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Agrawal S, Ameline B, Folpe AL, Azzato E, Astbury C, Mentzel T, Knapp C, Rütten A, Creytens D, Sukov W, Baumhoer D, Billings SD, Fritchie KJ. ALK-rearranged, CD34-positive spindle cell neoplasms resembling dermatofibrosarcoma protuberans: a study of seven cases. Histopathology 2024; 85:649-659. [PMID: 38867577 DOI: 10.1111/his.15239] [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: 02/28/2024] [Revised: 05/22/2024] [Accepted: 05/25/2024] [Indexed: 06/14/2024]
Abstract
AIMS The majority of dermatofibrosarcoma protuberans (DFSP) harbour PDGFB or PDGFD rearrangements. We encountered ALK expression/rearrangement in a PDGFB/D-negative CD34-positive spindle cell neoplasm with features similar to DFSP, prompting evaluation of ALK-rearrangements in DFSP and plaque-like CD34-positive dermal fibroma (P-LDF). METHODS AND RESULTS We searched the archives of academic institutions for cases previously coded as DFSP and P-LDF. NGS-naïve or PDGFB-negative DFSP were screened for ALK (clone D5F3) expression by immunohistochemistry. NGS or ALK FISH was performed on ALK-positive cases. Methylome profiling studies were performed and compared with conventional DFSP. One case of "DFSP" and two "P-LDF" with ALK expression were identified from the archives, while four cases were detected prospectively. These seven cases (6F:1M; 8 months to 76 years) arose in the dermis of the arm (two), scalp, eyelid, thigh, abdomen, and shoulder and ranged from 0.4 to 4.2 cm. Tumours were composed of spindled cells and displayed a storiform growth pattern. Cytologic atypia was absent, and mitotic figures were scarce (0-2/10 HPFs, high power fields). The lesional cells were diffusely positive for CD34 and ALK and negative for S100 protein. By NGS (n = 5), ALK fusion partners included DCTN1 (2), PLEKHH2, and CLIP2 in DFSP-like cases and FLNA in P-LDF-like lesions. ALK FISH was positive in one (of two) cases previously labelled P-LDF. Methylome profiling of two (of three) ALK-rearranged DFSP-like tumours showed clustering with conventional DFSP in the UMAP dimension reduction plot. To date, no tumour has recurred (n = 2; 26, 27 months). CONCLUSION We describe a cohort of novel ALK-rearranged tumours with morphologic features similar to DFSP.
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Affiliation(s)
- Shruti Agrawal
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Department of Dermatology, Mayo Clinic, Rochester, MN, USA
| | - Baptiste Ameline
- Bone Tumor Reference Center at the Institute for Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth Azzato
- Department of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Caroline Astbury
- Department of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Thomas Mentzel
- MVZ Dermatopathologie Friedrichshafen/Bodensee Part G, Friedrichshafen, Germany
| | - Calvin Knapp
- Department of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Arno Rütten
- MVZ Dermatopathologie Friedrichshafen/Bodensee Part G, Friedrichshafen, Germany
| | - David Creytens
- Department of Pathology, Ghent University and Ghent University Hospital, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - William Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Daniel Baumhoer
- Bone Tumor Reference Center at the Institute for Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Steven D Billings
- Department of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Karen J Fritchie
- Department of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA
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Maruta R, Sadato D, Yomota M, Gomikawa R, Motoi T, Sato T, Kino N, Kobayashi M, Hosomi Y. Case Report: Structurally Rare EML4-ALK Identified by Next Generation Sequencing in a Patient with NSCLC with Bilateral Ovarian Metastases. Onco Targets Ther 2024; 17:777-783. [PMID: 39345274 PMCID: PMC11430267 DOI: 10.2147/ott.s474134] [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: 05/07/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
The EML4-ALK oncogene is a fusion of the EML4 and ALK genes and is found in approximately 5-6% of the cases of non-small cell lung cancer (NSCLC). Herein, we present a unique case of lung adenocarcinoma with metastases to the bilateral ovaries harboring a rare EML4-ALK fusion gene variant in a 52-year-old patient. The patient had initially received a diagnosis of ovarian cancer, then had undergone neo-adjuvant chemotherapy followed by a surgical resection. Despite two cycles of adjuvant chemotherapy consisting of carboplatin and gemcitabine, CT revealed that the pleural effusion had increased from it before chemotherapy, and the shortness of breath worsened. Molecular profiling revealed an EML4-ALK rearrangement containing ALK -EML4 and ALK -NPR2 fusion genes. The diagnosis was changed to primary lung adenocarcinoma with metastases to the bilateral ovaries based on a pathological reevaluation. Treatment with alectinib, a second-generation ALK-tyrosine kinase inhibitor, led to a partial response of 18 months' duration, and the shortness of breath improved. No adverse events related to the alectinib therapy occurred. To assess the unique structure of the fusion genes, RNA sequencing was performed. An intronic sequence from both ALK and EML4 was found between ALK and EML4 exon, possibly because of an unusual insertion of a gene fragment derived from NRP2, indicated by the panel sequencing results. Variations in the drug response among EML4-ALK fusion variants highlight the importance of understanding their molecular structure. Further investigation is warranted to refine fusion gene detection methods and assess the therapeutic implications of rare fusion variants.
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Affiliation(s)
- Ryusuke Maruta
- Department of Respiratory Medicine, Tokyo Metropolitan Komagome Hospital, Bunkyo-ku, Japan
- Department of Respiratory Medicine, Tokyo Metropolitan Bokutoh Hospital, Sumida-ku, Japan
| | - Daichi Sadato
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Bunkyo-ku, Japan
| | - Makiko Yomota
- Department of Respiratory Medicine, Tokyo Metropolitan Komagome Hospital, Bunkyo-ku, Japan
| | - Ryu Gomikawa
- Department of Pathology, Tokyo Metropolitan Komagome Hospital, Bunkyo-ku, Japan
| | - Toru Motoi
- Department of Pathology, Tokyo Metropolitan Komagome Hospital, Bunkyo-ku, Japan
| | - Tatsuya Sato
- Department of Gynecology, Tokyo Metropolitan Komagome Hospital, Bunkyo-ku, Japan
| | - Nao Kino
- Department of Gynecology, Tokyo Metropolitan Komagome Hospital, Bunkyo-ku, Japan
| | - Masayoshi Kobayashi
- Department of Respiratory Medicine, Tokyo Metropolitan Bokutoh Hospital, Sumida-ku, Japan
| | - Yukio Hosomi
- Department of Respiratory Medicine, Tokyo Metropolitan Komagome Hospital, Bunkyo-ku, Japan
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3
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Wu K, Jiang H, Hicks DR, Liu C, Muratspahic E, Ramelot TA, Liu Y, McNally K, Gaur A, Coventry B, Chen W, Bera AK, Kang A, Gerben S, Lamb MYL, Murray A, Li X, Kennedy MA, Yang W, Schober G, Brierley SM, Gelb MH, Montelione GT, Derivery E, Baker D. Sequence-specific targeting of intrinsically disordered protein regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603480. [PMID: 39071356 PMCID: PMC11275711 DOI: 10.1101/2024.07.15.603480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
A general approach to design proteins that bind tightly and specifically to intrinsically disordered regions (IDRs) of proteins and flexible peptides would have wide application in biological research, therapeutics, and diagnosis. However, the lack of defined structures and the high variability in sequence and conformational preferences has complicated such efforts. We sought to develop a method combining biophysical principles with deep learning to readily generate binders for any disordered sequence. Instead of assuming a fixed regular structure for the target, general recognition is achieved by threading the query sequence through diverse extended binding modes in hundreds of templates with varying pocket depths and spacings, followed by RFdiffusion refinement to optimize the binder-target fit. We tested the method by designing binders to 39 highly diverse unstructured targets. Experimental testing of ~36 designs per target yielded binders with affinities better than 100 nM in 34 cases, and in the pM range in four cases. The co-crystal structure of a designed binder in complex with dynorphin A is closely consistent with the design model. All by all binding experiments for 20 designs binding diverse targets show they are highly specific for the intended targets, with no crosstalk even for the closely related dynorphin A and dynorphin B. Our approach thus could provide a general solution to the intrinsically disordered protein and peptide recognition problem.
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Kumar H, Kim P. Artificial intelligence in fusion protein three-dimensional structure prediction: Review and perspective. Clin Transl Med 2024; 14:e1789. [PMID: 39090739 PMCID: PMC11294035 DOI: 10.1002/ctm2.1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024] Open
Abstract
Recent advancements in artificial intelligence (AI) have accelerated the prediction of unknown protein structures. However, accurately predicting the three-dimensional (3D) structures of fusion proteins remains a difficult task because the current AI-based protein structure predictions are focused on the WT proteins rather than on the newly fused proteins in nature. Following the central dogma of biology, fusion proteins are translated from fusion transcripts, which are made by transcribing the fusion genes between two different loci through the chromosomal rearrangements in cancer. Accurately predicting the 3D structures of fusion proteins is important for understanding the functional roles and mechanisms of action of new chimeric proteins. However, predicting their 3D structure using a template-based model is challenging because known template structures are often unavailable in databases. Deep learning (DL) models that utilize multi-level protein information have revolutionized the prediction of protein 3D structures. In this review paper, we highlighted the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using DL models. We aim to explore both the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr-Rosetta and D-I-TASSER for modelling the 3D structures. HIGHLIGHTS: This review provides the overall pipeline and landscape of the prediction of the 3D structure of fusion protein. This review provides the factors that should be considered in predicting the 3D structures of fusion proteins using AI approaches in each step. This review highlights the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using deep learning models. This review explores the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr-Rosetta, and D-I-TASSER to model 3D structures.
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Affiliation(s)
- Himansu Kumar
- Department of Bioinformatics and Systems MedicineMcWilliams School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Pora Kim
- Department of Bioinformatics and Systems MedicineMcWilliams School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTexasUSA
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5
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Attwa MW, Abdelhameed AS, Kadi AA. An ultra-fast green ultra-high-performance liquid chromatography-tandem mass spectrometry method for estimating the in vitro metabolic stability of zotizalkib in human liver microsomes. J Sep Sci 2024; 47:e2400393. [PMID: 39087620 DOI: 10.1002/jssc.202400393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/10/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024]
Abstract
Zotizalkib (ZTK, TPX-0131) is a fourth-generation highly effective inhibitor of wild-type anaplastic lymphoma kinase (ALK) and ALK-resistant mutations that can penetrate the central nervous system. It exhibited greater potency compared to all five officially approved ALK inhibitors. The aim of this study was to develop a rapid, accurate, eco-friendly, and highly sensitive ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method for measuring the concentration of ZTK in human liver microsomes (HLMs). The validation aspects of the current UHPLC-MS/MS methodology in the HLMs were conducted in accordance with the bioanalytical method validation standards specified by the US Food and Drug Administration. ZTK and encorafenib were separated using an Agilent C8 column (Eclipse Plus) and an isocratic mobile phase. The calibration curve for the developed ZTK exhibited a linear relationship within the concentration range of 1-3000 ng/mL. The results from the Analytical Green-ness Metric Approach program (0.76) suggested that the created method demonstrated a significant degree of environmental sustainability. The in vitro half-life (t1/2) and intrinsic clearance (Clint) of ZTK were determined to be 15.79 min and 51.35 mL/min/kg, respectively that suggests the ZTK exhibits characteristics similar to those of a medication with a high extraction ratio. These approaches are crucial for the progress of novel pharmaceutical development, especially in improving metabolic stability.
