1
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DuBose E, Bevill SM, Mitchell DK, Sciaky N, Golitz BT, Dixon SAH, Rhodes SD, Bear JE, Johnson GL, Angus SP. Neratinib, a pan ERBB/HER inhibitor, restores sensitivity of PTEN-null, BRAFV600E melanoma to BRAF/MEK inhibition. Front Oncol 2024; 14:1191217. [PMID: 38854737 PMCID: PMC11159048 DOI: 10.3389/fonc.2024.1191217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/15/2024] [Indexed: 06/11/2024] Open
Abstract
Introduction Approximately 50% of melanomas harbor an activating BRAFV600E mutation. Standard of care involves a combination of inhibitors targeting mutant BRAF and MEK1/2, the substrate for BRAF in the MAPK pathway. PTEN loss-of-function mutations occur in ~40% of BRAFV600E melanomas, resulting in increased PI3K/AKT activity that enhances resistance to BRAF/MEK combination inhibitor therapy. Methods To compare the response of PTEN null to PTEN wild-type cells in an isogenic background, CRISPR/Cas9 was used to knock out PTEN in a melanoma cell line that harbors a BRAFV600E mutation. RNA sequencing, functional kinome analysis, and drug synergy screening were employed in the context of BRAF/MEK inhibition. Results RNA sequencing and functional kinome analysis revealed that the loss of PTEN led to an induction of FOXD3 and an increase in expression of the FOXD3 target gene, ERBB3/HER3. Inhibition of BRAF and MEK1/2 in PTEN null, BRAFV600E cells dramatically induced the expression of ERBB3/HER3 relative to wild-type cells. A synergy screen of epigenetic modifiers and kinase inhibitors in combination with BRAFi/MEKi revealed that the pan ERBB/HER inhibitor, neratinib, could reverse the resistance observed in PTEN null, BRAFV600E cells. Conclusions The findings indicate that PTEN null BRAFV600E melanoma exhibits increased reliance on ERBB/HER signaling when treated with clinically approved BRAFi/MEKi combinations. Future studies are warranted to test neratinib reversal of BRAFi/MEKi resistance in patient melanomas expressing ERBB3/HER3 in combination with its dimerization partner ERBB2/HER2.
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Affiliation(s)
- Evan DuBose
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Samantha M. Bevill
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Dana K. Mitchell
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Noah Sciaky
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Brian T. Golitz
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Shelley A. H. Dixon
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Steven D. Rhodes
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, United States
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
- Division of Pediatric Hematology/Oncology/Stem Cell Transplant, Indiana University School of Medicine, Indianapolis, IN, United States
| | - James E. Bear
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Gary L. Johnson
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Steven P. Angus
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, United States
- Division of Pediatric Hematology/Oncology/Stem Cell Transplant, Indiana University School of Medicine, Indianapolis, IN, United States
- Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
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2
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King AD, Deirawan H, Klein PA, Dasgeb B, Dumur CI, Mehregan DR. Next-generation sequencing in dermatology. Front Med (Lausanne) 2023; 10:1218404. [PMID: 37841001 PMCID: PMC10570430 DOI: 10.3389/fmed.2023.1218404] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Over the past decade, Next-Generation Sequencing (NGS) has advanced our understanding, diagnosis, and management of several areas within dermatology. NGS has emerged as a powerful tool for diagnosing genetic diseases of the skin, improving upon traditional PCR-based techniques limited by significant genetic heterogeneity associated with these disorders. Epidermolysis bullosa and ichthyosis are two of the most extensively studied genetic diseases of the skin, with a well-characterized spectrum of genetic changes occurring in these conditions. NGS has also played a critical role in expanding the mutational landscape of cutaneous squamous cell carcinoma, enhancing our understanding of its molecular pathogenesis. Similarly, genetic testing has greatly benefited melanoma diagnosis and treatment, primarily due to the high prevalence of BRAF hot spot mutations and other well-characterized genetic alterations. Additionally, NGS provides a valuable tool for measuring tumor mutational burden, which can aid in management of melanoma. Lastly, NGS demonstrates promise in improving the sensitivity of diagnosing cutaneous T-cell lymphoma. This article provides a comprehensive summary of NGS applications in the diagnosis and management of genodermatoses, cutaneous squamous cell carcinoma, melanoma, and cutaneous T-cell lymphoma, highlighting the impact of NGS on the field of dermatology.
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Affiliation(s)
- Andrew D. King
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Hany Deirawan
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| | | | - Bahar Dasgeb
- Department of Surgical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Catherine I. Dumur
- Bernhardt Laboratories, Sonic Healthcare Anatomic Pathology Division, Jacksonville, FL, United States
| | - Darius R. Mehregan
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
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3
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Gillis N, Etheridge AS, Patil SA, Hayes DN, Hayward MC, Auman JT, Parker JS, Innocenti F. Sequencing of genes of drug response in tumor DNA and implications for precision medicine in cancer patients. THE PHARMACOGENOMICS JOURNAL 2023:10.1038/s41397-023-00299-7. [PMID: 36709390 DOI: 10.1038/s41397-023-00299-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/30/2023]
Abstract
Tumor DNA sequencing is becoming standard-of-care for patient treatment decisions. We evaluated genotype concordance between tumor DNA and genomic DNA from blood and catalogued functional effects of somatic mutations in 21 drug response genes in 752 solid tumor patients. Using a threshold of 10% difference between tumor and blood DNA variant allele fraction (VAF), concordance for heterogenous genotype calls was 78% and increased to 97.5% using a 30% VAF threshold. Somatic mutations were observed in all 21 drug response genes, and 44% of patients had at least one somatic mutation in these genes. In tumor DNA, eight patients had a frameshift mutation in CYP2C8, which metabolizes taxanes. Overall, somatic copy number losses were more frequent than gains, including for CYP2C19 and CYP2D6 which had the most frequent copy number losses. However, copy number gains in TPMT were more than four times as common as losses. Seven % of patients had copy number gains in ABCB1, a multidrug resistance transporter of anti-cancer agents. These results demonstrate tumor-only DNA sequencing might not be reliable to call germline genotypes of drug response variants.
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Affiliation(s)
- Nancy Gillis
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.,Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Amy S Etheridge
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
| | - Sushant A Patil
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - D Neil Hayes
- Department of Medicine, Hematology/Oncology, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.,Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Michele C Hayward
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - J Todd Auman
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Federico Innocenti
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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4
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Bok I, Angarita A, Douglass SM, Weeraratna AT, Karreth FA. A Series of BRAF- and NRAS-Driven Murine Melanoma Cell Lines with Inducible Gene Modulation Capabilities. JID INNOVATIONS 2022; 2:100076. [PMID: 35146482 PMCID: PMC8819036 DOI: 10.1016/j.xjidi.2021.100076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/30/2021] [Accepted: 11/02/2021] [Indexed: 11/24/2022] Open
Abstract
Murine cancer cell lines are powerful research tools to complement studies in genetically engineered mouse models. We have established 21 melanoma cell lines from embryonic stem cell-genetically engineered mouse models driven by alleles that model the most frequent genetic alterations in human melanoma. In addition, these cell lines harbor regulatory alleles for the genomic integration of transgenes and the regulation of expression of such transgenes. In this study, we report a comprehensive characterization of these cell lines. Specifically, we validated melanocytic origin, driver allele recombination and expression, and activation of the oncogenic MAPK and protein kinase B pathways. We further tested tumor formation in syngeneic immunocompetent recipients as well as the functionality of the integrated Tet-ON system and recombination-mediated cassette exchange homing cassette. Finally, by deleting the transcription factor MAFG with an inducible CRISPR/Cas9 approach, we show the utility of the regulatory alleles for candidate gene modulation. These cell lines will be a valuable resource for studying melanoma biology and therapy.
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Key Words
- BCC, BrafV600E Cdkn2aΔ/Δ
- BPP, BrafV600E PtenΔ/Δ
- CHC, collagen homing cassette
- Dox, doxycycline
- ESC, embryonic stem cell
- FBS, fetal bovine serum
- GEMM, genetically engineered mouse model
- NCC, NrasQ61R Cdkn2aΔ/Δ
- NPP, NrasQ61R PtenΔ/Δ
- RMCE, recombination-mediated cassette exchange
- sgRNA, single-guide RNA
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Affiliation(s)
- Ilah Bok
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Cancer Biology PhD program, Department of Cell Biology, Microbiology and Molecular Biology, College of Arts and Sciences, University of South Florida, Tampa, Florida, USA
| | - Ariana Angarita
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Stephen M. Douglass
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ashani T. Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, University, Baltimore, Maryland, USA
| | - Florian A. Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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5
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Mose LE, Perou CM, Parker JS. Improved indel detection in DNA and RNA via realignment with ABRA2. Bioinformatics 2019; 35:2966-2973. [PMID: 30649250 PMCID: PMC6735753 DOI: 10.1093/bioinformatics/btz033] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 11/08/2018] [Accepted: 01/10/2019] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION Genomic variant detection from next-generation sequencing has become established as an extremely important component of research and clinical diagnoses in both cancer and Mendelian disorders. Insertions and deletions (indels) are a common source of variation and can frequently impact functionality, thus making their detection vitally important. While substantial effort has gone into detecting indels from DNA, there is still opportunity for improvement. Further, detection of indels from RNA-Seq data has largely been an afterthought and offers another critical area for variant detection. RESULTS We present here ABRA2, a redesign of the original ABRA implementation that offers support for realignment of both RNA and DNA short reads. The process results in improved accuracy and scalability including support for human whole genomes. Results demonstrate substantial improvement in indel detection for a variety of data types, including those that were not previously supported by ABRA. Further, ABRA2 results in broad improvements to variant calling accuracy across a wide range of post-processing workflows including whole genomes, targeted exomes and transcriptome sequencing. AVAILABILITY AND IMPLEMENTATION ABRA2 is implemented in a combination of Java and C/C++ and is freely available to all from: https://github.com/mozack/abra2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lisle E Mose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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6
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Filia A, Droop A, Harland M, Thygesen H, Randerson-Moor J, Snowden H, Taylor C, Diaz JMS, Pozniak J, Nsengimana J, Laye J, Newton-Bishop JA, Bishop DT. High-Resolution Copy Number Patterns From Clinically Relevant FFPE Material. Sci Rep 2019; 9:8908. [PMID: 31222134 PMCID: PMC6586881 DOI: 10.1038/s41598-019-45210-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/07/2019] [Indexed: 11/09/2022] Open
Abstract
Systematic tumour profiling is essential for biomarker research and clinically for assessing response to therapy. Solving the challenge of delivering informative copy number (CN) profiles from formalin-fixed paraffin embedded (FFPE) material, the only likely readily available biospecimen for most cancers, involves successful processing of small quantities of degraded DNA. To investigate the potential for analysis of such lesions, whole-genome CNVseq was applied to 300 FFPE primary tumour samples, obtained from a large-scale epidemiological study of melanoma. The quality and the discriminatory power of CNVseq was assessed. Libraries were successfully generated for 93% of blocks, with input DNA quantity being the only predictor of success (success rate dropped to 65% if <20 ng available); 3% of libraries were dropped because of low sequence alignment rates. Technical replicates showed high reproducibility. Comparison with targeted CN assessment showed consistency with the Next Generation Sequencing (NGS) analysis. We were able to detect and distinguish CN changes with a resolution of ≤10 kb. To demonstrate performance, we report the spectrum of genomic CN alterations (CNAs) detected at 9p21, the major site of CN change in melanoma. This successful analysis of CN in FFPE material using NGS provides proof of principle for intensive examination of population-based samples.
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Affiliation(s)
- Anastasia Filia
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
- Centre for Translational Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Alastair Droop
- MRC Medical Bioinformatics Centre, Leeds Institute of Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Helene Thygesen
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Juliette Randerson-Moor
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Helen Snowden
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Claire Taylor
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Joey Mark S Diaz
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Joanna Pozniak
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Jon Laye
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Julia A Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - D Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom.
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7
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Chera BS, Kumar S, Beaty BT, Marron D, Jefferys S, Green R, Goldman EC, Amdur R, Sheets N, Dagan R, Hayes DN, Weiss J, Grilley-Olson JE, Zanation A, Hackman T, Blumberg JM, Patel S, Weissler M, Tan XM, Parker JS, Mendenhall W, Gupta GP. Rapid Clearance Profile of Plasma Circulating Tumor HPV Type 16 DNA during Chemoradiotherapy Correlates with Disease Control in HPV-Associated Oropharyngeal Cancer. Clin Cancer Res 2019; 25:4682-4690. [PMID: 31088830 DOI: 10.1158/1078-0432.ccr-19-0211] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/22/2019] [Accepted: 05/08/2019] [Indexed: 12/17/2022]
Abstract
PURPOSE To identify a profile of circulating tumor human papilloma virus (HPV) DNA (ctHPVDNA) clearance kinetics that is associated with disease control after chemoradiotherapy (CRT) for HPV-associated oropharyngeal squamous cell carcinoma (OPSCC). EXPERIMENTAL DESIGN A multi-institutional prospective biomarker trial was conducted in 103 patients with (i) p16-positive OPSCC, (ii) M0 disease, and (iii) receipt of definitive CRT. Blood specimens were collected at baseline, weekly during CRT, and at follow-up visits. Optimized multianalyte digital PCR assays were used to quantify ctHPVDNA (types 16/18/31/33/35) in plasma. A control cohort of 55 healthy volunteers and 60 patients with non-HPV-associated malignancy was also analyzed. RESULTS Baseline plasma ctHPVDNA had high specificity (97%) and high sensitivity (89%) for detecting newly diagnosed HPV-associated OPSCC. Pretreatment ctHPV16DNA copy number correlated with disease burden, tumor HPV copy number, and HPV integration status. We define a ctHPV16DNA favorable clearance profile as having high baseline copy number (>200 copies/mL) and >95% clearance of ctHPV16DNA by day 28 of CRT. Nineteen of 67 evaluable patients had a ctHPV16DNA favorable clearance profile, and none had persistent or recurrent regional disease after CRT. In contrast, patients with adverse clinical risk factors (T4 or >10 pack years) and an unfavorable ctHPV16DNA clearance profile had a 35% actuarial rate of persistent or recurrent regional disease after CRT (P = 0.0049). CONCLUSIONS A rapid clearance profile of ctHPVDNA may predict likelihood of disease control in patients with HPV-associated OPSCC patients treated with definitive CRT and may be useful in selecting patients for deintensified therapy.
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Affiliation(s)
- Bhishamjit S Chera
- Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina. .,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Sunil Kumar
- Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Brian T Beaty
- Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - David Marron
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Lineberger Bioinformatics Core, University of North Carolina Hospitals, Chapel Hill, North Carolina
| | - Stuart Jefferys
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Lineberger Bioinformatics Core, University of North Carolina Hospitals, Chapel Hill, North Carolina
| | - Rebecca Green
- Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Emily C Goldman
- Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Robert Amdur
- Department of Radiation Oncology, University of Florida Hospitals, Gainesville, Florida
| | - Nathan Sheets
- Department of Radiation Oncology, UNC Rex Hospitals, Raleigh, North Carolina
| | - Roi Dagan
- University of Florida Health Proton Therapy Institute, Jacksonville, Florida
| | - D Neil Hayes
- West Cancer Center, University of Tennessee, Memphis, Tennessee
| | - Jared Weiss
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Division of Hematology Oncology, Department of Medicine, University of North Carolina, School of Medicine, Chapel Hill, North Carolina
| | - Juneko E Grilley-Olson
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Division of Hematology Oncology, Department of Medicine, University of North Carolina, School of Medicine, Chapel Hill, North Carolina
| | - Adam Zanation
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Trevor Hackman
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Jeffrey M Blumberg
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Samip Patel
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Mark Weissler
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Xianming M Tan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Lineberger Bioinformatics Core, University of North Carolina Hospitals, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - William Mendenhall
- Department of Radiation Oncology, University of Florida Hospitals, Gainesville, Florida
| | - Gaorav P Gupta
- Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina. .,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
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8
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BRAF
mutation leading to central nervous system rosai-dorfman disease. Ann Neurol 2018; 84:147-152. [DOI: 10.1002/ana.25281] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/25/2018] [Accepted: 06/27/2018] [Indexed: 11/07/2022]
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9
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Brighton HE, Angus SP, Bo T, Roques J, Tagliatela AC, Darr DB, Karagoz K, Sciaky N, Gatza ML, Sharpless NE, Johnson GL, Bear JE. New Mechanisms of Resistance to MEK Inhibitors in Melanoma Revealed by Intravital Imaging. Cancer Res 2018; 78:542-557. [PMID: 29180473 PMCID: PMC6132242 DOI: 10.1158/0008-5472.can-17-1653] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/06/2017] [Accepted: 11/10/2017] [Indexed: 11/16/2022]
Abstract
Targeted therapeutics that are initially effective in cancer patients nearly invariably engender resistance at some stage, an inherent challenge in the use of any molecular-targeted drug in cancer settings. In this study, we evaluated resistance mechanisms arising in metastatic melanoma to MAPK pathway kinase inhibitors as a strategy to identify candidate strategies to limit risks of resistance. To investigate longitudinal responses, we developed an intravital serial imaging approach that can directly visualize drug response in an inducible RAF-driven, autochthonous murine model of melanoma incorporating a fluorescent reporter allele (tdTomatoLSL). Using this system, we visualized formation and progression of tumors in situ, starting from the single-cell level longitudinally over time. Reliable reporting of the status of primary murine tumors treated with the selective MEK1/2 inhibitor (MEKi) trametinib illustrated a time-course of initial drug response and persistence, followed by the development of drug resistance. We found that tumor cells adjacent to bundled collagen had a preferential persistence in response to MEKi. Unbiased transcriptional and kinome reprogramming analyses from selected treatment time points suggested increased c-Kit and PI3K/AKT pathway activation in resistant tumors, along with enhanced expression of epithelial genes and epithelial-mesenchymal transition downregulation signatures with development of MEKi resistance. Similar trends were observed following simultaneous treatment with BRAF and MEK inhibitors aligned to standard-of-care combination therapy, suggesting these reprogramming events were not specific to MEKi alone. Overall, our results illuminate the integration of tumor-stroma dynamics with tissue plasticity in melanoma progression and provide new insights into the basis for drug response, persistence, and resistance.Significance: A longitudinal study tracks the course of MEKi treatment in an autochthonous imageable murine model of melanoma from initial response to therapeutic resistance, offering new insights into the basis for drug response, persistence, and resistance. Cancer Res; 78(2); 542-57. ©2017 AACR.
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Affiliation(s)
- Hailey E Brighton
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Steven P Angus
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Tao Bo
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jose Roques
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alicia C Tagliatela
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David B Darr
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kubra Karagoz
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Noah Sciaky
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael L Gatza
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Norman E Sharpless
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gary L Johnson
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - James E Bear
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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10
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Patel NM, Michelini VV, Snell JM, Balu S, Hoyle AP, Parker JS, Hayward MC, Eberhard DA, Salazar AH, McNeillie P, Xu J, Huettner CS, Koyama T, Utro F, Rhrissorrakrai K, Norel R, Bilal E, Royyuru A, Parida L, Earp HS, Grilley-Olson JE, Hayes DN, Harvey SJ, Sharpless NE, Kim WY. Enhancing Next-Generation Sequencing-Guided Cancer Care Through Cognitive Computing. Oncologist 2017; 23:179-185. [PMID: 29158372 PMCID: PMC5813753 DOI: 10.1634/theoncologist.2017-0170] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/06/2017] [Indexed: 11/20/2022] Open
Abstract
Next‐generation sequencing (NGS) has emerged as an affordable and reproducible means to query tumors for somatic genetic anomalies. To help interpret somatic NGS data, many institutions have created a molecular tumor board to analyze the results of NGS and make recommendations. This article evaluates the utility of cognitive computing systems to analyze data for clinical decision‐making. Background. Using next‐generation sequencing (NGS) to guide cancer therapy has created challenges in analyzing and reporting large volumes of genomic data to patients and caregivers. Specifically, providing current, accurate information on newly approved therapies and open clinical trials requires considerable manual curation performed mainly by human “molecular tumor boards” (MTBs). The purpose of this study was to determine the utility of cognitive computing as performed by Watson for Genomics (WfG) compared with a human MTB. Materials and Methods. One thousand eighteen patient cases that previously underwent targeted exon sequencing at the University of North Carolina (UNC) and subsequent analysis by the UNCseq informatics pipeline and the UNC MTB between November 7, 2011, and May 12, 2015, were analyzed with WfG, a cognitive computing technology for genomic analysis. Results. Using a WfG‐curated actionable gene list, we identified additional genomic events of potential significance (not discovered by traditional MTB curation) in 323 (32%) patients. The majority of these additional genomic events were considered actionable based upon their ability to qualify patients for biomarker‐selected clinical trials. Indeed, the opening of a relevant clinical trial within 1 month prior to WfG analysis provided the rationale for identification of a new actionable event in nearly a quarter of the 323 patients. This automated analysis took <3 minutes per case. Conclusion. These results demonstrate that the interpretation and actionability of somatic NGS results are evolving too rapidly to rely solely on human curation. Molecular tumor boards empowered by cognitive computing could potentially improve patient care by providing a rapid, comprehensive approach for data analysis and consideration of up‐to‐date availability of clinical trials. Implications for Practice. The results of this study demonstrate that the interpretation and actionability of somatic next‐generation sequencing results are evolving too rapidly to rely solely on human curation. Molecular tumor boards empowered by cognitive computing can significantly improve patient care by providing a fast, cost‐effective, and comprehensive approach for data analysis in the delivery of precision medicine. Patients and physicians who are considering enrollment in clinical trials may benefit from the support of such tools applied to genomic data.
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Affiliation(s)
- Nirali M Patel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Jeff M Snell
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Saianand Balu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alan P Hoyle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michele C Hayward
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David A Eberhard
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ashley H Salazar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Jia Xu
- IBM Watson Health, Cambridge, Massachusetts, USA
| | | | | | | | | | | | - Erhan Bilal
- IBM Research, Yorktown Heights, New York, USA
| | | | | | - H Shelton Earp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Juneko E Grilley-Olson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - D Neil Hayes
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Norman E Sharpless
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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11
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Wu SJ, Lin CT, Agathangelidis A, Lin LI, Kuo YY, Tien HF, Ghia P. Distinct molecular genetics of chronic lymphocytic leukemia in Taiwan: clinical and pathogenetic implications. Haematologica 2017; 102:1085-1090. [PMID: 28255015 PMCID: PMC5451340 DOI: 10.3324/haematol.2016.157552] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/16/2017] [Indexed: 11/09/2022] Open
Abstract
Differences in chronic lymphocytic leukemia between the Asian and the Western population are widely known. To further clarify these ethnic differences, we profiled the molecular genetics in a cohort of 83 newly diagnosed patients from Taiwan. In detail, we assessed: (i) the usage and the mutational status of the clonotypic immunoglobulin heavy-chain variable region (IgHV) genes, (ii) the presence of VH CDR3 stereotypes, and (iii) TP53, NOTCH1, SF3B1, BIRC3, and MYD88 mutations. The IgHV gene repertoire was biased and distinct from that observed in the West with the most common IgHV genes being IgHV3-23, IgHV3-7, and IgHV3-48 In terms of IgHV gene mutational status, 63.8% of patients carried mutated rearrangements, whereas 22.4% of patients were assigned to stereotyped subsets (6.9% to major subsets and 15.5% to minor ones). The frequencies of NOTCH1, SF3B1, BIRC3 and MYD88 mutations were 9.6%, 7.2%, 1.2%, and 2.4%, respectively; however, the frequency of TP53 mutations was significantly higher (20.5%). Patients with TP53 mutations or del(17p), SF3B1 mutations and unmutated IgHV had a worse outcome compared to the other patients. In conclusion, the differences observed in IgHV properties suggest different pathogenetic factors implicated in the development of chronic lymphocytic leukemia, while the high frequency of TP53 mutations could in part explain the dismal outcome of these patients in Taiwan.
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Affiliation(s)
- Shang-Ju Wu
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Ting Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Tai-Cheng Stem Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Andreas Agathangelidis
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Vita-Salute San Raffaele University and IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Liang-In Lin
- Department of Clinical Laboratory Science and Medical Technology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yuan-Yeh Kuo
- Graduate Institution of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Paolo Ghia
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Vita-Salute San Raffaele University and IRCCS San Raffaele Scientific Institute, Milan, Italy
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12
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Ozkaya N, Dogan A, Abdel-Wahab O. Identification and Targeting of Kinase Alterations in Histiocytic Neoplasms. Hematol Oncol Clin North Am 2017; 31:705-719. [PMID: 28673397 DOI: 10.1016/j.hoc.2017.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Histiocytic disorders represent clonal disorders of cells believed to be derived from the monocyte, macrophage, and/or dendritic cell lineage presenting with a range of manifestations. Although their nature as clonal versus inflammatory nonclonal conditions have long been debated, recent studies identified numerous somatic mutations that activate mitogen-activated protein kinase signaling in clinically and histologically diverse forms of histiocytosis. Clinical trials and case series have revealed that targeting aberrant kinase signaling using BRAF and/or MEK inhibitors may be effective. These findings suggest that a personalized approach in which patient-specific alterations are identified and targeted may be a critically important therapeutic approach.
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Affiliation(s)
- Neval Ozkaya
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Ahmet Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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13
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Hoggard TM, Henderson-Jackson E, Bui MM, Caracciolo J, Teer JK, Yoder S, Binitie O, Gonzalez RJ, Brohl AS, Reed DR. Myoepithelial carcinoma with RB1 mutation: remarkable chemosensitivity to carcinoma of unknown origin therapy. BMC Cancer 2017; 17:250. [PMID: 28390395 PMCID: PMC5385017 DOI: 10.1186/s12885-017-3249-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/31/2017] [Indexed: 12/30/2022] Open
Abstract
Background Myoepithelial carcinoma of soft tissue is a rare, malignant neoplasm that is morphologically and immunophenotypically similar to its counterpart in salivary gland. It demonstrates myoepithelial differentiation, possessing both epithelial and myogenic characteristics. Thought to be chemotherapy insensitive, the optimal treatment regimen of this tumor has yet to be established and only a select few cases in the literature discuss treatment efficacy in detail. Case presentation Here we present a case of a young adult with metastatic myoepithelial carcinoma with an initial excellent response to systemic therapy utilizing carboplatin and paclitaxel with continued complete response after 3 years. The patient also underwent complete surgical excision and received adjuvant radiation to the primary site of disease. Exome sequencing revealed an inactivating mutation in RB1 which we believe to be the first such mutation to be reported in this cancer type. Conclusions Given increasing evidence suggesting RB1 loss is associated with responsiveness to conventional chemotherapies, particularly platinum-based regimens, we hypothesize that this genetic feature predisposed chemosensitivity in our patient’s tumor.
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Affiliation(s)
- Timothy M Hoggard
- University of South Florida Morsani College of Medicine, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Evita Henderson-Jackson
- Department of Anatomic Pathology, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA.,Sarcoma Department, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Marilyn M Bui
- Department of Anatomic Pathology, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA.,Sarcoma Department, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Jamie Caracciolo
- Department of Diagnostic Imaging, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Odion Binitie
- Sarcoma Department, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA.,Adolescent and Young Adult Program; H. Lee Moffitt Cancer Center and Research Institute, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | | | - Andrew S Brohl
- Sarcoma Department, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Damon R Reed
- Sarcoma Department, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA. .,Chemical Biology and Molecular Medicine Program, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA. .,Adolescent and Young Adult Program; H. Lee Moffitt Cancer Center and Research Institute, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA.
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14
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Lee LH, Gasilina A, Roychoudhury J, Clark J, McCormack FX, Pressey J, Grimley MS, Lorsbach R, Ali S, Bailey M, Stephens P, Ross JS, Miller VA, Nassar NN, Kumar AR. Real-time genomic profiling of histiocytoses identifies early-kinase domain BRAF alterations while improving treatment outcomes. JCI Insight 2017; 2:e89473. [PMID: 28194436 DOI: 10.1172/jci.insight.89473] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Many patients with histiocytic disorders such as Langerhans cell histiocytosis (LCH) or Erdheim-Chester disease (ECD) have treatment-refractory disease or suffer recurrences. Recent findings of gene mutations in histiocytoses have generated options for targeted therapies. We sought to determine the utility of prospective sequencing of select genes to further characterize mutations and identify targeted therapies for patients with histiocytoses. Biopsies of 72 patients with a variety of histiocytoses underwent comprehensive genomic profiling with targeted DNA and RNA sequencing. Fifteen patients (21%) carried the known BRAF V600E mutation, and 11 patients (15%) carried various mutations in MAP2K1, which we confirm induce constitutive activation of extracellular signal-regulated kinase (ERK) and were sensitive to inhibitors of mitogen-activated protein kinase kinase (MEK, the product of MAP2K1). We also identified recurring ALK rearrangements, and 4 LCH patients with an uncommon in-frame deletion in BRAF (N486_P490del or N486_T491>K), resulting in constitutive activation of ERK with resistance to V600E-specific inhibitors. We subsequently describe clinical cases where patients with aggressive multisystem LCH experience dramatic and sustained responses to monotherapy with either dabrafenib or trametinib. These findings support our conclusion that comprehensive genomic profiling should be regularly applied to these disorders at diagnosis, and can positively impact clinical care.
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Affiliation(s)
- Lynn H Lee
- Cancer and Blood Diseases Institute, Division of Oncology, Cincinnati Children's Hospital Medical Center
| | - Anjelika Gasilina
- Cancer and Blood Diseases Institute, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center
| | - Jayeeta Roychoudhury
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center
| | - Jason Clark
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center
| | - Francis X McCormack
- Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Joseph Pressey
- Cancer and Blood Diseases Institute, Division of Oncology, Cincinnati Children's Hospital Medical Center
| | - Michael S Grimley
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center
| | - Robert Lorsbach
- Division of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Siraj Ali
- Foundation Medicine, Cambridge, Massachusetts, USA
| | - Mark Bailey
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | | | | | - Nicolas N Nassar
- Cancer and Blood Diseases Institute, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center
| | - Ashish R Kumar
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center
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15
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Next-Generation Sequencing Reveals Pathway Activations and New Routes to Targeted Therapies in Cutaneous Metastatic Melanoma. Am J Dermatopathol 2017; 39:1-13. [PMID: 28045747 DOI: 10.1097/dad.0000000000000729] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Comprehensive genomic profiling of clinical samples by next-generation sequencing (NGS) can identify one or more therapy targets for the treatment of metastatic melanoma (MM) with a single diagnostic test. METHODS NGS was performed on hybridization-captured, adaptor ligation-based libraries using DNA extracted from 4 formalin-fixed paraffin-embedded sections cut at 10 microns from 30 MM cases. The exons of 182 cancer-related genes were fully sequenced using the Illumina HiSeq 2000 at an average sequencing depth of 1098X and evaluated for genomic alterations (GAs) including point mutations, insertions, deletions, copy number alterations, and select gene fusions/rearrangements. Clinically relevant GAs (CRGAs) were defined as those identifying commercially available targeted therapeutics or therapies in registered clinical trials. RESULTS The 30 American Joint Committee on Cancer Stage IV MM included 17 (57%) male and 13 (43%) female patients with a mean age of 59.5 years (range 41-83 years). All MM samples had at least 1 GA, and an average of 2.7 GA/sample (range 1-7) was identified. The mean number of GA did not differ based on age or sex; however, on average, significantly more GAs were identified in amelanotic and poorly differentiated MM. GAs were most commonly identified in BRAF (12 cases, 40%), CDKN2A (6 cases, 20%), NF1 (8 cases, 26.7%), and NRAS (6 cases, 20%). CRGAs were identified in all patients, and represented 77% of the GA (64/83) detected. The median and mean CRGAs per tumor were 2 and 2.1, respectively (range 1-7). CONCLUSION Comprehensive genomic profiling of MM, using a single diagnostic test, uncovers an unexpectedly high number of CRGA that would not be identified by standard of care testing. Moreover, NGS has the potential to influence therapy selection and can direct patients to enter relevant clinical trials evaluating promising targeted therapies.
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16
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Harris G, O'Toole S, George P, Browett P, Print C. Massive parallel sequencing of solid tumours - challenges and opportunities for pathologists. Histopathology 2016; 70:123-133. [DOI: 10.1111/his.13067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Gavin Harris
- Department of Molecular Medicine and Pathology and Bioinformatics Institute; University of Auckland; Auckland New Zealand
- Canterbury Health Laboratories; Christchurch New Zealand
| | - Sandra O'Toole
- Department of Tissue Pathology and Diagnostic Oncology; Royal Prince Alfred Hospital; Camperdown NSW Australia
- Sydney Medical School; Sydney University; Sydney Australia
- The Kinghorn Cancer Centre; Garvan Institute of Medical Research; Darlinghurst NSW Australia
| | - Peter George
- Canterbury Health Laboratories; Christchurch New Zealand
| | - Peter Browett
- Department of Molecular Medicine and Pathology and Bioinformatics Institute; University of Auckland; Auckland New Zealand
| | - Cristin Print
- Department of Molecular Medicine and Pathology and Bioinformatics Institute; University of Auckland; Auckland New Zealand
- Maurice Wilkins Centre; c/o University of Auckland; Auckland New Zealand
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17
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Alternative genetic mechanisms of BRAF activation in Langerhans cell histiocytosis. Blood 2016; 128:2533-2537. [PMID: 27729324 DOI: 10.1182/blood-2016-08-733790] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/04/2016] [Indexed: 12/15/2022] Open
Abstract
Langerhans cell histiocytosis (LCH) is characterized by inflammatory lesions containing pathologic CD207+ dendritic cells with constitutively activated ERK. Mutually exclusive somatic mutations in MAPK pathway genes have been identified in ∼75% of LCH cases, including recurrent BRAF-V600E and MAP2K1 mutations. To elucidate mechanisms of ERK activation in the remaining 25% of patients, we performed whole-exome sequencing (WES, n = 6), targeted BRAF sequencing (n = 19), and/or whole-transcriptome sequencing (RNA-seq, n = 6) on 24 LCH patient samples lacking BRAF-V600E or MAP2K1 mutations. WES and BRAF sequencing identified in-frame BRAF deletions in the β3-αC loop in 6 lesions. RNA-seq revealed one case with an in-frame FAM73A-BRAF fusion lacking the BRAF autoinhibitory regulatory domain but retaining an intact kinase domain. High levels of phospho-ERK were detected in vitro in cells overexpressing either BRAF fusion or deletion constructs and ex vivo in CD207+ cells from lesions. ERK activation was resistant to BRAF-V600E inhibition, but responsive to both a second-generation BRAF inhibitor and a MEK inhibitor. These results support an emerging model of universal ERK-activating genetic alterations driving pathogenesis in LCH. A personalized approach in which patient-specific alterations are identified may be necessary to maximize benefit from targeted therapies for patients with LCH.
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18
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Seifert BA, O'Daniel JM, Amin K, Marchuk DS, Patel NM, Parker JS, Hoyle AP, Mose LE, Marron A, Hayward MC, Bizon C, Wilhelmsen KC, Evans JP, Earp HS, Sharpless NE, Hayes DN, Berg JS. Germline Analysis from Tumor-Germline Sequencing Dyads to Identify Clinically Actionable Secondary Findings. Clin Cancer Res 2016; 22:4087-4094. [PMID: 27083775 DOI: 10.1158/1078-0432.ccr-16-0015] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/27/2016] [Indexed: 01/03/2023]
Abstract
PURPOSE To evaluate germline variants in hereditary cancer susceptibility genes among unselected cancer patients undergoing tumor-germline sequencing. EXPERIMENTAL DESIGN Germline sequence data from 439 individuals undergoing tumor-germline dyad sequencing through the LCCC1108/UNCseq™ (NCT01457196) study were analyzed for genetic variants in 36 hereditary cancer susceptibility genes. These variants were analyzed as an exploratory research study to determine whether pathogenic variants exist within the germline of patients undergoing tumor-germline sequencing. Patients were unselected with respect to indicators of hereditary cancer predisposition. RESULTS Variants indicative of hereditary cancer predisposition were identified in 19 (4.3%) patients. For about half (10/19), these findings represent new diagnostic information with potentially important implications for the patient and their family. The others were previously identified through clinical genetic evaluation secondary to suspicion of a hereditary cancer predisposition. Genes with pathogenic variants included ATM, BRCA1, BRCA2, CDKN2A, and CHEK2 In contrast, a substantial proportion of patients (178, 40.5%) had Variants of Uncertain Significance (VUS), 24 of which had VUS in genes pertinent to the presenting cancer. Another 143 had VUS in other hereditary cancer genes, and 11 had VUS in both pertinent and nonpertinent genes. CONCLUSIONS Germline analysis in tumor-germline sequencing dyads will occasionally reveal significant germline findings that were clinically occult, which could be beneficial for patients and their families. However, given the low yield for unexpected germline variation and the large proportion of patients with VUS results, analysis and return of germline results should adhere to guidelines for secondary findings rather than diagnostic hereditary cancer testing. Clin Cancer Res; 22(16); 4087-94. ©2016 AACRSee related commentary by Mandelker, p. 3987.
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Affiliation(s)
- Bryce A Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Krunal Amin
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Daniel S Marchuk
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Nirali M Patel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Joel S Parker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Alan P Hoyle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Andrew Marron
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Michele C Hayward
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Christopher Bizon
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Kirk C Wilhelmsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A.,Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - James P Evans
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - H Shelton Earp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Norman E Sharpless
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - D Neil Hayes
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
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19
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Carson CC, Moschos SJ, Edmiston SN, Darr DB, Nikolaishvili-Feinberg N, Groben PA, Zhou X, Kuan PF, Pandey S, Chan KT, Jordan JL, Hao H, Frank JS, Hopkinson DA, Gibbs DC, Alldredge VD, Parrish E, Hanna SC, Berkowitz P, Rubenstein DS, Miller CR, Bear JE, Ollila DW, Sharpless NE, Conway K, Thomas NE. IL2 Inducible T-cell Kinase, a Novel Therapeutic Target in Melanoma. Clin Cancer Res 2016; 21:2167-76. [PMID: 25934889 DOI: 10.1158/1078-0432.ccr-14-1826] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE IL2 inducible T-cell kinase (ITK) promoter CpG sites are hypomethylated in melanomas compared with nevi. The expression of ITK in melanomas, however, has not been established and requires elucidation. EXPERIMENTAL DESIGN An ITK-specific monoclonal antibody was used to probe sections from deidentified, formalin-fixed paraffin-embedded tumor blocks or cell line arrays and ITK was visualized by IHC. Levels of ITK protein differed among melanoma cell lines and representative lines were transduced with four different lentiviral constructs that each contained an shRNA designed to knockdown ITK mRNA levels. The effects of the selective ITK inhibitor BI 10N on cell lines and mouse models were also determined. RESULTS ITK protein expression increased with nevus to metastatic melanoma progression. In melanoma cell lines, genetic or pharmacologic inhibition of ITK decreased proliferation and migration and increased the percentage of cells in the G0-G1 phase. Treatment of melanoma-bearing mice with BI 10N reduced growth of ITK-expressing xenografts or established autochthonous (Tyr-Cre/Pten(null)/Braf(V600E)) melanomas. CONCLUSIONS We conclude that ITK, formerly considered an immune cell-specific protein, is aberrantly expressed in melanoma and promotes tumor development and progression. Our finding that ITK is aberrantly expressed in most metastatic melanomas suggests that inhibitors of ITK may be efficacious for melanoma treatment. The efficacy of a small-molecule ITK inhibitor in the Tyr-Cre/Pten(null)/Braf(V600E) mouse melanoma model supports this possibility.
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Affiliation(s)
- Craig C Carson
- Department of Dermatology, The University of North Carolina, Chapel Hill, North Carolina
| | - Stergios J Moschos
- Department of Medicine, The University of North Carolina, Chapel Hill, North Carolina. Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina
| | - Sharon N Edmiston
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina
| | - David B Darr
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina
| | | | - Pamela A Groben
- Department of Pathology and Laboratory Medicine, The University of North Carolina, Chapel Hill, North Carolina
| | - Xin Zhou
- Department of Biostatistics, The University of North Carolina, Chapel Hill, North Carolina
| | - Pei Fen Kuan
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina. Department of Biostatistics, The University of North Carolina, Chapel Hill, North Carolina
| | - Shaily Pandey
- Department of Dermatology, The University of North Carolina, Chapel Hill, North Carolina
| | - Keefe T Chan
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina. Department of Cell Biology and Physiology, The University of North Carolina, Chapel Hill, North Carolina
| | - Jamie L Jordan
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina
| | - Honglin Hao
- Department of Dermatology, The University of North Carolina, Chapel Hill, North Carolina
| | - Jill S Frank
- Department of Surgery, The University of North Carolina, Chapel Hill, North Carolina
| | - Dennis A Hopkinson
- Department of Dermatology, The University of North Carolina, Chapel Hill, North Carolina
| | - David C Gibbs
- Department of Dermatology, The University of North Carolina, Chapel Hill, North Carolina
| | - Virginia D Alldredge
- Department of Dermatology, The University of North Carolina, Chapel Hill, North Carolina
| | - Eloise Parrish
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina
| | - Sara C Hanna
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina
| | - Paula Berkowitz
- Department of Dermatology, The University of North Carolina, Chapel Hill, North Carolina
| | - David S Rubenstein
- Department of Dermatology, The University of North Carolina, Chapel Hill, North Carolina. Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina
| | - C Ryan Miller
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina. Department of Pathology and Laboratory Medicine, The University of North Carolina, Chapel Hill, North Carolina. Department of Neurology, The University of North Carolina, Chapel Hill, North Carolina. Neuroscience Center, The University of North Carolina, Chapel Hill, North Carolina
| | - James E Bear
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina. Department of Cell Biology and Physiology, The University of North Carolina, Chapel Hill, North Carolina
| | - David W Ollila
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina. Department of Surgery, The University of North Carolina, Chapel Hill, North Carolina
| | - Norman E Sharpless
- Department of Medicine, The University of North Carolina, Chapel Hill, North Carolina. Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina
| | - Kathleen Conway
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina. Department of Epidemiology, The University of North Carolina, Chapel Hill, North Carolina
| | - Nancy E Thomas
- Department of Dermatology, The University of North Carolina, Chapel Hill, North Carolina. Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina.
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20
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Cost Effectiveness of Sequencing 34 Cancer-Associated Genes as an Aid for Treatment Selection in Patients with Metastatic Melanoma. Mol Diagn Ther 2016; 19:169-77. [PMID: 25926090 PMCID: PMC4469775 DOI: 10.1007/s40291-015-0140-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Objective To determine whether a next-generation sequencing (NGS) panel of 34 cancer-associated genes would cost-effectively aid in the treatment selection for patients with metastatic melanoma, compared with a single-site BRAF V600 mutation test. Methods A decision model was developed to estimate the costs and health outcomes of the two test strategies. The cost effectiveness of these two strategies was analyzed from a payer perspective over a 2-year time horizon with model parameters taken from the literature. Results In the base case, the gene sequencing panel strategy resulted in a cost of US$120,022 and 0.721 quality-adjusted life years (QALYs) per patient, whereas the single-site mutation test strategy resulted in a cost of US$128,965 and 0.704 QALYs. Thus, the gene sequencing panel strategy cost US$8943 less per patient and increased QALYs by 0.0174 per patient. Sensitivity analyses showed that, compared with the single-site mutation test strategy, the gene sequencing panel strategy had a 90.9 % chance of having reduced costs and increased QALYs, with the cost of the gene sequencing panel test having minimal effect on the incremental cost. Conclusion Compared with the single-site mutation test, the use of an NGS panel of 34 cancer-associated genes as an aid in selecting therapy for patients with metastatic melanoma reduced costs and increased QALYs. If the base-case results were applied to the 8900 patients diagnosed with metastatic melanoma in the USA each year, the gene sequencing panel strategy could result in an annual savings of US$79.6 million and a gain of 155 QALYs. Electronic supplementary material The online version of this article (doi:10.1007/s40291-015-0140-9) contains supplementary material, which is available to authorized users.
