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Chen Y, Lee K, Woo J, Kim DW, Keum C, Babbi G, Casadio R, Martelli PL, Savojardo C, Manfredi M, Shen Y, Sun Y, Katsonis P, Lichtarge O, Pejaver V, Seward DJ, Kamandula A, Bakolitsa C, Brenner SE, Radivojac P, O’Donnell-Luria A, Mooney SD, Jain S. Evaluating predictors of kinase activity of STK11 variants identified in primary human non-small cell lung cancers. RESEARCH SQUARE 2024:rs.3.rs-4587317. [PMID: 39011112 PMCID: PMC11247923 DOI: 10.21203/rs.3.rs-4587317/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Critical evaluation of computational tools for predicting variant effects is important considering their increased use in disease diagnosis and driving molecular discoveries. In the sixth edition of the Critical Assessment of Genome Interpretation (CAGI) challenge, a dataset of 28 STK11 rare variants (27 missense, 1 single amino acid deletion), identified in primary non-small cell lung cancer biopsies, was experimentally assayed to characterize computational methods from four participating teams and five publicly available tools. Predictors demonstrated a high level of performance on key evaluation metrics, measuring correlation with the assay outputs and separating loss-of-function (LoF) variants from wildtype-like (WT-like) variants. The best participant model, 3Cnet, performed competitively with well-known tools. Unique to this challenge was that the functional data was generated with both biological and technical replicates, thus allowing the assessors to realistically establish maximum predictive performance based on experimental variability. Three out of the five publicly available tools and 3Cnet approached the performance of the assay replicates in separating LoF variants from WT-like variants. Surprisingly, REVEL, an often-used model, achieved a comparable correlation with the real-valued assay output as that seen for the experimental replicates. Performing variant interpretation by combining the new functional evidence with computational and population data evidence led to 16 new variants receiving a clinically actionable classification of likely pathogenic (LP) or likely benign (LB). Overall, the STK11 challenge highlights the utility of variant effect predictors in biomedical sciences and provides encouraging results for driving research in the field of computational genome interpretation.
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Affiliation(s)
- Yile Chen
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, 98105, WA, USA
| | - Kyoungyeul Lee
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Junwoo Woo
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Dong-wook Kim
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Changwon Keum
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Rita Casadio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Pier Luigi Martelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Matteo Manfredi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843, TX, USA
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843, TX, USA
| | - Panagiotis Katsonis
- Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Olivier Lichtarge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - David J. Seward
- Department of Pathology, University of Vermont, Burlington, 5445, VT, USA
| | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
| | | | | | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
| | - Anne O’Donnell-Luria
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, 02115, MA, USA
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA
| | - Sean D. Mooney
- Center for Information Technology, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Shantanu Jain
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
- The Institute for Experiential AI, Northeastern University, Boston, 02115, MA, USA
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Ferrarone JR, Thomas J, Unni AM, Zheng Y, Nagiec MJ, Gardner EE, Mashadova O, Li K, Koundouros N, Montalbano A, Mustafa M, Cantley LC, Blenis J, Sanjana NE, Varmus H. Genome-wide CRISPR screens in spheroid culture reveal that the tumor suppressor LKB1 inhibits growth via the PIKFYVE lipid kinase. Proc Natl Acad Sci U S A 2024; 121:e2403685121. [PMID: 38743625 PMCID: PMC11127050 DOI: 10.1073/pnas.2403685121] [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: 02/22/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024] Open
Abstract
The tumor suppressor LKB1 is a serine/threonine protein kinase that is frequently mutated in human lung adenocarcinoma (LUAD). LKB1 regulates a complex signaling network that is known to control cell polarity and metabolism; however, the pathways that mediate the tumor-suppressive activity of LKB1 are incompletely defined. To identify mechanisms of LKB1-mediated growth suppression, we developed a spheroid-based cell culture assay to study LKB1-dependent growth. We then performed genome-wide CRISPR screens in spheroidal culture and found that LKB1 suppresses growth, in part, by activating the PIKFYVE lipid kinase. Finally, we used chemical inhibitors and a pH-sensitive reporter to determine that LKB1 impairs growth by promoting the internalization of wild-type EGFR in a PIKFYVE-dependent manner.
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Affiliation(s)
- John R. Ferrarone
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY10021
| | - Jerin Thomas
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
| | - Arun M. Unni
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
| | - Yuxiang Zheng
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
| | - Michal J. Nagiec
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
- Department of Pharmacology, Weill Cornell Medicine, New York, NY10021
| | - Eric E. Gardner
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
| | | | - Kate Li
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
| | - Nikos Koundouros
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
- Department of Pharmacology, Weill Cornell Medicine, New York, NY10021
| | - Antonino Montalbano
- New York Genome Center, New York, NY10013
- Department of Biology, New York University, New York, NY10003
| | - Meer Mustafa
- New York Genome Center, New York, NY10013
- Department of Biology, New York University, New York, NY10003
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
- Department of Medicine, Weill Cornell Medicine, New York, NY10021
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
- Department of Pharmacology, Weill Cornell Medicine, New York, NY10021
| | - Neville E. Sanjana
- New York Genome Center, New York, NY10013
- Department of Biology, New York University, New York, NY10003
| | - Harold Varmus
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY10021
- Department of Medicine, Weill Cornell Medicine, New York, NY10021
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Lagoudaki ED, Koutsopoulos AV, Sfakianaki M, Papadaki C, Manikis GC, Voutsina A, Trypaki M, Tsakalaki E, Fiolitaki G, Hatzidaki D, Yiachnakis E, Koumaki D, Mavroudis D, Tzardi M, Stathopoulos EN, Marias K, Georgoulias V, Souglakos J. LKB1 Loss Correlates with STING Loss and, in Cooperation with β-Catenin Membranous Loss, Indicates Poor Prognosis in Patients with Operable Non-Small Cell Lung Cancer. Cancers (Basel) 2024; 16:1818. [PMID: 38791897 PMCID: PMC11120022 DOI: 10.3390/cancers16101818] [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: 04/07/2024] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
To investigate the incidence and prognostically significant correlations and cooperations of LKB1 loss of expression in non-small cell lung cancer (NSCLC), surgical specimens from 188 metastatic and 60 non-metastatic operable stage I-IIIA NSCLC patients were analyzed to evaluate their expression of LKB1 and pAMPK proteins in relation to various processes. The investigated factors included antitumor immunity response regulators STING and PD-L1; pro-angiogenic, EMT and cell cycle targets, as well as metastasis-related (VEGFC, PDGFRα, PDGFRβ, p53, p16, Cyclin D1, ZEB1, CD24) targets; and cell adhesion (β-catenin) molecules. The protein expression levels were evaluated via immunohistochemistry; the RNA levels of LKB1 and NEDD9 were evaluated via PCR, while KRAS exon 2 and BRAFV600E mutations were evaluated by Sanger sequencing. Overall, loss of LKB1 protein expression was observed in 21% (51/248) patients and correlated significantly with histotype (p < 0.001), KRAS mutations (p < 0.001), KC status (concomitant KRAS mutation and p16 downregulation) (p < 0.001), STING loss (p < 0.001), and high CD24 expression (p < 0.001). STING loss also correlated significantly with loss of LKB1 expression in the metastatic setting both overall (p = 0.014) and in lung adenocarcinomas (LUACs) (p = 0.005). Additionally, LKB1 loss correlated significantly with a lack of or low β-catenin membranous expression exclusively in LUACs, both independently of the metastatic status (p = 0.019) and in the metastatic setting (p = 0.007). Patients with tumors yielding LKB1 loss and concomitant nonexistent or low β-catenin membrane expression experienced significantly inferior median overall survival of 20.50 vs. 52.99 months; p < 0.001 as well as significantly greater risk of death (HR: 3.32, 95% c.i.: 1.71-6.43; p <0.001). Our findings underscore the impact of the synergy of LKB1 with STING and β-catenin in NSCLC, in prognosis.
