is known about the functions of E5, we have shown that E5 displays the properties of a genuine gene. In addition, the role of E5 in the differential oncogenic potential of human PVs is supported by the sharp match between the type of E5 protein encoded in the PV genome and the infection phenotype we observe. Our results compile the current knowledge on PV diversity and present an ancient evolutionary timeline punctuated by evolutionary innovations in the history of this successful viral family.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

To better understand how PVs became oncogenic, a global family tree was constructed and a timeline was added to this tree. We found that PVs date back to at least 430 million years ago. By comparing the genomes of all known PVs, we found that the ancestral PVs were probably not able to induce cancer, as these viruses did not contain any of the PV oncogenes. These genes were thus acquired later during PV evolution, as shown in Figure 1. The major oncogenes, E6 and E7, are known to degrade human tumor suppressor proteins, which can eventually lead to the development of cancer. Despite of the presence of E6 and E7 in virtually all present day PV genomes infecting mammals, only a few PV lineages are responsible for cancer. Therefore, other factors than just the presence of these oncogenes must play a role in the ability of PVs to induce cancer.
The minor PV oncogene is E5, for which at the start of this study the functions and origin remained to be fully elucidated. By performing computational tests on the origin, we found that E6 and E7 appear to have arisen from a common ancestral DNA sequence, whereas the different E5 genes appear to have evolved multiple times independently through de novo gene evolution in a non-coding region in the PV genome. By performing multiple computational tests we showed that E5 is a functional protein. Moreover, the entrance of E5 in the ancestral genome of PVs infecting primates concurred with an event that was instrumental for the differential oncogenic potential of present-day PVs infecting humans (Figure 2). During this event, certain E6 and E7 proteins acquired the ability to degrade tumor suppressor proteins and thus facilitate the development of cancer in different tissues. This hypothesis is supported by the sharp match between the type of E5 protein encoded in the PV genome and the infection phenotype we observe (Figure 2).
By means of computational methods, the ancestral sequences of the E6 and E7 oncogenes of PV genomes infecting primates have been inferred. We investigated the structural properties of these ancestral sequences. Based on these analyses, the ancestor of PVs associated to mucosal lesions (Figure 2) appeared to be already able to degrade tumor suppressor proteins. However, not all PVs associated to mucosal lesions are carcinogenic, suggesting that other factors also play a role on the development of cancer.
Part of the results of the project have already been published in high impact peer-reviewed open access journals. Moreover, the results have been presented to scientist in different areas at national and international conferences and workshops. To communicate to the general public, our main findings were posted on Twitter and we have created a project website.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

It is argued that the ability to degrade tumor suppressor proteins is correlated with family tree grouping, and that this was inherited from the ancestor of PV infecting primates. Currently we are experimentally testing the binding affinity of the ancestral E6 proteins to different peptide sequences. The binding of E6 to these peptide sequences is in different ways involved in tumor progression in human cells. We expect that the results of this study will in fact indicate whether the ability to induce cancer is correlated with the family tree or whether there are additional factors that differentiate between closely related non-oncogenic and oncongenic PVs.
The recent discovery of PVs in different fish species has challenged our understanding of the origin of these viruses. These PVs consist of the minimal ancestral PV genome (without any oncogenes) and have been found to co-infect with polyomaviruses (PyVs). It is likely that PVs and PyVs share a common ancestor as they encode proteins sharing similar functions and domains. We are currently studying whether PVs, PyVs and other DNA viruses share a common ancestor. By unraveling the origin of these viruses, we expect to significantly contribute to the fields of virus evolution and genome evolution.
The results of this project have significantly improved our understanding of the evolutionary history of PVs. We expanded the current knowledge on the origin of PV genes and genomes and on how certain PVs evolved their oncogenic potential through their oncogenes. This research is not expected to result in patents but has a great potential of being exploited for future development of PV vaccines. Currently, only prophylactic (for prevention) vaccines against HPV are available and the oncogenes that are investigated in this project provide good opportunities to use for human cancer immunotherapy.

Figure 2

Figure 1