Periodic Reporting for period 1 - TETCOLON (Dissecting the role of the epigenetic regulator TET2 in colorectal cancer)
Reporting period: 2020-09-01 to 2022-08-31
Colorectal cancer (CRC) is the second leading cause for cancer-related deaths worldwide (GLOBOCAN, 2020) and its global incidence is on the rise. CRC is a complex disease characterized by the accumulation of genetic and epigenetic alterations in colonic epithelial cells. Elucidating the molecular and cellular mechanisms involved in CRC pathogenesis may lead to better prevention, diagnosis, prognosis, and more effective targeted therapies. Recently, due to the opportunity to chemically reverse the epigenetic changes, epigenetic therapies are emerging as promising treatment options.
The TET protein family dioxygenases (TET1-3) oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and subsequently to other oxidized forms of 5mC, in an active process that supports DNA demethylation and helps maintain epigenomic stability (Figure 1).
Emerging evidence indicates that TET1 is a tumorigenic driver in CRC and TET2 mutations have been identified in CRC by next generation sequencing approaches. In addition, CRCs frequently show loss of 5hmC but only a subset of these cancers has low TET1 expression, possibly involving other mechanisms, such as TET2 defects. These observations point to an important role of TET2 in CRC. However, whether TET2 defects contribute to CRC pathogenesis, or represent a bystander event, remains to be established.
This project aimed to investigate the role of TET2 in colorectal tumorigenesis with a multidisciplinary approach and an innovative technology, and to lay the groundwork for future translational studies. Specifically, the main objectives of this project were: 1) to investigate the functional consequences of TET2 defects in CRC, and 2) to determine the clinical significance of TET2 defects in human CRCs.
The findings made in the timeframe of TETCOLON project provided new knowledge on the molecular mechanisms and pathways implicated in the pathogenesis of CRC and they will likely be relevant for the clinical management of CRC patients.
The TET protein family dioxygenases (TET1-3) oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and subsequently to other oxidized forms of 5mC, in an active process that supports DNA demethylation and helps maintain epigenomic stability (Figure 1).
Emerging evidence indicates that TET1 is a tumorigenic driver in CRC and TET2 mutations have been identified in CRC by next generation sequencing approaches. In addition, CRCs frequently show loss of 5hmC but only a subset of these cancers has low TET1 expression, possibly involving other mechanisms, such as TET2 defects. These observations point to an important role of TET2 in CRC. However, whether TET2 defects contribute to CRC pathogenesis, or represent a bystander event, remains to be established.
This project aimed to investigate the role of TET2 in colorectal tumorigenesis with a multidisciplinary approach and an innovative technology, and to lay the groundwork for future translational studies. Specifically, the main objectives of this project were: 1) to investigate the functional consequences of TET2 defects in CRC, and 2) to determine the clinical significance of TET2 defects in human CRCs.
The findings made in the timeframe of TETCOLON project provided new knowledge on the molecular mechanisms and pathways implicated in the pathogenesis of CRC and they will likely be relevant for the clinical management of CRC patients.
In line with what described in the proposal, I set up a multidisciplinary approach (in silico and wet lab experiments) aimed to dissect the role of TET2 in CRC. Specifically, I modulated the level of TET2 expression in 2D and 3D cellular models of CRC and I characterized the functional effect of up- and down-regulation of TET2 in cell-based assays. Furthermore, by the data mining of the TCGA CRC dataset, I explored the correlations between the expression of TET2 genes and the molecular and clinico-pathological parameters of the tumors to assess the clinical significance of TET2 defects in human CRC cases. Our findings have contributed to better understand the role of the active DNA demethylation pathway in this tumor. Ongoing genome-wide gene expression and DNA methylation analysis, as well as data mining of a larger CRC dataset available through a collaboration with a biotech company, will lay the groundwork for future projects. Overall, over the time of this fellowship, not only I generated significant data towards the goal of the project, but also, I implemented new protocols and technologies of cellular biology and bioinformatics in the host laboratory and contributed to put in place new collaborations.
I have published a research article in the high impact journal Nature Communication (doi: 10.1038/s41467-022-29227-2) based on my previous collaborations and I wrote two scientific reviews: one was published in Clinical Cancer Research (doi: 10.1158/1078-0432.CCR-20-1741) and the other one is in press in Epigenomics. An additional research article and a review are in preparation for the special issue entitled “Genetics and Genomics of Gastrointestinal Cancers: From Prevention to Treatment” on Genes.
