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de Lima MC, de Castro CC, Aguiar KEC, Monte N, da Costa Nunes GG, da Costa ACA, Rodrigues JCG, Guerreiro JF, Ribeiro-dos-Santos Â, de Assumpção PP, Burbano RMR, Fernandes MR, dos Santos SEB, dos Santos NPC. Molecular Profile of Important Genes for Radiogenomics in the Amazon Indigenous Population. J Pers Med 2024; 14:484. [PMID: 38793065 PMCID: PMC11122349 DOI: 10.3390/jpm14050484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/13/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Radiotherapy is focused on the tumor but also reaches healthy tissues, causing toxicities that are possibly related to genomic factors. In this context, radiogenomics can help reduce the toxicity, increase the effectiveness of radiotherapy, and personalize treatment. It is important to consider the genomic profiles of populations not yet studied in radiogenomics, such as the indigenous Amazonian population. Thus, our objective was to analyze important genes for radiogenomics, such as ATM, TGFB1, RAD51, AREG, XRCC4, CDK1, MEG3, PRKCE, TANC1, and KDR, in indigenous people and draw a radiogenomic profile of this population. The NextSeq 500® platform was used for sequencing reactions; for differences in the allelic frequency between populations, Fisher's Exact Test was used. We identified 39 variants, 2 of which were high impact: 1 in KDR (rs41452948) and another in XRCC4 (rs1805377). We found four modifying variants not yet described in the literature in PRKCE. We did not find any variants in TANC1-an important gene for personalized medicine in radiotherapy-that were associated with toxicities in previous cohorts, configuring a protective factor for indigenous people. We identified four SNVs (rs664143, rs1801516, rs1870377, rs1800470) that were associated with toxicity in previous studies. Knowing the radiogenomic profile of indigenous people can help personalize their radiotherapy.
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Affiliation(s)
- Milena Cardoso de Lima
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
| | - Cinthia Costa de Castro
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
| | - Kaio Evandro Cardoso Aguiar
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
| | - Natasha Monte
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
| | - Giovanna Gilioli da Costa Nunes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
| | - Ana Caroline Alves da Costa
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
| | - Juliana Carla Gomes Rodrigues
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
| | - João Farias Guerreiro
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém 66075-110, PA, Brazil;
| | | | - Paulo Pimentel de Assumpção
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
| | - Rommel Mario Rodríguez Burbano
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
| | - Marianne Rodrigues Fernandes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
| | - Sidney Emanuel Batista dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém 66075-110, PA, Brazil;
| | - Ney Pereira Carneiro dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.C.d.L.); (C.C.d.C.); (K.E.C.A.); (N.M.); (G.G.d.C.N.); (A.C.A.d.C.); (J.C.G.R.); (J.F.G.); (P.P.d.A.); (R.M.R.B.); (M.R.F.)
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2
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Vannucchi M, Pennati V, Mencaroni C, Defraia C, Bardhi L, Castiglione F, Bellan C, Comin CE. KRAS Mutations Are Associated with Shortened Survival in Patients with Epithelioid Malignant Pleural Mesothelioma. Cancers (Basel) 2023; 15:cancers15072072. [PMID: 37046732 PMCID: PMC10093256 DOI: 10.3390/cancers15072072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive malignancy of the pleural surface that includes three major histologic subtypes, epitheliod, sarcomatoid and biphasic. Epithelioid mesothelioma is usually associated with better prognosis. The genetic mechanisms driving MPM, the possible target mutations and the correlation with overall survival remain largely unsettled. We performed target exome sequencing in 29 cases of MPM aimed at identifying somatic mutations and, eventually, their correlation with phenotypic traits and prognostic significance. We found that KRAS mutations, occurring in 13.7% of cases, were associated with shortened median survival (7.6 versus 32.6 months in KRAS wild-type; p = 0.005), as it was the occurrence of any ≥3 mutations (7.6 versus 37.6 months; p = 0.049). Conversely, the presence of KDR single nucleotide polymorphism p.V297I (rs2305948) resulted in a favorable variable for survival (NR versus 23.4 months; p = 0.026). With the intrinsic limitations of a small number of cases and patient heterogeneity, results of this study contribute to the characterization of the mutation profile of MPM and the impact of selected somatic mutations, and possibly KDR polymorphism, on prognosis.
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Affiliation(s)
- Margherita Vannucchi
- Section of Pathology, Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
- Correspondence:
| | - Veronica Pennati
- Division of Pathological anatomy, Department of Medical and Surgical Critical Care, University of Florence, 50121 Florence, Italy
| | - Clelia Mencaroni
- Division of Pathological anatomy, Department of Medical and Surgical Critical Care, University of Florence, 50121 Florence, Italy
| | - Chiara Defraia
- Section of Pathology, Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Ledi Bardhi
- Section of Pathology, Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Francesca Castiglione
- Division of Pathological anatomy, Department of Medical and Surgical Critical Care, University of Florence, 50121 Florence, Italy
| | - Cristiana Bellan
- Section of Pathology, Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Camilla Eva Comin
- Department of Experimental and Clinical Medicine, Section of Surgery, Histopathology and Molecular Pathology, University of Florence, 50121 Florence, Italy
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CD44, γ-H2AX, and p-ATM Expressions in Short-Term Ex Vivo Culture of Tumour Slices Predict the Treatment Response in Patients with Oral Squamous Cell Carcinoma. Int J Mol Sci 2022; 23:ijms23020877. [PMID: 35055060 PMCID: PMC8775909 DOI: 10.3390/ijms23020877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
Squamous cell carcinoma is the most common type of head and neck cancer (HNSCC) with a disease-free survival at 3 years that does not exceed 30%. Biomarkers able to predict clinical outcomes are clearly needed. The purpose of this study was to investigate whether a short-term culture of tumour fragments irradiated ex vivo could anticipate patient responses to chemo- and/or radiotherapies. Biopsies were collected prior to treatment from a cohort of 28 patients with non-operable tumours of the oral cavity or oropharynx, and then cultured ex vivo. Short-term biopsy slice culture is a robust method that keeps cells viable for 7 days. Different biomarkers involved in the stemness status (CD44) or the DNA damage response (pATM and γ-H2AX) were investigated for their potential to predict the treatment response. A higher expression of all these markers was predictive of a poor response to treatment. This allowed the stratification of responder or non-responder patients to treatment. Moreover, the ratio for the expression of the three markers 24 h after 4 Gy irradiation versus 0 Gy was higher in responder than in non-responder patients. Finally, combining these biomarkers greatly improved their predictive potential, especially when the γ-H2AX ratio was associated with the CD44 ratio or the pATM ratio. These results encourage further evaluation of these biomarkers in a larger cohort of patients.
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Volpe S, Pepa M, Zaffaroni M, Bellerba F, Santamaria R, Marvaso G, Isaksson LJ, Gandini S, Starzyńska A, Leonardi MC, Orecchia R, Alterio D, Jereczek-Fossa BA. Machine Learning for Head and Neck Cancer: A Safe Bet?-A Clinically Oriented Systematic Review for the Radiation Oncologist. Front Oncol 2021; 11:772663. [PMID: 34869010 PMCID: PMC8637856 DOI: 10.3389/fonc.2021.772663] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/25/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND PURPOSE Machine learning (ML) is emerging as a feasible approach to optimize patients' care path in Radiation Oncology. Applications include autosegmentation, treatment planning optimization, and prediction of oncological and toxicity outcomes. The purpose of this clinically oriented systematic review is to illustrate the potential and limitations of the most commonly used ML models in solving everyday clinical issues in head and neck cancer (HNC) radiotherapy (RT). MATERIALS AND METHODS Electronic databases were screened up to May 2021. Studies dealing with ML and radiomics were considered eligible. The quality of the included studies was rated by an adapted version of the qualitative checklist originally developed by Luo et al. All statistical analyses were performed using R version 3.6.1. RESULTS Forty-eight studies (21 on autosegmentation, four on treatment planning, 12 on oncological outcome prediction, 10 on toxicity prediction, and one on determinants of postoperative RT) were included in the analysis. The most common imaging modality was computed tomography (CT) (40%) followed by magnetic resonance (MR) (10%). Quantitative image features were considered in nine studies (19%). No significant differences were identified in global and methodological scores when works were stratified per their task (i.e., autosegmentation). DISCUSSION AND CONCLUSION The range of possible applications of ML in the field of HN Radiation Oncology is wide, albeit this area of research is relatively young. Overall, if not safe yet, ML is most probably a bet worth making.
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Affiliation(s)
- Stefania Volpe
- Division of Radiation Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Matteo Pepa
- Division of Radiation Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Mattia Zaffaroni
- Division of Radiation Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Federica Bellerba
- Molecular and Pharmaco-Epidemiology Unit, Department of Experimental Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Riccardo Santamaria
- Division of Radiation Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giulia Marvaso
- Division of Radiation Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Lars Johannes Isaksson
- Division of Radiation Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Sara Gandini
- Molecular and Pharmaco-Epidemiology Unit, Department of Experimental Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Anna Starzyńska
- Department of Oral Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Maria Cristina Leonardi
- Division of Radiation Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Roberto Orecchia
- Scientific Directorate, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Daniela Alterio
- Division of Radiation Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Barbara Alicja Jereczek-Fossa
- Division of Radiation Oncology, European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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Elbanna M, Chowdhury NN, Rhome R, Fishel ML. Clinical and Preclinical Outcomes of Combining Targeted Therapy With Radiotherapy. Front Oncol 2021; 11:749496. [PMID: 34733787 PMCID: PMC8558533 DOI: 10.3389/fonc.2021.749496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
In the era of precision medicine, radiation medicine is currently focused on the precise delivery of highly conformal radiation treatments. However, the tremendous developments in targeted therapy are yet to fulfill their full promise and arguably have the potential to dramatically enhance the radiation therapeutic ratio. The increased ability to molecularly profile tumors both at diagnosis and at relapse and the co-incident progress in the field of radiogenomics could potentially pave the way for a more personalized approach to radiation treatment in contrast to the current ‘‘one size fits all’’ paradigm. Few clinical trials to date have shown an improved clinical outcome when combining targeted agents with radiation therapy, however, most have failed to show benefit, which is arguably due to limited preclinical data. Several key molecular pathways could theoretically enhance therapeutic effect of radiation when rationally targeted either by directly enhancing tumor cell kill or indirectly through the abscopal effect of radiation when combined with novel immunotherapies. The timing of combining molecular targeted therapy with radiation is also important to determine and could greatly affect the outcome depending on which pathway is being inhibited.
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Affiliation(s)
- May Elbanna
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, United States.,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nayela N Chowdhury
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ryan Rhome
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, United States.,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Melissa L Fishel
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
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TP53 mutants and non-HPV16/18 genotypes are poor prognostic factors for concurrent chemoradiotherapy in locally advanced cervical cancer. Sci Rep 2021; 11:19261. [PMID: 34584128 PMCID: PMC8478905 DOI: 10.1038/s41598-021-98527-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022] Open
Abstract
Targeted sequencing for somatic mutations across the hotspots of 50 cancer-related genes was performed using biopsy specimens to investigate whether clinicopathological factors and genomic alterations correlated with prognosis in locally advanced cervical cancer. Seventy patients diagnosed with International Federation of Obstetrics and Gynecology (FIGO) stage III to IVA cervical cancer underwent radiotherapy or concurrent chemoradiotherapy at the National Cancer Center Hospital between January 2008 and December 2017. Mutations were detected in 47 of 70 [67% of cases; frequency of genetic alterations was as follows: PIK3CA (51%), FBXW7 (10%), PTEN (7.1%), and TP53 (5.7%)]. The Cancer Genome Atlas (TCGA) datasets showed a similar distribution of somatic mutations, but PIK3CA mutation frequency was significantly higher in our cohort than in TCGA datasets (P = 0.028). Patients with TP53 mutation were significantly related to poor progression-free survival (PFS) (hazard ratio [HR] = 3.53, P = 0.042). Patients with tumor diameters > 70 mm were associated with poor prognosis (HR = 2.96, P = 0.0048). Patients with non-HPV16/18 genotypes had worse prognosis than those with HPV16/18 genotypes (HR = 2.15, P = 0.030). Hence, patients with locally advanced cervical cancer, TP53 mutation, large tumor diameter, and non-HPV16/18 genotype were independently correlated with poor PFS, despite concurrent chemoradiotherapy.
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Brennan S, Baird AM, O’Regan E, Sheils O. The Role of Human Papilloma Virus in Dictating Outcomes in Head and Neck Squamous Cell Carcinoma. Front Mol Biosci 2021; 8:677900. [PMID: 34250016 PMCID: PMC8262095 DOI: 10.3389/fmolb.2021.677900] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/10/2021] [Indexed: 12/29/2022] Open
Abstract
The Human Papilloma Virus (HPV) is an oncogenic virus which is associated with the development of head and neck squamous cell carcinoma (HNSCC), predominantly within the oropharynx. Approximately 25% of oropharyngeal squamous cell carcinoma (OPSCC) cases worldwide are attributable to HPV infection, with an estimated 65% in the United States. Transmission is via exposure during sexual contact, with distinctive anatomical features of the tonsils providing this organ with a predilection for infection by HPV. No premalignant lesion is identifiable on clinical examination, thus no comparative histological features to denote the stages of carcinogenesis for HPV driven HNSCC are identifiable. This is in contrast to HPV-driven cervical carcinoma, making screening a challenge for the head and neck region. However, HPV proffers a favorable prognosis in the head and neck region, with better overall survival rates in contrast to its HPV negative counterparts. This has resulted in extensive research into de-intensifying therapies aiming to minimize the morbidity induced by standard concurrent chemo-radiotherapy without compromising efficacy. Despite the favorable prognosis, cases of recurrence and/or metastasis of HPV positive HNSCC do occur, and are linked with poor outcomes. HPV 16 is the most frequent genotype identified in HNSCC, yet there is limited research to date studying the impact of other HPV genotype with respect to overall survival. A similar situation pertains to genetic aberrations associated in those with HPV positive HNSCC who recur, with only four published studies to date. Somatic mutations in TSC2, BRIP1, NBN, TACC3, NFE2l2, STK11, HRAS, PIK3R1, TP63, and FAT1 have been identified in recurrent HPV positive OPSCC. Finding alternative therapeutic strategies for this young cohort may depend on upfront identification of HPV genotypes and mutations which are linked with worse outcomes, thus ensuring appropriate stratification of treatment regimens.
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Affiliation(s)
- Shane Brennan
- School of Medicine, Faculty of Health Sciences, Trinity College, Dublin, Ireland
| | - Anne-Marie Baird
- School of Medicine, Faculty of Health Sciences, Trinity College, Dublin, Ireland
| | - Esther O’Regan
- Department of Histopathology, St. James’s Hospital, Dublin, Ireland
| | - Orla Sheils
- School of Medicine, Faculty of Health Sciences, Trinity College, Dublin, Ireland
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Zaman N, Dass SS, DU Parcq P, Macmahon S, Gallagher L, Thompson L, Khorashad JS, LimbÄck-Stanic C. The KDR (VEGFR-2) Genetic Polymorphism Q472H and c-KIT Polymorphism M541L Are Associated With More Aggressive Behaviour in Astrocytic Gliomas. Cancer Genomics Proteomics 2021; 17:715-727. [PMID: 33099473 DOI: 10.21873/cgp.20226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND/AIM Better diagnostic and prognostic markers are required for a more accurate diagnosis and an earlier detection of glioma progression and for suggesting better treatment strategies. This retrospective study aimed to identify actionable gene variants to define potential markers of clinical significance. MATERIALS AND METHODS 56 glioblastomas (GBM) and 44 grade 2-3 astrocytomas were profiled with next generation sequencing (NGS) as part of routine diagnostic workup and bioinformatics analysis was used for the identification of variants. CD34 immunohistochemistry (IHC) was used to measure microvessel density (MVD) and Log-rank test to compare survival and progression in the presence or absence of these variants. RESULTS Bioinformatic analysis highlighted frequently occurring variants in genes involved in angiogenesis regulation (KDR, KIT, TP53 and PIK3CA), with the most common ones being KDR (rs1870377) and KIT (rs3822214). The KDR variant was associated with increased MVD and shorter survival in GBM. We did not observe any correlation between the KIT variant and MVD; however, there was an association with tumour grade. CONCLUSION This study highlights the role of single-nucleotide variants (SNVs) that may be considered non-pathogenic and suggests the prognostic significance for survival of KIT rs3822214 and KDR rs1870377 and potential importance in planning new treatment strategies for gliomas.
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Affiliation(s)
- Niyaz Zaman
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, U.K
| | - Serena Santhana Dass
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, U.K
| | - Persephone DU Parcq
- Department of Cell Pathology, Imperial College Healthcare NHS Trust, London, U.K
| | - Suzanne Macmahon
- Clinical Genomics, The Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, London, U.K
| | - Lewis Gallagher
- Clinical Genomics, The Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, London, U.K
| | - Lisa Thompson
- Clinical Genomics, The Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, London, U.K
| | - Jamshid S Khorashad
- Department of Immunology and Inflammation, Imperial College London, London, U.K
| | - Clara LimbÄck-Stanic
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, U.K. .,Department of Cell Pathology, Imperial College Healthcare NHS Trust, London, U.K
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9
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Moura ACD, Assad DX, Amorim Dos Santos J, Porto de Toledo I, Barra GB, Castilho RM, Squarize CH, Guerra ENS. Worldwide prevalence of PI3K-AKT-mTOR pathway mutations in head and neck cancer: A systematic review and meta-analysis. Crit Rev Oncol Hematol 2021; 160:103284. [PMID: 33675910 DOI: 10.1016/j.critrevonc.2021.103284] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 02/03/2021] [Accepted: 02/27/2021] [Indexed: 02/07/2023] Open
Abstract
A systematic review (SR) and meta-analysis were conducted to determine the prevalence of PI3K-AKT-mTOR signaling pathway mutations in patients with head and neck cancer (HNC). Overall, 105 studies comprising 8630 patients and 1306 mutations were selected. The estimated mutations prevalence was 13 % for PIK3CA (95 % confidence interval [CI] = 11-14; I2 = 82 %; p < 0.0001), 4% for PTEN (95 % CI = 3-5; I2 = 55 %; p < 0.0001), 3% for MTOR (95 % CI = 2-4; I2 = 5%; p = 0.40), and 2% for AKT (95 % CI = 1-2; I2 = 50 %; p = 0.0001). We further stratified the available data of the participants according to risk factors and tumor characteristics, including HPV infection, tobacco use, alcohol exposure, TNM stage, and histological tumor differentiation, and performed subgroup analysis. We identified significant associations between PI3K-AKT-mTOR pathway-associated mutations and advanced TNM stage (odds ratio [OR] = 0.20; 95 % CI = 0.09-0.44; I² = 71 %; p = 0.0001) and oropharyngeal HPV-positive tumors and PIK3CA mutations (OR = 17.48; 95 % CI = 4.20-72.76; I² = 69 %; p < 0.0002). No associations were found between alcohol and tobacco exposure, and tumor differentiation grade. This SR demonstrated that the PI3K-AKT-mTOR pathway emerges as a potential prognostic factor and could offer a molecular basis for future studies on therapeutic targeting in HNC patients.
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Affiliation(s)
- Adriana Castelo de Moura
- Laboratory of Oral Histopathology, Health Sciences Faculty, University of Brasília, Brasília, Brazil; Hospital Universitário de Brasília (HUB-UnB/Ebserh), Brasília, DF, Brazil; Hospital Santa Lúcia, Brasília, DF, Brazil
| | - Daniele Xavier Assad
- Laboratory of Oral Histopathology, Health Sciences Faculty, University of Brasília, Brasília, Brazil; Medical Oncology Department, Hospital Sírio-Libanês, Brasília, DF, Brazil
| | - Juliana Amorim Dos Santos
- Laboratory of Oral Histopathology, Health Sciences Faculty, University of Brasília, Brasília, Brazil
| | - Isabela Porto de Toledo
- Laboratory of Oral Histopathology, Health Sciences Faculty, University of Brasília, Brasília, Brazil
| | - Gustavo Barcelos Barra
- Sabin Medicina Diagnóstica, SAAN Quadra 03 Lotes 145/185, Brasília, 70632-340, DF, Brazil
| | - Rogerio Moraes Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, Division of Oral Pathology, Radiology and Medicine, University of Michigan School of Dentistry. Ann Arbor, 48109-1078, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Cristiane Helena Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, Division of Oral Pathology, Radiology and Medicine, University of Michigan School of Dentistry. Ann Arbor, 48109-1078, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Eliete Neves Silva Guerra
- Laboratory of Oral Histopathology, Health Sciences Faculty, University of Brasília, Brasília, Brazil; Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, Division of Oral Pathology, Radiology and Medicine, University of Michigan School of Dentistry. Ann Arbor, 48109-1078, MI, USA.
