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Baran JA, Bojarsky M, Halada S, Ricarte-Filho JC, Isaza A, Franco AT, Surrey LF, Bhatti T, Baloch Z, Adzick NS, Mostoufi-Moab S, Kazahaya K, Bauer AJ. Low-invasive somatic oncogenes and lymph node metastasis in pediatric papillary thyroid cancer: implications for prophylactic central neck dissection. Eur Thyroid J 2024; 13:e230265. [PMID: 38984999 PMCID: PMC11301529 DOI: 10.1530/etj-23-0265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/09/2024] [Indexed: 07/11/2024] Open
Abstract
Objective The American Thyroid Association (ATA) Pediatric Guidelines recommend selective, prophylactic central neck dissection (pCND) for patients with papillary thyroid carcinoma (PTC) based on tumor focality, tumor size, and the surgeon's experience. With the expansion of pre-surgical somatic oncogene testing and continued controversy over the benefits of pCND, oncogenic alteration data may provide an opportunity to stratify pCND. This study compared lymph node (LN) involvement in pediatric patients with PTC between tumors with low- and high-invasive-associated alterations to explore the potential utility of preoperative oncogenic alterations in the stratification of pCND. Methods This is retrospective cohort study of pediatric patients who underwent somatic oncogene testing post thyroidectomy for PTC between July 2003 and July 2022. Results Of 192 eligible PTC patients with postoperative somatic oncogene data, 19 tumors harbored somatic alterations associated with low-invasive disease (19/192, 10%), and 128 tumors harbored a BRAFV600E alteration (45/192, 23%) or an oncogenic fusion (83/192, 43%). Tumors with low-invasive alterations were less likely to present malignant preoperative cytology (2/18, 11%) than those with high-invasive alterations (97/124, 78%; P < 0.001). Twelve patients with low-invasive alterations had LNs dissected from the central neck (12/19, 63%) compared to 127 patients (127/128, 99%) with high-invasive alterations. LN metastasis was identified in two patients with low-invasive alterations (2/19, 11%) compared to 107 patients with high-invasive alterations (107/128, 84%; P < 0.001). Conclusion Pediatric patients with low-invasive somatic oncogenic alterations are at low risk for metastasis to central neck LNs. Our findings suggest that preoperative knowledge of somatic oncogene alterations provides objective data to stratify pediatric patients who may not benefit from pCND.
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Affiliation(s)
- Julia A Baran
- Division of Endocrinology and Diabetes, The Thyroid Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Mya Bojarsky
- Division of Endocrinology and Diabetes, The Thyroid Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stephen Halada
- Division of Endocrinology and Diabetes, The Thyroid Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Julio C Ricarte-Filho
- Division of Endocrinology and Diabetes, The Thyroid Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Amber Isaza
- Division of Endocrinology and Diabetes, The Thyroid Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Aime T Franco
- Division of Endocrinology and Diabetes, The Thyroid Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tricia Bhatti
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zubair Baloch
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - N Scott Adzick
- Department of Surgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sogol Mostoufi-Moab
- Division of Endocrinology and Diabetes, The Thyroid Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ken Kazahaya
- Division of Pediatric Otolaryngology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Otorhinolaryngology: Head and Neck Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrew J Bauer
- Division of Endocrinology and Diabetes, The Thyroid Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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2
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Gastier-Foster JM, Lutwama F, Mbabazi O, Mlenga S, Ulaya K, Namazzi R, Hollingsworth EF, Lopez-Terrada D, Fisher KE, Roy A, Allen CE, Poplack DG, Mzikamanda R, Ozuah N, Wasswa P. Rapid gene fusion testing using the NanoString nCounter platform to improve pediatric leukemia diagnoses in Sub-Saharan Africa. Front Oncol 2024; 14:1426638. [PMID: 38939333 PMCID: PMC11208450 DOI: 10.3389/fonc.2024.1426638] [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: 05/01/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Risk stratification and molecular targeting have been key to increasing cure rates for pediatric cancers in high-income countries. In contrast, precise diagnosis in low-resource settings is hindered by insufficient pathology infrastructure. The Global HOPE program aims to improve outcomes for pediatric cancer in Sub-Saharan Africa (SSA) by building local clinical care and diagnostic capacity. This study aimed to assess the feasibility of implementing molecular assays to improve leukemia diagnoses in SSA. Custom NanoString nCounter gene fusion assays, previously validated in the US, were used to test samples from suspected leukemia patients. The NanoString platform was chosen due to relatively low cost, minimal technical and bioinformatics expertise required, ability to test sub-optimal RNA, and rapid turnaround time. Fusion results were analyzed blindly, then compared to morphology and flow cytometry results. Of 117 leukemia samples, 74 were fusion-positive, 30 were negative, 7 were not interpretable, and 6 failed RNA quality. Nine additional samples were negative for leukemia by flow cytometry and negative for gene fusions. All 74 gene fusions aligned with the immunophenotype determined by flow cytometry. Fourteen samples had additional information available to further confirm the accuracy of the gene fusion results. The testing provided a more precise diagnosis in >60% of cases, and 9 cases were identified that could be treated with an available tyrosine kinase inhibitor, if detected at diagnosis. As risk-stratified and targeted therapies become more available in SSA, implementing this testing in real-time will enable the treatment of pediatric cancer to move toward incorporating risk stratification for optimized therapy.
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Affiliation(s)
- Julie M. Gastier-Foster
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Fredrick Lutwama
- Biomedical Research Centre, Makerere University, Kampala, Uganda
| | - Olive Mbabazi
- Biomedical Research Centre, Makerere University, Kampala, Uganda
| | - Steven Mlenga
- Baylor College of Medicine Children’s Foundation - Malawi, Lilongwe, Malawi
| | - Kennedy Ulaya
- Baylor College of Medicine Children’s Foundation - Malawi, Lilongwe, Malawi
| | - Ruth Namazzi
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - E. Faith Hollingsworth
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Dolores Lopez-Terrada
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Kevin E. Fisher
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Angshumoy Roy
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Carl E. Allen
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - David G. Poplack
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Rizine Mzikamanda
- Baylor College of Medicine Children’s Foundation - Malawi, Lilongwe, Malawi
| | - Nmazuo Ozuah
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Peter Wasswa
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
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3
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Suster D, Mackinnon AC, Ronen N, Mejbel HA, Harada S, Suster S. Non-Small Cell Lung Carcinoma With Clear Cell Features and FGFR3::TACC3 Gene Rearrangement : Clinicopathologic and Next Generation Sequencing Study of 7 Cases. Am J Surg Pathol 2024; 48:284-291. [PMID: 38084010 DOI: 10.1097/pas.0000000000002167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Seven cases of primary lung tumors characterized histologically by clear cell morphology and a distinctive FGFR3::TACC3 gene rearrangement are described. The tumors arose in 4 women and 3 men, aged 47 to 81 years (mean=68). They occurred in peripheral locations, predominantly subpleural, and ranged in size from 1.4 to 6.5 cm (mean=4.1 cm). All tumors showed a solid growth pattern with abundant central areas of necrosis and marked nuclear pleomorphism. The tumors demonstrated clear cell histology, with large cohesive tumor cells displaying atypical nuclei and abundant clear cytoplasm. Immunohistochemical stains identified a squamous phenotype in 5 cases and an adenocarcinoma phenotype in 2 cases. One case was a squamous cell carcinoma with focal glandular component, and one of the squamous cell carcinomas showed focal sarcomatoid changes. Next generation sequencing identified FGFR3::TACC3 gene rearrangements in all 7 cases. One case demonstrated a concurrent activating FGFR3 mutation and a second case demonstrated concurrent FGFR3 amplification. Two cases harbored a concurrent KRAS G12D mutation. One case harbored both KRAS and EGFR mutations, and 1 case had a concurrent TP53 mutation. Non-small cell lung carcinoma harboring FGFR3::TACC3 gene rearrangements is extremely rare, and this rearrangement may potentially be enriched in tumors that demonstrate clear cell histology. Identification of FGFR3::TACC3 in patients with lung carcinomas with clear cell features may be of importance as they could potentially be candidates for therapy with tyrosine kinase inhibitors.
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Affiliation(s)
- David Suster
- Department of Pathology, Rutgers New Jersey Medical School, Newark, NJ
| | - A Craig Mackinnon
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL
| | - Natali Ronen
- Department of Pathology, The Medical College of Wisconsin, Milwaukee, WI
| | - Haider A Mejbel
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL
- Department of Pathology, Emory University School of Medicine, Atlanta, GA
| | - Shuko Harada
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL
| | - Saul Suster
- Department of Pathology, The Medical College of Wisconsin, Milwaukee, WI
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4
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Bojarsky M, Baran JA, Halada S, Isaza A, Zhuang H, States L, Grant FD, Robbins S, Sisko L, Ricarte-Filho JC, Kazahaya K, Adzick NS, Mostoufi-Moab S, Bauer AJ. Outcomes of ATA Low-Risk Pediatric Thyroid Cancer Patients Not Treated With Radioactive Iodine Therapy. J Clin Endocrinol Metab 2023; 108:3338-3344. [PMID: 37265226 PMCID: PMC10655549 DOI: 10.1210/clinem/dgad322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
CONTEXT The American Thyroid Association (ATA) Pediatric Guidelines recommend patients not receive radioactive iodine therapy (RAIT) for differentiated thyroid cancer (DTC) confined to the thyroid. Since publication, there is ongoing concern whether withholding RAIT will result in a lower rate of remission. OBJECTIVE This study explores whether ATA low-risk patients treated with and without RAIT achieved similar remission rates. METHODS Medical records of patients <19 years old diagnosed with DTC and treated with total thyroidectomy between 2010 and 2020 were reviewed. Multivariate logistic regression was performed to evaluate factors influencing RAIT administration and remission rate. RESULTS Ninety-five patients with ATA low-risk DTC were analyzed: 53% (50/95) and 47% (45/95) were treated with and without RAIT, respectively. RAIT was used to treat 82% of patients before 2015 compared with 33% of patients after 2015 (P < .01). No significant difference in 1-year remission rate was found between patients treated with and without RAIT, 70% (35/50) vs 69% (31/45), respectively. With longer surveillance, remission rates increased to 82% and 76% for patients treated with and without RAIT, respectively. Median follow-up was 5.8 years (IQR 4.3-7.9, range 0.9-10.9) and 3.6 years (IQR 2.7-6.6; range 0.9-9.3) for both cohorts. No risk factors for persistent or indeterminate disease status were found, including RAIT administration, N1a disease, and surgery after 2015. CONCLUSION Withholding RAIT for pediatric patients with ATA low-risk DTC avoids exposure to radiation and does not have a negative impact on remission rates. Dynamic risk stratification at 1-year after initial treatment is a suitable time point to assess the impact of withholding RAIT for these patients.
