1
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Liu XL, Run-Hua Z, Pan JX, Li ZJ, Yu L, Li YL. Emerging therapeutic strategies for metastatic uveal melanoma: Targeting driver mutations. Pigment Cell Melanoma Res 2024; 37:411-425. [PMID: 38411373 DOI: 10.1111/pcmr.13161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/29/2023] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Uveal melanoma (UM) is the most common primary malignant intraocular tumor in adults. Although primary UM can be effectively controlled, a significant proportion of cases (40% or more) eventually develop distant metastases, commonly in the liver. Metastatic UM remains a lethal disease with limited treatment options. The initiation of UM is typically attributed to activating mutations in GNAQ or GNA11. The elucidation of the downstream pathways such as PKC/MAPK, PI3K/AKT/mTOR, and Hippo-YAP have provided potential therapeutic targets. Concurrent mutations in BRCA1 associated protein 1 (BAP1) or splicing factor 3b subunit 1 (SF3B1) are considered crucial for the acquisition of malignant potential. Furthermore, in preclinical studies, actionable targets associated with BAP1 loss or oncogenic mutant SF3B1 have been identified, offering promising avenues for UM treatment. This review aims to summarize the emerging targeted and epigenetic therapeutic strategies for metastatic UM carrying specific driver mutations and the potential of combining these approaches with immunotherapy, with particular focus on those in upcoming or ongoing clinical trials.
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Affiliation(s)
- Xiao-Lian Liu
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou, China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Zhou Run-Hua
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jing-Xuan Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhi-Jie Li
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Le Yu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yi-Lei Li
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou, China
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2
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Nakauma-González JA, Rijnders M, Noordsij MTW, Martens JWM, van der Veldt AAM, Lolkema MPJ, Boormans JL, van de Werken HJG. Whole-genome mapping of APOBEC mutagenesis in metastatic urothelial carcinoma identifies driver hotspot mutations and a novel mutational signature. Cell Genom 2024; 4:100528. [PMID: 38552621 PMCID: PMC11019362 DOI: 10.1016/j.xgen.2024.100528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 04/13/2024]
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) enzymes mutate specific DNA sequences and hairpin-loop structures, challenging the distinction between passenger and driver hotspot mutations. Here, we characterized 115 whole genomes of metastatic urothelial carcinoma (mUC) to identify APOBEC mutagenic hotspot drivers. APOBEC-associated mutations were detected in 92% of mUCs and were equally distributed across the genome, while APOBEC hotspot mutations (ApoHMs) were enriched in open chromatin. Hairpin loops were frequent targets of didymi (twins in Greek), two hotspot mutations characterized by the APOBEC SBS2 signature, in conjunction with an uncharacterized mutational context (Ap[C>T]). Next, we developed a statistical framework that identified ApoHMs as drivers in coding and non-coding genomic regions of mUCs. Our results and statistical framework were validated in independent cohorts of 23 non-metastatic UCs and 3,744 samples of 17 metastatic cancers, identifying cancer-type-specific drivers. Our study highlights the role of APOBEC in cancer development and may contribute to developing novel targeted therapy options for APOBEC-driven cancers.
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Affiliation(s)
- J Alberto Nakauma-González
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands.
| | - Maud Rijnders
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Minouk T W Noordsij
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Martijn P J Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Immunology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands.
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3
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Ruiz G, Enrico D, Mahmoud YD, Ruiz A, Cantarella MF, Leguina L, Barberis M, Beña A, Brest E, Starapoli S, Mendoza Bertelli A, Tsou F, Pupareli C, Coppola MP, Scocimarro A, Sena S, Levit P, Perfetti A, Aman E, Girotti MR, Arrieta O, Martín C, Salanova R. Association of PD-L1 expression with driver gene mutations and clinicopathological characteristics in non-small cell lung cancer: A real-world study of 10 441 patients. Thorac Cancer 2024; 15:895-905. [PMID: 38456253 PMCID: PMC11016406 DOI: 10.1111/1759-7714.15244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Programmed death ligand-1 (PD-L1) expression is a well-known predictive biomarker of response to immune checkpoint blockade in non-small cell lung cancer (NSCLC). However, there is limited evidence of the relationship between PD-L1 expression, clinicopathological features, and their association with major driver mutations in NSCLC patients in Latin America. METHODS This retrospective study included patients from Argentina with advanced NSCLC, and centralized evaluation of PD-L1 expression concurrently with genomic alterations in the driver genes EGFR, ALK, ROS1, BRAF, and/or KRAS G12C in FFPE tissue samples. RESULTS A total of 10 441 patients with advanced NSCLC were analyzed. Adenocarcinoma was the most frequent histological subtype (71.1%). PD-L1 expression was categorized as PD-L1 negative (45.1%), PD-L1 positive low-expression 1%-49% (32.3%), and PD-L1 positive high-expression ≥50% (22.6%). Notably, current smokers and males were more likely to have tumors with PD-L1 tumor proportion score (TPS) ≥50% and ≥ 80% expression, respectively (p < 0.001 and p = 0.013). Tumors with non-adenocarcinoma histology had a significantly higher median PD-L1 expression (p < 0.001). Additionally, PD-L1 in distant nodes was more likely ≥50% (OR 1.60 [95% CI: 1.14-2.25, p < 0.01]). In the multivariate analysis, EGFR-positive tumors were more commonly associated with PD-L1 low expression (OR 0.62 [95% CI: 0.51-0.75], p < 0.01), while ALK-positive tumors had a significant risk of being PD-L1 positive (OR 1.81 [95% CI: 1.30-2.52], p < 0.01). CONCLUSIONS PD-L1 expression was associated with well-defined clinicopathological and genomic features. These findings provide a comprehensive view of the expression of PD-L1 in patients with advanced NSCLC in a large Latin American cohort.
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Affiliation(s)
- Gonzalo Ruiz
- Pathology & Molecular Biology LaboratoriesBiomakersBuenos AiresArgentina
| | - Diego Enrico
- Thoracic Oncology Unit, Department of Medical OncologyAlexander Fleming Cancer InstituteBuenos AiresArgentina
- Clinical Research Unit, Department of Medical OncologyAlexander Fleming Cancer InstituteBuenos AiresArgentina
| | - Yamil D. Mahmoud
- Universidad Argentina de la Empresa (UADE), Instituto de Tecnología (INTEC)Buenos AiresArgentina
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos AiresArgentina
| | - Alan Ruiz
- Pathology & Molecular Biology LaboratoriesBiomakersBuenos AiresArgentina
| | | | - Laura Leguina
- Pathology & Molecular Biology LaboratoriesBiomakersBuenos AiresArgentina
| | - Mariana Barberis
- Pathology & Molecular Biology LaboratoriesBiomakersBuenos AiresArgentina
| | - Asunción Beña
- Pathology & Molecular Biology LaboratoriesBiomakersBuenos AiresArgentina
| | - Esteban Brest
- Pathology & Molecular Biology LaboratoriesBiomakersBuenos AiresArgentina
| | - Solange Starapoli
- Pathology & Molecular Biology LaboratoriesBiomakersBuenos AiresArgentina
| | | | - Florencia Tsou
- Thoracic Oncology Unit, Department of Medical OncologyAlexander Fleming Cancer InstituteBuenos AiresArgentina
- Clinical Research Unit, Department of Medical OncologyAlexander Fleming Cancer InstituteBuenos AiresArgentina
| | - Carmen Pupareli
- Thoracic Oncology Unit, Department of Medical OncologyAlexander Fleming Cancer InstituteBuenos AiresArgentina
- Clinical Research Unit, Department of Medical OncologyAlexander Fleming Cancer InstituteBuenos AiresArgentina
| | - María Pía Coppola
- Medical Oncology UnitHospital Zonal Especializado en Agudos y Crónicos Dr. Antonio CetrangoloBuenos AiresArgentina
| | - Alejandra Scocimarro
- Medical Oncology UnitHospital Zonal Especializado en Agudos y Crónicos Dr. Antonio CetrangoloBuenos AiresArgentina
| | - Susana Sena
- Medical Oncology DepartmentHospital AlemánBuenos AiresArgentina
| | - Patricio Levit
- Medical Oncology UnitUnión Personal‐Accord SaludBuenos AiresArgentina
| | - Aldo Perfetti
- Medical Oncology UnitUnión Personal‐Accord SaludBuenos AiresArgentina
- Medical Oncology DepartmentCentro de Educación Médica e Investigaciones Clínicas (CEMIC)Buenos AiresArgentina
| | - Enrique Aman
- Medical Oncology Unit, Swiss Medical GroupBuenos AiresArgentina
| | - María Romina Girotti
- Pathology & Molecular Biology LaboratoriesBiomakersBuenos AiresArgentina
- Universidad Argentina de la Empresa (UADE), Instituto de Tecnología (INTEC)Buenos AiresArgentina
| | - Oscar Arrieta
- Head of Thoracic Oncology UnitUnidad Funcional de Oncología Torácica, Instituto Nacional de Cancerología (INCan)Mexico CityMexico
| | - Claudio Martín
- Thoracic Oncology Unit, Department of Medical OncologyAlexander Fleming Cancer InstituteBuenos AiresArgentina
- Clinical Research Unit, Department of Medical OncologyAlexander Fleming Cancer InstituteBuenos AiresArgentina
| | - Rubén Salanova
- Pathology & Molecular Biology LaboratoriesBiomakersBuenos AiresArgentina
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4
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Reshkin SJ, Cardone RA, Koltai T. Genetic Signature of Human Pancreatic Cancer and Personalized Targeting. Cells 2024; 13:602. [PMID: 38607041 PMCID: PMC11011857 DOI: 10.3390/cells13070602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Pancreatic cancer is a highly lethal disease with a 5-year survival rate of around 11-12%. Surgery, being the treatment of choice, is only possible in 20% of symptomatic patients. The main reason is that when it becomes symptomatic, IT IS the tumor is usually locally advanced and/or has metastasized to distant organs; thus, early diagnosis is infrequent. The lack of specific early symptoms is an important cause of late diagnosis. Unfortunately, diagnostic tumor markers become positive at a late stage, and there is a lack of early-stage markers. Surgical and non-surgical cases are treated with neoadjuvant and/or adjuvant chemotherapy, and the results are usually poor. However, personalized targeted therapy directed against tumor drivers may improve this situation. Until recently, many pancreatic tumor driver genes/proteins were considered untargetable. Chemical and physical characteristics of mutated KRAS are a formidable challenge to overcome. This situation is slowly changing. For the first time, there are candidate drugs that can target the main driver gene of pancreatic cancer: KRAS. Indeed, KRAS inhibition has been clinically achieved in lung cancer and, at the pre-clinical level, in pancreatic cancer as well. This will probably change the very poor outlook for this disease. This paper reviews the genetic characteristics of sporadic and hereditary predisposition to pancreatic cancer and the possibilities of a personalized treatment according to the genetic signature.
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Affiliation(s)
- Stephan J. Reshkin
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy;
| | - Rosa Angela Cardone
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy;
| | - Tomas Koltai
- Oncomed, Via Pier Capponi 6, 50132 Florence, Italy
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5
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Perri F, Fusco R, Sabbatino F, Fasano M, Ottaiano A, Cascella M, Marciano ML, Pontone M, Salzano G, Maiello ME, Montano M, Calogero E, D'Aniello R, Maiolino P, Ciardiello F, Zotta A, Alfieri S, Ionna F. Translational Insights in the Landscape of Salivary Gland Cancers: Ready for a New Era? Cancers (Basel) 2024; 16:970. [PMID: 38473330 DOI: 10.3390/cancers16050970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Salivary gland carcinomas (SGCs) are rare neoplasms, representing less than 10% of all head and neck tumors, but they are extremely heterogeneous from the histological point of view, their clinical behavior, and their genetics. The guidelines regarding their treatment include surgery in most cases, which can also play an important role in oligometastatic disease. Where surgery cannot be used, systemic therapy comes into play. Systemic therapy for many years has been represented by polychemotherapy, but recently, with the affirmation of translational research, it can also count on targeted therapy, at least in some subtypes of SGCs. Interestingly, in some SGC histotypes, predominant mutations have been identified, which in some cases behave as "driver mutations", namely mutations capable of governing the carcinogenesis process. Targeting these driver mutations may be an effective therapeutic strategy. Nonetheless, it is not always possible to have drugs suitable for targeting driver mutations-and targeting driver mutations is not always accompanied by a clinical benefit. In this review, we will analyze the main mutations predominant in the various histotypes of SGCs.
