Periodic Reporting for period 2 - RETROFIT (Pinpointing novel molecular and cellular functions generated by retroelement onco-exaptation)
Berichtszeitraum: 2023-06-01 bis 2024-11-30
Retrotransposable elements (RTEs) are parasitic forms of DNA that have invaded our germline over the course of evolution and have now become a substantial part of our genetic constitution. There are over 4 million RTE insertions in the human genome, amounting to nearly half of our DNA. The genetic diversity provided by mobile genetic elements is a major force in the evolution of new molecular and cellular functions. RTEs can be co-opted in new functions that increase host fitness, a process termed exaptation. Notable exaptation events include the evolution of adaptive immunity and antibodies, and of placentation. However, the powerful evolutionary adaptability afforded by RTEs can be exploited by tumour cells, a process termed onco-exaptation, to promote oncogenesis.
This project aims to identify and characterise novel functions created by RTEs, with particular emphasis on immunity, infection and cancer. Such activities may derive from functions of canonical RTE proteins, such as the envelope glycoprotein or the reverse transcriptase of endogenous retroviruses, that are however distinct from their originally adapted or selected functions. They may also derive from the creation of novel function or from modification of the function of genes near or within which RTEs are integrated. Elucidation of novel physiological and pathological functions created by RTEs will be key to completing our understanding of how the immune system operates, how cancer initiates and progresses, and how the two intersect.
This project aims to identify and characterise novel functions created by RTEs, with particular emphasis on immunity, infection and cancer. Such activities may derive from functions of canonical RTE proteins, such as the envelope glycoprotein or the reverse transcriptase of endogenous retroviruses, that are however distinct from their originally adapted or selected functions. They may also derive from the creation of novel function or from modification of the function of genes near or within which RTEs are integrated. Elucidation of novel physiological and pathological functions created by RTEs will be key to completing our understanding of how the immune system operates, how cancer initiates and progresses, and how the two intersect.
A small number of impactful onco-exaptation events have been described in recent years underscoring their potential importance, but their true number is likely vastly underestimated owing to the challenges of RTE study.
RTE integrations are reasonably well recognised and annotated at the genome level. However, much less understood is their participation at the more complex transcriptome level, particularly where aberrant transcriptional patters are expected, such as in cancer. Without precise knowledge of the structure of transcripts that are initiated by or include RTEs, their transcriptional activity or any resulting protein products cannot be accurately defined. RTE-derived exons have been traditionally underrepresented in past transcriptome assembly efforts owing to exclusion of repetitive reads and loci. We therefore built a genome-guided de novo transcriptome assembly that captures the diversity of RTE transcripts. We have made use of the altered transcriptional landscape of cancer to identify RTE-overlapping transcripts that might have been harder to detect in other cellular states. This assembly doubled the number of previously annotated transcripts that include RTEs, several thousand of which were found expressed specifically in one or a few related cancer types, and captured a significant number of previously unannotated isoforms of known genes, with the potential to alter the canonical gene function or to gain novel function.
By applying a number of criteria, including evolutionary conservation, putative or known function the affected genes in cancer, predicted impact of RTE, expression pattern and correlation with clinical outcomes, we prioritised a number of possible onco-exaptation events. These are now been systematically evaluated in appropriate experimental systems. Up to this point of the project, we have characterised and reported three such events. These include the co-option of the Human Endogenous Retrovirus (HERV)-K(HML-2) envelope glycoprotein as a putative tumour-associated antigen targeted by antibodies during immunotherapy of lung adenocarcinomas, the HERV-H-driven ectopic expression of Calcium-binding protein Calbindin controlling senescence and inflammation in lung squamous cell carcinomas, and RTE-mediated reduction in the expression of several genes necessary for cellular fitness of esophageal adenocarcinomas.
RTE integrations are reasonably well recognised and annotated at the genome level. However, much less understood is their participation at the more complex transcriptome level, particularly where aberrant transcriptional patters are expected, such as in cancer. Without precise knowledge of the structure of transcripts that are initiated by or include RTEs, their transcriptional activity or any resulting protein products cannot be accurately defined. RTE-derived exons have been traditionally underrepresented in past transcriptome assembly efforts owing to exclusion of repetitive reads and loci. We therefore built a genome-guided de novo transcriptome assembly that captures the diversity of RTE transcripts. We have made use of the altered transcriptional landscape of cancer to identify RTE-overlapping transcripts that might have been harder to detect in other cellular states. This assembly doubled the number of previously annotated transcripts that include RTEs, several thousand of which were found expressed specifically in one or a few related cancer types, and captured a significant number of previously unannotated isoforms of known genes, with the potential to alter the canonical gene function or to gain novel function.
By applying a number of criteria, including evolutionary conservation, putative or known function the affected genes in cancer, predicted impact of RTE, expression pattern and correlation with clinical outcomes, we prioritised a number of possible onco-exaptation events. These are now been systematically evaluated in appropriate experimental systems. Up to this point of the project, we have characterised and reported three such events. These include the co-option of the Human Endogenous Retrovirus (HERV)-K(HML-2) envelope glycoprotein as a putative tumour-associated antigen targeted by antibodies during immunotherapy of lung adenocarcinomas, the HERV-H-driven ectopic expression of Calcium-binding protein Calbindin controlling senescence and inflammation in lung squamous cell carcinomas, and RTE-mediated reduction in the expression of several genes necessary for cellular fitness of esophageal adenocarcinomas.
We are continuing at pace our efforts to identify and mechanistically characterise individual cases of RTE co-option affecting or creating physiological and pathological functions. Made possible by recent methodological advances in the study of RTEs, we currently have a long list of candidate (onco-)exaptation events, which we aim to test functionally. Upon completion of the project we aim to build a genome-wide reference map of functionally validated RTE (onco-)exaptation events and pinpoint novel, targetable functions of RTEs in immunity, cancer and their intersection. Although RTE (onco-)exaptation candidate events are studied in isolation, so that their precise action is determined, coordinated activation of RTEs in cancer allows for more complex interactions of take place. We therefore aim to identify pathways co-opting RTEs that are co-ordinately regulated or display mutually exclusive patterns of expression, in order to build a network of their interaction.