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Affiliation(s)
- Eleni D. Lagoudaki
- Department of Pathology, University General Hospital of Heraklion, 71500 Heraklion, Greece; (A.V.K.); (M.T.); (E.N.S.)
- School of Medicine, University of Crete, 70013 Heraklion, Greece; (D.M.); (V.G.); (J.S.)
| | - Anastasios V. Koutsopoulos
- Department of Pathology, University General Hospital of Heraklion, 71500 Heraklion, Greece; (A.V.K.); (M.T.); (E.N.S.)
- School of Medicine, University of Crete, 70013 Heraklion, Greece; (D.M.); (V.G.); (J.S.)
| | - Maria Sfakianaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (M.S.); (C.P.); (A.V.); (M.T.); (E.T.); (G.F.); (D.H.)
| | - Chara Papadaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (M.S.); (C.P.); (A.V.); (M.T.); (E.T.); (G.F.); (D.H.)
| | - Georgios C. Manikis
- Foundation for Research and Technology Hellas (FORTH), 70013 Heraklion, Greece; (G.C.M.); (K.M.)
| | - Alexandra Voutsina
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (M.S.); (C.P.); (A.V.); (M.T.); (E.T.); (G.F.); (D.H.)
| | - Maria Trypaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (M.S.); (C.P.); (A.V.); (M.T.); (E.T.); (G.F.); (D.H.)
| | - Eleftheria Tsakalaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (M.S.); (C.P.); (A.V.); (M.T.); (E.T.); (G.F.); (D.H.)
| | - Georgia Fiolitaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (M.S.); (C.P.); (A.V.); (M.T.); (E.T.); (G.F.); (D.H.)
| | - Dora Hatzidaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (M.S.); (C.P.); (A.V.); (M.T.); (E.T.); (G.F.); (D.H.)
| | - Emmanuel Yiachnakis
- Laboratory of Bio-Medical Data Analysis Digital Applications and Interdisciplinary Approaches, University of Crete, 71003 Heraklion, Greece;
| | - Dimitra Koumaki
- Department of Dermatology, University General Hospital of Heraklion, Voutes, 71500 Heraklion, Greece;
| | - Dimitrios Mavroudis
- School of Medicine, University of Crete, 70013 Heraklion, Greece; (D.M.); (V.G.); (J.S.)
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (M.S.); (C.P.); (A.V.); (M.T.); (E.T.); (G.F.); (D.H.)
- Department of Medical Oncology, University General Hospital of Heraklion, 71500 Heraklion, Greece
| | - Maria Tzardi
- Department of Pathology, University General Hospital of Heraklion, 71500 Heraklion, Greece; (A.V.K.); (M.T.); (E.N.S.)
- School of Medicine, University of Crete, 70013 Heraklion, Greece; (D.M.); (V.G.); (J.S.)
| | - Efstathios N. Stathopoulos
- Department of Pathology, University General Hospital of Heraklion, 71500 Heraklion, Greece; (A.V.K.); (M.T.); (E.N.S.)
- School of Medicine, University of Crete, 70013 Heraklion, Greece; (D.M.); (V.G.); (J.S.)
| | - Kostas Marias
- Foundation for Research and Technology Hellas (FORTH), 70013 Heraklion, Greece; (G.C.M.); (K.M.)
| | - Vassilis Georgoulias
- School of Medicine, University of Crete, 70013 Heraklion, Greece; (D.M.); (V.G.); (J.S.)
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (M.S.); (C.P.); (A.V.); (M.T.); (E.T.); (G.F.); (D.H.)
- Department of Medical Oncology, University General Hospital of Heraklion, 71500 Heraklion, Greece
| | - John Souglakos
- School of Medicine, University of Crete, 70013 Heraklion, Greece; (D.M.); (V.G.); (J.S.)
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (M.S.); (C.P.); (A.V.); (M.T.); (E.T.); (G.F.); (D.H.)
- Department of Medical Oncology, University General Hospital of Heraklion, 71500 Heraklion, Greece
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Olsen A, Lebedeva A, Nosova P, Nikulin V, Sharova M, Ignatova E, Mileyko V, Ivanov M. Impact of the STK11/KRAS co-mutation on the response to immunotherapy in a real-world pan-cancer cohort. TUMORI JOURNAL 2024; 110:146-152. [PMID: 37817679 DOI: 10.1177/03008916231204441] [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] [Indexed: 10/12/2023]
Abstract
INTRODUCTION Immune checkpoint inhibitors are highly effective in treating various cancers. We analyzed the significance of the KRAS/STK11 co-mutation in relation to the efficacy of immune checkpoint inhibitors in pan-cancer patient cohort. METHODS We analyzed data from open-access research: MSK-IMPACT (molecular profiling data from patients receiving systemic antitumor therapy) and MSK-TMB (molecular profiling data from patients receiving immune checkpoint inhibitors). In both studies, high throughput sequencing was used for molecular profiling. RESULTS A total of 10,336 patients receiving antitumor therapy (MSK-IMPACT study) and 1661 patients receiving immune checkpoint inhibitors (MSK-TMB study) were included in the analysis. Co-mutation STK11/KRAS was found in 156 (1.5%) and 46 (2.8%) patients in the two studies, respectively. Most patients with the STK11/KRAS co-mutation had non-small cell lung cancer (83% and 85% in the two studies, respectively). Among non-small cell lung cancer patients, the STK11 mutation was associated with a worse outcome for patients receiving systemic antitumor therapy, but not immune checkpoint inhibition therapy (HR for OS 1.90 [95% CI 1.36-2.65] and 1.44 [95% CI 0.88-2.37]). Co-mutation STK11/KRAS was also not associated with patient outcome in any of the studies (HR for OS 0.93 [95% CI 0.56-1.52] and 1.09 [95% CI 0.54-2.19]). High tumor mutational burden was associated with better outcome in the cohort of patients receiving immune checkpoint inhibitors. An analogous analysis among patients in the pan-cancer cohort (excluding patients with non-small cell lung cancer) showed STK11 mutations and high tumor mutational burden have a predictive role for the efficacy of immune checkpoint inhibitors, but not STK11/KRAS co-mutation. CONCLUSIONS Co-mutation STK11/KRAS is common among patients with non-small cell lung cancer and is not an independent predictive marker for the efficacy of immune checkpoint inhibitors. Further studies are required to clarify the role of STK11 mutations in immune checkpoint inhibitor treatment response.
