1
|
Belcaid L, Bertelsen B, Wadt K, Tuxen I, Spanggaard I, Højgaard M, Benn Sørensen J, Ravn J, Lassen U, Cilius Nielsen F, Rohrberg K, Westmose Yde C. New pathogenic germline variants identified in mesothelioma. Lung Cancer 2023; 179:107172. [PMID: 36944283 DOI: 10.1016/j.lungcan.2023.03.008] [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: 11/15/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND Mesothelioma (MM) is associated with asbestos exposure, tumor heterogeneity and aggressive clinical behavior. Identification of germline pathogenic variants (PVs) in mesothelioma is relevant for identifying potential actionable targets and genetic counseling. METHODS 44 patients underwent whole exome sequencing (WES) or whole genome sequencing (WGS). Germline variants were selected according to association with inherited cancer using a 168-gene in silico panel, and variants classified according to ACMG/AMP classification as pathogenic (class 5) or likely pathogenic (class 4). RESULTS In total, 16 patients (36%) were found to carry pathogenic or likely pathogenic variants in 13 cancer associated genes (ATM, BAP1, BRCA2, CDKN2A, FANCA, FANCC, FANCD2, FANCM, MUTYH, NBN, RAD51B, SDHA and XPC). The germline PVs occurred in DNA repair pathways, including homologous recombination repair (HRR) (75%), nucleotide excision repair (6%), cell cycle regulatory (7%), base excision repair (6%), and hypoxic pathway (6%). Five (31%) patients with a germline PV had a first or second degree relative with mesothelioma compared to none for patients without a germline PV. Previously undiagnosed BRCA2 germline PVs were identified in two patients. Potential actionable targets based on the germline PVs were found in four patients (9%). CONCLUSION This study revealed a high frequency of germline PVs in patients with mesothelioma. Furthermore, we identified germline PVs in two genes (NBN & RAD51B) not previously associated with mesothelioma. The data support germline testing in mesothelioma and provide a rationale for additional investigation of the HRR pathway as a potential actionable target.
Collapse
Affiliation(s)
- Laila Belcaid
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark.
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Karin Wadt
- Dept. of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Ida Tuxen
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Iben Spanggaard
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Martin Højgaard
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Jens Benn Sørensen
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Jesper Ravn
- Dept. of Thoracic Surgery, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Ulrik Lassen
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | | | | |
Collapse
|
2
|
Borch A, Bjerregaard AM, Araujo Barbosa de Lima V, Østrup O, Yde CW, Eklund AC, Mau-Sørensen M, Barra C, Svane IM, Nielsen FC, Funt SA, Lassen U, Hadrup SR. Neoepitope load, T cell signatures and PD-L2 as combined biomarker strategy for response to checkpoint inhibition immunotherapy. Front Genet 2023; 14:1058605. [PMID: 37035751 PMCID: PMC10076713 DOI: 10.3389/fgene.2023.1058605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Immune checkpoint inhibition for the treatment of cancer has provided a breakthrough in oncology, and several new checkpoint inhibition pathways are currently being investigated regarding their potential to provide additional clinical benefit. However, only a fraction of patients respond to such treatment modalities, and there is an urgent need to identify biomarkers to rationally select patients that will benefit from treatment. In this study, we explore different tumor associated characteristics for their association with favorable clinical outcome in a diverse cohort of cancer patients treated with checkpoint inhibitors. We studied 29 patients in a basket trial comprising 12 different tumor types, treated with 10 different checkpoint inhibition regimens. Our analysis revealed that even across this diverse cohort, patients achieving clinical benefit had significantly higher neoepitope load, higher expression of T cell signatures, and higher PD-L2 expression, which also correlated with improved progression-free and overall survival. Importantly, the combination of biomarkers serves as a better predictor than each of the biomarkers alone. Basket trials are frequently used in modern immunotherapy trial design, and here we identify a set of biomarkers of potential relevance across multiple cancer types, allowing for the selection of patients that most likely will benefit from immune checkpoint inhibition.