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Affiliation(s)
- Mohamed W Attwa
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali S Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Adnan A Kadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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6
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Pashley SL, Papageorgiou S, O'Regan L, Barone G, Robinson SW, Lucken K, Straatman KR, Roig J, Fry AM. The mesenchymal morphology of cells expressing the EML4-ALK V3 oncogene is dependent on phosphorylation of Eg5 by NEK7. J Biol Chem 2024; 300:107144. [PMID: 38458397 PMCID: PMC11061729 DOI: 10.1016/j.jbc.2024.107144] [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: 09/22/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
Echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) oncogenic fusion proteins are found in approximately 5% of non-small cell lung cancers. Different EML4-ALK fusion variants exist with variant 3 (V3) being associated with a significantly higher risk than other common variants, such as variant 1 (V1). Patients with V3 respond less well to targeted ALK inhibitors, have accelerated rates of metastasis, and have poorer overall survival. A pathway has been described downstream of EML4-ALK V3 that is independent of ALK catalytic activity but dependent on the NEK9 and NEK7 kinases. It has been proposed that assembly of an EML4-ALK V3-NEK9-NEK7 complex on microtubules leads to cells developing a mesenchymal-like morphology and exhibiting enhanced migration. However, downstream targets of this complex remain unknown. Here, we show that the microtubule-based kinesin, Eg5, is recruited to interphase microtubules in cells expressing EML4-ALK V3, whereas chemical inhibition of Eg5 reverses the mesenchymal morphology of cells. Furthermore, we show that depletion of NEK7 interferes with Eg5 recruitment to microtubules in cells expressing EML4-ALK V3 and cell length is reduced, but this is reversed by coexpression of a phosphomimetic mutant of Eg5, in a site, S1033, phosphorylated by NEK7. Intriguingly, we also found that expression of Eg5-S1033D led to cells expressing EML4-ALK V1 adopting a more mesenchymal-like morphology. Together, we propose that Eg5 acts as a substrate of NEK7 in cells expressing EML4-ALK V3 and Eg5 phosphorylation promotes the mesenchymal morphology typical of these cells.
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Affiliation(s)
- Sarah L Pashley
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Savvas Papageorgiou
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Laura O'Regan
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Giancarlo Barone
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Susan W Robinson
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Kellie Lucken
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Kees R Straatman
- Advanced Imaging Facility, Core Biotechnology Services, University of Leicester, Leicester, UK
| | - Joan Roig
- Department of Cell & Developmental Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Andrew M Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
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7
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Wu Y, Guo J, Li W, Xiu X, Thirunavukarasu D, Wang Y, Wang K, Chen W, Yu Zhang D, Yang X, Fan C, Song P. Enhanced Detection of Novel Low-Frequency Gene Fusions via High-Yield Ligation and Multiplexed Enrichment Sequencing. Angew Chem Int Ed Engl 2024; 63:e202316484. [PMID: 38494435 DOI: 10.1002/anie.202316484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Panel-based methods are commonly employed for the analysis of novel gene fusions in precision diagnostics and new drug development in cancer. However, these methods are constrained by limitations in ligation yield and the enrichment of novel gene fusions with low variant allele frequencies. In this study, we conducted a pioneering investigation into the stability of double-stranded adapter DNA, resulting in improved ligation yield and enhanced conversion efficiency. Additionally, we implemented blocker displacement amplification, achieving a remarkable 7-fold enrichment of novel gene fusions. Leveraging the pre-enrichment achieved with this approach, we successfully applied it to Nanopore sequencing, enabling ultra-fast analysis of novel gene fusions within one hour with high sensitivity. This method offers a robust and remarkably sensitive mean of analyzing novel gene fusions, promising the discovery of pivotal biomarkers that can significantly improve cancer diagnostics and the development of new therapeutic strategies.
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Affiliation(s)
- Yi Wu
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinxiao Guo
- Shanghai Sixth People's Hospital Affiliated to, Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Wenjun Li
- NuProbe USA, Inc., 2575 West Bellfort Avenue, Ste. 200 Houston, TX 77054, USA
| | - Xuehao Xiu
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | | | - Yudong Wang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 322000, China
| | - Weiyu Chen
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 322000, China
| | - David Yu Zhang
- NuProbe USA, Inc., 2575 West Bellfort Avenue, Ste. 200 Houston, TX 77054, USA
| | - Xiurong Yang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Song
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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Myint KZ, Balasubramanian B, Venkatraman S, Phimsen S, Sripramote S, Jantra J, Choeiphuk C, Mingphruedhi S, Muangkaew P, Rungsakulkij N, Tangtawee P, Suragul W, Farquharson WV, Wongprasert K, Chutipongtanate S, Sanvarinda P, Ponpuak M, Poungvarin N, Janvilisri T, Suthiphongchai T, Yacqub-Usman K, Grabowska AM, Bates DO, Tohtong R. Therapeutic Implications of Ceritinib in Cholangiocarcinoma beyond ALK Expression and Mutation. Pharmaceuticals (Basel) 2024; 17:197. [PMID: 38399413 PMCID: PMC10892566 DOI: 10.3390/ph17020197] [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: 01/08/2024] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Cholangiocarcinoma (CCA) is a difficult-to-treat cancer, with limited therapeutic options and surgery being the only curative treatment. Standard chemotherapy involves gemcitabine-based therapies combined with cisplatin, oxaliplatin, capecitabine, or 5-FU with a dismal prognosis for most patients. Receptor tyrosine kinases (RTKs) are aberrantly expressed in CCAs encompassing potential therapeutic opportunity. Hence, 112 RTK inhibitors were screened in KKU-M213 cells, and ceritinib, an approved targeted therapy for ALK-fusion gene driven cancers, was the most potent candidate. Ceritinib's cytotoxicity in CCA was assessed using MTT and clonogenic assays, along with immunofluorescence, western blot, and qRT-PCR techniques to analyze gene expression and signaling changes. Furthermore, the drug interaction relationship between ceritinib and cisplatin was determined using a ZIP synergy score. Additionally, spheroid and xenograft models were employed to investigate the efficacy of ceritinib in vivo. Our study revealed that ceritinib effectively killed CCA cells at clinically relevant plasma concentrations, irrespective of ALK expression or mutation status. Ceritinib modulated multiple signaling pathways leading to the inhibition of the PI3K/Akt/mTOR pathway and activated both apoptosis and autophagy. Additionally, ceritinib and cisplatin synergistically reduced CCA cell viability. Our data show ceritinib as an effective treatment of CCA, which could be potentially explored in the other cancer types without ALK mutations.
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Affiliation(s)
- Kyaw Zwar Myint
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (K.Z.M.); (B.B.); (S.V.); (T.J.)
| | - Brinda Balasubramanian
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (K.Z.M.); (B.B.); (S.V.); (T.J.)
- Translational Medical Sciences Unit, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
| | - Simran Venkatraman
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (K.Z.M.); (B.B.); (S.V.); (T.J.)
| | - Suchada Phimsen
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; (S.P.); (C.C.)
| | - Supisara Sripramote
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.S.); (J.J.); (T.S.)
| | - Jeranan Jantra
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.S.); (J.J.); (T.S.)
| | - Chaiwat Choeiphuk
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; (S.P.); (C.C.)
| | - Somkit Mingphruedhi
- Hepato-Pancreatic-Biliary Surgery Unit, Department of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.M.); (P.M.); (N.R.); (P.T.); (W.S.); (W.V.F.)
| | - Paramin Muangkaew
- Hepato-Pancreatic-Biliary Surgery Unit, Department of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.M.); (P.M.); (N.R.); (P.T.); (W.S.); (W.V.F.)
| | - Narongsak Rungsakulkij
- Hepato-Pancreatic-Biliary Surgery Unit, Department of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.M.); (P.M.); (N.R.); (P.T.); (W.S.); (W.V.F.)
| | - Pongsatorn Tangtawee
- Hepato-Pancreatic-Biliary Surgery Unit, Department of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.M.); (P.M.); (N.R.); (P.T.); (W.S.); (W.V.F.)
| | - Wikran Suragul
- Hepato-Pancreatic-Biliary Surgery Unit, Department of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.M.); (P.M.); (N.R.); (P.T.); (W.S.); (W.V.F.)
| | - Watoo Vassanasiri Farquharson
- Hepato-Pancreatic-Biliary Surgery Unit, Department of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.M.); (P.M.); (N.R.); (P.T.); (W.S.); (W.V.F.)
| | - Kanokpan Wongprasert
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Somchai Chutipongtanate
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Pimtip Sanvarinda
- Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Marisa Ponpuak
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Naravat Poungvarin
- Department of Clinical Pathology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Tavan Janvilisri
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (K.Z.M.); (B.B.); (S.V.); (T.J.)
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.S.); (J.J.); (T.S.)
| | - Tuangporn Suthiphongchai
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.S.); (J.J.); (T.S.)
| | - Kiren Yacqub-Usman
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK; (K.Y.-U.); (A.M.G.); (D.O.B.)
| | - Anna M. Grabowska
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK; (K.Y.-U.); (A.M.G.); (D.O.B.)
| | - David O. Bates
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK; (K.Y.-U.); (A.M.G.); (D.O.B.)
| | - Rutaiwan Tohtong
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.S.); (J.J.); (T.S.)
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9
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Li Y, Yuan J, Lu J. Lung carcinoma with diffuse cysts repeatedly misdiagnosed as pulmonary infections and lymphoid interstitial pneumonia: A case report. Medicine (Baltimore) 2024; 103:e37002. [PMID: 38306516 PMCID: PMC10843309 DOI: 10.1097/md.0000000000037002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/29/2023] [Indexed: 02/04/2024] Open
Abstract
INTRODUCTION Diffuse cystic lung diseases comprise a heterogeneous group of pulmonary disorders, with most cases being benign and malignant instances being rare. CASE REPORT We present an unusual case of lung adenocarcinoma characterized by the progressive diffusion of cystic lesions. The patient, initially diagnosed with a pulmonary infection and lymphoid interstitial pneumonia, underwent repeated misdiagnoses. Ultimately, the diagnosis was confirmed using radial endobronchial ultrasound-guided-transbronchial cryobiopsy (rEBUS-TBCB). A 44-year-old male was admitted to the hospital with a persistent cough and expectoration of bloody sputum for over 6 months. Thoracic computed tomography revealed widespread cystic lesions and nodules. Despite multiple misdiagnoses, rEBUS-TBCB successfully confirmed the presence of lung adenocarcinoma and identified an echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) E13:A20 gene rearrangement. The patient was subsequently transferred to a local hospital for oral targeted drug therapy, which resulted in a favorable response. CONCLUSION In conclusions, transbronchial lung biopsies often provide inadequate specimens for confirming diffuse cystic lung diseases. In contrast, the utilization of rEBUS-guided TBCB offers superior diagnostic capabilities, as it enables the collection of larger lung biopsies with higher diagnostic yields and fewer complications compared to surgical lung biopsy.
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Affiliation(s)
- Yishi Li
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jinhe Yuan
- Pulmonary and Critical Care Medicine, Chongqing Fifth People’s Hospital, Chongqing, China
| | - Junyu Lu
- Pulmonary and Critical Care Medicine, Chongqing Fifth People’s Hospital, Chongqing, China
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10
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Zhang JZ, Nguyen WH, Greenwood N, Rose JC, Ong SE, Maly DJ, Baker D. Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution. Nat Biotechnol 2024:10.1038/s41587-023-02107-w. [PMID: 38273065 DOI: 10.1038/s41587-023-02107-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
The utility of genetically encoded biosensors for sensing the activity of signaling proteins has been hampered by a lack of strategies for matching sensor sensitivity to the physiological concentration range of the target. Here we used computational protein design to generate intracellular sensors of Ras activity (LOCKR-based Sensor for Ras activity (Ras-LOCKR-S)) and proximity labelers of the Ras signaling environment (LOCKR-based, Ras activity-dependent Proximity Labeler (Ras-LOCKR-PL)). These tools allow the detection of endogenous Ras activity and labeling of the surrounding environment at subcellular resolution. Using these sensors in human cancer cell lines, we identified Ras-interacting proteins in oncogenic EML4-Alk granules and found that Src-Associated in Mitosis 68-kDa (SAM68) protein specifically enhances Ras activity in the granules. The ability to subcellularly localize endogenous Ras activity should deepen our understanding of Ras function in health and disease and may suggest potential therapeutic strategies.
