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Misra C, Kaur J, Kumar M, Kaushik L, Chitkara D, Preet S, Wahajuddin M, Raza K. Docetaxel-tethered di-Carboxylic Acid Derivatised Fullerenes: A Promising Drug Delivery Approach for Breast Cancer. AAPS PharmSciTech 2024; 25:233. [PMID: 39358486 DOI: 10.1208/s12249-024-02955-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 09/23/2024] [Indexed: 10/04/2024] Open
Abstract
Docetaxel (DTX) has become widely accepted as a first-line treatment for metastatic breast cancer; however, the frequent development of resistance provides challenges in treating the disease.C60 fullerene introduces a unique molecular form of carbon, exhibiting attractive chemical and physical properties. Our study aimed to develop dicarboxylic acid-derivatized C60 fullerenes as a novel DTX delivery carrier. This study investigated the potential of water-soluble fullerenes to deliver the anti-cancer drug DTX through a hydrophilic linker. The synthesis was carried out using the Prato reaction. The spectroscopic analysis confirmed the successful conjugation of DTX molecules over fullerenes. The particle size of nanoconjugate was reported to be 122.13 ± 1.63 nm with a conjugation efficiency of 76.7 ± 0.14%. The designed conjugate offers pH-dependent release with significantly less plasma pH, ensuring maximum release at the target site. In-vitro cell viability studies demonstrated the enhanced cytotoxic nature of the developed nanoconjugate compared to DTX. These synthesized nanoscaffolds were highly compatible with erythrocytes, indicating the safer intravenous route administration. Pharmacokinetic studies confirmed the higher bioavailability (~ 6 times) and decreased drug clearance from the system vis-à-vis plain drug. The histological studies reveal that nanoconjugate-treated tumour cells exhibit similar morphology to normal cells. Therefore, it was concluded that this developed formulation would be a valuable option for clinical use.
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Affiliation(s)
- Charu Misra
- Department of Pharmacy, School of Chemical Science and Pharmacy, Central University of Rajasthan, Bandarsindri, Distt. Ajmer, Rajasthan, 305817, India
- Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, Faculty of Life Sciences, University of Bradford, Richmond Road, Bradford, BD7 1DP, UK
| | - Jasleen Kaur
- Department of Biophysics, Panjab University, Chandigarh, 160 014, India
| | - Manish Kumar
- Department of Pharmacy, School of Chemical Science and Pharmacy, Central University of Rajasthan, Bandarsindri, Distt. Ajmer, Rajasthan, 305817, India
| | - Lokesh Kaushik
- Department of Pharmacy, School of Chemical Science and Pharmacy, Central University of Rajasthan, Bandarsindri, Distt. Ajmer, Rajasthan, 305817, India
- ICFAI School of Pharmaceutical Sciences, The ICFAI University, Jaipur, Rajasthan, 302031, India
| | - Deepak Chitkara
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Rajasthan, 33031, India
| | - Simran Preet
- Department of Biophysics, Panjab University, Chandigarh, 160 014, India
| | - Muhammad Wahajuddin
- Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, Faculty of Life Sciences, University of Bradford, Richmond Road, Bradford, BD7 1DP, UK
| | - Kaisar Raza
- Department of Pharmacy, School of Chemical Science and Pharmacy, Central University of Rajasthan, Bandarsindri, Distt. Ajmer, Rajasthan, 305817, India.
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Ogbonnaya CN, Alsaedi BSO, Alhussaini AJ, Hislop R, Pratt N, Steele JD, Kernohan N, Nabi G. Radiogenomics Map-Based Molecular and Imaging Phenotypical Characterization in Localised Prostate Cancer Using Pre-Biopsy Biparametric MR Imaging. Int J Mol Sci 2024; 25:5379. [PMID: 38791417 PMCID: PMC11121591 DOI: 10.3390/ijms25105379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
To create a radiogenomics map and evaluate the correlation between molecular and imaging phenotypes in localized prostate cancer (PCa), using radical prostatectomy histopathology as a reference standard. Radiomic features were extracted from T2-weighted (T2WI) and Apparent Diffusion Coefficient (ADC) images of clinically localized PCa patients (n = 15) across different Gleason score-based risk categories. DNA extraction was performed on formalin-fixed, paraffin-embedded (FFPE) samples. Gene expression analysis of androgen receptor expression, apoptosis, and hypoxia was conducted using the Chromosome Analysis Suite (ChAS) application and OSCHIP files. The relationship between gene expression alterations and textural features was assessed using Pearson's correlation analysis. Receiver operating characteristic (ROC) analysis was utilized to evaluate the predictive accuracy of the model. A significant correlation was observed between radiomic texture features and copy number variation (CNV) of genes associated with apoptosis, hypoxia, and androgen receptor (p-value ≤ 0.05). The identified radiomic features, including Sum Entropy ADC, Inverse Difference ADC, Sum Variance T2WI, Entropy T2WI, Difference Variance T2WI, and Angular Secondary Moment T2WI, exhibited potential for predicting cancer grade and biological processes such as apoptosis and hypoxia. Incorporating radiomics and genomics into a prediction model significantly improved the prediction of prostate cancer grade (clinically significant prostate cancer), yielding an AUC of 0.95. Radiomic texture features significantly correlate with genotypes for apoptosis, hypoxia, and androgen receptor expression in localised prostate cancer. Integration of these into the prediction model improved prediction accuracy of clinically significant prostate cancer.
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Affiliation(s)
- Chidozie N. Ogbonnaya
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
| | | | - Abeer J. Alhussaini
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
| | - Robert Hislop
- Cytogenetic, Human Genetics Unit, NHS Tayside, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK; (R.H.); (N.P.)
| | - Norman Pratt
- Cytogenetic, Human Genetics Unit, NHS Tayside, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK; (R.H.); (N.P.)
| | - J. Douglas Steele
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
| | - Neil Kernohan
- Department of Pathology, NHS Tayside, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK;
| | - Ghulam Nabi
- Division of Imaging Science and Technology, School of Medicine, University of Dundee, Dundee DD1 4HN, UK; (C.N.O.); (A.J.A.); (J.D.S.)
