1
|
Kassir N, McDougall D, Kuruvilla D, Kim S, Kumar S, Rahman A, Ruf T, Cheeti S, Ankrom W. Exposure-Response Relationships for Pralsetinib in Patients with RET-Altered Thyroid Cancer or RET Fusion-Positive Nonsmall Cell Lung Cancer. J Clin Pharmacol 2024; 64:685-696. [PMID: 38337106 DOI: 10.1002/jcph.2409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
Pralsetinib is a highly potent oral kinase inhibitor of oncogenic RET (rearranged during transfection) fusions and mutations. Pralsetinib received approval from the United States Food and Drug Administration for the treatment of patients with metastatic RET fusion-positive non-small cell lung cancer (NSCLC), and received accelerated approval for the treatment of patients with RET fusion-positive thyroid cancer. Exposure-response (ER) analyses of efficacy were performed separately in patients with thyroid cancer and in patients with NSCLC, but data for all patients were pooled for the safety analysis. ER models were developed with time-varying exposure; the effect of covariates was also examined. For patients with NSCLC, a higher starting dose was associated with improved progression-free survival (PFS), but this improvement did not correlate with a higher exposure overall. Significant covariates included sex and baseline Eastern Cooperative Oncology Group (ECOG) score. For patients with thyroid cancer, a higher exposure was associated with improved PFS. Significant covariates included prior systemic cancer therapy and ECOG score. For safety, higher exposure was associated with a greater risk of grade ≥3 anemia, pneumonia, and lymphopenia. Patients with an ECOG score of ≥1 had an increased risk of grade ≥3 pneumonia. Non-White patients had a lower risk of grade ≥3 lymphopenia. ER analysis revealed that higher pralsetinib exposure was associated with improved PFS in thyroid cancer, but not in NSCLC. However, a higher starting dose (ie, 400 vs ≤300 mg daily) was correlated with better PFS for all indications. Higher exposure was also associated with an increased risk of grade ≥3 adverse events (AEs); however, the overall incidence of these events was acceptably low (≤20%). This analysis supports the use of a 400 mg starting dose of pralsetinib, allowing for dose reduction in the event of AEs.
Collapse
Affiliation(s)
| | | | | | - Sean Kim
- Blueprint Medicines Corporation, Cambridge, MA, USA
| | | | | | | | | | - Wendy Ankrom
- Blueprint Medicines Corporation, Cambridge, MA, USA
| |
Collapse
|
2
|
Moran JMT, Le LP, Nardi V, Golas J, Farahani AA, Signorelli S, Onozato ML, Foreman RK, Duncan LM, Lawrence DP, Lennerz JK, Dias-Santagata D, Hoang MP. Identification of fusions with potential clinical significance in melanoma. Mod Pathol 2022; 35:1837-1847. [PMID: 35871080 DOI: 10.1038/s41379-022-01138-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 12/24/2022]
Abstract
Though uncommon in melanoma, gene fusions may have therapeutic implications. Next generation sequencing-based clinical assays, designed to detect relevant gene fusions, mutations, and copy number changes, were performed on 750 melanomas (375 primary and 375 metastases) at our institution from 2014-2021. These included 599 (80%) cutaneous, 38 (5%) acral, 11 (1.5%) anorectal, 23 (3%) sinonasal, 27 (3.6%) eye (uveal/ conjunctiva), 11 (1.5%) genital (vulva/penile), and 41 (5.5%) melanomas of unknown primary. Sixteen fusions (2%) were detected in samples from 16 patients: 12/599 (2%) cutaneous, 2/38 (5%) acral, 1/9 (11%) vulva, 1/23(4.3%) sinonasal; and 12/16 (75%) fusions were potentially targetable. We identified two novel rearrangements: NAGS::MAST2 and NOTCH1::GNB1; and two fusions that have been reported in other malignancies but not in melanoma: CANT1::ETV4 (prostate cancer) and CCDC6::RET (thyroid cancer). Additional fusions, previously reported in melanoma, included: EML4::ALK, MLPH::ALK, AGAP3::BRAF, AGK::BRAF, CDH3::BRAF, CCT8::BRAF, DIP2B::BRAF, EFNB1::RAF1, LRCH3::RAF1, MAP4::RAF1, RUFY1::RAF1, and ADCY2::TERT. Fusion positive melanomas harbored recurrent alterations in TERT and CDKN2A, among others. Gene fusions were exceedingly rare (0.2%) in BRAF/RAS/NF1-mutant tumors and were detected in 5.6% of triple wild-type melanomas. Interestingly, gene rearrangements were significantly enriched within the subset of triple wild-type melanomas that harbor TERT promoter mutations (18% versus 2%, p < 0.0001). Thirteen (81%) patients were treated with immunotherapy for metastatic disease or in the adjuvant setting. Six of 12 (50%) patients with potentially actionable fusions progressed on immunotherapy, and 3/6 (50%) were treated with targeted agents (ALK and MEK inhibitors), 2 off-label and 1 as part of a clinical trial. One patient with an AGAP3::BRAF fusion positive melanoma experienced a 30-month long response to trametinib. We show that, detecting fusions, especially in triple wild-type melanomas with TERT promoter mutations, may have a clinically significant impact in patients with advanced disease who have failed front-line immunotherapy.
