Salta al contenuto principale

Laboratory of cancer epistranscriptomics

Isaia Barbieri - PI

Isaia Barbieri
Biographical sketch

2022-present AIRC Start-up Research Group leader, Molecular Biotechnology Center, University of Turin.

Team Barbieri
Main group members

  • Dr Roberta Chiavetta post-doctoral research associate

  • Dr Giorgio Cinque post-doctoral research associate

  • Niccoló Chiapasco Biotechnology master student

  • Domenico Ignoti Biotechnology master student

  • Maxim Bouvet Biotechnology master student

Research activity

The discovery of chemical modifications of histone proteins and DNA brought the field of epigenetics to the forefront, highlighting their impact on gene expression. Epigenetic marks are orchestrated by three classes of proteins: writers, erasers, and readers and are ultimately responsible for cell type specification during development and its maintenance in adult individuals. It is therefore unsurprising that many epigenetic modifications are dysregulated in multiple cancer types. Similarly, more than 100 different types of post-synthesis modifications have been discovered on RNA. All four RNA bases and the ribose sugar can be targets for these modifications (Figure 1). Ribosomal RNA (rRNA) and transfer RNA (tRNA) are notably the most extensively modified. It is worth noting that most research efforts have historically been centred on protein and DNA modifications, leaving modifications of RNA largely unexplored. The excitement surrounding this field is fuelled by the untapped biological insights related to the modifications themselves and their therapeutic potential. Multiple lines of evidence now suggest that the dysregulation of epitranscriptome pathways plays a role in the development of human diseases, including cancer. Consequently, several biotechnology companies have emerged with the goal of identifying pharmacological agents that target RNA epigenetic pathways. In our laboratory, we are characterizing RNA methyltransferases as potential targets in haematological malignancies and solid tumours. Our focus lies in both uncovering new biologically significant functions with clinical relevance and identifying new epitranscriptomic molecular mechanisms. Specifically, we are keen on exploring the functional interplay between epitranscriptomic and traditional epigenetic mechanisms. Our ultimate goal is to develop small molecule inhibitors targeting RNA enzymes catalytic activity and develop new potential therapeutic approaches for cancer treatment. Currently, the laboratory is dedicated to two primary lines of research: 

1. Targeting the m6A pathway in ALK-driven Anaplastic Large Cell lymphoma

Figure 1

Recently the m6A RNA modification pathway was implicated in several pathological contexts, including cancer (Figure 2). In particular, several studies showed that the m6A writers METTL3 and METTL16 are essential for the maintenance of Acute Myeloid Leukaemia (Figure 3). These findings sparked the interest in the generation of small molecule inhibitors targeting the m6A pathway. We are testing the effects of both genetic inactivation of METTL3 and small molecule METTL3 inhibitors in ALK-driven Anaplastic large cell lymphoma (ALCL) and characterizing the molecular mechanisms responsible for their effects. Our interest sparked from the observation that ALK signalling enhances the m6A machinery through upregulating the transcription of METTL3. We are testing newly developed METTL3 inhibitors as a potential strategy to inhibit ALK+ ALCL cell proliferation both in vitro and in vivo. We are studying their effects both alone and in combination with the ALK-inhibitor Crizotinib in different ALCL cell lines and patient-derived xenograft cells grown in vitro. Additionally, we are investigating the potential use of METTL3 inhibitors as a new approach to overcome primary and/or acquired Crizotinib resistance in both cellular models of acquired resistance and in patient-derived xenografts (PDX) established from pediatric Crizotinib-resistant lymphoma samples.

2. Characterize the role of the mRNA methyltransferase TGS1 in cancer

Figure 2

We identified Tgs1 as one of the top targets required for the proliferation of RN2C mouse acute myeloid leukemia cells through a dropout CRISPR-CAS9 screening approach Figure 3). This enzyme is responsible for converting 7-methylguanosine 5’-cap (m7G) into 2,2,7 trimethylguanosine (m2,2,7G) non specific cellular RNAs. High levels of TGS1 correlate with a poor prognosis in Aggressive childhood leukemia and TGS1 exhibits high expression in AML compared to other cancer types. TGS1 is responsible for di-methylating the 5’ cap of small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA), thereby regulating their nuclear localization. Additionally, we discovered that, in acute myeloid leukaemia cells, TGS1 can modify the cap of a specific group of 500 mRNAs encoding specifically for proteins involved in cellular metabolism such as selenoproteins and mitochondrial factors. Mechanistically the m2,2,7G cap modification increases the translational rate of these crucial metabolic factors. RNA-seq experiment in two TGS1-depleted AML cell lines and revealed that TGS1 silencing induces the reshaping of cellular oxygen metabolism pathways, as indicated by gene ontology analysis. This observation supports the involvement of selenoproteins and mitochondrial proteins, which primarily function is protecting against oxidative stress and regulating oxygen metabolism, respectively. Crucially, TGS1 is overexpressed in numerous cancer types. In the future we intend to explore the function of this enzyme and the m2,2,7G modification in these cancer types, with a particular focus on its impact on metabolic processes. 