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Workman AA, Green DC, Hughes EG, Shah PS, Cloutier JM, Marotti JD. Chondrolipoma of the Breast: A Myofibroblastoma Variant or a Distinct Lesion? Int J Surg Pathol 2024:10668969241231975. [PMID: 38356303 DOI: 10.1177/10668969241231975] [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: 02/16/2024]
Abstract
The entity commonly referred to as chondrolipoma is a rare and enigmatic breast lesion with unclear histogenesis and a complete lack of molecular characterization. It is uncertain whether it represents a hamartoma, choristoma, or a distinct neoplasm, including possibly a variant of mammary-type myofibroblastoma. We report two additional chondrolipomatous lesions of the breast. The lesions had varying histologic and immunohistochemical features similar to myofibroblastoma, including the loss of retinoblastoma (Rb) protein expression in one lesion. Molecular analysis by chromosomal microarray analysis performed on a second lesion did not demonstrate a loss of 13q14 or 16q typical of myofibroblastoma. Our findings further support the concept that at least a subset of breast lesions that historically have been classified as chondrolipoma are related to myofibroblastoma. However, the lack of myofibroblastoma-specific molecular alterations in one lesion suggests chondrolipomas may also have varying origins.
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Affiliation(s)
- Adrienne A Workman
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Donald C Green
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Edward G Hughes
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Parth S Shah
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Dartmouth Cancer Center, Lebanon, NH, USA
| | - Jeffrey M Cloutier
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jonathan D Marotti
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Dartmouth Cancer Center, Lebanon, NH, USA
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Webersinke G, Burghofer J, Malli T, Rammer M, Jahn SW, Niendorf A, Tavassoli FA, Moinfar F. TERT Promoter Mutation c.-124C>T Commonly Occurs in Low-Grade Fibromatosis-like Metaplastic Breast Carcinoma. Arch Pathol Lab Med 2023; 147:1451-1457. [PMID: 36897999 DOI: 10.5858/arpa.2022-0159-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 03/12/2023]
Abstract
CONTEXT.— Low-grade fibromatosis-like metaplastic carcinoma (FLMC) is a very rare subtype of triple-negative metaplastic (spindle cell) breast carcinoma. It is characterized by the proliferation of spindle cells closely resembling fibromatosis, which represents a benign fibroblastic/myofibroblastic breast proliferation. Unlike most triple-negative and basal-like breast cancers, FLMC has a very low potential for metastases, but demonstrates frequent local recurrences. OBJECTIVE.— To genetically characterize FLMC. DESIGN.— To this end, we analyzed 7 cases by targeted next-generation sequencing for 315 cancer-related genes and performed comparative microarray copy number analysis in 5 of these cases. RESULTS.— All cases shared TERT alterations (6 patients with recurrent c.-124C>T TERT promoter mutation and 1 patient with copy number gain encompassing the TERT locus), had oncogenic PIK3CA/PIK3R1 mutations (activation of the PI3K/AKT/mTOR pathway), and lacked mutations in TP53. TERT was overexpressed in all FLMCs. CDKN2A/B loss or mutation was observed in 4 of 7 cases (57%). Furthermore, tumors displayed chromosomal stability, with only few copy number variations and a low tumor mutational burden. CONCLUSIONS— We conclude that FLMCs typically show the recurrent TERT promoter mutation c.-124C>T, activation of the PI3K/AKT/mTOR pathway, low genomic instability, and wild-type TP53. In conjunction with previous data of metaplastic (spindle cell) carcinoma with and without fibromatosis-like morphology, FLMC is most likely distinguished by TERT promoter mutation. Thus, our data support the notion of a distinct subgroup within low-grade metaplastic breast cancer with spindle cell morphology and associated TERT mutations.
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Affiliation(s)
- Gerald Webersinke
- From the Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz/Hospital of the Sisters of Charity, Linz, Austria (Webersinke, Burghofer, Malli, Rammer)
| | - Jonathan Burghofer
- From the Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz/Hospital of the Sisters of Charity, Linz, Austria (Webersinke, Burghofer, Malli, Rammer)
| | - Theodora Malli
- From the Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz/Hospital of the Sisters of Charity, Linz, Austria (Webersinke, Burghofer, Malli, Rammer)
| | - Melanie Rammer
- From the Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz/Hospital of the Sisters of Charity, Linz, Austria (Webersinke, Burghofer, Malli, Rammer)
| | - Stephan Wenzel Jahn
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria (Jahn, Moinfar)
| | - Axel Niendorf
- Department of Pathology and Molecular Diagnostic, Hamburg-West, Hamburg, Germany (Niendorf)
| | - Fattaneh A Tavassoli
- Department of Pathology, Yale University School of Medicine, New Haven Connecticut (Tavassoli)
| | - Farid Moinfar
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria (Jahn, Moinfar)
- Department of Pathology and Molecular Pathology, Vinzenz Pathologieverbund Linz, Austria (Moinfar)
- The Vincent Academy of Pathology, Linz, Austria (Moinfar)
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5
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Mindiola Romero AE, Tafe LJ, Green DC, Deharvengt SJ, Winnick KN, Tsongalis GJ, Baker ML, Linos K, Levy JJ, Kerr DA. Utility of Retrospective Molecular Analysis in Diagnostically Challenging Mesenchymal Neoplasms. Int J Surg Pathol 2023; 31:1473-1484. [PMID: 36911994 DOI: 10.1177/10668969231157783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Introduction: Molecular analysis plays a growing role in the diagnosis of mesenchymal neoplasms. The aim of this study was to retrospectively apply broad, multiplex molecular assays (a solid tumor targeted next-generation sequencing [NGS]) assay and single nucleotide polymorphism [SNP] microarray) to selected tumors, exploring the current utility and limitations. Methods: We searched our database (2010-2020) for diagnostically challenging mesenchymal neoplasms. After histologic review of available slides, tissue blocks were selected for NGS, SNP microarray, or both. DNA and RNA were extracted using the AllPrep DNA/RNA FFPE Kit Protocol on the QIAcube instrument. The NGS platform used was the TruSight Tumor 170 (TST-170). For SNP array, copy number variant (CNV) analysis was performed using the OncoScanTM CNV Plus Assay. Results: DNA/RNA was successfully extracted from 50% of tumors (n = 10/20). Specimens not successfully extracted included 6 core biopsies, 3 incisional biopsies, and 1 resection; 4 were decalcified (3 hydrochloric acid, 1 ethylenediaminetetraacetic acid). Higher tumor proportion and number of tumor cells were parameters positively associated with sufficient DNA/RNA extraction whereas necrosis and decalcification were negatively associated with sufficient extraction. Molecular testing helped reach a definitive diagnosis in 50% of tumors (n = 5/10). Conclusions: Although the overall utility of this approach is limited, these molecular panels can be helpful in detecting a specific "driver" alteration.