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Affiliation(s)
| | | | - Polina Nosova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Margarita Sharova
- OncoAtlas, LLC, Moscow, Russia
- Research and Counseling Department, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina Ignatova
- OncoAtlas, LLC, Moscow, Russia
- Department of Oncogenetics, Institute of Higher and Additional Professional Education, Research Centre for Medical Genetics, Moscow, Russia
| | | | - Maxim Ivanov
- OncoAtlas, LLC, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
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Chen J, Zhu H, Chen S, Mi H. Apolipoprotein E is a Potential Biomarker for Predicting Cancer Prognosis and is Correlated with Immune Infiltration. Onco Targets Ther 2024; 17:199-214. [PMID: 38523659 PMCID: PMC10960509 DOI: 10.2147/ott.s447319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/12/2024] [Indexed: 03/26/2024] Open
Abstract
Background Apolipoprotein E (APOE) is a polymorphic protein that plays a role in lipoprotein transformation and metabolism. It is involved in numerous physiological processes within the body and is closely associated with tumor growth and metastasis. However, the role of APOE in pan-cancer has yet to be evaluated. Therefore, studying the association between APOE and various cancer types is crucial for providing a basis for individualized treatment strategies and clinical prognosis assessment. Methods We investigated the diagnostic and prognostic significance of APOE across 33 tumor types, as well as its correlation with tumor mutation burden (TMB) and microsatellite instability (MSI). Additionally, we employed the ESTIMATE and CIBERSORT algorithms to analyze the potential impact of APOE on the immune system. Furthermore, gene set enrichment analysis (GSEA) was conducted to explore its underlying physiological function. Results Based on observations from a pan-cancer dataset, APOE expression was significantly different between cancer and normal tissues, and was simultaneously associated with survival outcomes in terms of cancer type, clinical annotation, TMB, MSI, and TICs abundance. In addition, the results also showed that expression of APOE may respond to a variety of cancer chemotherapy. Conclusion The findings from this study strongly indicate a close association between APOE and tumor development. Moreover, APOE shows promise as a potential biomarker for predicting prognosis and response to immunotherapy in patients with pan-cancer.
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Affiliation(s)
- Jinji Chen
- Department of Urology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Herong Zhu
- Department of Urology, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan, People’s Republic of China
| | - Shaohua Chen
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Hua Mi
- Department of Urology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
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Lin K, Hu K, Chen Q, Wu J. The function and immune role of cuproptosis associated hub gene in Barrett's esophagus and esophageal adenocarcinoma. Biosci Trends 2023; 17:381-392. [PMID: 37866883 DOI: 10.5582/bst.2023.01164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Barrett's esophagus (BE) is a precancerous lesion of esophageal adenocarcinoma (EAC), with approximately 3-5% of patients developing EAC. Cuproptosis is a kind of programmed cell death phenomenon discovered in recent years, which is related to the occurrence and development of many diseases. However, its role in BE and EAC is not fully understood. We used single sample Gene Set Enrichment Analysis (ssGSEA) for differential analysis of BE in the database, followed by enrichment analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO) and GSEA, Protein-Protein Interaction (PPI), Weighted Gene Co-expression Network Analysis (WGCNA), Receiver Operating Characteristic Curve (ROC) and finally Quantitative Real Time Polymerase Chain Reaction (qRT-PCR) and immunohistochemistry (IHC) of clinical tissues. Two hub genes can be obtained by intersection of the results obtained from the cuproptosis signal analysis based on BE. The ROC curves of these two genes predicted EAC, and the Area Under the Curve (AUC) values could reach 0.950 and 0.946, respectively. The mRNA and protein levels of Centrosome associated protein E (CENPE) and Shc SH2 domain binding protein 1 (SHCBP1) were significantly increased in clinical EAC tissues. When they were grouped by protein expression levels, high expression of CENPE or SHCBP1 had a poor prognosis. The CENPE and SHCBP1 associated with cuproptosis may be a factor promoting the development of BE into EAC which associated with the regulation of NK cells and T cells.
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Affiliation(s)
- Kailin Lin
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ke Hu
- Department of Endocrinology, Minhang Hospital, Fudan University Shanghai, China
| | - Qiwen Chen
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiangchun Wu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
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Ferrarone JR, Thomas J, Unni AM, Zheng Y, Nagiec MJ, Gardner EE, Mashadova O, Li K, Koundouros N, Montalbano A, Mustafa M, Cantley LC, Blenis J, Sanjana NE, Varmus H. LKB1 suppresses growth and promotes the internalization of EGFR through the PIKFYVE lipid kinase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563158. [PMID: 37904985 PMCID: PMC10614957 DOI: 10.1101/2023.10.19.563158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The tumor suppressor LKB1 is a serine/threonine protein kinase that is frequently mutated in human lung adenocarcinoma (LUAD). LKB1 regulates a complex signaling network that is known to control cell polarity and metabolism; however, the pathways that mediate the tumor suppressive activity of LKB1 are incompletely defined. To identify mechanisms of LKB1- mediated growth suppression we developed a spheroid-based cell culture assay to study LKB1- dependent growth. Using this assay, along with genome-wide CRISPR screens and validation with orthogonal methods, we discovered that LKB1 suppresses growth, in part, by activating the PIKFYVE lipid kinase, which promotes the internalization of wild-type EGFR. Our findings reveal a new mechanism of regulation of EGFR, which may have implications for the treatment of LKB1 -mutant LUAD.
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Wankhede D, Bontoux C, Grover S, Hofman P. Prognostic Role of KRAS G12C Mutation in Non-Small Cell Lung Cancer: A Systematic Review and Meta-Analysis. Diagnostics (Basel) 2023; 13:3043. [PMID: 37835787 PMCID: PMC10572143 DOI: 10.3390/diagnostics13193043] [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: 08/17/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
KRAS G12C mutation (mKRAS G12C) is the most frequent KRAS point mutation in non-small cell lung cancer (NSCLC) and has been proven to be a predictive biomarker for direct KRAS G12C inhibitors in advanced solid cancers. We sought to determine the prognostic significance of mKRAS G12C in patients with NSCLC using the meta-analytic approach. A protocol is registered at the International Prospective Register for systematic reviews (CRD42022345868). PubMed, EMBASE, The Cochrane Library, and Clinicaltrials.gov.in were searched for prospective or retrospective studies reporting survival data for tumors with mKRAS G12C compared with either other KRAS mutations or wild-type KRAS (KRAS-WT). The hazard ratios (HRs) for overall survival (OS) or Disease-free survival (DFS) of tumors were pooled according to fixed or random-effects models. Sixteen studies enrolling 10,153 participants were included in the final analysis. mKRAS G12C tumors had poor OS [HR, 1.42; 95% CI, 1.10-1.84, p = 0.007] but similar DFS [HR 2.36, 95% CI 0.64-8.16] compared to KRAS-WT tumors. Compared to other KRAS mutations, mKRAS G12C tumors had poor DFS [HR, 1.49; 95% CI, 1.07-2.09, p < 0.0001] but similar OS [HR, 1.03; 95% CI, 0.84-1.26]. Compared to other KRAS mutations, high PD-L1 expression (>50%) [OR 1.37 95% CI 1.11-1.70, p = 0.004] was associated with mKRAS G12C tumors. mKRAS G12C is a promising prognostic factor for patients with NSCLC, negatively impacting survival. Prevailing significant heterogeneity and selection bias might reduce the validity of these findings. Concomitant high PD-L1 expression in these tumors opens doors for exciting therapeutic potential.
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Affiliation(s)
- Durgesh Wankhede
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christophe Bontoux
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Centre Hospitalier, Université Côte d’Azur, 06002 Nice, France;
| | - Sandeep Grover
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, 72076 Tübingen, Germany;
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Centre Hospitalier, Université Côte d’Azur, 06002 Nice, France;
- Institute for Research on Cancer and Ageing, Nice (IRCAN), INSERM U1081 and UMR CNRS 7284, Team 4, 06107 Nice, France;
- Hospital-Integrated Biobank BB-0033-00025, Pasteur Hospital, 06000 Nice, France
- University Hospital Federation OncoAge, CHU de Nice, University Côte d’Azur, 06000 Nice, France
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Zhang M, Yang H, Fu T, Meng M, Feng Y, Qu C, Li Z, Xing X, Li W, Ye M, Li S, Bu Z, Jia S. Liquid biopsy: circulating tumor DNA monitors neoadjuvant chemotherapy response and prognosis in stage II/III gastric cancer. Mol Oncol 2023; 17:1930-1942. [PMID: 37356061 PMCID: PMC10483607 DOI: 10.1002/1878-0261.13481] [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: 10/06/2022] [Revised: 03/09/2023] [Accepted: 06/23/2023] [Indexed: 06/27/2023] Open
Abstract
A good response to neoadjuvant chemotherapy (NACT) is strongly associated with a higher curative resection rate and favorable outcomes for patients with gastric cancer (GC). We examined the utility of serial circulating tumor DNA (ctDNA) testing for monitoring NACT response and prognosis in stage II-III GC. Seventy-nine patients were enrolled to receive two cycles of NACT following gastrectomy with D2-lymphadenectomy. Plasma at baseline, post-NACT, and after surgery, and tissue at pretreatment and surgery were collected. We used a 425-gene panel to detect genomic alterations (GAs). Results show that the mean cell-free DNA concentration of patients with clinical stage III was significantly higher than patients with stage II (15.43 ng·mL-1 vs 14.40 ng·mL-1 ). After receiving NACT and surgery, the overall detection rate of ctDNA gradually reduced (59.5%, 50.8%, and 47.4% for baseline, post-NACT, and postsurgery). The maximum variant allele frequency (max-VAF) and the number of GAs decreased from 0.50% to 0.08% and from 2.9 to 1.7 after NACT. For patients with a partial response after NACT, the max-VAF and the number of GAs declined significantly, but they increased for patients with progressive disease. Patients with detectable ctDNA at baseline, after NACT, or after surgery have a worse overall survival (OS) than patients with undetectable ctDNA. The estimated 3-year OS was 73% for the post-NACT ctDNA-negative patients and 34% for ctDNA-positive. Patients with perpetual negative ctDNA before and after NACT have the best prognosis. In conclusion, ctDNA was proposed as a potential biomarker to predict prognosis and monitor the NACT response for stage II-III GC patients.
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Affiliation(s)
- Meng Zhang
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Heli Yang
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Tao Fu
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Meizhu Meng
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Yi Feng
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Changda Qu
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Zhongwu Li
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Xiaofang Xing
- Department of Gastrointestinal Translational Research, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Wenmei Li
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Meiying Ye
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Sisi Li
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Zhaode Bu
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Shuqin Jia
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
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Sharma AE, Slack JC, Parra-Herran CE, Quade BJ, Shusterman S, Church AJ, Kolin DL, Carreon CK. STK11 Adnexal Tumor in an Adolescent Female: Diagnostic Pitfalls of a Recently Described Entity. Pediatr Dev Pathol 2023; 26:486-493. [PMID: 37334562 DOI: 10.1177/10935266231176681] [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] [Indexed: 06/20/2023]
Abstract
STK11 adnexal tumor is a recently described entity with less than 25 cases reported to date. These aggressive tumors typically occur in paratubal/paraovarian soft tissues, have characteristically striking morphologic and immunohistochemical heterogeneity, and harbor pathognomonic alterations in STK11. These occur almost exclusively in adult patients, with only one reported in a pediatric patient (to our knowledge). A previously healthy 16-year-old female presented with acute abdominal pain. Imaging studies revealed large bilateral solid and cystic adnexal masses, ascites, and peritoneal nodules. Following frozen section evaluation of a left ovarian surface nodule, bilateral salpingo-oophorectomy and tumor debulking were performed. Histologically, the tumor demonstrated distinctively variable cytoarchitecture, myxoid stroma, and mixed immunophenotype. A next generation sequencing-based assay identified a pathogenic STK11 mutation. We report the youngest patient to date with an STK11 adnexal tumor, highlighting key clinicopathologic and molecular features in order to contrast them with those of other pediatric intra-abdominal malignancies. This rare and unfamiliar tumor poses a considerable diagnostic challenge and requires a multidisciplinary integrated approach to diagnosis.
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Affiliation(s)
- Aarti E Sharma
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham & Women's Hospital/Harvard Medical School, Boston, MA, USA
| | - Jonathan C Slack
- Department of Pathology, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA
| | - Carlos E Parra-Herran
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham & Women's Hospital/Harvard Medical School, Boston, MA, USA
| | - Bradley J Quade
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham & Women's Hospital/Harvard Medical School, Boston, MA, USA
| | - Suzanne Shusterman
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Alanna J Church
- Department of Pathology, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA
| | - David L Kolin
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham & Women's Hospital/Harvard Medical School, Boston, MA, USA
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Swaminathan H, Saravanamurali K, Yadav SA. Extensive review on breast cancer its etiology, progression, prognostic markers, and treatment. Med Oncol 2023; 40:238. [PMID: 37442848 DOI: 10.1007/s12032-023-02111-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023]
Abstract
As the most frequent and vulnerable malignancy among women, breast cancer universally manifests a formidable healthcare challenge. From a biological and molecular perspective, it is a heterogenous disease and is stratified based on the etiological factors driving breast carcinogenesis. Notably, genetic predispositions and epigenetic impacts often constitute the heterogeneity of this disease. Typically, breast cancer is classified intrinsically into histological subtypes in clinical landscapes. These stratifications empower physicians to tailor precise treatments among the spectrum of breast cancer therapeutics. In this pursuit, numerous prognostic algorithms are extensively characterized, drastically changing how breast cancer is portrayed. Therefore, it is a basic requisite to comprehend the multidisciplinary rationales of breast cancer to assist the evolution of novel therapeutic strategies. This review aims at highlighting the molecular and genetic grounds of cancer additionally with therapeutic and phytotherapeutic context. Substantially, it also renders researchers with an insight into the breast cancer cell lines as a model paradigm for breast cancer research interventions.
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Affiliation(s)
- Harshini Swaminathan
- Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, 641021, Tamil Nadu, India
| | - K Saravanamurali
- Virus Research and Diagnostics Laboratory, Department of Microbiology, Coimbatore Medical College, Coimbatore, India
| | - Sangilimuthu Alagar Yadav
- Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, 641021, Tamil Nadu, India.
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12
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Pan M, Jiang C, Zhang Z, Achacoso N, Solorzano-Pinto AV, Tse P, Chung E, Suga JM, Thomas S, Habel LA. Sex- and Co-Mutation-Dependent Prognosis in Patients with SMARCA4-Mutated Malignancies. Cancers (Basel) 2023; 15:2665. [PMID: 37345003 DOI: 10.3390/cancers15102665] [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: 03/07/2023] [Revised: 04/12/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Whether sex and co-mutations impact prognosis of patients with SMARCA4-mutated (mutSMARCA4) malignancies is not clear. METHODS This cohort included patients from Northern California Kaiser Permanente with next-generation sequencing (NGS) performed from August 2020 to October 2022. We used Cox regression modeling to examine the association between sex and overall survival (OS), adjusting for demographics, performance status, Charlson comorbidity index, receipt of treatment, tumor mutation burden (TMB), and TP53, KRAS, CDKN2A, STK11, and Keap1 co-mutations. RESULTS Out of 9221 cases with NGS performed, 125 cases (1.4%) had a mutSMARCA4. The most common malignancies with a mutSMARCA4 were non-small cell lung cancer (NSCLC, 35.2%), esophageal and stomach adenocarcinoma (12.8%), and cancer of unknown primary (11.2%). The most common co-mutations were p53 (mutp53, 59.2%), KRAS (mutKRAS, 28.8%), CDKN2A (mutCDKN2A, 31.2%), STK11 (mutSTK11, 12.8%), and Keap1 (mutKeap1, 8.8%) mutations. Male patients had substantially worse OS than female patients both among the entire mutSMARCA4 cohort (HR = 1.71, [95% CI 0.92-3.18]) with a median OS of 3.0 versus 43.3 months (p < 0.001), and among the NSCLC subgroup (HR = 14.2, [95% CI 2.76-73.4]) with a median OS of 2.75 months versus un-estimable (p = 0.02). Among all patients with mutSMARCA4, mutp53 versus wtp53 (HR = 2.12, [95% CI 1.04-4.29]) and mutSTK11 versus wtSTK11 (HR = 2.59, [95% CI 0.87-7.73]) were associated with worse OS. Among the NSCLC subgroup, mutp53 versus wtp53 (HR = 0.35, [0.06-1.97]) and mutKRAS versus wtKRAS (HR = 0.04, [0.003-.45]) were associated with better OS, while mutCDKN2A versus wtCDKN2A (HR = 5.04, [1.12-22.32]), mutSTK11 versus wtSTK11 (HR = 13.10, [95% CI 1.16-148.26]), and mutKeap1 versus wtKeap1 (HR = 5.06, [95% CI 0.89-26.61}) were associated with worse OS. CONCLUSION In our cohort of patients with mutSMARCA4, males had substantially worse prognosis than females, while mutTP53, mutKRAS, mutCDKN2A, mutSTK11 and mutKeap1were differentially associated with prognosis among all patients and among the NSCLC subgroup. Our results, if confirmed, could suggest potentially unidentified mechanisms that underly this sex and co-mutation-dependent prognostic disparity among patients whose tumor bears a mutSMARCA4.
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Affiliation(s)
- Minggui Pan
- Department of Oncology and Hematology, Kaiser Permanente, Santa Clara, CA 94051, USA
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Chen Jiang
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Zheyang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, and National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361102, China
| | - Ninah Achacoso
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | | | - Pam Tse
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Elaine Chung
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Jennifer Marie Suga
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, CA 94589, USA
| | - Sachdev Thomas
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, CA 94589, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
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13
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Kong FS, Ren CY, Jia R, Zhou Y, Chen JH, Ma Y. Systematic pan-cancer analysis identifies SLC31A1 as a biomarker in multiple tumor types. BMC Med Genomics 2023; 16:61. [PMID: 36973786 PMCID: PMC10041742 DOI: 10.1186/s12920-023-01489-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Solute Carrier Family 31 Member 1 (SLC31A1) has recently been identified as a cuproptosis-regulatory gene. Recent studies have indicated that SLC31A1 may play a role in colorectal and lung cancer tumorigenesis. However, the role of SLC31A1 and its cuproptosis-regulatory functions in multiple tumor types remains to be further elucidated. METHODS Online websites and datasets such as HPA, TIMER2, GEPIA, OncoVar, and cProSite were used to extract data on SLC31A1 in multiple cancers. DAVID and BioGRID were used to conduct functional analysis and construct the protein-protein interaction (PPI) network, respectively. The protein expression data of SLC31A1 was obtained from the cProSite database. RESULTS The Cancer Genome Atlas (TCGA) datasets showed increased SLC31A1 expression in tumor tissues compared with non-tumor tissues in most tumor types. In patients with tumor types including adrenocortical carcinoma, low-grade glioma, or mesothelioma, higher SLC31A1 expression was associated with shorter overall survival and disease-free survival. S105Y was the most prevalent point mutation in SLC31A1 in TCGA pan-cancer datasets. Moreover, SLC31A1 expression was positively correlated with the infiltration of immune cells such as macrophages and neutrophils in tumor tissues in several tumor types. Functional enrichment analysis showed that SLC31A1 co-expressed genes were involved in protein binding, integral components of the membrane, metabolic pathways, protein processing, and endoplasmic reticulum. Copper Chaperone For Superoxide Dismutase, Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha and Solute Carrier Family 31 Member 2 were copper homeostasis-regulated genes shown in the PPI network, and their expression was positively correlated with SLC31A1. Analysis showed there was a correlation between SLC31A1 protein and mRNA in various tumors. CONCLUSIONS These findings demonstrated that SLC31A1 is associated with multiple tumor types and disease prognosis. SLC31A1 may be a potential key biomarker and therapeutic target in cancers.
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Affiliation(s)
- Fan-Sheng Kong
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Chun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Ruofan Jia
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Yuan Zhou
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China.
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China.
| | - Yaping Ma
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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14
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Xavier CB, Lopes CDH, Awni BM, Campos EF, Alves JPB, Camargo AA, Guardia GDA, Galante PAF, Jardim DL. Interplay between Tumor Mutational Burden and Mutational Profile and Its Effect on Overall Survival: A Pilot Study of Metastatic Patients Treated with Immune Checkpoint Inhibitors. Cancers (Basel) 2022; 14:cancers14215433. [PMID: 36358851 PMCID: PMC9657500 DOI: 10.3390/cancers14215433] [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: 08/27/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022] Open
Abstract
Purpose: Solid tumors harboring tumor mutational burden (TMB) ≥10 mutations per megabase (mut/Mb) received agnostic approval for pembrolizumab. This work aims to analyze the somatic mutational profile’s influence on the outcomes of patients with TMB-high tumors treated with immune checkpoint inhibitors (ICIs). Methods: This post-hoc analysis evaluated clinical and molecular features of patients with solid tumors treated with ICIs that could be either monoclonal antibody directed against programmed cell death protein-1 or monoclonal antibody directed against programmed cell death ligand 1 (anti-PD-1/anti-PD-L1), monoclonal antibody directed against cytotoxic T lymphocyte-associated antigen (anti-CTLA-4) or a combined treatment regimen including one anti-PD-1/anti-PD-L1 and one anti-CTLA-4 (ICIs combination). We performed OS analysis for TMB thresholds of ≥10, ≥20, and <10 mut/Mb. We assessed OS according to the mutational profile for a TMB ≥ 10 mut/Mb cutoff. For genes correlated with OS at the univariate assessment, we conducted a Cox multivariate analysis adjusted by median TMB, sex, age, microsatellite instability (MSI), and histology. Results: A total of 1661 patients were investigated; 488 with a TMB ≥10 mut/Mb (29.4%). The median OS was 42 months for TMB ≥10 or 20 mut/Mb, and 15 months for TMB <10 mut/Mb (p < 0.005). Among TMB ≥10 mut/Mb patients, mutations in E2F3 or STK11 correlated with worse OS, and mutations in NTRK3, PTPRD, RNF43, TENT5C, TET1, or ZFHX3 with better OS. These associations were confirmed with univariate and multivariate analyses (p < 0.05). Melanoma histology and TMB above the median endowed patients with better OS (p < 0.05), while MSI status, age, and gender did not have a statistically significant effect on OS. Conclusion: Combining TMB and mutation profiles in key cancer genes can better qualify patients for ICI treatment and predict their OS.