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Shah PA, Huang C, Li Q, Kazi SA, Byers LA, Wang J, Johnson FM, Frederick MJ. NOTCH1 Signaling in Head and Neck Squamous Cell Carcinoma. Cells 2020; 9:cells9122677. [PMID: 33322834 PMCID: PMC7764697 DOI: 10.3390/cells9122677] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
Biomarker-driven targeted therapies are lacking for head and neck squamous cell carcinoma (HNSCC), which is common and lethal. Efforts to develop such therapies are hindered by a genomic landscape dominated by the loss of tumor suppressor function, including NOTCH1 that is frequently mutated in HNSCC. Clearer understanding of NOTCH1 signaling in HNSCCs is crucial to clinically targeting this pathway. Structural characterization of NOTCH1 mutations in HNSCC demonstrates that most are predicted to cause loss of function, in agreement with NOTCH1's role as a tumor suppressor in this cancer. Experimental manipulation of NOTCH1 signaling in HNSCC cell lines harboring either mutant or wild-type NOTCH1 further supports a tumor suppressor function. Additionally, the loss of NOTCH1 signaling can drive HNSCC tumorigenesis and clinical aggressiveness. Our recent data suggest that NOTCH1 controls genes involved in early differentiation that could have different phenotypic consequences depending on the cancer's genetic background, including acquisition of pseudo-stem cell-like properties. The presence of NOTCH1 mutations may predict response to treatment with an immune checkpoint or phosphatidylinositol 3-kinase inhibitors. The latter is being tested in a clinical trial, and if validated, it may lead to the development of the first biomarker-driven targeted therapy for HNSCC.
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Affiliation(s)
- Pooja A. Shah
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (P.A.S.); (L.A.B.)
| | - Chenfei Huang
- Bobby R. Alford Department of Otolaryngology, Baylor College of Medicine, Houston, TX 77030, USA; (C.H.); (M.J.F.)
| | - Qiuli Li
- Department of Head and Neck Surgery, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China;
| | - Sawad A. Kazi
- School of Natural Sciences, University of Texas, Austin, TX 78712, USA;
| | - Lauren A. Byers
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (P.A.S.); (L.A.B.)
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA;
| | - Jing Wang
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA;
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Faye M. Johnson
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (P.A.S.); (L.A.B.)
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA;
- Correspondence: ; Tel.: +1-713–792-6363; Fax: +1-713-792-1220
| | - Mitchell J. Frederick
- Bobby R. Alford Department of Otolaryngology, Baylor College of Medicine, Houston, TX 77030, USA; (C.H.); (M.J.F.)
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11
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Scholl SM, Beal J, de Koning L, Girard E, Popovic M, de la Rochefordière A, Lecuru F, Fourchotte V, Ngo C, Floquet A, Berns EM, Kenter G, Gestraud P, von der Leyen H, Lecerf C, Puard V, Roman SR, Latouche A, Kereszt A, Balint B, Rouzier R, Kamal M. Genetic markers and phosphoprotein forms of beta-catenin pβ-Cat552 and pβ-Cat675 are prognostic biomarkers of cervical cancer. EBioMedicine 2020; 61:103049. [PMID: 33096476 PMCID: PMC7581879 DOI: 10.1016/j.ebiom.2020.103049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 09/21/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) remains a leading cause of gynaecological cancer-related mortality world wide and constitutes the third most common malignancy in women. The RAIDs consortium (http://www.raids-fp7.eu/) conducted a prospective European study [BioRAIDs (NCT02428842)] with the objective to stratify CC patients for innovative treatments. A "metagene" of genomic markers in the PI3K pathway and epigenetic regulators had been previously associated with poor outcome [2]. METHODS To detect new, more specific, targets for treatment of patients who resist standard chemo-radiation, a high-dimensional Cox model was applied to define dominant molecular variants, copy number variations, and reverse phase protein arrays (RPPA). FINDINGS Survival analysis on 89 patients with all omics data available, suggested loss-of-function (LOF) or activating molecular alterations in nine genes to be candidate biomarkers for worse prognosis in patients treated by chemo-radiation while LOF of ATRX, MED13 as well as CASP8 were associated with better prognosis. When protein expression data by RPPA were factored in, the supposedly low molecular weight and nuclear form, of beta-catenin, phosphorylated in Ser552 (pβ-Cat552), ranked highest for good prognosis, while pβ-Cat675 was associated with worse prognosis. INTERPRETATION These findings call for molecularly targeted treatments involving p53, Wnt pathway, PI3K pathway, and epigenetic regulator genes. Pβ-Cat552 and pβ-Cat675 may be useful biomarkers to predict outcome to chemo-radiation, which targets the DNA repair axis. FUNDING European Union's Seventh Program for research, technological development and demonstration (agreement N°304,810), the Fondation ARC pour la recherche contre le cancer.
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Affiliation(s)
- Suzy M Scholl
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France.
| | - Jonas Beal
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Leanne de Koning
- Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Elodie Girard
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Marina Popovic
- Oncology Institute of Vojvodina, Put doktora Goldmana, 421204 Sremska Kamenica, Serbia
| | | | - Fabrice Lecuru
- Department of Surgery, Institut Curie, PSL Research University, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Virginie Fourchotte
- Department of Surgery, Institut Curie, PSL Research University, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Charlotte Ngo
- Service de chirurgie cancérologique gynécologique et du sein, Hôpital Européen Georges Pompidou, APHP et faculté de médecine, Université Paris Descartes, France
| | - Anne Floquet
- Chirurgie onco-gynécologique and Oncology, Institut Bergonié, Centre Régional de Lutte contre le Cancer Bordeaux-Aquitaine, France
| | - Els Mjj Berns
- Dept Medical Oncology, Erasmus MC, 3000 CA Rotterdam, Netherlands
| | - Gemma Kenter
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Department of Gynaecologic Oncology Amsterdam, Amsterdam UMC and The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Pierre Gestraud
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Heiko von der Leyen
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Hannover Clinical Trial Center, Hannover Medical School Germany
| | - Charlotte Lecerf
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Vincent Puard
- Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Sergio Roman Roman
- Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Aurelien Latouche
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France; Conservatoire national des arts et métiers, Paris, France
| | - Attila Kereszt
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; SeqOmics Biotechnology Ltd, Vallalkozok utja 7, Morahalom, Hungary
| | - Balazs Balint
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Department of Translational Research, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
| | - Roman Rouzier
- Department of Surgery, Institut Curie, PSL Research University, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France; Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Maud Kamal
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, 75005 Paris & 92210 Saint-Cloud, France
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12
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Li Z, Wang M, Gu J, Zhao L, Guo Y, Zhang Z, Liu X. Missense Variants in Hypoxia-Induced VEGFA/VEGFR2 Signaling Predict the Outcome of Large Artery Atherosclerotic Stroke. Cell Mol Neurobiol 2020; 41:1217-1225. [PMID: 32506171 DOI: 10.1007/s10571-020-00890-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 05/28/2020] [Indexed: 11/30/2022]
Abstract
Collateral density variations are a major determinant of stroke outcome. Here, we explored the association of missense variants in hypoxia-induced VEGFA/VEGFR2 signaling and stroke outcome. We recruited 683 large artery atherosclerotic (LAA) stroke patients as the training set from Nanjing Stroke Registry Program between August 2013 and January 2016. To validate the findings from the training set, we recruited an additional 333 LAA stroke patients between February 2016 and January 2017 as the validation set. Genotyping of target SNPs (rs11549465 [HIF-1α], rs11549467 [HIF-1α], rs1870377 [VEGFR2], and rs2305948 [VEGFR2]) was conducted using a SNPscan method. Unfavorable outcome was defined as a modified Rankin Scale (mRS) score > 2 at three months after index event. In the training set, the AA genotype of rs1870377 led to a decreased risk of unfavorable outcomes in the recessive model (AA vs. TA + TT, OR 0.60, 95% CI 0.38-0.95, P = 0.031). This was confirmed in the validation set (OR 0.43, 95% CI 0.21-0.86, P = 0.017) and the combined set (OR 0.54, 95% CI 0.36-0.79, P = 0.002). We also found that A allele was a protective factor for stroke outcome in both validation set and combined set (OR 0.70, 95% CI 0.49-0.99, P = 0.044 and OR 0.77, 95% CI 0.63-0.94, P = 0.012, respectively). In silico analysis indicated that the rs1870377 variant led to structural alterations in VEGFR2 that may influence its activity. Our findings demonstrate that the rs1870377 in the hypoxia-induced VEGFA/VEGFR2 axis predicts the 3-month outcome of patients with LAA stroke.
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Affiliation(s)
- Zibao Li
- Department of Neurology, Jinling Hospital, Nanjing Medical University, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu, China.,Department of Neurology, Yijishan Hospital of Wannan Medical College, Wuhu, 241001, China
| | - Mengmeng Wang
- Department of Neurology, The First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, 213000, China
| | - Jinyu Gu
- Department of Neurology, Jinling Hospital, Nanjing Medical University, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu, China
| | - Li Zhao
- Department of Neurology, Yijishan Hospital of Wannan Medical College, Wuhu, 241001, China
| | - Yongtao Guo
- Department of Neurology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China
| | - Zhizhong Zhang
- Department of Neurology, Jinling Hospital, Nanjing Medical University, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu, China. .,Department of Neurology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China.
| | - Xinfeng Liu
- Department of Neurology, Jinling Hospital, Nanjing Medical University, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu, China. .,Department of Neurology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China.