Collapse
Affiliation(s)
- Jakob M T Moran
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Long P Le
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Josephine Golas
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander A Farahani
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sylvia Signorelli
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Maristela L Onozato
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ruth K Foreman
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lyn M Duncan
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Donald P Lawrence
- Division of Medical Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
3
|
Vishwanath D, Shanmugam A, Sundaresh M, Hariharan A, Saraf S, Bahadur U, Veeramachaneni V, Chandrasekhar N, Pillai V V, Bushan V, Shetty V, Subramaniam N, Kuriakose MA, Shivaprasad KS, Khadilkar K, Suresh A, Sum S, Lakhsmikantha A, Rekha PR, Zaidi SN, Gupta V, Kannan S. Development of a Low-cost NGS Test for the Evaluation of Thyroid Nodules. Indian J Surg Oncol 2022; 13:17-22. [PMID: 35462651 PMCID: PMC8986928 DOI: 10.1007/s13193-019-01000-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/25/2019] [Indexed: 10/25/2022] Open
Abstract
Ultrasound-guided fine needle aspiration cytology (FNAC) is the preferred method of identifying malignancy in palpable thyroid nodules using the Bethesda reporting system. However, in around 30-40% of FNACs (Bethesda categories III, IV, and V), the results are indeterminate and surgery is required to confirm malignancy. Out of those who undergo surgery, only 10-40% of patients in these categories are found to have malignancies, thus proving surgery to be unnecessary for some patients or to be incomplete in others. While molecular testing on thyroid FNAC material is part of the American Thyroid Association (ATA) guidelines in evaluating thyroid nodules, it is currently unavailable in India due to cost constraints. In this study, we prospectively collected FNAC samples from sixty-nine patients who presented with palpable thyroid nodules. We designed a cost-effective next-generation sequencing (NGS) test to query multiple variants in the DNA and RNA isolated from the fine needle aspirate. The identification of oncogenic variants was considered to be indicative of malignancy, and confirmed by surgical histopathology. The panel showed an overall sensitivity of 81.25% and a specificity of 100%, while in the case of Bethesda categories III, IV, and V, the sensitivity was higher (87.5%) and the specificity was established at 100%. The panel could thereby serve as a rule-in test for the diagnosis of thyroid cancer and therefore help identify patients who require surgery, especially in the indeterminate Bethesda categories III, IV, and V.
Collapse
Affiliation(s)
- Divya Vishwanath
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Ashwini Shanmugam
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Mahima Sundaresh
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Arun Hariharan
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Shradha Saraf
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Urvashi Bahadur
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Vamsi Veeramachaneni
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Naveen Chandrasekhar
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vijay Pillai V
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vidhya Bushan
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vivek Shetty
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Narayana Subramaniam
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Moni Abraham Kuriakose
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - K. S. Shivaprasad
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Kranti Khadilkar
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Amritha Suresh
- grid.506019.bMazumdar Shaw Medical Foundation, 258/A, Hosur Road Anekal, Taluk, Bommasandra Industrial Area, Bangalore, Karnataka 560099 India
| | - Sum Sum
- grid.506019.bMazumdar Shaw Medical Foundation, 258/A, Hosur Road Anekal, Taluk, Bommasandra Industrial Area, Bangalore, Karnataka 560099 India
| | - Akhila Lakhsmikantha
- grid.416504.20000 0004 1796 819XDepartment of Pathology & Laboratory Services, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Pobbisetty Radhakrishnagupta Rekha
- grid.416504.20000 0004 1796 819XDepartment of Pathology & Laboratory Services, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Shaesta Naseem Zaidi
- grid.416504.20000 0004 1796 819XDepartment of Pathology & Laboratory Services, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vaijayanti Gupta
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Subramanian Kannan
- grid.416504.20000 0004 1796 819XDepartment of Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| |
Collapse
|
4
|
Mayr L, Guntner AS, Madlener S, Schmook MT, Peyrl A, Azizi AA, Dieckmann K, Reisinger D, Stepien NM, Schramm K, Laemmerer A, Jones DTW, Ecker J, Sahm F, Milde T, Pajtler KW, Blattner-Johnson M, Strbac M, Dorfer C, Czech T, Kirchhofer D, Gabler L, Berger W, Haberler C, Müllauer L, Buchberger W, Slavc I, Lötsch-Gojo D, Gojo J. Cerebrospinal Fluid Penetration and Combination Therapy of Entrectinib for Disseminated ROS1/NTRK-Fusion Positive Pediatric High-Grade Glioma. J Pers Med 2020; 10:E290. [PMID: 33353026 PMCID: PMC7766483 DOI: 10.3390/jpm10040290] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
Targeting oncogenic fusion-genes in pediatric high-grade gliomas (pHGG) with entrectinib has emerged as a highly promising therapeutic approach. Despite ongoing clinical studies, to date, no reports on the treatment of cerebrospinal fluid (CSF) disseminated fusion-positive pHGG exist. Moreover, clinically important information of combination with other treatment modalities such as intrathecal therapy, radiotherapy and other targeted agents is missing. We report on our clinical experience of entrectinib therapy in two CSF disseminated ROS1/NTRK-fusion-positive pHGG cases. Combination of entrectinib with radiotherapy or intrathecal chemotherapy appears to be safe and has the potential to act synergistically with entrectinib treatment. In addition, we demonstrate CSF penetrance of entrectinib for the first time in patient samples suggesting target engagement even upon CSF dissemination. Moreover, in vitro analyses of two novel cell models derived from one case with NTRK-fusion revealed that combination therapy with either a MEK (trametinib) or a CDK4/6 (abemaciclib) inhibitor synergistically enhances entrectinib anticancer effects. In summary, our comprehensive study, including clinical experience, CSF penetrance and in vitro data on entrectinib therapy of NTRK/ROS1-fusion-positive pHGG, provides essential clinical and preclinical insights into the multimodal treatment of these highly aggressive tumors. Our data suggest that combined inhibition of NTRK/ROS1 and other therapeutic vulnerabilities enhances the antitumor effect, which should be followed-up in further preclinical and clinical studies.