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Affiliation(s)
- Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - William H Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Greenwood
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - John C Rose
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Dustin J Maly
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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11
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Bailey SM, Cross EM, Kinner-Bibeau L, Sebesta HC, Bedford JS, Tompkins CJ. Monitoring Genomic Structural Rearrangements Resulting from Gene Editing. J Pers Med 2024; 14:110. [PMID: 38276232 PMCID: PMC10817574 DOI: 10.3390/jpm14010110] [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: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The cytogenomics-based methodology of directional genomic hybridization (dGH) enables the detection and quantification of a more comprehensive spectrum of genomic structural variants than any other approach currently available, and importantly, does so on a single-cell basis. Thus, dGH is well-suited for testing and/or validating new advancements in CRISPR-Cas9 gene editing systems. In addition to aberrations detected by traditional cytogenetic approaches, the strand specificity of dGH facilitates detection of otherwise cryptic intra-chromosomal rearrangements, specifically small inversions. As such, dGH represents a powerful, high-resolution approach for the quantitative monitoring of potentially detrimental genomic structural rearrangements resulting from exposure to agents that induce DNA double-strand breaks (DSBs), including restriction endonucleases and ionizing radiations. For intentional genome editing strategies, it is critical that any undesired effects of DSBs induced either by the editing system itself or by mis-repair with other endogenous DSBs are recognized and minimized. In this paper, we discuss the application of dGH for assessing gene editing-associated structural variants and the potential heterogeneity of such rearrangements among cells within an edited population, highlighting its relevance to personalized medicine strategies.
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Affiliation(s)
- Susan M. Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Erin M. Cross
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | | | - Henry C. Sebesta
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Joel S. Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
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12
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Guan J, Chuang TP, Vikström A, Palmer RH, Hallberg B. ALK F1174S mutation impairs ALK kinase activity in EML4-ALK variant 1 and sensitizes EML4-ALK variant 3 to crizotinib. Front Oncol 2024; 13:1281510. [PMID: 38264745 PMCID: PMC10803553 DOI: 10.3389/fonc.2023.1281510] [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: 08/22/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Objective To assess the influence of F1174S mutation on kinase activity and drug sensitivity of the echinoderm microtubule-associated protein-like 4 (EML4) and anaplastic lymphoma kinase (ALK) fusion (EML4-ALK) variants 1 and 3. Methods We constructed mammalian expression plasmids of both wildtype and F1174 mutant EML4-ALK variants 1 and 3, and then characterized them with cell models by performing immunoblotting, neurite outgrowth assay, focus formation assay as well as protein stability assay. Drug sensitivity to ALK tyrosine kinase inhibitors was also compared between wildtype and F1174 mutant EML4-ALK fusions. In addition, we characterized the effect of different F1174 kinase domain mutations in the context of EML4-ALK fusions. Results In contrast to the oncogenic ALK-F1174S mutation that has been reported to be activating in the context of full-length ALK in neuroblastoma, EML4-ALK (F1174S) variant 1 exhibits impaired kinase activity leading to loss of oncogenicity. Furthermore, unlike the previously reported F1174C/L/V mutations, mutation of F1174 to S sensitizes EML4-ALK variants 3a and 3b to crizotinib. Conclusion These findings highlight the complexity of drug selection when treating patients harboring resistance mutations and suggest that the F1174S mutation in EML4-ALK variant 1 is likely not a potent oncogenic driver. Additional oncogenic driver or other resistance mechanisms should be considered in the case of EML4-ALK variant 1 with F1174S mutation.
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Affiliation(s)
- Jikui Guan
- Institute of Pediatric Medicine, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tzu-Po Chuang
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Vikström
- Department of Pulmonary Medicine, Linköping University Hospital, Linköping, Sweden
| | - Ruth H. Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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13
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Tjota MY, Segal JP, Wang P. Clinical Utility and Benefits of Comprehensive Genomic Profiling in Cancer. J Appl Lab Med 2024; 9:76-91. [PMID: 38167763 DOI: 10.1093/jalm/jfad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/28/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Comprehensive genomic profiling (CGP) with next-generation sequencing detects genetic alterations of hundreds of genes simultaneously and multiple molecular biomarkers with one test. In the personalized medicine era, CGP is increasingly used for cancer diagnosis, treatment selection, and prognosis prediction. CONTENT In this review, we summarize the benefits of CGP, clinical utility of CGP, and challenges of setting up CGP in the clinical laboratories. Besides the genetic alterations identified in the cancer-related genes, other biomarkers such as tumor mutational burden, microsatellite instability, and homologous recombination deficiency are critical for initiating targeted therapy. Compared with conventional tests, CGP uses less specimen and shortens the turnaround time if multiple biomarkers need to be tested. RNA fusion assay and liquid biopsy are helpful additions to DNA-based CGP by detecting fusions/splicing variants and complementing tissue-based CGP findings, respectively. SUMMARY Many previous hurdles for implementing CGP in the clinical laboratories have been gradually alleviated such as the decrease in sequencing cost, availability of both open-source and commercial bioinformatics tools, and improved reimbursement. These changes have helped to make CGP available to a greater population of cancer patients for improving characterization of their tumors and expanding their eligibility for clinical trials. Additionally, sequencing results of the hundreds of genes on CGP panels could be further analyzed to better understand the biology of various cancers and identify new biomarkers.
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Affiliation(s)
- Melissa Yuwono Tjota
- Department of Pathology, The University of Chicago, Chicago, IL 60637, United States
| | - Jeremy P Segal
- Department of Pathology, The University of Chicago, Chicago, IL 60637, United States
| | - Peng Wang
- Department of Pathology, The University of Chicago, Chicago, IL 60637, United States
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14
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Li J, Huang K, Ji H, Qian J, Lu H, Zhang Y, Russo A, Romero A, Urbanska EM, Tabbò F, Zhao X, Chu T. Efficacy of alectinib in lung adenocarcinoma patients with different anaplastic lymphoma kinase ( ALK) rearrangements and co-existing alterations-a retrospective cohort study. Transl Lung Cancer Res 2023; 12:2505-2519. [PMID: 38205204 PMCID: PMC10775000 DOI: 10.21037/tlcr-23-658] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/16/2023] [Indexed: 01/12/2024]
Abstract
Background Alectinib significantly improves survival of non-small cell lung cancer (NSCLC) patients with anaplastic lymphoma kinase (ALK)-rearrangement. In this study, we analyzed the effects of different ALK rearrangements and co-mutations on the efficacy of alectinib. Methods Using the electronic medical record system, we reviewed in terms of clinical and pathological features patients with advanced (IIIB/IV stage) ALK-rearranged NSCLC at Shanghai Chest Hospital between January 2018 and December 2021 who were treated with alectinib in first or second line and were assessed for objective response rate (ORR), disease control rate (DCR), and progression-free survival (PFS). Results A total of 66 patients were enrolled in the study, and 17 types of ALK rearrangements were detected, of which five types of ALK rearrangements responded well to alectinib. We classified ALK-rearrangements into four main types, namely echinoderm microtubule-associated protein-like 4 (EML4)-ALK (E6:A20), EML4-ALK (E13:A20), EML4-ALK (E20:A20), and others. There was no significant difference in ORR and DCR of these types (ORR: 31.3% vs. 13.0% vs. 18.2% vs. 17.6%, P=0.575; DCR: 93.8% vs. 95.6% vs. 100.0% vs. 88.2%, P=0.627). The 3-year PFS rates were 25.0% (4/16) vs. 13.0% (3/23) vs. 27.3% (3/11) vs. 18.8% (3/16) for EML4-ALK (E6:A20), EML4-ALK (E13:A20), EML4-ALK (E20:A20), and others, respectively (P=0.725). The results of co-mutation analysis showed that the median PFS (mPFS) for patients with tumors harboring TP53 mutations was 30.4 months, significantly shorter than that of patients with tumors without co-mutations and whose mPFS was not mature (P=0.026). TSC1 co-mutation was also identified as a detrimental factor in outcome, with a DCR of 60% vs. 100% (P=0.031), mPFS of 30.4 months vs. not applicable (P=0.160) in patients with vs. those without this co-mutation, respectively. The efficacy of alectinib in patients with brain metastases is comparable to that in patients without distant organ metastases. There were two cases with specific fusion types that also responded to alectinib; namely, double ALK-rearrangements: EML4-ALK (E13:A20) and MSH2-ALK (M7:A20), and with a rare fusion partner, SPECC1L-ALK (S8:A20). Their PFS were 8.7 and 38.0 months, respectively. Conclusions In this study, the efficacy of alectinib in different types of ALK-rearrangements varied slightly. TP53 and TSC1 co-mutations were identified as detrimental factors affecting efficacy. This study provides references for the response to alectinib in patients with different types of ALK rearrangements and co-mutation.
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Affiliation(s)
- Jiaqi Li
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kuofang Huang
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Ji
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Healthcare-Associated Infection Management, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jialin Qian
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haijiao Lu
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanan Zhang
- Department of Exosome, 3D Medicines Inc., Shanghai, China
| | - Alessandro Russo
- Medical Oncology Unit, Department of Onco-Hematology, Papardo Hospital, Messina, Italy
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro de Majadahonda, Madrid, Spain
| | - Edyta Maria Urbanska
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Fabrizio Tabbò
- Oncology Unit, Department of Medicine, Michele and Pietro Ferrero Hospital, Verduno, Italy
| | - Xiaoyu Zhao
- Department of Exosome, 3D Medicines Inc., Shanghai, China
| | - Tianqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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15
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Ploenzke M, Irizarry R. Reassessing pharmacogenomic cell sensitivity with multilevel statistical models. Biostatistics 2023; 24:901-921. [PMID: 35277956 PMCID: PMC10583722 DOI: 10.1093/biostatistics/kxac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 10/19/2023] Open
Abstract
Pharmacogenomic experiments allow for the systematic testing of drugs, at varying dosage concentrations, to study how genomic markers correlate with cell sensitivity to treatment. The first step in the analysis is to quantify the response of cell lines to variable dosage concentrations of the drugs being tested. The signal to noise in these measurements can be low due to biological and experimental variability. However, the increasing availability of pharmacogenomic studies provides replicated data sets that can be leveraged to gain power. To do this, we formulate a hierarchical mixture model to estimate the drug-specific mixture distributions for estimating cell sensitivity and for assessing drug effect type as either broad or targeted effect. We use this formulation to propose a unified approach that can yield posterior probability of a cell being susceptible to a drug conditional on being a targeted effect or relative effect sizes conditioned on the cell being broad. We demonstrate the usefulness of our approach via case studies. First, we assess pairwise agreements for cell lines/drugs within the intersection of two data sets and confirm the moderate pairwise agreement between many publicly available pharmacogenomic data sets. We then present an analysis that identifies sensitivity to the drug crizotinib for cells harboring EML4-ALK or NPM1-ALK gene fusions, as well as significantly down-regulated cell-matrix pathways associated with crizotinib sensitivity.
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Affiliation(s)
- Matt Ploenzke
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Building 2, 4th Floor, Boston, MA 02115
| | - Rafael Irizarry
- Department of Data Science, Dana Farber Cancer Institute, 450 Brookline Ave, CLSB 11007, Boston, MA 02215
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Yang Y, Lu B, Hu M, Wang Q, Jiang M, Zhang T, Liu Z. Mutation status analysis of 58 patients with advanced ALK fusion gene positive non small cell lung cancer. BMC Pulm Med 2023; 23:319. [PMID: 37658352 PMCID: PMC10472634 DOI: 10.1186/s12890-023-02618-x] [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: 03/05/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023] Open
Abstract
PURPOSE To analyze the characteristics and prognostic values of Anaplastic Lymphoma Kinase (ALK) fusion gene partner, gene subtype and abundance in tumor tissues of advanced Non Small Cell Lung Cancer (NSCLC) patients with positive ALK fusion gene and to explore the best treatment mode of ALK-Tyrosine Kinase Inhibitors(TKIs). METHODS Cases of advanced NSCLC patients with ALK positive confirmed by both Next Generation Sequencing (NGS) and immunohistochemistry were retrospectively collected. The relationships of Overall Survival (OS)/Progression Free Survival (PFS) between different mutation subtypes, mutation abundance, clinicopathological features were analyzed. OS/PFS between different treatment mode of ALK inhibitors were compared. RESULTS Fifty-eight patients were enrolled. There were diverse fusion partners. Five subtypes of Echinoderm Microtubule-associated protein-Like 4 gene (EML4)-ALK fusion mutation were detected: V1,V2,V3,V5 and V7. The mutation abundance ranged from 0.13 to 27.77%, with a median of 5.34%. The abundance of V2 and V5 was higher than V1 and V3 respectively. There was no difference in OS between the low abundance group(≤ 5.34%) and the high abundance group(>5.34%) (P = 0.434). PFS of second-generation ALK inhibitors as first-line treatment was longer than that of Crizotinib as first-line (P<0.001). Never smokers had longer OS than current smokers(P = 0.001). CONCLUSIONS There are differences in abundance between different fusion partners and subtypes in advanced NSCLC with positive ALK. OS is not associated with subtypes, mutation abundance and first line treatment option of either generation of ALK inhibitors. Smoking is a poor prognostic factor.