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13
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Radiomic biomarkers for head and neck squamous cell carcinoma. Strahlenther Onkol 2020; 196:868-878. [PMID: 32495038 DOI: 10.1007/s00066-020-01638-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/13/2020] [Indexed: 12/22/2022]
Abstract
Tumor heterogeneity is a well-known prognostic factor in head and neck squamous cell carcinoma (HNSCC). A major limitation of tissue- and blood-derived tumor markers is the lack of spatial resolution to image tumor heterogeneity. Tissue markers derived from tumor biopsies usually represent only a small tumor subregion at a single timepoint and are therefore often not representative of the tumors' biology or the biological alterations during and after treatment. Similarly, liquid biopsies give an overall picture of the tumors' secreted factors but completely lack any spatial resolution. Radiomics has the potential to give complete three-dimensional information about the tumor. We conducted a comprehensive literature search to assess the correlation of radiomics to tumor biology and treatment outcome in HNSCC and to assess current limitations of the radiomic biomarkers. In total, 25 studies that explored the ability of radiomics to predict tumor biology and phenotype in HNSCC and 28 studies that explored radiomics to predict post-treatment events were identified. Out of these 53 studies, only three failed to show a significant correlation. The major technical challenges are currently artifacts due to metal implants, non-standardized contrast injection, and delineation uncertainties. All studies to date were retrospective and none of the above-mentioned radiomics signatures have been validated in an independent cohort using an independent software implementation, which shows that transferability due to the numerous technical challenges is currently a major limitation. However, radiomics is a very young field and these studies hopefully pave the way for clinical implementation of radiomics for HNSCC in the future.
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14
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Ye J, Liao B, Jiang X, Dong Z, Hu S, Liu Y, Xiao M. Prognosis Value of Platelet Counts, Albumin and Neutrophil-Lymphocyte Ratio of Locoregional Recurrence in Patients with Operable Head and Neck Squamous Cell Carcinoma. Cancer Manag Res 2020; 12:731-741. [PMID: 32099469 PMCID: PMC6999764 DOI: 10.2147/cmar.s234618] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/03/2020] [Indexed: 12/12/2022] Open
Abstract
Background Peripheral blood inflammation factor neutrophil-lymphocyte ratio (NLR), platelet count (PLT) and nutritional factor serum albumin (ALB) have been proposed as prognostic markers of head and neck squamous carcinoma cancer (HNSCC) in recent years. In the current study, nomogram predict models based on pre-treatment hematological parameters and a modified risk-stratified score system have been built. Methods A total of 197 patients with oropharyngeal, hypopharyngeal and laryngeal cancers receiving multimodality treatment between 2012 and 2014 were included. The pre-treatment ALB, neutrophil, lymphocyte and platelet count (PLT) were detected. Cancer-specific survival and locoregional recurrence (LRC) by 5 years’ follow-up in the cases were obtained. To integrate clinical characteristics, we propose a modified risk-stratified score system. Kaplan–Meier method, proportional hazards COX model, logistic models were used to establish nomograms within external validation. Results Five-year LRC was decreased (p=0.004) for 140 patients with pre-treatment NLR <2.77. Five-year LRC and 5-year cancer-specific survival were decreased (p=0.031, p=0.021) with pre-treatment PLT ≥248×109/L. Comparison of univariate parametric models demonstrated that pre-treatment NLR evaluation and PLT>248×109/L were better among tested models. On Bayesian information criteria (BIC) analysis, the optimal prognostic model was then used to develop nomograms predicting 3- and 5-year LRC. The external validation of this predictive model was confirmed in 57 patients from another hospital. Conclusion Pre-treatment NLR elevation and PLT>248×109/L are promising predictors of prognosis in patients with operable HNSCC. Nomograms based on the pre-treatment hematological markers and modified risk-stratified score system provide distinct risk stratifications. There results provided the feasibility of anti-inflammatory and antiplatelet treatments for HNSCC patients.
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Affiliation(s)
- Jing Ye
- Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Bing Liao
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xiaohua Jiang
- Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zhihuai Dong
- Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Sunhong Hu
- Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yuehui Liu
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Mang Xiao
- Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
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15
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Neuropeptide receptor genes GHSR and NMUR1 are candidate epigenetic biomarkers and predictors for surgically treated patients with oropharyngeal cancer. Sci Rep 2020; 10:1007. [PMID: 31974445 PMCID: PMC6978330 DOI: 10.1038/s41598-020-57920-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/08/2020] [Indexed: 12/20/2022] Open
Abstract
Pathological staging and histological grading systems are useful, but imperfect, predictors of recurrence in head and neck squamous cell carcinoma (HNSCC). Aberrant promoter methylation is the main type of epigenetic modification that plays a role in the inactivation of tumor suppressor genes. To identify new potential prognostic markers, we investigated the promoter methylation status of five neuropeptide receptor genes. The methylation status of the target genes was compared with clinical characteristics in 278 cases; 72 hypopharyngeal cancers, 54 laryngeal cancers, 75 oropharyngeal cancers, and 77 oral cavity cancers were studied. We found that the NTSR1, NTSR2, GHSR, MLNR, and NMUR1 promoters were methylated in 47.8%, 46.8%, 54.3%, 39.2%, and 43.5% of the samples, respectively. GHSR and NMUR1 promoter methylation independently predicted recurrence in HNSCC. In patients with oropharyngeal cancer (n = 75), GHSR and NMUR1 promoter methylation significantly correlates with survival in surgically treated patients. We classified our patients as having a low, intermediate, or high-risk of death based on three factors: HPV status, and GHSR and NMUR1 promoter methylation. The disease-free survival (DFS) rates were 87.1%, 42.7%, and 17.0%, respectively. Combined data analysis of the methylation status of ten-eleven translocation (TET) family genes indicated a trend toward greater methylation indices as the number of TET methylation events increased. In the current study, we presented the relationship between the methylation status of the GHSR and NMUR1 genes and recurrence in HNSCC, specifically in risk classification of oropharyngeal carcinomas cases with HPV status.
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McIntyre B, Asahara T, Alev C. Overview of Basic Mechanisms of Notch Signaling in Development and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1227:9-27. [PMID: 32072496 DOI: 10.1007/978-3-030-36422-9_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Notch signaling is an evolutionarily conserved pathway associated with the development and differentiation of all metazoans. It is needed for proper germ layer formation and segmentation of the embryo and controls the timing and duration of differentiation events in a dynamic manner. Perturbations of Notch signaling result in blockades of developmental cascades, developmental anomalies, and cancers. An in-depth understanding of Notch signaling is thus required to comprehend the basis of development and cancer, and can be further exploited to understand and direct the outcomes of targeted cellular differentiation into desired cell types and complex tissues from pluripotent or adult stem and progenitor cells. In this chapter, we briefly summarize the molecular, evolutionary, and developmental basis of Notch signaling. We will focus on understanding the basics of Notch signaling and its signaling control mechanisms, its developmental outcomes and perturbations leading to developmental defects, as well as have a brief look at mutations of the Notch signaling pathway causing human hereditary disorders or cancers.
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Affiliation(s)
| | | | - Cantas Alev
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.
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17
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Jeon SH, Chie EK, Kim YJ, Lee KH, Lee HS, Kim MJ, Im SA, Kim JI, Kim TY. Targeted next-generation DNA sequencing identifies Notch signaling pathway mutation as a predictor of radiation response. Int J Radiat Biol 2019; 95:1640-1647. [PMID: 31525117 DOI: 10.1080/09553002.2019.1665212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Purpose: Identifying the association between somatic mutations and the radiation response of tumor is essential for understanding the mechanisms and practicing personalized radiotherapy. The present study aimed to discover specific genes or pathways that are associated with radiation response using targeted next-generation DNA sequencing.Material and methods: Fifty-five patients with various solid tumors whose specimen were sequenced using institutional panel which includes 148 cancer-related genes and received radiotherapy for a measurable tumor were analyzed. Patients with irradiated tumors in complete or partial remission for more than 6 months were defined as responders. Association between mutations including pathogenic single nucleotide variants and insertions/deletions in the 148 genes and 39 molecular pathways and radiation response was investigated.Results: Analyzing 17 responders and 38 non-responders, biologically effective dose (BED), but not concurrent chemotherapy, was associated with radiation response. No single gene correlated with radiation response. Mutations in Notch signaling pathway were associated with radiosensitivity after correction for multiple comparison (adjusted p = .094). When BED and Notch signaling pathway mutation were tested with logistic regression, both variables were associated with radiation response.Conclusions: Our results suggest that somatic mutations in Notch signaling pathway may be related to sensitivity to radiation, although these results should be validated in a larger and more homogeneous cohort.
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Affiliation(s)
- Seung Hyuck Jeon
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Korea
| | - Eui Kyu Chie
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Korea.,Institute of Radiation Medicine, Seoul National University Medical Research Center, Seoul, Korea
| | - Yi-Jun Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Korea
| | - Kyung-Hun Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun-Seob Lee
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Min Jung Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Seock-Ah Im
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Tae-You Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
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de Roest RH, Mes SW, Poell JB, Brink A, van de Wiel MA, Bloemena E, Thai E, Poli T, Leemans CR, Brakenhoff RH. Molecular Characterization of Locally Relapsed Head and Neck Cancer after Concomitant Chemoradiotherapy. Clin Cancer Res 2019; 25:7256-7265. [DOI: 10.1158/1078-0432.ccr-19-0628] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/23/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022]
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19
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Interference of tumour mutational burden with outcome of patients with head and neck cancer treated with definitive chemoradiation: a multicentre retrospective study of the German Cancer Consortium Radiation Oncology Group. Eur J Cancer 2019; 116:67-76. [PMID: 31173964 DOI: 10.1016/j.ejca.2019.04.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 04/09/2019] [Accepted: 04/12/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Tumour mutational burden (TMB) estimated from whole exome sequencing or comprehensive gene panels has previously been established as predictive factor of response to immune checkpoint inhibitors (ICIs). Its predictive value for the efficacy of concurrent chemoradiation (cCRTX), a potential combination partner of ICI, remains unknown. METHODS The accuracy of TMB estimation by an in-house 327-gene panel was established in the Cancer Genome Atlas (TCGA) head and neck squamous cell carcinoma (HNSCC) data set. Interference of TMB with outcome after cCRTX was determined in a multicentre cohort of patients with locally advanced HNSCC uniformly treated with cCRTX. Targeted next-generation sequencing was successfully applied in 101 formalin-fixed, paraffin-embedded pretreatment tumour samples. In a subset of cases (n = 40), tumour RNA was used for immune-related gene expression profiling by the nanoString platform. TMB was correlated with TP53 genotype, human papilloma virus (HPV) status, immune expression signatures and survival parameters. Results were validated in the TCGA HNSCC cohort. RESULTS A high accuracy of TMB estimation by the 327-gene panel was established. High TMB was significantly associated with an increased prevalence of TP53 mutations and immune gene expression patterns unrelated to T cell-inflamed gene expression profiles. Kaplan-Meier analysis revealed significantly reduced overall survival in the patient group with high TMB (hazard ratio for death: 1.79, 95% confidence interval: 1.02-3.14; P = 0.042) which remained significant after correcting for confounding factors in the multivariate model. The prognostic value of TMB was confirmed in the TCGA HNSCC cohort. CONCLUSION High TMB identifies HNSCC patients with poor outcome after cCRTX who might preferentially benefit from CRTX-ICI combinations.