Collapse
Affiliation(s)
- Lisa Mayr
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; (L.M.); (S.M.); (A.P.); (A.A.A.); (D.R.); (N.M.S.); (A.L.); (D.K.); (I.S.)
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (L.G.); (W.B.)
- Comprehensive Cancer Center-Central Nervous System Tumors Unit, Medical University of Vienna, 1090 Vienna, Austria
| | - Armin S. Guntner
- Institute of Analytical Chemistry, Johannes Kepler University, 4020 Linz, Austria; (A.S.G.); (W.B.)
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; (L.M.); (S.M.); (A.P.); (A.A.A.); (D.R.); (N.M.S.); (A.L.); (D.K.); (I.S.)
- Comprehensive Cancer Center-Central Nervous System Tumors Unit, Medical University of Vienna, 1090 Vienna, Austria
| | - Maria T. Schmook
- Division of Neuroradiology and Musculoskeletal Radiology, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria;
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; (L.M.); (S.M.); (A.P.); (A.A.A.); (D.R.); (N.M.S.); (A.L.); (D.K.); (I.S.)
| | - Amedeo A. Azizi
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; (L.M.); (S.M.); (A.P.); (A.A.A.); (D.R.); (N.M.S.); (A.L.); (D.K.); (I.S.)
| | - Karin Dieckmann
- Department of Radiotherapy, Medical University of Vienna, 1090 Vienna, Austria;
| | - Dominik Reisinger
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; (L.M.); (S.M.); (A.P.); (A.A.A.); (D.R.); (N.M.S.); (A.L.); (D.K.); (I.S.)
| | - Natalia M. Stepien
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; (L.M.); (S.M.); (A.P.); (A.A.A.); (D.R.); (N.M.S.); (A.L.); (D.K.); (I.S.)
| | - Kathrin Schramm
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; (K.S.); (D.T.W.J.); (T.M.); (K.W.P.); (M.B.-J.)
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Anna Laemmerer
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; (L.M.); (S.M.); (A.P.); (A.A.A.); (D.R.); (N.M.S.); (A.L.); (D.K.); (I.S.)
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (L.G.); (W.B.)
- Comprehensive Cancer Center-Central Nervous System Tumors Unit, Medical University of Vienna, 1090 Vienna, Austria
| | - David T. W. Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; (K.S.); (D.T.W.J.); (T.M.); (K.W.P.); (M.B.-J.)
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jonas Ecker
- Clinical Cooperation Unit Pediatric Oncology, Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany;
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany;
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Till Milde
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; (K.S.); (D.T.W.J.); (T.M.); (K.W.P.); (M.B.-J.)
- Clinical Cooperation Unit Pediatric Oncology, Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany;
| | - Kristian W. Pajtler
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; (K.S.); (D.T.W.J.); (T.M.); (K.W.P.); (M.B.-J.)
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Mirjam Blattner-Johnson
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; (K.S.); (D.T.W.J.); (T.M.); (K.W.P.); (M.B.-J.)
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Miroslav Strbac
- Department of Laboratory Medicine and Pathology, Tree Top Hospital, Hulhumale 23000, Maldives;
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria; (C.D.); (T.C.)
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria; (C.D.); (T.C.)
| | - Dominik Kirchhofer
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; (L.M.); (S.M.); (A.P.); (A.A.A.); (D.R.); (N.M.S.); (A.L.); (D.K.); (I.S.)
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (L.G.); (W.B.)
- Comprehensive Cancer Center-Central Nervous System Tumors Unit, Medical University of Vienna, 1090 Vienna, Austria
| | - Lisa Gabler
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (L.G.); (W.B.)
- Comprehensive Cancer Center-Central Nervous System Tumors Unit, Medical University of Vienna, 1090 Vienna, Austria
| | - Walter Berger
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (L.G.); (W.B.)
- Comprehensive Cancer Center-Central Nervous System Tumors Unit, Medical University of Vienna, 1090 Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria;
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria;
| | - Wolfgang Buchberger
- Institute of Analytical Chemistry, Johannes Kepler University, 4020 Linz, Austria; (A.S.G.); (W.B.)
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; (L.M.); (S.M.); (A.P.); (A.A.A.); (D.R.); (N.M.S.); (A.L.); (D.K.); (I.S.)
| | - Daniela Lötsch-Gojo
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (L.G.); (W.B.)
