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Koduru P, Chen W, Fuda F, Kaur G, Awan F, John S, Garcia R, Gagan J. RNASeq Analysis for Accurate Identification of Fusion Partners in Tumor Specific Translocations Detected by Standard FISH Probes in Hematologic Malignancies. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2024; 17:2632010X241230262. [PMID: 38371338 PMCID: PMC10874141 DOI: 10.1177/2632010x241230262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
Abstract
Background Fluorescence labeled DNA probes and in situ hybridization methods had shorter turn round time for results revolutionized their clinical application. Signals obtained from these probes are highly specific, yet they can produce fusion signals not necessarily representing fusion of actual genes due to other genes included in the probe design. In this study we evaluated discordance between cytogenetic, FISH and RNAseq results in 3 different patients with hematologic malignancies and illustrated the need to perform next generation sequencing (NGS) or RNASeq to accurately interpret FISH results. Methods Bone marrow or peripheral blood karyotypes and FISH were performed to detect recurring translocations associated with hematologic malignancies in clinical samples routinely referred to our clinical cytogenetics laboratory. When required, NGS was performed on DNA and RNA libraries to detect somatic alterations and gene fusions in some of these specimens. Discordance in results between these methods is further evaluated. Results For a patient with plasma cell leukemia standard FGFR3 / IGH dual fusion FISH assay detected fusion that was interpreted as FGFR3-positive leukemia, whereas NGS/RNASeq detected NSD2::IGH. For a pediatric acute lymphoblastic leukemia patient, a genetic diagnosis of PDGFRB-positive ALL was rendered because the PDGFRB break-apart probe detected clonal rearrangement, whereas NGS detected MEF2D::CSF1R. A MYC-positive B-prolymphocytic leukemia was rendered for another patient with a cytogenetically identified t(8;14) and MYC::IGH by FISH, whereas NGS detected a novel PVT1::RCOR1 not previously reported. Conclusions These are 3 cases in a series of several other concordant results, nevertheless, elucidate limitations when interpreting FISH results in clinical applications, particularly when other genes are included in probe design. In addition, when the observed FISH signals are atypical, this study illustrates the necessity to perform complementary laboratory assays, such as NGS and/or RNASeq, to accurately identify fusion genes in tumorigenic translocations.
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Affiliation(s)
- Prasad Koduru
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Weina Chen
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Franklin Fuda
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gurbakhash Kaur
- Internal Medicine (Division of Oncology), UT Southwestern Medical Center, Dallas, TX, USA
| | - Farrukh Awan
- Internal Medicine (Division of Oncology), UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel John
- Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rolando Garcia
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey Gagan
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
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Tsushima T, Terao T, Narita K, Fukumoto A, Ikeda D, Kamura Y, Kuzume A, Tabata R, Miura D, Takeuchi M, Matsue K. Clinical Characteristics and Outcomes of Cyclin D1-Positive AL Amyloidosis. Am J Clin Pathol 2023; 160:157-163. [PMID: 36940250 DOI: 10.1093/ajcp/aqad013] [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: 10/04/2022] [Accepted: 01/26/2023] [Indexed: 03/22/2023] Open
Abstract
OBJECTIVES To demonstrate the clinical features and prognostic impact of cyclin D1 positivity in patients with amyloid light chain amyloidosis (AL). METHODS We consecutively included 71 patients diagnosed with AL with cyclin D1 positivity between February 2008 and January 2022. t(11;14) was examined through interphase fluorescence in situ hybridization using bone marrow cells. RESULTS The median age of the patients was 73 years, and 53.5% were male. The underlying diseases included symptomatic multiple myeloma, smoldering multiple myeloma, Waldenström macroglobulinemia, and monoclonal gammopathy of undetermined significance, representing 33.8%, 26.8%, 2.8%, and 36.6%, respectively. The prevalence of cyclin D1 and t(11;14) was 38.0% and 34.7%, respectively. Higher frequency of light chain paraprotein type was seen in cyclin D1-positive patients with AL than in cyclin D1-negative patients (70.4% vs 18.2%). The median overall survival (OS) of patients with AL with and without cyclin D1 expression was 18.9 months and 73.1 months, respectively (P = .019). Early death occurred in 44.4% of cyclin D1-positive patients and 31.8% of cyclin D1-negative patients. Moreover, 83.3% of cyclin D1-positive patients and 21.4% of cyclin D1-negative patients died of cardiac causes. CONCLUSIONS Cyclin D1 immunohistochemistry accurately identified patients with t(11;14). Cyclin D1-positive patients had significantly inferior OS compared with cyclin D1-negative patients.
