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Ikram S, Sayyah E, Durdağı S. Identifying Potential SOS1 Inhibitors via Virtual Screening of Multiple Small Molecule Libraries against KRAS-SOS1 Interaction. Chembiochem 2024:e202400008. [PMID: 38622060 DOI: 10.1002/cbic.202400008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
The RAS-MAPK signaling pathway, crucial for cell proliferation and differentiation, involves key proteins KRAS and SOS1. Mutations in the KRAS and SOS1 genes are implicated in various cancer types, including pancreatic, lung, and juvenile myelomonocytic leukemia. There is considerable interest in identifying inhibitors targeting KRAS and SOS1 to explore potential therapeutic strategies for cancer treatment. In this study, advanced in silico techniques were employed to screen small molecule libraries at this interface, leading to the identification of promising lead compounds as potential SOS1 inhibitors. Comparative analysis of the average binding free energies of these predicted potent compounds with known SOS1 small molecule inhibitors revealed that the identified compounds display similar or even superior predicted binding affinities compared to the known inhibitors. These findings offer valuable insights into the potential of these compounds as candidates for further development as effective anti-cancer agents.
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Affiliation(s)
- Saima Ikram
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34734, Istanbul, Turkey
- Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HİTMER), Bahçeşehir University, 34734, İstanbul, Türkiye
| | - Ehsan Sayyah
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34734, Istanbul, Turkey
- Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HİTMER), Bahçeşehir University, 34734, İstanbul, Türkiye
| | - Serdar Durdağı
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34734, Istanbul, Turkey
- Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HİTMER), Bahçeşehir University, 34734, İstanbul, Türkiye
- Molecular Therapy Lab (MTL), Department of Pharmaceutical Chemistry, School of Pharmacy, Bahçeşehir University, 34353, Istanbul, Türkiye
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2
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Dhamelincourt E, Descourt R, Rousseau-Bussac G, Doubre H, Decroisette C, Demontrond P, Le Garff G, Falchero L, Huchot E, Vieillot S, Corre R, Kazulinski L, Bizieux A, Bigay-Gamé L, Morel H, Molinier O, Chouaïd C, Guisier F. Clinical Characteristics of Patients with Advanced ALK-Translocated Non-small Cell Lung Cancers and Long-Term Responses to Crizotinib (CRIZOLONG GFPC 05-19 Study). Target Oncol 2023; 18:905-914. [PMID: 37966566 DOI: 10.1007/s11523-023-01014-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Although ALK-translocated (ALK+) advanced non-small cell lung cancers (aNSCLCs) are currently treated with second- or third-generation ALK inhibitors (ALK-TKIs), some patients respond durably to the first-generation ALK-TKI crizotinib. OBJECTIVE This study aimed to describe the clinical characteristics of these long-term responders. PATIENTS AND METHODS This national, multicenter, retrospective, non-interventional study included patients with ALK+ aNSCLCs and long-term responses to first (L1)- or subsequent (≥ L2)-line crizotinib, defined, respectively, as treatments lasting > 18 and > 10 months. Median treatment duration (mDOT) was the primary endpoint. RESULTS A total of 85 patients (32 L1 and 53 ≥ L2 responders) from 23 centers were included (receiving crizotinib between 10/24/2011-10/02/2018): median age of 59 years, 83.6% non-smokers or ex-smokers, 85.9% performance status (PS) 0/1, 94.1% with adenocarcinomas, median of one metastatic site, and 22.4% with brain metastases (BMs). After median follow-up of 73.4 [95% confidence interval, 67.5-79.9] months, respective L1 and ≥ L2 mDOTs were 43.3 [26.7-56.8] and 29.6 [22.6-35.8] months, with overall survival (OS) not reached (NR) and 116.2 [83.4-NR] months. BM presence or absence did not affect mDOT (31.4 versus 32.9 months) but significantly impacted median OS (70.6 versus 158.6 months; p = 0.0008). Progression on crizotinib was paucisymptomatic (74.1%) and oligometastatic (34.8%), especially BMs (42.4%). After crizotinib discontinuation, 65 (76.5%) patients received subsequent systemic therapy: 57 (67.1%) with second-generation ALK-TKIs. Respective mDOTs of first- and second-line post-crizotinib ALK-TKIs lasted 19.4 [14.9-25.6] and 11.1 [4.8-17.9] months, respectively. CONCLUSIONS Most ALK+ aNSCLC patients with prolonged crizotinib efficacy had paucisymptomatic and oligometastatic disease without BMs. They subsequently benefited from a sequential strategy with other ALK-TKIs.