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Affiliation(s)
- Yuan Yang
- Oncology Department of Beijing Chest Hospital, Capital Medical University, 9 Beiguan Street, Tongzhou District, Beijing, PR China
| | - Baohua Lu
- Oncology Department of Beijing Chest Hospital, Capital Medical University, 9 Beiguan Street, Tongzhou District, Beijing, PR China.
| | - Mingming Hu
- Oncology Department of Beijing Chest Hospital, Capital Medical University, 9 Beiguan Street, Tongzhou District, Beijing, PR China
| | - Qunhui Wang
- Oncology Department of Beijing Chest Hospital, Capital Medical University, 9 Beiguan Street, Tongzhou District, Beijing, PR China
| | - Mei Jiang
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, 17 Qihelou Street, Dongcheng District, Beijing, PR China
| | - Tongmei Zhang
- Oncology Department of Beijing Chest Hospital, Capital Medical University, 9 Beiguan Street, Tongzhou District, Beijing, PR China
| | - Zhe Liu
- Oncology Department of Beijing Chest Hospital, Capital Medical University, 9 Beiguan Street, Tongzhou District, Beijing, PR China
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17
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Lu Y, Sun Z, Li H, Chen X, Li Y, Sun L, Yang F, Jiang G, Zhou J. Radiological evidence of rapid growth acceleration of a small part solid nodule found to be large-cell carcinoma of the lung. J Cardiothorac Surg 2023; 18:236. [PMID: 37488608 PMCID: PMC10364358 DOI: 10.1186/s13019-023-02290-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/15/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND With the widespread use of low-dose computed tomography for lung cancer screening, the detection rate of pulmonary lesions manifesting as ground-glass opacities (GGOs) has been increasing dramatically. The volume doubling time (VDT) has been introduced in clinical practice to monitor the potential growth rate of GGOs during long-term follow-up periods. CASE PRESENTATION A 72-year-old never-smoker female diagnosed with mixed GGO manifested abruptly accelerated growth with sudden decreased VDT from 400 to 36 days. A thoracoscopic left lower lobectomy with mediastinal lymph node dissection was performed, and the diagnosis was stage IB large-cell neuroendocrine carcinoma (LCNEC). Next-generation sequencing of the tumor highlights an EML4-ALK gene fusion. CONCLUSIONS The LCNEC may present as GGO with longer VDT in the early stage. VDT should calculate by the whole size either on the entire tumor diameter or on consolidation diameter. It is recommended that meticulous long-term follow-up with dynamic VDT monitoring may help select high-risk GGOs performing timely semi-elective surgical resection in clinical practice.
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Affiliation(s)
- Yunwei Lu
- Department of Thoracic Surgery, Peking University People's Hospital, No.11 Xizhimen South Street, Beijing, 100044, China
| | - Zewen Sun
- Department of Thoracic Surgery, Peking University People's Hospital, No.11 Xizhimen South Street, Beijing, 100044, China
| | - Hao Li
- Department of Thoracic Surgery, Peking University People's Hospital, No.11 Xizhimen South Street, Beijing, 100044, China
| | - Xiaofeng Chen
- Department of Thoracic Surgery, Peking University People's Hospital, No.11 Xizhimen South Street, Beijing, 100044, China
| | - Yun Li
- Department of Thoracic Surgery, Peking University People's Hospital, No.11 Xizhimen South Street, Beijing, 100044, China
| | - Lina Sun
- Department of Thoracic Surgery, Peking University People's Hospital, No.11 Xizhimen South Street, Beijing, 100044, China
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, No.11 Xizhimen South Street, Beijing, 100044, China
| | - Guanchao Jiang
- Department of Thoracic Surgery, Peking University People's Hospital, No.11 Xizhimen South Street, Beijing, 100044, China
| | - Jian Zhou
- Department of Thoracic Surgery, Peking University People's Hospital, No.11 Xizhimen South Street, Beijing, 100044, China.
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Peri A, Salomon N, Wolf Y, Kreiter S, Diken M, Samuels Y. The landscape of T cell antigens for cancer immunotherapy. NATURE CANCER 2023:10.1038/s43018-023-00588-x. [PMID: 37415076 DOI: 10.1038/s43018-023-00588-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/18/2023] [Indexed: 07/08/2023]
Abstract
The remarkable capacity of immunotherapies to induce durable regression in some patients with metastatic cancer relies heavily on T cell recognition of tumor-presented antigens. As checkpoint-blockade therapy has limited efficacy, tumor antigens have the potential to be exploited for complementary treatments, many of which are already in clinical trials. The surge of interest in this topic has led to the expansion of the tumor antigen landscape with the emergence of new antigen categories. Nonetheless, how different antigens compare in their ability to elicit efficient and safe clinical responses remains largely unknown. Here, we review known cancer peptide antigens, their attributes and the relevant clinical data and discuss future directions.
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Affiliation(s)
- Aviyah Peri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nadja Salomon
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Yochai Wolf
- Ella Lemelbaum Institute for Immuno-oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Sebastian Kreiter
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany.
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany.
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Wang M, Slatter S, Sussell J, Lin CW, Ogale S, Datta D, Butte AJ, Bazhenova L, Rudrapatna VA. ALK Inhibitor Treatment Patterns and Outcomes in Real-World Patients with ALK-Positive Non-Small-Cell Lung Cancer: A Retrospective Cohort Study. Target Oncol 2023:10.1007/s11523-023-00973-7. [PMID: 37341856 DOI: 10.1007/s11523-023-00973-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND Randomized trials have demonstrated that anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKIs) can be safe and efficacious treatments for patients with ALK-positive advanced non-small-cell lung cancer (aNSCLC). However, their safety, tolerability, effectiveness, and patterns of use in real-world patients remain understudied. OBJECTIVE We sought to assess the overall treatment pattern characteristics, safety, and effectiveness outcomes of real-world patients with ALK-positive aNSCLC receiving ALK TKIs. PATIENTS AND METHODS This retrospective cohort study using electronic health record data included adult patients with ALK-positive aNSCLC receiving ALK TKIs between January 2012 and November 2021 at a large tertiary medical center, University of California, San Francisco (UCSF), with alectinib or crizotinib as the initial ALK TKI therapy. Our primary endpoints included the incidence of treatment changes (treatment dose adjustments, interruptions, and discontinuations) during the initial ALK TKI treatment, the count and type of subsequent treatments, rates of serious adverse events (sAEs), and major adverse events (mAEs) leading to any ALK TKI treatment changes. Secondary endpoints included the hazard ratios (HRs) for median mAE-free survival (mAEFS), real-world progression-free survival (rwPFS), and overall survival (OS) when comparing alectinib with crizotinib. RESULTS The cohort consisted of 117 adult patients (70 alectinib and 47 crizotinib) with ALK-positive aNSCLC, with 24.8%, 17.9%, and 6.0% experiencing treatment dose adjustments, interruptions, and discontinuation, respectively. Of the 73 patients whose ALK TKI treatments were discontinued, 68 received subsequent treatments including newer generations of ALK TKIs, immune checkpoint inhibitors, and chemotherapies. The most common mAEs were rash (9.9%) and bradycardia (7.0%) for alectinib and liver toxicity (19.1%) for crizotinib. The most common sAEs were pericardial effusion (5.6%) and pleural effusion (5.6%) for alectinib and pulmonary embolism (6.4%) for crizotinib. Patients receiving alectinib versus crizotinib as their first ALK TKI treatment experienced significantly prolonged median rwPFS (29.3 versus 10.4 months) with an HR of 0.38 (95% CI 0.21-0.67), while prolonged median mAEFS (not reached versus 91.3 months) and OS (54.1 versus 45.8 months) were observed in patients receiving alectinib versus crizotinib but did not reach statistical significance. Yet, it is worth noting that there was a high degree of cross-over post-progression, which could significantly confound the overall survival measures. CONCLUSIONS We found that ALK TKIs were highly tolerable, and alectinib was associated with favorable survival outcomes with longer time to adverse events (AE) requiring medical interventions, disease progression, and death, in the context of real-world use. Proactive monitoring for adverse events such as rash, bradycardia, and hepatotoxicity may help further promote the safe and optimal use of ALK TKIs in the treatment of patients with aNSCLC.
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Affiliation(s)
- Michelle Wang
- Bakar Computational Health Sciences Institute, University of California San Francisco, UCSF Valley Tower, Box 2933 Room 21E, 490 Illinois Street, Floor 2, San Francisco, CA, 94143, USA
| | - Shadera Slatter
- Bakar Computational Health Sciences Institute, University of California San Francisco, UCSF Valley Tower, Box 2933 Room 21E, 490 Illinois Street, Floor 2, San Francisco, CA, 94143, USA
| | - Jesse Sussell
- Evidence for Access, Genentech Inc., South San Francisco, CA, USA
| | - Chia-Wei Lin
- Evidence for Access, Genentech Inc., South San Francisco, CA, USA
| | - Sarika Ogale
- Evidence for Access, Genentech Inc., South San Francisco, CA, USA
| | - Debajyoti Datta
- Bakar Computational Health Sciences Institute, University of California San Francisco, UCSF Valley Tower, Box 2933 Room 21E, 490 Illinois Street, Floor 2, San Francisco, CA, 94143, USA
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of California San Francisco, UCSF Valley Tower, Box 2933 Room 21E, 490 Illinois Street, Floor 2, San Francisco, CA, 94143, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Lyudmila Bazhenova
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Vivek A Rudrapatna
- Bakar Computational Health Sciences Institute, University of California San Francisco, UCSF Valley Tower, Box 2933 Room 21E, 490 Illinois Street, Floor 2, San Francisco, CA, 94143, USA.
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
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Shibata A, Shirohzu H, Iwakami Y, Abe T, Emura C, Aoki E, Ohgi T. Terminal bridging of siRNA duplex at the ribose 2' position controls strand bias and target sequence preference. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:468-477. [PMID: 37168798 PMCID: PMC10165404 DOI: 10.1016/j.omtn.2023.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/14/2023] [Indexed: 05/13/2023]
Abstract
Small interfering RNA (siRNA) and short hairpin RNA (shRNA) are widely used as RNA interference (RNAi) reagents. Recently, truncated shRNAs that trigger RNAi in a Dicer-independent manner have been developed. We generated a novel class of RNAi reagent, designated enforced strand bias (ESB) RNA, in which an siRNA duplex was chemically bridged between the 3' terminal overhang region of the guide strand and the 5' terminal nucleotide of the passenger strand. ESB RNA, which is chemically bridged at the 2' positions of ribose (2'-2' ESB RNA), functions in a Dicer-independent manner and was highly effective at triggering RNAi without the passenger strand-derived off-target effect. In addition, the 2'-2' ESB RNA exhibited a unique target sequence preference that differs from siRNA and silenced target sequences that could not be effectively suppressed by siRNA. Our results indicate that ESB RNA has the potential to be an effective RNAi reagent even when the target sequence is not suitable for siRNA.
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Affiliation(s)
- Atsushi Shibata
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
- Corresponding author Atsushi Shibata, Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan.
| | - Hisao Shirohzu
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
- Fukuoka Center for Disease Control and Prevention, Kurume, Fukuoka, Japan
| | - Yusuke Iwakami
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Tomoaki Abe
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Chisato Emura
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Eriko Aoki
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Tadaaki Ohgi
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
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Li JW, Zheng G, Kaye FJ, Wu L. PROTAC therapy as a new targeted therapy for lung cancer. Mol Ther 2023; 31:647-656. [PMID: 36415148 PMCID: PMC10014230 DOI: 10.1016/j.ymthe.2022.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/01/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
Despite recent advances in molecular therapeutics, lung cancer is still a leading cause of cancer deaths. Currently, limited targeted therapy options and acquired drug resistance present significant barriers in the treatment of patients with lung cancer. New strategies in drug development, including those that take advantage of the intracellular ubiquitin-proteasome system to induce targeted protein degradation, have the potential to advance the field of personalized medicine for patients with lung cancer. Specifically, small molecule proteolysis targeting chimeras (PROTACs), consisting of two ligands connected by a linker that bind to a target protein and an E3 ubiquitin ligase, have been developed against many cancer targets, providing promising opportunities for advanced lung cancer. In this review, we focus on the rationale for PROTAC therapy as a new targeted therapy and the current status of PROTAC development in lung cancer.