 

In the next few years we aim to develop the current projects and move our findings towards more translational models such as patient derived xenograft and mouse models, both in vitro and in vivo. Apart from this, we aim further identify and characterize epitranscriptomic factors in cancer. In particular, we will focus on performing CRISPR-CAS9 synthetic lethality screens, in the context of drug resistance, and screens to identify RNA enzymes involved in tumour progression mechanisms such as extravasation, angiogenesis and metastasis. Our findings will shed light on both epitranscriptomic mechanisms and their therapeutic potential in cancer.

  • 2022-2027 “Investigating RNA methylation in cancer” AIRC Start-Up grant, Italy

  •  2021-2022 “METTL3 inhibition as a novel therapeutic approach in ALK-driven ALCL both sensitive and resistant to ALK inhibition” Little princess trust project grant (UK) 

  • 2019-2020 “RNA methylation in SDH deficient Gastrointestinal stromal tumours ”Gist support UK (GSUK)/ Pathological society UK 

  • 2018-2022 “RNA methylation in Pediatric cancers” Start-up package Cancer research UK Cambridge center, paediatric program. (UK) 

  • 2017-2020 “Targeting m6A RNA methylation in AML.” The Kay Kendall Leukaemia Fund. (UK)

  • Dunsmore L et al., Controlled masking and targeted release of redox-cycling ortho-quinones via a C–C bond-cleaving 1,6-elimination. Nature Chemistry volume 14, pages 754–765 (2022) doi: 10.1038/s41557- 022-00964-7 

  • Leger A, Amaral PP, et al., RNA modifications detection by comparative Nanopore direct RNA sequencing. Nat Commun. 2021 Dec 10;12(1):7198. doi: 10.1038/ s41467-021-27393-3. 

  •  Miano V, Codino A, PandolfIni P and Barbieri I., The non-coding epitranscriptome in cancer. Briefings in Functional Genomics, Volume 20, Issue 2, March 2021, Pages 94–105, doi.org/10.1093/bfgp/elab003 

  • Prokoph N, et al., IL10RA Modulates Crizotinib Sensitivity in NPM1-ALK-positive Anaplastic Large Cell Lymphoma. Blood (2020) 136 (14): 1657–1669. doi: 10.1182/blood.2019003793. 

  •  Barbieri I & Kouzarides T. , Role of RNA modifications in cancer. Nat Rev Cancer 20, 303–322 (2020). doi. org/10.1038/s41568-020-0253-2 

  • PandolfIni L, Barbieri I et al., METTL1 Promotes letMicroRNA Processing via m7G Methylation, Mol Cell. 2019 Jun 20;74(6):1278-1290.e9. doi: 10.1016/j.molcel.2019.03.040.

  • Tzelepis K, et al., SRPK1 maintains acute myeloid leukaemia through effects on isoform usage of epigenetic regulators including BRD4. Nat Commun. 2018 Dec 19;9(1):5378. doi: 10.1038/s41467-018-07620-0. 

  • Barbieri I, Tzelepis K, PandolfIni L, et al.Promoter-bound METTL3 maintains myeloid leukaemia via m6A-dependent translation control. Nature. 2017 Dec 7;552(7683):126-131. doi: 10.1038/nature24678 

  • Wyspianska BS, Bannister AJ, Barbieri I et al., BET protein inhibition shows efficacy against JAK2V617F-driven neoplasms. Leukemia. 2014 Jan;28(1):88-97. doi: 10.1038/leu.2013.234. 

  • Barbieri I, Pensa S, et al., Constitutively active Stat3 enhances Neu-mediated migration and metastasis in mammary tumours via upregulation of Cten. Cancer Research, 2010 Mar 15;70(6):2558-67. doi: 10.1158/0008-5472.CAN-09-2840 

Scopus ID
Ultimo aggiornamento:
Share: