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Dissecting Molecular Heterogeneity of Circulating Tumor Cells (CTCs) from Metastatic Breast Cancer Patients through Copy Number Aberration (CNA) and Single Nucleotide Variant (SNV) Single Cell Analysis. Cancers (Basel) 2022; 14:cancers14163925. [PMID: 36010918 PMCID: PMC9405921 DOI: 10.3390/cancers14163925] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/11/2022] [Indexed: 12/27/2022] Open
Abstract
Circulating tumor cells' (CTCs) heterogeneity contributes to counteract their introduction in clinical practice. Through single-cell sequencing we aim at exploring CTC heterogeneity in metastatic breast cancer (MBC) patients. Single CTCs were isolated using DEPArray NxT. After whole genome amplification, libraries were prepared for copy number aberration (CNA) and single nucleotide variant (SNV) analysis and sequenced using Ion GeneStudio S5 and Illumina MiSeq, respectively. CTCs demonstrate distinctive mutational signatures but retain molecular traces of their common origin. CNA profiling identifies frequent aberrations involving critical genes in pathogenesis: gains of 1q (CCND1) and 11q (WNT3A), loss of 22q (CHEK2). The longitudinal single-CTC analysis allows tracking of clonal selection and the emergence of resistance-associated aberrations, such as gain of a region in 12q (CDK4). A group composed of CTCs from different patients sharing common traits emerges. Further analyses identify losses of 15q and enrichment of terms associated with pseudopodium formation as frequent and exclusive events. CTCs from MBC patients are heterogeneous, especially concerning their mutational status. The single-cell analysis allows the identification of aberrations associated with resistance, and is a candidate tool to better address treatment strategy. The translational significance of the group populated by similar CTCs should be elucidated.
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2
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Mutational analysis of hematologic neoplasms in 164 paired peripheral blood and bone marrow samples by next-generation sequencing. Blood Adv 2021; 4:4362-4365. [PMID: 32926123 DOI: 10.1182/bloodadvances.2020002306] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/07/2020] [Indexed: 01/30/2023] Open
Abstract
Key Points
Findings support use of PB samples for chronic myeloid neoplasms and for acute leukemias with sufficient circulating disease. In acute leukemias, BM appears to be superior to PB for monitoring measurable residual disease, even in the absence of BM excess blasts.
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3
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Scott AJ, Tokaz MC, Jacobs MF, Chinnaiyan AM, Phillips TJ, Wilcox RA. Germline variants discovered in lymphoma patients undergoing tumor profiling: a case series. Fam Cancer 2021; 20:61-65. [PMID: 32504211 PMCID: PMC7719097 DOI: 10.1007/s10689-020-00192-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/02/2020] [Indexed: 11/29/2022]
Abstract
Clinical tumor sequencing protocols often depend on obtaining germline DNA from patients to aid in the identification of de novo variants in the tumor, and therefore come with the possibility for the incidental discovery of germline variants. Ninety-one adult patients with lymphoma were consented and enrolled in MIONCOSEQ, an IRB-approved tumor profiling protocol that utilizes an exome sequencing platform. Charts were retrospectively reviewed for germline variants from sequencing results, personal and/or family history of cancer and genetic counseling referral. After review of the 91 lymphoma cases, seven (8%) cases revealed germline variants. Only one of these, CHEK2 p.I157T, has been previously recovered as a germline variant in lymphoma. Two of the seven patients received genetic counseling, two died before genetic counseling could be arranged and three did not follow-up with a genetics provider. None of the patients had a personal or family history that would have otherwise suggested an indication for cancer genetics referral, especially notable as lymphoma is not traditionally associated with inherited cancer syndromes. Importantly, as only two of seven patients had appropriate genetic counseling for their variant, timely genetic counseling should be a critical part of all tumor profiling platforms that use non-tumor DNA.