The outputs of my research were presented virtually at the department seminar series at the Host Institution and at the lab meetings during my secondment at the Helmholtz Diabetes Center of the Helmholtz Zentrum München (Munich, Germany). I was an invited speaker for the webinar focused on genome-wide methylation studies organized by the Italian Society of Human Genetics (SIGU) in 2020. I have attended the following workshop and conferences:
- First international workshop in sexual dimorphism (virtual edition), 2021
- Italian Association of Genetics Congress (virtual edition), 2021
- Italian conference on hereditary cancers-AIFEG (virtual edition); 2021
- 53rd European Society of Human Genetics Conference (virtual edition), 2021
- Italian Society of Human Genetics Congress (virtual edition), 2021
- 54th European Society of Human Genetics Conference (hybrid edition), 2022
- Italian conference on hereditary cancers-AIFET (former AIFEG) (in person); 2022
I have published a research article in the high impact journal Nature Communication (doi: 10.1038/s41467-022-29227-2) based on my previous collaborations and I wrote two scientific reviews: one was published in Clinical Cancer Research (doi: 10.1158/1078-0432.CCR-20-1741) and the other one is in press in Epigenomics. An additional research article and a review are in preparation for the special issue entitled “Genetics and Genomics of Gastrointestinal Cancers: From Prevention to Treatment” on Genes.
The outputs of my research were presented virtually at the department seminar series at the Host Institution and at the lab meetings during my secondment at the Helmholtz Diabetes Center of the Helmholtz Zentrum München (Munich, Germany). I was an invited speaker for the webinar focused on genome-wide methylation studies organized by the Italian Society of Human Genetics (SIGU) in 2020. I have attended the following workshop and conferences:
- First international workshop in sexual dimorphism (virtual edition), 2021
- Italian Association of Genetics Congress (virtual edition), 2021
- Italian conference on hereditary cancers-AIFEG (virtual edition); 2021
- 53rd European Society of Human Genetics Conference (virtual edition), 2021
- Italian Society of Human Genetics Congress (virtual edition), 2021
- 54th European Society of Human Genetics Conference (hybrid edition), 2022
- Italian conference on hereditary cancers-AIFET (former AIFEG) (in person); 2022
The findings of this project improved our understanding of the molecular mechanisms involved in reprogramming of DNA methylation patterns associated with colorectal carcinogenesis. This will contribute to better understand the molecular mechanisms of CRCs, to improve patients’ management and lead to a personalized approach for patients. In addition, since epigenetic alterations characterize several tumor types, the knowledge emerged from this study may advance the general understanding of the biology and therapy of cancer, beyond CRC. Overall, this will have a social impact in line with the objectives of Europe’s Beating cancer plan.
Over the course of the fellowship, I acquired new knowledge, leadership, and organizational skills; I set up new collaborations, I wrote scientific articles, and I gained experience in teaching and in supervising undergraduate and graduate students. These accomplishments have enforced my scientific maturity and independence and have contributed to launch a novel and innovative line of research at the host institution. Importantly, the above skills and knowledge have been an asset to be appointed as assistant professor (tenure-track) at host institution at the end of the fellowship.
Furthermore, I actively participated in the science popularization activities organized by the host institution for the European Researchers Night in 2021 including the following events: “Memory Game-Women & STEM” and “Guess Who?”. The latter was an event organized for bac, master, and PhD students to promote the research activities of the MSCA fellows and to publicize the opportunities offered by the MSCA fellowships, with more than 30 enthusiastic participants. In addition, I have been involved in events organized for high school students (e.g. “1hr with the researcher”) for the European Researchers Night in 2021 and 2022.
Over the course of the fellowship, I acquired new knowledge, leadership, and organizational skills; I set up new collaborations, I wrote scientific articles, and I gained experience in teaching and in supervising undergraduate and graduate students. These accomplishments have enforced my scientific maturity and independence and have contributed to launch a novel and innovative line of research at the host institution. Importantly, the above skills and knowledge have been an asset to be appointed as assistant professor (tenure-track) at host institution at the end of the fellowship.
Furthermore, I actively participated in the science popularization activities organized by the host institution for the European Researchers Night in 2021 including the following events: “Memory Game-Women & STEM” and “Guess Who?”. The latter was an event organized for bac, master, and PhD students to promote the research activities of the MSCA fellows and to publicize the opportunities offered by the MSCA fellowships, with more than 30 enthusiastic participants. In addition, I have been involved in events organized for high school students (e.g. “1hr with the researcher”) for the European Researchers Night in 2021 and 2022.