1
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Wei A, Border R, Fu B, Cullina S, Brandes N, Jang SK, Sankararaman S, Kenny E, Udler MS, Ntranos V, Zaitlen N, Arboleda V. Investigating the sources of variable impact of pathogenic variants in monogenic metabolic conditions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.09.14.23295564. [PMID: 37745486 PMCID: PMC10516069 DOI: 10.1101/2023.09.14.23295564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Over three percent of people carry a dominant pathogenic variant, yet only a fraction of carriers develop disease. Disease phenotypes from carriers of variants in the same gene range from mild to severe. Here, we investigate underlying mechanisms for this heterogeneity: variable variant effect sizes, carrier polygenic backgrounds, and modulation of carrier effect by genetic background (marginal epistasis). We leveraged exomes and clinical phenotypes from the UK Biobank and the Mt. Sinai BioMe Biobank to identify carriers of pathogenic variants affecting cardiometabolic traits. We employed recently developed methods to study these cohorts, observing strong statistical support and clinical translational potential for all three mechanisms of variable carrier penetrance and disease severity. For example, scores from our recent model of variant pathogenicity were tightly correlated with phenotype amongst clinical variant carriers, they predicted effects of variants of unknown significance, and they distinguished gain- from loss-of-function variants. We also found that polygenic scores predicted phenotypes amongst pathogenic carriers and that epistatic effects can exceed main carrier effects by an order of magnitude.
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2
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De Paolo R, Sarti S, Bernardi S, Cucco F, Tavosanis A, Pitto L, Poliseno L. Differential impact of BRAFV600E isoforms on tumorigenesis in a zebrafish model of melanoma. Cell Biosci 2023; 13:121. [PMID: 37393328 DOI: 10.1186/s13578-023-01064-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/05/2023] [Indexed: 07/03/2023] Open
Abstract
BRAFV600E comes as two main splicing variants. The well-studied ref isoform and the recently discovered X1 isoform are co-expressed in cancer cells and differ in terms of 3'UTR length and sequence, as well as C-term protein sequence. Here, we use a melanoma model in zebrafish to study the role played by each isoform in larval pigmentation, nevi formation, and their progression into melanoma tumours. We show that both BRAFV600E-ref and BRAFV600E-X1 proteins promote larval pigmentation and nevi formation, while melanoma-free survival curves performed in adult fish indicate that BRAFV600E-ref protein is a much stronger melanoma driver that BRAFV600E-X1 protein. Crucially, we also show that the presence of the 3'UTR suppresses the effect of ref protein. Our data highlight the necessity to undertake a systematic study of BRAFV600E isoforms, in order to uncover the full spectrum of their kinase-(in)dependent and coding-(in)dependent functions, hence to develop more informed strategies for therapeutic targeting.
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Affiliation(s)
- Raffaella De Paolo
- Institute of Clinical Physiology, CNR, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory (CRL), ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
| | - Samanta Sarti
- Institute of Clinical Physiology, CNR, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory (CRL), ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, USA
| | - Sara Bernardi
- Institute of Clinical Physiology, CNR, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory (CRL), ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- Department of Molecular Medicine and Neurobiology, IRCCS Fondazione Stella Maris, Pisa, Italy
| | | | - Andrea Tavosanis
- Institute of Clinical Physiology, CNR, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory (CRL), ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Laura Poliseno
- Institute of Clinical Physiology, CNR, Pisa, Italy.
- Oncogenomics Unit, Core Research Laboratory (CRL), ISPRO, Via Moruzzi 1, 56124, Pisa, Italy.
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3
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Marranci A, Prantera A, Masotti S, De Paolo R, Baldanzi C, Podda MS, Mero S, Vitiello M, Franchin C, Laezza M, Comelli L, Arrigoni G, Cervelli T, Del Pozzo G, Poliseno L. PARP1 negatively regulates MAPK signaling by impairing BRAF-X1 translation. J Hematol Oncol 2023; 16:33. [PMID: 37013641 PMCID: PMC10071733 DOI: 10.1186/s13045-023-01428-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
In human cells BRAF oncogene is invariably expressed as a mix of two coding transcripts: BRAF-ref and BRAF-X1. These two mRNA isoforms, remarkably different in the sequence and length of their 3'UTRs, are potentially involved in distinct post-transcriptional regulatory circuits. Herein, we identify PARP1 among the mRNA Binding Proteins that specifically target the X1 3'UTR in melanoma cells. Mechanistically, PARP1 Zinc Finger domain down-regulates BRAF expression at the translational level. As a consequence, it exerts a negative impact on MAPK pathway, and sensitizes melanoma cells to BRAF and MEK inhibitors, both in vitro and in vivo. In summary, our study unveils PARP1 as a negative regulator of the highly oncogenic MAPK pathway in melanoma, through the modulation of BRAF-X1 expression.