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Affiliation(s)
- Anthony J Scott
- Division of Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI, 48109, USA.
| | - Molly C Tokaz
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michelle F Jacobs
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Tycel J Phillips
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Ryan A Wilcox
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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4
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Personalized Treatment for Hematologic Diseases in Europe: An EHA Position Paper. Hemasphere 2020; 4:e474. [PMID: 32984771 PMCID: PMC7480966 DOI: 10.1097/hs9.0000000000000474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/05/2022] Open
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Abstract
Lung cancer causes more deaths annually than any other malignancy. A subset of non-small cell lung cancer (NSCLC) is driven by amplification and overexpression or activating mutation of the receptor tyrosine kinase (RTK) ERBB2 In some contexts, notably breast cancer, alternative splicing of ERBB2 causes skipping of exon 16, leading to the expression of an oncogenic ERBB2 isoform (ERBB2ΔEx16) that forms constitutively active homodimers. However, the broader implications of ERBB2 alternative splicing in human cancers have not been explored. Here, we have used genomic and transcriptomic analysis to identify elevated ERBB2ΔEx16 expression in a subset of NSCLC cases, as well as splicing site mutations facilitating exon 16 skipping and deletions of exon 16 in a subset of these lung tumors and in a number of other carcinomas. Supporting the potential of ERBB2ΔEx16 as a lung cancer driver, its expression transformed immortalized lung epithelial cells while a transgenic model featuring inducible ERBB2ΔEx16 specifically in the lung epithelium rapidly developed lung adenocarcinomas following transgene induction. Collectively, these observations indicate that ERBB2ΔEx16 is a lung cancer oncogene with potential clinical importance for a proportion of patients.
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Solimando AG, Annese T, Tamma R, Ingravallo G, Maiorano E, Vacca A, Specchia G, Ribatti D. New Insights into Diffuse Large B-Cell Lymphoma Pathobiology. Cancers (Basel) 2020; 12:cancers12071869. [PMID: 32664527 PMCID: PMC7408689 DOI: 10.3390/cancers12071869] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma (NHL), accounting for about 40% of all cases of NHL. Analysis of the tumor microenvironment is an important aspect of the assessment of the progression of DLBCL. In this review article, we analyzed the role of different cellular components of the tumor microenvironment, including mast cells, macrophages, and lymphocytes, in the tumor progression of DLBCL. We examined several approaches to confront the available pieces of evidence, whereby three key points emerged. DLBCL is a disease of malignant B cells spreading and accumulating both at nodal and at extranodal sites. In patients with both nodal and extranodal lesions, the subsequent induction of a cancer-friendly environment appears pivotal. The DLBCL cell interaction with mature stromal cells and vessels confers tumor protection and inhibition of immune response while delivering nutrients and oxygen supply. Single cells may also reside and survive in protected niches in the nodal and extranodal sites as a source for residual disease and relapse. This review aims to molecularly and functionally recapitulate the DLBCL–milieu crosstalk, to relate niche and pathological angiogenic constitution and interaction factors to DLBCL progression.
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Affiliation(s)
- Antonio Giovanni Solimando
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine ‘G. Baccelli’, University of Bari Medical School, 70124 Bari, Italy;
- Istituto di Ricovero e Cura a Carattere Scientifico-IRCCS Istituto Tumori “Giovanni Paolo II” of Bari, 70124 Bari, Italy
- Correspondence: (A.G.S.); (D.R.); Tel.: +39-3395626475 (A.G.S.); +39-080.5478326 (D.R.)
| | - Tiziana Annese
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs, University of Bari Medical School, 70124 Bari, Italy; (T.A.); (R.T.)
| | - Roberto Tamma
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs, University of Bari Medical School, 70124 Bari, Italy; (T.A.); (R.T.)
| | - Giuseppe Ingravallo
- Department of Emergency and Transplantation, Pathology Section, University of Bari Medical School, 70100 Bari, Italy; (G.I.); (E.M.)
| | - Eugenio Maiorano
- Department of Emergency and Transplantation, Pathology Section, University of Bari Medical School, 70100 Bari, Italy; (G.I.); (E.M.)
| | - Angelo Vacca
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine ‘G. Baccelli’, University of Bari Medical School, 70124 Bari, Italy;
| | - Giorgina Specchia
- Department of Emergency and Transplantation, Hematology Section, University of Bari Medical School, 70100 Bari, Italy;
| | - Domenico Ribatti
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs, University of Bari Medical School, 70124 Bari, Italy; (T.A.); (R.T.)
- Correspondence: (A.G.S.); (D.R.); Tel.: +39-3395626475 (A.G.S.); +39-080.5478326 (D.R.)
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7
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Bieg‐Bourne CC, Okamura R, Kurzrock R. Concordance between TP53 alterations in blood and tissue: impact of time interval, biopsy site, cancer type and circulating tumor DNA burden. Mol Oncol 2020; 14:1242-1251. [PMID: 32187847 PMCID: PMC7266274 DOI: 10.1002/1878-0261.12672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/13/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023] Open
Abstract
We examined the impact of spatial, temporal, histologic, and quantitative factors on concordance between TP53 alterations in tissue DNA vs in circulating tumor DNA (ctDNA). Four hundred and thirty-three patients underwent next-generation sequencing (NGS) in which both tissue and blood samples were evaluated. TP53 was detected in 258 of 433 patients (59.6%); 215 had tissue TP53 alterations (49.7%); 159, ctDNA (36.7%); and 116, both tissue and ctDNA (27.8%). Overall concordance rate between ctDNA and tissue biopsies for TP53 alterations was 67.2%; positive concordance was 45.0%. Overall concordance for TP53 did not vary among patients with ≤ 2 months vs > 6 months between test samples; however, positive concordance trended higher when time intervals between test samples were shorter, suggesting that the lack of difference in overall concordance may be due to the large number of negative/negative tests. There was a trend toward higher overall concordance based on biopsy site (metastatic vs primary) (P = 0.07) and significantly higher positive concordance if the tissue biopsy site was a metastatic lesion (P = 0.03). Positive concordance significantly decreased in noncolorectal cancer patients vs colorectal cancer patients (P = 0.02). Finally, higher %ctDNA was associated with higher concordance rates between blood and tissue (P < 0.001). Taken together, these data indicate that both blood and tissue DNA sequencing are necessary to evaluate the full scope of TP53 alterations, and that concordance rates may be related to multiple factors including, but not limited to, amount of ctDNA, histologic context, and site of tissue biopsy.
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Affiliation(s)
- Cheyennedra C. Bieg‐Bourne
- Center for Personalized Cancer TherapyMoores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | - Ryosuke Okamura
- Center for Personalized Cancer TherapyMoores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | - Razelle Kurzrock
- Center for Personalized Cancer TherapyMoores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
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Kim H, Yun JW, Lee ST, Kim HJ, Kim SH, Kim JW. Korean Society for Genetic Diagnostics Guidelines for Validation of Next-Generation Sequencing-Based Somatic Variant Detection in Hematologic Malignancies. Ann Lab Med 2019; 39:515-523. [PMID: 31240878 PMCID: PMC6660343 DOI: 10.3343/alm.2019.39.6.515] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/31/2019] [Accepted: 06/13/2019] [Indexed: 01/14/2023] Open
Abstract
Next-generation sequencing (NGS) is currently used in the clinical setting for targeted therapies and diagnosis of hematologic malignancies. Accurate detection of somatic variants is challenging because of tumor purity, heterogeneity, and the complexity of genetic alterations, with various issues ranging from high detection design to test implementation. This article presents guidelines developed through consensus among a panel of experts from the Korean Society for Genetic Diagnostics. They are based on experiences with the validation processes of NGS-based somatic panels for hematologic malignancies, with reference to previous international recommendations. These guidelines describe basic parameters with emphasis on the design of a validation protocol for NGS-based somatic panels to be used in practice. In addition, they suggest thresholds of key metrics, including minimum coverage, mean coverage with uniformity index, and minimum variant allele frequency, for the initial diagnosis of hematologic malignancies.
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Affiliation(s)
- Heyjin Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Korea
| | - Jae Won Yun
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Hee Jin Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun Hee Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong Won Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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9
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Garziera M, Roncato R, Montico M, De Mattia E, Gagno S, Poletto E, Scalone S, Canzonieri V, Giorda G, Sorio R, Cecchin E, Toffoli G. New Challenges in Tumor Mutation Heterogeneity in Advanced Ovarian Cancer by a Targeted Next-Generation Sequencing (NGS) Approach. Cells 2019; 8:cells8060584. [PMID: 31197119 PMCID: PMC6627128 DOI: 10.3390/cells8060584] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/06/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) technology has advanced knowledge of the genomic landscape of ovarian cancer, leading to an innovative molecular classification of the disease. However, patient survival and response to platinum-based treatments are still not predictable based on the tumor genetic profile. This retrospective study characterized the repertoire of somatic mutations in advanced ovarian cancer to identify tumor genetic markers predictive of platinum chemo-resistance and prognosis. Using targeted NGS, 79 primary advanced (III-IV stage, tumor grade G2-3) ovarian cancer tumors, including 64 high-grade serous ovarian cancers (HGSOCs), were screened with a 26 cancer-genes panel. Patients, enrolled between 1995 and 2011, underwent primary debulking surgery (PDS) with optimal residual disease (RD < 1 cm) and platinum-based chemotherapy as first-line treatment. We found a heterogeneous mutational landscape in some uncommon ovarian histotypes and in HGSOC tumor samples with relevance in predicting platinum sensitivity. In particular, we identified a poor prognostic signature in patients with HGSOC harboring concurrent mutations in two driver actionable genes of the panel. The tumor heterogeneity described, sheds light on the translational potential of targeted NGS approach for the identification of subgroups of patients with distinct therapeutic vulnerabilities, that are modulated by the specific mutational profile expressed by the ovarian tumor.