- Comprehensive Cancer Center-Central Nervous System Tumors Unit, Medical University of Vienna, 1090 Vienna, Austria
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria; (C.D.); (T.C.)
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; (L.M.); (S.M.); (A.P.); (A.A.A.); (D.R.); (N.M.S.); (A.L.); (D.K.); (I.S.)
- Comprehensive Cancer Center-Central Nervous System Tumors Unit, Medical University of Vienna, 1090 Vienna, Austria
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; (K.S.); (D.T.W.J.); (T.M.); (K.W.P.); (M.B.-J.)
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| |
Collapse
|
5
|
Odate T, Oishi N, Vuong HG, Mochizuki K, Kondo T. Genetic differences in follicular thyroid carcinoma between Asian and Western countries: a systematic review. Gland Surg 2020; 9:1813-1826. [PMID: 33224857 DOI: 10.21037/gs-20-356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Thyroid cancer is the most common endocrine malignancy, and follicular thyroid carcinoma (FTC) is the second most common thyroid cancer following papillary thyroid carcinoma (PTC). RAS mutation and PAX8/PPARγ rearrangement are the two representative genetic alterations in FTC, and there are studies from various countries on their regional frequencies. In this study, we systematically reviewed all available literature aiming to create a complete global map showing the frequencies of these common oncogenic drivers in FTC and to highlight the trends in Asian and Western countries. We performed a search in two electronic databases and identified 71 studies that fit our criteria from 1,329 studies found with our database search terms. There were 54 articles with 1,143 FTC patients and 39 articles with 764 FTC patients available for calculating the frequency of RAS mutation and PAX8/PPARγ rearrangement, respectively. NRAS mutation was the most frequent RAS mutation in all regions, followed by HRAS and KRAS mutation. The frequency of RAS mutation in Asian countries was higher than Western countries (34% vs. 27%, P=0.006) when the mutation detection method was not taken into account. In contrast, this difference in RAS mutation incidence between Asian and Western countries (28% vs. 25%, P=0.47) did not show up in our subgroup analysis incorporating only studies using direct sequencing method. The reported difference of RAS mutation frequency in the previous literature might not be due to the true prevalence of RAS mutation. They could be attributed to the difference in the detection method. As to PAX8/PPARγ rearrangement, Western countries overall had a much higher prevalence than Asian countries (23% vs. 4%, P<0.001), but some European countries had a low incidence, implying regional heterogeneity of PAX8/PPARγ rearrangement. A substantial lack of mutation data in FTC was found in several regions of the world such as Central Asia, Middle East, Africa, and Central and South America. Our results provide the most comprehensive global status of representative genetic alterations in FTC and highlight the similarities and differences between Asian and Western countries.
Collapse
Affiliation(s)
- Toru Odate
- Department of Pathology, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Naoki Oishi
- Department of Pathology, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Huy Gia Vuong
- Department of Pathology, Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | - Kunio Mochizuki
- Department of Pathology, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Tetsuo Kondo
- Department of Pathology, University of Yamanashi, Chuo, Yamanashi, Japan
| |
Collapse
|
6
|
Vellichirammal NN, Albahrani A, Banwait JK, Mishra NK, Li Y, Roychoudhury S, Kling MJ, Mirza S, Bhakat KK, Band V, Joshi SS, Guda C. Pan-Cancer Analysis Reveals the Diverse Landscape of Novel Sense and Antisense Fusion Transcripts. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:1379-1398. [PMID: 32160708 PMCID: PMC7044684 DOI: 10.1016/j.omtn.2020.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/03/2020] [Accepted: 01/14/2020] [Indexed: 01/26/2023]
Abstract
Gene fusions that contribute to oncogenicity can be explored for identifying cancer biomarkers and potential drug targets. To investigate the nature and distribution of fusion transcripts in cancer, we examined the transcriptome data of about 9,000 primary tumors from 33 different cancers in TCGA (The Cancer Genome Atlas) along with cell line data from CCLE (Cancer Cell Line Encyclopedia) using ChimeRScope, a novel fusion detection algorithm. We identified several fusions with sense (canonical, 39%) or antisense (non-canonical, 61%) transcripts recurrent across cancers. The majority of the recurrent non-canonical fusions found in our study are novel, unexplored, and exhibited highly variable profiles across cancers, with breast cancer and glioblastoma having the highest and lowest rates, respectively. Overall, 4,344 recurrent fusions were identified from TCGA in this study, of which 70% were novel. Additional analysis of 802 tumor-derived cell line transcriptome data across 20 cancers revealed significant variability in recurrent fusion profiles between primary tumors and corresponding cell lines. A subset of canonical and non-canonical fusions was validated by examining the structural variation evidence in whole-genome sequencing (WGS) data or by Sanger sequencing of fusion junctions. Several recurrent fusion genes identified in our study show promise for drug repurposing in basket trials and present opportunities for mechanistic studies.
