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Kashyap MK, Karathia H, Kumar D, Vera Alvarez R, Forero-Forero JV, Moreno E, Lujan JV, Amaya-Chanaga CI, Vidal NM, Yu Z, Ghia EM, Lengerke-Diaz PA, Achinko D, Choi MY, Rassenti LZ, Mariño-Ramírez L, Mount SM, Hannenhalli S, Kipps TJ, Castro JE. Aberrant spliceosome activity via elevated intron retention and upregulation and phosphorylation of SF3B1 in chronic lymphocytic leukemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102202. [PMID: 38846999 PMCID: PMC11154714 DOI: 10.1016/j.omtn.2024.102202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Splicing factor 3b subunit 1 (SF3B1) is the largest subunit and core component of the spliceosome. Inhibition of SF3B1 was associated with an increase in broad intron retention (IR) on most transcripts, suggesting that IR can be used as a marker of spliceosome inhibition in chronic lymphocytic leukemia (CLL) cells. Furthermore, we separately analyzed exonic and intronic mapped reads on annotated RNA-sequencing transcripts obtained from B cells (n = 98 CLL patients) and healthy volunteers (n = 9). We measured intron/exon ratio to use that as a surrogate for alternative RNA splicing (ARS) and found that 66% of CLL-B cell transcripts had significant IR elevation compared with normal B cells (NBCs) and that correlated with mRNA downregulation and low expression levels. Transcripts with the highest IR levels belonged to biological pathways associated with gene expression and RNA splicing. A >2-fold increase of active pSF3B1 was observed in CLL-B cells compared with NBCs. Additionally, when the CLL-B cells were treated with macrolides (pladienolide-B), a significant decrease in pSF3B1, but not total SF3B1 protein, was observed. These findings suggest that IR/ARS is increased in CLL, which is associated with SF3B1 phosphorylation and susceptibility to SF3B1 inhibitors. These data provide additional support to the relevance of ARS in carcinogenesis and evidence of pSF3B1 participation in this process.
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Affiliation(s)
- Manoj Kumar Kashyap
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Gurugram (HR) 122413, India
| | - Hiren Karathia
- Advanced Biomedical Computational Science and National Center for Advancing Translational Sciences, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Greenwood Genetic Center, Greenwood, SC, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Deepak Kumar
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Roberto Vera Alvarez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Eider Moreno
- Department of Internal Medicine, Division of Hematology-Oncology, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Juliana Velez Lujan
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | | | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zhe Yu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Emanuela M. Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Paula A. Lengerke-Diaz
- Department of Internal Medicine, Division of Hematology-Oncology, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Daniel Achinko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michael Y. Choi
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Laura Z. Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Leonardo Mariño-Ramírez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M. Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Januario E. Castro
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Department of Internal Medicine, Division of Hematology-Oncology, Mayo Clinic, Phoenix, AZ 85054, USA
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3
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Byrd JC, Hillmen P, O'Brien S, Barrientos JC, Reddy NM, Coutre S, Tam CS, Mulligan SP, Jaeger U, Barr PM, Furman RR, Kipps TJ, Thornton P, Moreno C, Montillo M, Pagel JM, Burger JA, Woyach JA, Dai S, Vezan R, James DF, Brown JR. Long-term follow-up of the RESONATE phase 3 trial of ibrutinib vs ofatumumab. Blood 2019; 133:2031-2042. [PMID: 30842083 PMCID: PMC6509542 DOI: 10.1182/blood-2018-08-870238] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/26/2019] [Indexed: 12/17/2022] Open
Abstract
Ibrutinib, a once-daily oral inhibitor of Bruton tyrosine kinase, has greatly improved outcomes for patients with chronic lymphocytic leukemia (CLL). The phase 3 RESONATE trial, which compared single-agent ibrutinib to ofatumumab in high-risk, relapsed patients with CLL, provided support for approval of ibrutinib in the United States and Europe. We describe long-term follow-up of patients treated in RESONATE, where continued superiority of progression-free survival (PFS) (hazard ratio [HR], 0.133; 95% confidence interval [CI], 0.099-0.178) was observed. Overall survival benefit continues (HR, 0.591; 95% CI, 0.378-0.926), although with decreased magnitude relative to that seen before crossover to ibrutinib was implemented for patients on ofatumumab (HR, 0.426; 95% CI, 0.220-0.823). Notably, overall response to ibrutinib increased over time, with 91% of patients attaining a response. The PFS benefit with ibrutinib was independent of baseline risk factors, although patients with ≥2 prior therapies had shorter PFS than those with <2 prior therapies, and the presence of TP53 or SF3B1 mutations showed a trend toward shorter PFS vs without these factors. Median duration of ibrutinib was 41 months, with 46% remaining on treatment at a median follow-up of 44 months. Grade ≥3 adverse events generally decreased over time, causing only a small proportion of patients to cease therapy. Ibrutinib was discontinued due to progressive disease in 27% of patients. This long-term study provides support for sustained efficacy and safety of ibrutinib in relapsed/refractory CLL and consideration of study provisions that allow crossover to investigational therapy when benefit has been clearly demonstrated. This trial was registered at www.clinicaltrials.gov as #NCT01578707.