Collapse
Affiliation(s)
- Annie Borch
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Anne-Mette Bjerregaard
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Department of Bioinformatics and Datamining, Novo Nordisk, Bagsvaerd, Denmark
| | | | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | | | | | | | - Carolina Barra
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Copenhagen University Hospital, Herlev, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Samuel A. Funt
- Weill Cornell Medical College, New York, NY, United States
| | - Ulrik Lassen
- Department of Oncology, Phase 1 Unit, Rigshospitalet, Copenhagen, Denmark
- *Correspondence: Ulrik Lassen, ; Sine Reker Hadrup,
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- *Correspondence: Ulrik Lassen, ; Sine Reker Hadrup,
| |
Collapse
|
3
|
Jacobsen IC, Spanggaard I, Højgaard M, Belcaid L, Qvortrup C, Yde CW, Schmidt AY, Nielsen FC, Willemoe GL, Dam MS, Lassen U, Staal Rohrberg K. Extensive genomic analysis in patients with KRAS-mutated solid tumors shows high frequencies of concurrent alterations and potential targets but has limited clinical impact. Acta Oncol 2022; 61:1499-1506. [PMID: 36529989 DOI: 10.1080/0284186x.2022.2156809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND This study aimed to investigate the distribution and frequency of concurrent alterations in different cancers across KRAS subtypes and in different KRAS subtypes across cancers, and to identify potentially actionable targets and patients who received targeted treatment matched to their genomic profile (GP). MATERIALS AND METHODS In this descriptive and single-center study, we included 188 patients with solid tumors harboring KRAS mutations in codon 12, 13, 61, 117, or 146, referred to the Phase 1 Unit, Rigshospitalet, Copenhagen, Denmark from mid-2016 to 2020. Genomic co-alterations were detected with whole-exome sequencing, RNA sequencing, SNP array, and mRNA expression array on fresh biopsies. The study is part of the Copenhagen Prospective Personalized Oncology study (NCT02290522). RESULTS The majority of patients had colorectal cancer (60.1%), non-small cell lung cancer (11.2%), or pancreatic cancer (10.6%). Most tumors were KRAS-mutated in codon 12 or 13 (93.7%) including G12D (27.1%), G12V (26.6%), G12C (11.7%), and G13D (11.2%). A total of 175 different co-alterations were found, most frequently pathogenic APC and TP53 mutations (55.9% and 46.4%, respectively) and high expression of CEACAM5 (73.4%). Different cancers and KRAS subtypes showed different patterns of co-alterations, and 157 tumors (83.5%) had potentially actionable targets with varying evidence of targetability (assessed using ESMO Scale for Clinical Actionability of molecular Targets). Of the 188 patients included in the study, 15 (7.4%) received treatment matched to their GP (e.g., immunotherapy and synthetic lethality drugs), of whom one had objective partial response according to Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. CONCLUSION Performing extensive genomic analysis in patients with known KRAS-mutated solid tumors may contribute with information to the genomic landscape of cancers and identify targets for immunotherapy or synthetic lethality drugs, but currently appears to have overall limited clinical impact, as few patients received targeted therapy matched to their GP.
Collapse
Affiliation(s)
- Ida Christine Jacobsen
- Phase 1 Unit, Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Iben Spanggaard
- Phase 1 Unit, Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Martin Højgaard
- Phase 1 Unit, Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Laïla Belcaid
- Phase 1 Unit, Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Camilla Qvortrup
- Phase 1 Unit, Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Christina Westmose Yde
- Center for Genomic Medicine, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Ane Yde Schmidt
- Center for Genomic Medicine, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Gro Linno Willemoe
- Department of Pathology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Mikkel Seidelin Dam
- Department of Diagnostic Radiology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Ulrik Lassen
- Phase 1 Unit, Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Staal Rohrberg
- Phase 1 Unit, Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
4
|
Bertelsen B, Tuxen IV, Yde CW, Gabrielaite M, Torp MH, Kinalis S, Oestrup O, Rohrberg K, Spangaard I, Santoni-Rugiu E, Wadt K, Mau-Sorensen M, Lassen U, Nielsen FC. High frequency of pathogenic germline variants within homologous recombination repair in patients with advanced cancer. NPJ Genom Med 2019; 4:13. [PMID: 31263571 PMCID: PMC6588611 DOI: 10.1038/s41525-019-0087-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/15/2019] [Indexed: 12/31/2022] Open
Abstract
Genomic screening of cancer patients for predisposing variants is traditionally based on age at onset, family history and type of cancer. Whereas the clinical guidelines have proven efficient in identifying families exhibiting classical attributes of hereditary cancer, the frequency of patients with alternative presentations is unclear. We identified and characterized germline variants in 636 patients with advanced solid cancer using whole exome sequencing. Pathogenic and likely pathogenic germline variants among 168 genes associated with hereditary cancer were considered. These variants were identified in 17.8% of the patients and within a wide range of cancer types. In particular, patients with mesothelioma, ovarian cancer, cervical cancer, urothelial cancer, and cancer of unknown primary origin displayed high frequencies of pathogenic variants. Variants were predominantly found in DNA-repair pathways and about half were within genes involved in homologous recombination repair. Twenty-two BRCA1 and BRCA2 germline variants were identified in 12 different cancer types, of which 10 (45%) were not previously identified in these patients based on the current clinical guidelines. Loss of heterozygosity and somatic second hits were identified in several of the affected genes, supporting possible causality for cancer development. A potential treatment target based on the pathogenic germline variant could be suggested in 25 patients (4%). The study demonstrates a high frequency of pathogenic germline variants in the homologous recombination pathway in patients with advanced solid cancers. We infer that genetic screening in this group of patients may reveal high-risk families and identify patients with potential PARP inhibitor sensitive tumors.
Collapse
Affiliation(s)
| | - Ida Viller Tuxen
- 2The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | | | | | | | - Savvas Kinalis
- 1Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Olga Oestrup
- 1Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Kristoffer Rohrberg
- 2The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | - Iben Spangaard
- 2The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | | | - Karin Wadt
- 4Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Morten Mau-Sorensen
- 2The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | - Ulrik Lassen
- 2The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | | |
Collapse
|
5
|
Ahlborn LB, Rohrberg KS, Gabrielaite M, Tuxen IV, Yde CW, Spanggaard I, Santoni-Rugiu E, Nielsen FC, Lassen U, Mau-Sorensen M, Østrup O. Application of cell-free DNA for genomic tumor profiling: a feasibility study. Oncotarget 2019; 10:1388-1398. [PMID: 30858924 PMCID: PMC6402712 DOI: 10.18632/oncotarget.26642] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/17/2019] [Indexed: 12/19/2022] Open
Abstract
Purpose Access to genomic tumor material is required to select patients for targeted therapies. However, tissue biopsies are not always feasible and therefore circulating cell-free DNA (cfDNA) has emerged as an alternative. Here we investigate the utility of cfDNA for genomic tumor profiling in the phase I setting. Study design Peripheral blood was collected from patients with advanced solid cancers eligible for phase I treatment. Patients failing the initial tissue biopsy due to inaccessible lesions or insufficient tumor cellularity (<10%) were included in the study. Genomic profiling of cfDNA including whole exome sequencing (WES) and somatic copy number alterations (SCNAs) analysis (OncoScan). Results Plasma cfDNA was pro- and retrospectively profiled from 24 and 20 patients, respectively. The median turnaround time was 29 days (N= 24, range 13-87 days) compared to tissue re-analyses of median 60 days (N= 6, range 29-98). Selected cancer-associated alterations (SCAAs) were identified in 70% (31/44) of patients, predominantly by WES due to the low sensitivity of OncoScan on cfDNA. Primarily, inaccessible cases of prostate and lung cancers could benefit from cfDNA profiling. In contrast, breast cancer patients showed a low level of tumor-specific cfDNA which might be due to cancer type and/or active treatment at the time of plasma collection. Conclusion Plasma cfDNA profiling using WES is feasible within a clinically relevant timeframe and represents an alternative to invasive tissue biopsies to identify possible treatment targets. Especially, difficult-to-biopsy cancers can benefit from cfDNA profiling, but tumor tissue remains the gold standard for molecular analyses.
Collapse
Affiliation(s)
- Lise B Ahlborn
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark.,Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Kristoffer S Rohrberg
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Migle Gabrielaite
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Ida V Tuxen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Christina W Yde
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Iben Spanggaard
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Ulrik Lassen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Morten Mau-Sorensen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| |
Collapse
|
6
|
Ratain MJ. The Molecular Profiling Lottery: More Accuracy, Less Precision, and No Cost. Clin Cancer Res 2018; 25:1136-1138. [DOI: 10.1158/1078-0432.ccr-18-3513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/22/2018] [Accepted: 11/30/2018] [Indexed: 11/16/2022]
|
7
|
Tuxen IV, Rohrberg KS, Oestrup O, Ahlborn LB, Schmidt AY, Spanggaard I, Hasselby JP, Santoni-Rugiu E, Yde CW, Mau-Sørensen M, Nielsen FC, Lassen U. Copenhagen Prospective Personalized Oncology (CoPPO)-Clinical Utility of Using Molecular Profiling to Select Patients to Phase I Trials. Clin Cancer Res 2018; 25:1239-1247. [PMID: 30274980 DOI: 10.1158/1078-0432.ccr-18-1780] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/21/2018] [Accepted: 09/27/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE We evaluated the clinical benefit of tumor molecular profiling to select treatment in the phase I setting. EXPERIMENTAL DESIGN Patients with advanced solid cancers and exhausted treatment options referred to a phase I unit were included in a prospective, single-center, single-arm open-label study (NCT02290522). Tumor biopsies were obtained for comprehensive genomic analysis including whole-exome sequencing and RNA sequencing. When possible, patients were treated with regimen matched to the genomic profile. Primary endpoint was progression-free survival (PFS). RESULTS From May 2013 to January 2017, a total of 591 patients were enrolled, with 500 patients undergoing biopsy. Genomic profiles were obtained in 460 patients and a potential actionable target was identified in 352 (70%) of 500 biopsied patients. A total of 101 patients (20%) received matched treatment based on either gene mutations or RNA expression levels of targets available in early clinical trials or off-label treatment. Objective response according to RECIST1.1 was observed in 15 of 101 patients (0% complete response, 15% partial response), with a median PFS of 12 weeks (95% confidence interval, 9.9-14.4). CONCLUSIONS Our study supports the feasibility of genomic profiling to select patients in the phase I setting and suggests that genomic matching can be beneficial for a minor subset of patients with no other treatment options. Randomized studies may validate this assumption.See related commentary by Ratain, p. 1136.
Collapse
Affiliation(s)
- Ida Viller Tuxen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | | | - Olga Oestrup
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Lise Barlebo Ahlborn
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Ane Yde Schmidt
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Iben Spanggaard
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | - Jane P Hasselby
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | | | | | - Morten Mau-Sørensen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | | | - Ulrik Lassen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark.