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Affiliation(s)
- Francesco Perri
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
| | - Roberta Fusco
- Medical Oncology Devision, IGEA S.p.A., 80013 Naples, Italy
| | - Francesco Sabbatino
- Medical Oncology Department, Università degli Studi di Salerno, Via Giovanni Paolo II, 132, 84084 Salerno, Italy
| | - Morena Fasano
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80128 Naples, Italy
| | - Alessandro Ottaiano
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
| | - Marco Cascella
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
| | - Maria Luisa Marciano
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
| | - Monica Pontone
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
| | - Giovanni Salzano
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Maria Elena Maiello
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
| | - Massimo Montano
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
| | - Ester Calogero
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
| | - Roberta D'Aniello
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
| | - Piera Maiolino
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
| | - Fortunato Ciardiello
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80128 Naples, Italy
| | - Alessia Zotta
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80128 Naples, Italy
| | - Salvatore Alfieri
- Head and Neck Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Franco Ionna
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Napoli, Italy
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Moura S, Hartl I, Brumovska V, Calabrese PP, Yasari A, Striedner Y, Bishara M, Mair T, Ebner T, Schütz GJ, Sevcsik E, Tiemann-Boege I. Exploring FGFR3 Mutations in the Male Germline: Implications for Clonal Germline Expansions and Paternal Age-Related Dysplasias. Genome Biol Evol 2024; 16:evae015. [PMID: 38411226 PMCID: PMC10898338 DOI: 10.1093/gbe/evae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
Delayed fatherhood results in a higher risk of inheriting a new germline mutation that might result in a congenital disorder in the offspring. In particular, some FGFR3 mutations increase in frequency with age, but there are still a large number of uncharacterized FGFR3 mutations that could be expanding in the male germline with potentially early- or late-onset effects in the offspring. Here, we used digital polymerase chain reaction to assess the frequency and spatial distribution of 10 different FGFR3 missense substitutions in the sexually mature male germline. Our functional assessment of the receptor signaling of the variants with biophysical methods showed that 9 of these variants resulted in a higher activation of the receptor´s downstream signaling, resulting in 2 different expansion behaviors. Variants that form larger subclonal expansions in a dissected postmortem testis also showed a positive correlation of the substitution frequency with the sperm donor's age, and a high and ligand-independent FGFR3 activation. In contrast, variants that measured high FGFR3 signaling and elevated substitution frequencies independent of the donor's age did not result in measurable subclonal expansions in the testis. This suggests that promiscuous signal activation might also result in an accumulation of mutations before the sexual maturation of the male gonad with clones staying relatively constant in size throughout time. Collectively, these results provide novel insights into our understanding of the mutagenesis of driver mutations and their resulting mosaicism in the male germline with important consequences for the transmission and recurrence of associated disorders.
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Affiliation(s)
- Sofia Moura
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, USA
| | - Ingrid Hartl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Peter P Calabrese
- Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Atena Yasari
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Theresa Mair
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Thomas Ebner
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Johannes Kepler University, 4020 Linz, Austria
| | | | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Vienna, Austria
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7
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Wang X, Kostrzewa C, Reiner A, Shen R, Begg C. Adaptation of a mutual exclusivity framework to identify driver mutations within oncogenic pathways. Am J Hum Genet 2024; 111:227-241. [PMID: 38232729 PMCID: PMC10870134 DOI: 10.1016/j.ajhg.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 01/19/2024] Open
Abstract
Distinguishing genomic alterations in cancer-associated genes that have functional impact on tumor growth and disease progression from the ones that are passengers and confer no fitness advantage have important clinical implications. Evidence-based methods for nominating drivers are limited by existing knowledge on the oncogenic effects and therapeutic benefits of specific variants from clinical trials or experimental settings. As clinical sequencing becomes a mainstay of patient care, applying computational methods to mine the rapidly growing clinical genomic data holds promise in uncovering functional candidates beyond the existing knowledge base and expanding the patient population that could potentially benefit from genetically targeted therapies. We propose a statistical and computational method (MAGPIE) that builds on a likelihood approach leveraging the mutual exclusivity pattern within an oncogenic pathway for identifying probabilistically both the specific genes within a pathway and the individual mutations within such genes that are truly the drivers. Alterations in a cancer-associated gene are assumed to be a mixture of driver and passenger mutations with the passenger rates modeled in relationship to tumor mutational burden. We use simulations to study the operating characteristics of the method and assess false-positive and false-negative rates in driver nomination. When applied to a large study of primary melanomas, the method accurately identifies the known driver genes within the RTK-RAS pathway and nominates several rare variants as prime candidates for functional validation. A comprehensive evaluation of MAGPIE against existing tools has also been conducted leveraging the Cancer Genome Atlas data.
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Affiliation(s)
- Xinjun Wang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Caroline Kostrzewa
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allison Reiner
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Colin Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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8
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Striedner Y, Arbeithuber B, Moura S, Nowak E, Reinhardt R, Muresan L, Salazar R, Ebner T, Tiemann-Boege I. Exploring the Micro-Mosaic Landscape of FGFR3 Mutations in the Ageing Male Germline and Their Potential Implications in Meiotic Differentiation. Genes (Basel) 2024; 15:191. [PMID: 38397181 PMCID: PMC10888257 DOI: 10.3390/genes15020191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Advanced paternal age increases the risk of transmitting de novo germline mutations, particularly missense mutations activating the receptor tyrosine kinase (RTK) signalling pathway, as exemplified by the FGFR3 mutation, which is linked to achondroplasia (ACH). This risk is attributed to the expansion of spermatogonial stem cells carrying the mutation, forming sub-clonal clusters in the ageing testis, thereby increasing the frequency of mutant sperm and the number of affected offspring from older fathers. While prior studies proposed a correlation between sub-clonal cluster expansion in the testis and elevated mutant sperm production in older donors, limited data exist on the universality of this phenomenon. Our study addresses this gap by examining the testis-expansion patterns, as well as the increases in mutations in sperm for two FGFR3 variants-c.1138G>A (p.G380R) and c.1948A>G (p.K650E)-which are associated with ACH or thanatophoric dysplasia (TDII), respectively. Unlike the ACH mutation, which showed sub-clonal expansion events in an aged testis and a significant increase in mutant sperm with the donor's age, as also reported in other studies, the TDII mutation showed focal mutation pockets in the testis but exhibited reduced transmission into sperm and no significant age-related increase. The mechanism behind this divergence remains unclear, suggesting potential pleiotropic effects of aberrant RTK signalling in the male germline, possibly hindering differentiation requiring meiosis. This study provides further insights into the transmission risks of micro-mosaics associated with advanced paternal age in the male germline.
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Affiliation(s)
- Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
| | - Barbara Arbeithuber
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Johannes Kepler University, 4020 Linz, Austria;
| | - Sofia Moura
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Elisabeth Nowak
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
| | - Ronja Reinhardt
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Leila Muresan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 2EL, UK;
- Faculty of Science and Engineering, Anglia Ruskin University, Cambridge CB1 1PT, UK
| | - Renato Salazar
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
| | - Thomas Ebner
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Johannes Kepler University, 4020 Linz, Austria;
| | - Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (Y.S.); (B.A.); (E.N.); (R.R.)
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Nourbakhsh M, Degn K, Saksager A, Tiberti M, Papaleo E. Prediction of cancer driver genes and mutations: the potential of integrative computational frameworks. Brief Bioinform 2024; 25:bbad519. [PMID: 38261338 PMCID: PMC10805075 DOI: 10.1093/bib/bbad519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/27/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
The vast amount of available sequencing data allows the scientific community to explore different genetic alterations that may drive cancer or favor cancer progression. Software developers have proposed a myriad of predictive tools, allowing researchers and clinicians to compare and prioritize driver genes and mutations and their relative pathogenicity. However, there is little consensus on the computational approach or a golden standard for comparison. Hence, benchmarking the different tools depends highly on the input data, indicating that overfitting is still a massive problem. One of the solutions is to limit the scope and usage of specific tools. However, such limitations force researchers to walk on a tightrope between creating and using high-quality tools for a specific purpose and describing the complex alterations driving cancer. While the knowledge of cancer development increases daily, many bioinformatic pipelines rely on single nucleotide variants or alterations in a vacuum without accounting for cellular compartments, mutational burden or disease progression. Even within bioinformatics and computational cancer biology, the research fields work in silos, risking overlooking potential synergies or breakthroughs. Here, we provide an overview of databases and datasets for building or testing predictive cancer driver tools. Furthermore, we introduce predictive tools for driver genes, driver mutations, and the impact of these based on structural analysis. Additionally, we suggest and recommend directions in the field to avoid silo-research, moving towards integrative frameworks.
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Affiliation(s)
- Mona Nourbakhsh
- Cancer Systems Biology, Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Astrid Saksager
- Cancer Systems Biology, Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Institute, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Systems Biology, Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark
- Cancer Structural Biology, Danish Cancer Institute, 2100 Copenhagen, Denmark
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10
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Peters L, Venkatachalam A, Ben-Neriah Y. Tissue-Predisposition to Cancer Driver Mutations. Cells 2024; 13:106. [PMID: 38247798 PMCID: PMC10814991 DOI: 10.3390/cells13020106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Driver mutations are considered the cornerstone of cancer initiation. They are defined as mutations that convey a competitive fitness advantage, and hence, their mutation frequency in premalignant tissue is expected to exceed the basal mutation rate. In old terms, that translates to "the survival of the fittest" and implies that a selective process underlies the frequency of cancer driver mutations. In that sense, each tissue is its own niche that creates a molecular selective pressure that may favor the propagation of a mutation or not. At the heart of this stands one of the biggest riddles in cancer biology: the tissue-predisposition to cancer driver mutations. The frequency of cancer driver mutations among tissues is non-uniform: for instance, mutations in APC are particularly frequent in colorectal cancer, and 99% of chronic myeloid leukemia patients harbor the driver BCR-ABL1 fusion mutation, which is rarely found in solid tumors. Here, we provide a mechanistic framework that aims to explain how tissue-specific features, ranging from epigenetic underpinnings to the expression of viral transposable elements, establish a molecular basis for selecting cancer driver mutations in a tissue-specific manner.
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Affiliation(s)
| | | | - Yinon Ben-Neriah
- Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research (IMRIC), The Faculty of Medicine, Hebrew University of Jerusalem, P.O. Box 12272, Jerusalem 91120, Israel; (L.P.); (A.V.)
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11
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Ermakov MS, Kashofer K, Regauer S. Different Mutational Landscapes in Human Papillomavirus-Induced and Human Papillomavirus-Independent Invasive Penile Squamous Cell Cancers. Mod Pathol 2023; 36:100250. [PMID: 37353203 DOI: 10.1016/j.modpat.2023.100250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/21/2023] [Accepted: 06/14/2023] [Indexed: 06/25/2023]
Abstract
Penile squamous cell carcinomas (SCC) are rare cancers that arise after transforming human papillomavirus (HPV) infections or independent of HPV in the background of chronic dermatoses. Limited knowledge about genetic alterations driving penile carcinogenesis comes from studies of mainly small cohorts of typically mixed etiology. In this comparative genetic study of HPV-induced and HPV-independent invasive penile SCC of 156 patients from a single institution in a low-incidence country, hotspots of 50 cancer-relevant genes were analyzed with targeted next-generation sequencing. Seventy-nine of 156 SCC were classified as HPV induced, and 77 of 156 SCC arose independent of HPV. Only 28 (35%) of 79 HPV-induced penile SCC, but 69 (90%) of 77 HPV-independent SCC carried somatic gene mutations. PIK3CA, FGFR3, and FBXW7 mutations occurred in both groups in similar numbers as seen in other human cancers. In contrast, mutations in TP53 (44/77; 57%), CDKN2A (35/77; 45%), and HRAS (13/77; 17%) genes occurred with one exception of a HIV positive patient exclusively in HPV-independent SCC with a frequent co-occurrence of TP53 and CDKN2A mutations (28/77; 42%). Mutations in multiple genes occurred in 9 (11%) of 79 HPV-induced SCC versus 47 (62%) of 77 HPV-independent SCC (χ2; P < .001). More than one mutation per gene (multi hits) was characteristic for HPV-independent SCC in 14 (18%) of 77 compared with only 3 (4%) of 79 HPV-induced SCC (χ2; P < .001). The total number of mutations in HPV-induced penile SCC (47 mutations) was significantly lower than that in HPV-independent SCC (143 mutations; Welsh test; P < .001). The presence of somatic driver gene mutations did not correlate with the age of patients, histology, or tumor stage of the primary SCC in either etiologic group, suggesting that acquisition of driver gene mutations is an early event after invasion. This large cohort analysis identified characteristic differences in mutational landscapes for the 2 etiologies. While genetic mutations in tumor suppressor genes drive HPV-independent penile carcinogenesis, oncogenic action of E6 and E7 substitute for mutations in HPV-induced SCC. A subgroup of patients with advanced SCC may be candidates for targeted therapy and clinical trials, although the majority of advanced penile SCC remain a therapeutic challenge.
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Affiliation(s)
- Mikhail S Ermakov
- Diagnostic and Research Institute of Pathology, Medical University Graz, MedCampus Graz, Graz, Austria
| | - Karl Kashofer
- Diagnostic and Research Institute of Pathology, Medical University Graz, MedCampus Graz, Graz, Austria.
| | - Sigrid Regauer
- Diagnostic and Research Institute of Pathology, Medical University Graz, MedCampus Graz, Graz, Austria.
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12
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Nourbakhsh M, Saksager A, Tom N, Chen XS, Colaprico A, Olsen C, Tiberti M, Papaleo E. A workflow to study mechanistic indicators for driver gene prediction with Moonlight. Brief Bioinform 2023; 24:bbad274. [PMID: 37551622 PMCID: PMC10516357 DOI: 10.1093/bib/bbad274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/28/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023] Open
Abstract
Prediction of driver genes (tumor suppressors and oncogenes) is an essential step in understanding cancer development and discovering potential novel treatments. We recently proposed Moonlight as a bioinformatics framework to predict driver genes and analyze them in a system-biology-oriented manner based on -omics integration. Moonlight uses gene expression as a primary data source and combines it with patterns related to cancer hallmarks and regulatory networks to identify oncogenic mediators. Once the oncogenic mediators are identified, it is important to include extra levels of evidence, called mechanistic indicators, to identify driver genes and to link the observed gene expression changes to the underlying alteration that promotes them. Such a mechanistic indicator could be for example a mutation in the regulatory regions for the candidate gene. Here, we developed new functionalities and released Moonlight2 to provide the user with a mutation-based mechanistic indicator as a second layer of evidence. These functionalities analyze mutations in a cancer cohort to classify them into driver and passenger mutations. Those oncogenic mediators with at least one driver mutation are retained as the final set of driver genes. We applied Moonlight2 to the basal-like breast cancer subtype, lung adenocarcinoma and thyroid carcinoma using data from The Cancer Genome Atlas. For example, in basal-like breast cancer, we found four oncogenes (COPZ2, SF3B4, KRTCAP2 and POLR2J) and nine tumor suppressor genes (KIR2DL4, KIF26B, ARL15, ARHGAP25, EMCN, GMFG, TPK1, NR5A2 and TEK) containing a driver mutation in their promoter region, possibly explaining their deregulation. Moonlight2R is available at https://github.com/ELELAB/Moonlight2R.
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Affiliation(s)
- Mona Nourbakhsh
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby, Denmark
| | - Astrid Saksager
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby, Denmark
| | - Nikola Tom
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby, Denmark
| | - Xi Steven Chen
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Catharina Olsen
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Reproduction and Genetics
- Brussels Interuniversity Genomics High Throughput core (BRIGHTcore), VUB-ULB, Brussels 1090, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB)2, Brussels 1050, Belgium
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Institute, Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby, Denmark
- Cancer Structural Biology, Danish Cancer Institute, Copenhagen, Denmark
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13
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Stopa KB, Łoziński F, Kusiak AA, Litewka J, Krzysztofik D, Mosiołek S, Morys J, Ferdek PE, Jakubowska MA. Driver Mutations of Pancreatic Cancer Affect Ca 2+ Signaling and ATP Production. Function (Oxf) 2023; 4:zqad035. [PMID: 37575483 PMCID: PMC10413928 DOI: 10.1093/function/zqad035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 08/15/2023] Open
Abstract
Glandular pancreatic epithelia of the acinar or ductal phenotype may seem terminally differentiated, but they are characterized by remarkable cell plasticity. Stress-induced trans-differentiation of these cells has been implicated in the mechanisms of carcinogenesis. Current consensus links pancreatic ductal adenocarcinoma with onco-transformation of ductal epithelia, but under the presence of driver mutations in Kras and Trp53, also with trans-differentiation of pancreatic acini. However, we do not know when, in the course of cancer progression, physiological functions are lost by mutant acinar cells, nor can we assess their capacity for the production of pancreatic juice components. Here, we investigated whether two mutations-KrasG12D and Trp53R172H-present simultaneously in acinar cells of KPC mice (model of oncogenesis) influence cytosolic Ca2+ signals. Since Ca2+ signals control the cellular handling of digestive hydrolases, any changes that affect intracellular signaling events and cell bioenergetics might have an impact on the physiology of the pancreas. Our results showed that physiological doses of acetylcholine evoked less regular Ca2+ oscillations in KPC acinar cells compared to the control, whereas responses to supramaximal concentrations were markedly reduced. Menadione elicited Ca2+ signals of different frequencies in KPC cells compared to control cells. Finally, Ca2+ extrusion rates were significantly inhibited in KPC cells, likely due to the lower basal respiration and ATP production. Cumulatively, these findings suggest that driver mutations affect the signaling capacity of pancreatic acinar cells even before the changes in the epithelial cell morphology become apparent.
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Affiliation(s)
- Kinga B Stopa
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7A, 30-387 Kraków, Poland
- Doctoral School of Exact and Biological Sciences, Jagiellonian University, ul. Łojasiewicza 11, 30-348 Kraków, Poland
| | - Filip Łoziński
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7A, 30-387 Kraków, Poland
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Agnieszka A Kusiak
- Doctoral School of Exact and Biological Sciences, Jagiellonian University, ul. Łojasiewicza 11, 30-348 Kraków, Poland
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Jacek Litewka
- Doctoral School of Exact and Biological Sciences, Jagiellonian University, ul. Łojasiewicza 11, 30-348 Kraków, Poland
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Daria Krzysztofik
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7A, 30-387 Kraków, Poland
- Doctoral School of Exact and Biological Sciences, Jagiellonian University, ul. Łojasiewicza 11, 30-348 Kraków, Poland
| | - Sylwester Mosiołek
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7A, 30-387 Kraków, Poland
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Jan Morys
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7A, 30-387 Kraków, Poland
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Paweł E Ferdek
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Monika A Jakubowska
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7A, 30-387 Kraków, Poland
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14
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Urlić I, Jovičić MŠ, Ostojić K, Ivković A. Cellular and Genetic Background of Osteosarcoma. Curr Issues Mol Biol 2023; 45:4344-4358. [PMID: 37232745 DOI: 10.3390/cimb45050276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/28/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023] Open
Abstract
Osteosarcoma describes a tumor of mesenchymal origin with an annual incidence rate of four to five people per million. Even though chemotherapy treatment has shown success in non-metastatic osteosarcoma, metastatic disease still has a low survival rate of 20%. A targeted therapy approach is limited due to high heterogeneity of tumors, and different underlying mutations. In this review, we will summarize new advances obtained by new technologies, such as next generation sequencing and single-cell sequencing. These new techniques have enabled better assessment of cell populations within osteosarcoma, as well as an understanding of the molecular pathogenesis. We also discuss the presence and properties of osteosarcoma stem cells-the cell population within the tumor that is responsible for metastasis, recurrence, and drug resistance.
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Affiliation(s)
- Inga Urlić
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Marijana Šimić Jovičić
- Department of Paediatric Orthopaedics, Children's Hospital Zagreb, 10000 Zagreb, Croatia
| | - Karla Ostojić
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Alan Ivković
- Department of Orthopaedics and Traumatology, University Hospital Sveti Duh, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Professional Study in Physiotherapy, University of Applied Health Sciences, 10000 Zagreb, Croatia
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15
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Ju S, Cui Z, Hong Y, Wang X, Mu W, Xie Z, Zeng X, Su L, Lin X, Zhang Z, Zhang Q, Song X, You S, Chen R, Chen W, Xu C, Zhao J. Detection of multiple types of cancer driver mutations using targeted RNA sequencing in nonsmall cell lung cancer. Cancer 2023. [PMID: 37096747 DOI: 10.1002/cncr.34804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/24/2022] [Accepted: 09/28/2022] [Indexed: 04/26/2023]
Abstract
BACKGROUND DNA-based next-generation sequencing has been widely used in the selection of target therapies for patients with nonsmall cell lung cancer (NSCLC). RNA-based next-generation sequencing has been proven to be valuable in detecting fusion and exon-skipping mutations and is recommended by National Comprehensive Cancer Network guidelines for these mutation types. METHODS The authors developed an RNA-based hybridization panel targeting actionable driver oncogenes in solid tumors. Experimental and bioinformatics pipelines were optimized for the detection of fusions, single-nucleotide variants (SNVs), and insertion/deletion (indels). In total, 1253 formalin-fixed, paraffin-embedded samples from patients with NSCLC were analyzed by DNA and RNA panel sequencing in parallel to assess the performance of the RNA panel in detecting multiple types of mutations. RESULTS In analytical validation, the RNA panel achieved a limit of detection of 1.45-3.15 copies per nanogram for SNVs and 0.21-6.48 copies per nanogram for fusions. In 1253 formalin-fixed, paraffin-embedded NSCLC samples, the RNA panel identified a total of 124 fusion events and 26 MET exon 14-skipping events, in which 14 fusions and six MET exon 14-skipping mutations were missed by DNA panel sequencing. By using the DNA panel as the reference, the positive percent agreement and the positive predictive value of the RNA panel were 98.08% and 98.62%, respectively, for detecting targetable SNVs and 98.15% and 99.38%, respectively, for detecting targetable indels. CONCLUSIONS Parallel DNA and RNA sequencing analyses demonstrated the accuracy and robustness of the RNA sequencing panel in detecting multiple types of clinically actionable mutations. The simplified experimental workflow and low sample consumption will make RNA panel sequencing a potentially effective method in clinical testing.
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Affiliation(s)
- Sheng Ju
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zihan Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuanyuan Hong
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Xiaoqing Wang
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Weina Mu
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Zhuolin Xie
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xuexia Zeng
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Lin Su
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Xiaojing Lin
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Zhuo Zhang
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Qi Zhang
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Xiaofeng Song
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Songxia You
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Ruixin Chen
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Weizhi Chen
- GeneCast Biotechnology Research Institute, Beijing, China
| | - Chun Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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16
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Herrera-Juárez M, Serrano-Gómez C, Bote-de-Cabo H, Paz-Ares L. Targeted therapy for lung cancer: Beyond EGFR and ALK. Cancer 2023; 129:1803-1820. [PMID: 37073562 DOI: 10.1002/cncr.34757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 04/20/2023]
Abstract
Precision oncology comprises the set of strategies that aim to design the best cancer treatment based on tumor biology. A recognized subset of patients with non-small cell lung cancer (NSCLC) harbor actionable genomic aberrations that can benefit from targeted therapy. In lung cancer, epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) rearrangements are well characterized oncogenic drivers for which the therapeutic use of tyrosine kinase inhibitors has demonstrated improved outcomes compared with chemotherapy. Other druggable targets are also well characterized, and effective inhibitors have been developed and commercialized, leading to a paradigm shift in NSCLC treatment. Here, the authors provide a review of the oncogenic role of the most relevant molecular alterations in NSCLC and emerging treatments in this setting beyond EGFR-driven and ALK-driven diseases.
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Affiliation(s)
- Mercedes Herrera-Juárez
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | - Helena Bote-de-Cabo
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Luis Paz-Ares
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Medicine, Complutense University, Madrid, Spain
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17
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Ostroverkhova D, Przytycka TM, Panchenko AR. Cancer driver mutations: predictions and reality. Trends Mol Med 2023:S1471-4914(23)00067-9. [PMID: 37076339 DOI: 10.1016/j.molmed.2023.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Cancer cells accumulate many genetic alterations throughout their lifetime, but only a few of them drive cancer progression, termed driver mutations. Driver mutations may vary between cancer types and patients, can remain latent for a long time and become drivers at particular cancer stages, or may drive oncogenesis only in conjunction with other mutations. The high mutational, biochemical, and histological tumor heterogeneity makes driver mutation identification very challenging. In this review we summarize recent efforts to identify driver mutations in cancer and annotate their effects. We underline the success of computational methods to predict driver mutations in finding novel cancer biomarkers, including in circulating tumor DNA (ctDNA). We also report on the boundaries of their applicability in clinical research.
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Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Teresa M Przytycka
- National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada; Department of Biology and Molecular Sciences, Queen's University, Kingston, ON, Canada; School of Computing, Queen's University, Kingston, ON, Canada; Ontario Institute of Cancer Research, Toronto, ON, Canada.
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18
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Abstract
Genomic studies of human disorders are often performed by distinct research communities (i.e., focused on rare diseases, common diseases, or cancer). Despite underlying differences in the mechanistic origin of different disease categories, these studies share the goal of identifying causal genomic events that are critical for the clinical manifestation of the disease phenotype. Moreover, these studies face common challenges, including understanding the complex genetic architecture of the disease, deciphering the impact of variants on multiple scales, and interpreting noncoding mutations. Here, we highlight these challenges in depth and argue that properly addressing them will require a more unified vocabulary and approach across disease communities. Toward this goal, we present a unified perspective on relating variant impact to various genomic disorders.
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Affiliation(s)
- Sushant Kumar
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics & Data Science, Yale University, New Haven, CT 06520, USA.
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19
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Zhong J, Bai H, Wang Z, Duan J, Zhuang W, Wang D, Wan R, Xu J, Fei K, Ma Z, Zhang X, Wang J. Treatment of advanced non-small cell lung cancer with driver mutations: current applications and future directions. Front Med 2023; 17:18-42. [PMID: 36848029 DOI: 10.1007/s11684-022-0976-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/05/2022] [Indexed: 03/01/2023]
Abstract
With the improved understanding of driver mutations in non-small cell lung cancer (NSCLC), expanding the targeted therapeutic options improved the survival and safety. However, responses to these agents are commonly temporary and incomplete. Moreover, even patients with the same oncogenic driver gene can respond diversely to the same agent. Furthermore, the therapeutic role of immune-checkpoint inhibitors (ICIs) in oncogene-driven NSCLC remains unclear. Therefore, this review aimed to classify the management of NSCLC with driver mutations based on the gene subtype, concomitant mutation, and dynamic alternation. Then, we provide an overview of the resistant mechanism of target therapy occurring in targeted alternations ("target-dependent resistance") and in the parallel and downstream pathways ("target-independent resistance"). Thirdly, we discuss the effectiveness of ICIs for NSCLC with driver mutations and the combined therapeutic approaches that might reverse the immunosuppressive tumor immune microenvironment. Finally, we listed the emerging treatment strategies for the new oncogenic alternations, and proposed the perspective of NSCLC with driver mutations. This review will guide clinicians to design tailored treatments for NSCLC with driver mutations.
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Affiliation(s)
- Jia Zhong
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Di Wang
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Rui Wan
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Jiachen Xu
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Kailun Fei
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Zixiao Ma
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Xue Zhang
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, 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, 100021, China.
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20
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Barbagallo C, Stella M, Broggi G, Russo A, Caltabiano R, Ragusa M. Genetics and RNA Regulation of Uveal Melanoma. Cancers (Basel) 2023; 15:775. [PMID: 36765733 PMCID: PMC9913768 DOI: 10.3390/cancers15030775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Uveal melanoma (UM) is the most common intraocular malignant tumor and the most frequent melanoma not affecting the skin. While the rate of UM occurrence is relatively low, about 50% of patients develop metastasis, primarily to the liver, with lethal outcome despite medical treatment. Notwithstanding that UM etiopathogenesis is still under investigation, a set of known mutations and chromosomal aberrations are associated with its pathogenesis and have a relevant prognostic value. The most frequently mutated genes are BAP1, EIF1AX, GNA11, GNAQ, and SF3B1, with mutually exclusive mutations occurring in GNAQ and GNA11, and almost mutually exclusive ones in BAP1 and SF3B1, and BAP1 and EIF1AX. Among chromosomal aberrations, monosomy of chromosome 3 is the most frequent, followed by gain of chromosome 8q, and full or partial loss of chromosomes 1 and 6. In addition, epigenetic mechanisms regulated by non-coding RNAs (ncRNA), namely microRNAs and long non-coding RNAs, have also been investigated. Several papers investigating the role of ncRNAs in UM have reported that their dysregulated expression affects cancer-related processes in both in vitro and in vivo models. This review will summarize current findings about genetic mutations, chromosomal aberrations, and ncRNA dysregulation establishing UM biology.
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Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| | - Giuseppe Broggi
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia—Section of Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Andrea Russo
- Department of Ophthalmology, University of Catania, 95123 Catania, Italy
| | - Rosario Caltabiano
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia—Section of Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
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21
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Kim D, Ha D, Lee K, Lee H, Kim I, Kim S. An evolution-based machine learning to identify cancer type-specific driver mutations. Brief Bioinform 2023; 24:6961611. [PMID: 36575568 DOI: 10.1093/bib/bbac593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/18/2022] [Accepted: 12/03/2022] [Indexed: 12/29/2022] Open
Abstract
Identifying cancer type-specific driver mutations is crucial for illuminating distinct pathologic mechanisms across various tumors and providing opportunities of patient-specific treatment. However, although many computational methods were developed to predict driver mutations in a type-specific manner, the methods still have room to improve. Here, we devise a novel feature based on sequence co-evolution analysis to identify cancer type-specific driver mutations and construct a machine learning (ML) model with state-of-the-art performance. Specifically, relying on 28 000 tumor samples across 66 cancer types, our ML framework outperformed current leading methods of detecting cancer driver mutations. Interestingly, the cancer mutations identified by sequence co-evolution feature are frequently observed in interfaces mediating tissue-specific protein-protein interactions that are known to associate with shaping tissue-specific oncogenesis. Moreover, we provide pre-calculated potential oncogenicity on available human proteins with prediction scores of all possible residue alterations through user-friendly website (http://sbi.postech.ac.kr/w/cancerCE). This work will facilitate the identification of cancer type-specific driver mutations in newly sequenced tumor samples.
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Affiliation(s)
| | | | | | | | - Inhae Kim
- ImmunoBiome Inc., Pohang, South Korea
| | - Sanguk Kim
- Department of Life Sciences.,Artificial Intelligence Graduate Program, Pohang University of Science and Technology, Pohang 790-784, South Korea.,Institute of Convergence Research and Education in Advanced Technology, Yonsei University, Seoul 120-149, South Korea
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22
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Tabor JK, Onoichenco A, Narayan V, Wernicke AG, D’Amico RS, Vojnic M. Brain metastasis screening in the molecular age. Neurooncol Adv 2023; 5:vdad080. [PMID: 37484759 PMCID: PMC10358433 DOI: 10.1093/noajnl/vdad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
The incidence of brain metastases (BM) amongst cancer patients has been increasing due to improvements in therapeutic options and an increase in overall survival. Molecular characterization of tumors has provided insights into the biology and oncogenic drivers of BM and molecular subtype-based screening. Though there are currently some screening and surveillance guidelines for BM, they remain limited. In this comprehensive review, we review and present epidemiological data on BM, their molecular characterization, and current screening guidelines. The molecular subtypes with the highest BM incidence are epithelial growth factor receptor-mutated non-small cell lung cancer (NSCLC), BRCA1, triple-negative (TN), and HER2+ breast cancers, and BRAF-mutated melanoma. Furthermore, BMs are more likely to present asymptomatically at diagnosis in oncogene-addicted NSCLC and BRAF-mutated melanoma. European screening standards recommend more frequent screening for oncogene-addicted NSCLC patients, and clinical trials are investigating screening for BM in hormone receptor+, HER2+, and TN breast cancers. However, more work is needed to determine optimal screening guidelines for other primary cancer molecular subtypes. With the advent of personalized medicine, molecular characterization of tumors has revolutionized the landscape of cancer treatment and prognostication. Incorporating molecular characterization into BM screening guidelines may allow physicians to better identify patients at high risk for BM development and improve patient outcomes.
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Affiliation(s)
| | | | - Vinayak Narayan
- Department of Neurological Surgery, Lenox Hill Hospital, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, NY, USA
| | - A Gabriella Wernicke
- Department of Radiation Medicine, Lenox Hill Hospital, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, NY, USA
| | - Randy S D’Amico
- Department of Neurological Surgery, Lenox Hill Hospital, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, NY, USA
| | - Morana Vojnic
- Corresponding Author: Morana Vojnic, MD, MBA, 210 East 64th Street, Floor 4, New York, NY 10065, USA ()
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23
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Abbou N, Piazzola P, Gabert J, Ernest V, Arcani R, Couderc AL, Tichadou A, Roche P, Farnault L, Colle J, Ouafik L, Morange P, Costello R, Venton G. Impact of Molecular Biology in Diagnosis, Prognosis, and Therapeutic Management of BCR::ABL1-Negative Myeloproliferative Neoplasm. Cells 2022; 12:cells12010105. [PMID: 36611899 PMCID: PMC9818322 DOI: 10.3390/cells12010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
BCR::ABL1-negative myeloproliferative neoplasms (MPNs) include three major subgroups-polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF)-which are characterized by aberrant hematopoietic proliferation with an increased risk of leukemic transformation. Besides the driver mutations, which are JAK2, CALR, and MPL, more than twenty additional mutations have been identified through the use of next-generation sequencing (NGS), which can be involved with pathways that regulate epigenetic modifications, RNA splicing, or DNA repair. The aim of this short review is to highlight the impact of molecular biology on the diagnosis, prognosis, and therapeutic management of patients with PV, ET, and PMF.
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Affiliation(s)
- Norman Abbou
- Molecular Biology Laboratory, North University Hospital, 13015 Marseille, France
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
| | - Pauline Piazzola
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Jean Gabert
- Molecular Biology Laboratory, North University Hospital, 13015 Marseille, France
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
| | - Vincent Ernest
- Hematology Laboratory, Timone University Hospital, 13005 Marseille, France
| | - Robin Arcani
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
- Department of Internal Medicine, Timone University Hospital, 13005 Marseille, France
| | - Anne-Laure Couderc
- Department of Geriatrics, South University Hospital, 13005 Marseille, France
| | - Antoine Tichadou
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Pauline Roche
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Laure Farnault
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Julien Colle
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - L’houcine Ouafik
- CNRS, INP, Institute of Neurophysiopathol, Aix-Marseille Université, 13005 Marseille, France
- APHM, CHU Nord, Service d’Onco-Biologie, Aix-Marseille Université, 13005 Marseille, France
| | - Pierre Morange
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
- Hematology Laboratory, Timone University Hospital, 13005 Marseille, France
| | - Régis Costello
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
- TAGC, INSERM, UMR1090, Aix-Marseille University, 13005 Marseille, France
| | - Geoffroy Venton
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
- TAGC, INSERM, UMR1090, Aix-Marseille University, 13005 Marseille, France
- Correspondence: ; Tel.: +33-4-91-38-41-52
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24
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Hilzenrat RA, Yip S, Melosky B, Ho C, Laskin J, Sun S, Choi JJ, McGuire AL. Disparate Time-to-Treatment and Varied Incidence of Actionable Non-Small Cell Lung Cancer Molecular Alterations in British Columbia: A Historical Cohort Study. Curr Oncol 2022; 30:145-156. [PMID: 36661661 PMCID: PMC9858228 DOI: 10.3390/curroncol30010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Background: non-small cell lung cancer (NSCLC) outcomes remain suboptimal for early-stage disease despite emerging advances in systemic therapy for the peri-operative period. Next-generation sequencing (NGS) identifies driver mutations for which targeted therapies have been developed that improve survival. The BC lung cancer screening program, which was initiated in May 2022, is expected to identify people with early and late stages of NSCLC. It is crucial to first understand the molecular epidemiology and patterns of time to initiate treatment across its five health authorities (HA) to optimize the delivery of care for NSCLC in BC. In this way, we may harness the benefits of targeted therapy for more people with NSCLC as novel advances in therapy continue to emerge. Objective: to compare (a) the frequency of actionable NSCLC molecular alterations among HAs and (b) the time to treatment initiation. Methods: a retrospective observational study was conducted with prospectively collected data from the BC CGL Database. Adults with late stage NSCLC who underwent targeted NGS were included for the time period from May 2020 to June 2021. Demographics, actionable molecular alterations, PDL-1 expression, and time to treatment across HAs were examined. Using appropriate statistical tests for comparison among HAs, p>0.05 was deemed significant. Results: 582 patients underwent NGS/IHC and analysis during the study period. The mean age was 71 (10.1), and 326 (56%) patients were female. A significantly higher proportion of all EGFRm+ were identified within Vancouver Coastal Health (VCHA) and Fraser Health Authority (FHA) compared to the other health authorities (p < 0.001). This also holds true for common sensitizing EGFRm+ alone (p < 0.001) and for sensitizing EGFRm+ when adjusted for females and smoker status (OR 0.75; 95% CI 0.62, 0.92; p = 0.005). Patients residing within the Northern, Interior, and Island HAs were less likely to receive treatment at the same rate as those in VCHA and FHA HAs. Conclusion: actionable NSCLC driver mutations are present in all regional HAs, with disparity noted in time to initiate treatment between HAs. This provides evidence for the importance of molecular testing for patients in all BC HAs to guide personalized and timely NSCLC treatment.
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Affiliation(s)
- Roy Avraham Hilzenrat
- Department of Surgery, Division of Thoracic Surgery, Vancouver Coastal Health, University of British Columbia, 2775 Laurel Street, Vancouver, BC V5Z 1M9, Canada
| | - Stephen Yip
- Cancer Genetics & Genomic Laboratory, BC Cancer—Vancouver Centre, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Barbara Melosky
- Department of Medicine, Division of Medical Oncology, BC Cancer Vancouver Centre, University of British Columbia, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Cheryl Ho
- Department of Medicine, Division of Medical Oncology, BC Cancer Vancouver Centre, University of British Columbia, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Janessa Laskin
- Department of Medicine, Division of Medical Oncology, BC Cancer Vancouver Centre, University of British Columbia, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Sophie Sun
- Department of Medicine, Division of Medical Oncology, BC Cancer Vancouver Centre, University of British Columbia, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - James J. Choi
- Department of Surgery, Division of Thoracic Surgery, Vancouver Coastal Health, University of British Columbia, 2775 Laurel Street, Vancouver, BC V5Z 1M9, Canada
| | - Anna L. McGuire
- Department of Surgery, Division of Thoracic Surgery, Vancouver Coastal Health, University of British Columbia, 2775 Laurel Street, Vancouver, BC V5Z 1M9, Canada
- Vancouver Coastal Health Research Institute, 2635 Laurel Street, Vancouver, BC V5Z 1M9, Canada
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25
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Zhao J, Wu Y, Chen MJ, Xu Y, Zhong W, Wang MZ. Characterization of driver mutations in Chinese non-small cell lung cancer patients using a novel targeted sequencing panel. J Thorac Dis 2022; 14:4669-4684. [PMID: 36647494 PMCID: PMC9840037 DOI: 10.21037/jtd-22-909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/04/2022] [Indexed: 12/05/2022]
Abstract
Background The identification of driver mutations has greatly promoted the precise diagnosis and treatment of non-small cell lung cancer (NSCLC), but there is lack of targeted sequencing panels specifically designed and applied to Chinese NSCLC patients. This study aimed to design and validate of a novel sequencing panel for comprehensive characterization of driver mutations in Chinese NSCLC patients, facilitating further exploration of downstream pathway alterations and therapeutic utility. Methods A novel target sequencing panel including 21 driver genes was designed and examined in a cohort of 260 Chinese NSCLC patients who underwent surgery in Peking Union Medical College Hospital (PUMCH). Genetic alterations were identified and further analyzed for driver mutations, downstream pathways and therapeutic utilities. Results The most frequently identified driver mutations in PUMCH NSCLC cohort were on genes TP53 (28%), EGFR (27%) and PIK3CA (19%) for lung adenocarcinoma (LUAD), and TP53 (41%), PIK3CA (14%) and CDKN2A (13%) for lung squamous cell carcinoma (LUSC), respectively. Downstream pathway analysis revealed common pathways like G1_AND_S1_PHASES pathway were shared not only between LUAD and LUSC patients, but also among three different NSCLC cohorts, while other pathways were subtype-specific, like the unique enrichment of SHC1_EVENT_IN_EGFR_SIGNALING pathway in LUAD patients, and P38_ALPHA_BETA_DOWNSTREAM pathway in LUSC patients, respectively. About 60% of both LUAD and LUSC patients harbored driver mutations as sensitive biomarkers for different targeted therapies, covering not only frequent mutations like EGFR L858R mutation, but also rare mutations like BRAF D594N mutation. Conclusions Our study provides a novel target sequencing panel suitable for Chinese NSCLC patients, which can effectively identify driver mutations, analyze downstream pathway alterations and predict therapeutic utility. Overall it is promising to further optimize and apply this panel in clinic with convenience and effectiveness.
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Affiliation(s)
- Jing Zhao
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Yang Wu
- School of Medicine, Tsinghua University, Beijing, China
| | - Min-Jiang Chen
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Yan Xu
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Wei Zhong
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Meng-Zhao Wang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
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26
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Rivas S, Marín A, Samtani S, González-Feliú E, Armisén R. MET Signaling Pathways, Resistance Mechanisms, and Opportunities for Target Therapies. Int J Mol Sci 2022; 23:ijms232213898. [PMID: 36430388 PMCID: PMC9697723 DOI: 10.3390/ijms232213898] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The MET gene, known as MET proto-oncogene receptor tyrosine kinase, was first identified to induce tumor cell migration, invasion, and proliferation/survival through canonical RAS-CDC42-PAK-Rho kinase, RAS-MAPK, PI3K-AKT-mTOR, and β-catenin signaling pathways, and its driver mutations, such as MET gene amplification (METamp) and the exon 14 skipping alterations (METex14), activate cell transformation, cancer progression, and worse patient prognosis, principally in lung cancer through the overactivation of their own oncogenic and MET parallel signaling pathways. Because of this, MET driver alterations have become of interest in lung adenocarcinomas since the FDA approval of target therapies for METamp and METex14 in 2020. However, after using MET target therapies, tumor cells develop adaptative changes, favoring tumor resistance to drugs, the main current challenge to precision medicine. Here, we review a link between the resistance mechanism and MET signaling pathways, which is not only limited to MET. The resistance impacts MET parallel tyrosine kinase receptors and signals shared hubs. Therefore, this information could be relevant in the patient's mutational profile evaluation before the first target therapy prescription and follow-up to reduce the risk of drug resistance. However, to develop a resistance mechanism to a MET inhibitor, patients must have access to the drugs. For instance, none of the FDA approved MET inhibitors are registered as such in Chile and other developing countries. Constant cross-feeding between basic and clinical research will thus be required to meet future challenges imposed by the acquired resistance to targeted therapies.
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Affiliation(s)
- Solange Rivas
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7550000, Chile
| | - Arnaldo Marín
- Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Suraj Samtani
- Departamento de Oncología Médica, Clínica Las Condes, Santiago 7550000, Chile
- Hospital Félix Bulnes, Santiago 9080000, Chile
| | - Evelin González-Feliú
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7550000, Chile
| | - Ricardo Armisén
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7550000, Chile
- Correspondence:
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Zografos E, Dimitrakopoulos FI, Koutras A. Prognostic Value of Circulating Tumor DNA (ctDNA) in Oncogene-Driven NSCLC: Current Knowledge and Future Perspectives. Cancers (Basel) 2022; 14:cancers14194954. [PMID: 36230877 PMCID: PMC9563444 DOI: 10.3390/cancers14194954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Personalized medicine has significantly changed the clinical outcome of oncogene-driven non-small cell lung cancer (NSCLC) due to the efficacy of molecular targeted therapies. Despite the advances in the management of this group of patients, the need for powerful biomarkers with the potential for a real-time assessment of the tumor genomic profile as well as for detecting and monitoring minimal residual disease (MRD) remains unmet. The aim of this article is to present the current knowledge and the future perspectives regarding the prognostic value of ctDNA in NSCLC, focusing on the most common druggable driver mutations, including those in epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), c-ros oncogene 1 (ROS1), rearranged during transfection (RET), kirsten rat sarcoma virus (KRAS), B-Raf proto-oncogene (BRAF), and mesenchymal epithelial transition factor receptor (MET) genes. Abstract As we enter an unprecedented era of personalized medicine, molecular targeted therapies have the potential to induce improved survival outcome in patients with non-small cell lung cancer (NSCLC). However, a significant percentage of oncogene-driven NSCLC patients will relapse even after definitive treatment, whereas chronic and durable response to targeted therapies is a less common event in advanced-stage lung cancer. This phenomenon could be attributed to minimal residual disease (MRD), defined as a population of disseminated tumor cells that survive during the course or after treatment, eventually leading to recurrence and limiting patient survival. Circulating tumor DNA (ctDNA) is a powerful biomarker for MRD detection and monitoring and is a non-invasive approach of treating cancer, and especially NSCLC, based on a real-time assessment of the tumor genomic landscape. In this review, we present the key findings of studies that have used ctDNA with regard to its prognostic value and in respect to the most common druggable driver mutations of genes in NSCLC, such as epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), c-ros oncogene 1 (ROS1), rearranged during transfection (RET), Kirsten rat sarcoma virus (KRAS), B-Raf proto-oncogene (BRAF), and mesenchymal epithelial transition factor receptor (MET).
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Affiliation(s)
- Eleni Zografos
- Division of Oncology, University Hospital of Patras, University of Patras, 26504 Patras, Greece
- Molecular Oncology Laboratory, Division of Oncology, Department of Medicine, University of Patras, 26504 Patras, Greece
| | - Foteinos-Ioannis Dimitrakopoulos
- Division of Oncology, University Hospital of Patras, University of Patras, 26504 Patras, Greece
- Molecular Oncology Laboratory, Division of Oncology, Department of Medicine, University of Patras, 26504 Patras, Greece
- Correspondence: ; Tel.: +30-2610-999535
| | - Angelos Koutras
- Division of Oncology, University Hospital of Patras, University of Patras, 26504 Patras, Greece
- Molecular Oncology Laboratory, Division of Oncology, Department of Medicine, University of Patras, 26504 Patras, Greece
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28
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Abdelghani M, Hammami H, Zidi W, Amouri H, Othmen HBH, Farrah A, Menif S. Hematological relevance of JAK2 V617F and calreticulin mutations in Tunisian patients with essential thrombocythemia. J Clin Lab Anal 2022; 36:e24522. [PMID: 35754115 PMCID: PMC9396186 DOI: 10.1002/jcla.24522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/28/2022] [Accepted: 05/01/2022] [Indexed: 11/14/2022] Open
Abstract
Background The genetic investigation of essential thrombocythemia(ET) has highlighted the presence of driver mutations in ET. Janus kinase JAK2V617F and calreticulin(CALR) mutations are the most frequent driver mutations and have significantly improved the molecular diagnosis of ET. The impact of genetic heterogeneity on clinical features has not been fully elucidated. This is the first study which aimed to determine the frequency of JAK2V617F and CALR exon9 mutations in Tunisian ET patients and to establish the correlation between hematological characteristics and mutational status. Methods This study included Tunisian patients suspected with ET and was conducted between September 2017 and March 2021. Genomic DNA of patients was isolated from peripheral blood samples. JAK2V617F was detected by AS‐PCR and CALR mutations were detected by PCR/direct sequencing. Clinical and hematological characteristics were also analyzed. Results Two hundred and fifty ET patients were enrolled in this study. JAK2V617F mutation was found in 166/250 (66.4%) of patients, whereas CALR mutations were detected in 27/84 (32.1%) patients without JAK2V617F. Compared with JAK2V617F‐positive patients, those with CALR mutations showed lower hemoglobin level and lower leucocytes count (p = 0.007 and p = 0.004,respectively). CALR type 2 was the most frequent mutation of CALR detected in 55.55% of CALR mutated. Six of seven patients with thrombotic events harbored JAK2V617F mutation. Conclusion The prevalence of driver mutations JAK2V617F or CALR mutations was 77.2% in Tunisian ET patients. Moreover, patients with JAK2 V617F mutation had a higher risk of thrombosis. The mutational status is necessary to improve the diagnosis and contribute to the therapeutic decisions.
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Affiliation(s)
- Maroua Abdelghani
- LR16IPT07, Molecular and Cellular Hematology Laboratory, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia.,Faculty of Mathematics, Physics and Natural Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Haifa Hammami
- LR16IPT07, Molecular and Cellular Hematology Laboratory, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia.,Faculty of Mathematics, Physics and Natural Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Wiem Zidi
- Laboratory of Biochemistry, Rabta Hospital, Tunis, Tunisia
| | - Hassiba Amouri
- LR16IPT07, Molecular and Cellular Hematology Laboratory, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hind Ben Hadj Othmen
- LR16IPT07, Molecular and Cellular Hematology Laboratory, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ahlem Farrah
- LR16IPT07, Molecular and Cellular Hematology Laboratory, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samia Menif
- LR16IPT07, Molecular and Cellular Hematology Laboratory, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
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29
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Sukhanova M, Obeidin F, Streich L, Alexiev BA. Inflammatory leiomyosarcoma/rhabdomyoblastic tumor: a report of two cases with novel genetic findings. Genes Chromosomes Cancer 2022; 61:653-661. [PMID: 35655404 PMCID: PMC9545443 DOI: 10.1002/gcc.23072] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 12/01/2022] Open
Abstract
Inflammatory leiomyosarcoma (ILMS) is a malignant neoplasm showing smooth muscle differentiation, a prominent inflammatory infiltrate, and near‐haploidization. These tumors have significant pathologic and genetic overlap with the recently described “inflammatory rhabdomyoblastic tumor (IRT),” suggesting that ILMS and IRT may belong to one entity. Herein, we describe two cases of ILMS/IRT with attention to new cytogenetic and sequencing findings. The tumors were composed of sheets and fascicles of variably pleomorphic tumor cells showing spindled and epithelioid to rhabdoid morphology and a prominent histiocyte‐rich inflammatory infiltrate typical of ILMS/IRT. In case 1, chromosomal microarray analysis showed a near‐haploid pattern with loss of heterozygosity resulting from loss of one copy of all autosomes except for chromosomes 5, 20, 21, and 22. Case 2 showed areas with high‐grade rhabdomyosarcomatous transformation. In this case, the low‐grade tumor component revealed a hyper‐diploid pattern with loss of heterozygosity for most of autosomes but with a normal diploid copy number state except for chromosomes 5, 20, and 22, which showed a relative gain. The high‐grade tumor component showed a similar pattern of copy‐neutral loss of heterozygosity with additional abnormalities, including mosaic segmental gains at 1p, 5p, 8q, 9p, 20q, and segmental loss at 8p. Next‐generation sequencing identified sequence variants in NF1, TP53, SMARCA4, KRAS, and MSH6. MSH6 variant was confirmed as germline, consistent with the diagnosis of hereditary nonpolyposis colorectal cancer (HNPCC) syndrome in one of our study patients and suggestive that ILMS/IRT might be part of the HNPCC cancer spectrum.
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Affiliation(s)
- Madina Sukhanova
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, 251 East Huron St, Chicago, Illinois, United States
| | - Farres Obeidin
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, 251 East Huron St, Chicago, Illinois, United States
| | - Lukas Streich
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, 251 East Huron St, Chicago, Illinois, United States
| | - Borislav A Alexiev
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, 251 East Huron St, Chicago, Illinois, United States
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30
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Mo X, Niu Q, Ivanov AA, Tsang YH, Tang C, Shu C, Li Q, Qian K, Wahafu A, Doyle SP, Cicka D, Yang X, Fan D, Reyna MA, Cooper LAD, Moreno CS, Zhou W, Owonikoko TK, Lonial S, Khuri FR, Du Y, Ramalingam SS, Mills GB, Fu H. Systematic discovery of mutation-directed neo-protein-protein interactions in cancer. Cell 2022; 185:1974-1985.e12. [PMID: 35512704 DOI: 10.1016/j.cell.2022.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/27/2022] [Accepted: 04/08/2022] [Indexed: 12/12/2022]
Abstract
Comprehensive sequencing of patient tumors reveals genomic mutations across tumor types that enable tumorigenesis and progression. A subset of oncogenic driver mutations results in neomorphic activity where the mutant protein mediates functions not engaged by the parental molecule. Here, we identify prevalent variant-enabled neomorph-protein-protein interactions (neoPPI) with a quantitative high-throughput differential screening (qHT-dS) platform. The coupling of highly sensitive BRET biosensors with miniaturized coexpression in an ultra-HTS format allows large-scale monitoring of the interactions of wild-type and mutant variant counterparts with a library of cancer-associated proteins in live cells. The screening of 17,792 interactions with 2,172,864 data points revealed a landscape of gain of interactions encompassing both oncogenic and tumor suppressor mutations. For example, the recurrent BRAF V600E lesion mediates KEAP1 neoPPI, rewiring a BRAFV600E/KEAP1 signaling axis and creating collateral vulnerability to NQO1 substrates, offering a combination therapeutic strategy. Thus, cancer genomic alterations can create neo-interactions, informing variant-directed therapeutic approaches for precision medicine.
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Affiliation(s)
- Xiulei Mo
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Qiankun Niu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrey A Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Yiu Huen Tsang
- Division of Oncologic Science, Oregon Health Sciences University School of Medicine, Portland, OR 97239, USA
| | - Cong Tang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Urology, The First Affiliated Hospital, Medical School of Xi'An Jiaotong University, Xi'an, Shannxi 710061, PRC
| | - Changfa Shu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Gynecology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, PRC
| | - Qianjin Li
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kun Qian
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alafate Wahafu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurosurgery, the First Affiliated Hospital of Xi'An Jiaotong University, Xi'an, PRC
| | - Sean P Doyle
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Danielle Cicka
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xuan Yang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dacheng Fan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Matthew A Reyna
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lee A D Cooper
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Carlos S Moreno
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA; Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Wei Zhou
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Taofeek K Owonikoko
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Fadlo R Khuri
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA; Department of Internal Medicine, Division of Hematology and Oncology, American University of Beirut, Beirut, 1107-2020, Lebanon
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | | | - Gordon B Mills
- Division of Oncologic Science, Oregon Health Sciences University School of Medicine, Portland, OR 97239, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA.
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31
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Petrov I, Alexeyenko A. Individualized discovery of rare cancer drivers in global network context. eLife 2022; 11:74010. [PMID: 35593700 PMCID: PMC9159755 DOI: 10.7554/elife.74010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
Late advances in genome sequencing expanded the space of known cancer driver genes several-fold. However, most of this surge was based on computational analysis of somatic mutation frequencies and/or their impact on the protein function. On the contrary, experimental research necessarily accounted for functional context of mutations interacting with other genes and conferring cancer phenotypes. Eventually, just such results become ‘hard currency’ of cancer biology. The new method, NEAdriver employs knowledge accumulated thus far in the form of global interaction network and functionally annotated pathways in order to recover known and predict novel driver genes. The driver discovery was individualized by accounting for mutations’ co-occurrence in each tumour genome – as an alternative to summarizing information over the whole cancer patient cohorts. For each somatic genome change, probabilistic estimates from two lanes of network analysis were combined into joint likelihoods of being a driver. Thus, ability to detect previously unnoticed candidate driver events emerged from combining individual genomic context with network perspective. The procedure was applied to 10 largest cancer cohorts followed by evaluating error rates against previous cancer gene sets. The discovered driver combinations were shown to be informative on cancer outcome. This revealed driver genes with individually sparse mutation patterns that would not be detectable by other computational methods and related to cancer biology domains poorly covered by previous analyses. In particular, recurrent mutations of collagen, laminin, and integrin genes were observed in the adenocarcinoma and glioblastoma cancers. Considering constellation patterns of candidate drivers in individual cancer genomes opens a novel avenue for personalized cancer medicine.
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Affiliation(s)
- Iurii Petrov
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Solna, Sweden
| | - Andrey Alexeyenko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Solna, Sweden.,Evi-networks, enskild konsultföretag, Huddinge, Sweden
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32
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Andrades R, Recamonde-Mendoza M. Machine learning methods for prediction of cancer driver genes: a survey paper. Brief Bioinform 2022; 23:6551145. [PMID: 35323900 DOI: 10.1093/bib/bbac062] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/21/2022] Open
Abstract
Identifying the genes and mutations that drive the emergence of tumors is a critical step to improving our understanding of cancer and identifying new directions for disease diagnosis and treatment. Despite the large volume of genomics data, the precise detection of driver mutations and their carrying genes, known as cancer driver genes, from the millions of possible somatic mutations remains a challenge. Computational methods play an increasingly important role in discovering genomic patterns associated with cancer drivers and developing predictive models to identify these elements. Machine learning (ML), including deep learning, has been the engine behind many of these efforts and provides excellent opportunities for tackling remaining gaps in the field. Thus, this survey aims to perform a comprehensive analysis of ML-based computational approaches to identify cancer driver mutations and genes, providing an integrated, panoramic view of the broad data and algorithmic landscape within this scientific problem. We discuss how the interactions among data types and ML algorithms have been explored in previous solutions and outline current analytical limitations that deserve further attention from the scientific community. We hope that by helping readers become more familiar with significant developments in the field brought by ML, we may inspire new researchers to address open problems and advance our knowledge towards cancer driver discovery.
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Affiliation(s)
- Renan Andrades
- Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre/RS, Brazil.,Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre/RS, Brazil
| | - Mariana Recamonde-Mendoza
- Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre/RS, Brazil.,Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre/RS, Brazil
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Abstract
Contrary to earlier beliefs, every cell in the individual is genetically different due to somatic mutations. Consequently, tissues become a mixture of cells with distinct genomes, a phenomenon termed somatic mosaicism. Recent advances in genome sequencing technology have unveiled possible causes of mutations and how they shape the unique mutational landscape of the tissues. Moreover, the analysis of sequencing data in combination with clinical information has revealed the impacts of somatic mosaicism on disease processes. In this review, we discuss somatic mosaicism in various tissues and its clinical implications for human disease.
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Affiliation(s)
- Hayato Ogawa
- Department of Cardiology, Meijo Hospital, Nagoya, Japan
- Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keita Horitani
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Medicine II, Kansai Medical University, Hirakata, Japan
| | - Yasuhiro Izumiya
- Department of Cardiovascular Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan;
| | - Soichi Sano
- Department of Cardiovascular Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan;
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34
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Li P, Yang R, Wang D, Wang L, Wang S, Liu C, Li J, Li L, Liu C, Tong Y, Wang Y. Clinical and genetic characteristics of early-stage multiple primary and independent primary lung adenocarcinoma patients. Asia Pac J Clin Oncol 2022; 18:e420-e426. [PMID: 35098658 DOI: 10.1111/ajco.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/07/2021] [Indexed: 11/28/2022]
Abstract
AIMS The difference between multiple primary lung cancers (MPLC) and intrapulmonary metastasis (IM) in patients with lung cancer is vital but controversial. Moreover, the genetic and clinical significance difference between MPLC and independent primary lung cancers (IPLC) patients is unknown. METHODS This study retrospectively researched clinical and genetic data of MPLC and IPLC patients from January 2019 to May 2021 at the affiliated hospital of Qingdao University, China. Ninety-four tissue samples from 41 early-stage patients with MPLC, and 94 tissue samples from 94 early-stage patients with IPLC were performed to targeted sequencing. RESULTS A total of 36 patients (88%) showed inconsistent driver mutations, and five MPLC patients (12%) shared single identical EGFR/BRAF/TP53 hotspot mutations in the early stage. In MPLC patients, high-frequency mutations included EGFR (63%), TP53 (12%), BRAF (12%), KRAS (10%), ERBB2 (4%), PIK3CA (3%), and MET (3%). In IPLC patients, high-frequency mutations included EGFR (55%), TP53(26%), KRAS (13%), MAP2K1 (5%), PIK3CA (4%), ERBB2 (4%), NF1 (4%), RET (3%), and BRAF (2%). The higher BRAF and fewer TP53 mutations may be related to the lower malignancy in MPLC patients. CONCLUSIONS The accuracy of pathological diagnosis in patients with early-stage MPLC does not need comprehensive molecular evaluation to supplement histology for differentiating early-stage MPLC and IM. Meanwhile, the molecular difference between MPLC and IPLC may be helpful to study the mechanism of MPLC pathogenesis.
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Affiliation(s)
- Peng Li
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ronghua Yang
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Dong Wang
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lingjie Wang
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Sai Wang
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Chuan Liu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Jinlong Li
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Ling Li
- Yinfeng Gene Technology Co., Ltd., Jinan, China
| | - Chuang Liu
- Yinfeng Gene Technology Co., Ltd., Jinan, China
| | - Yan Tong
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Yongjie Wang
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
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35
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Harada D, Takigawa N. Oligoprogression in Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:5823. [PMID: 34830977 DOI: 10.3390/cancers13225823] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Several retrospective studies present evidence of oligoprogressive disease (OPD) in patients with non-small cell lung cancer (NSCLC) with driver mutations such as EGFR. The strategy of local ablative therapy (LAT) with radiotherapy, followed by the continuation of the same anticancer drug therapy beyond progression disease, is recommended in the current NCCN guideline. Although evidence of the use of this strategy in the treatment of the driver mutation-negative NSCLC is missing, LAT with radiotherapy for OPD after combination therapy of immune checkpoint inhibitor with cytotoxic chemotherapy is expected. Tumors outside of the radiation field may further respond to the immune checkpoint inhibitors due to an abscopal effect. In the future, to achieve long-term survival in advanced NSCLC, it will be important to validate this treatment strategy via prospective comparative studies and to actively implement it in clinical practice. Abstract We reviewed the literature on oligoprogressive disease (OPD) and local ablative therapy (LAT) in patients with advanced non-small cell lung cancer (NSCLC). The frequency of OPD varies depending on its definition and is estimated to be between 15–47%. The implications of the strategy of continuing the same anticancer agents beyond progressive disease after LAT with radiation therapy for OPD are based on the concept of progression in which only a small number of lesions, not more than about four, proliferate after chemotherapy. In the case of OPD harboring driver mutations such as EGFR, prospective studies are underway. However, evidence from retrospective studies support this strategy, which is currently recommended in some guidelines. The prognosis in OPD cases during the administration of an immune checkpoint inhibitor (ICI) is relatively promising. Additionally, LAT with radiation for OPD after the first-line treatment of ICI with cytotoxic chemotherapy may overcome the resistance to the combination drug therapy due to an abscopal effect. To achieve long-term survival in advanced-stage NSCLC, it is important to verify the optimal method and timing of the therapy through prospective comparative studies as well as patient selection based on patient characteristics and biomarker levels.