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Affiliation(s)
- Andrea Marranci
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy.
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy.
- Fondazione Pisana per la Scienza ONLUS, 56017, Pisa, Italy.
| | - Antonella Prantera
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
| | - Simona Masotti
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
| | - Raffaella De Paolo
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
| | - Caterina Baldanzi
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
| | - Maurizio S Podda
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
| | - Serena Mero
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- Molecular Medicine and Neurobiology, IRCCS Fondazione Stella Maris, 56128, Pisa, Italy
| | - Marianna Vitiello
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- Genetics, Department of Biology, University of Pisa, 56126, Pisa, Italy
| | - Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Padua, Italy
| | - Mariavittoria Laezza
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
| | - Laura Comelli
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Padua, Italy
| | - Tiziana Cervelli
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
| | - Giovanna Del Pozzo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
| | - Laura Poliseno
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy.
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy.
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4
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Matsui JK, Perlow HK, Raj RK, Nalin AP, Lehrer EJ, Kotecha R, Trifiletti DM, McClelland S, Kendra K, Williams N, Owen DH, Presley CJ, Thomas EM, Beyer SJ, Blakaj DM, Ahluwalia MS, Raval RR, Palmer JD. Treatment of Brain Metastases: The Synergy of Radiotherapy and Immune Checkpoint Inhibitors. Biomedicines 2022; 10:2211. [PMID: 36140312 PMCID: PMC9496359 DOI: 10.3390/biomedicines10092211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/27/2022] Open
Abstract
Brain metastases are a devastating sequela of common primary cancers (e.g., lung, breast, and skin) and have limited effective therapeutic options. Previously, systemic chemotherapy failed to demonstrate significant benefit in patients with brain metastases, but in recent decades, targeted therapies and more recently immune checkpoint inhibitors (ICIs) have yielded promising results in preclinical and clinical studies. Furthermore, there is significant interest in harnessing the immunomodulatory effects of radiotherapy (RT) to synergize with ICIs. Herein, we discuss studies evaluating the impact of RT dose and fractionation on the immune response, early studies supporting the synergistic interaction between RT and ICIs, and ongoing clinical trials assessing the benefit of combination therapy in patients with brain metastases.
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Affiliation(s)
| | - Haley K. Perlow
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Rohit K. Raj
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Ansel P. Nalin
- College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Eric J. Lehrer
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rupesh Kotecha
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
| | | | - Shearwood McClelland
- Departments of Radiation Oncology and Neurological Surgery, University Hospitals Seidman Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kari Kendra
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Nicole Williams
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Dwight H. Owen
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Carolyn J. Presley
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Evan M. Thomas
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Sasha J. Beyer
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Dukagjin M. Blakaj
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Manmeet S. Ahluwalia
- Department of Medical Oncology, Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
| | - Raju R. Raval
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Joshua D. Palmer
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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5
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Honkala A, Malhotra SV, Kummar S, Junttila MR. Harnessing the predictive power of preclinical models for oncology drug development. Nat Rev Drug Discov 2021; 21:99-114. [PMID: 34702990 DOI: 10.1038/s41573-021-00301-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 12/21/2022]
Abstract
Recent progress in understanding the molecular basis of cellular processes, identification of promising therapeutic targets and evolution of the regulatory landscape makes this an exciting and unprecedented time to be in the field of oncology drug development. However, high costs, long development timelines and steep rates of attrition continue to afflict the drug development process. Lack of predictive preclinical models is considered one of the key reasons for the high rate of attrition in oncology. Generating meaningful and predictive results preclinically requires a firm grasp of the relevant biological questions and alignment of the model systems that mirror the patient context. In doing so, the ability to conduct both forward translation, the process of implementing basic research discoveries into practice, as well as reverse translation, the process of elucidating the mechanistic basis of clinical observations, greatly enhances our ability to develop effective anticancer treatments. In this Review, we outline issues in preclinical-to-clinical translatability of molecularly targeted cancer therapies, present concepts and examples of successful reverse translation, and highlight the need to better align tumour biology in patients with preclinical model systems including tracking of strengths and weaknesses of preclinical models throughout programme development.