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Affiliation(s)
- Jennifer W Li
- Department of Medicine, Brown University, Providence, RI 02912, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Frederic J Kaye
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA; UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Lizi Wu
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
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22
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Aepala MR, Peiris MN, Jiang Z, Yang W, Meyer AN, Donoghue DJ. Nefarious NTRK oncogenic fusions in pediatric sarcomas: Too many to Trk. Cytokine Growth Factor Rev 2022; 68:93-106. [PMID: 36153202 DOI: 10.1016/j.cytogfr.2022.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 01/30/2023]
Abstract
Neurotrophic Tyrosine Receptor Kinase (NTRK) genes undergo chromosomal translocations to create novel open reading frames coding for oncogenic fusion proteins; the N-terminal portion, donated by various partner genes, becomes fused to the tyrosine kinase domain of either NTRK1, NTRK2, or NTRK3. NTRK fusion proteins have been identified as driver oncogenes in a wide variety of tumors over the past three decades, including Pediatric Gliomas, Papillary Thyroid Carcinoma, Spitzoid Neoplasms, Glioblastoma, and additional tumors. Importantly, NTRK fusions function as drivers of pediatric sarcomas, accounting for approximately 15% of childhood cancers including Infantile Fibrosarcoma (IFS), a subset of pediatric soft tissue sarcoma (STS). While tyrosine kinase inhibitors (TKIs), such as larotrectinib and entrectinib, have demonstrated profound results against NTRK fusion-positive cancers, acquired resistance to these TKIs has resulted in the formation of gatekeeper, solvent-front, and compound mutations. We present a comprehensive compilation of oncogenic fusions involving NTRKs focusing specifically on pediatric STS, examining their biological signaling pathways and mechanisms of activation. The importance of an obligatory dimerization or multimerization domain, invariably donated by the N-terminal fusion partner, is discussed using characteristic fusions that occur in pediatric sarcomas. In addition, examples are presented of oncogenic fusion proteins in which the N-terminal partners may contribute additional biological activities beyond an oligomerization domain. Lastly, therapeutic approaches to the treatment of pediatric sarcoma will be presented, using first generation and second-generation agents such as selitrectinib and repotrectinib.
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Affiliation(s)
- Megha R Aepala
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0367, USA
| | - Malalage N Peiris
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0367, USA
| | - Zian Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0367, USA
| | - Wei Yang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0367, USA
| | - April N Meyer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0367, USA
| | - Daniel J Donoghue
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0367, USA; UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0367, USA.
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23
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Nesteryuk V, Hamdani O, Gong R, Almog N, Alexander BM, Soosman S, Yoneda K, Ali SM, Borowsky AD, Riess JW. A Common Cell of Origin for Inflammatory Myofibroblastic Tumor and Lung Adenocarcinoma with ALK rearrangement. Clin Lung Cancer 2022; 23:e550-e555. [PMID: 36253270 DOI: 10.1016/j.cllc.2022.09.001] [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: 03/26/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 01/27/2023]
Abstract
This case signifies the importance of obtaining tumor comprehensive genomic profiling (CGP) as it has utility in cancer type classification and helping in diagnosing recurrence/metastasis or separately occurring primary tumors. CGP can also help guiding treatment as in this case separately occurring Inflammatory Myofibroblastic Tumor had ALK fusion and responded to crizotinib. As treatment progresses, new biopsies should be obtained and CGP used to evaluate for appearance of any new genomic alterations, in order to guide further therapy.
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Affiliation(s)
- Vasyl Nesteryuk
- Department of Medicine.Division of Hematology/Oncology, UC Davis School of Medicine, UC Davis Comprehensive Cancer Center, Davis, CA
| | - Omar Hamdani
- Clinical Genomics Scientist, Clinical Development and Medical Affairs, Foundation Medicine, Inc., Cambridge, MA
| | - Raymond Gong
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Davis, CA
| | - Nava Almog
- Clinical Genomics Scientist, Clinical Development and Medical Affairs, Foundation Medicine, Inc., Cambridge, MA
| | - Brian M Alexander
- Clinical Genomics Scientist, Clinical Development and Medical Affairs, Foundation Medicine, Inc., Cambridge, MA
| | | | - Ken Yoneda
- Department of Medicine. Division of Pulmonary and Critical Care Medicine,UC Davis School of Medicine, UC Davis Comprehensive Cancer Center, Davis, CA
| | - Siraj M Ali
- Clinical Genomics Scientist, Clinical Development and Medical Affairs, Foundation Medicine, Inc., Cambridge, MA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Davis, CA
| | - Jonathan W Riess
- Department of Medicine.Division of Hematology/Oncology, UC Davis School of Medicine, UC Davis Comprehensive Cancer Center, Davis, CA.
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Que D, Zou H, Mao B, Zhang H, Liang W, Liu Q, Ke L, Guo L, Xie Q. Pathological complete remission in ALK-positive lung cancer patient after multiple lines of conversion therapy. Front Oncol 2022; 12:967675. [DOI: 10.3389/fonc.2022.967675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
IntroductionTraditional therapeutic approaches for the treatment of advanced non-small-cell lung cancer (NSCLC) are based on chemotherapy. However, the discovery and understanding of oncogenic driver alterations has led to the development of targeted therapies that have substantially improved patient outcomes. Still, to date, there have been no reports of patients with advanced anaplastic lymphoma kinase (ALK)-positive lung cancer achieving clinical complete response (cCR) in the systemic lesion and pathological complete remission (pCR) in primary lung lesion after multiple lines of conversion therapy.MethodsIn this case, a 55-year-old man was diagnosed with ALK-positive, stage IV lung adenocarcinoma using immunohistochemistry and next generation sequencing (NGS) tests.ResultsCrizotinib and two other ATP-competitive ALK inhibitors, ceritinib and alectinib, were used respectively as first-line, second-line, and third-line therapy. The patient received treatment with crizotinib and achieved partial response (PR), but 5 months later the efficacy was evaluated as progressive disease (PD). Ceritinib was used as the second-line treatment, but the disease progressed 6 months later. Alectinib was used as the third-line treatment, but the efficacy was evaluated as PD. From April 2019 to November 2019, the patient received 4 cycles of induction chemotherapy with pemetrexed/carboplatin/bevacizumab and then switched to pemetrexed/bevacizumab as the fourth-line treatment, and received the fifth line treatment, cetuximab/paclitaxel liposome/nedaplatin, for 1 cycle, but the disease still progressed. Then the patient received the sixth line of treatment, camrelizumab/lorlatinib, for 9 antitumor cycles, resulting in PR. The patient underwent surgery followed by maintenance treatment with lorlatinib and achieved cCR. To our knowledge, this is the first documented case of cCR in a patient with ALK-positive advanced lung adenocarcinoma treated with multiple lines of therapy followed by surgical treatment.DiscussionThis case reveals the possible survival benefit of immunotherapy after multiple line treatment in ALK-positive advanced lung adenocarcinoma, indicating that it is possible find new therapeutic targets based on NGS molecular detection and provide precise therapeutic strategies for clinical practice when drug resistance or progression occurs in cancer therapy.
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Integration of CRISPR/Cas9 with artificial intelligence for improved cancer therapeutics. J Transl Med 2022; 20:534. [PMID: 36401282 PMCID: PMC9673220 DOI: 10.1186/s12967-022-03765-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022] Open
Abstract
Gene editing has great potential in treating diseases caused by well-characterized molecular alterations. The introduction of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)–based gene-editing tools has substantially improved the precision and efficiency of gene editing. The CRISPR/Cas9 system offers several advantages over the existing gene-editing approaches, such as its ability to target practically any genomic sequence, enabling the rapid development and deployment of novel CRISPR-mediated knock-out/knock-in methods. CRISPR/Cas9 has been widely used to develop cancer models, validate essential genes as druggable targets, study drug-resistance mechanisms, explore gene non-coding areas, and develop biomarkers. CRISPR gene editing can create more-effective chimeric antigen receptor (CAR)-T cells that are durable, cost-effective, and more readily available. However, further research is needed to define the CRISPR/Cas9 system’s pros and cons, establish best practices, and determine social and ethical implications. This review summarizes recent CRISPR/Cas9 developments, particularly in cancer research and immunotherapy, and the potential of CRISPR/Cas9-based screening in developing cancer precision medicine and engineering models for targeted cancer therapy, highlighting the existing challenges and future directions. Lastly, we highlight the role of artificial intelligence in refining the CRISPR system's on-target and off-target effects, a critical factor for the broader application in cancer therapeutics.
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Wang T, Wei L, Lu Q, Shao Y, You S, Yin JC, Wang S, Shao Y, Chen Z, Wang Z. Landscape of potentially targetable receptor tyrosine kinase fusions in diverse cancers by DNA-based profiling. NPJ Precis Oncol 2022; 6:84. [DOI: 10.1038/s41698-022-00325-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
AbstractRecurrent fusions of receptor tyrosine kinases (RTKs) are often driving events in tumorigenesis that carry important diagnostic value and are potentially targetable by the increasing number of tyrosine kinase inhibitors (TKIs). Here, we characterized the spectrum of 1324 RTK fusions with intact kinase domains in solid tumors by DNA-based high-throughput sequencing. Overall, the prevalence of RTK fusions were 4.7%, with variable frequencies and diverse genomic structures and fusion partners across cancer types. Cancer types, such as thyroid cancers, urological cancers and neuroendocrine tumors are selective in the RTK fusions they carry, while others exhibit highly complex spectra of fusion events. Notably, most RTKs were promiscuous in terms of the partner genes they recombine with. A large proportion of RTK fusions had one of the breakpoints localized to intergenic regions. Comprehensive genomic profiling revealed differences in co-mutational patterns pre- and post-TKI treatments across various RTK fusions. At baseline, multiple cases were detected with co-occurring RTK fusions or concomitant oncogenic mutations in driver genes, such as KRAS and EGFR. Following TKI resistance, we observed differences in potential on- and off-target resistance mutations among fusion variants. For example, the EML4-ALK v3 variant displayed more complex on-target resistance mechanisms, which might explain the reduced survival outcome compared with the v1 variant. Finally, we identified two lung cancer patients with MET+ and NTRK1+ tumors, respectively, who responded well to crizotinib treatment. Taken together, our findings demonstrate the diagnostic and prognostic values of screening for RTK fusions using DNA-based sequencing in solid tumors.
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Evaluating Real World Mutational Differences Between Hispanics and Asians in NSCLC at a Large Academic Institution in Los Angeles. Clin Lung Cancer 2022; 23:e443-e452. [PMID: 35902325 DOI: 10.1016/j.cllc.2022.06.007] [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: 02/24/2022] [Revised: 06/03/2022] [Accepted: 06/16/2022] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Hispanics living in the United States have higher rates of Epidermal Growth Factor Receptor (EGFR) mutations compared with Non-Hispanic Whites. While this higher incidence is like Asian patients living in the United States, the outcomes for Hispanic patients differ. We looked to compare the variances in mutational profiles between Hispanics and Asians in Los Angeles. PATIENTS AND METHODS Three hundred ninety three non-small cell lung cancer (NSCLC) patients treated at Los Angeles County + University of Southern California (LAC + USC) Medical Center and Norris Comprehensive Cancer Center who received comprehensive genomic profiling (CGP) were evaluated from July 2017 to August 2020. CGP was done using tissue biopsies (n = 211) from Caris Life Sciences and liquid biopsies (n = 231) from Guardant Health. Multivariate logistic regression evaluated the role of race between Hispanics and Asians. RESULTS In the Hispanic cohort (n = 90), 50.0% were male, median age of diagnosis was 62, 54.5% were non-smokers, and 85.5% had adenocarcinoma. In Asians (n = 142), 47.5% were male, median age of diagnosis was 65, 59.6% were non-smokers, and 83.8% had adenocarcinoma. Hispanic patients had greater prevalence of Kirsten rat sarcoma virus (KRAS) mutations (odds ratio [OR] 4.42, 95% confidence interval [95% CI]: 1.63-12.83) and lesser prevalence of EGFR mutations (OR 0.31, 95% CI: 0.16-0.59). There were a greater proportion of Hispanic smokers with KRAS mutations (14/41; 34.1%) than Asian smokers (4/58; 6.9%). CONCLUSION We saw a greater percentage of Hispanics with KRAS mutations despite similar smoking percentages along with a greater percentage of Asians with EGFR mutations. This study shows that ethnic and racial backgrounds of the patient can influence the effects of potentially carcinogenic exposures leading to variances of mutation frequency of NSCLC among different ethnicities.