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Affiliation(s)
- Mya Bojarsky
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julia A Baran
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stephen Halada
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Amber Isaza
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hongming Zhuang
- Division of Nuclear Medicine, Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa States
- Division of Nuclear Medicine, Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Section Oncologic Imaging, Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Frederick D Grant
- Division of Nuclear Medicine, Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stephanie Robbins
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lindsay Sisko
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julio C Ricarte-Filho
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ken Kazahaya
- Division of Pediatric Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Otorhinolaryngology: Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - N Scott Adzick
- Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sogol Mostoufi-Moab
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Andrew J Bauer
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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5
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Chen S, Gallant S, Cunningham MJ, Robson CD, Church AJ, Perez-Atayde AR, Al-Ibraheemi A. CTNNB1 and APC Mutations in Sinonasal Myxoma : Expanding the Spectrum of Tumors Driven By WNT/β-catenin Pathway. Am J Surg Pathol 2023; 47:1291-1300. [PMID: 37589277 DOI: 10.1097/pas.0000000000002112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Sinonasal myxoma (SNM) is a rare, benign mesenchymal neoplasm with distinct clinicopathologic features and aberrant nuclear localization of β-catenin by immunohistochemistry. The molecular underpinnings have been linked to that of a "myxoid variant" of desmoid fibromatosis. Herein, we describe a series of 8 cases of SNM and propose clinical and biologic differences compared with desmoid fibromatosis. Our patient cohort is comprised of 5 males and 3 females (age range: 10 mo to 12 y), 6 of whom are aged less than or equal to 24 months. All presented with facial swelling, reflecting lesions involving the maxillary bone, and all underwent resection. All tumors were variably cellular and comprised of bland spindled to stellate cells in a profusely myxoid background with diffuse nuclear β-catenin expression. All cases of SNM were analyzed by next-generation sequencing using the Oncopanel assay. Three cases failed sequencing, 2 of 5 successful cases exhibited exon 3 CTNNB1 alterations involving the ubiquitin recognition motif, and 3 had adenomatous polyposis coli ( APC ) deletions. One patient had APC germline testing which was negative. No germline testing was available for the remaining 7 patients. Follow-up data over a range of 1 month to 23 years was available for 7 of the 8 SNMs. One case patient had local recurrence, and all were alive without evidence of disease. This is in contrast to the high recurrence rate typically seen in desmoid fibromatosis, particularly after resection. Our findings expand the spectrum of tumors with underlying WNT/β-catenin pathway and highlight the histologic, clinical, and genetic differences of SNM compared with desmoid fibromatosis. APC deletion raises the possibility of underlying germline alteration and familial adenomatous polyposis.
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Affiliation(s)
- Sonja Chen
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Sara Gallant
- Departments of Otolaryngology and Communication Enhancement
- Harvard Medical School, Boston, MA
| | - Michael J Cunningham
- Departments of Otolaryngology and Communication Enhancement
- Harvard Medical School, Boston, MA
| | | | - Alanna J Church
- Pathology and Laboratory Medicine, Boston Children's Hospital
- Harvard Medical School, Boston, MA
| | - Antonio R Perez-Atayde
- Pathology and Laboratory Medicine, Boston Children's Hospital
- Harvard Medical School, Boston, MA
| | - Alyaa Al-Ibraheemi
- Pathology and Laboratory Medicine, Boston Children's Hospital
- Harvard Medical School, Boston, MA
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6
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Xu E, Stone SL, Zhong Y, Golenberg N, Qiu L, Abdullaev Z, Aldape K, Bagley L, Halpern CH, Amankulor N, Nasrallah MP. A novel ARIH1::BRAF fusion in a glioma. J Neuropathol Exp Neurol 2023; 82:966-969. [PMID: 37742132 PMCID: PMC11009502 DOI: 10.1093/jnen/nlad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2023] Open
Affiliation(s)
- Emily Xu
- Department of Clinical Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sara Lynn Stone
- Department of Clinical Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yiming Zhong
- Department of Clinical Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Netta Golenberg
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Liming Qiu
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Linda Bagley
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Casey H Halpern
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nduka Amankulor
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - MacLean P Nasrallah
- Department of Clinical Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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7
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Baran JA, Halada S, Bauer AJ, Li Y, Isaza A, Patel T, Sisko L, Ginsberg JP, Kazahaya K, Adzick NS, Mostoufi-Moab S. Thyroid Ultrasound Screening in Childhood Cancer Survivors following Radiotherapy. Horm Res Paediatr 2023; 97:243-253. [PMID: 37722360 PMCID: PMC11151990 DOI: 10.1159/000531241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 05/16/2023] [Indexed: 09/20/2023] Open
Abstract
INTRODUCTION Childhood cancer survivors (CCS) are at risk for radiotherapy (RT) late effects, including second malignancies. Optimal screening for differentiated thyroid cancer (DTC) in CCS post-RT remains controversial. We assessed the outcome of thyroid ultrasound (US) surveillance in CCS exposed to RT. METHODS 306 CCS were surveilled with thyroid US between 2002-2021. Surveillance was dependent on age at the time of primary diagnosis, interval from receipt of RT, and individual provider. Thyroid US, clinicopathologic features, and outcomes were described. Cutpoints of CCS RT age associated with varying risk of nodule presentation were explored. The selected cutpoints were used to define age categories, which were then used to compare thyroid nodule-related outcomes. Risk factors for thyroid nodule(s) were evaluated using multivariate logistic regression (odds ratio [OR] [95% confidence interval]). RESULTS The most common CCS diagnoses were leukemia (32%), CNS tumor (26%), and neuroblastoma (18%). Patients received TBI (45%) and/or RT to craniospinal (44%), chest (11%), and neck regions (6%). About 49% (n = 150) of patients had thyroid nodule(s). Forty-four patients underwent surgery, and 28 had DTC: 19 with American Thyroid Association (ATA) low-risk classification, 2 with ATA intermediate-risk, and 7 with ATA high-risk disease. Age cutpoint analyses identified cutpoints 3 and 10; hence, ≤3, >3 to ≤10, and >10 years were used. Of the 9 patients with intermediate- or high-risk disease, 8 were ≤10 years and 1 was >10 years at the time of RT. Female sex (OR = 1.62 [1.13-2.12] p = 0.054) and greater interval between RT and first US (OR = 1.10 [1.04-1.16] p = 0.001) were independent risk factors for nodule presentation. CONCLUSIONS Thyroid US surveillance may be beneficial for CCS exposed to RT at younger ages (≤10 years) for earlier detection of DTC, prior to developing advanced metastatic disease.
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Affiliation(s)
- Julia A Baran
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,
| | - Stephen Halada
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Andrew J Bauer
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yimei Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amber Isaza
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tasleema Patel
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lindsay Sisko
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jill P Ginsberg
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ken Kazahaya
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Pediatric Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Otorhinolaryngology: Head and Neck Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - N Scott Adzick
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sogol Mostoufi-Moab
- Division of Endocrinology and Diabetes, The Thyroid Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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8
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Schieffer KM, Moccia A, Bucknor BA, Stonerock E, Jayaraman V, Jenkins H, McKinney A, Koo SC, Mathew MT, Mardis ER, Lee K, Reshmi SC, Cottrell CE. Expanding the Clinical Utility of Targeted RNA Sequencing Panels beyond Gene Fusions to Complex, Intragenic Structural Rearrangements. Cancers (Basel) 2023; 15:4394. [PMID: 37686670 PMCID: PMC10486946 DOI: 10.3390/cancers15174394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Gene fusions are a form of structural rearrangement well established as driver events in pediatric and adult cancers. The identification of such events holds clinical significance in the refinement, prognostication, and provision of treatment in cancer. Structural rearrangements also extend beyond fusions to include intragenic rearrangements, such as internal tandem duplications (ITDs) or exon-level deletions. These intragenic events have been increasingly implicated as cancer-promoting events. However, the detection of intragenic rearrangements may be challenging to resolve bioinformatically with short-read sequencing technologies and therefore may not be routinely assessed in panel-based testing. Within an academic clinical laboratory, over three years, a total of 608 disease-involved samples (522 hematologic malignancy, 86 solid tumors) underwent clinical testing using Anchored Multiplex PCR (AMP)-based RNA sequencing. Hematologic malignancies were evaluated using a custom Pan-Heme 154 gene panel, while solid tumors were assessed using a custom Pan-Solid 115 gene panel. Gene fusions, ITDs, and intragenic deletions were assessed for diagnostic, prognostic, or therapeutic significance. When considering gene fusions alone, we report an overall diagnostic yield of 36% (37% hematologic malignancy, 41% solid tumors). When including intragenic structural rearrangements, the overall diagnostic yield increased to 48% (48% hematologic malignancy, 45% solid tumor). We demonstrate the clinical utility of reporting structural rearrangements, including gene fusions and intragenic structural rearrangements, using an AMP-based RNA sequencing panel.
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Affiliation(s)
- Kathleen M. Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Amanda Moccia
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Brianna A. Bucknor
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Heather Jenkins
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Aimee McKinney
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Selene C. Koo
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Mariam T. Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Shalini C. Reshmi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Catherine E. Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
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9
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Gubbiotti MA, Madsen PJ, Tucker AM, Abdullaev Z, Aldape K, Shekdar K, Yang A, Minturn JE, Santi M, Viaene AN. ZFTA-fused supratentorial ependymoma with a novel fusion partner, DUX4. J Neuropathol Exp Neurol 2023; 82:668-671. [PMID: 37218333 PMCID: PMC10501467 DOI: 10.1093/jnen/nlad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Affiliation(s)
- Maria A Gubbiotti
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Peter J Madsen
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Alexander M Tucker
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zied Abdullaev
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kenneth Aldape
- Laboratory of Pathology and Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Karuna Shekdar
- Department of Radiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Adeline Yang
- Department of Pediatrics, Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jane E Minturn
- Department of Pediatrics, Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Angela N Viaene
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Gubbiotti MA, Santi M, Storm PB, Li M, Xu F, Abdullaev Z, Aldape K, Viaene AN. First-time identification of a KIF5B-NTRK2 fusion in extraventricular neurocytoma. J Neuropathol Exp Neurol 2023; 82:272-275. [PMID: 36655517 PMCID: PMC10167923 DOI: 10.1093/jnen/nlad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Maria A Gubbiotti
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Philip B Storm
- Department of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Marilyn Li
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Feng Xu
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zied Abdullaev
- Laboratory of Pathology and Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Kenneth Aldape
- Laboratory of Pathology and Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Angela N Viaene
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
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11
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Tran TH, Tasian SK. Clinical screening for Ph-like ALL and the developing role of TKIs. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2022; 2022:594-602. [PMID: 36485164 PMCID: PMC9821133 DOI: 10.1182/hematology.2022000357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a common subtype of B-lineage acute lymphoblastic leukemia (B-ALL) with increasing frequency across the age spectrum. Characterized by a kinase-activated gene expression profile and driven by a variety of genetic alterations involving cytokine receptors and kinases, Ph-like ALL is associated with high rates of residual disease and relapse in patients treated with conventional chemotherapy. In this case-based review, we describe the biology of the 2 major ABL-class and JAK pathway genetic subtypes of Ph-like ALL, discuss current diagnostic testing methodologies, and highlight targeted inhibitor and chemo/immunotherapy approaches under clinical investigation in children, adolescents, and adults with these high-risk leukemias.
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Affiliation(s)
- Thai Hoa Tran
- Division of Pediatric Hematology-Oncology, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics and Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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12
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Smith ME, Surrey LF, Zhang PJ, Weinstein GS, LiVolsi VA. Molecular identification of an ETV6-RET fusion in a secretory carcinoma associated with a pleomorphic adenoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2022; 134:733-738. [PMID: 35915042 DOI: 10.1016/j.oooo.2022.04.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/01/2022] [Accepted: 04/17/2022] [Indexed: 12/13/2022]
Abstract
Pleomorphic adenoma (PA) is the most common neoplasm of the salivary glands. Although several carcinomas have been reported to arise from PA, only 1 case of salivary gland secretory carcinoma (SC) ex pleomorphic adenoma has been previously reported. SC is a newly described salivary gland tumor harboring an ETV6-NTRK3 translocation, which is classically observed in secretory carcinoma of the breast, although other translocations have recently been observed. We report the first case of the molecular identification of a rare ETV6-RET translocation in an SC arising from a PA in the submandibular salivary gland (SC ex PA). Our results add to the diversity of tumors that are associated with PA and contribute to the molecular characterization of SC, which will have implications on its diagnosis, prognosis, and treatment.
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Affiliation(s)
- Maria E Smith
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Zhang
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory S Weinstein
- Department of Otorhinolaryngology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia A LiVolsi
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA.
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13
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Xu F, Viaene AN, Ruiz J, Schubert J, Wu J, Chen J, Cao K, Fu W, Bagatell R, Fan Z, Long A, Pagliaroli L, Zhong Y, Luo M, Kreiger PA, Surrey LF, Wertheim GB, Cole KA, Li MM, Santi M, Storm PB. Novel ATXN1/ATXN1L::NUTM2A fusions identified in aggressive infant sarcomas with gene expression and methylation patterns similar to CIC-rearranged sarcoma. Acta Neuropathol Commun 2022; 10:102. [PMID: 35836290 PMCID: PMC9281131 DOI: 10.1186/s40478-022-01401-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
CIC-rearranged sarcomas are newly defined undifferentiated soft tissue tumors with CIC-associated fusions, and dismal prognosis. CIC fusions activate PEA3 family genes, ETV1/4/5, leading to tumorigenesis and progression. We report two high-grade CNS sarcomas of unclear histological diagnosis and one disseminated tumor of unknown origin with novel fusions and similar gene-expression/methylation patterns without CIC rearrangement. All three patients were infants with aggressive diseases, and two experienced rapid disease deterioration and death. Whole-transcriptome sequencing identified an ATXN1-NUTM2A fusion in the two CNS tumors and an ATXN1L-NUTM2A fusion in case 3. ETV1/4/5 and WT1 overexpression were observed in all three cases. Methylation analyses predicted CIC-rearranged sarcoma for all cases. Retrospective IHC staining on case 2 demonstrated ETV4 and WT1 overexpression. ATXN1 and ATXN1L interact with CIC forming a transcription repressor complex. We propose that ATXN1/ATXN1L-associated fusions disrupt their interaction with CIC and decrease the transcription repressor complex, leading to downstream PEA3 family gene overexpression. These three cases with novel ATXN1/ATXN1L-associated fusions and features of CIC-rearranged sarcomas may further expand the scope of "CIC-rearranged" sarcomas to include non-CIC rearrangements. Additional cases are needed to demonstrate if ATXN1/ATXN1L-NUTM2A fusions are associated with younger age and more aggressive diseases.
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Affiliation(s)
- Feng Xu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Angela N Viaene
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jenny Ruiz
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jeffrey Schubert
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jinhua Wu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiani Chen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Weixuan Fu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rochelle Bagatell
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhiqian Fan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ariel Long
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Luca Pagliaroli
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yiming Zhong
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Portia A Kreiger
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gerald B Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristina A Cole
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Phillip B Storm
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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14
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Wolff HB, Steeghs EMP, Mfumbilwa ZA, Groen HJM, Adang EM, Willems SM, Grünberg K, Schuuring E, Ligtenberg MJL, Tops BBJ, Coupé VMH. Cost-Effectiveness of Parallel Versus Sequential Testing of Genetic Aberrations for Stage IV Non-Small-Cell Lung Cancer in the Netherlands. JCO Precis Oncol 2022; 6:e2200201. [PMID: 35834758 PMCID: PMC9307305 DOI: 10.1200/po.22.00201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
PURPOSE A large number of targeted treatment options for stage IV nonsquamous non–small-cell lung cancer with specific genetic aberrations in tumor DNA is available. It is therefore important to optimize diagnostic testing strategies, such that patients receive adequate personalized treatment that improves survival and quality of life. The aim of this study is to assess the efficacy (including diagnostic costs, turnaround time (TAT), unsuccessful tests, percentages of correct findings, therapeutic costs, and therapeutic effectiveness) of parallel next generation sequencing (NGS)–based versus sequential single-gene–based testing strategies routinely used in patients with metastasized non–small-cell lung cancer in the Netherlands. METHODS A diagnostic microsimulation model was developed to simulate 100,000 patients with prevalence of genetic aberrations, extracted from real-world data from the Dutch Pathology Registry. These simulated patients were modeled to undergo different testing strategies composed of multiple tests with different test characteristics including single-gene and panel tests, test accuracy, the probability of an unsuccessful test, and TAT. Diagnostic outcomes were linked to a previously developed treatment model, to predict average long-term survival, quality-adjusted life-years (QALYs), costs, and cost-effectiveness of parallel versus sequential testing. RESULTS NGS-based parallel testing for all actionable genetic aberrations is on average €266 cheaper than single-gene–based sequential testing, and detects additional relevant targetable genetic aberrations in 20.5% of the cases, given a TAT of maximally 2 weeks. Therapeutic costs increased by €8,358, and 0.12 QALYs were gained, leading to an incremental cost-effectiveness ratio of €69,614/QALY for parallel versus sequential testing. CONCLUSION NGS-based parallel testing is diagnostically superior over single-gene–based sequential testing, as it is cheaper and more effective than sequential testing. Parallel testing remains cost-effective with an incremental cost-effectiveness ratio of 69,614 €/QALY upon inclusion of therapeutic costs and long-term outcomes.
