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Kwon R, Yeung CCS. Advances in next-generation sequencing and emerging technologies for hematologic malignancies. Haematologica 2024; 109:379-387. [PMID: 37584286 PMCID: PMC10828783 DOI: 10.3324/haematol.2022.282442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/17/2023] [Indexed: 08/17/2023] Open
Abstract
Innovations in molecular diagnostics have often evolved through the study of hematologic malignancies. Examples include the pioneering characterization of the Philadelphia chromosome by cytogenetics in the 1970s, the implementation of polymerase chain reaction for high-sensitivity detection and monitoring of mutations and, most recently, targeted next- generation sequencing to drive the prognostic and therapeutic assessment of leukemia. Hematologists and hematopath- ologists have continued to advance in the past decade with new innovations improving the type, amount, and quality of data generated for each molecule of nucleic acid. In this review article, we touch on these new developments and discuss their implications for diagnostics in hematopoietic malignancies. We review advances in sequencing platforms and library preparation chemistry that can lead to faster turnaround times, novel sequencing techniques, the development of mobile laboratories with implications for worldwide benefits, the current status of sample types, improvements to quality and reference materials, bioinformatic pipelines, and the integration of machine learning and artificial intelligence into mol- ecular diagnostic tools for hematologic malignancies.
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Affiliation(s)
- Regina Kwon
- Department of Laboratory Medicine and Pathology, University of Washington
| | - Cecilia C. S. Yeung
- Department of Laboratory Medicine and Pathology, University of Washington
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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Chen SN, Mai ZY, Mai JN, Liang W, Dong ZX, Ju FE, Chan SH, Fang Z, Xu Y, Uziel O, He C, Zhang XD, Zheng Y. E2F2 modulates cell adhesion through the transcriptional regulation of PECAM1 in multiple myeloma. Br J Haematol 2023; 202:840-855. [PMID: 37365680 DOI: 10.1111/bjh.18958] [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: 12/08/2022] [Revised: 05/26/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023]
Abstract
Multiple myeloma (MM) is the second most common haematological malignancy. Despite the development of new drugs and treatments in recent years, the therapeutic outcomes of patients are not satisfactory. It is necessary to further investigate the molecular mechanism underlying MM progression. Herein, we found that high E2F2 expression was correlated with poor overall survival and advanced clinical stages in MM patients. Gain- and loss-of-function studies showed that E2F2 inhibited cell adhesion and consequently activated cell epithelial-to-mesenchymal transition (EMT) and migration. Further experiments revealed that E2F2 interacted with the PECAM1 promoter to suppress its transcriptional activity. The E2F2-knockdown-mediated promotion of cell adhesion was significantly reversed by the repression of PECAM1 expression. Finally, we observed that silencing E2F2 significantly inhibited viability and tumour progression in MM cell models and xenograft mouse models respectively. This study demonstrates that E2F2 plays a vital role as a tumour accelerator by inhibiting PECAM1-dependent cell adhesion and accelerating MM cell proliferation. Therefore, E2F2 may serve as a potential independent prognostic marker and therapeutic target for MM.
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Affiliation(s)
- Shu-Na Chen
- Department of Hematology, Institute of Hematology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Sun Yat-Sen University, Shenzhen, China
| | - Zhi-Ying Mai
- Department of Hematology, Institute of Hematology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Sun Yat-Sen University, Shenzhen, China
| | - Jun-Na Mai
- Department of Hematology, Institute of Hematology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Weiyao Liang
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Sun Yat-Sen University, Shenzhen, China
| | - Zhao-Xia Dong
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Sun Yat-Sen University, Shenzhen, China
| | - Fei-Er Ju
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Sun Yat-Sen University, Shenzhen, China
| | - Sze-Hoi Chan
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Sun Yat-Sen University, Shenzhen, China
| | - Zhigang Fang
- Department of Hematology, Institute of Hematology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yichuan Xu
- Department of Hematology, Institute of Hematology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Orit Uziel
- The Felsenstein Medical Research Center, Institute of Hematology Rabin Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chengwei He
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China
| | - Xing-Ding Zhang
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Sun Yat-Sen University, Shenzhen, China
| | - Yongjiang Zheng
- Department of Hematology, Institute of Hematology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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Ansari-Pour N, Samur M, Flynt E, Gooding S, Towfic F, Stong N, Estevez MO, Mavrommatis K, Walker B, Morgan G, Munshi N, Avet-Loiseau H, Thakurta A. Whole-genome analysis identifies novel drivers and high-risk double-hit events in relapsed/refractory myeloma. Blood 2023; 141:620-633. [PMID: 36223594 PMCID: PMC10163277 DOI: 10.1182/blood.2022017010] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022] Open
Abstract
Large-scale analyses of genomic data from patients with newly diagnosed multiple myeloma (ndMM) have been undertaken, however, large-scale analysis of relapsed/refractory MM (rrMM) has not been performed. We hypothesize that somatic variants chronicle the therapeutic exposures and clonal structure of myeloma from ndMM to rrMM stages. We generated whole-genome sequencing (WGS) data from 418 tumors (386 patients) derived from 6 rrMM clinical trials and compared them with WGS from 198 unrelated patients with ndMM in a population-based case-control fashion. We identified significantly enriched events at the rrMM stage, including drivers (DUOX2, EZH2, TP53), biallelic inactivation (TP53), noncoding mutations in bona fide drivers (TP53BP1, BLM), copy number aberrations (CNAs; 1qGain, 17pLOH), and double-hit events (Amp1q-ISS3, 1qGain-17p loss-of-heterozygosity). Mutational signature analysis identified a subclonal defective mismatch repair signature enriched in rrMM and highly active in high mutation burden tumors, a likely feature of therapy-associated expanding subclones. Further analysis focused on the association of genomic aberrations enriched at different stages of resistance to immunomodulatory agent (IMiD)-based therapy. This analysis revealed that TP53, DUOX2, 1qGain, and 17p loss-of-heterozygosity increased in prevalence from ndMM to lenalidomide resistant (LENR) to pomalidomide resistant (POMR) stages, whereas enrichment of MAML3 along with immunoglobulin lambda (IGL) and MYC translocations distinguished POM from the LEN subgroup. Genomic drivers associated with rrMM are those that confer clonal selective advantage under therapeutic pressure. Their role in therapy evasion should be further evaluated in longitudinal patient samples, to confirm these associations with the evolution of clinical resistance and to identify molecular subsets of rrMM for the development of targeted therapies.
