1
|
Luo Q, Raulston EG, Prado MA, Wu X, Gritsman K, Whalen KS, Yan K, Booth CAG, Xu R, van Galen P, Doench JG, Shimony S, Long HW, Neuberg DS, Paulo JA, Lane AA. Targetable leukaemia dependency on noncanonical PI3Kγ signalling. Nature 2024:10.1038/s41586-024-07410-3. [PMID: 38720074 DOI: 10.1038/s41586-024-07410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Phosphoinositide-3-kinase-γ (PI3Kγ) is implicated as a target to repolarize tumour-associated macrophages and promote antitumour immune responses in solid cancers1-4. However, cancer cell-intrinsic roles of PI3Kγ are unclear. Here, by integrating unbiased genome-wide CRISPR interference screening with functional analyses across acute leukaemias, we define a selective dependency on the PI3Kγ complex in a high-risk subset that includes myeloid, lymphoid and dendritic lineages. This dependency is characterized by innate inflammatory signalling and activation of phosphoinositide 3-kinase regulatory subunit 5 (PIK3R5), which encodes a regulatory subunit of PI3Kγ5 and stabilizes the active enzymatic complex. We identify p21 (RAC1)-activated kinase 1 (PAK1) as a noncanonical substrate of PI3Kγ that mediates this cell-intrinsic dependency and find that dephosphorylation of PAK1 by PI3Kγ inhibition impairs mitochondrial oxidative phosphorylation. Treatment with the selective PI3Kγ inhibitor eganelisib is effective in leukaemias with activated PIK3R5. In addition, the combination of eganelisib and cytarabine prolongs survival over either agent alone, even in patient-derived leukaemia xenografts with low baseline PIK3R5 expression, as residual leukaemia cells after cytarabine treatment have elevated G protein-coupled purinergic receptor activity and PAK1 phosphorylation. Together, our study reveals a targetable dependency on PI3Kγ-PAK1 signalling that is amenable to near-term evaluation in patients with acute leukaemia.
Collapse
Affiliation(s)
- Qingyu Luo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Evangeline G Raulston
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Miguel A Prado
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Xiaowei Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kira Gritsman
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Karley S Whalen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kezhi Yan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Christopher A G Booth
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ran Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Peter van Galen
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shai Shimony
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Hematology, Rabin Medical Center, Tel Aviv Faculty of Medicine, Tel Aviv, Israel
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
2
|
Gorfinkel L, Raghunandan S, Watkins B, Hebert K, Neuberg DS, Bratrude B, Betz K, Yu A, Choi SW, Davis J, Duncan C, Giller R, Grimley M, Harris AC, Jacobsohn D, Lalefar N, Farhadfar N, Pulsipher MA, Shenoy S, Petrovic A, Schultz KR, Yanik GA, Blazar BR, Horan JT, Langston A, Kean LS, Qayed M. Overlap chronic GVHD is associated with adverse survival outcomes compared to classic chronic GVHD. Bone Marrow Transplant 2024; 59:680-687. [PMID: 38383714 DOI: 10.1038/s41409-024-02245-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/20/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Chronic graft-versus-host-disease (cGVHD) is divided into two subtypes: classic (absence of acute GVHD features) and overlap cGVHD ('ocGVHD'), in which both chronic and acute GVHD clinical features are present simultaneously. While worse outcomes with ocGVHD have been reported, there are few recent analyses. We performed a secondary analysis of data from the ABA2 trial (N = 185), in which detailed GVHD data were collected prospectively and systematically adjudicated. Analyses included cumulative incidence of classic versus ocGVHD, their specific organ manifestations, global disease severity scores, non-relapse mortality (NRM), disease-free survival (DFS) and overall survival (OS) in these two cGVHD subtypes. Of 92 patients who developed cGVHD, 35 were classified as ocGVHD. The 1-year cumulative incidence, organ involvement, and global severity of classic and ocGVHD were similar between ABA2 patients receiving CNI/MTX+placebo and CNI/MTX+abatacept; thus, cohorts were combined for ocGVHD evaluation. This analysis identified ocGVHD as having significantly higher severity at presentation and at maximum global severity compared to classic cGVHD. OS and DFS were significantly lower for ocGVHD versus classic cGVHD. OcGVHD is associated with increased cGVHD severity scores, and is associated with decreased OS and DFS compared to classic cGVHD, underscoring the high risks with this cGVHD subtype.
Collapse
Affiliation(s)
- Lev Gorfinkel
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sharmila Raghunandan
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, and Emory University, Atlanta, GA, USA
| | - Benjamin Watkins
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, and Emory University, Atlanta, GA, USA
| | - Kyle Hebert
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brandi Bratrude
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kayla Betz
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alison Yu
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Jeffrey Davis
- BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Christine Duncan
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Roger Giller
- Center for Cancer and Blood Disorders, Children Hospital of Colorado, University of Colorado, Aurora, CO, USA
| | - Michael Grimley
- University of Cincinnati College of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | | | - Nahal Lalefar
- University of California San Francisco, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | | | | | - Shalini Shenoy
- Washington University School of Medicine, St Louis, MO, USA
| | | | - Kirk R Schultz
- BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | | | - Bruce R Blazar
- University of Minnesota, Department of Pediatrics, Division of Blood and Marrow Transplantation, Minneapolis, MN, USA
| | - John T Horan
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amelia Langston
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Leslie S Kean
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Muna Qayed
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, and Emory University, Atlanta, GA, USA.
| |
Collapse
|
3
|
Shimony S, Keating JH, Fay CJ, Luskin MR, Neuberg DS, LeBoeuf NR, Lane AA. Organ Involvement in Adults with BPDCN is Associated with Sun Exposure History, TET2 and RAS Mutations, and Survival. Blood Adv 2024:bloodadvances.2024012797. [PMID: 38603567 DOI: 10.1182/bloodadvances.2024012797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/15/2024] [Accepted: 04/07/2024] [Indexed: 04/13/2024] Open
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) can involve skin, bone marrow (BM), central nervous system (CNS), and non-CNS extramedullary sites. Preclinical models demonstrated clonal advantage of TET2-mutated plasmacytoid dendritic cells exposed to UV radiation. However, whether sun exposure, disease characteristics, and patient survival are clinically related is unclear. We classified 66 BPDCN patients based on organ involvement at diagnosis as skin only (n=19), systemic plus skin (n=33), or systemic only (n=14). BM involvement was absent, microscopic (<5%), or overt (≥5%). UV exposure history was based on clinical and demographic data. Patients with skin only BPDCN were more frequently ≥75 years (47% vs. 19%, p=0.032) and had lower rates of complex karyotype (0 vs. 32%, p=0.022) and mutated NRAS (0 vs. 29%, p=0.044). Conversely, those in the systemic only group had lower UV exposure (23% vs. 59%, p=0.03) and fewer TET2 mutations (33% vs. 72%, p=0.051). With median follow-up of 42 months, the median overall survival (OS) was 23.5, 20.4, and 17.5 months for skin only, systemic plus skin, and systemic only, respectively. Patients with no BM involvement had better OS vs. overt BM involvement (median OS 27.3 vs. 15.0 months, p=0.033) and comparable to those with microscopic BM involvement (27.3 vs. 23.5 months, p=0.6). Overt BM involvement remained significant for OS in a multivariable analysis adjusted for baseline characteristics and treatment. In summary, BPDCN clinical characteristics are associated with disease genetics and survival. These data are useful to estimate prognosis for individual patients and may indicate informative subtyping of BPDCN.
Collapse
Affiliation(s)
- Shai Shimony
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Julia H Keating
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | | | - Marlise R Luskin
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Donna S Neuberg
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Nicole R LeBoeuf
- Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Andrew A Lane
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States
| |
Collapse
|
4
|
Shimony S, Bewersdorf JP, Shallis RM, Liu Y, Schaefer EJ, Zeidan AM, Goldberg AD, Stein EM, Marcucci G, Lindsley RC, Chen EC, Ramos Perez J, Stein A, DeAngelo DJ, Neuberg DS, Stone RM, Ball B, Stahl M. Hypomethylating agents plus venetoclax compared with intensive induction chemotherapy regimens in molecularly defined secondary AML. Leukemia 2024; 38:762-768. [PMID: 38378841 DOI: 10.1038/s41375-024-02175-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Molecularly defined secondary acute myeloid leukemia is associated with a prior myeloid neoplasm and confers a worse prognosis. We compared outcomes of molecularly defined secondary AML patients (n = 395) treated with daunorubicin and cytarabine (7 + 3, n = 167), liposomal daunorubicin and cytarabine (CPX-351, n = 66) or hypomethylating agents (HMA) + venetoclax (VEN) (n = 162). Median overall survival (OS) was comparable between treatment groups among patients aged >60 years. In a multivariable model HMA + VEN vs. 7 + 3 was associated with better OS (hazard ratio [HR] 0.64 [95% confidence interval (CI) 0.42-0.98, p = 0.041]), whereas CPX-351 vs. 7 + 3 was not (HR 0.79 [CI 95% 0.50-1.25, p = 0.31]). Allogeneic hematopoietic stem cell transplantation, BCOR and IDH mutations were associated with improved OS; older age, prior myeloid disease, NRAS/KRAS mutations, EZH2 mutation, and monosomal karyotype were associated with worse OS. When analyzed in each treatment separately, the IDH co-mutations benefit was seen with 7 + 3 and the detrimental effect of NRAS/KRAS co-mutations with HMA + VEN and CPX-351. In pairwise comparisons adjusted for age, HMA + VEN was associated with improved OS vs. 7 + 3 in patients with SF3B1 mutation and improved OS vs. CPX-351 in those with RNA splicing factor mutations. In molecularly defined secondary AML treatment with HMA + VEN might be preferred but could further be guided by co-mutations.
Collapse
Affiliation(s)
- Shai Shimony
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Rabin Medical Center and Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Jan Philipp Bewersdorf
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rory M Shallis
- Yale Cancer Center and Smilow Cancer Hospital, New Haven, CT, USA
| | - Yiwen Liu
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Eva J Schaefer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Amer M Zeidan
- Yale Cancer Center and Smilow Cancer Hospital, New Haven, CT, USA
| | - Aaron D Goldberg
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eytan M Stein
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Guido Marcucci
- Department of Hematology and HCT, City of Hope National Medical Center, Duarte, CA, USA
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Evan C Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jorge Ramos Perez
- Department of Hematology and HCT, City of Hope National Medical Center, Duarte, CA, USA
| | - Anthony Stein
- Department of Hematology and HCT, City of Hope National Medical Center, Duarte, CA, USA
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donna S Neuberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Ball
- Department of Hematology and HCT, City of Hope National Medical Center, Duarte, CA, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
5
|
Langenau DM, Keefe MD, Storer NY, Guyon JR, Kutok JL, Le X, Goessling W, Neuberg DS, Kunkel LM, Zon LI. Corrigendium: Effects of RAS on the genesis of embryonal rhabdomyosarcoma. Genes Dev 2024; 38:289. [PMID: 38631822 PMCID: PMC11065167 DOI: 10.1101/gad.351747.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
|
6
|
Lane AA, Garcia JS, Raulston EG, Garzon JL, Galinsky I, Baxter EW, Leonard R, DeAngelo DJ, Luskin MR, Reilly CR, Stahl M, Stone RM, Vedula RS, Wadleigh MM, Winer ES, Mughal T, Brooks C, Gupta IV, Stevenson KE, Neuberg DS, Ren S, Keating J, Konopleva M, Stein A, Pemmaraju N. Phase 1b trial of tagraxofusp in combination with azacitidine with or without venetoclax in acute myeloid leukemia. Blood Adv 2024; 8:591-602. [PMID: 38052038 PMCID: PMC10837492 DOI: 10.1182/bloodadvances.2023011721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 12/07/2023] Open
Abstract
ABSTRACT CD123, a subunit of the interleukin-3 receptor, is expressed on ∼80% of acute myeloid leukemias (AMLs). Tagraxofusp (TAG), recombinant interleukin-3 fused to a truncated diphtheria toxin payload, is a first-in-class drug targeting CD123 approved for treatment of blastic plasmacytoid dendritic cell neoplasm. We previously found that AMLs with acquired resistance to TAG were re-sensitized by the DNA hypomethylating agent azacitidine (AZA) and that TAG-exposed cells became more dependent on the antiapoptotic molecule BCL-2. Here, we report a phase 1b study in 56 adults with CD123-positive AML or high-risk myelodysplastic syndrome (MDS), first combining TAG with AZA in AML/MDS, and subsequently TAG, AZA, and the BCL-2 inhibitor venetoclax (VEN) in AML. Adverse events with 3-day TAG dosing were as expected, without indication of increased toxicity of TAG or AZA+/-VEN in combination. The recommended phase 2 dose of TAG was 12 μg/kg/day for 3 days, with 7-day AZA +/- 21-day VEN. In an expansion cohort of 26 patients (median age 71) with previously untreated European LeukemiaNet adverse-risk AML (50% TP53 mutated), triplet TAG-AZA-VEN induced response in 69% (n=18/26; 39% complete remission [CR], 19% complete remission with incomplete count recovery [CRi], 12% morphologic leukemia-free state [MLFS]). Among 13 patients with TP53 mutations, 7/13 (54%) achieved CR/CRi/MLFS (CR = 4, CRi = 2, MLFS = 1). Twelve of 17 (71%) tested responders had no flow measurable residual disease. Median overall survival and progression-free survival were 14 months (95% CI, 9.5-NA) and 8.5 months (95% CI, 5.1-NA), respectively. In summary, TAG-AZA-VEN shows encouraging safety and activity in high-risk AML, including TP53-mutated disease, supporting further clinical development of TAG combinations. The study was registered on ClinicalTrials.gov as #NCT03113643.
Collapse
Affiliation(s)
- Andrew A. Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Jacqueline S. Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Evangeline G. Raulston
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Jada L. Garzon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Ilene Galinsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Emilie W. Baxter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Rebecca Leonard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Daniel J. DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Marlise R. Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Christopher R. Reilly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Richard M. Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Rahul S. Vedula
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Martha M. Wadleigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Eric S. Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Tariq Mughal
- Division of Hematology-Oncology, Tufts University School of Medicine, Boston, MA
- Stemline Therapeutics, New York, NY
| | | | | | | | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Siyang Ren
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Julia Keating
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Anthony Stein
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA
| | - Naveen Pemmaraju
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| |
Collapse
|
7
|
Maurer K, Park CY, Mani S, Borji M, Penter L, Jin Y, Zhang JY, Shin C, Brenner JR, Southard J, Krishna S, Lu W, Lyu H, Abbondanza D, Mangum C, Olsen LR, Neuberg DS, Bachireddy P, Farhi SL, Li S, Livak KJ, Ritz J, Soiffer RJ, Wu CJ, Azizi E. Coordinated Immune Cell Networks in the Bone Marrow Microenvironment Define the Graft versus Leukemia Response with Adoptive Cellular Therapy. bioRxiv 2024:2024.02.09.579677. [PMID: 38405900 PMCID: PMC10888840 DOI: 10.1101/2024.02.09.579677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Understanding how intra-tumoral immune populations coordinate to generate anti-tumor responses following therapy can guide precise treatment prioritization. We performed systematic dissection of an established adoptive cellular therapy, donor lymphocyte infusion (DLI), by analyzing 348,905 single-cell transcriptomes from 74 longitudinal bone-marrow samples of 25 patients with relapsed myeloid leukemia; a subset was evaluated by protein-based spatial analysis. In acute myelogenous leukemia (AML) responders, diverse immune cell types within the bone-marrow microenvironment (BME) were predicted to interact with a clonally expanded population of ZNF683 + GZMB + CD8+ cytotoxic T lymphocytes (CTLs) which demonstrated in vitro specificity for autologous leukemia. This population, originating predominantly from the DLI product, expanded concurrently with NK and B cells. AML nonresponder BME revealed a paucity of crosstalk and elevated TIGIT expression in CD8+ CTLs. Our study highlights recipient BME differences as a key determinant of effective anti-leukemia response and opens new opportunities to modulate cell-based leukemia-directed therapy.
Collapse
|
8
|
Bird GH, Patten JJ, Zavadoski W, Barucci N, Godes M, Moyer BM, Owen CD, DaSilva-Jardine P, Neuberg DS, Bowen RA, Davey RA, Walensky LD. A stapled lipopeptide platform for preventing and treating highly pathogenic viruses of pandemic potential. Nat Commun 2024; 15:274. [PMID: 38177138 PMCID: PMC10766962 DOI: 10.1038/s41467-023-44361-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024] Open
Abstract
The continued emergence of highly pathogenic viruses, which either thwart immune- and small molecule-based therapies or lack interventions entirely, mandates alternative approaches, particularly for prompt and facile pre- and post-exposure prophylaxis. Many highly pathogenic viruses, including coronaviruses, employ the six-helix bundle heptad repeat membrane fusion mechanism to achieve infection. Although heptad-repeat-2 decoys can inhibit viral entry by blocking six-helix bundle assembly, the biophysical and pharmacologic liabilities of peptides have hindered their clinical development. Here, we develop a chemically stapled lipopeptide inhibitor of SARS-CoV-2 as proof-of-concept for the platform. We show that our lead compound blocks infection by a spectrum of SARS-CoV-2 variants, exhibits mucosal persistence upon nasal administration, demonstrates enhanced stability compared to prior analogs, and mitigates infection in hamsters. We further demonstrate that our stapled lipopeptide platform yields nanomolar inhibitors of respiratory syncytial, Ebola, and Nipah viruses by targeting heptad-repeat-1 domains, which exhibit strikingly low mutation rates, enabling on-demand therapeutic intervention to combat viral outbreaks.
Collapse
Affiliation(s)
- Gregory H Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - J J Patten
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | | | | | - Marina Godes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Benjamin M Moyer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Callum D Owen
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | | | - Donna S Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Richard A Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| |
Collapse
|
9
|
Penter L, Borji M, Nagler A, Lyu H, Lu WS, Cieri N, Maurer K, Oliveira G, Al'Khafaji AM, Garimella KV, Li S, Neuberg DS, Ritz J, Soiffer RJ, Garcia JS, Livak KJ, Wu CJ. Integrative genotyping of cancer and immune phenotypes by long-read sequencing. Nat Commun 2024; 15:32. [PMID: 38167262 PMCID: PMC10762175 DOI: 10.1038/s41467-023-44137-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to improve cell lineage identification. Due to constraints of short-read sequencing, current methods to detect natural genetic barcodes often require cumbersome primer panels and early commitment to targets. Here we devise a flexible long-read sequencing workflow and analysis pipeline, termed nanoranger, that starts from intermediate single-cell cDNA libraries to detect cell lineage-defining features, including single-nucleotide variants, fusion genes, isoforms, sequences of chimeric antigen and TCRs. Through systematic analysis of these classes of natural 'barcodes', we define the optimal targets for nanoranger, namely those loci close to the 5' end of highly expressed genes with transcript lengths shorter than 4 kB. As proof-of-concept, we apply nanoranger to longitudinal tracking of subclones of acute myeloid leukemia (AML) and describe the heterogeneous isoform landscape of thousands of marrow-infiltrating immune cells. We propose that enhanced cellular genotyping using nanoranger can improve the tracking of single-cell tumor and immune cell co-evolution.
Collapse
Grants
- P01 CA229092 NCI NIH HHS
- P50 CA101942 NCI NIH HHS
- UM1 CA186709 NCI NIH HHS
- U24 CA224316 NCI NIH HHS
- U24 CA224331 NCI NIH HHS
- U24 CA224285 NCI NIH HHS
- R50 CA251956 NCI NIH HHS
- U24 CA224309 NCI NIH HHS
- U24 CA224319 NCI NIH HHS
- K08 CA245209 NCI NIH HHS
- This work was supported by National Institutes of Health, National Cancer Institute grant P01CA229092 (CJW), UM1CA186709 (Principal Investigator: Geoffrey Shapiro), National Cancer Institute Cancer Therapy Evaluation Program, Bristol-Myers Squibb, and LLS Therapy Accelerator Program. L.P. was supported by a research fellowship from the German Research Foundation (DFG, PE 3127/1-1) and is a Scholar of the American Society of Hematology, participant in the BIH Charité Digital Clinician Scientist Program funded by the DFG, the Charité – Universitätsmedizin Berlin, and the Berlin Institute of Health at Charité (BIH) and is supported by the Max-Eder program of the German Cancer Aid. A.A. is supported by the Broad Institute IGNITE award. K.M. is suppored by the ASCO YIA award. G.O. was supported by the Claudia Adams Barr Program for Innovative Cancer Research and by DF/HCC Kidney Cancer SPORE P50 CA101942. S.L. is supported by the National Institutes of Health, National Cancer Institute Research Specialist Award (R50CA251956). JSG is supported by the Conquer Cancer Foundation Career Development Award, Leukemia and Lymphoma Society Translational Research Program Award, and NIH K08CA245209. NCI CTEP provided study drug (Ipilimumab) support. This work was further supported by the CIMAC-CIDC Network. Scientific and financial support for the CIMAC-CIDC Network is provided through National Institutes of Health, National Cancer Institute Cooperative Agreements U24CA224319 (to the Icahn School of Medicine at Mount Sinai CIMAC), U24CA224331 (to the Dana-Farber Cancer Institute CIMAC), U24CA224285 (to the MD Anderson Cancer Center CIMAC), U24CA224309 (to the Stanford University CIMAC), and U24CA224316 (to the CIDC at Dana-Farber Cancer Institute). The CIMAC-CIDC website is found at https://cimac-network.org/.
Collapse
Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Mehdi Borji
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adi Nagler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Haoxiang Lyu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wesley S Lu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katie Maurer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aziz M Al'Khafaji
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Kiran V Garimella
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| |
Collapse
|
10
|
Luo Q, Raulston EG, Prado MA, Wu X, Gritsman K, Yan K, Booth CAG, Xu R, van Galen P, Doench JG, Shimony S, Long HW, Neuberg DS, Paulo JA, Lane AA. Targetable leukemia dependency on noncanonical PI3Kγ signaling. bioRxiv 2023:2023.12.15.571909. [PMID: 38328043 PMCID: PMC10849582 DOI: 10.1101/2023.12.15.571909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Phosphoinositide 3-kinase gamma (PI3Kγ) is implicated as a target to repolarize tumor-associated macrophages and promote anti-tumor immune responses in solid cancers. However, cancer cell-intrinsic roles of PI3Kγ are unclear. Here, by integrating unbiased genome-wide CRISPR interference screening with functional analyses across acute leukemias, we define a selective dependency on the PI3Kγ complex in a high-risk subset that includes myeloid, lymphoid, and dendritic lineages. This dependency is characterized by innate inflammatory signaling and activation of phosphoinositide 3-kinase regulatory subunit 5 ( PIK3R5 ), which encodes a regulatory subunit of PI3Kγ and stabilizes the active enzymatic complex. Mechanistically, we identify p21 (RAC1) activated kinase 1 (PAK1) as a noncanonical substrate of PI3Kγ that mediates this cell-intrinsic dependency independently of Akt kinase. PI3Kγ inhibition dephosphorylates PAK1, activates a transcriptional network of NFκB-related tumor suppressor genes, and impairs mitochondrial oxidative phosphorylation. We find that treatment with the selective PI3Kγ inhibitor eganelisib is effective in leukemias with activated PIK3R5 , either at baseline or by exogenous inflammatory stimulation. Notably, the combination of eganelisib and cytarabine prolongs survival over either agent alone, even in patient-derived leukemia xenografts with low baseline PIK3R5 expression, as residual leukemia cells after cytarabine treatment have elevated G protein-coupled purinergic receptor activity and PAK1 phosphorylation. Taken together, our study reveals a targetable dependency on PI3Kγ/PAK1 signaling that is amenable to near-term evaluation in patients with acute leukemia.
Collapse
|
11
|
Welch JJG, Flamand Y, Stevenson KE, Neuberg DS, Athale UH, Kelly KM, Laverdiere C, Michon B, Place AE, Sallan SE, Silverman LB, Vrooman LM. Impairment of health-related quality of life for children with acute lymphoblastic leukemia over the first year of therapy: A report from the DFCI ALL Consortium. Pediatr Blood Cancer 2023; 70:e30560. [PMID: 37461125 DOI: 10.1002/pbc.30560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/28/2023] [Accepted: 07/02/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Children treated for acute lymphoblastic leukemia (ALL) receive prolonged treatment, resulting in toxicities that affect health-related quality of life (HR-QoL). Longitudinal assessment of HR-QoL allows improved understanding of experiences with ALL. PROCEDURE Parent-proxy and child self-report HR-QoL over the first year of chemotherapy were evaluated in the context of DFCI Protocol 05-001, a phase 3 therapeutic trial for childhood ALL. HR-QoL was assessed with the Pediatric Quality-of-Life inventory (PedsQL) domains for Pain and Hurt, Procedural Anxiety, Treatment Anxiety, Emotional Functioning, General Fatigue, and Sleep/Rest Fatigue. RESULTS Total of 281 subjects participated, with 141 contributing at least one child report and 280 at least one parent report. Children with ALL experienced impairment in HR-QoL by both patient and parent report compared to the published PedsQL reference population at each time point on each subscale. Agreement between parent and child assessment of HR-QoL impairment was high, particularly among those for whom HR-QoL was not impaired. During the consolidation phase, which included intensive asparaginase administration, multivariable models demonstrated more impairment in Treatment Anxiety and Procedural Anxiety for children treated with intramuscular asparaginase than intravenous asparaginase, but randomized groups were otherwise similar in HR-QoL. Impairments in fatigue, both General and Sleep/Rest, were evident throughout and worse during intensive asparaginase therapy. CONCLUSIONS This report examines HR-QoL for children with ALL during treatment longitudinally by parent and patient report across multiple domains. Children with ALL demonstrated substantial impairment in HR-QoL, particularly related to fatigue during intensive consolidation therapy including asparaginase.
Collapse
Affiliation(s)
- Jennifer J G Welch
- Division of Pediatric Hematology/Oncology, Hasbro Children's Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Yael Flamand
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kristen E Stevenson
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Uma H Athale
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Kara M Kelly
- Department of Pediatrics, Roswell Park Comprehensive Cancer Center, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
| | - Caroline Laverdiere
- Department of Pediatrics, Division of Pediatric Hematology Oncology, Charles Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte Justine, Montreal, Quebec, Canada
| | - Bruno Michon
- Division of Hematology-Oncology, Centre Hospitalier Universitaire de Quebec, Quebec City, Quebec, Canada
| | - Andrew E Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Stephen E Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Lynda M Vrooman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| |
Collapse
|
12
|
Shimony S, Flamand Y, Valtis YK, Place AE, Silverman LB, Vrooman LM, Brunner AM, Sallan SE, Stone RM, Wadleigh M, Neuberg DS, DeAngelo DJ, Luskin MR. Effect of BMI on toxicities and survival among adolescents and young adults treated on DFCI Consortium ALL trials. Blood Adv 2023; 7:5234-5245. [PMID: 37432068 PMCID: PMC10500474 DOI: 10.1182/bloodadvances.2023009976] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/24/2023] [Accepted: 05/16/2023] [Indexed: 07/12/2023] Open
Abstract
Adolescent and young adults (AYAs) with acute lymphoblastic leukemia (ALL) treated with asparaginase-containing pediatric regimens are commonly overweight or obese. We studied the association of body mass index (BMI) on outcomes of 388 AYAs aged 15 to 50 years treated on Dana-Farber Cancer Institute (DFCI) consortium regimens (2008-2021). BMI was normal in 207 (53.3%) and overweight/obese in 181 (46.7%). Patients who were overweight or obese experienced higher nonrelapse mortality (NRM; 4-year, 11.7% vs 2.8%, P = .006), worse event-free survival (4-year, 63% vs 77%, P = .003), and worse overall survival (OS; 4-year, 64% vs 83%, P = .0001). Because younger (aged 15-29 years) AYAs more frequently had a normal BMI (79% vs 20%, P < .0001), we conducted separate analyses in each BMI group. We found excellent OS among younger and older (30-50 years) AYAs with normal BMI (4-year OS, 83% vs 85%, P = .89). Conversely, in AYAs who were overweight/obese, worse outcomes were seen in older AYAs (4-year OS, 55% vs 73%, P = .023). Regarding toxicity, AYAs who were overweight/obese experienced higher rates of grade 3/4 hepatotoxicity and hyperglycemia (60.7% vs 42.2%, P = .0005, and 36.4% vs 24.4%, P = .014, respectively) but had comparable rates of hypertriglyceridemia (29.5% vs 24.4%, P = .29). In a multivariable analysis, higher BMI was associated with worse OS, hypertriglyceridemia was associated with improved OS, and age was not associated with OS. In conclusion, among AYAs treated on DFCI Consortium ALL regimens, elevated BMI was associated with increased toxicity, increased NRM, and decreased OS. The deleterious effect of elevated BMI was more pronounced in older AYAs.
Collapse
Affiliation(s)
- Shai Shimony
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Hematology Department, Rabin Medical Center and Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Flamand
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Yannis K. Valtis
- Department of Medicine, Memorial Sloan Kettering Cancer Institute, New York, NY
| | - Andrew E. Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Boston, MA
| | - Lewis B. Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Boston, MA
| | - Lynda M. Vrooman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Boston, MA
| | - Andrew M. Brunner
- Leukemia Department, Hematology/Oncology, Massachusetts General Hospital, Boston, MA
| | - Stephen E. Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children’s Hospital, Boston, MA
| | - Richard M. Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Martha Wadleigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Daniel J. DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Marlise R. Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| |
Collapse
|
13
|
Shimony S, Fell G, Chen EC, Tsai HK, Wadleigh M, Winer ES, Garcia JS, Luskin MR, Stahl M, Neuberg DS, DeAngelo DJ, Lindsley RC, Stone RM. FLT3-ITD does not predict inferior prognosis in acute myeloid leukemia patients aged ≥60 years. Blood Adv 2023; 7:5354-5358. [PMID: 37163357 PMCID: PMC10509660 DOI: 10.1182/bloodadvances.2023009748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/01/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023] Open
Affiliation(s)
- Shai Shimony
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Rabin Medical Center and Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Geoffrey Fell
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Evan C. Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Martha Wadleigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Eric S. Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Marlise R. Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Daniel J. DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Richard M. Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| |
Collapse
|
14
|
Bachireddy P, Azizi E, Burdziak C, Nguyen VN, Ennis CS, Maurer K, Park CY, Choo ZN, Li S, Gohil SH, Ruthen NG, Ge Z, Keskin DB, Cieri N, Livak KJ, Kim HT, Neuberg DS, Soiffer RJ, Ritz J, Alyea EP, Peer D, Wu CJ. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Cell Rep 2023; 42:113011. [PMID: 37556329 PMCID: PMC10618917 DOI: 10.1016/j.celrep.2023.113011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023] Open
Affiliation(s)
| | - Elham Azizi
- Correspondence: (P.B.), (E.A.), (D.P.), (C.J.W.)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dana Peer
- Correspondence: (P.B.), (E.A.), (D.P.), (C.J.W.)
| | | |
Collapse
|
15
|
Takahashi T, Al-Kofahi M, Jaber M, Bratrude B, Betz K, Suessmuth Y, Yu A, Neuberg DS, Choi SW, Davis J, Duncan C, Giller R, Grimley M, Harris AC, Jacobsohn D, Lalefar N, Farhadfar N, Pulsipher MA, Shenoy S, Petrovic A, Schultz KR, Yanik GA, Blazar BR, Horan JT, Watkins B, Langston A, Qayed M, Kean LS. Higher abatacept exposure after transplant decreases acute GVHD risk without increasing adverse events. Blood 2023; 142:700-710. [PMID: 37319437 PMCID: PMC10797507 DOI: 10.1182/blood.2023020035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023] Open
Abstract
In the ABA2 study, the T-cell costimulation blockade agent, abatacept, was safe and effective in preventing acute graft-versus-host disease (aGVHD) after unrelated-donor hematopoietic cell transplant (HCT), leading to US Food and Drug Administration approval. Here, we performed a determination of abatacept pharmacokinetics (PK), which enabled an examination of how abatacept exposure-response relationships affected clinical outcomes. We performed a population PK analysis of IV abatacept using nonlinear mixed-effect modeling and assessed the association between abatacept exposure and key transplant outcomes. We tested the association between the trough after dose 1 (Ctrough_1) and grade (GR) 2 or 4 aGVHD (GR2-4 aGVHD) through day +100. An optimal Ctrough_1 threshold was identified via recursive partitioning and classification tree analysis. This demonstrated that abatacept PK was characterized by a 2-compartment model with first-order elimination. The ABA2 dosing regimen was based on previous work targeting a steady-state abatacept trough of 10 μg/mL. However, a higher Ctrough_1 (≥39 μg/mL, attained in ∼60% of patients on ABA2) was associated with a favorable GR2-4 aGVHD risk (hazard ratio, 0.35; 95% confidence interval, 0.19-0.65; P < .001), with a Ctrough_1 <39 μg/mL associated with GR2-4 aGVHD risk indistinguishable from placebo (P = .37). Importantly, no significant association was found between Ctrough_1 and key safety indicators, including relapse, and cytomegalovirus or Epstein-Barr virus viremia. These data demonstrate that a higher abatacept Ctrough_1 (≥39 μg/mL) was associated with a favorable GR2-4 aGVHD risk, without any observed exposure-toxicity relationships. This trial was registered at www.clinicaltrials.gov as #NCT01743131.