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Affiliation(s)
- Henri B Wolff
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, VU Amsterdam, Amsterdam, the Netherlands
| | - Elisabeth M P Steeghs
- Department of Pathology, Radboudumc, Nijmegen, the Netherlands.,Department of Pathology, Antoni van Leeuwenhoek Hospital, the Netherlands Cancer Institute, Amsterdam, the Netherlands.,Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Zakile A Mfumbilwa
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, VU Amsterdam, Amsterdam, the Netherlands
| | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Eddy M Adang
- Department of Epidemiology, Biostatistics and HTA, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Stefan M Willems
- Department of Pathology and Medical Biology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,PALGA Foundation, Houten, the Netherlands
| | | | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboudumc, Nijmegen, the Netherlands.,Department of Human Genetics, and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Bilthoven, the Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, VU Amsterdam, Amsterdam, the Netherlands
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15
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Franco AT, Ricarte-Filho JC, Isaza A, Jones Z, Jain N, Mostoufi-Moab S, Surrey L, Laetsch TW, Li MM, DeHart JC, Reichenberger E, Taylor D, Kazahaya K, Adzick NS, Bauer AJ. Fusion Oncogenes Are Associated With Increased Metastatic Capacity and Persistent Disease in Pediatric Thyroid Cancers. J Clin Oncol 2022; 40:1081-1090. [PMID: 35015563 PMCID: PMC8966969 DOI: 10.1200/jco.21.01861] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/07/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE In 2014, data from a comprehensive multiplatform analysis of 496 adult papillary thyroid cancer samples reported by The Cancer Genome Atlas project suggested that reclassification of thyroid cancer into molecular subtypes, RAS-like and BRAF-like, better reflects clinical behavior than sole reliance on pathologic classification. The aim of this study was to categorize the common oncogenic variants in pediatric differentiated thyroid cancer (DTC) and investigate whether mutation subtype classification correlated with the risk of metastasis and response to initial therapy in pediatric DTC. METHODS Somatic cancer gene panel analysis was completed on DTC from 131 pediatric patients. DTC were categorized into RAS-mutant (H-K-NRAS), BRAF-mutant (BRAF p.V600E), and RET/NTRK fusion (RET, NTRK1, and NTRK3 fusions) to determine differences between subtype classification in regard to pathologic data (American Joint Committee on Cancer TNM) as well as response to therapy 1 year after initial treatment had been completed. RESULTS Mutation-based subtype categories were significant in most variables, including age at diagnosis, metastatic behavior, and the likelihood of remission at 1 year. Patients with RET/NTRK fusions were significantly more likely to have advanced lymph node and distant metastasis and less likely to achieve remission at 1 year than patients within RAS- or BRAF-mut subgroups. CONCLUSION Our data support that genetic subtyping of pediatric DTC more accurately reflects clinical behavior than sole reliance on pathologic classification with patients with RET/NTRK fusions having worse outcomes than those with BRAF-mutant disease. Future trials should consider inclusion of molecular subtype into risk stratification.
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Affiliation(s)
- Aime T Franco
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Julio C Ricarte-Filho
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amber Isaza
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Zachary Jones
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
- Deceased
| | - Neil Jain
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sogol Mostoufi-Moab
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lea Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Theodore W Laetsch
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Erin Reichenberger
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ken Kazahaya
- Division of Pediatric Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA
| | - N Scott Adzick
- Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Andrew J Bauer
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
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16
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Ricarte-Filho JC, Halada S, O'Neill A, Casado-Medrano V, Laetsch TW, Franco AT, Bauer AJ. The clinical aspect of NTRK-fusions in pediatric papillary thyroid cancer. Cancer Genet 2022; 262-263:57-63. [PMID: 35092884 PMCID: PMC8931989 DOI: 10.1016/j.cancergen.2022.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/09/2021] [Accepted: 01/18/2022] [Indexed: 12/26/2022]
Abstract
Although adult and pediatric papillary thyroid cancer (PTC) share similar oncogenic drivers, they differ in the pathological features and outcomes of the disease. In adults with PTC, the most frequent genetic alterations are mutually exclusive point mutations in BRAFV600E or the RAS family with BRAFV600E commonly associated with invasive disease and decreased response to radioiodine therapy. In pediatric PTC, fusion oncogenes involving chromosomal translocations in tyrosine kinase (TK) receptors, most commonly RET and NTRK, are often found in patients with lateral neck and distant metastases. This brief report reviews clinical data from a single-institute's cohort of NTRK-driven pediatric PTC cases with an updated review of the literature and comparison to adult NTRK-driven PTC.
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Affiliation(s)
- Julio C Ricarte-Filho
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Buerger Center, 12-149, Philadelphia, PA 19104, United States
| | - Stephen Halada
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Buerger Center, 12-149, Philadelphia, PA 19104, United States
| | - Alison O'Neill
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Buerger Center, 12-149, Philadelphia, PA 19104, United States
| | - Victoria Casado-Medrano
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Buerger Center, 12-149, Philadelphia, PA 19104, United States
| | - Theodore W Laetsch
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Aime T Franco
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Buerger Center, 12-149, Philadelphia, PA 19104, United States; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Andrew J Bauer
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Buerger Center, 12-149, Philadelphia, PA 19104, United States.
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17
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Hu W, Yuan L, Zhang X, Ni Y, Hong D, Wang Z, Li X, Ling Y, Zhang C, Deng W, Tian M, Ding R, Song C, Li J, Zhang X. Development and validation of an RNA sequencing panel for gene fusions in soft tissue sarcoma. Cancer Sci 2022; 113:1843-1854. [PMID: 35238118 PMCID: PMC9128172 DOI: 10.1111/cas.15317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/08/2022] [Accepted: 02/24/2022] [Indexed: 11/29/2022] Open
Abstract
Gene fusions are one of the most common genomic alterations in soft tissue sarcomas (STS), which contain more than 70 subtypes. In this study, a custom-designed RNA sequencing panel including 67 genes was developed and validated to identify gene fusions in STS. Totally 92 STS samples were analyzed using the RNA panel and 95.7% (88/92) successfully passed all the quality control parameters. Fusion transcripts were detected in 60.2% (53/88) of samples, including three novel fusions (MEG3-PLAG1, SH3BP1-NTRK1, and RPSAP52-HMGA2). The panel demonstrated excellent analytic accuracy, with 93.9% sensitivity and 100% specificity. The intra-assay, inter-assay, and personnel consistencies were all 100.0% in 4 samples and 3 replicates. In addition, different variants of ESWR1-FLI, COL1A1-PDGFB, NAB2-STAT6, and SS18-SSX were also identified in the corresponding subtypes of STS. In combination with histological and molecular diagnosis, 14.8% (13/88) patients finally changed preliminary histology-based classification. Collectively, this RNA panel developed in our study shows excellent performance on RNA from formalin-fixed, paraffin-embedded samples and can complement DNA-based assay, thereby facilitating precise diagnosis and novel fusion detection.
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Affiliation(s)
- Wanming Hu
- Department of Pathology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Li Yuan
- Department of Pathology, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Xinke Zhang
- Department of Pathology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yang Ni
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210042, China.,Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, 210042, China
| | - Dongchun Hong
- Department of Medical Melanoma and Sarcoma, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Zhicai Wang
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research &, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Xiaomin Li
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210042, China
| | - Yuan Ling
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210042, China
| | - Chao Zhang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210042, China
| | - Wanglong Deng
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210042, China
| | - Minqi Tian
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210042, China
| | - Ran Ding
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210042, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210042, China.,Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, 210042, China
| | - Jianmin Li
- Department of Orthopedics, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Xing Zhang
- Department of Medical Melanoma and Sarcoma, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
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18
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Chang WI, Lin C, Liguori N, Honeyman JN, DeNardo B, El-Deiry W. Molecular Targets for Novel Therapeutics in Pediatric Fusion-Positive Non-CNS Solid Tumors. Front Pharmacol 2022; 12:747895. [PMID: 35126101 PMCID: PMC8811504 DOI: 10.3389/fphar.2021.747895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/03/2021] [Indexed: 12/31/2022] Open
Abstract
Chromosomal fusions encoding novel molecular drivers have been identified in several solid tumors, and in recent years the identification of such pathogenetic events in tumor specimens has become clinically actionable. Pediatric sarcomas and other rare tumors that occur in children as well as adults are a group of heterogeneous tumors often with driver gene fusions for which some therapeutics have already been developed and approved, and others where there is opportunity for progress and innovation to impact on patient outcomes. We review the chromosomal rearrangements that represent oncogenic events in pediatric solid tumors outside of the central nervous system (CNS), such as Ewing Sarcoma, Rhabdomyosarcoma, Fibrolamellar Hepatocellular Carcinoma, and Renal Cell Carcinoma, among others. Various therapeutics such as CDK4/6, FGFR, ALK, VEGF, EGFR, PDGFR, NTRK, PARP, mTOR, BRAF, IGF1R, HDAC inhibitors are being explored among other novel therapeutic strategies such as ONC201/TIC10.