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Use of ALK-tyrosine kinase inhibitors (ALK TKI) in clinical practice, overall survival, and treatment duration - a Swedish nationwide retrospective study. Acta Oncol 2022; 61:1354-1361. [PMID: 36368902 DOI: 10.1080/0284186x.2022.2133972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The real-world treatment and outcomes of patients with anaplastic lymphoma kinase positive (ALK+) advanced non-small cell lung cancer treated with ALK Tyrosine Kinase Inhibitor (TKI) drugs in Sweden is not well described. MATERIAL AND METHODS A retrospective population-based cohort study was conducted using Swedish national registers. All patients with a filled prescription for an ALK TKI between January 2012 and October 2020 were included. The sequencing of ALK TKI and duration of treatment (DOT) were described, and overall survival (OS) was estimated using the Kaplan-Meier method. Patients were stratified based on treatment with frontline chemotherapy, presence of CNS metastases prior to the first ALK TKI, and generation of ALK TKI agent. RESULTS Among the total of 579 patients, 549 (95%) underwent a therapy sequence in line with current clinical practice with 204 (37%) patients receiving frontline chemotherapy. Single-line ALK TKI was given to 366 patients (crizotinib: 211; alectinib: 146; ceritinib: 9), whereas 128 patients received two different ALK TKI (frontline crizotinib: 100, alectinib: 24, ceritinib: 4); 40 patients received three lines and 15 patients four ALK TKI lines or more. With frontline chemotherapy, the mean (standard deviation) DOT was 1.07 (1.25) years for the entire TKI therapy sequence compared to 1.23 (1.28) years with frontline ALK TKI. The median (95% confidence interval) OS was 1.83 (1.48-2.13) years for the entire cohort, 1.44 (0.89-1.98) years for patients given frontline chemotherapy, and 2.02 (1.60-2.58) years for patients given frontline ALK TKI. CONCLUSION This study provides a unique overview of the patient population treated with ALK TKI in Sweden and reveals the treatment patterns applied in real clinical practice. More research is needed when longer follow-up data are available for later-generation ALK TKI, to fully understand ALK TKI sequencing and its effect on patient survival in a real-world setting.
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[Consensus on Postoperative Recurrence Prediction of Non-small Cell Lung Cancer
Based on Molecular Markers]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2022; 25:701-714. [PMID: 36285390 PMCID: PMC9619343 DOI: 10.3779/j.issn.1009-3419.2022.102.44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Significant progress has been made in lung cancer screening, surgery, chemoradiation, targeted therapy, and immunotherapy recently. Surgical resection is the most important treatment for localized non-small cell lung cancer (NSCLC) so far, but there are still many patients who develop local recurrence or distant metastases within 5 years of surgery. Currently, the risk factors of recurrence in patients with NSCLC are mainly based on clinical and pathological features, which hardly identify patients at high risk of recurrence accurately. With the development of new detection technologies, a number of molecular markers that may have a predictive risk of recurrence in NSCLC have been discovered over the years. In order to summarize the molecular markers related to postoperative recurrence in NSCLC patients, we have formulated a consensus on the prediction of postoperative recurrence of NSCLC based on molecular markers. This consensus mainly focuses on the early stage NSCLC patients, discusses and summarizes the risk factors of disease recurrence from the molecular level. It is hoped that more and more valuable information can be provided for the management of patients, so as to provide more guidance for the perioperative management of the patients with early stage NSCLC in the future.
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Jiang J, Zhao C, Zhang F, Liu Z, Zhou K, Ren X, Wan Y. ALK inhibitors in ALK-rearranged non-small cell lung cancer with and without brain metastases: systematic review and network meta-analysis. BMJ Open 2022; 12:e060782. [PMID: 36123063 PMCID: PMC9486327 DOI: 10.1136/bmjopen-2022-060782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES To systematically evaluate the efficacy and safety of anaplastic lymphoma kinase (ALK) inhibitors in ALK-rearranged positive non-small cell lung cancer (NSCLC) with brain metastases, and update the overall survival (OS) outcomes of the second-generation and third-generation ALK (ALK-2ndG/3rdG) inhibitors versus first-generation (ALK-1stG) inhibitors. DESIGN The study is in accordance with the Preferred Reporting Items for Systematic Review and Meta-analysis guidelines. Randomised controlled trials (RCTs) published up to 3 November 2021 were retrieved from PubMed, EMBASE, Cochrane Library and ClinicalTrials.gov. SETTING RCTs from any country and healthcare setting. PARTICIPANTS Patients with advanced ALK-positive NSCLC with or without brain metastases. INTERVENTIONS AND COMPARISONS The interventions were ALK-2ndG/3rdG; the control arm was ALK-1stG or crizotinib. PRIMARY AND SECONDARY OUTCOME MEASURES Primary outcomes included median progression-free survival and median OS. Secondary outcomes included systemic objective response rate, intracranial response rate and rate of grade ≥3 adverse events (AEs). RESULTS A total of 12 RCTs involving 3156 patients were analysed. Compared with ALK-1stG (crizotinib), ALK-2ndG (alectinib, brigatinib, ceritinib and ensartinib) significantly improved the OS (HR: 0.72, 95% CI: 0.57 to 0.90, p=0.004) and intracranial response of patients with any brain metastases, especially with measurable (diameter ≥10 mm) brain metastases. Network meta-analysis demonstrated that ALK-3rdG (lorlatinib) had superior efficacy for patients with brain lesions, but performed a distinct side-effect profile. Moreover, alectinib showed superior efficacy and lower toxicity in ALK-positive NSCLC. CONCLUSION Treatment with ALK-2ndG inhibitors significantly improved OS compared with crizotinib, and alectinib has less severe AEs than any other ALK inhibitors with moderate-high efficacy. The limited OS follow-up and inadequate sample sizes might contribute to having no statistically significant difference in OS of lorlatinib versus crizotinib. More high-quality and longer follow-up RCTs are warranted to prove our findings. PROSPERO REGISTRATION NUMBER CRD42021292245.
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Affiliation(s)
- Jun Jiang
- Department of Health Service, Base of Health Service, Fourth Military Medical University, Xi'an, China
- Department of Respiratory and Critical Care, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Cong Zhao
- Department of Neurology, Air Force Medical Center of PLA, Beijing, China
| | - Fang Zhang
- Department of Respiratory and Critical Care, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Zhenhua Liu
- Department of Health Service, Base of Health Service, Fourth Military Medical University, Xi'an, China
| | - Kaiyuan Zhou
- Department of Health Service, Base of Health Service, Fourth Military Medical University, Xi'an, China
| | - Xinling Ren
- Department of Respiratory and Critical Care, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
- Department of Pulmonary Medicine, Shenzhen General Hospital, Shenzhen University, Shenzhen, China
| | - Yi Wan
- Department of Health Service, Base of Health Service, Fourth Military Medical University, Xi'an, China
- Department of Health Statistics, Fourth Military Medical University, Xi'an, China
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31
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Nguyen L, Van Hoeck A, Cuppen E. Machine learning-based tissue of origin classification for cancer of unknown primary diagnostics using genome-wide mutation features. Nat Commun 2022; 13:4013. [PMID: 35817764 PMCID: PMC9273599 DOI: 10.1038/s41467-022-31666-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/23/2022] [Indexed: 12/25/2022] Open
Abstract
Cancers of unknown primary (CUP) origin account for ∼3% of all cancer diagnoses, whereby the tumor tissue of origin (TOO) cannot be determined. Using a uniformly processed dataset encompassing 6756 whole-genome sequenced primary and metastatic tumors, we develop Cancer of Unknown Primary Location Resolver (CUPLR), a random forest TOO classifier that employs 511 features based on simple and complex somatic driver and passenger mutations. CUPLR distinguishes 35 cancer (sub)types with ∼90% recall and ∼90% precision based on cross-validation and test set predictions. We find that structural variant derived features increase the performance and utility for classifying specific cancer types. With CUPLR, we could determine the TOO for 82/141 (58%) of CUP patients. Although CUPLR is based on machine learning, it provides a human interpretable graphical report with detailed feature explanations. The comprehensive output of CUPLR complements existing histopathological procedures and can enable improved diagnostics for CUP patients.
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Affiliation(s)
- Luan Nguyen
- University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Arne Van Hoeck
- University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Edwin Cuppen
- University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
- Hartwig Medical Foundation, Science Park 408, 1098 XH, Amsterdam, The Netherlands.
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32
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Hamdan A, Ewing A. Unravelling the tumour genome: The evolutionary and clinical impacts of structural variants in tumourigenesis. J Pathol 2022; 257:479-493. [PMID: 35355264 PMCID: PMC9321913 DOI: 10.1002/path.5901] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/16/2022] [Accepted: 03/28/2022] [Indexed: 11/15/2022]
Abstract
Structural variants (SVs) represent a major source of aberration in tumour genomes. Given the diversity in the size and type of SVs present in tumours, the accurate detection and interpretation of SVs in tumours is challenging. New classes of complex structural events in tumours are discovered frequently, and the definitions of the genomic consequences of complex events are constantly being refined. Detailed analyses of short-read whole-genome sequencing (WGS) data from large tumour cohorts facilitate the interrogation of SVs at orders of magnitude greater scale and depth. However, the inherent technical limitations of short-read WGS prevent us from accurately detecting and investigating the impact of all the SVs present in tumours. The expanded use of long-read WGS will be critical for improving the accuracy of SV detection, and in fully resolving complex SV events, both of which are crucial for determining the impact of SVs on tumour progression and clinical outcome. Despite the present limitations, we demonstrate that SVs play an important role in tumourigenesis. In particular, SVs contribute significantly to late-stage tumour development and to intratumoural heterogeneity. The evolutionary trajectories of SVs represent a window into the clonal dynamics in tumours, a comprehensive understanding of which will be vital for influencing patient outcomes in the future. Recent findings have highlighted many clinical applications of SVs in cancer, from early detection to biomarkers for treatment response and prognosis. As the methods to detect and interpret SVs improve, elucidating the full breadth of the complex SV landscape and determining how these events modulate tumour evolution will improve our understanding of cancer biology and our ability to capitalise on the utility of SVs in the clinical management of cancer patients. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Alhafidz Hamdan
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Ailith Ewing
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
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33
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Lei Y, Lei Y, Shi X, Wang J. EML4‑ALK fusion gene in non‑small cell lung cancer (Review). Oncol Lett 2022; 24:277. [PMID: 35928804 PMCID: PMC9344266 DOI: 10.3892/ol.2022.13397] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a malignant tumor with a high morbidity and mortality rate that is a threat to human health. With the development of molecular targeted research, breakthroughs have been made on the molecular mechanism of lung cancer. The echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) fusion gene is one of the most important pathogenic driver genes of NSCLC discovered thus far. Four generations of targeted drugs for EML4-ALK have been developed, with patients benefiting significantly from these drugs. Therefore, EML4-ALK has become a research hotspot in NSCLC. The aim of the present study is to introduce the current research progress of EML4-ALK and its association with NSCLC.
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Affiliation(s)
- Yu Lei
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Yan Lei
- Department of Respiratory Medicine, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Xiang Shi
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Jingjing Wang
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
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34
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Huang L, Liao Z, Liu Z, Chen Y, Huang T, Xiao H. Application and Prospect of CRISPR/Cas9 Technology in Reversing Drug Resistance of Non-Small Cell Lung Cancer. Front Pharmacol 2022; 13:900825. [PMID: 35620280 PMCID: PMC9127258 DOI: 10.3389/fphar.2022.900825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer drug resistance has always been a major factor affecting the treatment of non-small cell lung cancer, which reduces the quality of life of patients. The clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) technology, as an efficient and convenient new gene-editing technology, has provided a lot of help to the clinic and accelerated the research of cancer and drug resistance. In this review, we introduce the mechanisms of drug resistance in non-small cell lung cancer (NSCLC), discuss how the CRISPR/Cas9 system can reverse multidrug resistance in NSCLC, and focus on drug resistance gene mutations. To improve the prognosis of NSCLC patients and further improve patients' quality of life, it is necessary to utilize the CRISPR/Cas9 system in systematic research on cancer drug resistance.