Collapse
Affiliation(s)
| | - Abrar Albahrani
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jasjit K Banwait
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; Bioinformatics and Systems Biology Core. University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nitish K Mishra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - You Li
- HitGen, South Keyuan Road 88, Chengdu, China
| | - Shrabasti Roychoudhury
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mathew J Kling
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shantaram S Joshi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; Bioinformatics and Systems Biology Core. University of Nebraska Medical Center, Omaha, NE 68198, USA.
| |
Collapse
|
7
|
Ferguson SD, Zhou S, Huse JT, de Groot JF, Xiu J, Subramaniam DS, Mehta S, Gatalica Z, Swensen J, Sanai N, Spetzler D, Heimberger AB. Targetable Gene Fusions Associate With the IDH Wild-Type Astrocytic Lineage in Adult Gliomas. J Neuropathol Exp Neurol 2019; 77:437-442. [PMID: 29718398 PMCID: PMC5961205 DOI: 10.1093/jnen/nly022] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Gene fusions involving oncogenes have been reported in gliomas and may serve as novel therapeutic targets. Using RNA-sequencing, we interrogated a large cohort of gliomas to assess for the incidence of targetable genetic fusions. Gliomas (n = 390) were profiled using the ArcherDx FusionPlex Assay. Fifty-two gene targets were analyzed and fusions with preserved kinase domains were investigated. Overall, 36 gliomas (9%) harbored a total of 37 potentially targetable fusions, the majority of which were found in astrocytomas (n = 34). Within this lineage 11% (25/235) of glioblastomas, 12% (5/42) of anaplastic astrocytomas, 8% (2/25) of grade II astrocytomas, and 33% (2/6) of pilocytic astrocytoma harbored targetable fusions. Fusions were significantly more frequent in IDH wild-type tumors (12%, n = 31/261) relative to IDH mutants (4%; n = 4/109) (p = 0.011). No fusions were seen in oligodendrogliomas. The most frequently observed therapeutically targetable fusions were in FGFR (n = 12), MET (n = 11), and NTRK (n = 8). Several additional novel fusions that have not been previously described in gliomas were identified including EGFR:VWC2 and FGFR3:NBR1. In summary, targetable gene fusions are enriched in IDH wild-type high-grade astrocytic tumors, which will influence enrollment in and interpretation of clinical trials of glioma patients.
Collapse
Affiliation(s)
- Sherise D Ferguson
- Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shouhao Zhou
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason T Huse
- Department of Neuropathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John F de Groot
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Deepa S Subramaniam
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Shwetal Mehta
- Barrow Neurological Institute and Barrow Neurosurgical Associates, Phoenix, Arizona
| | | | | | - Nader Sanai
- Barrow Neurological Institute and Barrow Neurosurgical Associates, Phoenix, Arizona
| | | | | |
Collapse
|
8
|
Detection of RET rearrangements in papillary thyroid carcinoma using RT-PCR and FISH techniques - A molecular and clinical analysis. Eur J Surg Oncol 2019; 45:1018-1024. [DOI: 10.1016/j.ejso.2018.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/22/2018] [Accepted: 11/12/2018] [Indexed: 12/26/2022] Open
|
9
|
Celestino R, Nome T, Pestana A, Hoff AM, Gonçalves AP, Pereira L, Cavadas B, Eloy C, Bjøro T, Sobrinho-Simões M, Skotheim RI, Soares P. CRABP1, C1QL1 and LCN2 are biomarkers of differentiated thyroid carcinoma, and predict extrathyroidal extension. BMC Cancer 2018; 18:68. [PMID: 29321030 PMCID: PMC5763897 DOI: 10.1186/s12885-017-3948-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 12/20/2017] [Indexed: 01/21/2023] Open
Abstract
Background The prognostic variability of thyroid carcinomas has led to the search for accurate biomarkers at the molecular level. Follicular thyroid carcinoma (FTC) is a typical example of differentiated thyroid carcinomas (DTC) in which challenges are faced in the differential diagnosis. Methods We used high-throughput paired-end RNA sequencing technology to study four cases of FTC with different degree of capsular invasion: two minimally invasive (mFTC) and two widely invasive FTC (wFTC). We searched by genes differentially expressed between mFTC and wFTC, in an attempt to find biomarkers of thyroid cancer diagnosis and/or progression. Selected biomarkers were validated by real-time quantitative PCR in 137 frozen thyroid samples and in an independent dataset (TCGA), evaluating the diagnostic and the prognostic performance of the candidate biomarkers. Results We identified 17 genes significantly differentially expressed between mFTC and wFTC. C1QL1, LCN2, CRABP1 and CILP were differentially expressed in DTC in comparison with normal thyroid tissues. LCN2 and CRABP1 were also differentially expressed in DTC when compared with follicular thyroid adenoma. Additionally, overexpression of LCN2 and C1QL1 were found to be independent predictors of extrathyroidal extension in DTC. Conclusions We conclude that the underexpression of CRABP1 and the overexpression of LCN2 may be useful diagnostic biomarkers in thyroid tumours with questionable malignity, and the overexpression of LCN2 and C1QL1 may be useful for prognostic purposes. Electronic supplementary material The online version of this article (10.1186/s12885-017-3948-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ricardo Celestino
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, P.O.Box 4953 Nydalen, 0424, Oslo, Norway.,School of Allied Health Technologies, Polytechnic of Porto, Rua Dr. António Bernardino de Almeida, 400, 4200-072, Porto, Portugal
| | - Torfinn Nome
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, P.O.Box 4953 Nydalen, 0424, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0424, Oslo, Norway
| | - Ana Pestana
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,ICBAS - Abel Salazar Biomedical Sciences Institute of the University of Porto, 4050-313, Porto, Portugal
| | - Andreas M Hoff
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, P.O.Box 4953 Nydalen, 0424, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0424, Oslo, Norway
| | - A Pedro Gonçalves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,ICBAS - Abel Salazar Biomedical Sciences Institute of the University of Porto, 4050-313, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Luísa Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Bruno Cavadas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Catarina Eloy
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Trine Bjøro
- Department of Medical Biochemistry, Norwegian Radium Hospital, Oslo University Hospital, 0424, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway
| | - Manuel Sobrinho-Simões
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Department of Pathology, Medical Faculty, University of Porto, 4200-319, Porto, Portugal.,Department of Pathology, Centro Hospitalar de São João, 4200-319, Porto, Portugal
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, P.O.Box 4953 Nydalen, 0424, Oslo, Norway. .,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0424, Oslo, Norway.