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Affiliation(s)
- Andres E Mindiola Romero
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
- Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Laura J Tafe
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
- Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Donald C Green
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Sophie J Deharvengt
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Kimberly N Winnick
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Gregory J Tsongalis
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
- Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Michael L Baker
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
- Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Konstantinos Linos
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
- Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Joshua J Levy
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
- Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Darcy A Kerr
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
- Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
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Batavia AA, Rutishauser D, Sobottka B, Schraml P, Beerenwinkel N, Moch H. Biallelic ELOC-Inactivated Renal Cell Carcinoma: Molecular Features Supporting Classification as a Distinct Entity. Mod Pathol 2023; 36:100194. [PMID: 37088333 DOI: 10.1016/j.modpat.2023.100194] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 04/25/2023]
Abstract
Approximately 70% of clear cell renal cell carcinoma (ccRCC) is characterized by the biallelic inactivation of von Hippel-Lindau (VHL) on chromosome 3p. ELOC-mutated (Elongin C-mutated) renal cell carcinoma containing biallelic ELOC inactivations with chromosome 8q deletions is considered a novel subtype of renal cancer possessing a morphologic overlap with ccRCC, renal cell carcinoma (RCC) with fibromyomatous stroma exhibiting Tuberous Sclerosis Complex (TSC)/mammalian Target of Rapamycin (mTOR) mutations, and clear cell papillary tumor. However, the frequency and consequences of ELOC alterations in wild-type VHL and mutated VHL RCC are unclear. In this study, we characterize 123 renal tumors with clear cell morphology and known VHL mutation status to assess the morphologic and molecular consequences of ELOC inactivation. Using OncoScan and whole-exome sequencing, we identify 18 ELOC-deleted RCCs, 3 of which contain ELOC mutations resulting in the biallelic inactivation of ELOC. Biallelic ELOC and biallelic VHL aberrations were mutually exclusive; however, 2 ELOC-mutated RCCs showed monoallelic VHL alterations. Furthermore, no mutations in TSC1, TSC2, or mTOR were identified in ELOC-mutated RCC with biallelic ELOC inactivation. Using High Ambiguity Driven biomolecular DOCKing, we report a novel ELOC variant containing a duplication event disrupting ELOC-VHL interaction alongside the frequently seen Y79C alteration. Using hyper reaction monitoring mass spectrometry, we show RCCs with biallelic ELOC alterations have significantly reduced ELOC expression but similar carbonic anhydrase 9 and vascular endothelial growth factor A expression compared with classical ccRCC with biallelic VHL inactivation. The absence of biallelic VHL and TSC1, TSC2, or mTOR inactivation in RCC with biallelic ELOC inactivation (ELOC mutation in combination with ELOC deletions on chromosome 8q) supports the notion of a novel, molecularly defined tumor entity.
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Affiliation(s)
- Aashil A Batavia
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dorothea Rutishauser
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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Stevens C, Hightower A, Buxbaum SG, Falzarano SM, Rhie SK. Genomic, epigenomic, and transcriptomic signatures of prostate cancer between African American and European American patients. Front Oncol 2023; 13:1079037. [PMID: 36937425 PMCID: PMC10018228 DOI: 10.3389/fonc.2023.1079037] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Prostate cancer is the second most common cancer in men in the United States, and racial disparities are greatly observed in the disease. Specifically, African American (AA) patients have 60% higher incidence and mortality rates, in addition to higher grade and stage prostate tumors, than European American (EA) patients. In order to narrow the gap between clinical outcomes for these two populations, genetic and molecular signatures contributing to this disparity have been characterized. Over the past decade, profiles of prostate tumor samples from different ethnic groups have been developed using molecular and functional assays coupled with next generation sequencing or microarrays. Comparative genome-wide analyses of genomic, epigenomic, and transcriptomic profiles from prostate tumor samples have uncovered potential race-specific mutations, copy number alterations, DNA methylation, and gene expression patterns. In this study, we reviewed over 20 published studies that examined the aforementioned molecular contributions to racial disparities in AA and EA prostate cancer patients. The reviewed genomic studies revealed mutations, deletions, amplifications, duplications, or fusion genes differentially enriched in AA patients relative to EA patients. Commonly reported genomic alterations included mutations or copy number alterations of FOXA1, KMT2D, SPOP, MYC, PTEN, TP53, ZFHX3, and the TMPRSS2-ERG fusion. The reviewed epigenomic studies identified that CpG sites near the promoters of PMEPA1, RARB, SNRPN, and TIMP3 genes were differentially methylated between AA and EA patients. Lastly, the reviewed transcriptomic studies identified genes (e.g. CCL4, CHRM3, CRYBB2, CXCR4, GALR1, GSTM3, SPINK1) and signaling pathways dysregulated between AA and EA patients. The most frequently found dysregulated pathways were involved in immune and inflammatory responses and neuroactive ligand signaling. Overall, we observed that the genomic, epigenomic, and transcriptomic alterations evaluated between AA and EA prostate cancer patients varied between studies, highlighting the impact of using different methods and sample sizes. The reported genomic, epigenomic, and transcriptomic alterations do not only uncover molecular mechanisms of tumorigenesis but also provide researchers and clinicians valuable resources to identify novel biomarkers and treatment modalities to improve the disparity of clinical outcomes between AA and EA patients.