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Affiliation(s)
- Naser Ansari-Pour
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Mehmet Samur
- Dana-Farber Cancer Institute, Boston, MA
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, NJ
| | - Sarah Gooding
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Department of Haematology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | | | | | - Maria Ortiz Estevez
- Predictive Sciences, BMS Center for Innovation and Translational Research Europe, A Bristol Myers Squibb Company, Sevilla, Spain
| | | | - Brian Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, IN
| | - Gareth Morgan
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY
| | - Nikhil Munshi
- Dana-Farber Cancer Institute, Boston, MA
- VA Boston Healthcare System, West Roxbury, MA
- Harvard Medical School, Boston, MA
| | | | - Anjan Thakurta
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Bristol Myers Squibb, Summit, NJ
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Disease, University of Oxford, Oxford, United Kingdom
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Karagoz K, Stokes M, Ortiz-Estévez M, Towfic F, Flynt E, Gooding S, Pierceall W, Thakurta A. Multiple Myeloma Patient Tumors With High Levels of Cereblon Exon-10 Deletion Splice Variant Upregulate Clinically Targetable Pro-Inflammatory Cytokine Pathways. Front Genet 2022; 13:831779. [PMID: 35222546 PMCID: PMC8864318 DOI: 10.3389/fgene.2022.831779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/14/2022] [Indexed: 12/13/2022] Open
Abstract
Immunomodulatory drugs (IMiDs), including lenalidomide and pomalidomide, are used in the routine treatment for multiple myeloma (MM) patients. Cereblon (CRBN) is the direct molecular target of IMiDs. While CRBN is not an essential gene for MM cell proliferation, the frequency of CRBN genetic aberrations, including mutation, copy number loss, and exon-10 (which includes a portion of the IMiD-binding domain) splicing, have been reported to incrementally increase in later-line patients. CRBN exon-10 splicing has also been shown to be associated with decreased progression-free survival in both newly diagnosed and relapsed refractory MM patients. Although we did not find significant general splicing defects among patients with CRBN exon-10 splice variant when compared to those expressing the full-length transcript, we identified upregulated TNFA signaling via NFKB, inflammatory response, and IL-10 signaling pathways in patients with exon-10 splice variant across various data sets—all potentially promoting tumor growth via chronic growth signals. We examined master regulators that mediate transcriptional programs in CRBN exon-10 splice variant patients and identified BATF, EZH2, and IKZF1 as the key candidates across the four data sets. Upregulated downstream targets of BATF, EZH2, and IKZF1 are components of TNFA signaling via NFKB, IL2/STAT5 signaling pathways, and IFNG response pathways. Previously, BATF-mediated transcriptional regulation was associated with venetoclax sensitivity in MM. Interestingly, we found that an EZH2 sensitivity gene expression signature also correlated with high BATF or venetoclax sensitivity scores in these tumors. Together, these data provide a rationale for investigating EZH2 inhibitors or venetoclax in combination with the next generation CRBN-targeting agents, such as CELMoDs, for patients overexpressing the CRBN exon-10 splice variant.
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Affiliation(s)
- Kubra Karagoz
- Translational Medicine, Bristol Myers Squibb, Summit, NJ, United States
| | - Matthew Stokes
- Translational Medicine, Bristol Myers Squibb, Summit, NJ, United States
| | - María Ortiz-Estévez
- Bristol Myers Squibb Center for Innovation and Translational Research Europe, Sevilla, Spain
| | - Fadi Towfic
- Bristol Myers Squibb, San Diego, CA, United States
| | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, NJ, United States
| | - Sarah Gooding
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Department of Haematology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.,Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | - William Pierceall
- Translational Medicine, Bristol Myers Squibb, Summit, NJ, United States
| | - Anjan Thakurta
- Translational Medicine, Bristol Myers Squibb, Summit, NJ, United States.,Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
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