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Affiliation(s)
- Takafumi Tsushima
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Toshiki Terao
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Kentaro Narita
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Ami Fukumoto
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Daisuke Ikeda
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Yuya Kamura
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Ayumi Kuzume
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Rikako Tabata
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Daisuke Miura
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Masami Takeuchi
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Kosei Matsue
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
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Furukawa Y, Kikuchi J. Molecular basis of clonal evolution in multiple myeloma. Int J Hematol 2020; 111:496-511. [DOI: 10.1007/s12185-020-02829-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/16/2020] [Indexed: 12/12/2022]
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Gao M, Li C, Xiao H, Dong H, Jiang S, Fu Y, Gong L. hsa_circ_0007841: A Novel Potential Biomarker and Drug Resistance for Multiple Myeloma. Front Oncol 2019; 9:1261. [PMID: 31803627 PMCID: PMC6877741 DOI: 10.3389/fonc.2019.01261] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Purpose: Circular RNA (circRNA) is a key regulatory factor in the development and progression of human tumors. However, the working mechanism and clinical significance of most circRNAs remain unknown in human cancers, including multiple myeloma (MM). Patients and Methods: This study employs high-throughput circRNA microarray with bioinformatics to identify differentially expressed circRNAs in patients with MM. The hsa_circ_0007841 expressions were observed in the MM tissues of 86 patients. Drug-resistant cell lines and pathological features were also detected. In addition, the relationship between hsa_circ_0007841 expressions in the MM tissues and the pathological features of patients with MM were evaluated and role of hsa_circ_0007841 as a potential biomarker and therapeutic target was assessed. Results: The results show that in the MM cell lines and drug-resistant cell lines, hsa_circ_0007841 expression was significantly upregulated, which was closely associated with disease prognosis. Specifically, hsa_circ_0007841 upregulation was correlated with chromosomal aberrations such as gain 1q21, t (4:14) and mutations in ATR and IRF4 genes. This finding was corroborated in large samples. Finally, bioinformatics analysis showed that eight differentially expressed miRNAs and 10 candidate mRNAs interacted with hsa_circ_0007841, shedding some new light on the basic functional research. Conclusion: This study may be the first to report that hsa_circ_0007841 is significantly upregulated in MM. It also suggests that hsa_circ_0007841 may be a novel biomarker for MM and its involvement in the progression of MM.
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Affiliation(s)
- Meng Gao
- The Third Xiangya Hospital of Central South University, Changsha, China
| | - Chengyuan Li
- The Third Xiangya Hospital of Central South University, Changsha, China
| | - Han Xiao
- The Third Xiangya Hospital of Central South University, Changsha, China
| | - Hang Dong
- The Third Xiangya Hospital of Central South University, Changsha, China
| | - Siyi Jiang
- The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yunfeng Fu
- The Third Xiangya Hospital of Central South University, Changsha, China
| | - Liying Gong
- The Third Xiangya Hospital of Central South University, Changsha, China
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Murase T, Ri M, Narita T, Fujii K, Masaki A, Iida S, Inagaki H. Immunohistochemistry for identification of CCND1, NSD2, and MAF gene rearrangements in plasma cell myeloma. Cancer Sci 2019; 110:2600-2606. [PMID: 31218784 PMCID: PMC6676137 DOI: 10.1111/cas.14109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/01/2019] [Accepted: 06/17/2019] [Indexed: 01/03/2023] Open
Abstract
The t(11;14)/CCND1‐IGH, t(4;14)/NSD2(MMSET)‐IGH, and t(14;16)/IGH‐MAF gene rearrangements detected by fluorescence in situ hybridization (FISH) are used for risk stratification in patients with multiple myeloma (MM). Compared with conventional FISH techniques using fresh cells, immunohistochemistry (IHC) is much more cost‐ and time‐efficient, and can be readily applied to routinely prepared formalin‐fixed, paraffin‐embedded (FFPE) materials. In this study, we performed tissue FISH and IHC employing FFPE specimens, and examined the usefulness of IHC as a tool for detecting CCND1,NSD2, and MAF gene rearrangements. CD138 signals were used to identify plasma cells in tissue FISH and IHC analyses. With cohort 1 (n = 70), we performed tissue FISH and subsequently IHC, and determined IHC cut‐off points. In this cohort, the sensitivity and specificity for the 3 molecules were ≥.90 and ≥.96, respectively. With cohort 2, using MM cases with an unknown gene status (n = 120), we performed IHC, and the gene status was estimated using the cut‐off points determined with cohort 1. The subsequent FISH analysis showed that the sensitivity and specificity for the 3 molecules were ≥.92 and ≥.98, respectively. CCND1, NSD2, and MAF gene rearrangements were estimated accurately by IHC, suggesting that conventional FISH assays can be replaced by IHC.
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Affiliation(s)
- Takayuki Murase
- Department of Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Masaki Ri
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Tomoko Narita
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Keiichiro Fujii
- Department of Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Ayako Masaki
- Department of Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Shinsuke Iida
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Hiroshi Inagaki
- Department of Pathology and Molecular Diagnostics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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