| |
Collapse
|
8
|
Ahlborn LB, Tuxen IV, Mouliere F, Kinalis S, Schmidt AY, Rohrberg KS, Santoni-Rugiu E, Nielsen FC, Lassen U, Yde CW, Oestrup O, Mau-Sorensen M. Circulating tumor DNA as a marker of treatment response in BRAF V600E mutated non-melanoma solid tumors. Oncotarget 2018; 9:32570-32579. [PMID: 30220966 PMCID: PMC6135692 DOI: 10.18632/oncotarget.25948] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/29/2018] [Indexed: 01/31/2023] Open
Abstract
Purpose We evaluated longitudinal tracking of BRAF V600E in circulating cell-free DNA (cfDNA) as a marker of treatment response to BRAF inhibitor (BRAFi) combination therapies in non-melanoma solid tumors included in the Copenhagen Prospective Personalized Oncology (CoPPO) program. Experimental design Patients with BRAF V600E-mutated tumors were treated with combination therapies including BRAFi. Quantification of mutant cfDNA from plasma was determined and correlated to clinical outcomes. Exome sequencing was performed to identify possible resistance mutations. Results Twenty-three patients had BRAF-mutated tumors out of 455 patients included in CoPPO and 17 started BRAFi combination (EGFRi/MEKi) therapy. Tumor responses were achieved in 8 out of 16 evaluable patients and the median overall- and progression-free survival (OS and PFS) was 15 and 4.8 months, respectively. Longitudinal measurements of BRAF V600E-mutant cfDNA indicated disease progression prior to radiological evaluation and a reduction in the mutant fraction of more than 50% after 4 and 12 weeks of therapy was associated with a significantly longer PFS (p=0.003 and p=0.029) and OS (p=0.029 and p=0.017). Furthermore, the baseline mutant fraction and total level of cfDNA positively correlated with tumor burden (p=0.026 and p=0.024). Finally, analysis of cfDNA at progression revealed novel mutations potentially affecting the MAPK pathway. Conclusion BRAFi combination therapies showed a response rate of 50% in BRAF V600E-mutated non-melanoma tumors. The fraction of BRAF-mutant cfDNA represent a sensitive indicator for clinical outcomes with plasma collected at week 4 and 12 as crucial time points for monitoring response and disease progression.
Collapse
Affiliation(s)
- Lise Barlebo Ahlborn
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark.,Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Ida Viller Tuxen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Savvas Kinalis
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Ane Y Schmidt
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Kristoffer Staal Rohrberg
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Ulrik Lassen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | | | - Olga Oestrup
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Morten Mau-Sorensen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| |
Collapse
|
9
|
Global trends in the distribution of cancer types among patients in oncology phase I trials, 1991-2015. Invest New Drugs 2018; 37:166-174. [PMID: 30083961 DOI: 10.1007/s10637-018-0654-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 07/31/2018] [Indexed: 12/26/2022]
Abstract
Background Systematic analyses regarding cancer types of patients enrolled in oncology phase I trials are scarce. The global distribution, time-dependent change, and regional differences were evaluated. Methods A systematic search of the PubMed database, in which all single-agent phase I trials permitting the enrollment of all-comer patients with any type of solid tumor published between January 1991 and December 2015 were specified, was performed. Trials expected to enroll specific patient populations were excluded according to predefined criteria. Results Eight hundred and sixty-six eligible trials, which had enrolled 29,112 advanced solid tumor patients, were identified. Colorectal (n = 7510; 25.8%) and lung cancer (n = 3212; 11.0%) were the most prevalent solid tumors, followed by sarcoma (n = 1756; 6.0%), breast cancer (n = 1623; 5.6%), and renal cancer (n = 1589; 5.5%). The proportion of patients with either colorectal or lung cancer tended to decrease over time. The proportion of trials, in which patients with either of these two cancers accounted for ≥50.0% of the total number of patients in each trial, also decreased: 33 of 67 trials (31/67) (46.3%) in 1991-1995, 58/142 (40.8%) in 1996-2000, 59/223 (26.5%) in 2001-2005, 38/189 (20.1%) in 2006-2010, and 41/245 (16.7%) in 2011-2015. Instead, the proportion of patients with various types of cancer increased, leading to diversification of enrolled patients. Conclusions The distribution of cancer types among patients in phase I trials has changed. The comprehensive review of the distribution of solid tumor types could contribute to flexible trial designs and optimal patient recruitment.
Collapse
|
10
|
Sundar R, Custodio A, Petruckevich A, Chénard-Poirier M, Ameratunga M, Collins D, Lim J, Kaye SB, Tunariu N, Banerji U, de Bono J, Lopez J. Clinical Outcome of Patients with Advanced Biliary Tract Cancer in a Dedicated Phase I Unit. Clin Oncol (R Coll Radiol) 2018; 30:185-191. [PMID: 29224898 DOI: 10.1016/j.clon.2017.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/19/2017] [Accepted: 11/22/2017] [Indexed: 11/25/2022]
Abstract
AIMS Advanced biliary tract carcinomas (ABC) are malignancies with limited effective therapies for advanced disease. There is little published evidence of outcomes of ABC patients participating in phase I clinical trials. MATERIALS AND METHODS Patient characteristics, treatment details and outcomes of ABC patients treated at a dedicated phase I unit were captured and analysed from case and trial records. RESULTS In total, 123 ABC patients were included in the study, of which 48 patients participated in 41 different phase I trials; 75 (61%) did not participate due to rapid disease progression or patient choice. Molecular characterisation of tumours using a targeted panel was conducted in 15 (31%), yielding several potentially actionable mutations, including BRCA, PIK3CA, FGFR, AKT and PTEN loss. Of the 39 evaluable patients there was one exceptional responder. Eighteen (46%) other patients achieved stable disease as their best response, with a clinical benefit rate at 4 months of 10%. Treatment was generally well tolerated with grade 3 or 4 adverse events only observed in eight patients (17 %), of which six were drug related and led to trial discontinuation in one (3%), with no toxicity-related deaths. CONCLUSION Carefully selected ABC patients have been found to tolerate experimental phase I clinical trials without excess toxicity. The aggressive nature of this disease warrants consideration of early referral to a phase I unit. Future work will require comprehensive molecular profiling in an attempt to understand the biology underlying the exceptional responders and to match patients in real-time to targeted therapies.