| | - Paula Soares
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal. .,Department of Pathology, Medical Faculty, University of Porto, 4200-319, Porto, Portugal.
| |
Collapse
|
10
|
Najafian A, Noureldine S, Azar F, Atallah C, Trinh G, Schneider EB, Tufano RP, Zeiger MA. RAS Mutations, and RET/PTC and PAX8/PPAR-gamma Chromosomal Rearrangements Are Also Prevalent in Benign Thyroid Lesions: Implications Thereof and A Systematic Review. Thyroid 2017; 27:39-48. [PMID: 27750019 DOI: 10.1089/thy.2016.0348] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Molecular markers associated with thyroid malignancy are increasingly being used as differential diagnostic tools for thyroid nodules. However, little has been reported recently regarding the prevalence of these markers in benign lesions. The literature was systematically reviewed to examine studies that reported on the prevalence of these markers in benign thyroid lesions. METHODS Appropriate studies published between January 1, 2000, and April 30, 2015, and cataloged in PubMed, Embase, Cochrane, Scopus, and Web of Science databases were searched for by combining different keywords for "thyroid tumor" with both general and specific keywords for "molecular marker" by using "AND" as the Boolean operator. All studies meeting criteria that reported the prevalence of RAS mutations, and RET/PTC and PAX8/PPAR-gamma chromosomal rearrangements in benign thyroid lesions were included for study. RESULTS A total of 64 articles (including 8162 patients, of whom 42.5% had benign lesions) that met all the study criteria were systematically reviewed and abstracted. Among 35 studies examining RAS mutations, the reported prevalence of RAS mutation in benign lesions ranged from 0% to 48%. In 38 studies examining RET/PTC rearrangements, the prevalence in benign lesions ranged from 0% to 68%. PAX8/PPAR-gamma rearrangements were examined in 27 studies, with the prevalence in benign lesions ranging from 0% to 55%. CONCLUSION The presence of these biomarkers and the tremendous variation in reports of their prevalence in benign lesions suggests the need for caution when including these markers in diagnostic decisions. Further understanding of the importance of these markers, as well as newly discovered markers of thyroid malignancy, may be required in order to avoid overtreatment of patients with benign thyroid tumors.
Collapse
Affiliation(s)
- Alireza Najafian
- 1 Endocrine Surgery, Department of Surgery, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Salem Noureldine
- 2 Division of Head and Neck Endocrine Surgery, Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Faris Azar
- 1 Endocrine Surgery, Department of Surgery, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Chady Atallah
- 1 Endocrine Surgery, Department of Surgery, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Gina Trinh
- 2 Division of Head and Neck Endocrine Surgery, Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Eric B Schneider
- 1 Endocrine Surgery, Department of Surgery, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Ralph P Tufano
- 2 Division of Head and Neck Endocrine Surgery, Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Martha A Zeiger
- 1 Endocrine Surgery, Department of Surgery, The Johns Hopkins University School of Medicine , Baltimore, Maryland
- 3 Department of Oncology, The Johns Hopkins University School of Medicine , Baltimore, Maryland
- 4 Department of Cellular and Molecular Medicine, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| |
Collapse
|
11
|
Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers. Proc Natl Acad Sci U S A 2016; 113:13768-13773. [PMID: 27856756 DOI: 10.1073/pnas.1606220113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Tumor genomes are mosaics of somatic structural variants (SVs) that may contribute to the activation of oncogenes or inactivation of tumor suppressors, for example, by altering gene copy number amplitude. However, there are multiple other ways in which SVs can modulate transcription, but the general impact of such events on tumor transcriptional output has not been systematically determined. Here we use whole-genome sequencing data to map SVs across 600 tumors and 18 cancers, and investigate the relationship between SVs, copy number alterations (CNAs), and mRNA expression. We find that 34% of CNA breakpoints can be clarified structurally and that most amplifications are due to tandem duplications. We observe frequent swapping of strong and weak promoters in the context of gene fusions, and find that this has a measurable global impact on mRNA levels. Interestingly, several long noncoding RNAs were strongly activated by this mechanism. Additionally, SVs were confirmed in telomere reverse transcriptase (TERT) upstream regions in several cancers, associated with elevated TERT mRNA levels. We also highlight high-confidence gene fusions supported by both genomic and transcriptomic evidence, including a previously undescribed paired box 8 (PAX8)-nuclear factor, erythroid 2 like 2 (NFE2L2) fusion in thyroid carcinoma. In summary, we combine SV, CNA, and expression data to provide insights into the structural basis of CNAs as well as the impact of SVs on gene expression in tumors.