Collapse
Affiliation(s)
- Takuto Takahashi
- Division Hematology/Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN
| | - Mahmoud Al-Kofahi
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN
| | - Mutaz Jaber
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN
| | - Brandi Bratrude
- Division Hematology/Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Kayla Betz
- Division Hematology/Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Yvonne Suessmuth
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA
- Department of Pediatrics, Emory University, Atlanta, GA
| | - Alison Yu
- Division Hematology/Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Sung W. Choi
- Department of Pediatrics, University of Michigan, Ann Arbor, MI
| | - Jeffrey Davis
- BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Christine Duncan
- Division Hematology/Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Roger Giller
- Center for Cancer and Blood Disorders, Children Hospital of Colorado, University of Colorado, Aurora, CO
| | - Michael Grimley
- Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Andrew C. Harris
- Pediatric Bone Marrow Transplant and Cellular Therapy Program, MSK Kids, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Jacobsohn
- Division of Blood and Marrow Transplantation, Center for Cancer and Blood Disorders, Children’s National Health System, Washington, DC
| | - Nahal Lalefar
- Division of Pediatric Hematology/Oncology, UCSF Benioff Children’s Hospital Oakland, University of California San Francisco, Oakland, CA
| | - Nosha Farhadfar
- Division of Hematology/Oncology, University of Florida College of Medicine, Gainesville, FL
| | - Michael A. Pulsipher
- Huntsman Cancer Institute, Spencer Fox Eccles School of Medicine, Primary Children’s Hospital, University of Utah, Salt Lake City, UT
| | - Shalini Shenoy
- Division Hematology/Oncology, Washington University School of Medicine, St Louis, MO
| | - Aleksandra Petrovic
- Department of Pediatrics, Seattle Children’s Hospital and Fred Hutch Cancer Center, Seattle, WA
| | - Kirk R. Schultz
- BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | | | - Bruce R. Blazar
- Division of Blood and Marrow Transplant & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - John T. Horan
- Division Hematology/Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Benjamin Watkins
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA
- Department of Pediatrics, Emory University, Atlanta, GA
| | | | - Muna Qayed
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA
- Department of Pediatrics, Emory University, Atlanta, GA
| | - Leslie S. Kean
- Division Hematology/Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| |
Collapse
|
16
|
Neilan TG, Quinaglia T, Onoue T, Mahmood SS, Drobni ZD, Gilman HK, Smith A, Heemelaar JC, Brahmbhatt P, Ho JS, Sama S, Svoboda J, Neuberg DS, Abramson JS, Hochberg EP, Barnes JA, Armand P, Jacobsen ED, Jacobson CA, Kim AI, Soumerai JD, Han Y, Friedman RS, Lacasce AS, Ky B, Landsburg D, Nasta S, Kwong RY, Jerosch-Herold M, Redd RA, Hua L, Januzzi JL, Asnani A, Mousavi N, Scherrer-Crosbie M. Atorvastatin for Anthracycline-Associated Cardiac Dysfunction: The STOP-CA Randomized Clinical Trial. JAMA 2023; 330:528-536. [PMID: 37552303 PMCID: PMC10410476 DOI: 10.1001/jama.2023.11887] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/12/2023] [Indexed: 08/09/2023]
Abstract
Importance Anthracyclines treat a broad range of cancers. Basic and retrospective clinical data have suggested that use of atorvastatin may be associated with a reduction in cardiac dysfunction due to anthracycline use. Objective To test whether atorvastatin is associated with a reduction in the proportion of patients with lymphoma receiving anthracyclines who develop cardiac dysfunction. Design, Setting, and Participants Double-blind randomized clinical trial conducted at 9 academic medical centers in the US and Canada among 300 patients with lymphoma who were scheduled to receive anthracycline-based chemotherapy. Enrollment occurred between January 25, 2017, and September 10, 2021, with final follow-up on October 10, 2022. Interventions Participants were randomized to receive atorvastatin, 40 mg/d (n = 150), or placebo (n = 150) for 12 months. Main Outcomes and Measures The primary outcome was the proportion of participants with an absolute decline in left ventricular ejection fraction (LVEF) of ≥10% from prior to chemotherapy to a final value of <55% over 12 months. A secondary outcome was the proportion of participants with an absolute decline in LVEF of ≥5% from prior to chemotherapy to a final value of <55% over 12 months. Results Of the 300 participants randomized (mean age, 50 [SD, 17] years; 142 women [47%]), 286 (95%) completed the trial. Among the entire cohort, the baseline mean LVEF was 63% (SD, 4.6%) and the follow-up LVEF was 58% (SD, 5.7%). Study drug adherence was noted in 91% of participants. At 12-month follow-up, 46 (15%) had a decline in LVEF of 10% or greater from prior to chemotherapy to a final value of less than 55%. The incidence of the primary end point was 9% (13/150) in the atorvastatin group and 22% (33/150) in the placebo group (P = .002). The odds of a 10% or greater decline in LVEF to a final value of less than 55% after anthracycline treatment was almost 3 times greater for participants randomized to placebo compared with those randomized to atorvastatin (odds ratio, 2.9; 95% CI, 1.4-6.4). Compared with placebo, atorvastatin also reduced the incidence of the secondary end point (13% vs 29%; P = .001). There were 13 adjudicated heart failure events (4%) over 24 months of follow-up. There was no difference in the rates of incident heart failure between study groups (3% with atorvastatin, 6% with placebo; P = .26). The number of serious related adverse events was low and similar between groups. Conclusions and Relevance Among patients with lymphoma treated with anthracycline-based chemotherapy, atorvastatin reduced the incidence of cardiac dysfunction. This finding may support the use of atorvastatin in patients with lymphoma at high risk of cardiac dysfunction due to anthracycline use. Trial Registration ClinicalTrials.gov Identifier: NCT02943590.
Collapse
Affiliation(s)
- Tomas G. Neilan
- Cardiovascular Imaging Research Center, Division of Cardiology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
- Division of Cardiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Thiago Quinaglia
- Cardiovascular Imaging Research Center, Division of Cardiology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Takeshi Onoue
- Division of Cardiology, Hospital of the University of Pennsylvania, Philadelphia
| | - Syed S. Mahmood
- Cardiovascular Imaging Research Center, Division of Cardiology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Zsofia D. Drobni
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Hannah K. Gilman
- Cardiovascular Imaging Research Center, Division of Cardiology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Amanda Smith
- Division of Cardiology, Hospital of the University of Pennsylvania, Philadelphia
| | - Julius C. Heemelaar
- Cardiovascular Imaging Research Center, Division of Cardiology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Priya Brahmbhatt
- Division of Cardiology, Hospital of the University of Pennsylvania, Philadelphia
| | - Jor Sam Ho
- Cardiovascular Imaging Research Center, Division of Cardiology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Supraja Sama
- Cardiovascular Imaging Research Center, Division of Cardiology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Jakub Svoboda
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jeremy S. Abramson
- Division of Hematology-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Ephraim P. Hochberg
- Division of Hematology-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Jefferey A. Barnes
- Division of Hematology-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Philippe Armand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eric D. Jacobsen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Caron A. Jacobson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Austin I. Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacob D. Soumerai
- Division of Hematology-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Yuchi Han
- Division of Cardiology, Hospital of the University of Pennsylvania, Philadelphia
| | - Robb S. Friedman
- Division of Hematology-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Ann S. Lacasce
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bonnie Ky
- Division of Cardiology, Hospital of the University of Pennsylvania, Philadelphia
| | - Dan Landsburg
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia
| | - Sunita Nasta
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Philadelphia
| | - Raymond Y. Kwong
- Cardiology Division, Brigham and Women’s Hospital, Boston, Massachusetts
| | | | - Robert A. Redd
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lanqi Hua
- Division of Cardiology, Massachusetts General Hospital, Harvard Medical School, Boston
- Cardiac Ultrasound Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston
| | - James L. Januzzi
- Division of Cardiology, Massachusetts General Hospital, Harvard Medical School, Boston
- Heart Failure Trials, Baim Institute for Clinical Research, Boston, Massachusetts
| | - Aarti Asnani
- Division of Cardiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Negareh Mousavi
- Division of Cardiology, McGill University Hospital, Montreal, Quebec, Canada
| | | |
Collapse
|
17
|
Osei MA, Merz LE, Ren S, Neuberg DS, Achebe M, Rodriguez JA, Langer AL. Persistence of Unequal Access to Classical Hematology Telemedicine Visits by Race and Other Demographics During the COVID-19 Pandemic. Telemed J E Health 2023; 29:1266-1271. [PMID: 36607804 PMCID: PMC10495195 DOI: 10.1089/tmj.2022.0505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 01/07/2023] Open
Abstract
Background: Unequal access to telemedicine services exacerbates health inequities and was evident at the start of the COVID-19 pandemic. We sought to explore whether unequal access persisted within a classical hematology division beyond the peak of COVID-19. Methods: Patient demographics by virtual visit type (telephone only [TO] or video only [VO]) between March 2020 and December 2021 were analyzed using adjusted odds ratio (aOR). Results: Of 8,207 patients, 18.4% had TO and 28.4% had VO visits. Fewer Black (21.8%; aOR 0.5 [0.4-0.62]), Hispanic or Latino (18.8%; 0.45 [0.34-0.59]), Spanish-speaking (7.6%; 0.32 [0.19-0.54]), high school (21.2%; 0.64 [0.52-0.78]), and older (24.2%) patients used VO compared with White (30.6%), English-speaking (29.5%), college (31%), postgraduate (34.9%), and younger (35.4%) patients. Conclusions: Groups that historically experience health inequities had fewer VO visits during and beyond the pandemic peak. Thus, there is a need to continue digital inclusion efforts to promote video access equity.
Collapse
Affiliation(s)
- Miriam A. Osei
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lauren E. Merz
- Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Siyang Ren
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Maureen Achebe
- Division of Hematology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jorge A. Rodriguez
- Division of General Internal Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA
| | - Arielle L. Langer
- Division of Hematology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| |
Collapse
|
18
|
Wachter F, Hebert K, Pikman Y, Yang J, Shah B, Bledsoe J, Shimamura A, Neuberg DS, Pollard JA, Lehmann LE. Impact of cytoreduction and remission status on hematopoietic cell transplantation outcomes in pediatric myelodysplastic syndrome and related disorders. Pediatr Blood Cancer 2023:e30530. [PMID: 37369986 DOI: 10.1002/pbc.30530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND The role of cytoreduction prior to hematopoietic cell transplant (HCT) for patients with pediatric myelodysplastic syndrome (MDS) and related disorders remains unclear. PROCEDURE We performed a single-center retrospective analysis of pre-transplant disease management and subsequent HCT outcome for pediatric patients with MDS and related disorders who underwent HCT between 2010 and 2020. RESULTS Total 62 patients (median age 11 years) with idiopathic MDS (n = 16), MDS secondary to an underlying germline condition (n = 11), secondary acute myeloid leukemia (n = 9), myeloproliferative neoplasms (n = 8), and treatment-related myeloid neoplasms (n = 18) received an allogeneic HCT. Cytoreduction prior to HCT was performed in 30/62 (48%) patients; this subset of patients had higher risk disease characteristics, including a higher blast count on presentation. In the overall cohort, use of cytoreduction before HCT was associated with higher rates of relapse (cumulative incidence of relapse 24 months post HCT: 48.1% [27.5%-66.1%]) for those who received cytoreduction versus 16.6% (5.9%-32.1%) for those who did not (p = .03). There was a trend toward decreased overall survival (OS) for those patients who received cytoreduction (24 months post HCT 57.1% vs. 75.3%, respectively; p = .06). OS for patients who received cytoreduction and attained measurable residual disease (MRD) negativity prior to HCT was superior compared to those with persistent disease (24 months post HCT 63.9% [36%-81.2%] vs. 33.3% [7.8%-62.3%], respectively; p = .04). CONCLUSION Cytoreduction did not provide survival benefit in our overall cohort, but its increased use in children with higher risk disease impacted the analysis. Patients receiving cytoreduction and achieving MRD-negative status before HCT demonstrated improved OS compared to those with persistent disease.
Collapse
Affiliation(s)
- Franziska Wachter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kyle Hebert
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jiemin Yang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Binita Shah
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jacob Bledsoe
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Akiko Shimamura
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jessica A Pollard
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Leslie E Lehmann
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
19
|
Penter L, Liu Y, Wolff JO, Yang L, Taing L, Jhaveri A, Southard J, Patel M, Cullen NM, Pfaff KL, Cieri N, Oliveira G, Kim-Schulze S, Ranasinghe S, Leonard R, Robertson T, Morgan EA, Chen HX, Song MH, Thurin M, Li S, Rodig SJ, Cibulskis C, Gabriel S, Bachireddy P, Ritz J, Streicher H, Neuberg DS, Hodi FS, Davids MS, Gnjatic S, Livak KJ, Altreuter J, Michor F, Soiffer RJ, Garcia JS, Wu CJ. Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease. Blood 2023; 141:1817-1830. [PMID: 36706355 PMCID: PMC10122106 DOI: 10.1182/blood.2022018246] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/29/2023] Open
Abstract
The challenge of eradicating leukemia in patients with acute myelogenous leukemia (AML) after initial cytoreduction has motivated modern efforts to combine synergistic active modalities including immunotherapy. Recently, the ETCTN/CTEP 10026 study tested the combination of the DNA methyltransferase inhibitor decitabine together with the immune checkpoint inhibitor ipilimumab for AML/myelodysplastic syndrome (MDS) either after allogeneic hematopoietic stem cell transplantation (HSCT) or in the HSCT-naïve setting. Integrative transcriptome-based analysis of 304 961 individual marrow-infiltrating cells for 18 of 48 subjects treated on study revealed the strong association of response with a high baseline ratio of T to AML cells. Clinical responses were predominantly driven by decitabine-induced cytoreduction. Evidence of immune activation was only apparent after ipilimumab exposure, which altered CD4+ T-cell gene expression, in line with ongoing T-cell differentiation and increased frequency of marrow-infiltrating regulatory T cells. For post-HSCT samples, relapse could be attributed to insufficient clearing of malignant clones in progenitor cell populations. In contrast to AML/MDS bone marrow, the transcriptomes of leukemia cutis samples from patients with durable remission after ipilimumab monotherapy showed evidence of increased infiltration with antigen-experienced resident memory T cells and higher expression of CTLA-4 and FOXP3. Altogether, activity of combined decitabine and ipilimumab is impacted by cellular expression states within the microenvironmental niche of leukemic cells. The inadequate elimination of leukemic progenitors mandates urgent development of novel approaches for targeting these cell populations to generate long-lasting responses. This trial was registered at www.clinicaltrials.gov as #NCT02890329.
Collapse
Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | | | - Lin Yang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Aashna Jhaveri
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Jackson Southard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA
| | - Manishkumar Patel
- Human Immune Monitoring Center at the Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole M. Cullen
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Kathleen L. Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center at the Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Rebecca Leonard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Taylor Robertson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Elizabeth A. Morgan
- Harvard Medical School, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Helen X. Chen
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | - Minkyung H. Song
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | - Magdalena Thurin
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA
| | - Scott J. Rodig
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Carrie Cibulskis
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Stacey Gabriel
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | | | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Howard Streicher
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - F. Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sacha Gnjatic
- Human Immune Monitoring Center at the Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kenneth J. Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA
| | | | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Robert J. Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Jacqueline S. Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| |
Collapse
|
20
|
Fell GG, Nathan DG, Neuberg DS. Correcting the Record on Anemia of Aging--a Statistical Reanalysis. Blood Adv 2023:495203. [PMID: 37013955 PMCID: PMC10365935 DOI: 10.1182/bloodadvances.2023010311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Affiliation(s)
- Geoffrey G Fell
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | | | - Donna S Neuberg
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| |
Collapse
|
21
|
Penter L, ten Hacken E, Southard J, Lareau CA, Ludwig LS, Li S, Neuberg DS, Livak KJ, Wu CJ. Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models. Cancer Res 2023; 83:667-672. [PMID: 36469010 PMCID: PMC9988704 DOI: 10.1158/0008-5472.can-22-0275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/13/2022] [Accepted: 06/07/2022] [Indexed: 12/13/2022]
Abstract
Murine models are indispensable tools for functional genomic studies and preclinical testing of novel therapeutic approaches. Mitochondrial single-cell assay for transposase-accessible chromatin using sequencing (mtscATAC-seq) enables the dissection of cellular heterogeneity and clonal dynamics by capturing chromatin accessibility, copy-number variations (CNV), and mitochondrial DNA (mtDNA) mutations, yet its applicability to murine studies remains unexplored. By leveraging mtscATAC-seq in novel chronic lymphocytic leukemia and Richter syndrome mouse models, we report the detection of mtDNA mutations, particularly in highly proliferative murine cells, alongside CNV and chromatin state changes indicative of clonal evolution upon secondary transplant. This study thus demonstrates the feasibility and utility of multi-modal single-cell and natural barcoding approaches to characterize murine cancer models. SIGNIFICANCE mtDNA mutations can serve as natural barcodes to enable lineage tracing in murine cancer models, which can be used to provide new insights into disease biology and to identify therapeutic vulnerabilities.
Collapse
Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Elisa ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Jackson Southard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Caleb A. Lareau
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Leif S. Ludwig
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenneth J. Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
22
|
ten Hacken E, Sewastianik T, Yin S, Hoffmann GB, Gruber M, Clement K, Penter L, Redd RA, Ruthen N, Hergalant S, Sholokhova A, Fell G, Parry EM, Broséus J, Guieze R, Lucas F, Hernández-Sánchez M, Baranowski K, Southard J, Joyal H, Billington L, Regis FFD, Witten E, Uduman M, Knisbacher BA, Li S, Lyu H, Vaisitti T, Deaglio S, Inghirami G, Feugier P, Stilgenbauer S, Tausch E, Davids MS, Getz G, Livak KJ, Bozic I, Neuberg DS, Carrasco RD, Wu CJ. In Vivo Modeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities. Blood Cancer Discov 2023; 4:150-169. [PMID: 36468984 PMCID: PMC9975769 DOI: 10.1158/2643-3230.bcd-22-0082] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/16/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Transformation to aggressive disease histologies generates formidable clinical challenges across cancers, but biological insights remain few. We modeled the genetic heterogeneity of chronic lymphocytic leukemia (CLL) through multiplexed in vivo CRISPR-Cas9 B-cell editing of recurrent CLL loss-of-function drivers in mice and recapitulated the process of transformation from indolent CLL into large cell lymphoma [i.e., Richter syndrome (RS)]. Evolutionary trajectories of 64 mice carrying diverse combinatorial gene assortments revealed coselection of mutations in Trp53, Mga, and Chd2 and the dual impact of clonal Mga/Chd2 mutations on E2F/MYC and interferon signaling dysregulation. Comparative human and murine RS analyses demonstrated tonic PI3K signaling as a key feature of transformed disease, with constitutive activation of the AKT and S6 kinases, downmodulation of the PTEN phosphatase, and convergent activation of MYC/PI3K transcriptional programs underlying enhanced sensitivity to MYC/mTOR/PI3K inhibition. This robust experimental system presents a unique framework to study lymphoid biology and therapy. SIGNIFICANCE Mouse models reflective of the genetic complexity and heterogeneity of human tumors remain few, including those able to recapitulate transformation to aggressive disease histologies. Herein, we model CLL transformation into RS through multiplexed in vivo gene editing, providing key insight into the pathophysiology and therapeutic vulnerabilities of transformed disease. This article is highlighted in the In This Issue feature, p. 101.