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Affiliation(s)
- Marica Garziera
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Rossana Roncato
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Marcella Montico
- Scientific Directorate, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Elena De Mattia
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Sara Gagno
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Elena Poletto
- Medical Oncology, "Santa Maria della Misericordia" University Hospital, ASUIUD, 33100 Udine, Italy.
| | - Simona Scalone
- Medical Oncology Unit C, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Vincenzo Canzonieri
- Pathology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Giorgio Giorda
- Gynecological Oncology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Roberto Sorio
- Medical Oncology Unit C, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Erika Cecchin
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
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A germline variant of TP53 in paediatric diffuse leptomeningeal glioneuronal tumour. Childs Nerv Syst 2019; 35:1021-1027. [PMID: 30937530 DOI: 10.1007/s00381-019-04128-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/18/2019] [Indexed: 12/22/2022]
Abstract
PURPOSE Diffuse leptomeningeal glioneuronal tumour (DLGNT) is an extremely rare tumour involving the neuroaxis. At present, its exact pathogenesis and associated factors remain incompletely characterised. Recent molecular investigations in a small cohort have offered some insights into this disease. However, the role of germline findings has not yet been fully explored in affected patients. The authors present a case of DLGNT, focusing on the clinical and molecular features with reference to current disease knowledge. METHODS A 4-year-old male presented with raised intracranial pressure symptoms secondary to extensive leptomeningeal disease of the brain and spine. Preliminary impression was that of an inflammatory lesion. RESULTS A lumbar biopsy of the lesion confirmed DLGNT on routine diagnostic examination. Further molecular analysis of his tumour and blood demonstrated a previously unreported TP53 exon 5 (c.147V > I) germline variant. Based on the latest DLGNT molecular subtyping classification, his tumour falls into the group with better clinical outcome. However, his germline findings may add an extra layer of uncertainty to his overall prognosis. CONCLUSION Given that much remains unknown in many rare paediatric tumours at this stage, isolated findings found in an individual may be of significance. Supplementary genetic information, together with tumour molecular analysis, add to our current understanding of this uncommon disease. This case highlights the benefit of combined clinical and molecular efforts, including germline testing, especially for children affected by such challenging neoplasms.
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11
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Janku F, Diamond EL, Goodman AM, Raghavan VK, Barnes TG, Kato S, Abdel-Wahab O, Durham BH, Meric-Bernstam F, Kurzrock R. Molecular Profiling of Tumor Tissue and Plasma Cell-Free DNA from Patients with Non-Langerhans Cell Histiocytosis. Mol Cancer Ther 2019; 18:1149-1157. [PMID: 31015311 PMCID: PMC6548628 DOI: 10.1158/1535-7163.mct-18-1244] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/16/2018] [Accepted: 04/05/2019] [Indexed: 12/18/2022]
Abstract
The BRAF V600E mutation and BRAF inhibitor responsiveness characterize ∼50% of patients with the non-Langerhans cell histiocytosis (non-LCH) Erdheim-Chester disease (ECD). We interrogated the non-LCH molecular landscape [ECD, n = 35; Rosai-Dorfman disease (RDD), n = 3; mixed ECD/RDD, n = 1] using BRAF V600E PCR and/or next-generation sequencing [tissue and cell-free DNA (cfDNA) of plasma and/or urine]. Of 34 evaluable patients, 17 (50%) had the BRAF V600E mutation. Of 31 patients evaluable for non-BRAF V600E alterations, 18 (58%) had ≥1 alteration and 12 putative non-BRAF V600E MAPK pathway alterations: atypical BRAF mutation; GNAS, MAP2K1, MAP2K2, NF1, and RAS mutations; RAF1 or ERBB2 amplifications; LMNA-NTRK1 (TRK inhibitor-sensitive) and CAPZA2-BRAF fusions. Four patients had JAK2, MPL ASXL1, U2AF1 alterations, which can correlate with myeloid neoplasms, a known ECD predisposition, and one developed myelofibrosis 13 months after cfDNA testing. Therefore, our multimodal comprehensive genomics reveals clinically relevant alterations and suggests that MAPK activation is a hallmark of non-LCH.