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Affiliation(s)
- Alexander Honkala
- Department of Cell Development & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Sanjay V Malhotra
- Department of Cell Development & Cancer Biology, Oregon Health & Science University, Portland, OR, USA.,Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Shivaani Kummar
- Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. .,Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA.
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6
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Lee CS, Miao E, Das K, Seetharamu N. Clinical efficacy with dabrafenib and trametinib in a T599_V600insT poorly differentiated metastatic thyroid carcinoma. BMJ Case Rep 2021; 14:e243264. [PMID: 34413035 PMCID: PMC8378374 DOI: 10.1136/bcr-2021-243264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2021] [Indexed: 11/04/2022] Open
Abstract
BRAF (v-raf murine sarcoma viral oncogene homolog B1) and MEK (mitogen-activated protein kinase kinase) inhibitors have been shown to improve clinical outcomes in tumours presenting with mutations in the BRAF gene. The most common form of BRAF mutation is V600E/K and has been shown to occur in thyroid cancers. Treatment data for patients harbouring less frequent BRAF mutations are limited. In vitro studies have shown that mutations in codons 599-601 increase kinase activity similar to that in V600E mutations, which suggests that BRAF and MEK inhibitors could be an effective treatment option. Here, we report a case of a patient with thyroid carcinoma harbouring a rare amino acid insertion in codon 599 of the BRAF gene (T599_V600insT) treated with a BRAF and MEK inhibitor.
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Affiliation(s)
- Chung-Shien Lee
- Division of Medical Oncology and Hematology, Northwell Health Cancer Institute, Lake Success, New York, USA
- Clinical Health Professions, St John's University, Queens, New York, USA
| | - Emily Miao
- Pharmacy Department, North Shore University Hospital, Manhasset, New York, USA
| | - Kasturi Das
- Division of Cytopathology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Greenvale, New York, USA
| | - Nagashree Seetharamu
- Division of Medical Oncology and Hematology, Northwell Health Cancer Institute, Lake Success, New York, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
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7
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Li H, Yang L, Lai Y, Wang X, Han X, Liu S, Wang D, Li X, Hu N, Kong Y, Si L, Li Z. Genetic alteration of Chinese patients with rectal mucosal melanoma. BMC Cancer 2021; 21:623. [PMID: 34044811 PMCID: PMC8161925 DOI: 10.1186/s12885-021-08383-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/13/2021] [Indexed: 12/23/2022] Open
Abstract
Background Rectal mucosal melanoma (RMM) is a rare and highly aggressive disease with a poor prognosis. Due to the rarity of RMM, there are few studies focusing on its genetic mechanism. This retrospective study aimed to analyze the genetic spectrum and prognosis of RMM in China and lay a foundation for targeted therapy. Methods 36 patients with primary RMM from Peking University Cancer Hospital were enrolled in this study. The Next-generation sequencing (NGS) data of the tumor samples were fitted into the TruSight™ Oncology 500 (TSO500) Docker pipeline to detect genomic variants. Then, the univariate and multivariate Cox hazard analysis were performed to evaluate the correlations of the variants with the overall survival (OS), along with Kaplan-Meier and log-rank test to determine their significance. Results BRAF mutations, NRG1 deletions and mitotic index were significant prognostic factors in the univariate analysis. In multivariable analysis of the OS-related prognostic factors in primary RMM patients, it revealed 2 significant alterations: BRAF mutations [HR 7.732 (95%CI: 1.735–34.456), P = 0.007] and NRG1 deletions [HR 14.976 (95%CI: 2.305–97.300), P = 0.005]. Conclusions This is the first study to show genetic alterations exclusively to Chinese patients with RMM. We confirmed genetic alterations of RMM differ from cutaneous melanoma (CM). Our study indicates that BRAF and NRG1 were correlated with a poor prognostic of RMM and may be potential therapeutic targets for RMM treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08383-6.