Collapse
Affiliation(s)
- Elisa ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Tomasz Sewastianik
- Harvard Medical School, Boston, Massachusetts
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | | | - Michaela Gruber
- CEMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité – Universitätsmedizin Berlin (corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany
| | - Robert A. Redd
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Neil Ruthen
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sébastien Hergalant
- Inserm UMRS1256 Nutrition-Génétique et Exposition aux Risques Environnementaux (N-GERE), Université de Lorraine, Nancy, France
| | - Alanna Sholokhova
- Department of Applied Mathematics, University of Washington, Seattle, Washington
| | - Geoffrey Fell
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Erin M. Parry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Julien Broséus
- Inserm UMRS1256 Nutrition-Génétique et Exposition aux Risques Environnementaux (N-GERE), Université de Lorraine, Nancy, France
- Université de Lorraine, CHRU-Nancy, Service d'Hématologie Biologique, Pôle Laboratoires, Nancy, France
| | | | - Fabienne Lucas
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, Madrid, Spain
| | - Kaitlyn Baranowski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jackson Southard
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Heather Joyal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Leah Billington
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Fara Faye D. Regis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elizabeth Witten
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mohamed Uduman
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Binyamin A. Knisbacher
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Haoxiang Lyu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tiziana Vaisitti
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Silvia Deaglio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Pierre Feugier
- Inserm UMRS1256 Nutrition-Génétique et Exposition aux Risques Environnementaux (N-GERE), Université de Lorraine, Nancy, France
- Université de Lorraine, CHRU-Nancy, Service d'Hématologie Biologique, Pôle Laboratoires, Nancy, France
| | - Stephan Stilgenbauer
- Department III of Internal Medicine III, Division of CLL, Ulm University, Ulm, Germany
| | - Eugen Tausch
- Department III of Internal Medicine III, Division of CLL, Ulm University, Ulm, Germany
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Kenneth J. Livak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ivana Bozic
- Department of Applied Mathematics, University of Washington, Seattle, Washington
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ruben D. Carrasco
- Harvard Medical School, Boston, Massachusetts
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| |
Collapse
|
23
|
Knisbacher BA, Lin Z, Hahn CK, Nadeu F, Duran-Ferrer M, Stevenson KE, Tausch E, Delgado J, Barbera-Mourelle A, Taylor-Weiner A, Bousquets-Muñoz P, Diaz-Navarro A, Dunford A, Anand S, Kretzmer H, Gutierrez-Abril J, López-Tamargo S, Fernandes SM, Sun C, Sivina M, Rassenti LZ, Schneider C, Li S, Parida L, Meissner A, Aguet F, Burger JA, Wiestner A, Kipps TJ, Brown JR, Hallek M, Stewart C, Neuberg DS, Martín-Subero JI, Puente XS, Stilgenbauer S, Wu CJ, Campo E, Getz G. Molecular map of chronic lymphocytic leukemia and its impact on outcome. Nat Genet 2022; 54:1664-1674. [PMID: 35927489 PMCID: PMC10084830 DOI: 10.1038/s41588-022-01140-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/21/2022] [Indexed: 01/02/2023]
Abstract
Recent advances in cancer characterization have consistently revealed marked heterogeneity, impeding the completion of integrated molecular and clinical maps for each malignancy. Here, we focus on chronic lymphocytic leukemia (CLL), a B cell neoplasm with variable natural history that is conventionally categorized into two subtypes distinguished by extent of somatic mutations in the heavy-chain variable region of immunoglobulin genes (IGHV). To build the 'CLL map,' we integrated genomic, transcriptomic and epigenomic data from 1,148 patients. We identified 202 candidate genetic drivers of CLL (109 new) and refined the characterization of IGHV subtypes, which revealed distinct genomic landscapes and leukemogenic trajectories. Discovery of new gene expression subtypes further subcategorized this neoplasm and proved to be independent prognostic factors. Clinical outcomes were associated with a combination of genetic, epigenetic and gene expression features, further advancing our prognostic paradigm. Overall, this work reveals fresh insights into CLL oncogenesis and prognostication.
Collapse
Affiliation(s)
| | - Ziao Lin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard University, Cambridge, MA, USA
| | - Cynthia K Hahn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Alex Barbera-Mourelle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | - Pablo Bousquets-Muñoz
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Ander Diaz-Navarro
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | | | | | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jesus Gutierrez-Abril
- Computational Oncology Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sara López-Tamargo
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clare Sun
- Laboratory of Lymphoid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mariela Sivina
- Department of Leukemia, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Laura Z Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | | | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Jan A Burger
- Department of Leukemia, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Adrian Wiestner
- Laboratory of Lymphoid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michael Hallek
- Center for Molecular Medicine, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf and German CLL Study Group, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | | | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Hematopathology Section, Laboratory of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
24
|
Fell G, Rosko AE, Abel GA, Dumontier C, Higby KJ, Murillo A, Neuberg DS, Burd CE, Lane AA. Peripheral blood CD3 + T-cell gene expression biomarkers correlate with clinical frailty in patients with haematological malignancies. Br J Haematol 2022; 199:100-105. [PMID: 35766906 PMCID: PMC10462450 DOI: 10.1111/bjh.18336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 11/26/2022]
Abstract
Older patients with cancer often receive treatment regimens based on their age without considering other objective factors that may influence outcomes. Assessment of frailty can identify older patients who are robust and therefore more likely to benefit from intensive treatment, or conversely, frail and might instead be offered alternative approaches. However, such assessment requires specialised training and dedicated clinical resources. Alternative quantitative biomarkers associated with frailty are lacking. Here, we asked if expression signatures of 74 immune cell, ageing, and senescence-related messenger RNAs in purified peripheral blood T cells could identify associations with clinical frailty in patients with haematological malignancies. We studied 69 patients between the ages of 36 and 92 years (median 76 years) with leukaemia, lymphoma, or multiple myeloma, across two institutions. Expression of four genes (aryl hydrocarbon receptor [AHR], CD27, CD28, and interleukin-2 receptor subunit alpha [IL2RA; CD25]) in T cells was associated with frailty, independent of age. An expression-based regression model had 76% sensitivity and 90% specificity to assign a patient as robust. These data identify measurable peripheral blood correlates of clinical frailty and suggest biomarkers for future prospective assessment.
Collapse
Affiliation(s)
- Geoffrey Fell
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ashley E. Rosko
- Division of Hematology, The Ohio State University, Columbus, Ohio, USA
| | - Gregory A. Abel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Clark Dumontier
- New England Geriatric Research Education and Clinical Center, VA Boston Healthcare System, Boston, Massachusetts, USA
- Division of Aging, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kelly J. Higby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Anays Murillo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Christin E. Burd
- Departments of Molecular Genetics; Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Andrew A. Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
25
|
Athale UH, Flamand Y, Blonquist T, Stevenson KE, Spira M, Asselin BL, Clavell LA, Cole PD, Kelly KM, Laverdiere C, Leclerc JM, Michon B, Schorin MA, Welch JJG, Harris MH, Neuberg DS, Sallan SE, Silverman LB. Predictors of thrombosis in children receiving therapy for acute lymphoblastic leukemia: Results from Dana-Farber Cancer Institute ALL Consortium trial 05-001. Pediatr Blood Cancer 2022; 69:e29581. [PMID: 35316569 DOI: 10.1002/pbc.29581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/20/2021] [Accepted: 01/06/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND/OBJECTIVES Although thromboembolism (TE) is a serious complication in patients with acute lymphoblastic leukemia (ALL), thromboprophylaxis is not commonly used due to the inherent bleeding risk in this population. Identifying prothrombotic risk factors will help target thromboprophylaxis to those at highest thrombotic risk. We aimed to define predictors and the impact of TE on ALL outcome in children (1-18 years) treated on the Dana-Farber Cancer Institute ALL 05-001 trial. METHODS Clinical and laboratory data including TE events were prospectively collected. PCR-based allelic discrimination assay identified single-nucleotide polymorphisms (SNP) for prothrombin G20210A (rs1799963) and Factor V G1691A (rs6025). Univariate and multivariable competing risk regression models evaluated the effect of diagnostic clinical (age, sex, body mass index, ALL-immunophenotype, risk group) and laboratory variables (presenting leukocyte count, blood group, SNPs) on the cumulative incidence of TE. Cox regression modeling explored the impact of TE on survival. RESULTS Of 794 patients [median age 4.97 (range, 1.04-17.96) years; males 441], 100 developed TE; 25-month cumulative incidence 13.0% (95% CI, 10.7%-15.5%). Univariate analyses identified older age (≥10 years), presenting leucocyte count, T-ALL, high-risk ALL, and non-O blood group as risk factors. Age and non-O blood group were independent predictors of TE on multivariable regression; the blood group impact being most evident in patients 1-5 years of age (P = 0.011). TE did not impact survival. Induction TE was independently associated with induction failure (OR 6.45; 95% CI, 1.64-25.47; P = 0.008). CONCLUSION We recommend further evaluation of these risk factors and consideration of thromboprophylaxis for patients ≥10 years (especially those ≥15 years) when receiving asparaginase.
Collapse
Affiliation(s)
- Uma H Athale
- Division of Hematology/Oncology, McMaster Children's Hospital, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Yael Flamand
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Traci Blonquist
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kristen E Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Menachem Spira
- Department of Pediatrics, New York-Presbyterian Hospital, New York, New York
| | - Barbara L Asselin
- Department of Pediatrics, University of Rochester Medical Center and School of Medicine, Rochester, New York
| | | | - Peter D Cole
- Division of Pediatric Hematology/Oncology, Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Kara M Kelly
- Roswell Park Comprehensive Cancer Center, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Caroline Laverdiere
- Hematology-Oncology Division, Charles Bruneau Cancer Center, Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Jean-Marie Leclerc
- Hematology-Oncology Division, Charles Bruneau Cancer Center, Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Bruno Michon
- Centre Hospitalier Universitaire de Quebec, Sainte-Foy, Quebec, Canada
| | | | - Jennifer J G Welch
- Pediatric Hematology Oncology, Hasbro Children's Hospital/Brown University, Providence, Rhode Island
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Donna S Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stephen E Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, Massachusetts
| |
Collapse
|
26
|
Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Yadollahpour P, Reeves JW, Mohan R, Drokhlyansky E, Van Wittenberghe N, Ashenberg O, Farhi SL, Schapiro D, Divakar P, Miller E, Zollinger DR, Eng G, Schenkel JM, Su J, Shiau C, Yu P, Freed-Pastor WA, Abbondanza D, Mehta A, Gould J, Lambden C, Porter CBM, Tsankov A, Dionne D, Waldman J, Cuoco MS, Nguyen L, Delorey T, Phillips D, Barth JL, Kem M, Rodrigues C, Ciprani D, Roldan J, Zelga P, Jorgji V, Chen JH, Ely Z, Zhao D, Fuhrman K, Fropf R, Beechem JM, Loeffler JS, Ryan DP, Weekes CD, Ferrone CR, Qadan M, Aryee MJ, Jain RK, Neuberg DS, Wo JY, Hong TS, Xavier R, Aguirre AJ, Rozenblatt-Rosen O, Mino-Kenudson M, Castillo CFD, Liss AS, Ting DT, Jacks T, Regev A. Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment. Nat Genet 2022; 54:1178-1191. [PMID: 35902743 DOI: 10.1038/s41588-022-01134-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 06/16/2022] [Indexed: 12/24/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here, we construct a high-resolution molecular landscape of the cellular subtypes and spatial communities that compose PDAC using single-nucleus RNA sequencing and whole-transcriptome digital spatial profiling (DSP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment naive. We uncovered recurrent expression programs across malignant cells and fibroblasts, including a newly identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities with distinct contributions from malignant, fibroblast and immune subtypes: classical, squamoid-basaloid and treatment enriched. Our refined molecular and cellular taxonomy can provide a framework for stratification in clinical trials and serve as a roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.
Collapse
Affiliation(s)
- William L Hwang
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karthik A Jagadeesh
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jimmy A Guo
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,School of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Hannah I Hoffman
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard-MIT MD/PhD and Health Sciences and Technology Program, Harvard Medical School, Boston, MA, USA
| | - Payman Yadollahpour
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Rahul Mohan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Denis Schapiro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Institute for Computational Biomedicine and Institute of Pathology, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
| | | | | | | | - George Eng
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason M Schenkel
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer Su
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carina Shiau
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick Yu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William A Freed-Pastor
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Arnav Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Joshua Gould
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | | | - Julia Waldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lan Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Toni Delorey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Devan Phillips
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Jaimie L Barth
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marina Kem
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clifton Rodrigues
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Debora Ciprani
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jorge Roldan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Piotr Zelga
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vjola Jorgji
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan H Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zackery Ely
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | | | - Jay S Loeffler
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David P Ryan
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Colin D Weekes
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Motaz Qadan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rakesh K Jain
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jennifer Y Wo
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theodore S Hong
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew J Aguirre
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Andrew S Liss
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David T Ting
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Genentech, South San Francisco, CA, USA.
| |
Collapse
|
27
|
Purroy N, Tong YE, Lemvigh CK, Cieri N, Li S, Parry EM, Zhang W, Rassenti LZ, Kipps TJ, Slager SL, Kay NE, Lesnick C, Shanafelt TD, Ghia P, Scarfò L, Livak KJ, Kharchenko PV, Neuberg DS, Olsen LR, Fan J, Gohil SH, Wu CJ. Single-cell analysis reveals immune dysfunction from the earliest stages of CLL that can be reversed by ibrutinib. Blood 2022; 139:2252-2256. [PMID: 35020831 PMCID: PMC8990375 DOI: 10.1182/blood.2021013926] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/22/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Noelia Purroy
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
| | - Yuzhou Evelyn Tong
- Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
- Program in Health Sciences and Technology, Harvard Medical School-Massachusetts Institute of Technology, Boston, MA
| | - Camilla K Lemvigh
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicoletta Cieri
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
| | - Shuqiang Li
- Broad Institute, Cambridge, MA
- Translational Immunogenomics Laboratory, Dana Farber Cancer Institute, Boston, MA
| | - Erin M Parry
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
| | - Wandi Zhang
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Laura Z Rassenti
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Thomas J Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | | | - Neil E Kay
- Department of Health Sciences Research and
- Department of Medicine, Mayo Clinic, Rochester, MN
| | | | | | - Paolo Ghia
- Division of Experimental Oncology, Department of Onco-Hematology, Università Vita-Salute San Raffaele-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan Italy
| | - Lydia Scarfò
- Division of Experimental Oncology, Department of Onco-Hematology, Università Vita-Salute San Raffaele-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan Italy
| | - Kenneth J Livak
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Translational Immunogenomics Laboratory, Dana Farber Cancer Institute, Boston, MA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Lars Rønn Olsen
- Program in Health Sciences and Technology, Harvard Medical School-Massachusetts Institute of Technology, Boston, MA
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
| | - Satyen H Gohil
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
- Department of Academic Haematology, University College London, United Kingdom; and
| | - Catherine J Wu
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| |
Collapse
|
28
|
Biran A, Yin S, Kretzmer H, Ten Hacken E, Parvin S, Lucas F, Uduman M, Gutierrez C, Dangle N, Billington L, Regis FF, Rassenti LZ, Mohammad A, Hoffmann GB, Stevenson K, Zheng M, Witten E, Fernandes SM, Tausch E, Sun C, Stilgenbauer S, Brown JR, Kipps TJ, Aster JC, Gnirke A, Neuberg DS, Letai A, Wang L, Carrasco RD, Meissner A, Wu CJ. Activation of Notch and Myc Signaling via B-cell-Restricted Depletion of Dnmt3a Generates a Consistent Murine Model of Chronic Lymphocytic Leukemia. Cancer Res 2021; 81:6117-6130. [PMID: 34686499 PMCID: PMC8678341 DOI: 10.1158/0008-5472.can-21-1273] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/18/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by disordered DNA methylation, suggesting these epigenetic changes might play a critical role in disease onset and progression. The methyltransferase DNMT3A is a key regulator of DNA methylation. Although DNMT3A somatic mutations in CLL are rare, we found that low DNMT3A expression is associated with more aggressive disease. A conditional knockout mouse model showed that homozygous depletion of Dnmt3a from B cells results in the development of CLL with 100% penetrance at a median age of onset of 5.3 months, and heterozygous Dnmt3a depletion yields a disease penetrance of 89% with a median onset at 18.5 months, confirming its role as a haploinsufficient tumor suppressor. B1a cells were confirmed as the cell of origin of disease in this model, and Dnmt3a depletion resulted in focal hypomethylation and activation of Notch and Myc signaling. Amplification of chromosome 15 containing the Myc gene was detected in all CLL mice tested, and infiltration of high-Myc-expressing CLL cells in the spleen was observed. Notably, hyperactivation of Notch and Myc signaling was exclusively observed in the Dnmt3a CLL mice, but not in three other CLL mouse models tested (Sf3b1-Atm, Ikzf3, and MDR), and Dnmt3a-depleted CLL were sensitive to pharmacologic inhibition of Notch signaling in vitro and in vivo. Consistent with these findings, human CLL samples with lower DNMT3A expression were more sensitive to Notch inhibition than those with higher DNMT3A expression. Altogether, these results suggest that Dnmt3a depletion induces CLL that is highly dependent on activation of Notch and Myc signaling. SIGNIFICANCE: Loss of DNMT3A expression is a driving event in CLL and is associated with aggressive disease, activation of Notch and Myc signaling, and enhanced sensitivity to Notch inhibition.