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Affiliation(s)
- Claire Stevens
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
| | - Alexandria Hightower
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
| | - Sarah G. Buxbaum
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
- Department of Epidemiology and Biostatistics, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A&M University, Tallahassee, FL, United States
| | - Sara M. Falzarano
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Suhn K. Rhie
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
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8
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Comparative Molecular Genetics of Odontogenic Keratocysts in Sporadic and Syndromic Patients. Mod Pathol 2023; 36:100002. [PMID: 36788060 DOI: 10.1016/j.modpat.2022.100002] [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: 07/04/2022] [Revised: 08/26/2022] [Accepted: 09/17/2022] [Indexed: 01/19/2023]
Abstract
Odontogenic keratocysts (OKCs) are common cysts of odontogenic origin that usually occur as a single nonsyndromic cyst in isolation (sporadic) or as syndromic multiple cysts as a manifestation of naevoid basal cell carcinoma syndrome. Alterations involving the PTCH gene are the most commonly identified factor associated with up to 85% and 84% of naevoid basal cell carcinoma syndrome and sporadic cases, respectively. Other Hedgehog pathway and non-Hedgehog pathway-associated genes have been implicated in the pathogenesis of OKCs. This pilot study used the Affymetrix OncoScan molecular assay to perform a comparative genomic analysis between 4 sporadic and 3 syndromic cases of OKC to identify molecular drivers that may be common and/or distinct in these 2 groups. The majority of alterations detected in both groups were copy number neutral loss of heterozygosity. Despite distinct molecular signatures observed in both groups, copy number neutral loss of heterozygosity alterations involving chromosome 9q affecting not only PTCH but also the NOTCH1 gene were detected in all syndromic and 3 sporadic cases. Loss of heterozygosity alterations involving 16p11.2 affecting genes not previously described in OKCs were also detected in all syndromic and 3 sporadic cases. Furthermore, alterations on 22q11.23 and 10q22.1 were also detected in both groups. Of note, alterations on 1p13.3, 2q22.1, and 6p21.33 detected in sporadic cases were absent in all syndromic cases. This study demonstrates that a more common group of genes may be affected in both groups of OKCs, whereas other alterations may be useful in distinguishing sporadic from syndromic cysts. These findings should be validated in larger OKC cohorts to improve molecular diagnosis and subsequent patient management.
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9
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Gupta S, Sukov WR, Vanderbilt CM, Shen W, Herrera-Hernandez L, Lohse CM, Thompson RH, Boorjian SA, Leibovich BC, Jimenez RE, Cheville JC. A contemporary guide to chromosomal copy number profiling in the diagnosis of renal cell carcinoma. Urol Oncol 2022; 40:512-524. [PMID: 34092479 DOI: 10.1016/j.urolonc.2021.04.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/06/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023]
Abstract
The routine clinical implementation of molecular methods other than fluorescence in situ hybridization in the evaluation of renal neoplasia is currently limited, as the current standard of care primarily involves a combination of morphologic and immunophenotypic analysis of such tumors. Amongst various molecular techniques, global copy number profiling using single nucleotide polymorphism-based microarrays, colloquially referred to as SNP-arrays, is being increasingly utilized to profile renal tumors, as several subtypes have characteristic recurrent patterns of copy number alterations. Recurrent copy number alterations in common tumor types include loss of chromosome 3p in clear cell renal cell carcinoma (RCC), gain of chromosomes 7 and 17 in papillary RCC and multiple losses in chromosomes 1, 2, 6, 10, 13, 17, and 21 in chromophobe RCC. Such assays are being increasingly utilized in the clinical setting. Herein, we discuss some common clinical applications of such testing that includes high yield diagnostic and prognostic applications. Diagnostic utility includes evaluation of tumor types that are primarily defined by underlying copy number alterations, establishing the underlying subtype in high grade dedifferentiated (unclassified) renal tumors, as well as assessment of loss of heterozygosity, which is an important component in the workup for germline alterations in tumor suppressor genes. Universal adoption of these techniques across clinical laboratories will likely be significantly affected by variables such as cost, reimbursement, and turnaround time.
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Affiliation(s)
- Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wei Shen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Christine M Lohse
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | | | | | | | - Rafael E Jimenez
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - John C Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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10
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A comprehensive genomic and transcriptomic dataset of triple-negative breast cancers. Sci Data 2022; 9:587. [PMID: 36153392 PMCID: PMC9509351 DOI: 10.1038/s41597-022-01681-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/09/2022] [Indexed: 11/28/2022] Open
Abstract
Molecular subtyping of triple-negative breast cancer (TNBC) is essential for understanding the mechanisms and discovering actionable targets of this highly heterogeneous type of breast cancer. We previously performed a large single-center and multiomics study consisting of genomics, transcriptomics, and clinical information from 465 patients with primary TNBC. To facilitate reusing this unique dataset, we provided a detailed description of the dataset with special attention to data quality in this study. The multiomics data were generally of high quality, but a few sequencing data had quality issues and should be noted in subsequent data reuse. Furthermore, we reconduct data analyses with updated pipelines and the updated version of the human reference genome from hg19 to hg38. The updated profiles were in good concordance with those previously published in terms of gene quantification, variant calling, and copy number alteration. Additionally, we developed a user-friendly web-based database for convenient access and interactive exploration of the dataset. Our work will facilitate reusing the dataset, maximize the values of data and further accelerate cancer research. Measurement(s) | RNA expression profiling • whole-exome sequencing (WES) • somatic mutations • copy number alterations (CNAs) | Technology Type(s) | RNA sequencing • DNA sequencing • OncoScan CNV assay | Factor Type(s) | Intervention or procedure | Sample Characteristic - Organism | Homo sapiens | Sample Characteristic - Location | China |
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11
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Han LM, Weiel JJ, Longacre TA, Folkins AK. DICER1-associated Tumors in the Female Genital Tract: Molecular Basis, Clinicopathologic Features, and Differential Diagnosis. Adv Anat Pathol 2022; 29:297-308. [PMID: 35778792 DOI: 10.1097/pap.0000000000000351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
DICER1 syndrome is a tumor predisposition syndrome in which patients are at an increased risk of developing a wide variety of benign and malignant neoplasms with a hallmark constellation of pediatric pleuropulmonary blastoma, cystic nephroma, and thyroid lesions. DICER1 encodes an RNA endoribonuclease that is crucial to the processing of microRNA and may play a role in the maturation of Müllerian tissue. Within the gynecologic tract, germline mutations in DICER1 are associated with an array of rare tumors, including Sertoli-Leydig cell tumor, embryonal rhabdomyosarcoma of the cervix, gynandroblastoma, and juvenile granulosa cell tumor, which typically present in childhood, adolescence, or early adulthood. In addition, somatic DICER1 mutations have been described in rare gynecologic tumors such as adenosarcoma, Sertoli cell tumor, ovarian fibrosarcoma, cervical primitive neuroectodermal tumor, carcinosarcoma, and germ cell tumors. In light of the significant association with multiple neoplasms, genetic counseling should be considered for patients who present with a personal or family history of these rare DICER1-associated gynecologic tumors. This review highlights the most current understanding of DICER1 genetic alterations and describes the clinical, histopathologic, and immunohistochemical features and differential diagnoses for gynecologic tumors associated with DICER1 mutation.
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Affiliation(s)
- Lucy M Han
- Department of Pathology, Stanford University, Stanford, CA
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12
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Pei J, Flieder DB, Talarchek JN, Cooper HS, Patchefsky AS, Wei S. Clinical Application of Chromosome Microarray Analysis in the Diagnosis of Lipomatous Tumors. Appl Immunohistochem Mol Morphol 2021; 29:592-598. [PMID: 33734108 DOI: 10.1097/pai.0000000000000923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/27/2021] [Indexed: 11/25/2022]
Abstract
Well-differentiated liposarcoma/atypical lipomatous tumor (WDLS/ALT) and dedifferentiated liposarcoma (DDLS) have characteristic supernumerary ring and giant marker chromosomes involving the chromosomal region 12q13-15 which contains MDM2 (12q15), CDK4 (12q14.1), HMGA2 (12q14.3), YEATS4 (12q15), CPM (12q15), and FRS2 (12q15). Detecting MDM2 amplification by fluorescence in situ hybridization (FISH) is considered to be the gold standard for the diagnosis of WDLS/ALT and DDLS. In this study, formalin fixed paraffin embedded clinical specimens (16 liposarcomas and 19 benign lipomatous tumors) were used to detect MDM2 amplification and other chromosomal alterations in WDLS/ALT and DDLS by single nucleotide polymorphism-based chromosome microarray (CMA). All 16 liposarcomas showed MDM2 amplification with a MDM2/cep12 ratio from 2.4 to 8.4 by CMA. Ten (62.5%) of these cases had CDK4/cep12 ratio ≥2.0. All the cases without CDK4 amplification were from the thigh. The MDM2/cep12 ratio of all the benign lipomatous tumors (19/19) was within the normal limits. Twenty-one of the 35 benign lipomatous tumors and liposarcomas were also tested for MDM2 amplification by FISH. All the FISH results were consistent with the CMA results (100%). Along with MDM2 amplification, all 16 liposarcomas (100%) also showed amplification of YEATS4, CPM and FRS2. Only 11 of 16 (69%) cases showed HMGA2 amplification. In conclusion, this study demonstrated that CMA on routine formalin fixed paraffin embedded tissue is a sensitive and specific clinical test for detection of MDM2 gene amplification. Moreover, CMA allows simultaneous detection of genomic changes of interest including CDK4 and others, which provides enriched information for diagnosing lipomatous tumors.
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Affiliation(s)
- Jianming Pei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA
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Akazawa K, Kagara N, Sota Y, Motooka D, Nakamura S, Miyake T, Tanei T, Naoi Y, Shimoda M, Kim SJ, Noguchi S, Shimazu K. Comparison of the multigene panel test and OncoScan™ for the determination of HER2 amplification in breast cancer. Oncol Rep 2021; 46:217. [PMID: 34396441 DOI: 10.3892/or.2021.8168] [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: 12/09/2020] [Accepted: 05/26/2021] [Indexed: 11/06/2022] Open
Abstract
The diagnostic accuracy of the multigene panel test (MPT) and OncoScan™ in the determination of HER2 amplification in breast tumors remains controversial. In the present study, HER2 copy number was analyzed using both MPT and OncoScan™ in 45 breast tumors and was compared with that in fluorescent in situ hybridization (FISH) analysis. Tumors with low cellularity were examined using tumor cell enrichment and fluorescence‑activated cell sorting. Both MPT and OncoScan™ exhibited significant correlations with FISH with respect to the determination of HER2 amplification in breast tumors. However, the correlation coefficient was significantly higher for the comparison of MPT and FISH (r=0.770) compared with that between OncoScan™ and FISH (r=0.564). The accuracy of MPT (93.3%) was slightly higher compared with that in OncoScan™ (84.4%) in determining the HER2 status, which was mostly explained by the higher sensitivity of MPT in tumors with low cellularity (83.3 vs. 33.3%), but not in those with high cellularity (81.8 vs. 72.7%). The specificity was 100% for both tests. The MPT exhibited higher sensitivity in the determination of the amplification of other genes, including MYC, fibroblast growth factor receptor 1 and GATA binding protein 3 in tumors with low cellularity compared with that in tumors with high cellularity. OncoScan™ exhibited low sensitivity without tumor cell enrichment. The results suggested that MPT could be a promising method to determine HER2 status in breast tumors and that it could exhibit improved accuracy compared with that in OncoScan™ in tumors with low cellularity.