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Affiliation(s)
- Huan Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Fucheng Road No.52, Haidian District, Peking, 100142, Beijing, People's Republic of China
| | - Lujing Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Fucheng Road No.52, Haidian District, Peking, 100142, Beijing, People's Republic of China
| | - Yumei Lai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Fucheng Road No.52, Haidian District, Peking, 100142, Beijing, People's Republic of China
| | - Xintong Wang
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, 100176, People's Republic of China
| | - Xinyin Han
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
| | - Siyao Liu
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, 100176, People's Republic of China
| | - Dongliang Wang
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, 100176, People's Republic of China
| | - Xiaojuan Li
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, 100176, People's Republic of China
| | - Nana Hu
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, 100176, People's Republic of China
| | - Yan Kong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Fucheng Road No.52, Haidian District, 100142, Beijing, People's Republic of China.
| | - Lu Si
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Fucheng Road No.52, Haidian District, 100142, Beijing, People's Republic of China.
| | - Zhongwu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Fucheng Road No.52, Haidian District, Peking, 100142, Beijing, People's Republic of China.
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8
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Argenziano G, Brancaccio G, Moscarella E, Dika E, Fargnoli MC, Ferrara G, Longo C, Pellacani G, Peris K, Pimpinelli N, Quaglino P, Rongioletti F, Simonacci M, Zalaudek I, Calzavara Pinton P. Management of cutaneous melanoma: comparison of the leading international guidelines updated to the 8th American Joint Committee on Cancer staging system and workup proposal by the Italian Society of Dermatology. GIORN ITAL DERMAT V 2021; 155:126-145. [PMID: 32394673 DOI: 10.23736/s0392-0488.19.06383-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Giuseppe Argenziano
- Unit of Dermatology, Luigi Vanvitelli University of Campania, Naples, Italy -
| | | | - Elvira Moscarella
- Unit of Dermatology, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Emi Dika
- Unit of Dermatology (DIMES), University of Bologna, Bologna, Italy
| | - Maria C Fargnoli
- Department of Dermatology, University of L'Aquila, L'Aquila, Italy
| | - Gerardo Ferrara
- Unit of Anatomic Pathology, Hospital of Macerata, Area Vasta 3 ASUR Marche, Macerata, Italy
| | - Caterina Longo
- Department of Dermatology, University of Modena and Reggio Emilia, Modena, Italy.,Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Centro Oncologico ad Alta Tecnologia Diagnostica-Dermatologia, Reggio Emilia, Italy
| | - Giovanni Pellacani
- Department of Dermatology, University of Modena and Reggio Emilia, Modena, Italy
| | - Ketty Peris
- Institute of Dermatology, Sacred Heart Catholic University, Rome, Italy.,A. Gemelli University Polyclinic, IRCCS and Foundation, Rome, Italy
| | - Nicola Pimpinelli
- Unit of Dermatology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Pietro Quaglino
- Dermatologic Clinic, Department of Medical Sciences, University of Turin Medical School, Turin, Italy
| | - Franco Rongioletti
- Unit of Dermatology, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Marco Simonacci
- Unit of Dermatology, Hospital of Macerata, Area Vasta 3 ASUR Marche, Macerata, Italy
| | - Iris Zalaudek
- Department of Dermatology, University Hospital of Trieste, Trieste, Italy
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9
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Abstract
The protein-coding regions of mRNAs have the information to make proteins and hence have been at the center of attention for understanding altered protein functions in disease states, including cancer. Indeed, the discovery of genomic alterations and driver mutations that change protein levels and/or activity has been pivotal in our understanding of cancer biology. However, to better understand complex molecular mechanisms that are deregulated in cancers, we also need to look at non-coding parts of mRNAs, including 3'UTRs (untranslated regions), which control mRNA stability, localization, and translation efficiency. Recently, these rather overlooked regions of mRNAs are gaining attention as mounting evidence provides functional links between 3'UTRs, protein functions, and cancer-related molecular mechanisms. Here, roles of 3'UTRs in cancer biology and mechanisms that result in cancer-specific 3'-end isoform variants will be reviewed. An increased appreciation of 3'UTRs may help the discovery of new ways to explain as of yet unknown oncogene activation and tumor suppressor inactivation cases in cancers, and provide new avenues for diagnostic and therapeutic applications.
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Affiliation(s)
- Ayse Elif Erson-Bensan
- Department of Biological Sciences and Cancer Systems Biology Laboratory, Middle East Technical University (METU, ODTU), Dumlupinar Blv No: 1, Universiteler Mah, 06800, Ankara, Turkey.