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Affiliation(s)
- Wen-I Chang
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- Pediatric Hematology/Oncology, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, United States
- *Correspondence: Wen-I Chang, ; Wafik El-Deiry,
| | - Claire Lin
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Nicholas Liguori
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Joshua N. Honeyman
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, United States
- Pediatric Surgery, The Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Bradley DeNardo
- Pediatric Hematology/Oncology, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, United States
| | - Wafik El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, United States
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- Hematology/Oncology Division, Department of Medicine, Lifespan Health System and Brown University, Providence, RI, United States
- *Correspondence: Wen-I Chang, ; Wafik El-Deiry,
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19
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Lang SS, Kumar NK, Madsen P, Gajjar AA, Gajjar E, Resnick AC, Storm PB. Neurotrophic Tyrosine Receptor Kinase Fusion in Pediatric Central Nervous System Tumors. Cancer Genet 2022; 262-263:64-70. [DOI: 10.1016/j.cancergen.2022.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/29/2021] [Accepted: 01/18/2022] [Indexed: 12/16/2022]
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20
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Davis JL, Al‐Ibraheemi A, Rudzinski ER, Surrey LF. Mesenchymal neoplasms with NTRK and other kinase gene alterations. Histopathology 2021; 80:4-18. [DOI: 10.1111/his.14443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/20/2022]
Affiliation(s)
- Jessica L Davis
- Department of Pathology Oregon Health & Science University Portland OregonUSA
| | - Alyaa Al‐Ibraheemi
- Department of Pathology Boston Children’s Hospital Boston MassachusettsUSA
| | - Erin R Rudzinski
- Department of Laboratories Seattle Children’s Hospital Seattle WashingtonUSA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine The Children’s Hospital of Philadelphia Philadelphia Pennsylvania USA
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21
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Kotch C, Fisher MJ, Lin F, Zhong Y, Gallo D, Fan Z, Chen J, Santi M, Li MM. Atypical teratoid rhabdoid tumor in a child with neurofibromatosis type 2: A novel dual diagnosis. Cancer Genet 2021; 262-263:1-4. [PMID: 34972035 DOI: 10.1016/j.cancergen.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/24/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022]
Abstract
Neurofibromatosis type 2 (NF2) is a genetic disorder characterized by the development of tumors of the nervous system and is associated with NF2 gene alterations. Atypical teratoid rhabdoid tumor (ATRT) is a malignant central nervous system tumor that occurs primarily in children less than 3 years of age. The majority of cases of ATRT demonstrate genomic alterations of SMARCB1, a core member of the SWI/SNF chromatin-remodeling complex and tumor suppressor gene. SMARCB1 inactivation in ATRT is occasionally associated with somatic NF2 deletion; however, concurrent germline NF2 mutations have not been reported. Herein, we describe the case of a 3-year-old patient who presented with an intracranial mass. Next generation sequencing analysis of tumor identified homozygous deletions of the entire SMARCB1 gene and exon 7 to exon 14 of NF2 gene with whole chromosome 22 loss of heterozygosity (LOH). Multiplex Ligation-dependent Probe Amplification (MLPA) assay performed on blood identified a germline heterozygous intragenic deletion of NF2 exon 7 to exon 14; a somatic chromosome 22 LOH led to the homozygous deletion. SMARCB1 MLPA assay of blood showed no deletion. This cascade represents a novel, "four-hit" mechanism of SMARCB1 inactivation resulting in ATRT and the first known dual diagnosis of NF2 and ATRT.
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Affiliation(s)
- Chelsea Kotch
- Department of Pediatrics, Division of Oncology, Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA 19104, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Michael J Fisher
- Department of Pediatrics, Division of Oncology, Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA 19104, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Yiming Zhong
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Dan Gallo
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Zhiqian Fan
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jiani Chen
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Mariarita Santi
- Division of Anatomic Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Marilyn M Li
- Department of Pediatrics, Division of Oncology, Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA 19104, United States; Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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22
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Whole-transcriptome analysis in acute lymphoblastic leukemia: a report from the DFCI ALL Consortium Protocol 16-001. Blood Adv 2021; 6:1329-1341. [PMID: 34933343 PMCID: PMC8864659 DOI: 10.1182/bloodadvances.2021005634] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/27/2021] [Indexed: 11/25/2022] Open
Abstract
RNA-seq is feasible in the context of a prospective clinical trial for de novo ALL within a clinically sensitive turnaround time. RNA-seq identified several genetic alterations not detected by conventional methods that confer potential prognostic and therapeutic impact.
The molecular hallmark of childhood acute lymphoblastic leukemia (ALL) is characterized by recurrent, prognostic genetic alterations, many of which are cryptic by conventional cytogenetics. RNA sequencing (RNA-seq) is a powerful next-generation sequencing technology that can simultaneously identify cryptic gene rearrangements, sequence mutations and gene expression profiles in a single assay. We examined the feasibility and utility of incorporating RNA-seq into a prospective multicenter phase 3 clinical trial for children with newly diagnosed ALL. The Dana-Farber Cancer Institute ALL Consortium Protocol 16-001 enrolled 173 patients with ALL who consented to optional studies and had samples available for RNA-seq. RNA-seq identified at least 1 alteration in 157 patients (91%). Fusion detection was 100% concordant with results obtained from conventional cytogenetic analyses. An additional 56 gene fusions were identified by RNA-seq, many of which confer prognostic or therapeutic significance. Gene expression profiling enabled further molecular classification into the following B-cell ALL (B-ALL) subgroups: high hyperdiploid (n = 36), ETV6-RUNX1/-like (n = 31), TCF3-PBX1 (n = 7), KMT2A-rearranged (KMT2A-R; n = 5), intrachromosomal amplification of chromosome 21 (iAMP21) (n = 1), hypodiploid (n = 1), Philadelphia chromosome (Ph)-positive/Ph-like (n = 16), DUX4-R (n = 11), PAX5 alterations (PAX5 alt; n = 11), PAX5 P80R (n = 1), ZNF384-R (n = 4), NUTM1-R (n = 1), MEF2D-R (n = 1), and others (n = 10). RNA-seq identified 141 nonsynonymous mutations in 93 patients (54%); the most frequent were RAS-MAPK pathway mutations. Among 79 patients with both low-density array and RNA-seq data for the Philadelphia chromosome-like gene signature prediction, results were concordant in 74 patients (94%). In conclusion, RNA-seq identified several clinically relevant genetic alterations not detected by conventional methods, which supports the integration of this technology into front-line pediatric ALL trials. This trial was registered at www.clinicaltrials.gov as #NCT03020030.
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23
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Tran TH, Tasian SK. Has Ph-like ALL Superseded Ph+ ALL as the Least Favorable Subtype? Best Pract Res Clin Haematol 2021; 34:101331. [PMID: 34865703 DOI: 10.1016/j.beha.2021.101331] [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: 11/24/2022]
Abstract
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a subset of high-risk B-ALL associated with high relapse risk and inferior clinical outcomes across the pediatric-to-adult age spectrum. Ph-like ALL is characterized by frequent IKZF1 alterations and a kinase-activated gene expression profile similar to that of Philadelphia chromosome-positive (Ph+) ALL, yet lacks the canonical BCR-ABL1 rearrangement. Advances in high-throughput sequencing technologies during the past decade have unraveled the genomic landscape of Ph-like ALL, revealing a diverse array of kinase-activating translocations and mutations that may be amenable to targeted therapies that have set a remarkable precision medicine paradigm for patients with Ph + ALL. Collaborative scientific efforts to identify and characterise Ph-like ALL during the past decade has directly informed current precision medicine trials investigating the therapeutic potential of tyrosine kinase inhibitor-based therapies for children, adolescents, and adults with Ph-like ALL, although the most optimal treatment paradigm for this high-risk group of patients has yet to be established. Herein, we describe the epidemiology, clinical features, and biology of Ph-like ALL, highlight challenges in implementing pragmatic and cost-effective diagnostic algorithms in the clinic, and describe the milieu of treatment strategies under active investigation that strive to decrease relapse risk and improve long-term survival for patients with Ph-like ALL as has been successfully achieved for those with Ph + ALL.
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Affiliation(s)
- Thai Hoa Tran
- Division of Pediatric Hematology-Oncology, Charles-Bruneau Cancer Center, CHU Sainte-Justine, Montreal, QC, Canada; Department of Pediatrics, University of Montreal, Montreal, QC, Canada
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics and Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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24
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Harada S, Caliò A, Janowski KM, Morlote D, Rodriguez Pena MD, Canete-Portillo S, Harbi D, DeFrank G, Magi-Galluzzi C, Netto GJ, Martignoni G, Mackinnon AC. Diagnostic utility of one-stop fusion gene panel to detect TFE3/TFEB gene rearrangement and amplification in renal cell carcinomas. Mod Pathol 2021; 34:2055-2063. [PMID: 34148064 DOI: 10.1038/s41379-021-00858-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
MiT family translocation renal cell carcinoma (MiT-RCC) harbors translocations involving the TFE3 or TFEB genes. RCC with TFEB amplification is also identified and is associated with a more aggressive clinical course. Accurate diagnosis of MiT-RCC is crucial for patient management. In this study, we evaluated the performance of the Archer FusionPlex assay for detection of MiT-RCC with TFE3 or TFEB translocations and TFEB amplifications. RNA was extracted from 49 RCC FFPE tissue samples with known TFE3/TFEB status (26 TFE3 FISH positive, 12 TFEB FISH positive, 4 TFEB amplified (1 case both split and amplified), and 8 FISH negative) using the Covaris extraction kit. Target enriched cDNA libraries were prepared using the Archer FusionPlex kit and sequenced on the Illumina NextSeq 550. We demonstrate that the age of the specimen, quality of RNA, and sequencing metrics are important for fusion detection. Fusions were identified in 20 of 21 cases less than 2 years old, and TFE3/TFEB rearrangements were detected in all cases with Fusion QC ≥ 100. The assay identified intrachromosomal inversions in two cases (TFE3-RBM10 and NONO-TFE3), usually difficult to identify by FISH assays. TFEB mRNA expression and the TFEB/TFE3 mRNA expression ratio were significantly higher in RCCs with TFEB fusion and TFEB gene amplification compared to tumors without TFEB fusion or amplification. A cutoff TFEB/TFE3 ratio of 0.5 resulted in 97.3% concordance to FISH results with no false negatives. Our study demonstrates that the FusionPlex assay successfully identifies TFE3 and TFEB fusions including intrachromosomal inversions. Age of the specimen and certain sequencing metrics are important for successful fusion detection. Furthermore, mRNA expression levels may be used for predicting cases harboring TFEB amplification, thereby streamlining testing. This assay enables accurate molecular detection of multiple subtypes of MiT-RCCs in a convenient workflow.