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Affiliation(s)
- Lu Huang
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhi Liao
- Department of Gynecology and Obstetrics, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Zhixi Liu
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Yan Chen
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - Tingwenli Huang
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Hongtao Xiao
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
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35
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Ding Y, Sun C, Su W, Miao C, He X, Wang JS, Zhang ZH. Detecting anaplastic lymphoma kinase (ALK) gene rearrangements with next-generation sequencing remains a reliable approach in patients with non-small-cell lung cancer. Virchows Arch 2022; 481:405-419. [PMID: 35624360 DOI: 10.1007/s00428-022-03339-y] [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: 01/05/2022] [Revised: 04/12/2022] [Accepted: 05/12/2022] [Indexed: 11/24/2022]
Abstract
Next-generation sequencing (NGS) is rapidly becoming routine in clinical oncology practice to identify therapeutic biomarkers, including gene rearrangements in anaplastic lymphoma kinase (ALK). Our study investigated the concordance of ALK positivity evaluated by DNA-based NGS with orthogonal ALK testing methods such as fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and RNA-based NGS (RNA-NGS). Thirty-eight patients with lung adenocarcinoma who were detected with ALK rearrangements using DNA-NGS and also had adequate tissue samples submitted for FISH, IHC, and RNA-NGS, were included in this study. Of the 38 patients, RNA samples from 3 patients failed quality control for RNA-NGS. The concordance of ALK positivity was calculated relative to DNA-NGS results. The concordance rates were 97.1% (34/35) for RNA-NGS, 94.7% (36/38) for IHC, and 97.4% (37/38) for FISH. DNA-NGS detected single ALK rearrangements in 14 (35.0%) patients and complex ALK rearrangements in 26 (65.0%). RNA-NGS detected only single transcripts of the primary ALK fusions. A novel LANCL1-ALK (L7:A20) detected using DNA-NGS was detected as EML4-ALK (E13:A20) transcripts using RNA-NGS. Interestingly, patients with single ALK rearrangements were more likely to be detected with atypical isolated red signals (p < 0.001), while patients with complex ALK rearrangements were more likely to be detected with atypical split red and green signals less than 2 signal diameters apart (p < 0.001). Our study highlights the reliability of NGS in the accurate detection of specific ALK fusion variants and concomitant mutations that are crucial for individualized treatment decisions in patients with lung cancer.
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Affiliation(s)
- Ying Ding
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Chang Sun
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, 210029, China
| | - Wei Su
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, 210029, China
| | - Chen Miao
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xiao He
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jin-Song Wang
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210000, China
| | - Zhi-Hong Zhang
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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36
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Multiple Genetic Alterations as Resistance Mechanism during Second-Line Lorlatinib for Advanced ALK-Rearranged Lung Adenocarcinoma: A Case Report. Diagnostics (Basel) 2022; 12:diagnostics12030682. [PMID: 35328235 PMCID: PMC8947659 DOI: 10.3390/diagnostics12030682] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 12/12/2022] Open
Abstract
Second and third-generation ALK-TKI inhibitors have showed better activity and have replaced crizotinib in most of cases of advanced ALK-rearranged lung adenocarcinoma. The emergence of resistance adversely affects also the activity of these newer drugs; in particular, lorlatinib often shows multiple and complex resistance mechanisms. The case reported here highlights the importance of reassessing the biomolecular profile during the disease course, both by tissutal and liquid biopsy, with the aim of improving the knowledge of these resistance mechanisms, and so identifying new drugs or sequences able to optimize the management of these patients.
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37
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Takeda-Miyata N, Miyagawa-Hayashino A, Hamada S, Nagamine M, Fujii T, Imura T, Tsunezuka H, Shimomura M, Yamaguchi T, Yanada M, Inoue M, Konishi E. A clinicopathologic and molecular analysis of five cases of bronchiolar adenoma with rare mutations. Pathol Int 2022; 72:273-282. [PMID: 35234319 DOI: 10.1111/pin.13213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/25/2022] [Indexed: 11/30/2022]
Abstract
Bronchiolar adenoma (BA) is a rare benign lung tumor that shows proliferation of bland bronchiolar-type epithelium containing a continuous layer of basal cells. This tumor entity has been newly added to the recent World Health Organization (WHO) classification 5th edition. This entity encompasses a spectrum of lesions: the classic ciliated muconodular papillary tumor (CMPT) and the non-classic CMPT. Although BA is reported to have driver mutations including BRAF V600E, EGFR, and KRAS, the molecular profile of BA is still incompletely understood. Five resected BAs at our institutions were analyzed. The BA lesions were subdivided into two groups: three proximal-type BAs and two distal-type BAs. NRAS codon 12/13 mutation and EML4 exon 20-ALK exon 20 fusion were found in two of the three proximal-types. BRAF V600E mutation was found in one of the two distal-types. Two cases coexisted with lung adenocarcinoma, with EGFR exon 19 deletion and KRAS mutation, respectively. No recurrence was observed at a median of 12 months (range 2-84 months) of follow-up. BA has uncommon variants of mutation seen in lung adenocarcinoma. NRAS mutation and ALK fusion partner has not been reported previously. The present cases may reinforce the distinctive biology of BA from lung adenocarcinoma.
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Affiliation(s)
- Naoko Takeda-Miyata
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Aya Miyagawa-Hayashino
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | | | - Michiko Nagamine
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomomi Fujii
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Tetsuya Imura
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroaki Tsunezuka
- Department of Surgery, Division of Thoracic Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masanori Shimomura
- Department of Surgery, Division of Thoracic Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | | | - Masashi Yanada
- Department of Thoracic Surgery, Otsu City Hospital, Shiga, Japan
| | - Masayoshi Inoue
- Department of Surgery, Division of Thoracic Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eiichi Konishi
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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38
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Lorlatinib for Previously Treated ALK-Positive Advanced Non-Small Cell Lung Cancer: Primary Efficacy and Safety From a Phase 2 Study in China. J Thorac Oncol 2022; 17:816-826. [DOI: 10.1016/j.jtho.2022.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 11/22/2022]
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Review of Therapeutic Strategies for Anaplastic Lymphoma Kinase-Rearranged Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14051184. [PMID: 35267492 PMCID: PMC8909087 DOI: 10.3390/cancers14051184] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer (NSCLC) was first reported in 2007. Following the development of crizotinib as a tyrosine kinase inhibitor (TKI) targeting ALK, the treatment of advanced NSCLC with ALK-rearrangements has made remarkable progress. Currently, there are five ALK-TKIs approved by the FDA, and the development of new agents, including fourth-generation TKI, is ongoing. Clinical trials with angiogenesis inhibitors and immune checkpoint inhibitors are also underway, and further progress in the treatment of ALK-rearranged advanced NSCLC is expected. The purpose of this manuscript is to provide information on the recent clinical trials of ALK-TKIs, angiogenesis inhibitors, immune checkpoint inhibitors, and chemotherapy, to describe tissue and liquid biopsy as a method to investigate the mechanisms of resistance against ALK-TKIs and suggest a proposed treatment algorithm. Abstract Non-small cell lung cancer (NSCLC) with anaplastic lymphoma kinase rearrangement (ALK) was first reported in 2007. ALK-rearranged NSCLC accounts for about 3–8% of NSCLC. The first-line therapy for ALK-rearranged advanced NSCLC is tyrosine kinase inhibitors (TKI) targeting ALK. Following the development of crizotinib, the first ALK-TKI, patient prognosis has been greatly improved. Currently, five TKIs are approved by the FDA. In addition, clinical trials of the novel TKI, ensartinib, and fourth-generation ALK-TKI for compound ALK mutation are ongoing. Treatment with angiogenesis inhibitors and immune checkpoint inhibitors is also being studied. However, as the disease progresses, cancers tend to develop resistance mechanisms. In addition to ALK mutations, other mechanisms, including the activation of bypass signaling pathways and histological transformation, cause resistance, and the identification of these mechanisms is important in selecting subsequent therapy. Studies on tissue and liquid biopsy have been reported and are expected to be useful tools for identifying resistance mechanisms. The purpose of this manuscript is to provide information on the recent clinical trials of ALK-TKIs, angiogenesis inhibitors, immune checkpoint inhibitors, and chemotherapy to describe tissue and liquid biopsy as a method to investigate the mechanisms of resistance against ALK-TKIs and suggest a proposed treatment algorithm.
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RNA-Seq for the detection of gene fusions in solid tumors: development and validation of the JAX FusionSeq™ 2.0 assay. J Mol Med (Berl) 2022; 100:323-335. [PMID: 35013752 DOI: 10.1007/s00109-021-02149-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 10/19/2022]
Abstract
Whole transcriptome sequencing (RNA-Seq) has gained prominence for the detection of fusions in solid tumors. Here, we describe the development and validation of an in-house RNA-Seq-based test system (FusionSeq™ 2.0) for the detection of clinically actionable gene fusions, in formalin-fixed paraffin-embedded (FFPE) specimens, using seventy tumor samples with varying fusion status. Conditions were optimized for RNA input of 50 ng, shown to be adequate to call known fusions at as low as 20% neoplastic content. Evaluation of assay performance between FFPE and fresh-frozen (FF) tissues exhibited little to no difference in fusion calling capability. Performance analysis of the assay validation data determined 100% accuracy, sensitivity, specificity, and reproducibility. This clinically developed and validated RNA-Seq-based approach for fusion detection in FPPE samples was shown to be on par if not superior to off-the-shelf commercially offered assays. With gene fusions implicated in a variety of cancer types, offering high-quality, low-cost molecular testing services for FFPE specimens will serve to best benefit the patient and the advancement of precision medicine in molecular oncology. KEY MESSAGES: A custom RNA-Seq-based test system (FusionSeq™ 2.0) for the detection of clinically actionable gene fusions, Evaluation of assay performance between FFPE and fresh-frozen (FF) tissues exhibited little to no difference in fusion calling capability. The assay can be performed with low RNA input and neoplastic content. Performance characteristics of the assay validation data determined 100% accuracy, sensitivity, specificity, and reproducibility.
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Iriagac Y, Cavdar E, Karaboyun K, Tacar S, Akkoc Mustafayev F, Celik E, Avci O, Okutur S, Koral L, Demirci N, Ozgun A, Seber E. Decrease in estimated glomerular filtration rates in non-small cell lung cancer patients treated with crizotinib. J Cancer Res Ther 2022. [DOI: 10.4103/jcrt.jcrt_1276_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Pathak N, Chitikela S, Malik PS. Recent advances in lung cancer genomics: Application in targeted therapy. ADVANCES IN GENETICS 2021; 108:201-275. [PMID: 34844713 DOI: 10.1016/bs.adgen.2021.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genomic characterization of lung cancer has not only improved our understanding of disease biology and carcinogenesis but also revealed several therapeutic opportunities. Targeting tumor dependencies on specific genomic alterations (oncogene addiction) has accelerated the therapeutic developments and significantly improved the outcomes even in advanced stage of disease. Identification of genomic alterations predicting response to specific targeted treatment is the key to success for this "personalized treatment" approach. Availability of multiple choices of therapeutic options for specific genomic alterations highlight the importance of optimum sequencing of drugs. Multiplex gene testing has become mandatory in view of constantly increasing number of therapeutic targets and effective treatment options. Influence of genomic characteristics on response to immunotherapy further makes comprehensive genomic profiling necessary before therapeutic decision making. A comprehensive elucidation of resistance mechanisms and directed treatments have made the continuum of care possible and transformed this deadly disease into a chronic condition. Liquid biopsy-based approach has made the dynamic monitoring of disease possible and enabled treatment optimizations accordingly. Current lung cancer management is the perfect example of "precision-medicine" in clinical oncology.
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Affiliation(s)
- Neha Pathak
- Department of Medical Oncology, Dr. B.R.A.I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Sindhura Chitikela
- Department of Medical Oncology, Dr. B.R.A.I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Prabhat Singh Malik
- Department of Medical Oncology, Dr. B.R.A.I.R.C.H., All India Institute of Medical Sciences, New Delhi, India.