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10
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Sarti S, De Paolo R, Ippolito C, Pucci A, Pitto L, Poliseno L. Inducible modulation of miR-204 levels in a zebrafish melanoma model. Biol Open 2020; 9:bio053785. [PMID: 33037013 PMCID: PMC7657466 DOI: 10.1242/bio.053785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/22/2020] [Indexed: 11/20/2022] Open
Abstract
Here, we present miniCoopR-I, an inducible upgrade of the constitutive miniCoopR vector. We developed miniCoopR-I-sponge-204 and miniCoopR-I-pre-miR-204 vectors and we successfully tested them for their ability to achieve time- (embryo/juvenile/adult) and space- (melanocytic lineage) restricted inhibition/overexpression of miR-204, a positive modulator of pigmentation previously discovered by us. Furthermore, melanoma-free survival curves performed on induced fish at the adult stage indicate that miR-204 overexpression accelerates the development of BRAFV600E-driven melanoma. miniCoopR-I allows study of the impact that coding and non-coding modulators of pigmentation exert on melanomagenesis in adult zebrafish, uncoupling it from the impact that they exert on melanogenesis during embryonic development.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Samanta Sarti
- Oncogenomics Unit, CRL-ISPRO, Pisa 56124, Italy
- Institute of Clinical Physiology, CNR, Pisa 56124, Italy
| | - Raffaella De Paolo
- Oncogenomics Unit, CRL-ISPRO, Pisa 56124, Italy
- Institute of Clinical Physiology, CNR, Pisa 56124, Italy
- University of Siena, Siena 53100, Italy
| | - Chiara Ippolito
- Unit of Histology and Human Embryology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa 56126, Italy
| | - Angela Pucci
- Histopathology Department, Pisa University Hospital, Pisa 56126, Italy
| | - Letizia Pitto
- Institute of Clinical Physiology, CNR, Pisa 56124, Italy
| | - Laura Poliseno
- Oncogenomics Unit, CRL-ISPRO, Pisa 56124, Italy
- Institute of Clinical Physiology, CNR, Pisa 56124, Italy
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11
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Detection of BRAF V600E Mutation in Ganglioglioma and Pilocytic Astrocytoma by Immunohistochemistry and Real-Time PCR-Based Idylla Test. DISEASE MARKERS 2020; 2020:8880548. [PMID: 32879641 PMCID: PMC7448243 DOI: 10.1155/2020/8880548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/21/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022]
Abstract
The BRAF V600E mutation is an important oncological target in certain central nervous system (CNS) tumors, for which a possible application of BRAF-targeted therapy grows continuously. In the present study, we aim to determine the prevalence of BRAF V600E mutations in a series of ganglioglioma (GG) and pilocytic astrocytoma (PA) cases. Simultaneously, we decided to verify whether the combination of fully automated tests—BRAF-VE1 immunohistochemistry (IHC) and Idylla BRAF mutation assay—may be useful to accurately predict it in the case of specified CNS tumors. The study included 49 formalin-fixed, paraffin-embedded tissues, of which 15 were GG and 34 PA. Immunohistochemistry with anti-BRAF V600E (VE1) antibody was performed on tissue sections using the VentanaBenchMark ULTRA platform. All positive or equivocal cases on IHC and selected negative ones were further assessed using the Idylla BRAF mutation assay coupled with the Idylla platform. The BRAF-VE1 IHC was positive in 6 (6/49; 12.3%) and negative in 39 samples (39/49; 79.6%). The interpretation of immunostaining results was complicated in 4 cases, of which 1 tested positive for the Idylla BRAF mutation assay. Therefore, the overall positivity rate was 14.3%. This included 2 cases of GG and 5 cases of PA. Our study found that BRAF V600E mutations are moderately frequent in PA and GG and that for these tumor entities, IHC VE1 is suitable for screening purposes, but all negative, equivocal, and weak positive cases should be further tested with molecular biology techniques, of which the Idylla system seems to be a promising tool.