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Affiliation(s)
- Shuko Harada
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Anna Caliò
- Department of Diagnostic and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Karen M Janowski
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Diana Morlote
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Sofia Canete-Portillo
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Djamel Harbi
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gina DeFrank
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - George J Netto
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Guido Martignoni
- Department of Diagnostic and Public Health, Section of Pathology, University of Verona, Verona, Italy.,Department of Pathology, Pederzoli Hospital, Peschiera del Garda, Italy
| | - Alexander C Mackinnon
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
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25
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Aref-Eshghi E, Lin F, Li MM, Zhong Y. The oncogenic roles of NTRK fusions and methods of molecular diagnosis. Cancer Genet 2021; 258-259:110-119. [PMID: 34710798 DOI: 10.1016/j.cancergen.2021.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/23/2021] [Accepted: 10/16/2021] [Indexed: 10/20/2022]
Abstract
The NTRK gene family is composed of NTRK1, NTRK2, and NTRK3, which encode three tropomyosin-receptor kinases, belonging to a class of tyrosine kinase receptors. These proteins are known to play roles in cell proliferation, differentiation, apoptosis, and survival. Fusions involving the NTRK genes are long known as drivers in many tumors. Although they occur in less than 5% of all malignancies, their occurrence in a great diversity of tumors has been documented. Several rare tumors including infantile fibrosarcoma, secretory breast carcinoma, and mammary analogue secretory carcinoma are accompanied by NTRK fusions in more than 90% of cases, demonstrating a diagnostic value for the NTRK fusion testing in these tumors. More recently, the development of effective targeted therapies has created a demand for their detection in all malignancies. A variety of approaches are available for testing including immunohistochemistry, fluorescence in situ hybridization (FISH), reverse transcription polymerase chain reaction (RT-PCR), and DNA- and RNA-based next-generation sequencing (NGS). This article reviews the molecular biology and tumorigenesis of NTRK fusions, their prevalence and clinical significance with a focus on available methods for fusion detection. The advantages and limitations of different technologies, the best practice algorithms for NTRK fusion detection, and the future direction of NTRK testing are also discussed.
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Affiliation(s)
- Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Yiming Zhong
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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26
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Sun L, McNulty SN, Evenson MJ, Zhu X, Robinson J, Mann PR, Duncavage EJ, Pfeifer JD. Clinical Implications of a Targeted RNA-Sequencing Panel in the Detection of Gene Fusions in Solid Tumors. J Mol Diagn 2021; 23:1749-1760. [PMID: 34562614 DOI: 10.1016/j.jmoldx.2021.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/09/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
The detection of recurrent gene fusions can help confirm diagnoses in solid tumors, particularly when the morphology and staining are unusual or nonspecific, and can guide therapeutic decisions. Although fluorescence in situ hybridization and PCR are often used to identify fusions, the rearrangement must be suspected, with only a few prioritized probes run. We hypothesized that the Illumina TruSight RNA Fusion Panel, which detects fusions of 507 genes and their partners, would uncover fusions with greater sensitivity than other approaches, leading to changes in diagnosis, prognosis, or therapy. Targeted RNA sequencing was performed on formalin-fixed, paraffin-embedded sarcoma and carcinoma cases in which fluorescence in situ hybridization, RT-PCR, or DNA-based sequencing was conducted during the diagnostic workup. Of 153 cases, 138 (90%) were sequenced with adequate quality control metrics. A total of 101 of 138 (73%) cases were concordant by RNA sequencing and the prior test method. RNA sequencing identified an additional 30 cases (22%) with fusions that were not detected by conventional methods. In seven cases (5%), the additional fusion information provided by RNA sequencing would have altered the diagnosis and management. A total of 19 novel fusion pairs (not previously described in the literature) were discovered (14%). Overall, the findings show that a targeted RNA-sequencing method can detect gene fusions in formalin-fixed, paraffin-embedded specimens with high sensitivity.
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Affiliation(s)
- Lulu Sun
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
| | - Samantha N McNulty
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J Evenson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Xiaopei Zhu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Joshua Robinson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Patrick R Mann
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - John D Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
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27
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Abstract
The detection of gene rearrangements in pediatric leukemia is an essential component of the work-up, with implications for accurate diagnosis, proper risk stratification, and therapeutic decisions, including the use of targeted therapies. The traditional methods of karyotype and fluorescence in situ hybridization are still valuable, but many new assays are also available, with different strengths and weaknesses. These assays include next-generation sequencing-based assays that have the potential for highly multiplexed and/or unbiased detection of rearrangements.
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Affiliation(s)
- Marian H Harris
- Department of Pathology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA.
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28
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Lalonde E, Rentas S, Wertheim G, Cao K, Surrey LF, Lin F, Zhao X, Obstfeld A, Aplenc R, Luo M, Li MM. Clinical impact of genomic characterization of 15 patients with acute megakaryoblastic leukemia-related malignancies. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005975. [PMID: 33832921 PMCID: PMC8040732 DOI: 10.1101/mcs.a005975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/26/2021] [Indexed: 01/30/2023] Open
Abstract
Acute megakaryoblastic leukemia (AMKL) is a rare subtype of acute myeloid leukemia but is approximately 500 times more likely to develop in children with Down syndrome (DS) through transformation of transient abnormal myelopoiesis (TAM). This study investigates the clinical significance of genomic heterogeneity of AMKL in children with and without DS and in children with TAM. Genomic evaluation of nine patients with DS-related TAM or AMKL, and six patients with non-DS AMKL, included conventional cytogenetics and a comprehensive next-generation sequencing panel for single-nucleotide variants/indels and copy-number variants in 118 genes and fusions involving 110 genes. Recurrent gene fusions were found in all patients with non-DS, including two individuals with complex genomes and either a NUP98–KDM5A or a KMT2A–MLLT6 fusion, and the remaining harbored a CBFA2T3–GLIS2 fusion, which arose from both typical and atypical cytogenetic mechanisms. These fusions guided treatment protocols and resulted in a change in diagnosis in two patients. The nine patients with DS had constitutional trisomy 21 and somatic GATA1 mutations, and those with DS-AMKL had two to four additional clinically significant somatic mutations. Comprehensive genomic characterization provides critical information for diagnosis, risk stratification, and treatment decisions for patients with AMKL. Continued genetic and clinical characterization of these rare cancers will aid in improving patient management.
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Affiliation(s)
- Emilie Lalonde
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Stefan Rentas
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Gerald Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Xiaonan Zhao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Amrom Obstfeld
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Richard Aplenc
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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29
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Fusion transcript discovery using RNA sequencing in formalin-fixed paraffin-embedded specimen. Crit Rev Oncol Hematol 2021; 160:103303. [DOI: 10.1016/j.critrevonc.2021.103303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
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30
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Pikman Y, Tasian SK, Sulis ML, Stevenson K, Blonquist TM, Apsel Winger B, Cooper TM, Pauly M, Maloney KW, Burke MJ, Brown PA, Gossai N, McNeer JL, Shukla NN, Cole PD, Kahn JM, Chen J, Barth MJ, Magee JA, Gennarini L, Adhav AA, Clinton CM, Ocasio-Martinez N, Gotti G, Li Y, Lin S, Imamovic A, Tognon CE, Patel T, Faust HL, Contreras CF, Cremer A, Cortopassi WA, Garrido Ruiz D, Jacobson MP, Dharia NV, Su A, Robichaud AL, Saur Conway A, Tarlock K, Stieglitz E, Place AE, Puissant A, Hunger SP, Kim AS, Lindeman NI, Gore L, Janeway KA, Silverman LB, Tyner JW, Harris MH, Loh ML, Stegmaier K. Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium. Cancer Discov 2021; 11:1424-1439. [PMID: 33563661 DOI: 10.1158/2159-8290.cd-20-0564] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/25/2020] [Accepted: 01/14/2021] [Indexed: 11/16/2022]
Abstract
Despite a remarkable increase in the genomic profiling of cancer, integration of genomic discoveries into clinical care has lagged behind. We report the feasibility of rapid identification of targetable mutations in 153 pediatric patients with relapsed/refractory or high-risk leukemias enrolled on a prospective clinical trial conducted by the LEAP Consortium. Eighteen percent of patients had a high confidence Tier 1 or 2 recommendation. We describe clinical responses in the 14% of patients with relapsed/refractory leukemia who received the matched targeted therapy. Further, in order to inform future targeted therapy for patients, we validated variants of uncertain significance, performed ex vivo drug-sensitivity testing in patient leukemia samples, and identified new combinations of targeted therapies in cell lines and patient-derived xenograft models. These data and our collaborative approach should inform the design of future precision medicine trials. SIGNIFICANCE: Patients with relapsed/refractory leukemias face limited treatment options. Systematic integration of precision medicine efforts can inform therapy. We report the feasibility of identifying targetable mutations in children with leukemia and describe correlative biology studies validating therapeutic hypotheses and novel mutations.See related commentary by Bornhauser and Bourquin, p. 1322.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics and Abramson Cancer Center at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maria Luisa Sulis
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, New York
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kristen Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Traci M Blonquist
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Beth Apsel Winger
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Todd M Cooper
- Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, Washington
| | - Melinda Pauly
- Division of Hematology/Oncology, Emory University, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Kelly W Maloney
- Children's Hospital Colorado, University of Colorado Cancer Center, Aurora, Colorado
| | - Michael J Burke
- Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | | | - Nathan Gossai
- Center for Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota
| | | | - Neerav N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter D Cole
- Children's Hospital at Montefiore, Bronx, New York
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Justine M Kahn
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, New York
| | - Jing Chen
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, New York
- Children's Cancer Institute, Joseph M. Sanzari Children's Hospital, Hackensack University Medical Center, Hackensack, New Jersey
| | | | - Jeffrey A Magee
- Division of Pediatric Hematology/Oncology, Washington University/St. Louis Children's Hospital, St. Louis, Missouri
| | | | - Asmani A Adhav
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Catherine M Clinton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Giacomo Gotti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yuting Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alma Imamovic
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Cristina E Tognon
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Tasleema Patel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Haley L Faust
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cristina F Contreras
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Anjali Cremer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- University Hospital Frankfurt, Department of Hematology/Oncology, Frankfurt/Main, Germany
| | - Wilian A Cortopassi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Angela Su
- INSERM UMR 944, IRSL, St Louis Hospital, Paris, France
| | - Amanda L Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Amy Saur Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Katherine Tarlock
- Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, Washington
| | - Elliot Stieglitz
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Andrew E Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | | | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics and Abramson Cancer Center at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lia Gore
- Children's Hospital Colorado, University of Colorado Cancer Center, Aurora, Colorado
| | - Katherine A Janeway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Jeffrey W Tyner
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Mignon L Loh
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
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31
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Zhao X, Kotch C, Fox E, Surrey LF, Wertheim GB, Baloch ZW, Lin F, Pillai V, Luo M, Kreiger PA, Pogoriler JE, Linn RL, Russo PA, Santi M, Resnick AC, Storm PB, Hunger SP, Bauer AJ, Li MM. NTRK Fusions Identified in Pediatric Tumors: The Frequency, Fusion Partners, and Clinical Outcome. JCO Precis Oncol 2021; 1:PO.20.00250. [PMID: 34036219 PMCID: PMC8140782 DOI: 10.1200/po.20.00250] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/26/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022] Open
Abstract
Neurotrophic tyrosine receptor kinase (NTRK) fusions have been described as
oncogenic drivers in a variety of tumors. However, little is known about the
overall frequency of NTRK fusion in unselected pediatric tumors. Here, we
assessed the frequency, fusion partners, and clinical course in pediatric
patients with NTRK fusion–positive tumors.