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Nussinov R, Zhang M, Maloney R, Tsai CJ, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2021; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey.,Department of Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey.,Koc University Research Center for Translational Medicine, School of Medicine, Koc University, Istanbul, Turkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
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37
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Richardson RB, Anghel CV, Deng DS. Profound synchrony of age-specific incidence rates and tumor suppression for different cancer types as revealed by the multistage-senescence model of carcinogenesis. Aging (Albany NY) 2021; 13:23545-23578. [PMID: 34695806 PMCID: PMC8580351 DOI: 10.18632/aging.203651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/07/2021] [Indexed: 12/27/2022]
Abstract
The age-specific trend of cancer incidence rates, but not its magnitude, is well described employing the multistage theory of carcinogenesis by Armitage and Doll in combination with the senescence model of Pompei and Wilson. We derived empirical parameters of the multistage-senescence model from U.S. Surveillance, Epidemiology, and End Results (SEER) incidence data from 2000–2003 and 2010–2013 for The Cancer Genome Atlas (TCGA) cancer types. Under the assumption of a constant tumor-specific transition rate between stages, there is an extremely strong linear relationship (P < 0.0001) between the number of stages and the stage transition rate. The senescence tumor suppression factor for 20 non-reproductive cancers is remarkably consistent (0.0099±0.0005); however, five female reproductive cancers have significantly higher tumor suppression. The peak incidence rate for non-reproductive cancers occurs at a younger age for cancers with fewer stages and their carcinogenic stages are of longer duration. Driver gene mutations are shown to contribute on average only about a third of the carcinogenic stages of different tumor types. A tumor’s accumulated incidence, calculated using a two-variable (age, stage) model, is strongly associated with intrinsic cancer risk. During both early adulthood and senescence, the pace of tumor suppression appears to be synchronized across most cancer types, suggesting the presence of overlapping evolutionary processes.
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Affiliation(s)
- Richard B Richardson
- Radiobiology and Health Branch, Canadian Nuclear Laboratories (CNL), Chalk River Laboratories, Chalk River, ON K0J 1J0, Canada.,Medical Physics Unit, Cedars Cancer Centre, McGill University Health Centre - Glen Site, Montreal, QC H4A 3J1, Canada
| | - Catalina V Anghel
- Computational Techniques Branch, Canadian Nuclear Laboratories (CNL), Chalk River Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Dennis S Deng
- Computational Techniques Branch, Canadian Nuclear Laboratories (CNL), Chalk River Laboratories, Chalk River, ON K0J 1J0, Canada
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38
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Smit W, Heijmans J. The concerted action of oncogenic driver mutations directs global translation in intestinal epithelial cells. Mol Cell Oncol 2021; 8:1879614. [PMID: 34616863 DOI: 10.1080/23723556.2021.1879614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Oncogenic transformation of colorectal cancer cells is driven by a set of mutations that cause aberrant signaling of growth factor-receptor pathways. Using organoids, we demonstrate that the most frequent driver mutations in APC, KRAS, SMAD4, and TP53 are enhancers of the global mRNA translational capacity, which is linked to intestinal cell growth in an mTOR-dependent manner.
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Affiliation(s)
- Wouter Smit
- Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jarom Heijmans
- Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Internal Medicine and Hematology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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39
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Flores SK, Estrada-Zuniga CM, Thallapureddy K, Armaiz-Peña G, Dahia PLM. Insights into Mechanisms of Pheochromocytomas and Paragangliomas Driven by Known or New Genetic Drivers. Cancers (Basel) 2021; 13:cancers13184602. [PMID: 34572828 PMCID: PMC8467373 DOI: 10.3390/cancers13184602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/12/2021] [Accepted: 09/12/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Pheochromocytomas and paragangliomas are rare neuroendocrine tumors that are often hereditary. Although research has advanced considerably, significant gaps still persist in understanding risk factors, predicting metastatic potential and treating aggressive tumors. The study of rare mutations can provide new insights into how pheochromocytomas and paragangliomas develop. In this review, we provide examples of such rare events and how they can inform our understanding of the spectrum of mutations that can lead to these tumors and improve our ability to provide a genetic diagnosis. Abstract Pheochromocytomas and paragangliomas are rare tumors of neural crest origin. Their remarkable genetic diversity and high heritability have enabled discoveries of bona fide cancer driver genes with an impact on diagnosis and clinical management and have consistently shed light on new paradigms in cancer. In this review, we explore unique mechanisms of pheochromocytoma and paraganglioma initiation and management by drawing from recent examples involving rare mutations of hypoxia-related genes VHL, EPAS1 and SDHB, and of a poorly known susceptibility gene, TMEM127. These models expand our ability to predict variant pathogenicity, inform new functional domains, recognize environmental-gene connections, and highlight persistent therapeutic challenges for tumors with aggressive behavior.
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Affiliation(s)
- Shahida K. Flores
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (S.K.F.); (C.M.E.-Z.); (K.T.); (G.A.-P.)
| | - Cynthia M. Estrada-Zuniga
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (S.K.F.); (C.M.E.-Z.); (K.T.); (G.A.-P.)
| | - Keerthi Thallapureddy
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (S.K.F.); (C.M.E.-Z.); (K.T.); (G.A.-P.)
| | - Gustavo Armaiz-Peña
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (S.K.F.); (C.M.E.-Z.); (K.T.); (G.A.-P.)
| | - Patricia L. M. Dahia
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (S.K.F.); (C.M.E.-Z.); (K.T.); (G.A.-P.)
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Correspondence:
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Patil K, Jordan EJ, Park JH, Suresh K, Smith CM, Lemmon AA, Mossé YP, Lemmon MA, Radhakrishnan R. Computational studies of anaplastic lymphoma kinase mutations reveal common mechanisms of oncogenic activation. Proc Natl Acad Sci U S A 2021; 118:e2019132118. [PMID: 33674381 DOI: 10.1073/pnas.2019132118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
High-risk tumors are genomically heterogeneous, harboring gene amplifications and mutations. The activation status of mutated proteins in cancer can profoundly impact disease progression, patient response, and drug sensitivity. Yet, outside of a few hotspot mutations, functional studies of clinically observed mutations are not commonly pursued. We report a combined experimental profiling and computational analysis of the effects of clinically observed and “test” mutations in the kinase domain of anaplastic lymphoma kinase (ALK), a known oncogenic driver in pediatric neuroblastoma. We find that the activation status of the mutated protein is a good indicator of the transforming ability in NIH 3T3 cells. We also report biophysical as well as data-driven models with predictive power to profile these mutant kinases in silico. Kinases play important roles in diverse cellular processes, including signaling, differentiation, proliferation, and metabolism. They are frequently mutated in cancer and are the targets of a large number of specific inhibitors. Surveys of cancer genome atlases reveal that kinase domains, which consist of 300 amino acids, can harbor numerous (150 to 200) single-point mutations across different patients in the same disease. This preponderance of mutations—some activating, some silent—in a known target protein make clinical decisions for enrolling patients in drug trials challenging since the relevance of the target and its drug sensitivity often depend on the mutational status in a given patient. We show through computational studies using molecular dynamics (MD) as well as enhanced sampling simulations that the experimentally determined activation status of a mutated kinase can be predicted effectively by identifying a hydrogen bonding fingerprint in the activation loop and the αC-helix regions, despite the fact that mutations in cancer patients occur throughout the kinase domain. In our study, we find that the predictive power of MD is superior to a purely data-driven machine learning model involving biochemical features that we implemented, even though MD utilized far fewer features (in fact, just one) in an unsupervised setting. Moreover, the MD results provide key insights into convergent mechanisms of activation, primarily involving differential stabilization of a hydrogen bond network that engages residues of the activation loop and αC-helix in the active-like conformation (in >70% of the mutations studied, regardless of the location of the mutation).
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Kan Y, Jiang L, Tang J, Guo Y, Guo F. A systematic view of computational methods for identifying driver genes based on somatic mutation data. Brief Funct Genomics 2021; 20:333-343. [PMID: 34312663 DOI: 10.1093/bfgp/elab032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 11/13/2022] Open
Abstract
Abnormal changes of driver genes are serious for human health and biomedical research. Identifying driver genes, exactly from enormous genes with mutations, promotes accurate diagnosis and treatment of cancer. A lot of works about uncovering driver genes have been developed over the past decades. By analyzing previous works, we find that computational methods are more efficient than traditional biological experiments when distinguishing driver genes from massive data. In this study, we summarize eight common computational algorithms only using somatic mutation data. We first group these methods into three categories according to mutation features they apply. Then, we conclude a general process of nominating candidate cancer driver genes. Finally, we evaluate three representative methods on 10 kinds of cancer derived from The Cancer Genome Atlas Program and five Chinese projects from the International Cancer Genome Consortium. In addition, we compare results of methods with various parameters. Evaluation is performed from four perspectives, including CGC, OG/TSG, Q-value and QQQuantile-Quantileplot. To sum up, we present algorithms using somatic mutation data in order to offer a systematic view of various mutation features and lay the foundation of methods based on integration of mutation information and other types of data.
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Affiliation(s)
- Yingxin Kan
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Limin Jiang
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jijun Tang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,School of Computational Science and Engineering, University of South Carolina, Columbia, U.S
| | - Yan Guo
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, U.S
| | - Fei Guo
- School of Computer Science and Engineering, Central South University, Changsha, China
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Gu Y, Ji Y, Jiang H, Qiu G. Clinical Effect of Driver Mutations of KRAS, CDKN2A/P16, TP53, and SMAD4 in Pancreatic Cancer: A Meta-Analysis. Genet Test Mol Biomarkers 2021; 24:777-788. [PMID: 33347393 DOI: 10.1089/gtmb.2020.0078] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Objective: To evaluate the prognostic value of driver mutations in the KRAS, CDKN2A/P16, TP53, and SMAD4 genes in pancreatic cancer to aid in the design of therapeutic strategies. Search Strategy: A systematic search was conducted using PubMed, MEDLINE, Springer, and Cochrane library to identify eligible studies published between January 1990 and June 2018 that reported an association between driver mutations in these genes and survival data. Inclusion Criteria: Articles which passed the primary screen were further scrutinized for the presence of all the following items: (1) cohort studies or case-control studies, evaluating the relationship between driver mutations and cancer; (2) cancer diagnoses clearly proved; and (3) hazard ratios (HR) and 95% confidence intervals (CIs) were characterized by sufficient information. Data Extraction and Analysis: Selection of included articles, data extraction, and methodological quality assessments were, respectively, conducted by two authors. Results: The meta-analysis was composed of 17 studies on the P53, 8 on SMAD4, 7 on CDKN2A/P16, and 2 on KRAS, containing 3373 samples. Our pooled results demonstrated that the patients with overexpression of the P53 (HR = 1.249, 95% CI = 1.003-1.554, p = 0.047), SMAD4 (HR = 1.397, 95% CI = 1.015-1.922, p = 0.040), CDKN2A/P16 (HR = 0.916, 95% CI = 0.583-1.439, p = 0.704), and KRAS (HR = 1.68, 95% CI = 1.27-2.22, p < 0.001) mutations all had poorer overall survival. Conclusion: This systematic review and meta-analysis supports the use of driver mutations in the P53, SMAD4, and KRAS genes as prognostic markers for pancreatic cancer.