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Overcoming Resistance to Therapies Targeting the MAPK Pathway in BRAF-Mutated Tumours. JOURNAL OF ONCOLOGY 2020; 2020:1079827. [PMID: 32411231 PMCID: PMC7199609 DOI: 10.1155/2020/1079827] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/21/2019] [Accepted: 11/29/2019] [Indexed: 12/12/2022]
Abstract
Overactivation of the mitogen-activated protein kinase (MAPK) pathway is an important driver of many human cancers. First line, FDA-approved therapies targeting MAPK signalling, which include BRAF and MEK inhibitors, have variable success across cancers, and a significant number of patients quickly develop resistance. In recent years, a number of preclinical studies have reported alternative methods of overcoming resistance, which include promoting apoptosis, modulating autophagy, and targeting mitochondrial metabolism. This review summarizes mechanisms of resistance to approved MAPK-targeted therapies in BRAF-mutated cancers and discusses novel preclinical approaches to overcoming resistance.
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Systemic therapy for brain metastases. Crit Rev Oncol Hematol 2019; 142:44-50. [PMID: 31357143 DOI: 10.1016/j.critrevonc.2019.07.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 06/30/2019] [Accepted: 07/14/2019] [Indexed: 02/07/2023] Open
Abstract
Metastases from cells outside of the central nervous system are the most common cancer found in the brain and are commonly associated with poor prognosis. Although cancer treatment is improving overall, central nervous system metastases are becoming more prevalent and require finesse to properly treat. Physicians must consider the biology of the primary tumor and the complex neurological environment that the metastasis resides in. This can be further complicated by the fact that the practice of cancer management is constantly evolving and therapy that works outside of the blood-brain barrier may not be effective inside of it. Therefore, this review seeks to update the reader on recent advancements made on the three most common sources of brain metastases: lung cancer, breast cancer, and melanoma. Each of these malignancies has been the subject of intriguing and novel avenues of therapy which are reviewed here.
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Marranci A, D'Aurizio R, Vencken S, Mero S, Guzzolino E, Rizzo M, Pitto L, Pellegrini M, Chiorino G, Greene CM, Poliseno L. Systematic evaluation of the microRNAome through miR-CATCHv2.0 identifies positive and negative regulators of BRAF-X1 mRNA. RNA Biol 2019; 16:865-878. [PMID: 30929607 DOI: 10.1080/15476286.2019.1600934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Here we present miR-CATCHv2.0, an implemented experimental method that allows the identification of the microRNA species directly bound to an RNA of interest. After cross-linking of microRNA::RNA::Ago2 complexes using formaldehyde, the RNA is fragmented using sonication and then subjected to affinity purification using two sets of biotinylated tiling probes (ODD and EVEN). Finally, enriched microRNA species are retrieved by means of small RNA sequencing coupled with an ad hoc analytical workflow. In BRAFV600E mutant A375 melanoma cells, miR-CATCHv2.0 allowed us to identify 20 microRNAs that target X1, the most abundant isoform of BRAF mRNA. These microRNAs fall into different functional classes, according to the effect that they exert (decrease/increase in BRAFV600E mRNA and protein levels) and to the mechanism they use to achieve it (destabilization/stabilization of X1 mRNA or decrease/increase in its translation). microRNA-induced variations in BRAFV600E protein levels are most of the times coupled to consistent variations in pMEK levels, in melanoma cell proliferation in vitro and in sensitivity to the BRAF inhibitor vemurafenib in a xenograft model in zebrafish. However, microRNAs exist that uncouple the degree of activation of the ERK pathway from the levels of BRAFV600E protein. Our study proposes miR-CATCHv2.0 as an effective tool for the identification of direct microRNA-target interactions and, by using such a tool, unveils the complexity of the post-transcriptional regulation to which BRAFV600E and the ERK pathway are subjected in melanoma cells.