Collapse
Affiliation(s)
- R Sundar
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK; National University Health System, Singapore
| | - A Custodio
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK
| | - A Petruckevich
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK
| | - M Chénard-Poirier
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK
| | - M Ameratunga
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK
| | - D Collins
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK
| | - J Lim
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK; National University Health System, Singapore
| | - S B Kaye
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK
| | - N Tunariu
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK
| | - U Banerji
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK
| | - J de Bono
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK
| | - J Lopez
- Royal Marsden Hospital & The Institute of Cancer Research, London, UK.
| |
Collapse
|
11
|
Krolewski AS, Skupien J, Rossing P, Warram JH. Fast renal decline to end-stage renal disease: an unrecognized feature of nephropathy in diabetes. Kidney Int 2017; 91:1300-1311. [PMID: 28366227 PMCID: PMC5429989 DOI: 10.1016/j.kint.2016.10.046] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/11/2016] [Accepted: 10/19/2016] [Indexed: 01/22/2023]
Abstract
A new model of diabetic nephropathy in type 1 diabetes emerged from our studies of Joslin Clinic patients. The dominant feature is progressive renal decline, not albuminuria. This decline is a unidirectional process commencing while patients have normal renal function and, in the majority, progressing steadily (linearly) to end-stage renal disease (ESRD). While an individual's rate of renal decline is constant, the estimated glomerular filtration rate (eGFR) slope varies widely among individuals from -72 to -3.0 ml/min/year. Kidney Disease: Improving Global Outcomes guidelines define rapid progression as rate of eGFR declines > 5 ml/min/year, a value exceeded by 80% of patients in Joslin's type 1 diabetes ESRD cohort. The extraordinary range of slopes within the rapid progression category prompted us to partition it into "very fast," "fast" and "moderate" decline. We showed, for the first time, that very fast and fast decline from normal eGFR to ESRD within 2 to 10 years constitutes 50% of the Joslin cohort. In this review we present data about frequency of fast decliners in both diabetes types, survey some mechanisms underlying fast renal decline, discuss methods of identifying patients at risk and comment on the need for effective therapeutic interventions. Whether the initiating mechanism of fast renal decline affects glomerulus, tubule, interstitium or vasculature is unknown. Since no animal model mimics progressive renal decline, studies in humans are needed. Prospective studies searching for markers predictive of the rate of renal decline yield findings that may make detection of fast decliners feasible. Identifying such patients will be the foundation for developing effective individualized methods to prevent or delay onset of ESRD in diabetes.
Collapse
Affiliation(s)
- Andrzej S Krolewski
- Research Division of Joslin Diabetes Center, Boston, Massachusetts, USA; Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
| | - Jan Skupien
- Department of Metabolic Diseases, Jagellonian University Medical College, Krakow, Poland
| | - Peter Rossing
- Steno Diabetes Center, Gentofte, Denmark; University of Copenhagen, Faculty of Health, Copenhagen, Denmark
| | - James H Warram
- Research Division of Joslin Diabetes Center, Boston, Massachusetts, USA
| |
Collapse
|
12
|
Østrup O, Ahlborn LB, Lassen U, Mau-Sørensen M, Nielsen FC. Detection of copy number alterations in cell-free tumor DNA from plasma. BBA CLINICAL 2017; 7:120-126. [PMID: 28417079 PMCID: PMC5390666 DOI: 10.1016/j.bbacli.2017.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/21/2017] [Accepted: 03/28/2017] [Indexed: 12/22/2022]
Abstract
Background Somatic copy number alterations (SCNAs) occurring in tumors can provide information about tumor classification, patient's outcome or treatment targets. Liquid biopsies, incl. plasma samples containing circulating cell-free tumor DNA (ccfDNA) can be used to assess SCNAs for clinical purposes, however specify and reliability of methods have to be tested. Methods SNP microarrays (Affymetrix) were used to generate whole-genome copy number profiles from plasma ccfDNA (OncoScan) and paired tumor biopsies (CytoScan) from ten patients with metastatic cancers. Numerical, segmental and focal SCNAs were assessed using ASCAT/TuScan and SNP-FASST2. Results Aberrations in ccfDNA in 4 patients resembled numerical (76%) and segmental (80%) aberrations in tDNA. Three patients represented low correlation due to postponed sampling time, ccfDNA quality and possible treatment interference. Breakpoints of high-amplitude amplification were assessed with high accuracy and relative breakpoints difference of only 7% (0.02–37%). Similarly, biallelic losses were reliably detected. Array was 100% successful in detection of SCNAs on clinically relevant genes compared to SCNAs in tumor biopsies. Tracking of SCNAs changes during the treatment course of one patient also indicated that apoptosis/necrosis of non-cancerous cells presumably induced by treatment can influence ccfDNA composition and introduce false-negative findings into the analysis of liquid biopsies. Conclusions Genomic alterations detected in ccfDNA from liquid biopsies by comprehensive SNP array are reliable source for information for stratification of patients for targeted treatment. General significance Clinically relevant SCNAs can be detected in ccfDNA with high resolution and can therefore serve as an alternative to tumor biopsy in defining treatment targets. Genome-wide copy number alterations can be detected in tumor ccfDNA isolated from blood. Alterations in ccfDNA reflect alterations in corresponding tumor. Array-based technology assigns alterations break-points with high precision. Composition of ccfDNA can be altered by treatment.