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Affiliation(s)
- Camila B. Xavier
- Oncology Center, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | | | - Beatriz M. Awni
- Oncology Center, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Eduardo F. Campos
- Oncology Center, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | | | - Anamaria A. Camargo
- Molecular Oncology Center, Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Gabriela D. A. Guardia
- Molecular Oncology Center, Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Pedro A. F. Galante
- Molecular Oncology Center, Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Denis L. Jardim
- Oncology Center, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
- Correspondence: ; Tel.: +55-11-99-707-2594
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15
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Guo H, Zhang J, Qin C, Yan H, Liu T, Hu H, Tang S, Tang S, Zhou H. Biomarker-Targeted Therapies in Non-Small Cell Lung Cancer: Current Status and Perspectives. Cells 2022; 11:3200. [PMID: 36291069 PMCID: PMC9600447 DOI: 10.3390/cells11203200] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 07/25/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC) is one of the most common malignancies and the leading causes of cancer-related death worldwide. Despite many therapeutic advances in the past decade, NSCLC remains an incurable disease for the majority of patients. Molecular targeted therapies and immunotherapies have significantly improved the prognosis of NSCLC. However, the vast majority of advanced NSCLC develop resistance to current therapies and eventually progress. In this review, we discuss current and potential therapies for NSCLC, focusing on targeted therapies and immunotherapies. We highlight the future role of metabolic therapies and combination therapies in NSCLC.
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Affiliation(s)
- Haiyang Guo
- Department of Thoracic Surgery, Suining Central Hospital, Suining 629099, China
- Institute of Surgery, Graduate School, Chengdu University of TCM, Chengdu 610075, China
| | - Jun Zhang
- Department of Thoracic Surgery, Suining Central Hospital, Suining 629099, China
- Institute of Surgery, Graduate School, Zunyi Medical University, Zunyi 563003, China
| | - Chao Qin
- Department of Thoracic Surgery, Suining Central Hospital, Suining 629099, China
- Institute of Surgery, Graduate School, Zunyi Medical University, Zunyi 563003, China
| | - Hang Yan
- Department of Thoracic Surgery, Suining Central Hospital, Suining 629099, China
- Institute of Surgery, Graduate School, Zunyi Medical University, Zunyi 563003, China
| | - Tao Liu
- Department of Thoracic Surgery, Suining Central Hospital, Suining 629099, China
- Institute of Surgery, Graduate School, Zunyi Medical University, Zunyi 563003, China
| | - Haiyang Hu
- Department of Thoracic Surgery, Suining Central Hospital, Suining 629099, China
- Institute of Surgery, Graduate School, Zunyi Medical University, Zunyi 563003, China
| | - Shengjie Tang
- Department of Thoracic Surgery, Suining Central Hospital, Suining 629099, China
| | - Shoujun Tang
- Department of Thoracic Surgery, Suining Central Hospital, Suining 629099, China
| | - Haining Zhou
- Department of Thoracic Surgery, Suining Central Hospital, Suining 629099, China
- Institute of Surgery, Graduate School, Chengdu University of TCM, Chengdu 610075, China
- Institute of Surgery, Graduate School, Zunyi Medical University, Zunyi 563003, China
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Halima A, Vuong W, Chan TA. Next-generation sequencing: unraveling genetic mechanisms that shape cancer immunotherapy efficacy. J Clin Invest 2022; 132:154945. [PMID: 35703181 PMCID: PMC9197511 DOI: 10.1172/jci154945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Immunity is governed by fundamental genetic processes. These processes shape the nature of immune cells and set the rules that dictate the myriad complex cellular interactions that power immune systems. Everything from the generation of T cell receptors and antibodies, control of epitope presentation, and recognition of pathogens by the immunoediting of cancer cells is, in large part, made possible by core genetic mechanisms and the cellular machinery that they encode. In the last decade, next-generation sequencing has been used to dissect the complexities of cancer immunity with potent effect. Sequencing of exomes and genomes has begun to reveal how the immune system recognizes “foreign” entities and distinguishes self from non-self, especially in the setting of cancer. High-throughput analyses of transcriptomes have revealed deep insights into how the tumor microenvironment affects immunotherapy efficacy. In this Review, we discuss how high-throughput sequencing has added to our understanding of how immune systems interact with cancer cells and how cancer immunotherapies work.
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Affiliation(s)
- Ahmed Halima
- Department of Radiation Oncology, Taussig Cancer Institute, and
| | - Winston Vuong
- Department of Radiation Oncology, Taussig Cancer Institute, and
| | - Timothy A Chan
- Department of Radiation Oncology, Taussig Cancer Institute, and.,Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio, USA.,National Center for Regenerative Medicine, Cleveland, Ohio, USA
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17
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Malhotra J, Ryan B, Patel M, Chan N, Guo Y, Aisner J, Jabbour SK, Pine S. Clinical outcomes and immune phenotypes associated with STK11 co-occurring mutations in non-small cell lung cancer. J Thorac Dis 2022; 14:1772-1783. [PMID: 35813711 PMCID: PMC9264081 DOI: 10.21037/jtd-21-1377] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/24/2021] [Indexed: 11/06/2022]
Abstract
Background STK11 mutation in non-small cell lung cancer (NSCLC) is associated with worse survival as well as primary resistance to PD-1/PD-L1 targeting immunotherapy. We hypothesize that co-occurring mutations and tumor mutation burden (TMB) may impact response to therapy and prognosis. Methods Forty-one patients with STK11-mutated NSCLC seen in our Thoracic oncology clinic with available next-generation sequencing tumor data were included in the analysis. Data from the Cancer Genome Atlas (TCGA) was used for survival and immune gene expression analysis. Overall and progression-free survival (PFS) was estimated by the Kaplan-Meier method and compared using a log-rank test. Results In the 41 patients included, common co-occurring alterations with STK11 were KRAS (54%), TP53 (44%), CDKN2A (37%) and KEAP1 (27%). Overall 17 patients received locoregional therapy with surgery or radiation with median OS of 8.6 years and there was no significant difference in clinical outcomes with KRAS and TP53 co-occurring mutations. Response to both chemotherapy and immunotherapy was poor across all co-occurring mutations. However, TP53 co-mutation was associated with improved clinical benefit with immunotherapy. Patients with higher TMB had longer PFS with immunotherapy. In TCGA survival analysis, tumors with STK11 mutation with or without KRAS co-mutation were associated with worse survival (P<0.05) but tumors with STK11/TP53 co-mutation did not have worst survival compared to STK11 wild type tumors. Moreover, co-occurring mutations had significant effect on intratumoral immune status with both STK11 alone and STK11/KRAS co-mutated tumors showing more enrichment for wound healing immune subtype while STK11/TP53 co-mutated tumors showed more enrichment for IFN-g immune subtype. Conclusions Our retrospective analysis in patients with STK11-mutated NSCLC found that both TMB and co-occurring mutations may be predictors for response to immunotherapy with worse outcomes in patients with low TMB or KRAS co-mutation and improved outcomes with TP53 co-mutation. Patients with STK11-mutated NSCLC also demonstrate chemotherapy resistance but have similar outcomes with localized treatment compared to STK11 wild type tumors. Moreover, co-mutations with KRAS or TP53 significantly alter tumor immune landscape of STK11-mutated tumors and therefore response to immunotherapy.
