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Lin AL, Rudneva VA, Richards AL, Zhang Y, Woo HJ, Cohen M, Tisnado J, Majd N, Wardlaw SL, Page-Wilson G, Sengupta S, Chow F, Goichot B, Ozer BH, Dietrich J, Nachtigall L, Desai A, Alano T, Ogilive S, Solit DB, Bale TA, Rosenblum M, Donoghue MTA, Geer EB, Tabar V. Genome-wide loss of heterozygosity predicts aggressive, treatment-refractory behavior in pituitary neuroendocrine tumors. Acta Neuropathol 2024; 147:85. [PMID: 38758238 PMCID: PMC11101347 DOI: 10.1007/s00401-024-02736-8] [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: 02/21/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
Abstract
Pituitary neuroendocrine tumors (PitNETs) exhibiting aggressive, treatment-refractory behavior are the rare subset that progress after surgery, conventional medical therapies, and an initial course of radiation and are characterized by unrelenting growth and/or metastatic dissemination. Two groups of patients with PitNETs were sequenced: a prospective group of patients (n = 66) who consented to sequencing prior to surgery and a retrospective group (n = 26) comprised of aggressive/higher risk PitNETs. A higher mutational burden and fraction of loss of heterozygosity (LOH) was found in the aggressive, treatment-refractory PitNETs compared to the benign tumors (p = 1.3 × 10-10 and p = 8.5 × 10-9, respectively). Within the corticotroph lineage, a characteristic pattern of recurrent chromosomal LOH in 12 specific chromosomes was associated with treatment-refractoriness (occurring in 11 of 14 treatment-refractory versus 1 of 14 benign corticotroph PitNETs, p = 1.7 × 10-4). Across the cohort, a higher fraction of LOH was identified in tumors with TP53 mutations (p = 3.3 × 10-8). A machine learning approach identified loss of heterozygosity as the most predictive variable for aggressive, treatment-refractory behavior, outperforming the most common gene-level alteration, TP53, with an accuracy of 0.88 (95% CI: 0.70-0.96). Aggressive, treatment-refractory PitNETs are characterized by significant aneuploidy due to widespread chromosomal LOH, most prominently in the corticotroph tumors. This LOH predicts treatment-refractoriness with high accuracy and represents a novel biomarker for this poorly defined PitNET category.
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Affiliation(s)
- Andrew L Lin
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vasilisa A Rudneva
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hyung Jun Woo
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Cohen
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamie Tisnado
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nazanin Majd
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon L Wardlaw
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Gabrielle Page-Wilson
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Soma Sengupta
- Department of Neurology and Neurosurgery, University of North Carolina, Chapel Hill, NC, USA
| | - Frances Chow
- Department of Neurology, Keck School of Medicine at University of Southern California Medical Center, Los Angeles, CA, USA
| | - Bernard Goichot
- Department of Endocrinology, Les Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Byram H Ozer
- Department of Oncology, Sibley Memorial Hospital/Johns Hopkins, Washington, DC, USA
| | - Jorg Dietrich
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Lisa Nachtigall
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Arati Desai
- Department of Medicine, University of Pennsylvania Medical Center, Philadelphia, PA, USA
| | - Tina Alano
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shahiba Ogilive
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tejus A Bale
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Rosenblum
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eliza B Geer
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Viviane Tabar
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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2
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Dermawan JK, Chiang S, Singer S, Jadeja B, Hensley ML, Tap WD, Movva S, Maki RG, Antonescu CR. Developing Novel Genomic Risk Stratification Models in Soft Tissue and Uterine Leiomyosarcoma. Clin Cancer Res 2024; 30:2260-2271. [PMID: 38488807 PMCID: PMC11096044 DOI: 10.1158/1078-0432.ccr-24-0148] [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: 01/15/2024] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 05/16/2024]