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21
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Weiss S, Hanniford D, Hernando E, Osman I. Revisiting determinants of prognosis in cutaneous melanoma. Cancer 2015; 121:4108-23. [PMID: 26308244 PMCID: PMC4666819 DOI: 10.1002/cncr.29634] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 11/10/2022]
Abstract
The American Joint Committee on Cancer staging system for cutaneous melanoma is based on primary tumor thickness and the presence of ulceration, mitoses, lymph node spread, and distant metastases as determinants of prognosis. Although this cutaneous melanoma staging system has evolved over time to more accurately reflect patient prognosis, improvements are still needed, because current understanding of the particular factors (genetic mutation, expression alteration, host response, etc) that are critical for predicting patient outcomes is incomplete. Given the clinical and biologic heterogeneity of primary melanomas, new prognostic tools are needed to more precisely identify patients who are most likely to develop advanced disease. Such tools would affect clinical surveillance strategies and aid in patient selection for adjuvant therapy. The authors reviewed the literature on prognostic molecular and immunologic markers in primary cutaneous melanoma, their associations with clinicopathologic and survival outcomes, and their potential for incorporation into current staging models. Overall, the studies considered in this review did not define prognostic markers that could be readily incorporated into the current staging system. Therefore, efforts should be continued in these and other directions to maximize the likelihood of identifying clinically useful prognostic biomarkers for cutaneous melanoma.
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Affiliation(s)
- Sarah Weiss
- Department of Medical Oncology, New York University School of Medicine, New York, NY
- Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY
| | - Douglas Hanniford
- Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY
- Department of Pathology, New York University School of Medicine, New York, NY
| | - Eva Hernando
- Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY
- Department of Pathology, New York University School of Medicine, New York, NY
| | - Iman Osman
- Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY
- Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY
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22
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Field MA, Cho V, Andrews TD, Goodnow CC. Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies. PLoS One 2015; 10:e0143199. [PMID: 26600436 PMCID: PMC4658170 DOI: 10.1371/journal.pone.0143199] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/02/2015] [Indexed: 12/21/2022] Open
Abstract
A diversity of tools is available for identification of variants from genome sequence data. Given the current complexity of incorporating external software into a genome analysis infrastructure, a tendency exists to rely on the results from a single tool alone. The quality of the output variant calls is highly variable however, depending on factors such as sequence library quality as well as the choice of short-read aligner, variant caller, and variant caller filtering strategy. Here we present a two-part study first using the high quality 'genome in a bottle' reference set to demonstrate the significant impact the choice of aligner, variant caller, and variant caller filtering strategy has on overall variant call quality and further how certain variant callers outperform others with increased sample contamination, an important consideration when analyzing sequenced cancer samples. This analysis confirms previous work showing that combining variant calls of multiple tools results in the best quality resultant variant set, for either specificity or sensitivity, depending on whether the intersection or union, of all variant calls is used respectively. Second, we analyze a melanoma cell line derived from a control lymphocyte sample to determine whether software choices affect the detection of clinically important melanoma risk-factor variants finding that only one of the three such variants is unanimously detected under all conditions. Finally, we describe a cogent strategy for implementing a clinical variant detection pipeline; a strategy that requires careful software selection, variant caller filtering optimizing, and combined variant calls in order to effectively minimize false negative variants. While implementing such features represents an increase in complexity and computation the results offer indisputable improvements in data quality.
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Affiliation(s)
- Matthew A. Field
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- National Computational Infrastructure, Australian National University, Canberra, ACT, Australia
| | - Vicky Cho
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Australian Phenomics Facility, Australian National University, Canberra, ACT, Australia
| | - T. Daniel Andrews
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- National Computational Infrastructure, Australian National University, Canberra, ACT, Australia
| | - Chris C. Goodnow
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Immunogenomics Group, Immunology Research Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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23
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Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC. PLoS One 2015; 10:e0129280. [PMID: 26076459 PMCID: PMC4468211 DOI: 10.1371/journal.pone.0129280] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/06/2015] [Indexed: 01/21/2023] Open
Abstract
The recent FDA approval of the MiSeqDx platform provides a unique opportunity to develop targeted next generation sequencing (NGS) panels for human disease, including cancer. We have developed a scalable, targeted panel-based assay termed UNCseq, which involves a NGS panel of over 200 cancer-associated genes and a standardized downstream bioinformatics pipeline for detection of single nucleotide variations (SNV) as well as small insertions and deletions (indel). In addition, we developed a novel algorithm, NGScopy, designed for samples with sparse sequencing coverage to detect large-scale copy number variations (CNV), similar to human SNP Array 6.0 as well as small-scale intragenic CNV. Overall, we applied this assay to 100 snap-frozen lung cancer specimens lacking same-patient germline DNA (07–0120 tissue cohort) and validated our results against Sanger sequencing, SNP Array, and our recently published integrated DNA-seq/RNA-seq assay, UNCqeR, where RNA-seq of same-patient tumor specimens confirmed SNV detected by DNA-seq, if RNA-seq coverage depth was adequate. In addition, we applied the UNCseq assay on an independent lung cancer tumor tissue collection with available same-patient germline DNA (11–1115 tissue cohort) and confirmed mutations using assays performed in a CLIA-certified laboratory. We conclude that UNCseq can identify SNV, indel, and CNV in tumor specimens lacking germline DNA in a cost-efficient fashion.
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24
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Lee JJ, Sholl LM, Lindeman NI, Granter SR, Laga AC, Shivdasani P, Chin G, Luke JJ, Ott PA, Hodi FS, Mihm MC, Lin JY, Werchniak AE, Haynes HA, Bailey N, Liu R, Murphy GF, Lian CG. Targeted next-generation sequencing reveals high frequency of mutations in epigenetic regulators across treatment-naïve patient melanomas. Clin Epigenetics 2015; 7:59. [PMID: 26221190 PMCID: PMC4517542 DOI: 10.1186/s13148-015-0091-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/27/2015] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Recent developments in genomic sequencing have advanced our understanding of the mutations underlying human malignancy. Melanoma is a prototype of an aggressive, genetically heterogeneous cancer notorious for its biologic plasticity and predilection towards developing resistance to targeted therapies. Evidence is rapidly accumulating that dysregulated epigenetic mechanisms (DNA methylation/demethylation, histone modification, non-coding RNAs) may play a central role in the pathogenesis of melanoma. Therefore, we sought to characterize the frequency and nature of mutations in epigenetic regulators in clinical, treatment-naïve, patient melanoma specimens obtained from one academic institution. RESULTS Targeted next-generation sequencing for 275 known and investigative cancer genes (of which 41 genes, or 14.9 %, encoded an epigenetic regulator) of 38 treatment-naïve patient melanoma samples revealed that 22.3 % (165 of 740) of all non-silent mutations affected an epigenetic regulator. The most frequently mutated genes were BRAF, MECOM, NRAS, TP53, MLL2, and CDKN2A. Of the 40 most commonly mutated genes, 12 (30.0 %) encoded epigenetic regulators, including genes encoding enzymes involved in histone modification (MECOM, MLL2, SETD2), chromatin remodeling (ARID1B, ARID2), and DNA methylation and demethylation (TET2, IDH1). Among the 38 patient melanoma samples, 35 (92.1 %) harbored at least one mutation in an epigenetic regulator. The genes with the highest number of total UVB-signature mutations encoded epigenetic regulators, including MLL2 (100 %, 16 of 16) and MECOM (82.6 %, 19 of 23). Moreover, on average, epigenetic genes harbored a significantly greater number of UVB-signature mutations per gene than non-epigenetic genes (3.7 versus 2.4, respectively; p = 0.01). Bioinformatics analysis of The Cancer Genome Atlas (TCGA) melanoma mutation dataset also revealed a frequency of mutations in the 41 epigenetic genes comparable to that found within our cohort of patient melanoma samples. CONCLUSIONS Our study identified a high prevalence of somatic mutations in genes encoding epigenetic regulators, including those involved in DNA demethylation, histone modification, chromatin remodeling, and microRNA processing. Moreover, UVB-signature mutations were found more commonly among epigenetic genes than in non-epigenetic genes. Taken together, these findings further implicate epigenetic mechanisms, particularly those involving the chromatin-remodeling enzyme MECOM/EVI1 and histone-modifying enzyme MLL2, in the pathobiology of melanoma.