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Affiliation(s)
- Yujun Gu
- Department of Ultrasound Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou City, China
| | - Yayun Ji
- Department of Interventional Ultrasound, Xianyang Central Hospital, Xianyang City, China
| | - Hui Jiang
- Medical Imaging Department, Zhaoqing Medical College, Zhaoqing City, China
| | - Ganbin Qiu
- Medical Imaging Department, Zhaoqing Medical College, Zhaoqing City, China
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Betancourt LH, Gil J, Sanchez A, Doma V, Kuras M, Murillo JR, Velasquez E, Çakır U, Kim Y, Sugihara Y, Parada IP, Szeitz B, Appelqvist R, Wieslander E, Welinder C, de Almeida NP, Woldmar N, Marko‐Varga M, Eriksson J, Pawłowski K, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Lindberg H, Oskolas H, Lee B, Berge E, Sjögren M, Eriksson C, Kim D, Kwon HJ, Knudsen B, Rezeli M, Malm J, Hong R, Horvath P, Szász AM, Tímár J, Kárpáti S, Horvatovich P, Miliotis T, Nishimura T, Kato H, Steinfelder E, Oppermann M, Miller K, Florindi F, Zhou Q, Domont GB, Pizzatti L, Nogueira FCS, Szadai L, Németh IB, Ekedahl H, Fenyö D, Marko‐Varga G. The Human Melanoma Proteome Atlas-Complementing the melanoma transcriptome. Clin Transl Med 2021; 11:e451. [PMID: 34323402 PMCID: PMC8299047 DOI: 10.1002/ctm2.451] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/12/2022] Open
Abstract
The MM500 meta-study aims to establish a knowledge basis of the tumor proteome to serve as a complement to genome and transcriptome studies. Somatic mutations and their effect on the transcriptome have been extensively characterized in melanoma. However, the effects of these genetic changes on the proteomic landscape and the impact on cellular processes in melanoma remain poorly understood. In this study, the quantitative mass-spectrometry-based proteomic analysis is interfaced with pathological tumor characterization, and associated with clinical data. The melanoma proteome landscape, obtained by the analysis of 505 well-annotated melanoma tumor samples, is defined based on almost 16 000 proteins, including mutated proteoforms of driver genes. More than 50 million MS/MS spectra were analyzed, resulting in approximately 13,6 million peptide spectrum matches (PSMs). Altogether 13 176 protein-coding genes, represented by 366 172 peptides, in addition to 52 000 phosphorylation sites, and 4 400 acetylation sites were successfully annotated. This data covers 65% and 74% of the predicted and identified human proteome, respectively. A high degree of correlation (Pearson, up to 0.54) with the melanoma transcriptome of the TCGA repository, with an overlap of 12 751 gene products, was found. Mapping of the expressed proteins with quantitation, spatiotemporal localization, mutations, splice isoforms, and PTM variants was proven not to be predicted by genome sequencing alone. The melanoma tumor molecular map was complemented by analysis of blood protein expression, including data on proteins regulated after immunotherapy. By adding these key proteomic pillars, the MM500 study expands the knowledge on melanoma disease.
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Abstract
BACKGROUND Predictive testing is a crucial part of the complete diagnostic process of non-small cell lung cancer (NSCLC) and a necessary requirement in order to determine proper course of treatment. However, the possibilities of testing and the spectrum of examined markers are quickly evolving as a result of the progress in diagnostic and therapeutic possibilities, and as such it is necessary to regularly update the current guidelines to achieve proper standards of care in routine practice. PURPOSE To provide a complex overview of the current problematics of predictive testing in NSCLC at a molecular level, considering also the evaluation of PD-L1 expression based on the international and national guidelines. To summarize the current state of predictive testing employed in NSCLC in the Czech Republic. CONCLUSION Predictive testing in NSCLC is a part of routine diagnostic practice; however, as a result of the expanding spectrum of diagnostic and therapeutic possibilities, it is undergoing significant development. The existing method of the sequential testing of individual markers is becoming unsuitable; given the increasing number of potential predictors and complex molecular testing, the use of new generation sequencing appears to represent a more suitable solution. The immunohistochemical evaluation of PD-L1 expression is also a necessary part of predictive testing in NSCLC.
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Abstract
AREAS COVERED This review provides an overview regarding the current scenario and knowledge of the CCA genomic landscape and the potentially actionable molecular aberrations in each CCA subtype. EXPERT OPINION The establishment and advances of high-throughput methodologies applied to genetic and epigenetic profiling are changing many cancer types' therapeutic landscape , including CCA.The large body of data generated must be interpreted appropriately and eventually implemented in clinical practice. The following advancements toward precision medicine in CCA management will require designing better clinical trials with improved methods to stratify biliary tumor patients.
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Affiliation(s)
- Antonio Cigliano
- Department of Medical, Surgery and Experimental Sciences, Division of Experimental Pathology and Oncology, University of Sassari, Italy
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California, USA
| | - Diego F. Calvisi
- Institute of Pathology, University of Regensburg, Regensburg, Germany
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Roy U, Raghavan SC. Deleterious point mutations in T-cell acute lymphoblastic leukemia: Mechanistic insights into leukemogenesis. Int J Cancer 2021; 149:1210-1220. [PMID: 33634864 DOI: 10.1002/ijc.33527] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/11/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is characterized by the leukemogenic transformation of immature T cells, which accumulate an array of genetic and epigenetic lesions, leading to a sustained proliferation of abnormal T cells. Genetic alterations in the DNA repair genes, protooncogenes, transcription factors, and epigenetic modifiers have been studied in the past decade using next-generation sequencing and high-resolution copy number arrays. While other genomic lesions like chromosomal rearrangements, inversions, insertions, and gene fusions have been well studied at functional level, the mechanism of generation of driver mutations in T-ALL is the subject of current investigation. Novel oncogenic mutations in the TP53, BRCA2, PTEN, IL7R, RAS, NOTCH1, ETV6, BCL11B, WT1, DNMT3A, PRC2, PHF6, USP7, KDM6A and an array of other genes disrupt the genetic and epigenetic homeostasis in T-ALL. In this review, we have summarized the mechanistic role of deleterious driver mutations in T-ALL initiation and progression. We speculate that the formation of non-B DNA structures could be one of the primary reasons for the occurrence of different genomic lesions seen in T-ALL, which warrants further investigation. Understanding the mechanism behind the genesis of oncogenic mutations will pave the way to develop targeted therapies that can improve the overall survival and treatment outcome.
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Affiliation(s)
- Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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Salem D, Chelvanambi M, Storkus WJ, Fecek RJ. Cutaneous Melanoma: Mutational Status and Potential Links to Tertiary Lymphoid Structure Formation. Front Immunol 2021; 12:629519. [PMID: 33746966 PMCID: PMC7970117 DOI: 10.3389/fimmu.2021.629519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 02/11/2021] [Indexed: 12/21/2022] Open
Abstract
Recent advances in immunotherapy have enabled rapid evolution of novel interventional approaches designed to reinvigorate and expand patient immune responses against cancer. An emerging approach in cancer immunology involves the conditional induction of tertiary lymphoid structures (TLS), which are non-encapsulated ectopic lymphoid structures forming at sites of chronic, pathologic inflammation. Cutaneous melanoma (CM), a highly-immunogenic form of solid cancer, continues to rise in both incidence and mortality rate, with recent reports supporting a positive correlation between the presence of TLS in melanoma and beneficial treatment outcomes amongst advanced-stage patients. In this context, TLS in CM are postulated to serve as dynamic centers for the initiation of robust anti-tumor responses within affected regions of active disease. Given their potential importance to patient outcome, significant effort has been recently devoted to gaining a better understanding of TLS neogenesis and the influence these lymphoid organs exert within the tumor microenvironment. Here, we briefly review TLS structure, function, and response to treatment in the setting of CM. To uncover potential tumor-intrinsic mechanisms that regulate TLS formation, we have taken the novel perspective of evaluating TLS induction in melanomas impacted by common driver mutations in BRAF, PTEN, NRAS, KIT, PRDM1, and MITF. Through analysis of The Cancer Genome Atlas (TCGA), we show expression of DNA repair proteins (DRPs) including BRCA1, PAXIP, ERCC1, ERCC2, ERCC3, MSH2, and PMS2 to be negatively correlated with expression of pro-TLS genes, suggesting DRP loss may favor TLS development in support of improved patient outcome and patient response to interventional immunotherapy.
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Affiliation(s)
- Deepak Salem
- Department of Microbiology, Lake Erie College of Osteopathic Medicine at Seton Hill, Greensburg, PA, United States
| | - Manoj Chelvanambi
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Walter J Storkus
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Dermatology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Ronald J Fecek
- Department of Microbiology, Lake Erie College of Osteopathic Medicine at Seton Hill, Greensburg, PA, United States
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Abstract
The prognosis of patients with solid tumours has remarkably improved with the development of molecular-targeted drugs and immune checkpoint inhibitors. However, the improvements in the prognosis of pancreatic cancer and biliary tract cancer is delayed compared to other carcinomas, and the 5-year survival rates of distal-stage disease are approximately 10 and 20%, respectively. However, a comprehensive analysis of tumour cells using The Cancer Genome Atlas (TCGA) project has led to the identification of various driver mutations. Evidently, few mutations exist across organs, and basket trials targeting driver mutations regardless of the primary organ are being actively conducted. Such basket trials not only focus on the gate keeper-type oncogene mutations, such as HER2 and BRAF, but also focus on the caretaker-type tumour suppressor genes, such as BRCA1/2, mismatch repair-related genes, which cause hereditary cancer syndrome. As oncogene panel testing is a vital approach in routine practice, clinicians should devise a strategy for improved understanding of the cancer genome. Here, the gene mutation profiles of pancreatic cancer and biliary tract cancer have been outlined and the current status of tumour-agnostic therapy in these cancers has been reported.
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Affiliation(s)
- Shunsuke Kato
- Department of Clinical Oncology, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
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Yang X, Jiang L, Jin Y, Li P, Hou Y, Yun J, Wu C, Sun W, Fan X, Kuang D, Wang W, Ni J, Mao A, Tang W, Liu Z, Wang J, Xiao S, Li Y, Lin D. PD-L1 Expression in Chinese Patients with Advanced Non-Small Cell Lung Cancer (NSCLC): A Multi-Center Retrospective Observational Study. J Cancer 2021; 12:7390-7398. [PMID: 35003359 PMCID: PMC8734414 DOI: 10.7150/jca.63003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/03/2021] [Indexed: 11/22/2022] Open
Abstract
Objective: This study aimed to investigate the prevalence of tumor programmed death-ligand 1 (PD-L1) expression in Chinese patients with advanced Non-Small Cell Lung Cancer (NSCLC). Methods: Tumor tissues with histologically confirmed stage IIIB/IV NSCLC were retrospectively obtained from 10 centers in China. PD-L1 expression was determined using the PD-L1 IHC 22C3 pharmDx kit (Agilent, Santa Clara, CA, USA) and the samples were repetitively assayed with the PD-L1 IHC 22C3 Ab concentrate (Agilent, Santa Clara, CA, USA). Results: Out of 901 patients who met the inclusion criteria, 879 (97.6%) had evaluable PD-L1 data. The number of patients with a PD-L1 tumor proportion score (TPS) < 1%, 1-49%, and ≥ 50% (corresponding to PD-L1 non-expression, low expression, and high expression) was 424 (48.2%), 266 (30.3%), and 189 (21.5%), respectively. PD-L1 expression was more likely to be found in patients younger than 75 years, men, current or former smokers, those with good performance status (PS) scores, and those with a wild-type epidermal growth factor receptor (EGFR). PD-L1 TPS ≥ 50% and ≥ 1% were respectively 28.0% and 50.2% among patients negative for both EGFR mutation and anaplastic lymphoma kinase (ALK) rearrangement. PD-L1 expression determined using the 22C3 antibody concentrate and pharmDx kit had comparable results. Conclusions: The prevalence of PD‑L1 expression in advanced NSCLC was consistent with that reported in the global EXPRESS study. Age, gender, smoking history, PS scores, and EGFR/ALK mutation status affected PD-L1 expression. The 22C3 antibody concentrate appears to be an alternative reagent for the PD-L1 assay.
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Affiliation(s)
- Xin Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lili Jiang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yan Jin
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Peng Li
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yingyong Hou
- Zhongshan Hospital of Fudan University, Shanghai, China
| | - Jingping Yun
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenyong Sun
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Xiangshan Fan
- Nanjing Drum Tower Hospital, Nanjing, Jiangsu, China
| | - Dong Kuang
- Department of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Weiya Wang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jinsong Ni
- The first hospital of Jilin University - The Eastern Division, Changchun, Jilin, China
| | - Anhua Mao
- Medical Affairs Department, MSD China, Shanghai, China
| | - Wenmin Tang
- Medical Affairs Department, MSD China, Shanghai, China
| | - Zhenhua Liu
- Medical Affairs Department, MSD China, Shanghai, China
| | - Jiali Wang
- Medical Affairs Department, MSD China, Shanghai, China
| | - Suijun Xiao
- Medical Affairs Department, MSD China, Shanghai, China
| | - Yuan Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- ✉ Corresponding authors: Prof. Dongmei Lin, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China; Prof. Yuan Li, Fudan University Cancer Hospital. 270 Dongan Road, Xuhui District, Shanghai, China;
| | - Dongmei Lin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
- ✉ Corresponding authors: Prof. Dongmei Lin, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China; Prof. Yuan Li, Fudan University Cancer Hospital. 270 Dongan Road, Xuhui District, Shanghai, China;
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Abstract
The management of advanced nonsmall cell lung cancer (NSCLC) patients is becoming increasingly complex with the identification of driver mutations/rearrangements and development/availability of appropriate targeted therapies. In 2017, an expert group of medical oncologists with expertise in treating lung cancer used data from published literature and experience to arrive at practical consensus recommendations on treatment of advanced NSCLC for use by the community oncologists. This was published subsequently in the Indian Journal of Cancer with a plan to be updated annually. The present document is an update to the 2017 document.
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Affiliation(s)
- Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
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