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Affiliation(s)
- Xiaonan Zhao
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Chelsea Kotch
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth Fox
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gerald B Wertheim
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Zubair W Baloch
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Vinodh Pillai
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Portia A Kreiger
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jennifer E Pogoriler
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Rebecca L Linn
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Pierre A Russo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Adam C Resnick
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Phillip B Storm
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Stephen P Hunger
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Andrew J Bauer
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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32
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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33
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Zhong Y, Lin F, Xu F, Schubert J, Wu J, Wainwright L, Zhao X, Cao K, Fan Z, Chen J, Lang SS, Kennedy BC, Viaene AN, Santi M, Resnick AC, Storm PB, Li MM. Genomic characterization of a PPP1CB-ALK fusion with fusion gene amplification in a congenital glioblastoma. Cancer Genet 2020; 252-253:37-42. [PMID: 33341678 DOI: 10.1016/j.cancergen.2020.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/22/2020] [Accepted: 12/06/2020] [Indexed: 12/26/2022]
Abstract
ALK (Anaplastic lymphoma kinase) fusion proteins are oncogenic and have been seen in various tumors. PPP1CB-ALK fusions are rare but have been reported in a few patients with low- or high-grade gliomas. However, little is known regarding the mechanism of fusion formation and genomic break points of this fusion. We performed genomic characterization of a PPP1CB-ALK fusion with fusion gene amplification in a congenital glioblastoma. The PPP1CB-ALK consists of exons 1-5 of PPP1CB and exons 20-29 of ALK. The genomic translocation breakpoints were determined by real-time quantitative PCR (RT-qPCR) and Sanger sequencing of genomic DNA. Next generation sequencing, RT-qPCR and fluorescence in situ hybridization analyses demonstrated PPP1CB-ALK amplification. Copy number analyses of genes between PPP1CB and ALK using RT-qPCR suggest that the PPP1CB-ALK is likely the result of local chromothripsis followed by episomal amplification. Transcriptome sequencing demonstrated high-level SOX2 expression and predicted WNT/β-catenin pathway activation, suggesting possible therapeutic approaches.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Feng Xu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jeff Schubert
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jinhua Wu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Luanne Wainwright
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Xiaonan Zhao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Zhiqian Fan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jiani Chen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Shih-Shan Lang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Benjamin C Kennedy
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Angela N Viaene
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Adam C Resnick
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Phillip B Storm
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
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34
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Lopez-Nunez O, Cafferata B, Santi M, Ranganathan S, Pearce TM, Kulich SM, Bailey KM, Broniscer A, Rossi S, Zin A, Nasrallah MP, Li MM, Zhong Y, Miele E, Alaggio R, Surrey LF. The spectrum of rare central nervous system (CNS) tumors with EWSR1-non-ETS fusions: experience from three pediatric institutions with review of the literature. Brain Pathol 2020; 31:70-83. [PMID: 32997853 PMCID: PMC8018079 DOI: 10.1111/bpa.12900] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/02/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022] Open
Abstract
The group of CNS mesenchymal (non‐meningothelial) and primary glial/neuronal tumors in association with EWSR1‐non‐ETS rearrangements comprises a growing spectrum of entities, mostly reported in isolation with incomplete molecular profiling. Archival files from three pediatric institutions were queried for unusual cases of pediatric (≤21 years) CNS EWSR1‐rearranged tumors confirmed by at least one molecular technique. Extra‐axial tumors and cases with a diagnosis of Ewing sarcoma (EWSR1‐ETS family fusions) were excluded. Additional studies, including anchored multiplex‐PCR with next‐generation sequencing and DNA methylation profiling, were performed as needed to determine fusion partner status and brain tumor methylation class, respectively. Five cases (median 17 years) were identified (M:F of 3:2). Location was parenchymal (n = 3) and undetermined (n = 2) with topographic distributions including posterior fossa (n = 1), frontal (n = 1), temporal (n = 1), parietal (n = 1) and occipital (n = 1) lobes. Final designation with fusion findings included desmoplastic small round cell tumor (EWSR1‐WT1; n = 1) and tumors of uncertain histogenesis (EWSR1‐CREM, n = 1; EWSR1‐CREB1, n = 1; EWSR1‐PLAGL1, n = 1; and EWSR1‐PATZ1, n = 1). Tumors showed a wide spectrum of morphology and biologic behavior. For EWSR1‐CREM, EWSR1‐PLAGL1 and EWSR1‐PATZ1 tumors, no significant methylation scores were reached in the known brain tumor classes. Available outcome (4/5) was reported as favorable (n = 2) and unfavorable (n = 2) with a median follow‐up of 30 months. In conclusion, we describe five primary EWSR1‐non‐ETS fused CNS tumors exhibiting morphologic and biologic heterogeneity and we highlight the clinical importance of determining specific fusion partners to improve diagnostic accuracy, treatment and monitoring. Larger prospective clinicopathological and molecular studies are needed to determine the prognostic implications of histotypes, anatomical location, fusion partners, breakpoints and methylation profiles in patients with these rare tumors.
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Affiliation(s)
- Oscar Lopez-Nunez
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA.,Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Barbara Cafferata
- General Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padova, Padova, Italy
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Sarangarajan Ranganathan
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Thomas M Pearce
- Division of Neuropathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Scott M Kulich
- Division of Neuropathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Kelly M Bailey
- Division of Pediatric Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Alberto Broniscer
- Division of Pediatric Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Sabrina Rossi
- Department of Pathology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angelica Zin
- Institute of Pediatric Research (IRP), Fondazione Città della Speranza, Padova, Italy
| | - MacLean P Nasrallah
- General Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padova, Padova, Italy
| | - Marilyn M Li
- General Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padova, Padova, Italy
| | - Yiming Zhong
- General Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padova, Padova, Italy
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rita Alaggio
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Department of Pathology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lea F Surrey
- General Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padova, Padova, Italy
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35
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How I treat relapsed acute lymphoblastic leukemia in the pediatric population. Blood 2020; 136:1803-1812. [DOI: 10.1182/blood.2019004043] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/11/2020] [Indexed: 01/04/2023] Open
Abstract
Abstract
Relapsed acute lymphoblastic leukemia (ALL) has remained challenging to treat in children, with survival rates lagging well behind those observed at initial diagnosis. Although there have been some improvements in outcomes over the past few decades, only ∼50% of children with first relapse of ALL survive long term, and outcomes are much worse with second or later relapses. Recurrences that occur within 3 years of diagnosis and any T-ALL relapses are particularly difficult to salvage. Until recently, treatment options were limited to intensive cytotoxic chemotherapy with or without site-directed radiotherapy and allogeneic hematopoietic stem cell transplantation (HSCT). In the past decade, several promising immunotherapeutics have been developed, changing the treatment landscape for children with relapsed ALL. Current research in this field is focusing on how to best incorporate immunotherapeutics into salvage regimens and investigate long-term survival and side effects, and when these might replace HSCT. As more knowledge is gained about the biology of relapse through comprehensive genomic profiling, incorporation of molecularly targeted therapies is another area of active investigation. These advances in treatment offer real promise for less toxic and more effective therapy for children with relapsed ALL, and we present several cases highlighting contemporary treatment decision-making.