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Affiliation(s)
- Andrea Marranci
- a Institute of Clinical Physiology , CNR , Pisa , Italy.,b Oncogenomics Unit, Core Research Laboratory , ISPRO , Pisa , Italy.,c Signal Transduction Unit, Core Research Laboratory , ISPRO , Siena , Italy
| | | | - Sebastian Vencken
- e Department of Clinical Microbiology , Royal College of Surgeon in Ireland , Dublin , Ireland
| | - Serena Mero
- a Institute of Clinical Physiology , CNR , Pisa , Italy.,b Oncogenomics Unit, Core Research Laboratory , ISPRO , Pisa , Italy
| | | | - Milena Rizzo
- a Institute of Clinical Physiology , CNR , Pisa , Italy
| | - Letizia Pitto
- a Institute of Clinical Physiology , CNR , Pisa , Italy
| | | | - Giovanna Chiorino
- f Cancer Genomics Lab , Fondazione Edo ed Elvo Tempia , Biella , Italy
| | - Catherine M Greene
- e Department of Clinical Microbiology , Royal College of Surgeon in Ireland , Dublin , Ireland
| | - Laura Poliseno
- a Institute of Clinical Physiology , CNR , Pisa , Italy.,b Oncogenomics Unit, Core Research Laboratory , ISPRO , Pisa , Italy
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15
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Grassinger JM, Merz S, Aupperle-Lellbach H, Erhard H, Klopfleisch R. Correlation of BRAF Variant V595E, Breed, Histological Grade and Cyclooxygenase-2 Expression in Canine Transitional Cell Carcinomas. Vet Sci 2019; 6:vetsci6010031. [PMID: 30893857 PMCID: PMC6466154 DOI: 10.3390/vetsci6010031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 12/20/2022] Open
Abstract
The presence of BRAF variant V595E, as well as an increased cyclooxygenase-2 (COX-2) expression in canine transitional cell carcinoma (TCC) are well-described in the literature. The aim of the present study was to investigate the correlation between breed (terrier versus non-terrier dogs), histological grade, COX-2 expression, and BRAF mutation in canine TCC. Therefore, transmural TCC biopsies from 65 dogs (15 terriers, 50 non-terriers) were graded histologically into low- and high-grade. Immunohistochemical evaluation of the intensity of COX-2 expression was performed using an immunoreactive score (IRS). Exon 15 of chromosome 16 was examined for the BRAF variant c.1799T>A by TaqMan® SNP assay. TCC was low-grade in 20 cases (one terrier, 19 non-terriers) and high-grade in 45 cases (14 terriers, 31 non-terriers). Contrary to humans, histological grade was not significantly correlated to the intensity of COX-2 expression. BRAF mutation was detected in 11/15 (73%) TCC of terriers and in 18/50 (36%) TCC of non-terriers. Histological grade and BRAF mutation were not correlated significantly (p = 0.2912). Terriers had a considerably higher prevalence of high-grade tumors (p < 0.0001), as well as of BRAF mutation (p ≤ 0.05) compared to non-terriers. In non-terriers, neoplasms with BRAF mutation showed a significantly higher intensity of COX-2 expression than those without BRAF mutation (p ≤ 0.05). In conclusion, in contrast to humans, testing for BRAF mutation in canine TCC is a sensitive diagnostic method especially in terriers (73%) and may be recommended as a screening test. However, evidence of BRAF mutation in canine TCC is not a predictor for the histological grade. Moreover, a positive correlation between histological grade and the intensity of COX-2 expression was not found. Further studies are necessary to clarify the clinical and prognostic relevance of the elevated intensity of COX-2 expression of TCC with BRAF mutation detected in non-terriers.
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Affiliation(s)
| | - Sophie Merz
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany.
| | | | - Hanna Erhard
- Laboklin GmbH & Co. KG, 97688 Bad Kissingen, Germany.
| | - Robert Klopfleisch
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany.
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Lubrano S, Comelli L, Piccirilli C, Marranci A, Dapporto F, Tantillo E, Gemignani F, Gutkind JS, Salvetti A, Chiorino G, Cozza G, Chiariello M, Galli A, Poliseno L, Cervelli T. Development of a yeast-based system to identify new hBRAFV600E functional interactors. Oncogene 2018; 38:1355-1366. [PMID: 30237439 DOI: 10.1038/s41388-018-0496-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 07/30/2018] [Accepted: 08/14/2018] [Indexed: 11/09/2022]
Abstract
BRAFV600E is a mutant Ser-Thr protein kinase that plays a crucial role in many types of cancer, including melanoma. Despite several aspects of BRAFV600E biology have been already elucidated, the proteins that regulate its expression and activity remain largely unknown, hampering our capacity to control its unrestrained effects. Here, we propose yeast Saccharomyces cerevisiae as a model system that can be used to achieve a better understanding of the regulation of human BRAFV600E.By showing that in osmotic stress conditions hBRAFV600E can rescue the growth of strains carrying a double or triple deletion in MAPKKK belonging to the HOG pathway, we demonstrate that this oncogenic kinase is active in yeast even if it does not have an ortholog. Moreover, we report that, in the yeast ptp3∆ptc1∆ strain that is deleted in the genes encoding for two phosphatases responsible for Hog1 de-phoshorylation, hBRAFV600E mimics the toxicity observed in the presence of constitutive Hog1 activation. Finally, we exploit such a toxicity to perform a functional screening of a human cDNA library, looking for cDNAs able to rescue yeast growth. In this way, we identify SMIM10, a mitochondrial protein that in melanoma cells selectively downregulates BRAFV600E RNA and protein levels, by acting indirectly at the post-transcriptional level. Upon SMIM10 overexpression, BRAFV600E melanoma cells show disrupted mitochondrial structure/function and undergo senescence. They also show decreased ability to proliferate and form colonies, as well as increased sensitivity to the BRAF inhibitor vemurafenib. Interestingly, the analysis of TCGA melanoma samples indicates that patients with higher SMIM10 levels have a better prognosis. Therefore, these data suggest that SMIM10 exerts an oncosuppressive role in melanoma cells.Taken together, our results unveil the potential of S. cerevisiae to study hBRAFV600E, to populate the network of its functional interactors and, in doing so, to uncover new cancer-associated genes with therapeutic potential.