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Affiliation(s)
- Kaori Akazawa
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita‑shi, Osaka 565‑0871, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita‑shi, Osaka 565‑0871, Japan
| | - Yoshiaki Sota
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita‑shi, Osaka 565‑0871, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita‑shi, Osaka 565‑0871, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita‑shi, Osaka 565‑0871, Japan
| | - Tomohiro Miyake
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita‑shi, Osaka 565‑0871, Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita‑shi, Osaka 565‑0871, Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita‑shi, Osaka 565‑0871, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita‑shi, Osaka 565‑0871, Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita‑shi, Osaka 565‑0871, Japan
| | - Shinzaburo Noguchi
- Hyogo Prefectural Nishinomiya Hospital, Nishinomiya, Hyogo 662‑0918, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita‑shi, Osaka 565‑0871, Japan
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Fruncillo S, Su X, Liu H, Wong LS. Lithographic Processes for the Scalable Fabrication of Micro- and Nanostructures for Biochips and Biosensors. ACS Sens 2021; 6:2002-2024. [PMID: 33829765 PMCID: PMC8240091 DOI: 10.1021/acssensors.0c02704] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since the early 2000s, extensive research has been performed to address numerous challenges in biochip and biosensor fabrication in order to use them for various biomedical applications. These biochips and biosensor devices either integrate biological elements (e.g., DNA, proteins or cells) in the fabrication processes or experience post fabrication of biofunctionalization for different downstream applications, including sensing, diagnostics, drug screening, and therapy. Scalable lithographic techniques that are well established in the semiconductor industry are now being harnessed for large-scale production of such devices, with additional development to meet the demand of precise deposition of various biological elements on device substrates with retained biological activities and precisely specified topography. In this review, the lithographic methods that are capable of large-scale and mass fabrication of biochips and biosensors will be discussed. In particular, those allowing patterning of large areas from 10 cm2 to m2, maintaining cost effectiveness, high throughput (>100 cm2 h-1), high resolution (from micrometer down to nanometer scale), accuracy, and reproducibility. This review will compare various fabrication technologies and comment on their resolution limit and throughput, and how they can be related to the device performance, including sensitivity, detection limit, reproducibility, and robustness.
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Affiliation(s)
- Silvia Fruncillo
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Xiaodi Su
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
- Department of Chemistry, National University of Singapore, Block S8, Level 3, 3 Science Drive, Singapore 117543, Singapore
| | - Hong Liu
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Lu Shin Wong
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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15
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Roth LM, Czernobilsky B, Roth DJ, Cheng L. Highly differentiated follicular thyroid-type carcinoma of the ovary reconsidered. J Clin Pathol 2021; 74:553-557. [PMID: 34162686 DOI: 10.1136/jclinpath-2021-207447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/25/2021] [Accepted: 05/03/2021] [Indexed: 11/04/2022]
Affiliation(s)
- Lawrence M Roth
- Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | - David J Roth
- Independent Researcher, Cambridge, Massachusetts, USA
| | - Liang Cheng
- Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
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16
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Apellaniz-Ruiz M, McCluggage WG, Foulkes WD. DICER1-associated embryonal rhabdomyosarcoma and adenosarcoma of the gynecologic tract: Pathology, molecular genetics, and indications for molecular testing. Genes Chromosomes Cancer 2020; 60:217-233. [PMID: 33135284 DOI: 10.1002/gcc.22913] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 12/21/2022] Open
Abstract
Gynecologic sarcomas are uncommon neoplasms, the majority occurring in the uterus. Due to the diverse nature of these, the description of "new" morphological types and the rarity of some of them, pathological diagnosis and treatment is often challenging. Finding genetic alterations specific to, and frequently occurring, in a certain type can aid in the diagnosis. DICER1 is a highly conserved ribonuclease crucial in the biogenesis of microRNAs and mutations in DICER1 (either somatic or germline) have been detected in a wide range of sarcomas including genitourinary embryonal rhabdomyosarcomas (ERMS) and adenosarcomas. Importantly, DICER1-associated sarcomas share morphological features irrespective of the site of origin such that the pathologist can strongly suspect a DICER1 association. A review of the literature shows that almost all gynecologic ERMS reported (outside of the vagina) harbor DICER1 alterations, while approximately 20% of adenosarcomas also do so. These two tumor types exhibit significant morphological overlap and DICER1 tumor testing may be helpful in distinguishing between them, because a negative result makes ERMS unlikely. Given that germline pathogenic DICER1 variants are frequent in uterine (corpus and cervix) ERMS and pathogenic germline variants in this gene cause a hereditary cancer predisposition syndrome (DICER1 syndrome), patients diagnosed with these neoplasms should be referred to medical genetic services. Cooperation between pathologists and geneticists is crucial and will help in improving the diagnosis and management of these uncommon sarcomas.
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Affiliation(s)
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
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17
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Chromosomal microarray analysis of benign mesenchymal tumors with RB1 deletion. Hum Pathol 2020; 102:88-93. [PMID: 32800346 DOI: 10.1016/j.humpath.2020.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 02/07/2023]
Abstract
Spindle cell lipomas/pleomorphic lipomas, mammary-type myofibroblastomas, and cellular angiofibromas are benign mesenchymal tumors that demonstrate histologically overlapping features but with varying anatomic locations and an uncertain etiologic relationship. These tumors have also been found to have an overlapping molecular profile with shared 13q14 deletions, which is the location of the tumor suppressor gene RB1 that encodes the retinoblastoma protein. Molecular studies thus far have largely focused on the RB1 locus, using primarily immunohistochemistry and fluorescence in situ hybridization to characterize RB1 status. However, further characterization of the molecular profile of these lesions, including genome-wide copy number variation, remains to be well defined. The goal of this study is to further characterize the specific RB1 deletions seen in spindle cell lipomas/pleomorphic lipomas, cellular angiofibromas, and mammary-type myofibroblastomas as well as to evaluate these neoplasms for additional molecular abnormalities using the OncoScan™ CNV Plus Assay, which is used for clinical use as a whole-genome copy number microarray-based assay. Ten of eleven cases demonstrated deletion of the RB1 gene with varying deletion size and breakpoints. The majority of additional genetic alterations were chromosomal losses and loss of heterozygosity with rare chromosomal gains. Although only a small subset of mesenchymal neoplasms was evaluated, the principle of creating a novel pairing of the molecular method with the tumor type represents a promising avenue for further study in a variety of tumors.