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20
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Budach V, Tinhofer I. Novel prognostic clinical factors and biomarkers for outcome prediction in head and neck cancer: a systematic review. Lancet Oncol 2019; 20:e313-e326. [DOI: 10.1016/s1470-2045(19)30177-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 01/16/2023]
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21
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Dogan S, Xu B, Middha S, Vanderbilt CM, Bowman AS, Migliacci J, Morris LGT, Seshan VE, Ganly I. Identification of prognostic molecular biomarkers in 157 HPV-positive and HPV-negative squamous cell carcinomas of the oropharynx. Int J Cancer 2019; 145:3152-3162. [PMID: 31093971 DOI: 10.1002/ijc.32412] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022]
Abstract
The incidence of oropharyngeal squamous cell carcinoma (OPSCC) has been increasing due to high-risk HPV infection. We explored the significance of genetic alterations in HPV-positive (HPV-P) and HPV-negative (HPV-N) OPSCC patients on long-term outcome. A total of 157 cases of primary resected OPSCC diagnosed from 1978 to 2005 were subjected to a targeted exome sequencing by MSK-IMPACT™ interrogating somatic mutations in 410 cancer-related genes. Mutational profiles were correlated to recurrence and survival outcomes. OPSCC included 47% HPV-positive (HPV-P) and 53% HPV-negative (HPV-N) tumors arising in the base of tongue (BOT, 43%), palatine tonsil (30%) and soft palate (SP, 27%). HPV negative status, SP location and smoking were associated with poorer outcome. Poorer overall survival was found in NOTCH1-mutated HPV-P (p = 0.039), and in SOX2-amplified HPV-N cases (p = 0.036). Chromosomal arm gains in 8p and 8q, and 16q loss were more common in HPV-P (p = 0.005, 0.04 and 0.01, respectively), while 9p, 18q and 21q losses were more frequent in HPV-N OPSCC (p = 0.006, 0.002 and 0.01, respectively). Novel, potentially functional JAK3, MYC and EP300 intragenic deletions were found in HPV-P, and FOXP1, CDKN2A, CCND1 and RUNX1 intragenic deletions and one FGFR3 inversion were detected in HPV-N tumors. HPV-N/TP53-wild-type OPSCC harbored recurrent mutations in NOTCH1/3/4 (39%), PIK3CA, FAT1 and TERT. In comparison to their oral and laryngeal counterparts, HPV-N OPSCC were genetically distinct. In OPSCC, HPV status, tumor subsite and smoking determine outcome. Risk-stratification can be further refined based on the mutational signature, namely, NOTCH1 and SOX2 mutation status.
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Affiliation(s)
- Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jocelyn Migliacci
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ian Ganly
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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22
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Hess AK, Jöhrens K, Zakarneh A, Balermpas P, Von Der Grün J, Rödel C, Weichert W, Hummel M, Keilholz U, Budach V, Tinhofer I. Characterization of the tumor immune micromilieu and its interference with outcome after concurrent chemoradiation in patients with oropharyngeal carcinomas. Oncoimmunology 2019; 8:1614858. [PMID: 31413922 DOI: 10.1080/2162402x.2019.1614858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Intra-tumoral CD8 + T-cell infiltration in squamous cell carcinoma of the head and neck (HNSCC) has previously been linked to the efficacy of cisplatin-based chemoradiation (CDDP-CRTX) and immune checkpoint inhibitor (ICI) monotherapy. Further detailed characterization of the tumor immune-micromilieu and its influence on outcome may guide the development of CRTX-ICI combinations. METHODS Comprehensive immune transcriptome analysis was applied to a training set of tumor specimens from oropharyngeal squamous cell carcinoma (OPSCC) patients treated with CDDP-CRTX in the ARO-0401 phase III study (n = 33). A composite immune signature risk score (ISRS) for survival prediction was developed, and subsequently validated in two independent OPSCC cohorts treated with either CDDP-CRTX (n = 36) or mitomycin-based CRTX (MMC-CRTX, n = 31). Further validation of the ISRS was performed in the OPSCC subset (n = 79) of the TCGA HNSCC cohort. Potential interference between immune signatures and HPV status was evaluated in multivariate Cox regression models. RESULTS Significant differences according to the 3-y OS status in the abundance of tumor-infiltrating T- and B-cells, and the expression levels of 51 immune-related genes were observed. A risk score based on 13 differentially expressed genes involved in cytokine signaling, T-cell effector functions and the TNFR pathway was established as robust predictive factor of OS. Its predictive power was superior to the 6-gene interferon-gamma signature of ICI efficacy and independent of the HPV status. CONCLUSIONS This study further elucidates the complex interaction of the tumor immune microenvironment with the efficacy of CDDP-CRTX in OPSCC. The results suggest immune markers for selection of patients treated with CRTX-ICI combinations.
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Affiliation(s)
- Anne-Kathrin Hess
- Department of Radiooncology and Radiotherapy, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Korinna Jöhrens
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Andre Zakarneh
- Department of Otorhinolaryngology, Sankt Gertrauden-Krankenhaus, Berlin, Germany
| | - Panagiotis Balermpas
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK) partner site Frankfurt, Department of Radiation Oncology, University Hospital Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Jens Von Der Grün
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK) partner site Frankfurt, Department of Radiation Oncology, University Hospital Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Claus Rödel
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK) partner site Frankfurt, Department of Radiation Oncology, University Hospital Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Wilko Weichert
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK) partner site Munich, Institute of Pathology, Technical University Munich, Munich, Germany
| | - Michael Hummel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ulrich Keilholz
- Berlin Institute of Health, Comprehensive Cancer Center Charité, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Volker Budach
- Department of Radiooncology and Radiotherapy, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) partner site Berlin, Berlin, Germany
| | - Ingeborg Tinhofer
- Department of Radiooncology and Radiotherapy, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) partner site Berlin, Berlin, Germany
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23
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Zwirner K, Hilke FJ, Demidov G, Socarras Fernandez J, Ossowski S, Gani C, Thorwarth D, Riess O, Zips D, Schroeder C, Welz S. Radiogenomics in head and neck cancer: correlation of radiomic heterogeneity and somatic mutations in TP53, FAT1 and KMT2D. Strahlenther Onkol 2019; 195:771-779. [PMID: 31123786 DOI: 10.1007/s00066-019-01478-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 05/10/2019] [Indexed: 12/17/2022]
Abstract
PURPOSE Genetic tumour profiles and radiomic features can be used to complement clinical information in head and neck squamous cell carcinoma (HNSCC) patients. Radiogenomics imply the potential to investigate complementarity or interrelations of radiomic and genomic features, and prognostic factors might be determined. The aim of our study was to explore radiogenomics in HNSCC. METHODS For 20 HNSCC patients treated with primary radiochemotherapy, next-generation sequencing (NGS) of tumour and corresponding normal tissue was performed. In total, 327 genes were investigated by panel sequencing. Radiomic features were extracted from computed tomography data. A hypothesis-driven approach was used for radiogenomic correlations of selected image-based heterogeneity features and well-known driver gene mutations in HNSCC. RESULTS The most frequently mutated driver genes in our cohort were TP53 (involved in cell cycle control), FAT1 (Wnt signalling, cell-cell contacts, migration) and KMT2D (chromatin modification). Radiomic features of heterogeneity did not correlate significantly with somatic mutations in TP53 or KMT2D. However, somatic mutations in FAT1 and smaller primary tumour volumes were associated with reduced radiomic intra-tumour heterogeneity. CONCLUSION The landscape of somatic variants in our cohort is well in line with previous reports. An association of somatic mutations in FAT1 with reduced radiomic tumour heterogeneity could potentially elucidate the previously described favourable outcomes of these patients. Larger studies are needed to validate this exploratory data in the future.