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Affiliation(s)
| | - Renaud Descourt
- Institut de Cancérologie, Hôpital Morvan, CHU de Brest, Brest, France
| | | | - Hélène Doubre
- Service d'Oncologie Thoracique, Hôpital Foch, Suresnes, France
| | | | | | | | - Lionel Falchero
- Service de Pneumologie, Hôpital Nord-Ouest de Villefranche-sur-Saône, Gleizé, France
| | - Eric Huchot
- Service de Pneumologie, CHU Saint-Pierre, La Réunion, France
| | - Sabine Vieillot
- Service d'Oncologie, Clinique Saint Pierre, Perpignan, France
| | - Romain Corre
- Service de Pneumologie, CH Quimper, Quimper, France
| | - Laure Kazulinski
- Service de Pneumologie, CH du Cotentin Cherbourg, Cherbourg, France
| | - Acya Bizieux
- Service de Pneumologie, CH La Roche-sur-Yon, La Roche-sur-Yon, France
| | | | - Hugues Morel
- Service de Pneumologie, CH Orléans, Orléans, France
| | | | - Christos Chouaïd
- Service de Pneumologie, Centre Hospitalier Intercommunal, Créteil, France
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Xia J, Chen S, Zhang Z, Wang J. Identification of a novel RSRC1-ALK (R6: A20) fusion using next-generation sequencing technique. Cancer Genet 2023; 278-279:18-23. [PMID: 37572583 DOI: 10.1016/j.cancergen.2023.08.003] [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: 04/21/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Non-small-cell lung cancer (NSCLC) patients with anaplastic lymphoma kinase (ALK) fusion showed promising responses to ALK tyrosine kinase inhibitors (TKIs). In this study, fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), next generation sequencing (NGS) and Sanger sequencing were performed to identify the presence of ALK fusion, to investigate whether the patient may benefit from TKI therapy. Postoperative pathological analysis indicated invasive adenocarcinoma with mainly mucinous type and partial micropapillary type in left lower lung. Minimally invasive adenocarcinoma was seen in left upper lung, with mainly acinar type. NGS detected a novel RSRC1-ALK (R6: A20) fusion in left lower lobe sample, which was presented as the fusion of exon 6 of RSRC1 and exon 20 of ALK gene. Sanger sequencing validated the fusion. Break rearrangement signal of ALK gene was detected in 80% of tumor cells. Immunohistochemistry showed ALK positive expression in lung. For the treatment, the patient received ensartinib hydrochloride with a dose of 225 mg per day. He was in a state of progression-free survival for at least 24 months in follow-up with no complications. NGS can be used for exploring treatment options for NSCLC patients with ALK fusion.
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Affiliation(s)
- Jingjing Xia
- Department of Medical Examination, Huai'an First People's Hospital, Nanjing Medical University, Huai'an 223300, PR China
| | - Sheng Chen
- Department of Thoracic Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an 223300, PR China
| | | | - Jipeng Wang
- Department of Respiration, Huai'an First People's Hospital, Nanjing Medical University, Huai'an 223300, PR China.
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Sun W, Zheng J, Zhou J, Zhou J. A non-small cell lung carcinoma patient responded to crizotinib therapy after alectinib-induced interstitial lung disease. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:583-587. [PMID: 37899398 PMCID: PMC10630055 DOI: 10.3724/zdxbyxb-2023-0319] [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: 07/10/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023]
Abstract
A 54-year-old, non-smoking woman was diagnosed as stage ⅣB adenocarcinoma with widespread bone metastasis (cT4N2M1c) in the First Affiliated Hospital, Zhejiang University School of Medicine. Immunohistochemistry result showed the presence of anaplastic lymphoma kinase (ALK) gene rearrangement; next-generation sequencing (NGS) indicated EML4-ALK fusion (E6:A20) with concurrent CCDC148-ALK (C1:A20), PKDCC-ALK (Pintergenic:A20)and VIT-ALK (V15:A20) fusions. After 32 weeks of alectinib treatment, the patient complained cough and exertional chest distress but had no sign of infection. Computed tomography (CT) showed bilateral diffuse ground glass opacities, suggesting a diagnosis of alectinib-related interstitial lung disease (ILD). Following corticosteroid treatment and discontinuation of alectinib, clinical presentations and CT scan gradually improved, but the primary lung lesions enlarged during the regular follow-up. The administration of crizotinib was then initiated and the disease was stable for 25 months without recurrence of primary lung lesions and ILD.