Collapse
MESH Headings
- Animals
- Anti-Bacterial Agents/pharmacology
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Proliferation
- DNA Methyltransferase 3A/genetics
- DNA Methyltransferase 3A/metabolism
- DNA Methyltransferase 3A/physiology
- Daptomycin/pharmacology
- Disease Models, Animal
- Drug Resistance, Neoplasm
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Mice
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Prognosis
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- RNA-Seq
- Receptors, Notch/antagonists & inhibitors
- Receptors, Notch/genetics
- Receptors, Notch/metabolism
- Survival Rate
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Anat Biran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Elisa Ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Salma Parvin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Fabienne Lucas
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mohamed Uduman
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Catherine Gutierrez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Nathan Dangle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Leah Billington
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Fara Faye Regis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Laura Z Rassenti
- Moores Cancer Center, University of California San Diego Health, La Jolla, California
| | - Arman Mohammad
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Kristen Stevenson
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mei Zheng
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Witten
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Thomas J Kipps
- Moores Cancer Center, University of California San Diego Health, La Jolla, California
| | - John C Aster
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Ruben D Carrasco
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| |
Collapse
|
29
|
Wood WA, Marks P, Plovnick RM, Hewitt K, Neuberg DS, Walters S, Dolan BK, Tucker EA, Abrams CS, Thompson AA, Anderson KC, Kluetz P, Farrell A, Rivera D, Gertzog M, Pappas G. ASH Research Collaborative: a real-world data infrastructure to support real-world evidence development and learning healthcare systems in hematology. Blood Adv 2021; 5:5429-5438. [PMID: 34673922 PMCID: PMC9153041 DOI: 10.1182/bloodadvances.2021005902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/02/2021] [Indexed: 12/03/2022] Open
Abstract
The ASH Research Collaborative is a nonprofit organization established through the American Society of Hematology's commitment to patients with hematologic conditions and the science that informs clinical care and future therapies. The ASH Research Collaborative houses 2 major initiatives: (1) the Data Hub and (2) the Clinical Trials Network (CTN). The Data Hub is a program for hematologic diseases in which networks of clinical care delivery sites are developed in specific disease areas, with individual patient data contributed through electronic health record (EHR) integration, direct data entry through electronic data capture, and external data sources. Disease-specific data models are constructed so that data can be assembled into analytic datasets and used to enhance clinical care through dashboards and other mechanisms. Initial models have been built in multiple myeloma (MM) and sickle cell disease (SCD) using the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) and Fast Healthcare Interoperability Resources (FHIR) standards. The Data Hub also provides a framework for development of disease-specific learning communities (LC) and testing of health care delivery strategies. The ASH Research Collaborative SCD CTN is a clinical trials accelerator that creates efficiencies in the execution of multicenter clinical trials and has been initially developed for SCD. Both components are operational, with the Data Hub actively aggregating source data and the SCD CTN reviewing study candidates. This manuscript describes processes involved in developing core features of the ASH Research Collaborative to inform the stakeholder community in preparation for expansion to additional disease areas.
Collapse
Affiliation(s)
- William A Wood
- Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Peter Marks
- U.S. Food and Drug Administration, Silver Spring, MD
| | | | | | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | | | - Brendan K Dolan
- The University of Wisconsin School of Medicine and Public Health, Madison, WI
| | | | - Charles S Abrams
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Kenneth C Anderson
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Paul Kluetz
- U.S. Food and Drug Administration, Silver Spring, MD
| | - Ann Farrell
- U.S. Food and Drug Administration, Silver Spring, MD
| | - Donna Rivera
- U.S. Food and Drug Administration, Silver Spring, MD
| | | | | |
Collapse
|
30
|
Penter L, Gohil SH, Lareau C, Ludwig LS, Parry EM, Huang T, Li S, Zhang W, Livitz D, Leshchiner I, Parida L, Getz G, Rassenti LZ, Kipps TJ, Brown JR, Davids MS, Neuberg DS, Livak KJ, Sankaran VG, Wu CJ. Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History. Cancer Discov 2021; 11:3048-3063. [PMID: 34112698 PMCID: PMC8660953 DOI: 10.1158/2159-8290.cd-21-0276] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/04/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022]
Abstract
While cancers evolve during disease progression and in response to therapy, temporal dynamics remain difficult to study in humans due to the lack of consistent barcodes marking individual clones in vivo. We employ mitochondrial single-cell assay for transposase-accessible chromatin with sequencing to profile 163,279 cells from 9 patients with chronic lymphocytic leukemia (CLL) collected across disease course and utilize mitochondrial DNA (mtDNA) mutations as natural genetic markers of cancer clones. We observe stable propagation of mtDNA mutations over years in the absence of strong selective pressure, indicating clonal persistence, but dramatic changes following tight bottlenecks, including disease transformation and relapse posttherapy, paralleled by acquisition of copy-number variants and changes in chromatin accessibility and gene expression. Furthermore, we link CLL subclones to distinct chromatin states, providing insight into nongenetic sources of relapse. mtDNA mutations thus mirror disease history and provide naturally occurring genetic barcodes to enable patient-specific study of cancer subclonal dynamics. SIGNIFICANCE Single-cell multi-omic profiling of CLL reveals the utility of somatic mtDNA mutations as in vivo barcodes, which mark subclones that can evolve over time along with changes in accessible chromatin and gene expression profiles to capture dynamics of disease evolution. See related commentary by Hilton and Scott, p. 2965. This article is highlighted in the In This Issue feature, p. 2945.
Collapse
Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Hematology, Oncology, and Tumor Immunology, Charité – Universitätsmedizin Berlin (CVK), Berlin, Germany
| | - Satyen H. Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Academic Haematology, University College London Cancer Institute, London, United Kingdom
- Department of Haematology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Caleb Lareau
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Leif S. Ludwig
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Berlin Institute of Health at Charité — Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany
| | - Erin M. Parry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Teddy Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Dimitri Livitz
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Ignaty Leshchiner
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Laxmi Parida
- IBM TJ Watson Research Center, Yorktown Heights, New York, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Laura Z. Rassenti
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenneth J. Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Vijay G. Sankaran
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| |
Collapse
|
31
|
Bachireddy P, Azizi E, Burdziak C, Nguyen VN, Ennis CS, Maurer K, Park CY, Choo ZN, Li S, Gohil SH, Ruthen NG, Ge Z, Keskin DB, Cieri N, Livak KJ, Kim HT, Neuberg DS, Soiffer RJ, Ritz J, Alyea EP, Pe'er D, Wu CJ. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Cell Rep 2021; 37:109992. [PMID: 34758319 PMCID: PMC9035342 DOI: 10.1016/j.celrep.2021.109992] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 06/23/2021] [Accepted: 10/21/2021] [Indexed: 01/06/2023] Open
Abstract
To elucidate mechanisms by which T cells eliminate leukemia, we study donor lymphocyte infusion (DLI), an established immunotherapy for relapsed leukemia. We model T cell dynamics by integrating longitudinal, multimodal data from 94,517 bone marrow-derived single T cell transcriptomes in addition to chromatin accessibility and single T cell receptor sequencing from patients undergoing DLI. We find that responsive tumors are defined by enrichment of late-differentiated T cells before DLI and rapid, durable expansion of early differentiated T cells after treatment, highly similar to "terminal" and "precursor" exhausted subsets, respectively. Resistance, in contrast, is defined by heterogeneous T cell dysfunction. Surprisingly, early differentiated T cells in responders mainly originate from pre-existing and novel clonotypes recruited to the leukemic microenvironment, rather than the infusion. Our work provides a paradigm for analyzing longitudinal single-cell profiling of scenarios beyond adoptive cell therapy and introduces Symphony, a Bayesian approach to infer regulatory circuitry underlying T cell subsets, with broad relevance to exhaustion antagonists across cancers.
Collapse
Affiliation(s)
- Pavan Bachireddy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Hematopoietic Biology & Malignancy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Cancer Prevention and Research Institute of Texas (CPRIT) Scholar in Cancer Research, Austin, TX 78701, USA.
| | - Elham Azizi
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Biomedical Engineering and Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA.
| | - Cassandra Burdziak
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Vinhkhang N Nguyen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Christina S Ennis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Katie Maurer
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Cameron Y Park
- Department of Biomedical Engineering and Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Zi-Ning Choo
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Satyen H Gohil
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Neil G Ruthen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zhongqi Ge
- Department of Hematopoietic Biology & Malignancy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Derin B Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicoletta Cieri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Haesook T Kim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Edwin P Alyea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Parker Institute of Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
32
|
Beauchamp EM, Leventhal M, Bernard E, Hoppe ER, Todisco G, Creignou M, Gallì A, Castellano CA, McConkey M, Tarun A, Wong W, Schenone M, Stanclift C, Tanenbaum B, Malolepsza E, Nilsson B, Bick AG, Weinstock JS, Miller M, Niroula A, Dunford A, Taylor-Weiner A, Wood T, Barbera A, Anand S, Psaty BM, Desai P, Cho MH, Johnson AD, Loos R, MacArthur DG, Lek M, Neuberg DS, Lage K, Carr SA, Hellstrom-Lindberg E, Malcovati L, Papaemmanuil E, Stewart C, Getz G, Bradley RK, Jaiswal S, Ebert BL. ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing. Blood Cancer Discov 2021; 2:500-517. [PMID: 34568833 DOI: 10.1158/2643-3230.bcd-20-0224] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Clonal hematopoiesis results from somatic mutations in cancer driver genes in hematopoietic stem cells. We sought to identify novel drivers of clonal expansion using an unbiased analysis of sequencing data from 84,683 persons and identified common mutations in the 5-methylcytosine reader, ZBTB33, as well as in YLPM1, SRCAP, and ZNF318. We also identified these mutations at low frequency in myelodysplastic syndrome patients. Zbtb33 edited mouse hematopoietic stem and progenitor cells exhibited a competitive advantage in vivo and increased genome-wide intron retention. ZBTB33 mutations potentially link DNA methylation and RNA splicing, the two most commonly mutated pathways in clonal hematopoiesis and MDS.
Collapse
Affiliation(s)
- Ellen M Beauchamp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Matthew Leventhal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Elsa Bernard
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emma R Hoppe
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Gabriele Todisco
- Department of Molecular Medicine, University of Pavia, and Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Creignou
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Gallì
- Department of Molecular Medicine, University of Pavia, and Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Cecilia A Castellano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Marie McConkey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Akansha Tarun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Waihay Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Monica Schenone
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Caroline Stanclift
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Benjamin Tanenbaum
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Edyta Malolepsza
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Björn Nilsson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Department of Laboratory Medicine, Lund University, 221 84, Sweden
| | - Alexander G Bick
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Mendy Miller
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Abhishek Niroula
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Andrew Dunford
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Amaro Taylor-Weiner
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Timothy Wood
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Alex Barbera
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA.,Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Pinkal Desai
- Division of Hematology & Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Andrew D Johnson
- National Heart, Lung, and Blood Institute Center for Population Studies, The Framingham Heart Study, Framingham, MA, USA
| | - Ruth Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Daniel G MacArthur
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia.,Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Monkol Lek
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kasper Lage
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Eva Hellstrom-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, and Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chip Stewart
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA, USA
| |
Collapse
|
33
|
Bloehdorn J, Braun A, Taylor-Weiner A, Jebaraj BMC, Robrecht S, Krzykalla J, Pan H, Giza A, Akylzhanova G, Holzmann K, Scheffold A, Johnston HE, Yeh RF, Klymenko T, Tausch E, Eichhorst B, Bullinger L, Fischer K, Weisser M, Robak T, Schneider C, Gribben J, Dahal LN, Carter MJ, Elemento O, Landau DA, Neuberg DS, Cragg MS, Benner A, Hallek M, Wu CJ, Döhner H, Stilgenbauer S, Mertens D. Multi-platform profiling characterizes molecular subgroups and resistance networks in chronic lymphocytic leukemia. Nat Commun 2021; 12:5395. [PMID: 34518531 PMCID: PMC8438057 DOI: 10.1038/s41467-021-25403-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
Knowledge of the genomic landscape of chronic lymphocytic leukemia (CLL) grows increasingly detailed, providing challenges in contextualizing the accumulated information. To define the underlying networks, we here perform a multi-platform molecular characterization. We identify major subgroups characterized by genomic instability (GI) or activation of epithelial-mesenchymal-transition (EMT)-like programs, which subdivide into non-inflammatory and inflammatory subtypes. GI CLL exhibit disruption of genome integrity, DNA-damage response and are associated with mutagenesis mediated through activation-induced cytidine deaminase or defective mismatch repair. TP53 wild-type and mutated/deleted cases constitute a transcriptionally uniform entity in GI CLL and show similarly poor progression-free survival at relapse. EMT-like CLL exhibit high genomic stability, reduced benefit from the addition of rituximab and EMT-like differentiation is inhibited by induction of DNA damage. This work extends the perspective on CLL biology and risk categories in TP53 wild-type CLL. Furthermore, molecular targets identified within each subgroup provide opportunities for new treatment approaches.
Collapse
Affiliation(s)
| | - Andrejs Braun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | | | - Sandra Robrecht
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Julia Krzykalla
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Heng Pan
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Adam Giza
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Gulnara Akylzhanova
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Annika Scheffold
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Harvey E Johnston
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - Ru-Fang Yeh
- Biostatistics, Genentech Inc., South San Francisco, CA, USA
| | - Tetyana Klymenko
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Eugen Tausch
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Barbara Eichhorst
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Lars Bullinger
- Medical Clinic for Hematology, Oncology and Tumor Biology, Charité University Hospital, Berlin, Germany
| | - Kirsten Fischer
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Martin Weisser
- Roche Pharma Research and Early Development, Penzberg, Germany
| | - Tadeusz Robak
- Department of Hematology, Medical University of Lodz, Lodz, Poland
| | | | - John Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lekh N Dahal
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
- Department of Pharmacology and Therapeutics, Faculty of Life and Health Sciences, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mathew J Carter
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Dan A Landau
- Cancer Genomics and Evolutionary Dynamics, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Donna S Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark S Cragg
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Michael Hallek
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Hartmut Döhner
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | | | - Daniel Mertens
- Department of Internal Medicine III, University of Ulm, Ulm, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
34
|
Miller PG, Sperling AS, Brea EJ, Leick MB, Fell GG, Jan M, Gohil SH, Tai YT, Munshi NC, Wu CJ, Neuberg DS, Maus MV, Jacobson C, Gibson CJ, Ebert BL. Clonal hematopoiesis in patients receiving chimeric antigen receptor T-cell therapy. Blood Adv 2021; 5:2982-2986. [PMID: 34342642 PMCID: PMC8361461 DOI: 10.1182/bloodadvances.2021004554] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/04/2021] [Indexed: 11/20/2022] Open
Abstract
Chimeric antigen receptor (CAR) T-cells have emerged as an efficacious modality in patients with non-Hodgkin lymphoma (NHL) and multiple myeloma (MM). Clonal hematopoiesis of indeterminate potential (CHIP), a state in which mutations in hematopoietic cells give rise to a clonal population of cells, is more common in patients exposed to cytotoxic therapies, has been shown to influence inflammatory immune programs, and is associated with an adverse prognosis in patients with NHL and MM receiving autologous transplantation. We therefore hypothesized that CHIP could influence clinical outcomes in patients receiving CAR T-cell therapy. In a cohort of 154 patients with NHL or MM receiving CAR T-cells, we found that CHIP was present in 48% of patients and associated with increased rates of complete response and cytokine release syndrome severity, but only in patients younger than age 60 years. Despite these differences, CHIP was not associated with a difference in progression-free or overall survival, regardless of age. Our data suggest that CHIP can influence CAR T-cell biology and clinical outcomes, but, in contrast to autologous transplantation, CHIP was not associated with worse survival and should not be a reason to exclude individuals from receiving this potentially life-prolonging treatment.