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Affiliation(s)
- Simone Lubrano
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy.,Institute of Clinical Physiology, IFC-CNR, Pisa, Italy.,Department of Biology, University of Pisa, Pisa, Italy
| | - Laura Comelli
- Institute of Clinical Physiology, IFC-CNR, Pisa, Italy
| | | | - Andrea Marranci
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy.,Institute of Clinical Physiology, IFC-CNR, Pisa, Italy
| | | | - Elena Tantillo
- Scuola Normale Superiore, Pisa, Italy.,FPS-Pisa Science Foundation, Pisa, Italy
| | | | - J Silvio Gutkind
- Department of Pharmacology, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Alessandra Salvetti
- Unit of Experimental Biology and Genetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Giovanna Chiorino
- Lab of Cancer Genomics, Fondazione Edo and Elvo Tempia, Biella, Italy
| | - Giorgio Cozza
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Mario Chiariello
- Institute of Clinical Physiology, IFC-CNR, Pisa, Italy.,Signal Transduction Unit, Core Research Laboratory, ISPRO, Siena, Italy
| | - Alvaro Galli
- Institute of Clinical Physiology, IFC-CNR, Pisa, Italy.
| | - Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy. .,Institute of Clinical Physiology, IFC-CNR, Pisa, Italy.
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Rosati E, Baldoni S, De Falco F, Del Papa B, Dorillo E, Rompietti C, Albi E, Falzetti F, Di Ianni M, Sportoletti P. NOTCH1 Aberrations in Chronic Lymphocytic Leukemia. Front Oncol 2018; 8:229. [PMID: 29998084 PMCID: PMC6030253 DOI: 10.3389/fonc.2018.00229] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/05/2018] [Indexed: 01/13/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is an incurable B-cell neoplasm characterized by highly variable clinical outcomes. In recent years, genomic and molecular studies revealed a remarkable heterogeneity in CLL, which mirrored the clinical diversity of this disease. These studies profoundly enhanced our understanding of leukemia cell biology and led to the identification of new biomarkers with potential prognostic and therapeutic significance. Accumulating evidence indicates a key role of deregulated NOTCH1 signaling and NOTCH1 mutations in CLL. This review highlights recent discoveries that improve our understanding of the pathophysiological NOTCH1 signaling in CLL and the clinical impact of NOTCH1 mutations in retrospective and prospective trials. In addition, we discuss the rationale for a therapeutic strategy aiming at inhibiting NOTCH1 signaling in CLL, along with an overview on the currently available NOTCH1-directed approaches.
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Affiliation(s)
- Emanuela Rosati
- Department of Experimental Medicine, Biosciences and Medical Embryology Section, University of Perugia, Perugia, Italy
| | - Stefano Baldoni
- Department of Life, Hematology Section, Health and Environmental Sciences, University of L'Aquila, Perugia, Italy
| | - Filomena De Falco
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Beatrice Del Papa
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Erica Dorillo
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Chiara Rompietti
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Elisa Albi
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Franca Falzetti
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Mauro Di Ianni
- Department of Medicine and Aging Sciences, University of Chieti Pescara, Chieti, Italy.,Department of Hematology, Transfusion Medicine and Biotechnologies, Ospedale Civile, Pescara, Italy
| | - Paolo Sportoletti
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
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