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Spasova V, Mladenov B, Rangelov S, Hammoudeh Z, Nesheva D, Serbezov D, Staneva R, Hadjidekova S, Ganev M, Balabanski L, Vazharova R, Slavov C, Toncheva D, Antonova O. Clinical impact of copy number variation changes in bladder cancer samples. Exp Ther Med 2021; 22:901. [PMID: 34257714 PMCID: PMC8243332 DOI: 10.3892/etm.2021.10333] [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: 11/30/2019] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to detect copy number variations (CNVs) related to tumour progression and metastasis of urothelial carcinoma through whole-genome scanning. A total of 30 bladder cancer samples staged from pTa to pT4 were included in the study. DNA was extracted from freshly frozen tissue via standard phenol-chloroform extraction and CNV analysis was performed on two alternative platforms (CytoChip Oligo aCGH, 4x44K and Infinium OncoArray-500K BeadChip; Illumina, Inc.). Data were analysed with BlueFuse Multi software and Karyostudio, respectively. The results highlight the role of genomic imbalances in regions containing genes with metastatic and proliferative potential for tumour invasion. A high level of genomic instability in uroepithelial tumours was observed and a total of 524 aberrations, including 175 losses and 349 gains, were identified. The most prevalent genetic imbalances affected the following regions: 1p, 1q, 2q, 4p, 4q, 5p, 5q, 6p, 6q, 7q, 8q, 9p, 9q, 10p, 10q, 11q, 13q and 17q. High-grade tumours more frequently harboured genomic imbalances (n=227) than low-grade tumours (n=103). A total of 36 CNVs in high-grade bladder tumours were detected in chromosomes 1-5, 8-11, 14, 17, 19 and 20. Furthermore, five loss of heterozygosity variants containing 176 genes were observed in high-grade bladder cancer and may be used as potential targets for precision therapy. Revealing specific chromosomal regions related to the metastatic potential of uroepithelial tumours may lay a foundation for implementing molecular CNV profiling of bladder tumours as part of a routine progression risk estimation strategy, thus expanding the personalized therapeutic approach.
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Affiliation(s)
- Victoria Spasova
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Boris Mladenov
- Department of Urology, UMBALSM N.I. Pirogov, 1606 Sofia, Bulgaria
| | - Simeon Rangelov
- Department of Urology, Tsaritsa Yoanna University Hospital, 1527 Sofia, Bulgaria
| | - Zora Hammoudeh
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Dimitar Serbezov
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Rada Staneva
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria.,Medical Genetics Laboratory, Nadezhda Women's Health Hospital, 1373 Sofia, Bulgaria
| | - Savina Hadjidekova
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria.,Medical Genetics Laboratory, Nadezhda Women's Health Hospital, 1373 Sofia, Bulgaria
| | - Mihail Ganev
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Lubomir Balabanski
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria.,Medical Genetics Laboratory, GARH Malinov, 1680 Sofia, Bulgaria
| | - Radoslava Vazharova
- Medical Genetics Laboratory, GARH Malinov, 1680 Sofia, Bulgaria.,Department of Biology, Medical Genetics and Microbiology, Faculty of Medicine, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
| | - Chavdar Slavov
- Department of Urology, Tsaritsa Yoanna University Hospital, 1527 Sofia, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Olga Antonova
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
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Kakarmath S, Heller HT, Alexander CA, Cibas ES, Krane JF, Barletta JA, Lindeman NI, Frates MC, Benson CB, Gawande AA, Cho NL, Nehs M, Moore FD, Marqusee E, Kim MI, Larsen PR, Kwong N, Angell TE, Alexander EK. Clinical, Sonographic, and Pathological Characteristics of RAS-Positive Versus BRAF-Positive Thyroid Carcinoma. J Clin Endocrinol Metab 2016; 101:4938-4944. [PMID: 27689252 PMCID: PMC5155682 DOI: 10.1210/jc.2016-2620] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Mutations in the BRAF and RAS oncogenes are responsible for most well-differentiated thyroid cancer. Yet, our clinical understanding of how BRAF-positive and RAS-positive thyroid cancers differ is incomplete. OBJECTIVE We correlated clinical, radiographic, and pathological findings from patients with thyroid cancer harboring a BRAF or RAS mutation. DESIGN Prospective cohort study. SETTING Academic, tertiary care hospital. PATIENTS A total of 101 consecutive patients with well-differentiated thyroid cancer. MAIN OUTCOME MEASURE We compared the clinical, sonographic, and pathological characteristics of patients with BRAF-positive cancer to those with RAS-positive cancer. RESULTS Of 101 patients harboring these mutations, 71 were BRAF-positive, whereas 30 were RAS-positive. Upon sonographic evaluation, RAS-positive nodules were significantly larger (P = .04), although BRAF-positive nodules were more likely to harbor concerning sonographic characteristics (hypoechogenicity [P < .001]; irregular margins [P = .04]). Cytologically, 70% of BRAF-positive nodules were classified positive for PTC, whereas 87% of RAS-positive nodules were indeterminate (P < .001). Histologically, 96% of RAS-positive PTC malignancies were follicular variants of PTC, whereas 70% of BRAF-positive malignancies were classical variants of PTC. BRAF-positive malignancies were more likely to demonstrate extrathyroidal extension (P = .003), lymphovascular invasion (P = .02), and lymph node metastasis (P < .001). CONCLUSIONS BRAF-positive malignant nodules most often demonstrate worrisome sonographic features and are frequently associated with positive or suspicious Bethesda cytology. In contrast, RAS-positive malignancy most often demonstrates indolent sonographic features and more commonly associates with lower risk, "indeterminate" cytology. Because BRAF and RAS mutations are the most common molecular perturbations associated with well-differentiated thyroid cancer, these findings may assist with improved preoperative risk assessment by suggesting the likely molecular profile of a thyroid cancer, even when postsurgical molecular analysis is unavailable.
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Affiliation(s)
- Sujay Kakarmath
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Howard T Heller
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Caroline A Alexander
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Edmund S Cibas
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Jeffrey F Krane
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Justine A Barletta
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Neal I Lindeman
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Mary C Frates
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Carol B Benson
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Atul A Gawande
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Nancy L Cho
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Matthew Nehs
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Francis D Moore
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Ellen Marqusee
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Mathew I Kim
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - P Reed Larsen
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Norra Kwong
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Trevor E Angell
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Erik K Alexander
- Thyroid Section, Division of Endocrinology, Hypertension, and Diabetes (S.K., T.E.A., N.K., C.A.A., E.M., M.I.K., P.R.L., E.K.A.), and Departments of Radiology (H.T.H., M.C.F., C.B.B.), Pathology (E.S.C., J.F.K., J.A.B., N.I.L.), and Surgery (A.A.G., N.L.C., M.N., F.D.M.), The Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
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