Collapse
Affiliation(s)
- Peter G Miller
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Adam S Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Division of Hematology, Brigham and Women's Hospital, Boston, MA
| | - Elliott J Brea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mark B Leick
- Cellular Immunotherapy Program, Massachusetts General Hospital Cancer Center, Boston, MA
| | - Geoffrey G Fell
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA
| | - Max Jan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Satyen H Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Academic Haematology, University College London Cancer Institute, London, United Kingdom; and
| | - Yu-Tzu Tai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Nikhil C Munshi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Donna S Neuberg
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA
| | - Marcela V Maus
- Cellular Immunotherapy Program, Massachusetts General Hospital Cancer Center, Boston, MA
| | - Caron Jacobson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Christopher J Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA
| |
Collapse
|
35
|
Völkel G, Laban S, Fürstberger A, Kühlwein SD, Ikonomi N, Hoffmann TK, Brunner C, Neuberg DS, Gaidzik V, Döhner H, Kraus JM, Kestler HA. Erratum to: Analysis, identification and visualization of subgroups in genomics. Brief Bioinform 2021; 22:6314775. [PMID: 34226916 PMCID: PMC8575006 DOI: 10.1093/bib/bbab280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
- Gunnar Völkel
- Institute of Medical Systems Biology (MSB), Ulm University, Ulm, Germany
| | - Simon Laban
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Axel Fürstberger
- MSB and deputy of Core Unit Bioinformatics, Ulm University, Ulm, Germany
| | - Silke D Kühlwein
- International Graduate School of Molecular Medicine, Ulm University, Germany
| | - Nensi Ikonomi
- International Graduate School of Molecular Medicine, Ulm University, Germany
| | - Thomas K Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Donna S Neuberg
- Department of Biostatistics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Verena Gaidzik
- Department of Internal Medicine III, Ulm University Medical Center, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Medical Center, Germany
| | | | - Hans A Kestler
- Institute of Medical Systems Biology, and head of Core Unit Bioinformatics, Ulm University, Ulm, Germany
| |
Collapse
|
36
|
Vrooman LM, Blonquist TM, Stevenson KE, Supko JG, Hunt SK, Cronholm SM, Koch V, Kay-Green S, Athale UH, Clavell LA, Cole PD, Harris MH, Kelly KM, Laverdiere C, Leclerc JM, Michon B, Place AE, Schorin MA, Welch JJG, Neuberg DS, Sallan SE, Silverman LB. Efficacy and Toxicity of Pegaspargase and Calaspargase Pegol in Childhood Acute Lymphoblastic Leukemia: Results of DFCI 11-001. J Clin Oncol 2021; 39:3496-3505. [PMID: 34228505 DOI: 10.1200/jco.20.03692] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
PURPOSE Dana-Farber Cancer Institute Acute Lymphoblastic Leukemia (ALL) Consortium Protocol 11-001 assessed efficacy and toxicity of calaspargase pegol (calaspargase), a novel pegylated asparaginase formulation with longer half-life, compared with the standard formulation pegaspargase. METHODS Patients age 1 to ≤ 21 years with newly diagnosed ALL or lymphoblastic lymphoma were randomly assigned to intravenous pegaspargase or calaspargase, 2,500 IU/m2/dose. Patients received one induction dose. Beginning week 7, pegaspargase was administered every 2 week for 15 doses and calaspargase every 3 week for 10 doses (30 weeks). Serum asparaginase activity (SAA) (≥ 0.1 IU/mL considered therapeutic) was assessed 4, 11, 18, and 25 days after the induction dose and before each postinduction dose. RESULTS Between 2012 and 2015, 239 eligible patients enrolled (230 ALL, nine lymphoblastic lymphoma); 120 were assigned to pegaspargase and 119 to calaspargase. After the induction dose, SAA was ≥ 0.1 IU/mL in ≥ 95% of patients on both arms 18 days after dosing. At day 25, more patients had SAA ≥ 0.1 IU/mL with calaspargase (88% v 17%; P ˂ .001). Postinduction, median nadir SAAs were similar (≥ 1.0 IU/mL) for both arms. Of 230 evaluable patients, 99% of pegaspargase and 95% of calaspargase patients achieved complete remission (P = .12), with no difference in frequency of high end-induction minimal residual disease among evaluable patients with B acute lymphoblastic leukemia (B-ALL). There were no differences in frequencies of asparaginase allergy, pancreatitis, thrombosis, or hyperbilirubinemia. With 5.3 years median follow-up, 5-year event-free survival for pegaspargase was 84.9% (SE ± 3.4%) and 88.1% (± SE 3.0%) for calaspargase (P = .65). CONCLUSION Every 3-week calaspargase had similar nadir SAA, toxicity, and survival outcomes compared with every 2-week pegaspargase. The high nadir SAA observed for both preparations suggest dosing strategies can be further optimized.
Collapse
Affiliation(s)
- Lynda M Vrooman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School Boston, MA
| | - Traci M Blonquist
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | | | - Jeffrey G Supko
- Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Sarah K Hunt
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Sarah M Cronholm
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Victoria Koch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Samantha Kay-Green
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Uma H Athale
- Division of Pediatric Hematology/Oncology, McMaster University, Hamilton, ON, Canada
| | - Luis A Clavell
- Division of Pediatric Oncology, San Jorge Children's Hospital, San Juan, Puerto Rico
| | - Peter D Cole
- Division of Pediatric Hematology/Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Kara M Kelly
- Department of Pediatric Oncology, Roswell Park Cancer Institute and Oishei Children's Hospital, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY
| | - Caroline Laverdiere
- Division of Hematology and Oncology, Hospital Sainte-Justine, University of Montreal, Montreal, Canada
| | - Jean-Marie Leclerc
- Division of Hematology and Oncology, Hospital Sainte-Justine, University of Montreal, Montreal, Canada
| | - Bruno Michon
- Division of Hematology-Oncology, Centre Hospitalier Universite de Quebec, Quebec City, Canada
| | - Andrew E Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School Boston, MA
| | | | - Jennifer J G Welch
- Division of Pediatric Hematology/Oncology, Hasbro Children's Hospital, Brown University Medical School, Providence, RI
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Stephen E Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School Boston, MA
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School Boston, MA
| |
Collapse
|
37
|
Sella T, Fell G, Miller PG, Gibson CJ, Rosenberg SM, Snow C, Stover DG, Ruddy KJ, Peppercorn JM, Schapira L, Borges VF, Come SE, Warner E, Neuberg DS, Ebert BL, Partridge AH. Testing for clonal hematopoiesis of indeterminate potential in breast cancer survivors. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.e24108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e24108 Background: Clonal hematopoiesis of Indeterminate Potential (CHIP) is associated with adverse clinical outcomes including increased risk of hematologic malignancies and heart disease. Limited data suggest an increased prevalence of CHIP in patients treated for solid tumors, particularly after exposure to radiation and chemotherapy. CHIP testing may inform risk-reduction strategies for cancer survivors. Little is known about patient knowledge, attitudes, and preferences regarding CHIP testing. Methods: We surveyed survivors without history of recurrence participating in an ongoing prospective cohort study of young women with breast cancer (BC). The survey was sent by email and included an introduction to CHIP including risk factors and clinical associations. Respondents then reviewed a vignette and were asked about CHIP testing preferences (definitely/probably test vs. definitely/probably not test) considering sequentially: 1) population-based 10-year risk of BC recurrence, hematological malignancy and heart disease; 2) estimated increase in these risks with CHIP; 3) current CHIP management; 4) a dedicated CHIP clinic; and 5) a theoretical CHIP treatment. Changes in preferences from the prior scenario were evaluated with the McNemar's test using a type I error rate of 5%. Results: 528/642 (82.2%) eligible women responded to the survey, at a median age of 46 (range: 31-54) years (median time from diagnosis: 108 months (range: 60-168)), and 88% were white. Most had stage 1/2 BC (78.8%) and had received chemotherapy (73.1%) and/or radiation (61.9%). 93.6% had never heard of CHIP prior to survey. After initial patient vignette presentation, most women (87.1%,) recommended CHIP testing if offered. Preferences for testing decreased (p<0.05) when considering population-based risks, with 11.1% shifting their preference from CHIP testing to not testing. After considering increased risks associated with CHIP, interest in testing increased (p<0.05), with 10.1% shifting their preference to testing. Interest significantly (p<0.05) increased with the possibility of managing CHIP through a clinic or a hypothetical CHIP treatment, with 7.2% and 14.1% switching their preferences towards testing, respectively. Finally, 75.8% responded that they themselves, after learning about CHIP and reviewing the vignette, would want to have CHIP testing; 28.2% reported that learning about CHIP and the associated risks caused them at least moderate anxiety. Conclusion: Few young BC survivors were aware of CHIP yet most indicated an interest in testing after learning about it. Testing preferences were influenced by risks presented and potential management strategies. Findings highlight the importance of effective risk communication and the need for adequate psychosocial support when considering testing for CHIP and other potential clinical biomarkers predictive of cancer and other medical risks in cancer survivors.
Collapse
Affiliation(s)
- Tal Sella
- Dana Farber Cancer Institute, Boston, MA
| | - Geoffrey Fell
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Peter Grant Miller
- Department of Medical Oncology, Dana-Farber Cancer Institute, Division of Hematology, Brigham and Women’s Hospital, Broad Institute of MIT and Harvard, Boston, MA
| | | | | | - Craig Snow
- Dana-Farber Cancer Institute, Boston, MA
| | - Daniel G. Stover
- Ohio State University Comprehensive Cancer Center, Division of Medical Oncology, Columbus, OH
| | | | | | - Lidia Schapira
- Stanford University and Stanford Cancer Institute, Stanford, CA
| | | | | | - Ellen Warner
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Donna S. Neuberg
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Benjamin Levine Ebert
- Brigham and Women's Hospital, Howard Hughes Medical Institute Bethesda and Broad Institute of MIT and Harvard, Boston, MA
| | | |
Collapse
|
38
|
Bernard E, Nannya Y, Hasserjian RP, Devlin SM, Tuechler H, Medina-Martinez JS, Yoshizato T, Shiozawa Y, Saiki R, Malcovati L, Levine MF, Arango JE, Zhou Y, Solé F, Cargo CA, Haase D, Creignou M, Germing U, Zhang Y, Gundem G, Sarian A, van de Loosdrecht AA, Jädersten M, Tobiasson M, Kosmider O, Follo MY, Thol F, Pinheiro RF, Santini V, Kotsianidis I, Boultwood J, Santos FPS, Schanz J, Kasahara S, Ishikawa T, Tsurumi H, Takaori-Kondo A, Kiguchi T, Polprasert C, Bennett JM, Klimek VM, Savona MR, Belickova M, Ganster C, Palomo L, Sanz G, Ades L, Della Porta MG, Elias HK, Smith AG, Werner Y, Patel M, Viale A, Vanness K, Neuberg DS, Stevenson KE, Menghrajani K, Bolton KL, Fenaux P, Pellagatti A, Platzbecker U, Heuser M, Valent P, Chiba S, Miyazaki Y, Finelli C, Voso MT, Shih LY, Fontenay M, Jansen JH, Cervera J, Atsuta Y, Gattermann N, Ebert BL, Bejar R, Greenberg PL, Cazzola M, Hellström-Lindberg E, Ogawa S, Papaemmanuil E. Author Correction: Implications of TP53 allelic state for genome stability, clinical presentation and outcomes in myelodysplastic syndromes. Nat Med 2021; 27:927. [PMID: 33948021 DOI: 10.1038/s41591-021-01367-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Elsa Bernard
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | | | - Sean M Devlin
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Juan S Medina-Martinez
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Ryunosuke Saiki
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.,Department of Hematology, IRCCS Fondazione Policlinico S. Matteo, Pavia, Italy
| | - Max F Levine
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan E Arango
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yangyu Zhou
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francesc Solé
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Catherine A Cargo
- Haematological Malignancy Diagnostic Service, St James's University Hospital, Leeds, UK
| | - Detlef Haase
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Maria Creignou
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gunes Gundem
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Araxe Sarian
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Martin Jädersten
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Tobiasson
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Olivier Kosmider
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin and Université de Paris, Université Paris Descartes, Paris, France
| | - Matilde Y Follo
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation Hannover Medical School, Hannover, Germany
| | - Ronald F Pinheiro
- Drug Research and Development Center, Federal University of Ceara, Ceara, Brazil
| | - Valeria Santini
- MDS Unit, Hematology, AOU Careggi, University of Florence, Florence, Italy
| | - Ioannis Kotsianidis
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - Jacqueline Boultwood
- Radcliffe Department of Medicine, University of Oxford and Oxford BRC Haematology Theme, Oxford, UK
| | - Fabio P S Santos
- Oncology-Hematology Center, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Julie Schanz
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Senji Kasahara
- Department of Hematology, Gifu Municipal Hospital, Gifu, Japan
| | - Takayuki Ishikawa
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Hisashi Tsurumi
- Department of Hematology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toru Kiguchi
- Department of Hematology, Chugoku Central Hospital, Fukuyama, Japan
| | - Chantana Polprasert
- Department of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - John M Bennett
- Lab. Medicine and Pathology, Hematology/Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - Virginia M Klimek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Monika Belickova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Christina Ganster
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Laura Palomo
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Guillermo Sanz
- Department of Hematology, Hospital Universitario y Politécnico La Fe, Valencia, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Lionel Ades
- Department of Hematology, Hôpital St Louis and Paris University, Paris, France
| | - Matteo Giovanni Della Porta
- Humanitas Clinical and Research Center-IRCCS, Humanitas Cancer Center, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Harold K Elias
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yesenia Werner
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Minal Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnès Viale
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katelynd Vanness
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Donna S Neuberg
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Kamal Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelly L Bolton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pierre Fenaux
- Department of Hematology, Hôpital St Louis and Paris University, Paris, France
| | - Andrea Pellagatti
- Radcliffe Department of Medicine, University of Oxford and Oxford BRC Haematology Theme, Oxford, UK
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular Therapy, University of Leipzig, Leipzig, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation Hannover Medical School, Hannover, Germany
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology and Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Shigeru Chiba
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Carlo Finelli
- Institute of Hematology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Maria Teresa Voso
- MDS Cooperative Group GROM-L, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Lee-Yung Shih
- Chang Gung Memorial Hospital at Linkou, Chang Gung University, Taoyuan City, Taiwan
| | - Michaela Fontenay
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin and Université de Paris, Université Paris Descartes, Paris, France
| | - Joop H Jansen
- Laboratory Hematology, Department LABGK, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - José Cervera
- Department of Hematology and Genetics Unit, University Hospital La Fe, Valencia, Spain
| | - Yoshiko Atsuta
- Japanese Data Center for Hematopoietic Cell Transplantation, Nagoya, Japan
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology and Howard Hughes Medical Institute, Dana-Farber Cancer Center, Boston, MA, USA
| | - Rafael Bejar
- UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.,Department of Hematology, IRCCS Fondazione Policlinico S. Matteo, Pavia, Italy
| | - Eva Hellström-Lindberg
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
39
|
Meizlish ML, Goshua G, Liu Y, Fine R, Amin K, Chang E, DeFilippo N, Keating C, Liu Y, Mankbadi M, McManus D, Wang SY, Price C, Bona RD, Ochoa Chaar CI, Chun HJ, Pine AB, Rinder HM, Siner JM, Neuberg DS, Owusu KA, Lee AI. Intermediate-dose anticoagulation, aspirin, and in-hospital mortality in COVID-19: A propensity score-matched analysis. Am J Hematol 2021; 96:471-479. [PMID: 33476420 PMCID: PMC8013588 DOI: 10.1002/ajh.26102] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 02/06/2023]
Abstract
Thrombotic complications occur at high rates in hospitalized patients with COVID-19, yet the impact of intensive antithrombotic therapy on mortality is uncertain. We examined in-hospital mortality with intermediate- compared to prophylactic-dose anticoagulation, and separately with in-hospital aspirin compared to no antiplatelet therapy, in a large, retrospective study of 2785 hospitalized adult COVID-19 patients. In this analysis, we established two separate, nested cohorts of patients (a) who received intermediate- or prophylactic-dose anticoagulation ("anticoagulation cohort", N = 1624), or (b) who were not on home antiplatelet therapy and received either in-hospital aspirin or no antiplatelet therapy ("aspirin cohort", N = 1956). To minimize bias and adjust for confounding factors, we incorporated propensity score matching and multivariable regression utilizing various markers of illness severity and other patient-specific covariates, yielding treatment groups with well-balanced covariates in each cohort. The primary outcome was cumulative incidence of in-hospital death. Among propensity score-matched patients in the anticoagulation cohort (N = 382), in a multivariable regression model, intermediate- compared to prophylactic-dose anticoagulation was associated with a significantly lower cumulative incidence of in-hospital death (hazard ratio 0.518 [0.308-0.872]). Among propensity-score matched patients in the aspirin cohort (N = 638), in a multivariable regression model, in-hospital aspirin compared to no antiplatelet therapy was associated with a significantly lower cumulative incidence of in-hospital death (hazard ratio 0.522 [0.336-0.812]). In this propensity score-matched, observational study of COVID-19, intermediate-dose anticoagulation and aspirin were each associated with a lower cumulative incidence of in-hospital death.
Collapse
Affiliation(s)
| | - George Goshua
- Section of Hematology, Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Yiwen Liu
- Dana‐Farber Cancer InstituteBostonMassachusettsUSA
| | - Rebecca Fine
- Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Kejal Amin
- Department of PharmacyYale‐New Haven HospitalNew HavenConnecticutUSA
| | - Eric Chang
- Section of Hematology, Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Nicholas DeFilippo
- Department of PharmacyYale‐New Haven HospitalNew HavenConnecticutUSA
- School of PharmacyUniversity of ConnecticutStorrsConnecticutUSA
| | - Craig Keating
- Joint Data Analytics TeamYale New Haven HospitalNew HavenConnecticutUSA
| | - Yuxin Liu
- Section of Hematology, Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Michael Mankbadi
- Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Dayna McManus
- Department of PharmacyYale‐New Haven HospitalNew HavenConnecticutUSA
| | - Stephen Y. Wang
- Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Christina Price
- Section of Allergy and Immunology, Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Robert D. Bona
- Section of Hematology, Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Cassius Iyad Ochoa Chaar
- Section of Vascular Surgery, Department of SurgeryYale School of MedicineNew HavenConnecticutUSA
| | - Hyung J. Chun
- Section of Cardiology, Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Alexander B. Pine
- Section of Hematology, Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Henry M. Rinder
- Section of Hematology, Department of MedicineYale School of MedicineNew HavenConnecticutUSA
- Department of Laboratory MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Jonathan M. Siner
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| | | | - Kent A. Owusu
- Department of PharmacyYale‐New Haven HospitalNew HavenConnecticutUSA
- Clinical RedesignYale New Haven HealthNew HavenConnecticutUSA
| | - Alfred Ian Lee
- Section of Hematology, Department of MedicineYale School of MedicineNew HavenConnecticutUSA
| |
Collapse
|
40
|
Lazarian G, Yin S, Ten Hacken E, Sewastianik T, Uduman M, Font-Tello A, Gohil SH, Li S, Kim E, Joyal H, Billington L, Witten E, Zheng M, Huang T, Severgnini M, Lefebvre V, Rassenti LZ, Gutierrez C, Georgopoulos K, Ott CJ, Wang L, Kipps TJ, Burger JA, Livak KJ, Neuberg DS, Baran-Marszak F, Cymbalista F, Carrasco RD, Wu CJ. A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation. Cancer Cell 2021; 39:380-393.e8. [PMID: 33689703 PMCID: PMC8034546 DOI: 10.1016/j.ccell.2021.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/25/2020] [Accepted: 02/04/2021] [Indexed: 12/20/2022]
Abstract
Hotspot mutation of IKZF3 (IKZF3-L162R) has been identified as a putative driver of chronic lymphocytic leukemia (CLL), but its function remains unknown. Here, we demonstrate its driving role in CLL through a B cell-restricted conditional knockin mouse model. Mutant Ikzf3 alters DNA binding specificity and target selection, leading to hyperactivation of B cell receptor (BCR) signaling, overexpression of nuclear factor κB (NF-κB) target genes, and development of CLL-like disease in elderly mice with a penetrance of ~40%. Human CLL carrying either IKZF3 mutation or high IKZF3 expression was associated with overexpression of BCR/NF-κB pathway members and reduced sensitivity to BCR signaling inhibition by ibrutinib. Our results thus highlight IKZF3 oncogenic function in CLL via transcriptional dysregulation and demonstrate that this pro-survival function can be achieved by either somatic mutation or overexpression of this CLL driver. This emphasizes the need for combinatorial approaches to overcome IKZF3-mediated BCR inhibitor resistance.