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Affiliation(s)
- Filip Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas, MD Anderson Cancer Center, Houston, Texas.
| | - Eli L Diamond
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Aaron M Goodman
- Center for Personalized Cancer Therapy, Division of Blood and Marrow Transplantation, Division of Hematology/Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Vaijayanthi Kandadai Raghavan
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Tamara G Barnes
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Shumei Kato
- Center for Personalized Cancer Therapy, Division of Blood and Marrow Transplantation, Division of Hematology/Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Omar Abdel-Wahab
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin H Durham
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, Division of Blood and Marrow Transplantation, Division of Hematology/Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, La Jolla, California
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12
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Huang M, Wei S. Overview of Molecular Testing of Cytology Specimens. Acta Cytol 2019; 64:136-146. [PMID: 30917368 DOI: 10.1159/000497187] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Utilizing cytology specimens for molecular testing has attracted increasing attention in the era of personalized medicine. Cytology specimens are clinically easier to access. The samples can be quickly and completely fixed in a very short time of fixation before tissue degradation occurs, compared to hours or days of fixation in surgical pathology specimens. In addition, cytology specimens can be fixed without formalin, which can significantly damage DNA and RNA. All these factors contribute to the superb quality of DNA and RNA in cytology specimens for molecular tests. STUDY DESIGN We summarize the most pertinent information in the literature regarding molecular testing in the field of cytopathology. RESULTS The first part focuses on the types of cytological specimens that can be used for molecular testing, including the advantages and limitations. The second section describes the common molecular tests and their clinical application. CONCLUSION Various types of cytology specimens are suitable for many molecular tests, which may require additional clinical laboratory validation.
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Affiliation(s)
- Min Huang
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Shuanzeng Wei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA,
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Galanina N, Bejar R, Choi M, Goodman A, Wieduwilt M, Mulroney C, Kim L, Yeerna H, Tamayo P, Vergilio JA, Mughal TI, Miller V, Jamieson C, Kurzrock R. Comprehensive Genomic Profiling Reveals Diverse but Actionable Molecular Portfolios across Hematologic Malignancies: Implications for Next Generation Clinical Trials. Cancers (Basel) 2018; 11:E11. [PMID: 30583461 PMCID: PMC6356731 DOI: 10.3390/cancers11010011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/11/2018] [Accepted: 12/11/2018] [Indexed: 12/21/2022] Open
Abstract
Background: The translation of genomic discoveries to the clinic is the cornerstone of precision medicine. However, incorporating next generation sequencing (NGS) of hematologic malignancies into clinical management remains limited. Methods: We describe 235 patients who underwent integrated NGS profiling (406 genes) and analyze the alterations and their potential actionability. Results: Overall, 227 patients (96.5%) had adequate tissue. Most common diagnoses included myelodysplastic syndrome (22.9%), chronic lymphocytic leukemia (17.2%), non-Hodgkin lymphoma (13.2%), acute myeloid leukemia (11%), myeloproliferative neoplasm (9.2%), acute lymphoblastic leukemia (8.8%), and multiple myeloma (7.5%). Most patients (N = 197/227 (87%)) harbored ≥1 genomic alteration(s); 170/227 (75%), ≥1 potentially actionable alteration(s) targetable by an FDA-approved (mostly off-label) or an investigational agent. Altogether, 546 distinct alterations were seen, most commonly involving TP53 (10.8%), TET2 (4.6%), and DNMT3A (4.2%). The median tumor mutational burden (TMB) was low (1.7 alterations/megabase); 12% of patients had intermediate or high TMB (higher TMB correlates with favorable response to anti-PD1/PDL1 inhibition in solid tumors). In conclusion, 96.5% of patients with hematologic malignancies have adequate tissue for comprehensive genomic profiling. Most patients had unique molecular signatures, and 75% had alterations that may be pharmacologically tractable with gene- or immune-targeted agents.
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Affiliation(s)
- Natalie Galanina
- Department of Medicine, Division of Hematology/Oncology and Center for Personalized Cancer Therapy, University of California San Diego, 3855 Health Science Drive #0987, La Jolla, CA 92093, USA.
| | - Rafael Bejar
- Department of Medicine, Division of Hematology/Oncology and Center for Personalized Cancer Therapy, University of California San Diego, 3855 Health Science Drive #0987, La Jolla, CA 92093, USA.
| | - Michael Choi
- Department of Medicine, Division of Hematology/Oncology and Center for Personalized Cancer Therapy, University of California San Diego, 3855 Health Science Drive #0987, La Jolla, CA 92093, USA.
| | - Aaron Goodman
- Department of Medicine, Division of Hematology/Oncology and Center for Personalized Cancer Therapy, University of California San Diego, 3855 Health Science Drive #0987, La Jolla, CA 92093, USA.