Collapse
Affiliation(s)
- Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen Ø, Denmark
| | - Lise Barlebo Ahlborn
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen Ø, Denmark.,Department of Oncology, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen Ø, Denmark
| | - Ulrik Lassen
- Department of Oncology, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen Ø, Denmark
| | - Morten Mau-Sørensen
- Department of Oncology, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen Ø, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen Ø, Denmark
| |
Collapse
|
13
|
Chang HR, Park HS, Ahn YZ, Nam S, Jung HR, Park S, Lee SJ, Balch C, Powis G, Ku JL, Kim YH. Improving gastric cancer preclinical studies using diverse in vitro and in vivo model systems. BMC Cancer 2016; 16:200. [PMID: 26955870 PMCID: PMC4784390 DOI: 10.1186/s12885-016-2232-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/29/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND "Biomarker-driven targeted therapy," the practice of tailoring patients' treatment to the expression/activity levels of disease-specific genes/proteins, remains challenging. For example, while the anti-ERBB2 monoclonal antibody, trastuzumab, was first developed using well-characterized, diverse in vitro breast cancer models (and is now a standard adjuvant therapy for ERBB2-positive breast cancer patients), trastuzumab approval for ERBB2-positive gastric cancer was largely based on preclinical studies of a single cell line, NCI-N87. Ensuing clinical trials revealed only modest patient efficacy, and many ERBB2-positive gastric cancer (GC) patients failed to respond at all (i.e., were inherently recalcitrant), or succumbed to acquired resistance. METHOD To assess mechanisms underlying GC insensitivity to ERBB2 therapies, we established a diverse panel of GC cells, differing in ERBB2 expression levels, for comprehensive in vitro and in vivo characterization. For higher throughput assays of ERBB2 DNA and protein levels, we compared the concordance of various laboratory quantification methods, including those of in vitro and in vivo genetic anomalies (FISH and SISH) and xenograft protein expression (Western blot vs. IHC), of both cell and xenograft (tissue-sectioned) microarrays. RESULTS The biomarker assessment methods strongly agreed, as did correlation between RNA and protein expression. However, although ERBB2 genomic anomalies showed good in vitro vs. in vivo correlation, we observed striking differences in protein expression between cultured cells and mouse xenografts (even within the same GC cell type). Via our unique pathway analysis, we delineated a signaling network, in addition to specific pathways/biological processes, emanating from the ERBB2 signaling cascade, as a potential useful target of clinical treatment. Integrated analysis of public data from gastric tumors revealed frequent (10 - 20 %) amplification of the genes NFKBIE, PTK2, and PIK3CA, each of which resides in an ERBB2-derived subpathway network. CONCLUSION Our comprehensive bioinformatics analyses of highly heterogeneous cancer cells, combined with tumor "omics" profiles, can optimally characterize the expression patterns and activity of specific tumor biomarkers. Subsequent in vitro and in vivo validation, of specific disease biomarkers (using multiple methodologies), can improve prediction of patient stratification according to drug response or nonresponse.
Collapse
Affiliation(s)
- Hae Ryung Chang
- New Experimental Therapeutics Branch, National Cancer Center of Korea, Ilsan, Goyang-si, Gyeonggi-do, Republic of Korea. .,Cancer Biology Research Laboratory, Institut Pasteur Korea, Bundang, Seongnam-si, Gyeonggi-do, Republic of Korea.
| | - Hee Seo Park
- Animal Sciences Branch, National Cancer Center of Korea, Ilsan, Goyang-si, Gyeonggi-do, Republic of Korea.
| | - Young Zoo Ahn
- New Experimental Therapeutics Branch, National Cancer Center of Korea, Ilsan, Goyang-si, Gyeonggi-do, Republic of Korea.
| | - Seungyoon Nam
- New Experimental Therapeutics Branch, National Cancer Center of Korea, Ilsan, Goyang-si, Gyeonggi-do, Republic of Korea. .,Department of Life Sciences, College of BioNano Technology, Gachon University, Sungnam, South Korea. .,College of Medicine, Gachon University, Incheon, South Korea.
| | - Hae Rim Jung
- New Experimental Therapeutics Branch, National Cancer Center of Korea, Ilsan, Goyang-si, Gyeonggi-do, Republic of Korea.