Collapse
Affiliation(s)
- Gregory Lazarian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; INSERM, U978, Université Paris 13, Bobigny, France; Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France
| | - Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Elisa Ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Tomasz Sewastianik
- Harvard Medical School, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Mohamed Uduman
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alba Font-Tello
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Satyen H Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Academic Haematology, University College London, London, UK
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ekaterina Kim
- Department of Leukemia, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heather Joyal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Leah Billington
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Elizabeth Witten
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mei Zheng
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Teddy Huang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mariano Severgnini
- Center for Immuno-Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Valerie Lefebvre
- Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France
| | | | - Catherine Gutierrez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Katia Georgopoulos
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Christopher J Ott
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, CA, USA
| | - Thomas J Kipps
- Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, USA
| | - Jan A Burger
- Department of Leukemia, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fanny Baran-Marszak
- INSERM, U978, Université Paris 13, Bobigny, France; Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France
| | - Florence Cymbalista
- INSERM, U978, Université Paris 13, Bobigny, France; Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France
| | - Ruben D Carrasco
- Harvard Medical School, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| |
Collapse
|
41
|
Burns MA, Place AE, Stevenson KE, Gutiérrez A, Forrest S, Pikman Y, Vrooman LM, Harris MH, Weinberg OK, Hunt SK, O'Brien JE, Asselin BL, Athale UH, Clavell LA, Cole PD, Gennarini LM, Kahn J, Kelly KM, Laverdiere C, Leclerc JM, Michon B, Schorin MA, Sulis ML, Welch JJG, Neuberg DS, Sallan SE, Silverman LB. Corrigendum. Pediatr Blood Cancer 2021; 68:e28885. [PMID: 33506554 DOI: 10.1002/pbc.28885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
42
|
Meizlish ML, Goshua G, Liu Y, Fine R, Amin K, Chang E, DeFilippo N, Keating C, Liu Y, Mankbadi M, McManus D, Wang S, Price C, Bona RD, Chaar CIO, Chun HJ, Pine AB, Rinder HM, Siner J, Neuberg DS, Owusu KA, Lee AI. Intermediate-dose anticoagulation, aspirin, and in-hospital mortality in COVID-19: a propensity score-matched analysis. medRxiv 2021:2021.01.12.21249577. [PMID: 33469595 PMCID: PMC7814841 DOI: 10.1101/2021.01.12.21249577] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Background Thrombotic complications occur at high rates in hospitalized patients with COVID-19, yet the impact of intensive antithrombotic therapy on mortality is uncertain. Research Question How does in-hospital mortality compare with intermediate- versus prophylactic-dose anticoagulation, and separately with in-hospital aspirin versus no antiplatelet therapy, in treatment of COVID-19? Study Design and Methods Using data from 2785 hospitalized adult COVID-19 patients, we established two separate, nested cohorts of patients (1) who received intermediate- or prophylactic-dose anticoagulation ("anticoagulation cohort", N = 1624), or (2) who were not on home antiplatelet therapy and received either in-hospital aspirin or no antiplatelet therapy ("aspirin cohort", N = 1956). Propensity score matching utilizing various markers of illness severity and other patient-specific covariates yielded treatment groups with well-balanced covariates in each cohort. The primary outcome was cumulative incidence of in-hospital death. Results Among propensity score-matched patients in the anticoagulation cohort (N = 382), in a multivariable regression model, intermediate- compared to prophylactic-dose anticoagulation was associated with a significantly lower cumulative incidence of in-hospital death (hazard ratio 0.518 [0.308-0.872]). Among propensity-score matched patients in the aspirin cohort (N = 638), in a multivariable regression model, in-hospital aspirin compared to no antiplatelet therapy was associated with a significantly lower cumulative incidence of in-hospital death (hazard ratio 0.522 [0.336-0.812]). Interpretation In this propensity score-matched, observational study of COVID-19, intermediate-dose anticoagulation and aspirin were each associated with a lower cumulative incidence of in-hospital death.
Collapse
Affiliation(s)
| | - George Goshua
- Section of Hematology, Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Yiwen Liu
- Dana-Farber Cancer Institute, Boston, MA
| | - Rebecca Fine
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Kejal Amin
- Department of Pharmacy, Yale-New Haven Hospital, New Haven, CT
| | - Eric Chang
- Section of Hematology, Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Nicholas DeFilippo
- Department of Pharmacy, Yale-New Haven Hospital, New Haven, CT
- School of Pharmacy, University of Connecticut, Storrs, CT
| | - Craig Keating
- Joint Data Analytics Team, Yale New Haven Hospital, New Haven, CT
| | - Yuxin Liu
- Section of Hematology, Department of Medicine, Yale School of Medicine, New Haven, CT
| | | | - Dayna McManus
- Department of Pharmacy, Yale-New Haven Hospital, New Haven, CT
| | - Stephen Wang
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Christina Price
- Section of Allergy and Immunology, Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Robert D. Bona
- Section of Hematology, Department of Medicine, Yale School of Medicine, New Haven, CT
| | | | - Hyung J. Chun
- Section of Cardiology, Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Alexander B. Pine
- Section of Hematology, Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Henry M. Rinder
- Section of Hematology, Department of Medicine, Yale School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Jonathan Siner
- Section of Pulmonary and Sleep Medicine, Department of Medicine, Yale School of Medicine, New Haven, CT
| | | | - Kent A. Owusu
- Department of Pharmacy, Yale-New Haven Hospital, New Haven, CT
- Clinical Redesign, Yale New Haven Health, New Haven, CT
| | - Alfred Ian Lee
- Section of Hematology, Department of Medicine, Yale School of Medicine, New Haven, CT
| |
Collapse
|
43
|
Burns MA, Place AE, Stevenson KE, Gutiérrez A, Forrest S, Pikman Y, Vrooman LM, Harris MH, Weinberg OK, Hunt SK, O’Brien JE, Asselin BL, Athale UH, Clavell LA, Cole PD, Gennarini LM, Kahn JM, Kelly KM, Laverdiere C, Leclerc JM, Michon B, Schorin MA, Sulis ML, Welch JJ, Neuberg DS, Sallan SE, Silverman LB. Identification of prognostic factors in childhood T-cell acute lymphoblastic leukemia: Results from DFCI ALL Consortium Protocols 05-001 and 11-001. Pediatr Blood Cancer 2021; 68:e28719. [PMID: 33026184 PMCID: PMC8369809 DOI: 10.1002/pbc.28719] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND/OBJECTIVES While outcomes for pediatric T-cell acute lymphoblastic leukemia (T-ALL) are favorable, there are few widely accepted prognostic factors, limiting the ability to risk stratify therapy. DESIGN/METHODS Dana-Farber Cancer Institute (DFCI) Protocols 05-001 and 11-001 enrolled pediatric patients with newly diagnosed B- or T-ALL from 2005 to 2011 and from 2012 to 2015, respectively. Protocol therapy was nearly identical for patients with T-ALL (N = 123), who were all initially assigned to the high-risk arm. End-induction minimal residual disease (MRD) was assessed by reverse transcription polymerase chain reaction (RT-PCR) or next-generation sequencing (NGS), but was not used to modify postinduction therapy. Early T-cell precursor (ETP) status was determined by flow cytometry. Cases with sufficient diagnostic DNA were retrospectively evaluated by targeted NGS of known genetic drivers of T-ALL, including Notch, PI3K, and Ras pathway genes. RESULTS The 5-year event-free survival (EFS) and overall survival (OS) for patients with T-ALL was 81% (95% CI, 73-87%) and 90% (95% CI, 83-94%), respectively. ETP phenotype was associated with failure to achieve complete remission, but not with inferior OS. Low end-induction MRD (<10-4 ) was associated with superior disease-free survival (DFS). Pathogenic mutations of the PI3K pathway were mutually exclusive of ETP phenotype and were associated with inferior 5-year DFS and OS. CONCLUSIONS Together, our findings demonstrate that ETP phenotype, end-induction MRD, and PI3K pathway mutation status are prognostically relevant in pediatric T-ALL and should be considered for risk classification in future trials. DFCI Protocols 05-001 and 11-001 are registered at www.clinicaltrials.gov as NCT00165087 and NCT01574274, respectively.
Collapse
Affiliation(s)
- Melissa A. Burns
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Andrew E. Place
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Kristen E. Stevenson
- Department of Biostatistics and Computational Biology,
Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Alejandro Gutiérrez
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Suzanne Forrest
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Lynda M. Vrooman
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Marian H. Harris
- Department of Pathology, Boston Children’s Hospital,
Harvard Medical School, Boston, MA
| | | | - Sarah K. Hunt
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
| | - Jane E. O’Brien
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
| | - Barbara L. Asselin
- Department of Pediatrics, Golisano Children’s
Hospital, University of Rochester Medical Center, Rochester, NY
| | - Uma H. Athale
- Division of Pediatric Hematology/Oncology, McMaster
University, Hamilton, ON, Canada
| | - Luis A. Clavell
- Division of Pediatric Oncology, San Jorge Children’s
Hospital, San Juan, Puerto Rico
| | - Peter D. Cole
- Division of Pediatric Hematology/Oncology, Rutgers Cancer
Institute of New Jersey, Rutgers ;Robert Wood Johnson School of Medicine, New
Brunswick, NJ
| | - Lisa M. Gennarini
- Division of Pediatric Hematology/Oncology,
Children’s Hospital at Montefiore, Bronx, NY
| | - Justine M. Kahn
- Division of Pediatric Hematology, Oncology, and Stem Cell
Transplantation, Columbia University, New York, NY
| | - Kara M. Kelly
- Department of Pediatric Oncology, Roswell Park
Comprehensive Cancer Center, University at Buffalo, Buffalo, NY
| | - Caroline Laverdiere
- Division of Hematology and Oncology, Hospital
Sainte-Justine, University of Montreal, Montreal, Canada
| | - Jean-Marie Leclerc
- Division of Hematology and Oncology, Hospital
Sainte-Justine, University of Montreal, Montreal, Canada
| | - Bruno Michon
- Division of Hematology-Oncology, Centre Hospitalier
Universite de Quebec, Quebec City, Canada
| | | | - Maria Luisa Sulis
- Pediatric Hematologic Malignancies Service, Department of
Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jennifer J.G. Welch
- Division of Pediatric Hematology-Oncology, Hasbro
Children’s Hospital, Warren Alpert Medical School of Brown University,
Providence, RI
| | - Donna S. Neuberg
- Department of Biostatistics and Computational Biology,
Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Stephen E. Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Lewis B. Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| |
Collapse
|
44
|
Kretzmer H, Biran A, Purroy N, Lemvigh CK, Clement K, Gruber M, Gu H, Rassenti L, Mohammad AW, Lesnick C, Slager SL, Braggio E, Shanafelt TD, Kay NE, Fernandes SM, Brown JR, Wang L, Li S, Livak KJ, Neuberg DS, Klages S, Timmermann B, Kipps TJ, Campo E, Gnirke A, Wu CJ, Meissner A. Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy. Blood Cancer Discov 2021; 2:54-69. [PMID: 33604581 PMCID: PMC7888194 DOI: 10.1158/2643-3230.bcd-19-0058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 10/28/2020] [Accepted: 11/18/2020] [Indexed: 01/09/2023] Open
Abstract
Most human cancers converge to a deregulated methylome with reduced global levels and elevated methylation at select CpG islands. To investigate the emergence and dynamics of the cancer methylome, we characterized genome-wide DNA methylation in pre-neoplastic monoclonal B cell lymphocytosis (MBL) and chronic lymphocytic leukemia (CLL), including serial samples collected across disease course. We detected the aberrant tumor-associated methylation landscape at CLL diagnosis and found no significantly differentially methylated regions in the high-count MBL-to-CLL transition. Patient methylomes showed remarkable stability with natural disease and post-therapy progression. Single CLL cells were consistently aberrantly methylated, indicating a homogeneous transition to the altered epigenetic state, and a distinct expression profile together with MBL cells compared to normal B cells. Our longitudinal analysis reveals the cancer methylome to emerge early, which may provide a platform for subsequent genetically-driven growth dynamics and together with its persistent presence suggests a central role in the normal-to-cancer transition.
Collapse
Affiliation(s)
- Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anat Biran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Noelia Purroy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Camilla K Lemvigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Michaela Gruber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Haematology and Haemostaseology, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Laura Rassenti
- Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | | | - Connie Lesnick
- Mayo Clinic, Division of Hematology, Rochester, Minnesota
| | - Susan L Slager
- Mayo Clinic, Division of Hematology, Rochester, Minnesota
| | | | | | - Neil E Kay
- Mayo Clinic, Division of Hematology, Rochester, Minnesota
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Monrovia, California
| | - Shuqiang Li
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kenneth J Livak
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Donna S Neuberg
- Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thomas J Kipps
- Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Elias Campo
- Lymphoid Neoplasm Program, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hematopathology Section, Hospital Clínic; Departament d'Anatomia Patològica, Universitat de Barcelona, Barcelona, Spain
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| |
Collapse
|
45
|
Zeng Z, Fu J, Cibulskis C, Jhaveri A, Gumbs C, Das B, Sanchez-Espiridion B, Janssens S, Taing L, Wang J, Lindsay J, Vilimas T, Zhang J, Tokheim C, Sahu A, Jiang P, Yan C, Duose DY, Cerami E, Chen L, Cohen D, Chen Q, Enos R, Huang X, Lee JJ, Liu Y, Neuberg DS, Nguyen C, Patterson C, Sarkar S, Shukla S, Tang M, Tsuji J, Uduman M, Wang X, Weirather JL, Yu J, Yu J, Zhang J, Zhang J, Meerzaman D, Thurin M, Futreal A, Karlovich C, Gabriel SB, Wistuba II, Liu XS, Wu CJ. Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network. Clin Cancer Res 2020; 27:5049-5061. [PMID: 33323402 DOI: 10.1158/1078-0432.ccr-20-3251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/24/2020] [Accepted: 12/08/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Whole-exome (WES) and RNA sequencing (RNA-seq) are key components of cancer immunogenomic analyses. To evaluate the consistency of tumor WES and RNA-seq profiling platforms across different centers, the Cancer Immune Monitoring and Analysis Centers (CIMAC) and the Cancer Immunologic Data Commons (CIDC) conducted a systematic harmonization study. EXPERIMENTAL DESIGN DNA and RNA were centrally extracted from fresh frozen and formalin-fixed paraffin-embedded non-small cell lung carcinoma tumors and distributed to three centers for WES and RNA-seq profiling. In addition, two 10-plex HapMap cell line pools with known mutations were used to evaluate the accuracy of the WES platforms. RESULTS The WES platforms achieved high precision (> 0.98) and recall (> 0.87) on the HapMap pools when evaluated on loci using > 50× common coverage. Nonsynonymous mutations clustered by tumor sample, achieving an index of specific agreement above 0.67 among replicates, centers, and sample processing. A DV200 > 24% for RNA, as a putative presequencing RNA quality control (QC) metric, was found to be a reliable threshold for generating consistent expression readouts in RNA-seq and NanoString data. MedTIN > 30 was likewise assessed as a reliable RNA-seq QC metric, above which samples from the same tumor across replicates, centers, and sample processing runs could be robustly clustered and HLA typing, immune infiltration, and immune repertoire inference could be performed. CONCLUSIONS The CIMAC collaborating laboratory platforms effectively generated consistent WES and RNA-seq data and enable robust cross-trial comparisons and meta-analyses of highly complex immuno-oncology biomarker data across the NCI CIMAC-CIDC Network.