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Affiliation(s)
- Wenjia Sun
- Department of Respiratory Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
| | - Jing Zheng
- Department of Respiratory Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Jianya Zhou
- Department of Respiratory Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
| | - Jianying Zhou
- Department of Respiratory Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
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Muñoz-Barrera A, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Lorenzo-Salazar JM, González-Montelongo R, García-Olivares V, Flores C. From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research. Life (Basel) 2022; 12:1939. [PMID: 36431075 PMCID: PMC9695713 DOI: 10.3390/life12111939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Next-generation sequencing (NGS) applications have flourished in the last decade, permitting the identification of cancer driver genes and profoundly expanding the possibilities of genomic studies of cancer, including melanoma. Here we aimed to present a technical review across many of the methodological approaches brought by the use of NGS applications with a focus on assessing germline and somatic sequence variation. We provide cautionary notes and discuss key technical details involved in library preparation, the most common problems with the samples, and guidance to circumvent them. We also provide an overview of the sequence-based methods for cancer genomics, exposing the pros and cons of targeted sequencing vs. exome or whole-genome sequencing (WGS), the fundamentals of the most common commercial platforms, and a comparison of throughputs and key applications. Details of the steps and the main software involved in the bioinformatics processing of the sequencing results, from preprocessing to variant prioritization and filtering, are also provided in the context of the full spectrum of genetic variation (SNVs, indels, CNVs, structural variation, and gene fusions). Finally, we put the emphasis on selected bioinformatic pipelines behind (a) short-read WGS identification of small germline and somatic variants, (b) detection of gene fusions from transcriptomes, and (c) de novo assembly of genomes from long-read WGS data. Overall, we provide comprehensive guidance across the main methodological procedures involved in obtaining sequencing results for the most common short- and long-read NGS platforms, highlighting key applications in melanoma research.
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Affiliation(s)
- Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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Therapeutic Advances of Rare ALK Fusions in Non-Small Cell Lung Cancer. Curr Oncol 2022; 29:7816-7831. [PMID: 36290895 PMCID: PMC9601201 DOI: 10.3390/curroncol29100618] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/05/2022] [Accepted: 10/13/2022] [Indexed: 01/11/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) accounts for approximately 85% of all lung cancer cases and is the leading cause of cancer-related death. Despite advances in chemotherapy and immunotherapy, the prognosis for advanced patients remains poor. The discovery of oncogenic driver mutations, such as anaplastic lymphoma kinase (ALK) mutations, means that a subset of patients has opportunities for targeted therapy. With the improvement of genetic testing coverage, more and more ALK fusion subtypes and ALK partners have been discovered, and more than 90 rare ALK fusion subtypes have been found in NSCLC. However, unlike the common fusion, echinoderm microtubule-associated protein-like 4 (EML4)-ALK, some rare ALK fusions such as striatin (STRN)-ALK and huntingtin interacting protein 1 (HIP1)-ALK, etc., the large-scale clinical data related to its efficacy are still immature. The clinical application of ALK-tyrosine kinase inhibitors (ALK-TKIs) mainly depends on the positivity of the ALK gene, regardless of the molecular characteristics of the fusion partner. Recent clinical studies in the ALK-positive NSCLC population have demonstrated differences in progression-free survival (PFS) among patients based on different ALK fusion subtypes. This article will introduce the biological characteristics of ALK fusion kinase and common detection methods of ALK fusion and focus on summarizing the differential responses of several rare ALK fusions to ALK-TKIs, and propose corresponding treatment strategies, so as to better guide the application of ALK-TKIs in rare ALK fusion population.