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Affiliation(s)
- Jyoti Malhotra
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Brid Ryan
- National Cancer Institute, Bethesda, MD, USA
| | - Malini Patel
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Nancy Chan
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Yanxiang Guo
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Joseph Aisner
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | | | - Sharon Pine
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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Wang X, Xu Z, Liu Z, Lin W, Cao Z, Feng X, Gao Y, He J. Characterization of the Immune Cell Infiltration Landscape Uncovers Prognostic and Immunogenic Characteristics in Lung Adenocarcinoma. Front Genet 2022; 13:902577. [PMID: 35677561 PMCID: PMC9168373 DOI: 10.3389/fgene.2022.902577] [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: 03/23/2022] [Accepted: 04/14/2022] [Indexed: 12/12/2022] Open
Abstract
The immune cell infiltration in TME has been reported to be associated with prognosis and immunotherapy efficiency of lung cancers. However, to date, the immune infiltrative landscape of lung adenocarcinoma (LUAD) has not been elucidated yet. Therefore, this study aimed to identify a new transcriptomic-based TME classification and develop a risk scoring system to predict the clinical outcomes of patients with LUAD. We applied “CIBERSORT” algorithm to analyze the transcriptomic data of LUAD samples and classified LUAD into four discrete subtypes according to the distinct immune cell infiltration patterns. Furthermore, we established a novel predictive tool (TMEscore) to quantify the immune infiltration patterns for each LUAD patient by principal component analysis. The TMEscore displayed as a reliable and independent prognostic biomarker for LUAD, with worse survival in TMEscrore-high patients and better survival in TMEscrore-low patients in both TCGA and other five GEO cohorts. In addition, enriched pathways and genomic alterations were also analyzed and compared in different TMEscore subgroups, and we observed that high TMEscore was significantly correlated with more aggressive molecular changes, while the low TMEscore subgroup enriched in immune active-related pathways. The TMEscore-low subtype showed overexpression of PD-1, CTLA4, and associations of other markers of sensitivity to immunotherapy, including TMB, immunophenoscore (IPS) analysis, and tumor immune dysfunction and exclusion (TIDE) algorithm. Conclusively, TMEscore is a promising and reliable biomarker to distinguish the prognosis, the molecular and immune characteristics, and the benefit from ICIs treatments in LUAD.
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Affiliation(s)
- Xin Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhenyi Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Zhilin Liu
- Department of Biostatistics, Peking University, Beijing, China
| | - Weihao Lin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Cao
- 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
| | - Xiaoli Feng
- 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
| | - Yibo Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Laboratory of Translational Medicine, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
- *Correspondence: Yibo Gao, ; Jie He,
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yibo Gao, ; Jie He,
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Zhou W, Yan LD, Yu ZQ, Li N, Yang YH, Wang M, Chen YY, Mao MX, Peng XC, Cai J. Role of STK11 in ALK‑positive non‑small cell lung cancer (Review). Oncol Lett 2022; 23:181. [PMID: 35527776 PMCID: PMC9073580 DOI: 10.3892/ol.2022.13301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/01/2022] [Indexed: 11/10/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) inhibitors have been shown to be effective in treating patients with ALK-positive non-small cell lung cancer (NSCLC), and crizotinib, ceritinib and alectinib have been approved as clinical first-line therapeutic agents. The availability of these inhibitors has also largely changed the treatment strategy for advanced ALK-positive NSCLC. However, patients still inevitably develop resistance to ALK inhibitors, leading to tumor recurrence or metastasis. The most critical issues that need to be addressed in the current treatment of ALK-positive NSCLC include the high cost of targeted inhibitors and the potential for increased toxicity and resistance to combination therapy. Recently, it has been suggested that the serine/threonine kinase 11 (STK11) mutation may serve as one of the biomarkers for immunotherapy in NSCLC. Therefore, the main purpose of this review was to summarize the role of STK11 in ALK-positive NSCLC. The present review also summarizes the treatment and drug resistance studies in ALK-positive NSCLC and the current status of STK11 research in NSCLC.
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Affiliation(s)
- Wen Zhou
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Lu-Da Yan
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Zhi-Qiong Yu
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Na Li
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Yong-Hua Yang
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Meng Wang
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Yuan-Yuan Chen
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Meng-Xia Mao
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Xiao-Chun Peng
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Jun Cai
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
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Daily Practice Assessment of KRAS Status in NSCLC Patients: A New Challenge for the Thoracic Pathologist Is Right around the Corner. Cancers (Basel) 2022; 14:cancers14071628. [PMID: 35406400 PMCID: PMC8996900 DOI: 10.3390/cancers14071628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary RAS mutation is the most frequent oncogenic alteration in human cancers and KRAS is the most frequently mutated, notably in non-small cell lung carcinomas (NSCLC). Various attempts to inhibit KRAS in the past were unsuccessful in these latter tumors. However, recently, several small molecules (AMG510, MRTX849, JNJ-74699157, and LY3499446) have been developed to specifically target KRAS G12C-mutated tumors, which seems promising for patient treatment and should soon be administered in daily practice for non-squamous (NS)-NSCLC. In this context, it will be mandatory to systematically assess the KRAS status in routine clinical practice, at least in advanced NS-NSCLC, leading to new challenges for thoracic oncologists. Abstract KRAS mutations are among the most frequent genomic alterations identified in non-squamous non-small cell lung carcinomas (NS-NSCLC), notably in lung adenocarcinomas. In most cases, these mutations are mutually exclusive, with different genomic alterations currently known to be sensitive to therapies targeting EGFR, ALK, BRAF, ROS1, and NTRK. Recently, several promising clinical trials targeting KRAS mutations, particularly for KRAS G12C-mutated NSCLC, have established new hope for better treatment of patients. In parallel, other studies have shown that NSCLC harboring co-mutations in KRAS and STK11 or KEAP1 have demonstrated primary resistance to immune checkpoint inhibitors. Thus, the assessment of the KRAS status in advanced-stage NS-NSCLC has become essential to setting up an optimal therapeutic strategy in these patients. This stimulated the development of new algorithms for the management of NSCLC samples in pathology laboratories and conditioned reorganization of optimal health care of lung cancer patients by the thoracic pathologists. This review addresses the recent data concerning the detection of KRAS mutations in NSCLC and focuses on the new challenges facing pathologists in daily practice for KRAS status assessment.
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Kaen DL, Minatta N, Russo A, Malapelle U, de Miguel-Pérez D, Rolfo C. Immunotherapy in Lung Cancer: Are the Promises of Long-Term Benefit Finally Met? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1342:113-142. [PMID: 34972964 DOI: 10.1007/978-3-030-79308-1_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the last few years, agents targeting immune checkpoints have shown potential to improve therapeutic outcomes in patients with lung cancer in multiple clinical settings. Inhibitors of PD-1/PD-L1 have been approved for the treatment of different types of lung cancer by the FDA either alone or in combination with chemotherapy or other immune checkpoint inhibitors, such as anti-CTLA-4 agents. The introduction of these agents in clinical practice has revolutionized the therapeutic approach to lung cancer, keeping the promises of long-term benefit in selected patient populations. The therapeutic indications of immunotherapy in lung cancer are rapidly growing, and multiple combinations entered clinical practice or are under active development. Furthermore, the quest for a reliable predictive biomarker is still ongoing to overcome the limits of currently approved tests for patients' selection. In this review, we summarized the current status and progress of anti-PD-1/PD-L1 agents in lung cancer treatment.
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Affiliation(s)
- Diego L Kaen
- Centro Oncologico Riojano (CORI), National University La Rioja, La Rioja, Argentina
| | - Nicolas Minatta
- Departament of Oncology, Hospital Italiano, Buenos Aires, Argentina
| | | | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Diego de Miguel-Pérez
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, Mount Sinai, New York, NY, USA.