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Affiliation(s)
- Kerstin Zwirner
- Department of Radiation Oncology, Medical Faculty and University Hospital, Eberhard Karls University, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany.
| | - Franz J Hilke
- Institute of Medical Genetics and Applied Genomics, Medical Faculty and University Hospital, Eberhard Karls University, Calwerstraße 7, 72076, Tübingen, Germany
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, Medical Faculty and University Hospital, Eberhard Karls University, Calwerstraße 7, 72076, Tübingen, Germany
| | - Jairo Socarras Fernandez
- Section for Biomedical Physics, Department of Radiation Oncology, Medical Faculty and University Hospital, Eberhard Karls University, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, Medical Faculty and University Hospital, Eberhard Karls University, Calwerstraße 7, 72076, Tübingen, Germany.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Cihan Gani
- Department of Radiation Oncology, Medical Faculty and University Hospital, Eberhard Karls University, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany.,German Cancer Research Center (DKFZ) partner site Tübingen, German Cancer Consortium (DKTK), Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany
| | - Daniela Thorwarth
- Section for Biomedical Physics, Department of Radiation Oncology, Medical Faculty and University Hospital, Eberhard Karls University, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany.,German Cancer Research Center (DKFZ) partner site Tübingen, German Cancer Consortium (DKTK), Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, Medical Faculty and University Hospital, Eberhard Karls University, Calwerstraße 7, 72076, Tübingen, Germany.,NGS Competence Center Tübingen (NCCT), Eberhard Karls University, Calwerstraße 7, 72076, Tübingen, Germany
| | - Daniel Zips
- Department of Radiation Oncology, Medical Faculty and University Hospital, Eberhard Karls University, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany.,German Cancer Research Center (DKFZ) partner site Tübingen, German Cancer Consortium (DKTK), Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, Medical Faculty and University Hospital, Eberhard Karls University, Calwerstraße 7, 72076, Tübingen, Germany
| | - Stefan Welz
- Department of Radiation Oncology, Medical Faculty and University Hospital, Eberhard Karls University, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany.,German Cancer Research Center (DKFZ) partner site Tübingen, German Cancer Consortium (DKTK), Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany
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24
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Mori T, Kobayashi K, Yoshimoto S. ASO Author Reflections: Precise p53 Analysis in Formalin-Fixed Paraffin-Embedded Specimens Can Predict Head and Neck Squamous Cell Carcinoma Outcomes. Ann Surg Oncol 2019; 26:614-615. [DOI: 10.1245/s10434-019-07433-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Indexed: 11/18/2022]
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25
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Goodman AM, Kato S, Chattopadhyay R, Okamura R, Saunders IM, Montesion M, Frampton GM, Miller VA, Daniels GA, Kurzrock R. Phenotypic and Genomic Determinants of Immunotherapy Response Associated with Squamousness. Cancer Immunol Res 2019; 7:866-873. [PMID: 31003990 DOI: 10.1158/2326-6066.cir-18-0716] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/10/2019] [Accepted: 04/16/2019] [Indexed: 12/25/2022]
Abstract
Advanced and metastatic squamous cell carcinomas (SCC) are common and difficult-to-treat malignancies. We assessed 75 immunotherapy-treated patients with SCC from a clinically annotated database of 2,651 patients, as well as 9,407 patients from a deidentified database for molecular features that might influence checkpoint blockade response. SCCs had higher tumor mutational burdens (TMB) than non-SCCs (P < 0.0001). Cutaneous SCCs had the highest TMB (P < 0.0001), with 41.3% demonstrating a very high TMB (≥50 mutations/Mb). In immunotherapy-treated patients with SCC, higher TMB (≥12 mutations/Mb) correlated with a trend to higher clinical benefit rate [stable disease ≥ 6 months or partial/complete remission; 60% vs. 29%; (high vs. low TMB); P = 0.06] and significantly longer median time-to-treatment failure (TTF; 9.9 vs. 4.4 months; P = 0.0058). Cutaneous SCCs had the highest clinical benefit [11/15 patients (73%) vs. 20/60 (33%) non-cutaneous (P = 0.008)], TTF (P = 0.0015), and overall survival (P = 0.06) with immunotherapy treatment. In conclusion, among a diverse set of SCCs, higher TMB and cutaneous disease associated with better immunotherapy outcome.
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Affiliation(s)
- Aaron M Goodman
- Department of Medicine, Division of Hematology/Oncology, University of California San Diego, La Jolla, California. .,Center for Personalized Cancer Therapy, University of California San Diego, La Jolla, California.,Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California
| | - Shumei Kato
- Department of Medicine, Division of Hematology/Oncology, University of California San Diego, La Jolla, California.,Center for Personalized Cancer Therapy, University of California San Diego, La Jolla, California
| | - Ranajoy Chattopadhyay
- Center for Personalized Cancer Therapy, University of California San Diego, La Jolla, California
| | - Ryosuke Okamura
- Center for Personalized Cancer Therapy, University of California San Diego, La Jolla, California
| | - Ila M Saunders
- Department of Pharmacology, University of California San Diego, La Jolla, California
| | | | | | | | - Gregory A Daniels
- Department of Medicine, Division of Hematology/Oncology, University of California San Diego, La Jolla, California
| | - Razelle Kurzrock
- Department of Medicine, Division of Hematology/Oncology, University of California San Diego, La Jolla, California.,Center for Personalized Cancer Therapy, University of California San Diego, La Jolla, California
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26
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Genetic Factors Associated with a Poor Outcome in Head and Neck Cancer Patients Receiving Definitive Chemoradiotherapy. Cancers (Basel) 2019; 11:cancers11040445. [PMID: 30934880 PMCID: PMC6521057 DOI: 10.3390/cancers11040445] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/24/2019] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
About half of advanced stage head and neck squamous cell carcinoma (HNSCC) patients can be cured by chemoradiotherapy. Patient outcome may be partially determined by the genetic alterations in HNSCC, rendering these alterations promising candidate prognostic factors and/or therapeutic targets. However, their relevance in patient outcome prognosis remains to be assessed in patients that receive standard-of-care chemoradiotherapy. We therefore tested whether frequent genetic alterations were associated with progression free survival (PFS) in advanced stage HNSCC patients who were uniformly treated with definitive platinum-based chemoradiotherapy. To this end, we performed targeted DNA sequencing on frozen pre-treatment tumor biopsy material from 77 patients with advanced stage oro- and hypopharyngeal carcinoma. This provided somatic point mutation and copy number aberration data of 556 genes. The most frequently mutated genes, TP53 (62%), CCND1 (51%), CDKN2A (30%) and PIK3CA (21%), were not associated with PFS. However, co-occurring CCND1 and CDKN2A mutations were associated with short PFS (HR 2.24, p = 0.028) in HPV-negative tumors. Furthermore, tumor mutational burden (sum of somatic point mutations) showed a trend towards decreased PFS (HR 1.9, p = 0.089), and chromosomal instability (CIN) was associated with shorter PFS (HR 2.3, p = 0.023), independent of HPV status. Our results show that tumor mutational burden, CIN markers, and co-occurring CCND1 and CDKN2A mutations are associated with chemoradiotherapy outcomes in advanced stage oro- and hypopharyngeal HNSCC patients, thereby highlighting their prognostic potential. Given their poor prognosis association and link to biological targets, they may also identify patients for novel targeted therapies and immunotherapies.
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27
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Jiang X, Ye J, Dong Z, Hu S, Xiao M. Novel genetic alterations and their impact on target therapy response in head and neck squamous cell carcinoma. Cancer Manag Res 2019; 11:1321-1336. [PMID: 30799957 PMCID: PMC6371928 DOI: 10.2147/cmar.s187780] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is highly variable by tumor site, histologic type, molecular characteristics, and clinical outcome. During recent years, emerging targeted therapies have been focused on driver genes. HNSCC involves several genetic alterations, such as co-occurrence, multiple feedback loops, and cross-talk communications. These different kinds of genetic alterations interact with each other and mediate targeted therapy response. In the current review, it is emphasized that future treatment strategy in HNSCC will not solely be based on "synthetic lethality" approaches directed against overactivated genes. More importantly, biologic, genetic, and epigenetic alterations of HNSCC will be taken into consideration to guide the therapy. The emerging genetic alterations in HNSCC and its effect on targeted therapy response are discussed in detail. Hopefully, novel combination regimens for the treatment of HNSCC can be developed.
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Affiliation(s)
- Xiaohua Jiang
- Department of Otolaryngology Head and Neck Surgery, Sir Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,
| | - Jing Ye
- Department of Otolaryngology Head and Neck Surgery, Sir Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,
| | - Zhihuai Dong
- Department of Otolaryngology Head and Neck Surgery, Sir Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,
| | - Sunhong Hu
- Department of Otolaryngology Head and Neck Surgery, Sir Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,
| | - Mang Xiao
- Department of Otolaryngology Head and Neck Surgery, Sir Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,
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Rettig EM, Bishop JA, Agrawal N, Chung CH, Sharma R, Zamuner F, Li RJ, Koch WM, Califano JA, Guo T, Gaykalova DA, Fakhry C. HEY1 is expressed independent of NOTCH1 and is associated with poor prognosis in head and neck squamous cell carcinoma. Oral Oncol 2018; 82:168-175. [PMID: 29909892 DOI: 10.1016/j.oraloncology.2018.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/12/2018] [Accepted: 05/25/2018] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Notch signaling is frequently altered in head and neck squamous cell carcinoma (HNSCC). However, the nature and clinical implications of this dysregulation are not well understood. We previously described an association of transcriptionally active NOTCH1 Intracellular Domain (NICD1) immunohistochemical (IHC) expression pattern with high-risk pathologic characteristics. Here we further characterize Notch signaling in HNSCC. MATERIALS AND METHODS IHC expression patterns and clinicopathologic associations of Notch pathway molecules were evaluated among 78 tumors with known NOTCH1 mutation status. IHC was performed for JAG1, a NOTCH1 activating ligand, and HEY1, an NICD1 transcriptional target and Notch pathway activation marker. IHC pattern and H-score (% staining × intensity) were recorded and compared to clinicopathologic characteristics and survival. Survival was analyzed using Kaplan Meier method and Cox proportional hazards models (HR). RESULTS JAG1 and NICD1 expression patterns were highly concordant among tumors without truncating NOTCH1 mutations (p < 0.001), but were dissimilar among tumors with truncating NOTCH1 mutations (p = 0.24). There was evidence for JAG1-independent NOTCH1 activation among seven tumors, all with wild-type NOTCH1. HEY1 expression was associated with neither JAG1 nor NICD1 expression, but was associated with NOTCH1 mutation status (p = 0.03). Twelve (16%) tumors expressed HEY1 but not NICD1. Higher HEY1 H-score was significantly associated with worse overall (adjusted hazard ratio [aHR] 2.0, 95% CI = 1.0-4.2) and disease-specific (aHR = 3.3, 95% CI = 1.4-7.9) survival, whereas JAG1 and NICD1 expression were not associated with survival. CONCLUSIONS These findings suggest both NOTCH1-dependent and -independent HEY1 regulation, and imply a previously unrecognized prognostic role for HEY1 in HNSCC.