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Affiliation(s)
- John C Byrd
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Peter Hillmen
- The Leeds Teaching Hospitals, St. James Institute of Oncology, Leeds, United Kingdom
| | - Susan O'Brien
- UC Irvine, Chao Family Comprehensive Cancer Center, Irvine, CA
| | | | | | - Steven Coutre
- Stanford University School of Medicine, Stanford, CA
| | - Constantine S Tam
- Department of Haematology, Peter MacCallum Cancer Centre and St. Vincent's Hospital, Melbourne, VIC, Australia
| | | | - Ulrich Jaeger
- Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Paul M Barr
- University of Rochester Medical Center, Rochester, NY
| | - Richard R Furman
- Weill Cornell Medical College/New York Presbyterian Hospital, New York, NY
| | | | | | - Carol Moreno
- Hospital de la Santa Creu Sant Pau, Barcelona, Spain
| | | | - John M Pagel
- Swedish Cancer Institute Hematologic Malignancies Program, Seattle, WA
| | - Jan A Burger
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Sandra Dai
- Pharmacyclics LLC, an AbbVie Company, Sunnyvale, CA; and
| | - Remus Vezan
- Pharmacyclics LLC, an AbbVie Company, Sunnyvale, CA; and
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4
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Mato AR, Foon KA, Feldman T, Schuster SJ, Svoboda J, Chow KF, Valentinetti M, Mrkulic M, Azzollini K, Gadaleta G, Bhattacharyya PK, Zenreich J, Pascual LN, Yannotti K, Kdiry S, Howlett C, Strelec L, Porter D, Bejot C, Goy A. Reduced-dose fludarabine, cyclophosphamide, and rituximab (FCR-Lite) plus lenalidomide, followed by lenalidomide consolidation/maintenance, in previously untreated chronic lymphocytic leukemia. Am J Hematol 2015; 90:487-92. [PMID: 25691474 DOI: 10.1002/ajh.23983] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 01/15/2023]
Abstract
Fludarabine, cyclophosphamide, and rituximab (FCR) remains the standard of care for fit chronic lymphocytic leukemia (CLL) patients requiring first therapy. However, side effects can be significant, and patients with poor risk features have inferior outcomes. The purpose of this study was to evaluate reduced-dose FCR (FCR-Lite) plus lenalidomide (FCR(2) ) followed by lenalidomide maintenance as a strategy to shorten immunochemotherapy in untreated CLL. Patients received four to six cycles of FCR(2) . Patients who were minimal residual disease (MRD) negative in peripheral blood (PB) and bone marrow (BM) initiated 12 months of lenalidomide maintenance after either four or six cycles (based on MRD status). The primary study endpoint was the complete response (CR) rate after four cycles of FCR(2) . Twenty patients were evaluable. After four cycles of FCR(2) , response rates were: CR, 45.0%; CR with incomplete blood count recovery (CRi), 5.0%; partial response (PR), 45.0%; and stable disease (SD), 5.0%. BM and PB samples from 27.8% and 52.9% of patients, respectively, were MRD negative. After six cycles, response rates were: CR, 58.3%; CRi, 16.7%; and PR, 25.0%. BM and PB samples from 50.0% and 72.7% of patients, respectively, were MRD negative. Overall, 75% of evaluable patients achieved a CR or CRi following FCR(2) . After 17.4 months of median follow-up, one progression and one death occurred. Our findings suggest that FCR(2) combines encouraging clinical activity with acceptable toxicity in previously untreated CLL. Lenalidomide can be safely added to FCR and may reduce chemotherapy exposure without compromising outcomes.