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Pons-Tostivint E, Lugat A, Fontenau JF, Denis MG, Bennouna J. STK11/LKB1 Modulation of the Immune Response in Lung Cancer: From Biology to Therapeutic Impact. Cells 2021; 10:cells10113129. [PMID: 34831355 PMCID: PMC8618117 DOI: 10.3390/cells10113129] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/28/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
The STK11/LKB1 gene codes for liver kinase B1 (STK11/LKB1), a highly conserved serine/threonine kinase involved in many energy-related cellular processes. The canonical tumor-suppressive role for STK11/LKB1 involves the activation of AMPK-related kinases, a master regulator of cell survival during stress conditions. In pre-clinical models, inactivation of STK11/LKB1 leads to the progression of lung cancer with the acquisition of metastatic properties. Moreover, preclinical and clinical data have shown that inactivation of STK11/LKB1 is associated with an inert tumor immune microenvironment, with a reduced density of infiltrating cytotoxic CD8+ T lymphocytes, a lower expression of PD-(L)1, and a neutrophil-enriched tumor microenvironment. In this review, we first describe the biological function of STK11/LKB1 and the role of its inactivation in cancer cells. We report descriptive epidemiology, co-occurring genomic alterations, and prognostic impact for lung cancer patients. Finally, we discuss recent data based on pre-clinical models and lung cancer cohorts analyzing the results of STK11/LKB1 alterations on the immune system and response or resistance to immune checkpoint inhibitors.
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Affiliation(s)
- Elvire Pons-Tostivint
- Medical Oncology Department, Nantes University Hospital, 44000 Nantes, France
- Center for Research in Cancerology and Immunology Nantes-Angers (CRCINA), University of Nantes, INSERM UMR 1232, 44000 Nantes, France; (A.L.); (J.-F.F.); (J.B.)
- Correspondence:
| | - Alexandre Lugat
- Center for Research in Cancerology and Immunology Nantes-Angers (CRCINA), University of Nantes, INSERM UMR 1232, 44000 Nantes, France; (A.L.); (J.-F.F.); (J.B.)
| | - Jean-François Fontenau
- Center for Research in Cancerology and Immunology Nantes-Angers (CRCINA), University of Nantes, INSERM UMR 1232, 44000 Nantes, France; (A.L.); (J.-F.F.); (J.B.)
| | | | - Jaafar Bennouna
- Center for Research in Cancerology and Immunology Nantes-Angers (CRCINA), University of Nantes, INSERM UMR 1232, 44000 Nantes, France; (A.L.); (J.-F.F.); (J.B.)
- Medical Oncology Department, Hopital Foch, 75073 Suresnes, France
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23
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An J, Yan M, Yu N, Chennamadhavuni A, Furqan M, Mott SL, Loeffler BT, Kruser T, Sita TL, Feldman L, Nguyen R, Pasquinelli M, Hanna NH, Abu Hejleh T. Outcomes of patients with stage III non-small cell lung cancer (NSCLC) that harbor a STK11 mutation. Transl Lung Cancer Res 2021; 10:3608-3615. [PMID: 34584860 DOI: 10.21037/tlcr-21-177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022]
Abstract
Background STK11 mutation (STK11m ) in patients (pts) with stage IV non-small cell lung cancer (NSCLC) is associated with inferior survival and poor response to immune checkpoint inhibitors (ICI). The significance of STK11m in stage III NSCLC pts treated with concurrent chemoradiation (CCRT) with or without consolidation ICI is unknown. Methods Stage III NSCLC patients who received CCRT and had known STK11 mutational status were included in this retrospective study. The data on the STK11m pts were collected from 4 cancer institutions. A cohort of pts with wild type STK11 (STK11w ) from the University of Iowa served as a comparison group. Patient demographics and clinical characteristics were collected. Cox regression models were used to explore the effect of STK11 mutation on survival. Results 75 pts with stage III NSCLC who had known STK11 mutational status were identified. 16/75 (21%) had STK11m . 5/16 with STK11 m did not receive CCRT so they were excluded from the analysis. The clinical and demographic characteristics for the 11 STK11m and 59 STK11w pts were not statistically different (STK11m vs. STK11w ): mean age: 57 vs. 64 yrs, non-squamous histology: 8/11 (73%) vs. 37/59 (63%), KRAS mutation: 3/11 (27%) vs. 11/59 (19%), TP53 mutation: 6/11 (55%) vs. 15/59 (25%), PD-L1 ≥50%: 1/8 (13%) vs. 10/32 (31%), and consolidation ICI 6/11 (55%) vs. 17/59 (29%). Regarding the 6 STK11m pts who received ICI (4 pembrolizumab, 2 durvalumab), the median number of ICI infusions was 8 (range, 3-17) vs. 6 (range, 1-25) in the 17 pts with STK11w who received ICI (durvalumab). After adjusting for performance status and cancer stage, multivariable analysis showed that progression free survival (PFS) for the STK11m pts was significantly worse than STK11 w pts (HR =2.25; 95% CI, 1.03-4.88, P=0.04), whereas overall survival (OS) showed no significant difference for STK11m vs. STK11w patients (HR 1.47, 95% CI, 0.49-4.38, P=0.49). Conclusions In stage III NSCLC patients who received CCRT, STK11m was associated with worse PFS compared to STK11w . Larger studies are needed to further explore the prognostic implications of STK11m in stage III NSCLC and whether ICI impacts survival for this subgroup.
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Affiliation(s)
- Josiah An
- Division of Hematology, Oncology, Blood & Marrow Transplantation, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Melissa Yan
- Division of Hematology and Oncology, Indiana University Health - Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Nanmeng Yu
- Division of Hematology, Oncology, Blood & Marrow Transplantation, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Adithya Chennamadhavuni
- Division of Hematology, Oncology, Blood & Marrow Transplantation, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Muhammad Furqan
- Division of Hematology, Oncology, Blood & Marrow Transplantation, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Sarah L Mott
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Bradley T Loeffler
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Timothy Kruser
- Turville Bay Radiation Oncology, SSM Health, Madison, WI, USA
| | - Timothy L Sita
- Department of Radiation Oncology, Northwestern Memorial Hospital, Chicago, IL, USA
| | - Lawrence Feldman
- Division of Hematology and Oncology, The University of Illinois at Chicago, Chicago, IL, USA
| | - Ryan Nguyen
- Division of Hematology and Oncology, The University of Illinois at Chicago, Chicago, IL, USA
| | - Mary Pasquinelli
- Division of Hematology and Oncology, The University of Illinois at Chicago, Chicago, IL, USA
| | - Nasser H Hanna
- Division of Hematology and Oncology, Indiana University Health - Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Taher Abu Hejleh
- Division of Hematology, Oncology, Blood & Marrow Transplantation, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
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24
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Abstract
STK11 encodes for the protein liver kinase B1, a serine/threonine kinase which is involved in a number of physiological processes including regulation of cellular metabolism, cell polarity and the DNA damage response. It acts as a tumour suppressor via multiple mechanisms, most classically through AMP-activated protein kinase-mediated inhibition of the mammalian target of rapamycin signalling pathway. Germline loss-of-function mutations in STK11 give rise to Peutz-Jeghers syndrome, which is associated with hamartomatous polyps of the gastrointestinal tract, mucocutaneous pigmentation and a substantially increased lifetime risk of many cancers. In the sporadic setting, STK11 mutations are commonly seen in a subset of adenocarcinomas of the lung in addition to a number of other tumours occurring at various sites. Mutations in STK11 have been associated with worse prognoses across a range of malignancies and may be a predictor of poor response to immunotherapy in a subset of lung cancers, though further studies are needed before the presence of STK11 mutations can be implemented as a routine clinical biomarker.
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Affiliation(s)
- Roman E Zyla
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Elan Hahn
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Anatomic Pathology, University Health Network, Toronto, Ontario, Canada
| | - Anjelica Hodgson
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada .,Anatomic Pathology, University Health Network, Toronto, Ontario, Canada
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