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Affiliation(s)
- Eleni M Rettig
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 N Caroline St., Baltimore, MD 21287, United States.
| | - Justin A Bishop
- Department of Pathology, Johns Hopkins University School of Medicine, 600 N Wolfe St., Baltimore, MD 21287, United States
| | - Nishant Agrawal
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 N Caroline St., Baltimore, MD 21287, United States
| | - Christine H Chung
- Department of Oncology, Johns Hopkins University School of Medicine, 401 N Broadway, Baltimore, MD 21287, United States
| | - Rajni Sharma
- Department of Pathology, Johns Hopkins University School of Medicine, 600 N Wolfe St., Baltimore, MD 21287, United States
| | - Fernando Zamuner
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 N Caroline St., Baltimore, MD 21287, United States
| | - Ryan J Li
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 N Caroline St., Baltimore, MD 21287, United States
| | - Wayne M Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 N Caroline St., Baltimore, MD 21287, United States
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 N Caroline St., Baltimore, MD 21287, United States
| | - Theresa Guo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 N Caroline St., Baltimore, MD 21287, United States
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 N Caroline St., Baltimore, MD 21287, United States
| | - Carole Fakhry
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 N Caroline St., Baltimore, MD 21287, United States; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St., Baltimore, MD 21205, United States
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29
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Kamran SC, Mouw KW. Applying Precision Oncology Principles in Radiation Oncology. JCO Precis Oncol 2018; 2:1800034. [PMID: 32914000 DOI: 10.1200/po.18.00034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Radiation therapy is a critical component in the curative management of many solid tumor types, and advances in radiation delivery techniques during the past decade have led to improved disease control and quality of life for patients. During the same period, remarkable advances have also been made in understanding the genomic landscape of tumors; however, treatment decisions in radiation oncology continue to depend primarily on clinical and histopathologic characteristics rather than on the genetic features of the tumor or the patient. With the development of novel genomic techniques and their increasing use in clinical practice, radiation oncology is uniquely positioned to leverage these advances to identify novel biomarkers that could inform radiation dose, field, and the use of concurrent systemic agents. Here, we summarize efforts to use genomic techniques to guide radiation decisions, and we highlight some of the current opportunities and challenges that exist in attempting to apply precision oncology principles in radiation oncology.
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Affiliation(s)
- Sophia C Kamran
- and , Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School; and , Harvard Radiation Oncology Program, Boston, MA
| | - Kent W Mouw
- and , Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School; and , Harvard Radiation Oncology Program, Boston, MA
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Clonal evolution and heterogeneity in metastatic head and neck cancer-An analysis of the Austrian Study Group of Medical Tumour Therapy study group. Eur J Cancer 2018; 93:69-78. [PMID: 29477794 DOI: 10.1016/j.ejca.2018.01.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/30/2017] [Accepted: 01/06/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Tumour heterogeneity and clonal evolution within a cancer patient are deemed responsible for relapse in malignancies and present challenges to the principles of targeted therapy, for which treatment modality is often decided based on the molecular pathology of the primary tumour. Nevertheless, the clonal architecture in distant relapse of head and neck cancer is fairly unknown. PATIENTS AND METHODS For this project, we analysed a cohort of 386 patients within the Austrian Registry of head and neck cancer. We identified 26 patients with material from the primary tumour, the distant metastasis after curative first-line treatment and a germline sample for analysis of clonal evolution. After pathological analyses, these samples were analysed using a targeted massively parallel sequencing (MPS) panel of 257 genes known to be recurrently mutated in head and neck cancer plus a genome-wide SNP-set. RESULTS Despite histological diagnosis of distant metastasis, no corresponding mutation in the supposed metastases was found in two of 23 (8.6%) evaluable patients suggesting a primary tumour of the lung instead of a distant metastasis of head and neck cancer. We observed a branched pattern of evolution in 31.6% of the analysed patients. This pattern was associated with a shorter time to distant metastasis, compared with a pattern of punctuated evolution. Structural genomic changes over time were also present in 7 of 12 (60%) evaluable patients with metachronous metastases. CONCLUSION Targeted MPS demonstrated substantial heterogeneity at the time of diagnosis and a complex pattern of evolution during disease progression in head and neck cancer. Copy number analyses revealed additional changes that were not detected by mutational analyses. Mutational and structural changes contribute to tumour heterogeneity at diagnosis and progression.
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Stangl S, Tontcheva N, Sievert W, Shevtsov M, Niu M, Schmid TE, Pigorsch S, Combs SE, Haller B, Balermpas P, Rödel F, Rödel C, Fokas E, Krause M, Linge A, Lohaus F, Baumann M, Tinhofer I, Budach V, Stuschke M, Grosu AL, Abdollahi A, Debus J, Belka C, Maihöfer C, Mönnich D, Zips D, Multhoff G. Heat shock protein 70 and tumor-infiltrating NK cells as prognostic indicators for patients with squamous cell carcinoma of the head and neck after radiochemotherapy: A multicentre retrospective study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG). Int J Cancer 2017; 142:1911-1925. [PMID: 29235112 PMCID: PMC5873418 DOI: 10.1002/ijc.31213] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/03/2017] [Accepted: 11/28/2017] [Indexed: 12/28/2022]
Abstract
Tumor cells frequently overexpress heat shock protein 70 (Hsp70) and present it on their cell surface, where it can be recognized by pre-activated NK cells. In our retrospective study the expression of Hsp70 was determined in relation to tumor-infiltrating CD56+ NK cells in formalin-fixed paraffin embedded (FFPE) tumor specimens of patients with SCCHN (N = 145) as potential indicators for survival and disease recurrence. All patients received radical surgery and postoperative cisplatin-based radiochemotherapy (RCT). In general, Hsp70 expression was stronger, but with variable intensities, in tumor compared to normal tissues. Patients with high Hsp70 expressing tumors (scores 3-4) showed significantly decreased overall survival (OS; p = 0.008), local progression-free survival (LPFS; p = 0.034) and distant metastases-free survival (DMFS; p = 0.044), compared to those with low Hsp70 expression (scores 0-2), which remained significant after adjustment for relevant prognostic variables. The adverse prognostic value of a high Hsp70 expression for OS was also observed in patient cohorts with p16- (p = 0.001), p53- (p = 0.0003) and HPV16 DNA-negative (p = 0.001) tumors. The absence or low numbers of tumor-infiltrating CD56+ NK cells also correlated with significantly decreased OS (p = 0.0001), LPFS (p = 0.0009) and DMFS (p = 0.0001). A high Hsp70 expression and low numbers of tumor-infiltrating NK cells have the highest negative predictive value (p = 0.00004). In summary, a strong Hsp70 expression and low numbers of tumor-infiltrating NK cells correlate with unfavorable outcome following surgery and RCT in patients with SCCHN, and thus serve as negative prognostic markers.
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Affiliation(s)
- Stefan Stangl
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,Department of Radiation Sciences (DRS), Helmholtz Zentrum Munich (HMGU), Institute of Innovative Radiotherapy (iRT), Munich, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Munich, Germany
| | | | - Wolfgang Sievert
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,Department of Radiation Sciences (DRS), Helmholtz Zentrum Munich (HMGU), Institute of Innovative Radiotherapy (iRT), Munich, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Munich, Germany
| | - Maxim Shevtsov
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,Department of Radiation Sciences (DRS), Helmholtz Zentrum Munich (HMGU), Institute of Innovative Radiotherapy (iRT), Munich, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Munich, Germany
| | - Minli Niu
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany
| | - Thomas E Schmid
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,Department of Radiation Sciences (DRS), Helmholtz Zentrum Munich (HMGU), Institute of Innovative Radiotherapy (iRT), Munich, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Munich, Germany
| | - Steffi Pigorsch
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,Department of Radiation Sciences (DRS), Helmholtz Zentrum Munich (HMGU), Institute of Innovative Radiotherapy (iRT), Munich, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Munich, Germany
| | - Stephanie E Combs
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,Department of Radiation Sciences (DRS), Helmholtz Zentrum Munich (HMGU), Institute of Innovative Radiotherapy (iRT), Munich, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Munich, Germany
| | - Bernhard Haller
- Institute of Medical Informatics, Statistics and Epidemiology, Technische Universität München (TUM), Munich, Germany
| | - Panagiotis Balermpas
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Frankfurt, Frankfurt, Germany
| | - Franz Rödel
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Frankfurt, Frankfurt, Germany
| | - Claus Rödel
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Frankfurt, Frankfurt, Germany
| | - Emmanouil Fokas
- Department of Radiotherapy and Oncology, Goethe University Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Frankfurt, Frankfurt, Germany
| | - Mechthild Krause
- OncoRay - National Centre for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Department of Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Dresden, Germany.,Helmholtz-Zentrum Dresden - Rossendorf, Institute of Radiooncology, Berlin, Germany
| | - Annett Linge
- OncoRay - National Centre for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Department of Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Dresden, Germany
| | - Fabian Lohaus
- OncoRay - National Centre for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Department of Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Dresden, Germany
| | - Michael Baumann
- OncoRay - National Centre for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Department of Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Dresden, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Heidelberg, Germany
| | - Inge Tinhofer
- Department of Radiooncology and Radiotherapy, Charite University Hospital Berlin, Berlin, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Berlin, Germany
| | - Volker Budach
- Department of Radiooncology and Radiotherapy, Charite University Hospital Berlin, Berlin, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Berlin, Germany
| | - Martin Stuschke
- Department of Radiotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Essen, Germany
| | - Anca-Ligia Grosu
- Department of Radiation Oncology, Medical Faculty, Medical Centre, University of Freiburg, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Freiburg, Germany
| | - Amir Abdollahi
- German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Heidelberg, Germany
| | - Jürgen Debus
- German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Heidelberg, Germany.,Department of Radiation Oncology, Heidelberg Ion Therapy Centre (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School, Heidelberg, Germany.,National Centre for Radiation Research Oncology (NCRO), University of Heidelberg Medical School, Heidelberg, Germany
| | - Claus Belka
- German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Munich, Germany.,National Centre for Radiation Research Oncology (NCRO), University of Heidelberg Medical School, Heidelberg, Germany.,Department of Radiation Oncology, University Hospital LMU Munich, Munich, Germany.,Clinical Cooperation Group (CCG) Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum, Munich, Germany
| | - Cornelius Maihöfer
- German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Munich, Germany.,National Centre for Radiation Research Oncology (NCRO), University of Heidelberg Medical School, Heidelberg, Germany.,Department of Radiation Oncology, University Hospital LMU Munich, Munich, Germany.,Clinical Cooperation Group (CCG) Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum, Munich, Germany
| | - David Mönnich
- Department of Radiation Oncology, Faculty of Medicine and University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany.,DKTK Consortium Tübingen, Tübingen, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Tübingen, Germany
| | - Daniel Zips
- Department of Radiation Oncology, Faculty of Medicine and University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany.,DKTK Consortium Tübingen, Tübingen, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Tübingen, Germany
| | - Gabriele Multhoff
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,Department of Radiation Sciences (DRS), Helmholtz Zentrum Munich (HMGU), Institute of Innovative Radiotherapy (iRT), Munich, Germany.,German Cancer Research Centre (DKFZ), Heidelberg and German Research Consortium (DKTK), Munich, Germany
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Tronik‐Le Roux D, Renard J, Vérine J, Renault V, Tubacher E, LeMaoult J, Rouas‐Freiss N, Deleuze J, Desgrandschamps F, Carosella ED. Novel landscape of HLA-G isoforms expressed in clear cell renal cell carcinoma patients. Mol Oncol 2017; 11:1561-1578. [PMID: 28815885 PMCID: PMC5664004 DOI: 10.1002/1878-0261.12119] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/21/2017] [Accepted: 07/29/2017] [Indexed: 12/14/2022] Open
Abstract
Immune checkpoints are powerful inhibitory molecules that promote tumor survival. Their blockade is now recognized as providing effective therapeutic benefit against cancer. Human leukocyte antigen G (HLA-G), a recently identified immune checkpoint, has been detected in many types of primary tumors and metastases, in malignant effusions as well as on tumor-infiltrating cells, particularly in patients with clear cell renal cell carcinoma (ccRCC). Here, in order to define a possible anticancer therapy, we used a molecular approach based on an unbiased strategy that combines transcriptome determination and immunohistochemical labeling, to analyze in-depth the HLA-G isoforms expressed in these tumors. We found that the expression of HLA-G is highly variable among tumors and distinct areas of the same tumor, testifying a marked inter- and intratumor heterogeneity. Moreover, our results generate an inventory of novel HLA-G isoforms which includes spliced forms that have an extended 5'-region and lack the transmembrane and alpha-1 domains. So far, these isoforms could not be detected by any method available and their assessment may improve the procedure by which tumors are analyzed. Collectively, our approach provides the first extensive portrait of HLA-G in ccRCC and reveals data that should prove suitable for the tailoring of future clinical applications.