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Ebrahimizadeh W, Guérard KP, Rouzbeh S, Bramhecha YM, Scarlata E, Brimo F, Patel PG, Jamaspishvili T, Aprikian AG, Berman D, Bartlett JMS, Chevalier S, Lapointe J. Design and Development of a Fully Synthetic Multiplex Ligation-Dependent Probe Amplification-Based Probe Mix for Detection of Copy Number Alterations in Prostate Cancer Formalin-Fixed, Paraffin-Embedded Tissue Samples. J Mol Diagn 2020; 22:1246-1263. [PMID: 32763409 DOI: 10.1016/j.jmoldx.2020.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/24/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
DNA copy number alterations (CNAs) are promising biomarkers to predict prostate cancer (PCa) outcome. However, fluorescence in situ hybridization (FISH) cannot assess complex CNA signatures because of low multiplexing capabilities. Multiplex ligation-dependent probe amplification (MLPA) can detect multiple CNAs in a single PCR assay, but PCa-specific probe mixes available commercially are lacking. Synthetic MLPA probes were designed to target 10 CNAs relevant to PCa: 5q15-21.1 (CHD1), 6q15 (MAP3K7), 8p21.2 (NKX3-1), 8q24.21 (MYC), 10q23.31 (PTEN), 12p13.1 (CDKN1B), 13q14.2 (RB1), 16p13.3 (PDPK1), 16q23.1 (GABARAPL2), and 17p13.1 (TP53), with 9 control probes. In cell lines, CNAs were detected when the cancer genome was as low as 30%. Compared with FISH in radical prostatectomy formalin-fixed, paraffin-embedded samples (n = 18: 15 cancers and 3 matched benign), the MLPA assay showed median sensitivity and specificity of 80% and 93%, respectively, across all CNAs assessed. In the validation set (n = 40: 20 tumors sampled in two areas), the respective sensitivity and specificity of MLPA compared advantageously with FISH and TaqMan droplet digital PCR (ddPCR) when assessing PTEN deletion (FISH: 85% and 100%; ddPCR: 100% and 83%) and PDPK1 gain (FISH: 100% and 92%; ddPCR: 93% and 100%). This new PCa probe mix accurately identifies CNAs by MLPA across multiple genes using low quality and quantities (50 ng) of DNA extracted from clinical formalin-fixed, paraffin-embedded samples.
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Affiliation(s)
- Walead Ebrahimizadeh
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Karl-Philippe Guérard
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Shaghayegh Rouzbeh
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Yogesh M Bramhecha
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Eleonora Scarlata
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Fadi Brimo
- Department of Pathology, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Palak G Patel
- Department of Pathology, Queen's University, Kingston, Ontario, Canada
| | | | - Armen G Aprikian
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - David Berman
- Department of Pathology, Queen's University, Kingston, Ontario, Canada
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Simone Chevalier
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jacques Lapointe
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
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Neill SG, Hauenstein J, Li MM, Liu YJ, Luo M, Saxe DF, Ligon AH. Copy number assessment in the genomic analysis of CNS neoplasia: An evidence-based review from the cancer genomics consortium (CGC) working group on primary CNS tumors. Cancer Genet 2020; 243:19-47. [PMID: 32203924 DOI: 10.1016/j.cancergen.2020.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/12/2020] [Accepted: 02/19/2020] [Indexed: 12/20/2022]
Abstract
The period from the 1990s to the 2010s has witnessed a burgeoning sea change in the practice of surgical neuropathology due to the incorporation of genomic data into the assessment of a range of central nervous system (CNS) neoplasms. This change has since matured into the adoption of genomic information into the definition of several World Health Organization (WHO)-established diagnostic entities. The data needed to accomplish the modern diagnosis of CNS neoplasia includes DNA copy number aberrations that may be assessed through a variety of mechanisms. Through a review of the relevant literature and professional practice guidelines, here we provide a condensed and scored overview of the most critical DNA copy number aberrations to assess for a selection of primary CNS neoplasms.
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Affiliation(s)
- Stewart G Neill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Jennifer Hauenstein
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Marilyn M Li
- Department of Pathology, Division of Genomic Diagnostics, Children's Hospital of Philadelphia and Perelman School of Medicine, Philadelphia, PA, United States
| | - Yajuan J Liu
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Minjie Luo
- Department of Pathology, Division of Genomic Diagnostics, Children's Hospital of Philadelphia and Perelman School of Medicine, Philadelphia, PA, United States
| | - Debra F Saxe
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Azra H Ligon
- Department of Pathology, Center for Advanced Molecular Diagnostics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, United States
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Patel SH, Batchala PP, Mrachek EKS, Lopes MBS, Schiff D, Fadul CE, Patrie JT, Jain R, Druzgal TJ, Williams ES. MRI and CT Identify Isocitrate Dehydrogenase (IDH)-Mutant Lower-Grade Gliomas Misclassified to 1p/19q Codeletion Status with Fluorescence in Situ Hybridization. Radiology 2020; 294:160-167. [DOI: 10.1148/radiol.2019191140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Van der Linden M, Raman L, Vander Trappen A, Dheedene A, De Smet M, Sante T, Creytens D, Lievens Y, Menten B, Van Dorpe J, Van Roy N. Detection of Copy Number Alterations by Shallow Whole-Genome Sequencing of Formalin-Fixed, Paraffin-Embedded Tumor Tissue. Arch Pathol Lab Med 2019; 144:974-981. [PMID: 31846367 DOI: 10.5858/arpa.2019-0010-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— In routine clinical practice, tumor tissue is stored in formalin-fixed, paraffin-embedded blocks. However, the use of formalin-fixed, paraffin-embedded tissue for genome analysis is challenged by poorer DNA quality and quantity. Although several studies have reported genome-wide massive parallel sequencing applied on formalin-fixed, paraffin-embedded samples for mutation analysis, copy number analysis is not yet commonly performed. OBJECTIVE.— To evaluate the use of formalin-fixed, paraffin-embedded tissue for copy number alteration detection using shallow whole-genome sequencing, more generally referred to as copy number variation sequencing. DESIGN.— We selected samples from 21 patients, covering a range of different tumor entities. The performance of copy number detection was compared across 3 setups: array comparative genomic hybridization in combination with fresh material; copy number variation sequencing on fresh material; and copy number variation sequencing on formalin-fixed, paraffin-embedded material. RESULTS.— Very similar copy number profiles between paired samples were obtained. Although formalin-fixed, paraffin-embedded profiles often displayed more noise, detected copy numbers seemed equally reliable if the tumor fraction was at least 20%. CONCLUSIONS.— Copy number variation sequencing of formalin-fixed, paraffin-embedded material represents a trustworthy method. It is very likely that copy number variation sequencing of routinely obtained biopsy material will become important for individual patient care and research. Moreover, the basic technology needed for copy number variation sequencing is present in most molecular diagnostics laboratories.