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7
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Li H, Deng Y, Chen B, Xiao Y, Yang J, Liu Q, Lin G. Identification of a novel RMST-ALK rearrangement in advanced lung adenocarcinoma and durable response to ceritinib: A case report. Front Oncol 2022; 12:913838. [PMID: 35978810 PMCID: PMC9376587 DOI: 10.3389/fonc.2022.913838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Next-generation sequencing technology has enabled the identification of fusion partners of anaplastic lymphoma kinase (ALK) in non-small cell lung cancer, and various ALK fusion partners have been confirmed. Here, a novel rhabdomyosarcoma 2-associated transcript (RMST)-ALK rearrangement was identified in an 80-year-old Chinese man with advanced lung adenocarcinoma. The patient was prescribed ceritinib and achieved a partial response, which has been sustained for more than 18 months. This is the first report of the RMST-ALK rearrangement, and we showed that a patient with lung adenocarcinoma carrying this rearrangement can benefit from ceritinib treatment; therefore, this is a significant finding in clinical practice.
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Affiliation(s)
- Hui Li
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yixiao Deng
- The Genetic Analysis Department, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Bin Chen
- Department of Interventional Radiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yajie Xiao
- The Genetic Analysis Department, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Jie Yang
- The Genetic Analysis Department, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Qionghui Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Qionghui Liu, ; Gengpeng Lin,
| | - Gengpeng Lin
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Qionghui Liu, ; Gengpeng Lin,
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8
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Tao H, Liu Z, Mu J, Gai F, Huang Z, Shi L. Concomitant novel ALK-SSH2, EML4-ALK and ARID2-ALK, EML4-ALK double-fusion variants and confer sensitivity to crizotinib in two lung adenocarcinoma patients, respectively. Diagn Pathol 2022; 17:27. [PMID: 35144623 PMCID: PMC8832643 DOI: 10.1186/s13000-022-01212-9] [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: 10/21/2021] [Accepted: 01/25/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction Anaplastic lymphoma kinase (ALK) gene rearrangements, have been identified in approximately 2-7% of patients with lung adenocarcinoma (LUAD). However, co-occurrence of double ALK fusions in one patient was rare. Herein, we reported two Chinese female LUAD patients with confirmed double ALK fusion variants by next generation sequencing. Case presentation Case 1, a 38-year-old female was diagnosed as peripheral LUAD in left upper lobe with synchronous multiple intrapulmonary metastases (pT2N0M1b, stage IVa). And case 2, a 58-year-old female had left lower lobe primary LUAD and synchronous multiple lung metastases (pT4N2M1b, stage IVa). In both patients, tumor cells displayed strong expression of ALK protein. Genetic profiling by next generation sequencing showed both patients concurrently harbored two types of ALK rearrangements. Case 1 had an unreported ALK-SSH2/EML4-ALK double fusions, and case 2 had an another novel ARID2-ALK/EML4‐ALK double fusions. Both of these patients responded to ALK inhibitor crizotinib. Conclusions Our study reported two novel ALK fusion partners never reported, which expands the knowledge of ALK fusion spectrum and provides insight into therapeutic options for patients with double ALK fusions.
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Affiliation(s)
- Hong Tao
- Department of Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zhe Liu
- Department of Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jing Mu
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Thoracic Tumor Research Institute, Beijing Tuberculosis, Beijing, China
| | - Fei Gai
- Department of Medical Business, Amoy Diagnostics Co., Ltd, Xiamen, China
| | - Zhan Huang
- Department of Medical Business, Amoy Diagnostics Co., Ltd, Xiamen, China
| | - Liang Shi
- Department of Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
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Kessler D, Gerlach D, Kraut N, McConnell DB. Targeting Son of Sevenless 1: The pacemaker of KRAS. Curr Opin Chem Biol 2021; 62:109-118. [PMID: 33848766 DOI: 10.1016/j.cbpa.2021.02.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 12/12/2022]
Abstract
Son of Sevenless (SOS) is a guanine nucleotide exchange factor that activates the important cell signaling switch KRAS. SOS acts as a pacemaker for KRAS, the beating heart of cancer, by catalyzing the "beating" from the KRAS(off) to the KRAS(on) conformation. Activating mutations in SOS1 are common in Noonan syndrome and oncogenic alterations in KRAS drive 1 in seven human cancers. Promising clinical efficacy has been observed for selective KRASG12C inhibitors, but the vast majority of oncogenic KRAS alterations remain undrugged. The discovery of a druggable pocket on SOS1 has led to potent SOS1 inhibitors such as BI-3406. SOS1 inhibition leads to antiproliferative effects against all major KRAS mutants. The first SOS1 inhibitor has entered clinical trials for KRAS-mutated cancers. In this review, we provide an overview of SOS1 function, its association with cancer and RASopathies, known SOS1 activators and inhibitors, and a future perspective is provided.