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Affiliation(s)
- Diana Tronik‐Le Roux
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- UMR_E5IUHHôpital Saint‐LouisUniversite Paris DiderotSorbonne Paris CiteFrance
| | - Julie Renard
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- UMR_E5IUHHôpital Saint‐LouisUniversite Paris DiderotSorbonne Paris CiteFrance
| | - Jérôme Vérine
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- Service d'Anatomo‐PathologieAP‐HP, Hôpital Saint‐LouisParisFrance
| | - Victor Renault
- Centre d'Etudes du Polymorphisme HumainFondation Jean DaussetParisFrance
| | - Emmanuel Tubacher
- Centre d'Etudes du Polymorphisme HumainFondation Jean DaussetParisFrance
| | - Joel LeMaoult
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- UMR_E5IUHHôpital Saint‐LouisUniversite Paris DiderotSorbonne Paris CiteFrance
| | - Nathalie Rouas‐Freiss
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- UMR_E5IUHHôpital Saint‐LouisUniversite Paris DiderotSorbonne Paris CiteFrance
| | - Jean‐François Deleuze
- Centre d'Etudes du Polymorphisme HumainFondation Jean DaussetParisFrance
- Centre National de GénotypageInstitut de GénomiqueCEAEvryFrance
| | - François Desgrandschamps
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- Service d'UrologieAP‐HP, Hôpital Saint‐LouisParisFrance
| | - Edgardo D. Carosella
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)Direction de la Recherche Fondamentale (DRF)Service de Recherche en Hemato‐Immunologie (SRHI)ParisFrance
- UMR_E5IUHHôpital Saint‐LouisUniversite Paris DiderotSorbonne Paris CiteFrance
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Niehr F, Eder T, Pilz T, Konschak R, Treue D, Klauschen F, Bockmayr M, Türkmen S, Jöhrens K, Budach V, Tinhofer I. Multilayered Omics-Based Analysis of a Head and Neck Cancer Model of Cisplatin Resistance Reveals Intratumoral Heterogeneity and Treatment-Induced Clonal Selection. Clin Cancer Res 2017; 24:158-168. [PMID: 29061642 DOI: 10.1158/1078-0432.ccr-17-2410] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/04/2017] [Accepted: 10/11/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Platinum-based drugs, in particular cisplatin (cis-diamminedichloridoplatinum(II), CDDP), are used for treatment of squamous cell carcinoma of the head and neck (SCCHN). Despite initial responses, CDDP treatment often results in chemoresistance, leading to therapeutic failure. The role of primary resistance at subclonal level and treatment-induced clonal selection in the development of CDDP resistance remains unknown.Experimental Design: By applying targeted next-generation sequencing, fluorescence in situ hybridization, microarray-based transcriptome, and mass spectrometry-based phosphoproteome analysis to the CDDP-sensitive SCCHN cell line FaDu, a CDDP-resistant subline, and single-cell derived subclones, the molecular basis of CDDP resistance was elucidated. The causal relationship between molecular features and resistant phenotypes was determined by siRNA-based gene silencing. The clinical relevance of molecular findings was validated in patients with SCCHN with recurrence after CDDP-based chemoradiation and the TCGA SCCHN dataset.Results: Evidence of primary resistance at clonal level and clonal selection by long-term CDDP treatment was established in the FaDu model. Resistance was associated with aneuploidy of chromosome 17, increased TP53 copy-numbers and overexpression of the gain-of-function (GOF) mutant variant p53R248L siRNA-mediated knockdown established a causal relationship between mutant p53R248L and CDDP resistance. Resistant clones were also characterized by increased activity of the PI3K-AKT-mTOR pathway. The poor prognostic value of GOF TP53 variants and mTOR pathway upregulation was confirmed in the TCGA SCCHN cohort.Conclusions: Our study demonstrates a link of intratumoral heterogeneity and clonal evolution as important mechanisms of drug resistance in SCCHN and establishes mutant GOF TP53 variants and the PI3K/mTOR pathway as molecular targets for treatment optimization. Clin Cancer Res; 24(1); 158-68. ©2017 AACR.
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Affiliation(s)
- Franziska Niehr
- Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) Partner Site Berlin, Berlin, Germany
| | - Theresa Eder
- Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) Partner Site Berlin, Berlin, Germany
| | - Tanja Pilz
- Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy, Berlin, Germany
| | - Robert Konschak
- Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) Partner Site Berlin, Berlin, Germany
| | - Denise Treue
- Charité, Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Frederick Klauschen
- German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) Partner Site Berlin, Berlin, Germany.,Charité, Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Michael Bockmayr
- Charité, Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Seval Türkmen
- Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Human Genetics, Berlin, Germany
| | - Korinna Jöhrens
- Charité, Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Volker Budach
- Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy, Berlin, Germany
| | - Ingeborg Tinhofer
- Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy, Berlin, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) Partner Site Berlin, Berlin, Germany
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Litwin TR, Clarke MA, Dean M, Wentzensen N. Somatic Host Cell Alterations in HPV Carcinogenesis. Viruses 2017; 9:v9080206. [PMID: 28771191 PMCID: PMC5580463 DOI: 10.3390/v9080206] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/12/2022] Open
Abstract
High-risk human papilloma virus (HPV) infections cause cancers in different organ sites, most commonly cervical and head and neck cancers. While carcinogenesis is initiated by two viral oncoproteins, E6 and E7, increasing evidence shows the importance of specific somatic events in host cells for malignant transformation. HPV-driven cancers share characteristic somatic changes, including apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC)-driven mutations and genomic instability leading to copy number variations and large chromosomal rearrangements. HPV-associated cancers have recurrent somatic mutations in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) and phosphatase and tensin homolog (PTEN), human leukocyte antigen A and B (HLA-A and HLA-B)-A/B, and the transforming growth factor beta (TGFβ) pathway, and rarely have mutations in the tumor protein p53 (TP53) and RB transcriptional corepressor 1 (RB1) tumor suppressor genes. There are some variations by tumor site, such as NOTCH1 mutations which are primarily found in head and neck cancers. Understanding the somatic events following HPV infection and persistence can aid the development of early detection biomarkers, particularly when mutations in precancers are characterized. Somatic mutations may also influence prognosis and treatment decisions.
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Affiliation(s)
- Tamara R Litwin
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA.
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA.
| | - Megan A Clarke
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA.
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA.
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD 20850, USA.
| | - Nicolas Wentzensen
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA.
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Bibault JE, Tinhofer I. The role of Next-Generation Sequencing in tumoral radiosensitivity prediction. Clin Transl Radiat Oncol 2017; 3:16-20. [PMID: 29658008 PMCID: PMC5893518 DOI: 10.1016/j.ctro.2017.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 12/30/2022] Open
Abstract
Next-Generation Sequencing cost has significantly decreased recently. NGS is used to comprehensively assess tumoral radiosensitivity. Personalized and dose-adapted radiotherapy could be achieved through the use of these technologies.
Technological advances have led to more precise radiation delivery, which has resulted in significant clinical gains. A better understanding of tumoral radiosensitivity is still needed to develop strategies and further personalize radiation treatments. Next-Generation Sequencing (NGS) and system biology have significantly transformed the field of oncology in the last two decades, but have only a few clinical applications in radiation oncology. This review describes the technical aspects and evolutions of NGS and discusses the latest clinical applications of genomics to predict tumoral radiosensitivity.
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Affiliation(s)
- Jean-Emmanuel Bibault
- Radiation Oncology Department, Georges Pompidou European Hospital, Assistance Publique - Hôpitaux de Paris, Paris Descartes University, Paris Sorbonne Cité, Paris, France.,INSERM UMR 1138 Team 22: Information Sciences to Support Personalized Medicine, Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - Ingeborg Tinhofer
- Department of Radiooncology and Radiotherapy, Charité University Hospital Berlin, Berlin, Germany
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