| | - Sungjin Park
- New Experimental Therapeutics Branch, National Cancer Center of Korea, Ilsan, Goyang-si, Gyeonggi-do, Republic of Korea. .,Department of Life Sciences, College of BioNano Technology, Gachon University, Sungnam, South Korea. .,College of Medicine, Gachon University, Incheon, South Korea.
| | - Sang Jin Lee
- Animal Sciences Branch, National Cancer Center of Korea, Ilsan, Goyang-si, Gyeonggi-do, Republic of Korea.
| | - Curt Balch
- Department of Pharmacology and Experimental Therapeutics, University of Toledo College of Pharmacy, Toledo, OH, USA.
| | - Garth Powis
- Cancer Center, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA.
| | - Ja-Lok Ku
- SNU Korean Cell Line Bank, Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
| | - Yon Hui Kim
- New Experimental Therapeutics Branch, National Cancer Center of Korea, Ilsan, Goyang-si, Gyeonggi-do, Republic of Korea. .,Cancer Biology Research Laboratory, Institut Pasteur Korea, Bundang, Seongnam-si, Gyeonggi-do, Republic of Korea.
| |
Collapse
|
14
|
Schiefer AI, Parlow L, Gabler L, Mesteri I, Koperek O, von Deimling A, Streubel B, Preusser M, Lehmann A, Kellner U, Pauwels P, Lambin S, Dietel M, Hummel M, Klauschen F, Birner P, Möbs M. Multicenter Evaluation of a Novel Automated Rapid Detection System of BRAF Status in Formalin-Fixed, Paraffin-Embedded Tissues. J Mol Diagn 2016; 18:370-377. [PMID: 26921540 DOI: 10.1016/j.jmoldx.2015.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 12/01/2015] [Accepted: 12/09/2015] [Indexed: 12/20/2022] Open
Abstract
The mutated BRAF oncogene represents a therapeutic target in malignant melanoma. Because BRAF mutations are also involved in the pathogenesis of other human malignancies, the use of specific BRAF inhibitors might also be extended to other diseases in the future. A prerequisite for the clinical application of BRAF inhibitors is the reliable detection of activating BRAF mutations in routine histopathological samples. In a multicenter approach, we evaluated a novel and fully automated PCR-based system (Idylla) capable of detecting BRAF V600 mutations in formalin-fixed, paraffin-embedded tissue within 90 minutes with high sensitivity. We analyzed a total of 436 samples with the Idylla system. Valid results were obtained in 421 cases (96.56%). Its performance was compared with conventional methods (pyrosequencing or Sanger sequencing). Concordant results were obtained in 406 cases (96.90%). Reanalysis of eight discordant samples by next-generation sequencing and/or pyrosequencing with newly extracted DNA and the BRAF RGQ Kit confirmed the Idylla result in seven cases, resulting in an overall agreement of 98.57%. In conclusion, the Idylla system is a highly reliable and sensitive platform for detection of BRAF V600 mutations in formalin-fixed, paraffin-embedded material, providing an efficient alternative to conventional diagnostic methods, particularly for routine diagnostics laboratories with limited experience in molecular pathology.
Collapse
Affiliation(s)
- Ana-Iris Schiefer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Laura Parlow
- Institute of Pathology, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Lisa Gabler
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | | | - Oskar Koperek
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, and Clinical Cooperation Unit Neuropathology, DKFZ and DKTK, Heidelberg, Germany
| | - Berthold Streubel
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Matthias Preusser
- Division of Oncology, Department of Internal Medicine I, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Annika Lehmann
- Institute of Pathology, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Udo Kellner
- Department of Pathology, Johannes Wesling Klinikum Minden, Minden, Germany
| | - Patrick Pauwels
- Department of Pathology, Antwerp University Hospital, Edegem, Belgium
| | - Suzan Lambin
- Department of Pathology, Antwerp University Hospital, Edegem, Belgium
| | - Manfred Dietel
- Institute of Pathology, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Michael Hummel
- Institute of Pathology, Charité-Universitaetsmedizin Berlin, Berlin, Germany.
| | - Frederick Klauschen
- Institute of Pathology, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Peter Birner
- Department of Pathology, Medical University of Vienna, Vienna, Austria.
| | - Markus Möbs
- Institute of Pathology, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| |
Collapse
|
15
|
|
16
|
Karki R, Pandya D, Elston RC, Ferlini C. Defining "mutation" and "polymorphism" in the era of personal genomics. BMC Med Genomics 2015; 8:37. [PMID: 26173390 PMCID: PMC4502642 DOI: 10.1186/s12920-015-0115-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 07/06/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The growing advances in DNA sequencing tools have made analyzing the human genome cheaper and faster. While such analyses are intended to identify complex variants, related to disease susceptibility and efficacy of drug responses, they have blurred the definitions of mutation and polymorphism. DISCUSSION In the era of personal genomics, it is critical to establish clear guidelines regarding the use of a reference genome. Nowadays DNA variants are called as differences in comparison to a reference. In a sequencing project Single Nucleotide Polymorphisms (SNPs) and DNA mutations are defined as DNA variants detectable in >1 % or <1 % of the population, respectively. The alternative use of the two terms mutation or polymorphism for the same event (a difference as compared with a reference) can lead to problems of classification. These problems can impact the accuracy of the interpretation and the functional relationship between a disease state and a genomic sequence. We propose to solve this nomenclature dilemma by defining mutations as DNA variants obtained in a paired sequencing project including the germline DNA of the same individual as a reference. Moreover, the term mutation should be accompanied by a qualifying prefix indicating whether the mutation occurs only in somatic cells (somatic mutation) or also in the germline (germline mutation). We believe this distinction in definition will help avoid confusion among researchers and support the practice of sequencing the germline and somatic tissues in parallel to classify the DNA variants thus defined as mutations.