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, CA 92093, USA.
| | - Matthew Wieduwilt
- Department of Medicine, Division of Hematology/Oncology and Center for Personalized Cancer Therapy, University of California San Diego, 3855 Health Science Drive #0987, La Jolla, CA 92093, USA.
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, CA 92093, USA.
| | - Carolyn Mulroney
- Department of Medicine, Division of Hematology/Oncology and Center for Personalized Cancer Therapy, University of California San Diego, 3855 Health Science Drive #0987, La Jolla, CA 92093, USA.
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, CA 92093, USA.
| | - Lisa Kim
- Department of Medicine, Division of Hematology/Oncology and Center for Personalized Cancer Therapy, University of California San Diego, 3855 Health Science Drive #0987, La Jolla, CA 92093, USA.
| | - Huwate Yeerna
- Department of Medicine, Division of Statistical Physics, University of California San Diego, La Jolla, CA 92093, USA.
| | - Pablo Tamayo
- Department of Medicine, Division of Statistical Physics, University of California San Diego, La Jolla, CA 92093, USA.
| | | | - Tariq I Mughal
- Foundation Medicine Inc., Cambridge, MA 02141, USA.
- Tufts University Medical Center, Boston, MA 02111, USA.
| | | | - Catriona Jamieson
- Department of Medicine, Division of Hematology/Oncology and Center for Personalized Cancer Therapy, University of California San Diego, 3855 Health Science Drive #0987, La Jolla, CA 92093, USA.
| | - Razelle Kurzrock
- Department of Medicine, Division of Hematology/Oncology and Center for Personalized Cancer Therapy, University of California San Diego, 3855 Health Science Drive #0987, La Jolla, CA 92093, USA.
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Galanina N, Kurzrock R. Successful implementation of genomically based treatment of chemotherapy refractory peripheral T-cell lymphoma (PTCL). Cancer Biol Ther 2018; 20:247-251. [PMID: 30307363 DOI: 10.1080/15384047.2018.1523857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND The treatment of peripheral T-cell lymphoma (PTCL) after failure of standard therapy represents a significant clinical challenge as the best approach has not been defined. The outcomes of patients with peripheral T-cell lymphoma (PTCL) after relapse, in the absence of hematopoietic stem-cell transplantation, are poor with median overall survival is less than six months. Thus, relapsed/refractory PTCL presents an area of unmet medical need. CASE PRESENTATION Herein, we report an 84-year old woman with stage IV PTCL with extensive involvement of the bowel and abdominal pain. She was treated with cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP) chemotherapy which was complicated by prolonged pancytopenia, without response. Disease progression was manifested by small bowel obstruction, for which she received palliative radiation therapy, further complicated by cardiac arrhythmia and sepsis. In the meantime, clinical-grade next generation sequencing of a lymph node (406 gene panel) showed six genomic alterations: NRAS Q61R, PTEN Q17*, CREBBP R768*, EP300 R1529*, SETD2 loss exons 19-21, along with an intermediate tumor mutational burden. Tissue PD-L1 staining was low positive by immunohistochemistry. The patient was discussed in Molecular Tumor Board with consensus opinion favoring a combination of the MEK inhibitor trametinib (for the NRAS alteration) and the checkpoint inhibitor nivolumab for the elevated mutational burden and PD-L1 positivity. Her abdominal pain resolved and she achieved a complete remission ongoing at 5+ months. Side effects at five months included only low-grade rash and peripheral edema. CONCLUSIONS Our observations suggest that matching patients with hematologic malignancies with customized combinations based on genomic sequencing warrants further study as a way to achieve and/or deepen responses, including in patients who are elderly and/or have refractory disease and significant disease-related complications.
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Affiliation(s)
- Natalie Galanina
- a Department of Medicine , Division of Hematology/Oncology , San Diego , CA , USA.,b Center for Personalized Cancer Therapy , University of California San Diego, Moores Cancer Center , San Diego , CA , USA
| | - Razelle Kurzrock
- a Department of Medicine , Division of Hematology/Oncology , San Diego , CA , USA.,b Center for Personalized Cancer Therapy , University of California San Diego, Moores Cancer Center , San Diego , CA , USA
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