Collapse
|
12
|
Abstract
Human cancer genomes harbour a variety of alterations leading to the deregulation of key pathways in tumour cells. The genomic characterization of tumours has uncovered numerous genes recurrently mutated, deleted or amplified, but gene fusions have not been characterized as extensively. Here we develop heuristics for reliably detecting gene fusion events in RNA-seq data and apply them to nearly 7,000 samples from The Cancer Genome Atlas. We thereby are able to discover several novel and recurrent fusions involving kinases. These findings have immediate clinical implications and expand the therapeutic options for cancer patients, as approved or exploratory drugs exist for many of these kinases. Kinases activated by gene fusions represent potentially important targets for the development of cancer drugs. Here, the authors develop a method for detecting gene fusion events in RNA sequencing data from The Cancer Genome Atlas and identify several novel recurrent fusions involving kinases.
Collapse
|
13
|
Smallridge RC, Chindris AM, Asmann YW, Casler JD, Serie DJ, Reddi HV, Cradic KW, Rivera M, Grebe SK, Necela BM, Eberhardt NL, Carr JM, McIver B, Copland JA, Thompson EA. RNA sequencing identifies multiple fusion transcripts, differentially expressed genes, and reduced expression of immune function genes in BRAF (V600E) mutant vs BRAF wild-type papillary thyroid carcinoma. J Clin Endocrinol Metab 2014; 99:E338-47. [PMID: 24297791 PMCID: PMC3913813 DOI: 10.1210/jc.2013-2792] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
CONTEXT The BRAF V600E mutation (BRAF-MUT) confers an aggressive phenotype in papillary thyroid carcinoma, but unidentified additional genomic abnormalities may be required for full phenotypic expression. OBJECTIVE RNA sequencing (RNA-Seq) was performed to identify genes differentially expressed between BRAF-MUT and BRAF wild-type (BRAF-WT) tumors and to correlate changes to patient clinical status. DESIGN BRAF-MUT and BRAF-WT tumors were identified in patients with T1N0 and T2-3N1 tumors evaluated in a referral medical center. Gene expression levels were determined (RNA-Seq) and fusion transcripts were detected. Multiplexed capture/detection and digital counting of mRNA transcripts (nCounter, NanoString Technologies) validated RNA-Seq data for immune system-related genes. PATIENTS BRAF-MUT patients included nine women, three men; nine were TNM stage I and three were stage III. Three (25%) had tumor infiltrating lymphocytes. BRAF-WT included five women, three men; all were stage I, and five (62.5%) had tumor infiltrating lymphocytes. RESULTS RNA-Seq identified 560 of 13 085 genes differentially expressed between BRAF-MUT and BRAF-WT tumors. Approximately 10% of these genes were related to MetaCore immune function pathways; 51 were underexpressed in BRAF-MUT tumors, whereas 4 (HLAG, CXCL14, TIMP1, IL1RAP) were overexpressed. The four most differentially overexpressed immune genes in BRAF-WT tumors (IL1B; CCL19; CCL21; CXCR4) correlated with lymphocyte infiltration. nCounter confirmed the RNA-Seq expression level data. Eleven different high-confidence fusion transcripts were detected (four interchromosomal; seven intrachromosomal) in 13 of 20 tumors. All in-frame fusions were validated by RT-PCR. CONCLUSION BRAF-MUT papillary thyroid cancers have reduced expression of immune/inflammatory response genes compared with BRAF-WT tumors and correlate with lymphocyte infiltration. In contrast, HLA-G and CXCL14 are overexpressed in BRAF-MUT tumors. Sixty-five percent of tumors had between one and three fusion transcripts. Functional studies will be required to determine the potential role of these newly identified genomic abnormalities in contributing to the aggressiveness of BRAF-MUT and BRAF-WT tumors.