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Affiliation(s)
- Malaïka Van der Linden
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Lennart Raman
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Ansel Vander Trappen
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Annelies Dheedene
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Matthias De Smet
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Tom Sante
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - David Creytens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Yolande Lievens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Björn Menten
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Jo Van Dorpe
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Nadine Van Roy
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
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22
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Olson N, Gularte-Mérida R, Selenica P, Da Cruz Paula A, Alemar B, Weigelt B, Lefferts J, Linos K. Molecular Characterization of a Rare Dedifferentiated Liposarcoma With Rhabdomyosarcomatous Differentiation in a 24 Year Old. Int J Surg Pathol 2019; 28:454-463. [PMID: 31801397 PMCID: PMC8302235 DOI: 10.1177/1066896919890401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aims. The aim of this study was to identify potential driver genetic alterations in a dedifferentiated liposarcoma (DDLPS) with rhabdomyosarcomatous differentiation. Methods and Results. A 24-year-old female underwent resection of an abdominal mass, which on a previous biopsy demonstrated rhabdomyosarcomatous differentiation concerning for embryonal rhabdomyosarcoma. Histologically the resected tumor displayed a high-grade sarcoma with rhabdomyosarcomatous differentiation in the background of well-differentiated liposarcoma consistent with DDLPS. Fluorescence in situ hybridization confirmed MDM2 amplification, as did array-based copy number profiling. Whole-exome sequencing revealed a somatic FGFR1 hotspot mutation and RNA sequencing an LMNB2-MAP2K6 fusion only within the dedifferentiated component. Conclusions. This study represents an in-depth examination of a rare DDLPS with rhabdomyosarcomatous differentiation in a young individual. Additionally, it is also instructive of a potential pitfall when assessing for MDM2 amplification in small biopsies. Despite exhaustive analysis, mutation and gene copy number analysis did not identify any molecular events that would underlie the rhabdomyoblastic differentiation. Our understanding of what causes some tumors to dedifferentiate as well as undergo divergent differentiation is limited, and larger studies are needed.
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Affiliation(s)
- Nicholas Olson
- Dartmouth-Hitchcock Medical Center and Geisel School of Medicine, Lebanon, NH, USA
| | | | - Pier Selenica
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,University of Maastricht, Maastricht, Netherlands
| | | | - Barbara Alemar
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joel Lefferts
- Dartmouth-Hitchcock Medical Center and Geisel School of Medicine, Lebanon, NH, USA
| | - Konstantinos Linos
- Dartmouth-Hitchcock Medical Center and Geisel School of Medicine, Lebanon, NH, USA
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23
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Genomic profile of breast sarcomas: a comparison with malignant phyllodes tumours. Breast Cancer Res Treat 2018; 174:365-373. [DOI: 10.1007/s10549-018-5067-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/20/2018] [Indexed: 01/04/2023]
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24
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Krieger N, Nabavi S, Waterman PD, Achacoso NS, Acton L, Schnitt SJ, Habel LA. Feasibility of analyzing DNA copy number variation in breast cancer tumor specimens from 1950 to 2010: how old is too old? Cancer Causes Control 2018; 29:305-314. [PMID: 29427260 DOI: 10.1007/s10552-018-1006-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/30/2018] [Indexed: 10/18/2022]
Abstract
PURPOSE The purpose of the study was to assess the feasibility of quantifying long-term trends in breast tumor DNA copy number variation (CNV) profiles. METHODS We evaluated CNV profiles in formalin-fixed paraffin-embedded (FFPE) tumor specimens from 30 randomly selected Kaiser Permanente Northern California health plan women members diagnosed with breast cancer from 1950 to 2010. Assays were conducted for five cases per decade who had available tumor blocks and pathology reports. RESULTS As compared to the tumors from the 1970s to 2000s, the older tumors dating back to the 1950s and 1960s were much more likely to (1) fail quality control, and (2) have fewer CNV events (average 23 and 31 vs. 58 to 69), fewer CNV genes (average 5.1 and 3.7k vs. 8.1 to 10.3k), shorter CNV length (average 2,440 and 3,300k vs. 5,740 to 9,280k), fewer high frequency Del genes (37 and 25% vs. 54 to 76%), and fewer high frequency high_Amp genes (20% vs. 56 to 73%). On average, assay interpretation took an extra 60 min/specimen for cases from the 1960s versus 20 min/specimen for the most recent tumors. CONCLUSIONS Assays conducted in the mid-2010s for CNVs may be feasible for FFPE tumor specimens dating back to the 1980s, but less feasible for older specimens.
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Affiliation(s)
- Nancy Krieger
- Dept of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Kresge 717, Boston, MA, 02130, USA.
| | - Sheida Nabavi
- Dept of Computer Science and Engineering, University of Connecticut, 371 Fairfield Way, Storrs, CT, 06269, USA
| | - Pamela D Waterman
- Dept of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02130, USA
| | - Ninah S Achacoso
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA, 94612, USA
| | - Luana Acton
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA, 94612, USA
| | - Stuart J Schnitt
- Dana-Farber Cancer Institute/Brigham and Women's Hospital Breast Oncology Program, Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, 02115, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA, 94612, USA
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25
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Dubuc AM, Ligon AH. From Prognostication to Personalized Medicine: Classification of Tumors of the Central Nervous System (CNS) Using Chromosomal Microarrays. CURRENT GENETIC MEDICINE REPORTS 2017. [DOI: 10.1007/s40142-017-0127-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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