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36
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Zhong Y, Schubert J, Wu J, Xu F, Lin F, Cao K, Zelley K, Luo M, Foster JB, Cole KA, MacFarland SP, Resnick AC, Storm PB, Li MM. A germline PALB2 pathogenic variant identified in a pediatric high-grade glioma. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005397. [PMID: 32554798 PMCID: PMC7476410 DOI: 10.1101/mcs.a005397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
PALB2 (partner and localizer of BRCA2) gene encodes a protein that colocalizes with BRCA2 in nuclear foci and likely permits the stable intranuclear localization and accumulation of BRCA2. PALB2 plays a critical role in maintaining genome integrity through its role in the Fanconi anemia and homologous recombination DNA repair pathways. It has a known loss-of-function disease mechanism. Biallelic PALB2 pathogenic variants have been described in autosomal recessive Fanconi anemia. Heterozygous pathogenic variants in PALB2 are associated with increased risk for female and male breast cancer and pancreatic cancer (Science 324: 217; Cancer Res 71: 2222–2229; N Engl J Med 371: 497–506). Heterozygous germline PALB2 mutations have also been observed in patients with medulloblastoma (Lancet Oncol 19: 785–798). However, PALB2-related cancer predisposition to high-grade gliomas has not been reported. Here we report a germline PALB2 pathogenic variant (c.509_510delGA, p.Arg170Ilefs*14, NM_024675.3) found in a pediatric patient with high-grade glioma. This variant was first identified by tumor sequencing using the Children's Hospital of Philadelphia (CHOP) Comprehensive Solid Tumor Panel and then confirmed to be a germline change using the CHOP Comprehensive Hereditary Cancer Panel on DNA from a blood sample of this patient. Parental studies showed that this variant was paternally inherited. Further studies are needed to illustrate if pathogenic variants in PALB2 convey increased risk to developing brain tumor. This case also highlights the potential of identifying germline mutation through tumor sequencing.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jeffrey Schubert
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Jinhua Wu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Feng Xu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kristin Zelley
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jessica B Foster
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kristina A Cole
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Suzanne P MacFarland
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Adam C Resnick
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Neurosurgery, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Phillip B Storm
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Neurosurgery, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
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Barua S, Wang G, Mansukhani M, Hsiao S, Fernandes H. Key considerations for comprehensive validation of an RNA fusion NGS panel. Pract Lab Med 2020; 21:e00173. [PMID: 32613069 PMCID: PMC7322345 DOI: 10.1016/j.plabm.2020.e00173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/19/2020] [Accepted: 05/28/2020] [Indexed: 12/28/2022] Open
Abstract
Objectives Validation of RNA-based NGS assays for the detection of therapeutically targetable gene fusions is challenging. Here, we report systematic validation and quality control monitoring of our targeted fusion panel for the detection of 17 clinically relevant fusion transcripts across several tumor types. We implemented this RNA Fusion Panel as a reflex test for tumors lacking DNA driver mutations. Design Forty-four formalin-fixed, paraffin-embedded (FFPE) or fresh-frozen lung, brain, soft tissue and skin tumors were used to determine the accuracy of the assay. Additional fusion-positive specimens and a calibrated reference standard were used to establish the precision, reproducibility and sensitivity of the assay. All aspects of the validation, including quality control metrics, were performed according to New York State guidelines. Results For the RNA fusion panel, accuracy, reproducibility and precision studies were above 99%. Reproducibility and sensitivity studies with the reference standard were helpful in identifying inconsistencies. The limit of detection for most RNA fusion transcripts was 50 copies. Application of the RNA fusion assay as a reflex test to 450 tumor samples lacking DNA driver mutations resulted in a 10% increase in diagnostic yield with minimal additional processing time. Conclusions The validated RNA fusion panel provides clinical utility in therapy selection for patients with solid tumors. By using a sequential testing approach, the RNA fusion assay complements the DNA hotspot assay in identifying clinically relevant variants across many tumor types with minimal additional increase in processing time. RNA fusion NGS panel uses anchored multiplex PCR to detect known and novel fusions. Pre- and post-sequencing quality control increases accuracy of results. Sequential testing of RNA, on samples without DNA variants is practical and cost-effective. Detection of novel RNA fusions expands the therapeutic landscape of tumors.
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Affiliation(s)
- Subit Barua
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Gary Wang
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Mahesh Mansukhani
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Susan Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
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Davis JL, Vargas SO, Rudzinski ER, López Marti JM, Janeway K, Forrest S, Winsnes K, Pinto N, Yang SE, VanSandt M, Boyd TK, Corless CL, Liu YJ, Surrey LF, Harris MH, Church A, Al-Ibraheemi A. Recurrent RET gene fusions in paediatric spindle mesenchymal neoplasms. Histopathology 2020; 76:1032-1041. [PMID: 31994201 DOI: 10.1111/his.14082] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/22/2020] [Accepted: 01/25/2020] [Indexed: 01/02/2023]
Abstract
AIMS The classification of paediatric spindle mesenchymal tumours is evolving, and the spectrum of so-called 'infantile fibrosarcoma' has expanded to include tumours with NTRK, BRAF and MET gene fusions. RET-rearranged paediatric spindle cell neoplasms are an emerging group; there is sparse literature on their clinical, pathological and genetic features, and their nosological place in the canon of soft tissue tumours is uncertain. In this study, we report five RET-rearranged paediatric spindle cell tumours with fusion partners MYH10, KIAA1217 and CLIP2. METHODS AND RESULTS The tumours occurred in the pelvic region, paraspinal region, kidney and subcutaneous tissue of hand and abdomen. The patients' ages ranged from 6 months to 13 years (median 1 year). The tumours were composed of monomorphic spindle cells arranged in a fascicular pattern. Lesional cells had minimally atypical ovoid or tapered nuclei and pale cytoplasm with indistinct borders. Necrosis was not identified. Mitoses numbered three to 12 per 10 high-power field. Cases showed inconsistent and variable expression of S100, CD34 and SMA. Clinical behaviour ranged from small lesions potentially cured by simple resection to large lesions exhibiting metastasis, but responsive to kinase inhibitor therapy. CONCLUSIONS Our findings help to define RET-rearranged spindle cell tumours. Although it is likely that these tumours comprise part of the morphological and clinical spectrum of infantile fibrosarcoma (IFS), identification of RET gene alteration is important for its unique therapeutic implications.
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Affiliation(s)
- Jessica L Davis
- Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - Sara O Vargas
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Erin R Rudzinski
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA
| | - Jessica M López Marti
- Department of Pathology, Hospital Nacional de Pediatria Juan P. Garrahan, Buenos Aires, Argentina
| | - Katherine Janeway
- Department of Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Suzanne Forrest
- Department of Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Katrina Winsnes
- Division of Pediatric Hematology and Oncology, Oregon Health and Science University/Doernbecher Children's Hospital, Portland, OR, USA
| | - Navin Pinto
- Cancer and Blood Disorders Center, Seattle Children's Hospital, University of Washington Medical Center and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sung E Yang
- Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - Mandy VanSandt
- Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - Theonia K Boyd
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | | | - Yajuan J Liu
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Alanna Church
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
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39
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Lopez-Nunez O, Surrey LF, Alaggio R, Fritchie KJ, John I. Novel PPP1CB-ALK fusion in spindle cell tumor defined by S100 and CD34 coexpression and distinctive stromal and perivascular hyalinization. Genes Chromosomes Cancer 2020; 59:495-499. [PMID: 32222087 DOI: 10.1002/gcc.22844] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/14/2020] [Accepted: 03/20/2020] [Indexed: 12/29/2022] Open
Abstract
A novel group of S100- and CD34-positive spindle cell tumors with distinctive stromal and perivascular hyalinization harboring recurrent gene fusions involving kinases including RAF1, BRAF, NTRK1/2/3, and RET have been recently reported. To our knowledge, no such cases harboring ALK rearrangements have been identified. We report a previously healthy 41-year-old male with a 12-cm intramuscular shoulder mass. The tumor was composed of bland-appearing spindled to epithelioid cells, arranged in a patternless pattern in a background of loose myxoid stroma containing striking amianthoid-like stromal collagen and perivascular rings. In accordance with the previously reported tumors, the tumor cells showed diffuse immunopositivity with S100 and CD34, while lacking SOX10 expression. Targeted RNA-based next-generation sequencing identified a novel serine/threonine-protein phosphatase PP1-beta-catalytic subunit (PPP1CB)-ALK fusion gene. Although ALK break-apart was not detected by FISH, likely due to a paracentric inversion of chromosome 2, the presence of the fusion was confirmed by Sanger sequencing showing a 10-bp linker between exon 6 of PPP1CB and intron 19 of ALK while maintaining reading frame. Subsequent ALK-1 immunostain exhibited diffuse cytoplasmic staining in the tumor cells. Our case expands the molecular genetic spectrum of the distinctive group of spindle cell tumors with CD34/S100+ immunophenotype, supporting the important role of various kinases as drivers of oncogenesis. Awareness of this entity including its unique morphologic and immunophenotypic features as well as its interchangeable kinase gene fusions is crucial for correct classification and potential targeted therapy, particularly in aggressive subsets.
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Affiliation(s)
- Oscar Lopez-Nunez
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Rita Alaggio
- Department of Pathology, Ospedale Pediatrico Bambino Gesù (OPBG), Rome, Italy
| | - Karen J Fritchie
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ivy John
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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