Collapse
Affiliation(s)
- Robert C Smallridge
- Department of Medicine (R.C.S.), Division of Endocrinology and Metabolism, Mayo Clinic, Jacksonville, Florida 32224; Department of Otorhinolaryngology-Head and Neck Surgery (A.M.C., J.D.C.), Mayo Clinic, Jacksonville, Florida 32224; Department of Health Sciences Research (Y.W.A., D.J.S.), Mayo Clinic, Jacksonville, Florida 32224; Department of Medicine, Division of Endocrinology (H.V.R., N.L.E., B.M.), Mayo Clinic, Rochester, Minnesota 55905; Department of Laboratory Medicine and Pathology (K.W.C., S.K.G.), Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, Minnesota 55905; Department of Laboratory Medicine and Pathology (M.R.), Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905; Department of Cancer Biology (B.N., J.M.C., J.A.C., E.A.T.), Mayo Clinic, Jacksonville, Florida 32224; and Department of Biochemistry and Molecular Biology (N.L.E.), Mayo Clinic, Rochester, Minnesota 55905
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Shah N, Lankerovich M, Lee H, Yoon JG, Schroeder B, Foltz G. Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data. BMC Genomics 2013; 14:818. [PMID: 24261984 PMCID: PMC4046790 DOI: 10.1186/1471-2164-14-818] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 11/04/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND RNA-seq has spurred important gene fusion discoveries in a number of different cancers, including lung, prostate, breast, brain, thyroid and bladder carcinomas. Gene fusion discovery can potentially lead to the development of novel treatments that target the underlying genetic abnormalities. RESULTS In this study, we provide comprehensive view of gene fusion landscape in 185 glioblastoma multiforme patients from two independent cohorts. Fusions occur in approximately 30-50% of GBM patient samples. In the Ivy Center cohort of 24 patients, 33% of samples harbored fusions that were validated by qPCR and Sanger sequencing. We were able to identify high-confidence gene fusions from RNA-seq data in 53% of the samples in a TCGA cohort of 161 patients. We identified 13 cases (8%) with fusions retaining a tyrosine kinase domain in the TCGA cohort and one case in the Ivy Center cohort. Ours is the first study to describe recurrent fusions involving non-coding genes. Genomic locations 7p11 and 12q14-15 harbor majority of the fusions. Fusions on 7p11 are formed in focally amplified EGFR locus whereas 12q14-15 fusions are formed by complex genomic rearrangements. All the fusions detected in this study can be further visualized and analyzed using our website: http://ivygap.swedish.org/fusions. CONCLUSIONS Our study highlights the prevalence of gene fusions as one of the major genomic abnormalities in GBM. The majority of the fusions are private fusions, and a minority of these recur with low frequency. A small subset of patients with fusions of receptor tyrosine kinases can benefit from existing FDA approved drugs and drugs available in various clinical trials. Due to the low frequency and rarity of clinically relevant fusions, RNA-seq of GBM patient samples will be a vital tool for the identification of patient-specific fusions that can drive personalized therapy.
Collapse
Affiliation(s)
- Nameeta Shah
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA USA
| | - Michael Lankerovich
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA USA
| | - Hwahyung Lee
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA USA
| | - Jae-Geun Yoon
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA USA
| | - Brett Schroeder
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA USA
| | - Greg Foltz
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA USA
| |
Collapse
|
15
|
Yang W, Wu JM, Bi AD, Ou-yang YC, Shen HH, Chirn GW, Zhou JH, Weiss E, Holman EP, Liao DJ. Possible formation of mitochondrial-RNA containing chimeric or trimeric RNA implies a post-transcriptional and post-splicing mechanism for RNA fusion. PLoS One 2013; 8:e77016. [PMID: 24204722 PMCID: PMC3811998 DOI: 10.1371/journal.pone.0077016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/26/2013] [Indexed: 12/16/2022] Open
Abstract
Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine.
Collapse
Affiliation(s)
- Wei Yang
- Guangxi Veterinary Research Institute, Nanning, Guangxi, P.R. China
- * E-mail: (WY); (DJL)
| | - Jian-min Wu
- Guangxi Veterinary Research Institute, Nanning, Guangxi, P.R. China
| | - An-ding Bi
- Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America
| | - Yong-chang Ou-yang
- Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America
| | - Hai-hong Shen
- School of life Sciences, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Gung-wei Chirn
- Biomedical Engineering Department, Boston University, Boston, Massachusetts, United States of America
| | | | - Emily Weiss
- Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America
| | - Emily Pauline Holman
- Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America
| | - D. Joshua Liao
- Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America
- * E-mail: (WY); (DJL)
| |
Collapse
|
16
|
Yuan C, Liu Y, Yang M, Liao DJ. New methods as alternative or corrective measures for the pitfalls and artifacts of reverse transcription and polymerase chain reactions (RT-PCR) in cloning chimeric or antisense-accompanied RNA. RNA Biol 2013; 10:958-67. [PMID: 23618925 PMCID: PMC4111735 DOI: 10.4161/rna.24570] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We established new methods for cloning cDNA ends that start with reverse transcription (RT) and soon proceed with the synthesis of the second cDNA strand, avoiding manipulations of fragile RNA. Our 3′-end cloning method does not involve poly-dT primers and polymerase chain reactions (PCR), is low in efficiency but high in fidelity and can clone those RNAs without a poly-A tail. We also established a cDNA protection assay to supersede RNA protection assay. The protected cDNA can be amplified, cloned and sequenced, enhancing sensitivity and fidelity. We report that RT product using gene-specific primer (GSP) cannot be gene- or strand-specific because RNA sample contains endogenous random primers (ERP). The gene-specificity may be improved by adding a linker sequence at the 5′-end of the GSP to prime RT and using the linker as a primer in the ensuing PCR. The strand-specificity may be improved by using strand-specific DNA oligos in our protection assay. The CDK4 mRNA and TSPAN31 mRNA are transcribed from the opposite DNA strands and overlap at their 3′ ends. Using this relationship as a model, we found that the overlapped sequence might serve as a primer with its antisense as the template to create a wrong-template extension in RT or PCR. We infer that two unrelated RNAs or cDNAs overlapping at the 5′- or 3′-end might create a spurious chimera in this way, and many chimeras with a homologous sequence may be such artifacts. The ERP and overlapping antisense together set complex pitfalls, which one should be aware of.
Collapse
Affiliation(s)
- Chengfu Yuan
- Hormel Institute, University of Minnesota, Austin, MN, USA
| | | | | | | |
Collapse
|