Collapse
Affiliation(s)
- Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Jingxin Fu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, China
| | | | - Aashna Jhaveri
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Biswajit Das
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Beatriz Sanchez-Espiridion
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jin Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, China
| | - James Lindsay
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tomas Vilimas
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Avinash Sahu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Peng Jiang
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | - Dzifa Yawa Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ethan Cerami
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Li Chen
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - David Cohen
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Qingrong Chen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | | | - Xin Huang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jack J Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cu Nguyen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | | | - Sharmistha Sarkar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sachet Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Junko Tsuji
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Mohamed Uduman
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xiaoman Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jason L Weirather
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jijun Yu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joyce Yu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | - Magdalena Thurin
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chris Karlovich
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | | | - Ignacio Ivan Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| |
Collapse
|
46
|
Bernard E, Nannya Y, Hasserjian RP, Devlin SM, Tuechler H, Medina-Martinez JS, Yoshizato T, Shiozawa Y, Saiki R, Malcovati L, Levine MF, Arango JE, Zhou Y, Solé F, Cargo CA, Haase D, Creignou M, Germing U, Zhang Y, Gundem G, Sarian A, van de Loosdrecht AA, Jädersten M, Tobiasson M, Kosmider O, Follo MY, Thol F, Pinheiro RF, Santini V, Kotsianidis I, Boultwood J, Santos FPS, Schanz J, Kasahara S, Ishikawa T, Tsurumi H, Takaori-Kondo A, Kiguchi T, Polprasert C, Bennett JM, Klimek VM, Savona MR, Belickova M, Ganster C, Palomo L, Sanz G, Ades L, Della Porta MG, Elias HK, Smith AG, Werner Y, Patel M, Viale A, Vanness K, Neuberg DS, Stevenson KE, Menghrajani K, Bolton KL, Fenaux P, Pellagatti A, Platzbecker U, Heuser M, Valent P, Chiba S, Miyazaki Y, Finelli C, Voso MT, Shih LY, Fontenay M, Jansen JH, Cervera J, Atsuta Y, Gattermann N, Ebert BL, Bejar R, Greenberg PL, Cazzola M, Hellström-Lindberg E, Ogawa S, Papaemmanuil E. Implications of TP53 allelic state for genome stability, clinical presentation and outcomes in myelodysplastic syndromes. Nat Med 2020; 26:1549-1556. [PMID: 32747829 PMCID: PMC8381722 DOI: 10.1038/s41591-020-1008-z] [Citation(s) in RCA: 323] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/07/2020] [Indexed: 01/19/2023]
Abstract
Tumor protein p53 (TP53) is the most frequently mutated gene in cancer1,2. In patients with myelodysplastic syndromes (MDS), TP53 mutations are associated with high-risk disease3,4, rapid transformation to acute myeloid leukemia (AML)5, resistance to conventional therapies6-8 and dismal outcomes9. Consistent with the tumor-suppressive role of TP53, patients harbor both mono- and biallelic mutations10. However, the biological and clinical implications of TP53 allelic state have not been fully investigated in MDS or any other cancer type. We analyzed 3,324 patients with MDS for TP53 mutations and allelic imbalances and delineated two subsets of patients with distinct phenotypes and outcomes. One-third of TP53-mutated patients had monoallelic mutations whereas two-thirds had multiple hits (multi-hit) consistent with biallelic targeting. Established associations with complex karyotype, few co-occurring mutations, high-risk presentation and poor outcomes were specific to multi-hit patients only. TP53 multi-hit state predicted risk of death and leukemic transformation independently of the Revised International Prognostic Scoring System (IPSS-R)11. Surprisingly, monoallelic patients did not differ from TP53 wild-type patients in outcomes and response to therapy. This study shows that consideration of TP53 allelic state is critical for diagnostic and prognostic precision in MDS as well as in future correlative studies of treatment response.
Collapse
Affiliation(s)
- Elsa Bernard
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | | | - Sean M Devlin
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Juan S Medina-Martinez
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Ryunosuke Saiki
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology, IRCCS Fondazione Policlinico S. Matteo, Pavia, Italy
| | - Max F Levine
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan E Arango
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yangyu Zhou
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francesc Solé
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Catherine A Cargo
- Haematological Malignancy Diagnostic Service, St James's University Hospital, Leeds, UK
| | - Detlef Haase
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Maria Creignou
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gunes Gundem
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Araxe Sarian
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Martin Jädersten
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Tobiasson
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Olivier Kosmider
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin and Université de Paris, Université Paris Descartes, Paris, France
| | - Matilde Y Follo
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation Hannover Medical School, Hannover, Germany
| | - Ronald F Pinheiro
- Drug Research and Development Center, Federal University of Ceara, Ceara, Brazil
| | - Valeria Santini
- MDS Unit, Hematology, AOU Careggi, University of Florence, Florence, Italy
| | - Ioannis Kotsianidis
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - Jacqueline Boultwood
- Radcliffe Department of Medicine, University of Oxford and Oxford BRC Haematology Theme, Oxford, UK
| | - Fabio P S Santos
- Oncology-Hematology Center, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Julie Schanz
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Senji Kasahara
- Department of Hematology, Gifu Municipal Hospital, Gifu, Japan
| | - Takayuki Ishikawa
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Hisashi Tsurumi
- Department of Hematology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toru Kiguchi
- Department of Hematology, Chugoku Central Hospital, Fukuyama, Japan
| | - Chantana Polprasert
- Department of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - John M Bennett
- Lab. Medicine and Pathology, Hematology/Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - Virginia M Klimek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Monika Belickova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Christina Ganster
- Clinics of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
| | - Laura Palomo
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Guillermo Sanz
- Department of Hematology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Lionel Ades
- Department of Hematology, Hôpital St Louis and Paris University, Paris, France
| | - Matteo Giovanni Della Porta
- Humanitas Clinical and Research Center-IRCCS, Humanitas Cancer Center, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Harold K Elias
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yesenia Werner
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Minal Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnès Viale
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katelynd Vanness
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Donna S Neuberg
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Kamal Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelly L Bolton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pierre Fenaux
- Department of Hematology, Hôpital St Louis and Paris University, Paris, France
| | - Andrea Pellagatti
- Radcliffe Department of Medicine, University of Oxford and Oxford BRC Haematology Theme, Oxford, UK
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular Therapy, University of Leipzig, Leipzig, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation Hannover Medical School, Hannover, Germany
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology and Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Shigeru Chiba
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Carlo Finelli
- Institute of Hematology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Maria Teresa Voso
- MDS Cooperative Group GROM-L, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Lee-Yung Shih
- Chang Gung Memorial Hospital at Linkou, Chang Gung University, Taoyuan City, Taiwan
| | - Michaela Fontenay
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin and Université de Paris, Université Paris Descartes, Paris, France
| | - Joop H Jansen
- Laboratory Hematology, Department LABGK, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - José Cervera
- Department of Hematology and Genetics Unit, University Hospital La Fe, Valencia, Spain
| | - Yoshiko Atsuta
- Japanese Data Center for Hematopoietic Cell Transplantation, Nagoya, Japan
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology and Howard Hughes Medical Institute, Dana-Farber Cancer Center, Boston, MA, USA
| | - Rafael Bejar
- UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology, IRCCS Fondazione Policlinico S. Matteo, Pavia, Italy
| | - Eva Hellström-Lindberg
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
47
|
Völkel G, Laban S, Fürstberger A, Kühlwein SD, Ikonomi N, Hoffmann TK, Brunner C, Neuberg DS, Gaidzik V, Döhner H, Kraus JM, Kestler HA. Analysis, identification and visualization of subgroups in genomics. Brief Bioinform 2020; 22:5909009. [PMID: 32954413 PMCID: PMC8138884 DOI: 10.1093/bib/bbaa217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
Motivation Cancer is a complex and heterogeneous disease involving multiple somatic mutations that accumulate during its progression. In the past years, the wide availability of genomic data from patients’ samples opened new perspectives in the analysis of gene mutations and alterations. Hence, visualizing and further identifying genes mutated in massive sets of patients are nowadays a critical task that sheds light on more personalized intervention approaches. Results Here, we extensively review existing tools for visualization and analysis of alteration data. We compare different approaches to study mutual exclusivity and sample coverage in large-scale omics data. We complement our review with the standalone software AVAtar (‘analysis and visualization of alteration data’) that integrates diverse aspects known from different tools into a comprehensive platform. AVAtar supplements customizable alteration plots by a multi-objective evolutionary algorithm for subset identification and provides an innovative and user-friendly interface for the evaluation of concurrent solutions. A use case from personalized medicine demonstrates its unique features showing an application on vaccination target selection. Availability AVAtar is available at: https://github.com/sysbio-bioinf/avatar Contact hans.kestler@uni-ulm.de, phone: +49 (0) 731 500 24 500, fax: +49 (0) 731 500 24 502
Collapse
Affiliation(s)
| | | | | | | | | | - Thomas K Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Donna S Neuberg
- Department of Biostatistics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Verena Gaidzik
- Department of Internal Medicine III, Ulm University Medical Center, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Medical Center, Germany
| | | | | |
Collapse
|
48
|
Knisbacher BA, Lin Z, Stewart C, Hahn CK, Stevenson KE, Neuberg DS, Martín-Subero JI, Puente XS, Campo E, Wu CJ, Getz G. Abstract 169: Discovery of clinically distinct CLL subgroups by integrative mapping of large-scale genetic, epigenetic, expression and clinical data. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Chronic lymphocytic leukemia (CLL) accounts for one third of all diagnosed leukemias. It exhibits tremendous clinical variability, ranging from indolent disease kinetics to a fast progressing aggressive disease. Two large-scale studies by our groups, each analyzing more than 500 CLL subjects, have shown that a large part of this clinical variability can be explained by underlying molecular features of the cancerous B-cells, including genetic and epigenetic alterations. Despite this progress, patients do not yet fully benefit from these discoveries in their treatment plans, and prognosis is not tailored to them based on the molecular features of their cancer. To achieve precision medicine, we compile a large dataset of multi-omic and clinical data from over 1100 CLL patients. Our extensive cohort confers power to detect novel driver genes, doubling the number of known drivers (114 total) and identifying drivers specific to major CLL subtypes, such as IGHV-mutated and IGHV-unmutated. The analysis identifies recurrent copy number alterations, order-of-event timing and mutational processes acting in CLL. We integrate these with expression data from 700 CLL RNA-seqs and epigenetic data to define molecular subtypes that present differential clinical outcomes. Altogether, this work delineates the molecular landscape of CLL and sets the stage for improved classification, prognostics and treatment of CLL patients.
Citation Format: Binyamin A. Knisbacher, Ziao Lin, Chip Stewart, Cynthia K. Hahn, Kristen E. Stevenson, Donna S. Neuberg, José I. Martín-Subero, Xose S. Puente, Elias Campo, Catherine J. Wu, Gad Getz. Discovery of clinically distinct CLL subgroups by integrative mapping of large-scale genetic, epigenetic, expression and clinical data [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 169.
Collapse
Affiliation(s)
| | - Ziao Lin
- 2Broad Institute of MIT and Harvard
- Harvard University, Cambridge, MA
| | - Chip Stewart
- 1Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard University, Cambridge, MA
| | - Cynthia K. Hahn
- 3Broad Institute of MIT and Harvard; Department of Medical Oncology, Dana-Farber Cancer Institute, MA
- Harvard University, Cambridge, MA
| | - Kristen E. Stevenson
- 4Department of Biostatistics and Computational Biology, DFCI, Boston, MA
- Harvard University, Cambridge, MA
| | - Donna S. Neuberg
- 4Department of Biostatistics and Computational Biology, DFCI, Boston, MA
- Harvard University, Cambridge, MA
| | - José I. Martín-Subero
- 5IDIBAPS, Barcelona; CIBERONC, Madrid; Universitat de Barcelona; ICREA, Barcelona, Spain
- Harvard University, Cambridge, MA
| | - Xose S. Puente
- 6Departamento de Bioquimica y Biologia Molecular, IUOPA, Universidad de Oviedo, Oviedo, Spain
- Harvard University, Cambridge, MA
| | - Elias Campo
- 7Hematopathology Section, Laboratory of Pathology, Hospital Clinic de Barcelona, Barcelona, Spain
- Harvard University, Cambridge, MA
| | - Catherine J. Wu
- 8Broad Institute of MIT and Harvard, Cambridge, MA; Department of Medical Oncology, DFCI, Boston; Department of Medicine, Brigham and Women's Hospital, Boston; Harvard Medical School, Boston, MA
- Harvard University, Cambridge, MA
| | - Gad Getz
- 9Broad Institute of MIT and Harvard, Cambridge; Harvard Medical School, Boston; Department of Pathology, MGH, Boston; Center for Cancer Research, MGH, Boston, MA
- Harvard University, Cambridge, MA
| |
Collapse
|
49
|
Carney BJ, Uhlmann EJ, Puligandla M, Mantia C, Weber GM, Neuberg DS, Zwicker JI. Anticoagulation after intracranial hemorrhage in brain tumors: Risk of recurrent hemorrhage and venous thromboembolism. Res Pract Thromb Haemost 2020; 4:860-865. [PMID: 32685895 PMCID: PMC7354400 DOI: 10.1002/rth2.12377] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/23/2020] [Accepted: 05/08/2020] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Intracranial hemorrhage (ICH) is a common and often devastating outcome in patients with brain tumors. Despite this, there is little evidence to guide anticoagulation management following an initial ICH event. OBJECTIVES To analyze the risk of recurrent hemorrhagic and thrombotic outcomes after an initial ICH event in patients with brain tumors and prior venous thromboembolism (VTE). PATIENTS AND METHODS A retrospective cohort study was performed. Radiographic images obtained after initial ICH were reviewed for the primary outcomes of recurrent ICH and VTE. RESULTS AND CONCLUSIONS A total of 79 patients with brain tumors who developed ICH on anticoagulation for VTE were analyzed. Fifty-four patients (68.4%) restarted anticoagulation following ICH. The cumulative incidence of recurrent ICH at 1 year was 6.1% (95% confidence interval [CI], 1.5-15.3) following reinitiation of anticoagulation. Following a major ICH (defined as an ICH >10 mL in size, causing symptoms, or requiring intervention), the rate of recurrent ICH upon reexposure to anticoagulation was 14.5% (95% CI, 2.1-38.35), whereas the rate of recurrent ICH following smaller ICH was 2.6% (95% CI, 0.2%-12.0%). Mortality following a recurrent ICH on anticoagulation was 67% at 30 days. The cumulative incidence of recurrent VTE was significantly lower in the restart cohort compared to patients who did not restart anticoagulation (8.1% vs 35.3%; P = .003). We conclude that resumption of anticoagulation is lowest among patients with metastatic brain tumors with small initial ICH. Following an initial major ICH, resumption of anticoagulation was associated with a high rate of recurrent ICH.
Collapse
Affiliation(s)
- Brian J. Carney
- Division of Hemostasis and ThrombosisBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Erik J. Uhlmann
- Department of NeurologyBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Maneka Puligandla
- Department of Data SciencesDana‐Farber Cancer InstituteBostonMassachusettsUSA
| | - Charlene Mantia
- Division of Hematology and OncologyBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Griffin M. Weber
- Interdisciplinary Medicine and BiotechnologyBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Donna S. Neuberg
- Department of Data SciencesDana‐Farber Cancer InstituteBostonMassachusettsUSA
| | - Jeffrey I. Zwicker
- Division of Hemostasis and ThrombosisBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMassachusettsUSA
| |
Collapse
|
50
|
Braun DA, Hou Y, Bakouny Z, Ficial M, Sant'Angelo M, Ross-Macdonald P, Jegede O, Sun M, Wind-Rotolo M, Pignon JC, Neuberg DS, Catalano PJ, Freeman GJ, Sharpe A, McDermott DF, Van Allen EM, Signoretti S, Wu CJ, Shukla SA, Choueiri TK. Immunogenomic characterization of advanced clear cell renal cell carcinoma treated with PD-1 blockade. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.5010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5010 Background: Immune checkpoint inhibitors targeting the PD-1 pathway have transformed the management of many advanced malignancies, including clear cell renal cell carcinoma (ccRCC), but the drivers and resistors of PD-1 response remain incompletely elucidated. Further, the common paradigm in solid tumor immunology that pre-existing CD8+ T cell infiltration, in combination with high numbers of nonsynonymous mutations (which, in the context of diverse HLA class I alleles, may be presented as neoantigens) drives response to PD-1 blockade, has not been thoroughly explored in ccRCC. Methods: We analyzed 592 tumors collected from advanced ccRCC patients enrolled in prospective clinical trials (CheckMate 009, CheckMate 010, CheckMate 025) of treatment with PD-1 blockade (n = 362) or mTOR inhibition (as control arm; n = 230) by whole-exome (n = 454) and RNA-sequencing (n = 311), integrated with CD8 immunofluorescence analysis (n = 219), to uncover the immunogenomic determinants of therapeutic response and survival. Wilcoxon rank-sum test was used to compare somatic alteration burden between clinical benefit (CB) v.s no CB (NCB); Fisher’s exact test was used to compare mutations and copy number alteration by infiltration state; and hazard ratio (HR) was calculated from Cox PH model for progression-free (PFS) and overall survival (OS) endpoints. All tests were at a significance level of p < 0.05. Results: Conventional genomic markers (tumor mutation burden, p = 0.81; neoantigen load, p = 0.47 for CB vs. NCB) and degree of CD8+ T cell infiltration (p = 0.88 for PFS; p = 0.65 for OS) were not associated with clinical response or altered survival with PD-1 blockade. These advanced ccRCC tumors were highly CD8+ T cell infiltrated, with only 22% having an immune desert phenotype and 5% with an immune excluded phenotype. Our analysis revealed that CD8+ T cell infiltrated tumors are depleted of clinically favorable PBRM1 mutations (p = 0.013) and enriched for unfavorable chromosomal losses of 9p21.3 (p < 0.001) when compared to non-infiltrated tumors. When found within infiltrated tumors, del(9p21.3) was associated with worse CB rate (36% (9/25) for del(9p21.3) vs. 88% (7/8) for wildtype at that locus, p = 0.017) and worse survival (HR = 2.38, p = 0.01 for PFS; HR = 2.44, p = 0.01 for OS) with PD-1 blockade. Conclusions: These data demonstrate how the potential interplay of immunophenotypes with somatic mutations and chromosomal alterations impacts therapeutic efficacy in advanced ccRCC.
Collapse
Affiliation(s)
| | - Yue Hou
- Dana-Farber Cancer Institute, Boston, MA
| | - Ziad Bakouny
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | - Maxine Sun
- Dana Farber Cancer Institute, Boston, MA
| | | | | | - Donna S. Neuberg
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | | | - David F. McDermott
- Beth Israel Deaconess Medical Center, Dana-Farber/Harvard Cancer Center, Boston, MA
| | | | | | | | | | - Toni K. Choueiri
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| |
Collapse
|