Collapse
Affiliation(s)
- Roshan Karki
- Danbury Hospital Research Institute, Western Connecticut Health Network, 131 West Street, Danbury, CT, 06810, USA
| | - Deep Pandya
- Danbury Hospital Research Institute, Western Connecticut Health Network, 131 West Street, Danbury, CT, 06810, USA
| | - Robert C Elston
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Cristiano Ferlini
- Danbury Hospital Research Institute, Western Connecticut Health Network, 131 West Street, Danbury, CT, 06810, USA.
| |
Collapse
|
17
|
Yang JJ, Wu YL. Insight into early-phase trials for lung cancer in the United States. CHINESE JOURNAL OF CANCER 2015; 34:288-94. [PMID: 26162603 PMCID: PMC4593356 DOI: 10.1186/s40880-015-0027-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/15/2015] [Indexed: 01/28/2023]
Abstract
Introduction Few data have been published comparing early-phase trials for lung cancer between China and the United States (US). This study was to investigate the differences of phase 1 trials for lung cancer between these two countries. Methods In 2014, a cross-sectional survey was conducted to compare phase 1 trials for lung cancer between the Guangdong Lung Cancer Institute (GLCI), the University of Wisconsin Carbone Cancer Center (UWCCC), and the University of Texas MD Anderson Cancer Center (MDACC). Results We found that the GLCI had a lower percentage of phase 1 lung cancer trials than the MDACC in December 2014 (23.8% [5/21] vs. 59.8% [28/47], P = 0.006) and the UWCCC in September 2014 (16.7% [3/18] vs. 34.8% [8/23], P = 0.345). Descriptive analyses were performed for early-phase trials conducted by the Cancer Therapy Evaluation Program at the National Cancer Institute (CTEP/NCI), the MDACC, and the Chinese Thoracic Oncology Group (CTONG). There were 149 ongoing early-phase trials in the Department of Investigational Cancer Therapeutics (Phase 1 program) at the MDACC in October 2014. In contrast, no phase 1 trials had been initiated by the CTONG since its establishment in 2007. Conclusions These data suggest that a significantly higher percentage of phase 1 trials for lung cancer were conducted in the US than in China. Early-phase oncology trials with robust preclinical data had a higher chance of being approved by the Investigational Drug Branch at the CTEP/NCI. Given the importance of early-phase oncology trials in developing innovative cancer medicines, such studies should be highly encouraged and strategically funded in China.
Collapse
Affiliation(s)
- Jin-Ji Yang
- Guangdong Lung Cancer Institute (GLCI), Guangdong General Hospital (GGH), Guangdong Academy of Medical Sciences (GAMS), Guangzhou, Guangdong, 510080, P.R. China.
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute (GLCI), Guangdong General Hospital (GGH), Guangdong Academy of Medical Sciences (GAMS), Guangzhou, Guangdong, 510080, P.R. China.
| |
Collapse
|
18
|
Osborn JL, Greer SF. Metastatic melanoma cells evade immune detection by silencing STAT1. Int J Mol Sci 2015; 16:4343-61. [PMID: 25690042 PMCID: PMC4346960 DOI: 10.3390/ijms16024343] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/11/2015] [Indexed: 12/31/2022] Open
Abstract
Transcriptional activation of major histocompatibility complex (MHC) I and II molecules by the cytokine, interferon γ (IFN-γ), is a key step in cell-mediated immunity against pathogens and tumors. Recent evidence suggests that suppression of MHC I and II expression on multiple tumor types plays important roles in tumor immunoevasion. One such tumor is malignant melanoma, a leading cause of skin cancer-related deaths. Despite growing awareness of MHC expression defects, the molecular mechanisms by which melanoma cells suppress MHC and escape from immune-mediated elimination remain unknown. Here, we analyze the dysregulation of the Janus kinase (JAK)/STAT pathway and its role in the suppression of MHC II in melanoma cell lines at the radial growth phase (RGP), the vertical growth phase (VGP) and the metastatic phase (MET). While RGP and VGP cells both express MHC II, MET cells lack not only MHC II, but also the critical transcription factors, interferon response factor (IRF) 1 and its upstream activator, signal transducer and activator of transcription 1 (STAT1). Suppression of STAT1 in vitro was also observed in patient tumor samples, suggesting STAT1 silencing as a global mechanism of MHC II suppression and immunoevasion.
Collapse
Affiliation(s)
- JoDi Lynn Osborn
- Division of Cellular Biology and Immunology, Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
| | - Susanna F Greer
- Division of Cellular Biology and Immunology, Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
| |
Collapse
|