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Affiliation(s)
- Anthony R. Mato
- Center for Chronic Lymphocytic Leukemia and Lymphoma Program, Abramson Cancer Center, University of Pennsylvania; Philadelphia Pennsylvania
| | - Kenneth A. Foon
- Department of Medical Affairs; Celgene Corporation; Summit New Jersey
| | - Tatyana Feldman
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Stephen J. Schuster
- Center for Chronic Lymphocytic Leukemia and Lymphoma Program, Abramson Cancer Center, University of Pennsylvania; Philadelphia Pennsylvania
| | - Jakub Svoboda
- Center for Chronic Lymphocytic Leukemia and Lymphoma Program, Abramson Cancer Center, University of Pennsylvania; Philadelphia Pennsylvania
| | - Kar Fai Chow
- Pathology Department; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Marisa Valentinetti
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Mary Mrkulic
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Kelly Azzollini
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Gabriella Gadaleta
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Pritish K. Bhattacharyya
- Pathology Department; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Joshua Zenreich
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Lauren-Nicole Pascual
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Kara Yannotti
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Sabrina Kdiry
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - Christina Howlett
- Department of Pharmacy and Clinical Services; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
- Department of Pharmacy Practice and Administration; Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey; Piscataway New Jersey
| | - Lauren Strelec
- Center for Chronic Lymphocytic Leukemia and Lymphoma Program, Abramson Cancer Center, University of Pennsylvania; Philadelphia Pennsylvania
| | - David Porter
- Center for Chronic Lymphocytic Leukemia and Lymphoma Program, Abramson Cancer Center, University of Pennsylvania; Philadelphia Pennsylvania
| | - Coleen Bejot
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
| | - André Goy
- Lymphoma Division; John Theurer Cancer Center at Hackensack University Medical Center; Hackensack New Jersey
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Ivanescu AM, Oprea M, Momanu R, Coles E, Colita A, Lupu AR. Prognosis Factors in Chronic Lymphocytic Leukemia. J Med Life 2012; 5:48-53. [PMID: 31803286 PMCID: PMC6880207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Chronic lymphocytic leukemia is still one of the most common hematologic malignancies. Finding a curative solution is the objective of numerous followed cases and clinical trials. Diagnosis is based on the interlocking of classic elements and newly identified prognostic factors but time to first treatment is still an open issue. CD38, ZAP 70, IgHV gene mutational status and cytogenetic changes are proven negatively influence the evolution of chronic lymphocytic leukemia. Whether through aggressive rapid evolution or by the difficulty of obtaining a complete remission or risk of early relapse, CLL is still important. Adapted to these prognostic factors, combined therapeutic regimens have proved to be effective in achieving a durable complete remission, new agents, with encouraging partial results, being studied. Requiring initial screening, for comparative purposes, a current and growing importance has minimal residual disease; its absence at the end of treatment represents a strong positive prognostic factor.
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Affiliation(s)
- A M Ivanescu
- Hematology Department, Coltea Clinical Hospital, Bucharest
| | - M Oprea
- Hematology Department, Coltea Clinical Hospital, Bucharest
| | | | - E Coles
- "Carol Davila" University of Medicine and Pharmacy, Bucharest
| | - A Colita
- Hematology Department, Coltea Clinical Hospital, Bucharest
- "Carol Davila" University of Medicine and Pharmacy, Bucharest
| | - A R Lupu
- Hematology Department, Coltea Clinical Hospital, Bucharest
- "Carol Davila" University of Medicine and Pharmacy, Bucharest
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