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Affiliation(s)
- Jonathan J. Lee
- />Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA
| | - Lynette M. Sholl
- />Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA
| | - Neal I. Lindeman
- />Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA
| | - Scott R. Granter
- />Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA
| | - Alvaro C. Laga
- />Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA
| | - Priyanka Shivdasani
- />Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA
| | - Gary Chin
- />Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA
| | - Jason J. Luke
- />Melanoma Center, Dana–Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA
| | - Patrick A. Ott
- />Melanoma Center, Dana–Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA
| | - F. Stephen Hodi
- />Melanoma Center, Dana–Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA
| | - Martin C. Mihm
- />Melanoma Center, Dana–Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA
| | - Jennifer Y. Lin
- />Melanoma Center, Dana–Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA
| | - Andrew E. Werchniak
- />Melanoma Center, Dana–Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA
| | - Harley A. Haynes
- />Melanoma Center, Dana–Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA
| | - Nancy Bailey
- />Melanoma Center, Dana–Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA
| | - Robert Liu
- />Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA
| | - George F. Murphy
- />Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA
| | - Christine G. Lian
- />Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA
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25
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Liu Y, Chen H, Sun Z, Chen X. Molecular mechanisms of ethanol-associated oro-esophageal squamous cell carcinoma. Cancer Lett 2015; 361:164-73. [PMID: 25766659 DOI: 10.1016/j.canlet.2015.03.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/04/2015] [Accepted: 03/04/2015] [Indexed: 02/06/2023]
Abstract
Alcohol drinking is a major etiological factor of oro-esophageal squamous cell carcinoma (OESCC). Both local and systemic effects of ethanol may promote carcinogenesis, especially among chronic alcoholics. However, molecular mechanisms of ethanol-associated OESCC are still not well understood. In this review, we summarize current understandings and propose three mechanisms of ethanol-associated OESCC: (1) Disturbance of systemic metabolism of nutrients: during ethanol metabolism in the liver, systemic metabolism of retinoids, zinc, iron and methyl groups is altered. These nutrients are known to be associated with the development of OESCC. (2) Disturbance of redox metabolism in squamous epithelial cells: when ethanol is metabolized in oro-esophageal squamous epithelial cells, reactive oxygen species are generated and produce oxidative damage. Meanwhile, ethanol may also disturb fatty-acid metabolism in these cells. (3) Disturbance of signaling pathways in squamous epithelial cells: due to its physico-chemical properties, ethanol changes cell membrane fluidity and shape, and may thus impact multiple signaling pathways. Advanced molecular techniques in genomics, epigenomics, metabolomics and microbiomics will help us elucidate how ethanol promotes OESCC.
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Affiliation(s)
- Yao Liu
- Department of Oral Medicine, Beijing Stomatological Hospital, Capital Medical University, Beijing 100050, China; Cancer Research Program, JLC-BBRI, North Carolina Central University, Durham, NC 27707, USA
| | - Hao Chen
- Cancer Research Program, JLC-BBRI, North Carolina Central University, Durham, NC 27707, USA
| | - Zheng Sun
- Department of Oral Medicine, Beijing Stomatological Hospital, Capital Medical University, Beijing 100050, China.
| | - Xiaoxin Chen
- Cancer Research Program, JLC-BBRI, North Carolina Central University, Durham, NC 27707, USA.
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26
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Abstract
Advances in the biology of melanoma have provided insights about chemoresistance and its genetic heterogeneity in parallel with advances in drug design, culminating in recent major treatment breakthroughs. Although clinical benefit of targeted therapies has been unquestionable, future advances are only possible if we understand the interplay between genetic aberrations and role of other crucial nongenetic changes yet to be identified by such projects as the Cancer Genome Atlas Project in Melanoma. Combination therapies, either among small molecule inhibitors themselves and/or with immunotherapies, may be the optimal strategy to prevent development of drug resistance inherently linked with such targeted therapies.
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27
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Burd CE, Liu W, Huynh MV, Waqas MA, Gillahan JE, Clark KS, Fu K, Martin BL, Jeck WR, Souroullas GP, Darr DB, Zedek DC, Miley MJ, Baguley BC, Campbell SL, Sharpless NE. Mutation-specific RAS oncogenicity explains NRAS codon 61 selection in melanoma. Cancer Discov 2014; 4:1418-29. [PMID: 25252692 PMCID: PMC4258185 DOI: 10.1158/2159-8290.cd-14-0729] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
UNLABELLED NRAS mutation at codons 12, 13, or 61 is associated with transformation; yet, in melanoma, such alterations are nearly exclusive to codon 61. Here, we compared the melanoma susceptibility of an NrasQ61R knock-in allele to similarly designed KrasG12D and NrasG12D alleles. With concomitant p16INK4a inactivation, KrasG12D or NrasQ61R expression efficiently promoted melanoma in vivo, whereas NrasG12D did not. In addition, NrasQ61R mutation potently cooperated with Lkb1/Stk11 loss to induce highly metastatic disease. Functional comparisons of NrasQ61R and NrasG12D revealed little difference in the ability of these proteins to engage PI3K or RAF. Instead, NrasQ61R showed enhanced nucleotide binding, decreased intrinsic GTPase activity, and increased stability when compared with NrasG12D. This work identifies a faithful model of human NRAS-mutant melanoma, and suggests that the increased melanomagenecity of NrasQ61R over NrasG12D is due to heightened abundance of the active, GTP-bound form rather than differences in the engagement of downstream effector pathways. SIGNIFICANCE This work explains the curious predominance in human melanoma of mutations of codon 61 of NRAS over other oncogenic NRAS mutations. Using conditional "knock-in" mouse models, we show that physiologic expression of NRASQ61R, but not NRASG12D, drives melanoma formation.
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Affiliation(s)
- Christin E Burd
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio. Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio
| | - Wenjin Liu
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina. The Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Minh V Huynh
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Meriam A Waqas
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio
| | - James E Gillahan
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio. Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio
| | - Kelly S Clark
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina. The Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Kailing Fu
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina. The Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Brit L Martin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio
| | - William R Jeck
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina. The Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - George P Souroullas
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina. The Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - David B Darr
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina. The Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Daniel C Zedek
- Department of Dermatology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Michael J Miley
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Sharon L Campbell
- The Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina. Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Norman E Sharpless
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina. The Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.
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