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Misove A, Vicha A, Zapotocky M, Malis J, Balko J, Nemeckova T, Szabova J, Kyncl M, Novakova-Kodetova D, Stolova L, Jencova P, Broz P, Krskova L. An unusual fusion gene EML4-ALK in a patient with congenital mesoblastic nephroma. Genes Chromosomes Cancer 2021; 60:837-840. [PMID: 34378283 DOI: 10.1002/gcc.22990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/20/2022] Open
Abstract
Congenital mesoblastic nephroma (CMN), the most common renal tumor of infancy, is a mesenchymal neoplasm histologically classified into classic, cellular, or mixed types. Most cellular CMNs harbor a characteristic ETV6-NTRK3 fusion. Here, we report an unusual congenital mesoblastic nephroma presenting in a newborn boy with a novel EML4-ALK gene fusion revealed by Anchored Multiplex RNA Sequencing Assay. The EML4-ALK gene fusion expands the genetic spectrum implicated in the pathogenesis of congenital mesoblastic nephroma, with yet another example of kinase oncogenic activation through chromosomal rearrangement. The methylation profile of the tumor corresponds with infantile fibrosarcoma showing the biological similarity of these two entities.
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Affiliation(s)
- Adela Misove
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Ales Vicha
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Michal Zapotocky
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Josef Malis
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Jan Balko
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Tereza Nemeckova
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Jana Szabova
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Martin Kyncl
- Department of Radiology, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Daniela Novakova-Kodetova
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Lucie Stolova
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Pavla Jencova
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
| | - Petr Broz
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
- BIOXSYS s.r.o., Na Kopecku 15, Usti nad Labem, Czech Republic
| | - Lenka Krskova
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University Prague and Faculty Hospital Motol, Prague, Czech Republic
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Seegobin K, Majeed U, Wiest N, Manochakian R, Lou Y, Zhao Y. Immunotherapy in Non-Small Cell Lung Cancer With Actionable Mutations Other Than EGFR. Front Oncol 2021; 11:750657. [PMID: 34926258 PMCID: PMC8671626 DOI: 10.3389/fonc.2021.750657] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022] Open
Abstract
While first line targeted therapies are the current standard of care treatment for non-small cell lung cancer (NSCLC) with actionable mutations, the cancer cells inevitably acquire resistance to these agents over time. Immune check-point inhibitors (ICIs) have improved the outcomes of metastatic NSCLC, however, its efficacy in those with targetable drivers is largely unknown. In this manuscript, we reviewed the published data on ICI therapies in NSCLC with ALK, ROS1, BRAF, c-MET, RET, NTRK, KRAS, and HER2 (ERBB2) alterations. We found that the objective response rates (ORRs) associated with ICI treatments in lung cancers harboring the BRAF (0-54%), c-MET (12-49%), and KRAS (18.7-66.7%) alterations were comparable to non-mutant NSCLC, whereas the ORRs in RET fusion NSCLC (less than10% in all studies but one) and ALK fusion NSCLC (0%) were relatively low. The ORRs reported in small numbers of patients and studies of ROS1 fusion, NTRK fusion, and HER 2 mutant NSCLC were 0-17%, 50% and 7-23%, respectively, making the efficacy of ICIs in these groups of patients less clear. In most studies, no significant correlation between treatment outcome and PD-L1 expression or tumor mutation burden (TMB) was identified, and how to select patients with NSCLC harboring actionable mutations who will likely benefit from ICI treatment remains unknown.
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Affiliation(s)
- Karan Seegobin
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Umair Majeed
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Nathaniel Wiest
- Department of Medicine, Mayo Clinic, Jacksonville, FL, United States
| | - Rami Manochakian
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Yanyan Lou
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Yujie Zhao
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
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Wang S, Luo R, Shi Y, Han X. The impact of the ALK fusion variant on clinical outcomes in EML4-ALK patients with NSCLC: a systematic review and meta-analysis. Future Oncol 2021; 18:385-402. [PMID: 34783600 DOI: 10.2217/fon-2021-0945] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background: Recent studies showed that ALK-fusion variants are associated with heterogeneous clinical outcomes. However, contradictory conclusions have been drawn in other studies showing no correlation between ALK variants and prognoses. Methods: A systematic review and meta-analysis was performed to evaluate the prognostic value of EML4-ALK fusion variants for patient outcomes. Results: 28 studies were included in the analysis. According to the pooled results, patients harboring variant 1 showed equivalent progression-free survival (PFS) and overall survival (OS) with non-v1 patients (hazard ratio [HR] for PFS: 0.91 [0.68-1.21]; p = 0.499; OS: 1.12 [0.73-1.72]; p = 0.610). Similarly, patients with v3 showed the same disease progress as non-v3 patients (pooled HR for PFS = 1.07 [0.72-1.58]; p = 0.741). However, pooled results for OS suggested that patients with v3 had worse survival than non-v3 patients (HR = 3.44 [1.42-8.35]; p = 0.006). Conclusion: Results suggest that patients with v1 exhibited no significant difference from non-v1 in terms of OS and PFS, while v3 was associated with shorter OS in ALK-positive patients with non-small cell lung cancer.
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Affiliation(s)
- Shasha Wang
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Rongrong Luo
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe & Rare Diseases, NMPA Key Laboratory for Clinical Research & Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100032, China
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46
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Liang Q, Xu H, Liu Y, Zhang W, Sun C, Hu M, Zhu Y, Tan S, Xu X, Wang S, Liu L. Coexistence of a novel NBEA-ALK, EML4-ALK double-fusion in a lung adenocarcinoma patient and response to alectinib: A case report. Lung Cancer 2021; 162:86-89. [PMID: 34763158 DOI: 10.1016/j.lungcan.2021.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
OBJECTIVES The echinoderm microtubule-associated protein-like 4 gene (EML4) and anaplastic lymphoma kinase gene (ALK) fusion is the most common ALK rearrangements in non-small cell lung cancer (NSCLC). Herein, we firstly report that coexistence of a novel Neurobeachin (NBEA)-ALK, EML4-ALK double-fusion is sensitive to alectinib. MATERIALS AND METHODS Hematoxylin-eosin staining (HE), fluorescent in situ hybridization (FISH), and next-generation sequencing (NGS) was performed on the biopsy sample. RESULTS The patient responded to alectinib as a second-line treatment and achieved stable disease for 11 months, without significant symptoms of toxicity. Significantly, the liquid biopsy also validated clinical benefit, with the disappearance of NBEA-ALK and EML4-ALK fusion variants. We also provided a comprehensive review of all 50 ALK fusion genes in NSCLC. CONCLUSION This is the first report on one patient with a novel NBEA-ALK, EML4-ALK double-ALK fusion beneficial from alectinib. Alectinib may be a viable therapeutic option for NSCLC patients with double-ALK fusion, and liquid biopsy could dynamically monitor clinical curative effect.
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Affiliation(s)
- Qi Liang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Huanhuan Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yiqian Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Weiming Zhang
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Chongqi Sun
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Meng Hu
- Department of Oncology, Liyang People's Hospital, Liyang 213300, China
| | - Yizhi Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shanyue Tan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xian Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Sumeng Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Lingxiang Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
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The genomic landscape of lung adenocarcinoma—insights towards personalized medicine. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2021. [DOI: 10.1007/s43538-021-00054-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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48
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Ou K, Liu X, Li W, Yang Y, Ying J, Yang L. ALK Rearrangement-Positive Pancreatic Cancer with Brain Metastasis Has Remarkable Response to ALK Inhibitors: A Case Report. Front Oncol 2021; 11:724815. [PMID: 34568053 PMCID: PMC8456297 DOI: 10.3389/fonc.2021.724815] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Patients with metastatic pancreatic cancer typically have poor prognosis due to the limited effectiveness of existing treatment options. ALK rearrangement–positive is rare in pancreatic cancer, but may occur in those with KRAS-wild type. We present a 34-year-old young man with ALK rearrangement–positive and KRAS-wild pancreatic cancer who had a remarkable response to crizotinib after resistance to prior chemotherapy and re-response to alectinib after brain metastases developed. This clinical observation suggests that comprehensive molecular profiling to guide targeted therapies is not only feasible, but also significantly improves survival outcomes for a subgroup of patients with pancreatic cancer.
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Affiliation(s)
- Kai Ou
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiu Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weihua Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Yang
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Gene Editing Screening and Research and Development (R&D) of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Abstract
Tyrosine kinase inhibitors of anaplastic lymphoma kinase (ALK-TKIs) including alectinib have been the standard therapy against ALK fusion gene-positive non–small cell lung cancers (NSCLCs). Many ALK fusion variants have been identified in NSCLCs, and the predominant variants are echinoderm microtubule-associated protein-like 4-ALK (EML4-ALK) variant 1 (V1), V2 and V3a/b. However, there have been conflicting reports on the clinical responses of these variants to ALK-TKIs, and there are few reports on other less common ALK variants. To examine the influence of ALK variants on the efficacy of ALK-TKIs, we analyzed the sensitivity to alectinib of eight types of ALK variant: three major variants (V1, V2 and V3a) and five less common variants (V4; kinesin family member 5-ALK; kinesin light chain 1-ALK; striatin, calmodulin-binding protein-ALK; and tropomyosin-receptor kinase fused gene-ALK). Analysis was done by cell-free kinase assays using the recombinant proteins and by cell, growth assays using murine Ba/F3 cells expressing ALK variants. The kinase activity of each recombinant protein was significantly inhibited by alectinib. Intracellular ALK phosphorylation levels and its downstream signaling mediators, STAT3 and ERK, were suppressed by alectinib in each ALK variant-expressing Ba/F3 cell. Each cellular proliferation was markedly inhibited by alectinib treatment. There was no significant difference in the IC50 values between cells, with a <3.6-fold difference in responsiveness. In conclusion, these eight ALK variants had similar sensitivity to alectinib in vitro, indicating that it may not be possible to predict the response to alectinib just by determination of the ALK variant type in ALK fusion-positive NSCLCs.
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50
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Personeni N, Smiroldo V, Giunta EF, Prete MG, Rimassa L, Bregni G, Sclafani F. Tackling Refractory Metastatic Colorectal Cancer: Future Perspectives. Cancers (Basel) 2021; 13:4506. [PMID: 34572729 PMCID: PMC8472765 DOI: 10.3390/cancers13184506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 01/09/2023] Open
Abstract
Substantial improvements have characterized the systemic treatment of metastatic colorectal cancer (mCRC) over the past 20 years. Besides strong evidence that supports the use of RAS and BRAF status as prognostic and predictive indicators of disease and response, novel technologies have made possible the incorporation of emerging biomarkers for the management of mCRC. On one hand, the discovery of point mutations, amplifications, fusions, and gene expression profiles highlights the genomic and dynamic complexity of CRC. On the other, such discoveries are leading to newer biomarker-driven strategies that add to existing anti-epidermal growth factor receptor (EGFR) and anti-angiogenic approaches. In addition, the availability of a wide molecular profiling has relevant implications for patient prognosis and treatment benefits. Here, we will review the molecular underpinnings and clinical data supporting novel targeted treatments under development for refractory mCRC harboring BRAF mutations, KRAS G12C mutations, HER2 amplification, and less common molecular alterations, such as the re-arrangements of NTRK, ALK, and ROS1. Additionally, we will discuss novel strategies driving the rechallenge of EGFR antibodies and the incorporation of newer anti-angiogenic agents in the therapeutic armamentarium.
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Affiliation(s)
- Nicola Personeni
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Milan, Italy; (N.P.); (M.G.P.)
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Milan, Italy;
| | - Valeria Smiroldo
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Milan, Italy;
| | - Emilio Francesco Giunta
- Medical Oncology Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via Pansini 5, 80131 Naples, Italy;
| | - Maria Giuseppina Prete
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Milan, Italy; (N.P.); (M.G.P.)
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Milan, Italy;
| | - Lorenza Rimassa
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Milan, Italy; (N.P.); (M.G.P.)
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Milan, Italy;
| | - Giacomo Bregni
- Department of Medical Oncology, Institut Jules Bordet–Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Bruxelles, Belgium; (G.B.); (F.S.)
| | - Francesco Sclafani
- Department of Medical Oncology, Institut Jules Bordet–Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Bruxelles, Belgium; (G.B.); (F.S.)
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