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Affiliation(s)
- Dirk Kessler
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120, Vienna, Austria
| | - Daniel Gerlach
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120, Vienna, Austria
| | - Norbert Kraut
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120, Vienna, Austria
| | - Darryl B McConnell
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120, Vienna, Austria.
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Bruno R, Fontanini G. Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review. Diagnostics (Basel) 2020; 10:diagnostics10080521. [PMID: 32726941 PMCID: PMC7460167 DOI: 10.3390/diagnostics10080521] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023] Open
Abstract
Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.
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Affiliation(s)
- Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy;
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy
- Correspondence:
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11
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Ma L, Zhang Q, Dong Y, Li H, Wang J. SPECC1L-ALK: A novel gene fusion response to ALK inhibitors in non-small cell lung cancer. Lung Cancer 2020; 143:97-100. [PMID: 32216970 DOI: 10.1016/j.lungcan.2020.03.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Li Ma
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, No. 97 Ma Chang, Tongzhou District, Beijing, 101149, China
| | - Quan Zhang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, No. 97 Ma Chang, Tongzhou District, Beijing, 101149, China
| | - Yujie Dong
- Departments of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Haoyang Li
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, No. 97 Ma Chang, Tongzhou District, Beijing, 101149, China
| | - Jinghui Wang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, No. 97 Ma Chang, Tongzhou District, Beijing, 101149, China.
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Ou SHI, Zhu VW, Nagasaka M. Catalog of 5' Fusion Partners in ALK-positive NSCLC Circa 2020. JTO Clin Res Rep 2020; 1:100015. [PMID: 34589917 PMCID: PMC8474466 DOI: 10.1016/j.jtocrr.2020.100015] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/17/2022] Open
Abstract
Since the discovery of anaplastic lymphoma kinase fusion-positive (ALK+) NSCLC in 2007, the methods to detect ALK+ NSCLC have evolved and expanded from fluorescence in situ hybridization and immunohistochemistry to next-generation DNA sequencing, targeted RNA sequencing, and whole transcriptome sequencing. As such, the deep sequencing methods have resulted in the expansion of distinct fusion partners identified in ALK+ NSCLC to 90 (one variant PLEKHM2-ALK is found in small cell lung cancer but included in this catalog) by the end of January 2020; about 65 of them (since 2018) and most of the recent novel fusion partners were reported from China. Thirty-four of the distinct fusion partners are located on the short arm of chromosome 2; 28 of these 34 fusion partners are located on 2p21-25, in which ALK is located on 2p23.2-p23.1. Many of these new ALK+ NSCLC fusion variants have responded to ALK tyrosine kinase inhibitors (TKIs). Several of these novel ALK fusion variants were identified as being resistant to EGFR TKIs or as dual 3'ALK fusions. In addition, at least 28 intergenic ALK rearrangements have also been reported, with three of them reported as responding to crizotinib. This review aims to serve as a central source of reference of fusion partners in ALK+ NSCLC for clinicians and scientists. We aim to update and improve the list going forward.
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Affiliation(s)
- Sai-Hong Ignatius Ou
- Department of Medicine, Division of Hematology-Oncology, Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, California
| | - Viola W. Zhu
- Department of Medicine, Division of Hematology-Oncology, Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, California
| | - Misako Nagasaka
- Department of Oncology, Karmanos Cancer Institute/Wayne State University School of Medicine, Detroit, Michigan
- Department of Advanced Medical Innovations, St. Marianna University Graduate School of Medicine, Kawasaki, Kanagawa, Japan
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