Abstract
PURPOSE Leiomyosarcomas (LMS) are clinically and molecularly heterogeneous tumors. Despite recent large-scale genomic studies, current LMS risk stratification is not informed by molecular alterations. We propose a clinically applicable genomic risk stratification model. EXPERIMENTAL DESIGN We performed comprehensive genomic profiling in a cohort of 195 soft tissue LMS (STLMS), 151 primary at presentation, and a control group of 238 uterine LMS (ULMS), 177 primary at presentation, with at least 1-year follow-up. RESULTS In STLMS, French Federation of Cancer Centers (FNCLCC) grade but not tumor size predicted progression-free survival (PFS) or disease-specific survival (DSS). In contrast, in ULMS, tumor size, mitotic rate, and necrosis were associated with inferior PFS and DSS. In STLMS, a 3-tier genomic risk stratification performed well for DSS: high risk: co-occurrence of RB1 mutation and chr12q deletion (del12q)/ATRX mutation; intermediate risk: presence of RB1 mutation, ATRX mutation, or del12q; low risk: lack of any of these three alterations. The ability of RB1 and ATRX alterations to stratify STLMS was validated in an external AACR GENIE cohort. In ULMS, a 3-tier genomic risk stratification was significant for both PFS and DSS: high risk: concurrent TP53 mutation and chr20q amplification/ATRX mutations; intermediate risk: presence of TP53 mutation, ATRX mutation, or amp20q; low risk: lack of any of these three alterations. Longitudinal sequencing showed that most molecular alterations were early clonal events that persisted during disease progression. CONCLUSIONS Compared with traditional clinicopathologic models, genomic risk stratification demonstrates superior prediction of clinical outcome in STLMS and is comparable in ULMS.
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Affiliation(s)
- Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Diagnostics Institute, Cleveland Clinic, Cleveland, Ohio
| | - Sarah Chiang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bhumika Jadeja
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Martee L Hensley
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Sujana Movva
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Robert G Maki
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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3
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Friedman CF, Manning-Geist BL, Zhou Q, Soumerai T, Holland A, Da Cruz Paula A, Green H, Ozsoy MA, Iasonos A, Hollmann T, Leitao MM, Mueller JJ, Makker V, Tew WP, O'Cearbhaill RE, Liu YL, Rubinstein MM, Troso-Sandoval T, Lichtman SM, Schram A, Kyi C, Grisham RN, Causa Andrieu P, Wherry EJ, Aghajanian C, Weigelt B, Hensley ML, Zamarin D. Nivolumab for mismatch-repair-deficient or hypermutated gynecologic cancers: a phase 2 trial with biomarker analyses. Nat Med 2024; 30:1330-1338. [PMID: 38653864 PMCID: PMC11108776 DOI: 10.1038/s41591-024-02942-7] [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: 07/12/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
Programmed death-1 (PD-1) inhibitors are approved for therapy of gynecologic cancers with DNA mismatch repair deficiency (dMMR), although predictors of response remain elusive. We conducted a single-arm phase 2 study of nivolumab in 35 patients with dMMR uterine or ovarian cancers. Co-primary endpoints included objective response rate (ORR) and progression-free survival at 24 weeks (PFS24). Secondary endpoints included overall survival (OS), disease control rate (DCR), duration of response (DOR) and safety. Exploratory endpoints included biomarkers and molecular correlates of response. The ORR was 58.8% (97.5% confidence interval (CI): 40.7-100%), and the PFS24 rate was 64.7% (97.5% one-sided CI: 46.5-100%), meeting the pre-specified endpoints. The DCR was 73.5% (95% CI: 55.6-87.1%). At the median follow-up of 42.1 months (range, 8.9-59.8 months), median OS was not reached. One-year OS rate was 79% (95% CI: 60.9-89.4%). Thirty-two patients (91%) had a treatment-related adverse event (TRAE), including arthralgia (n = 10, 29%), fatigue (n = 10, 29%), pain (n = 10, 29%) and pruritis (n = 10, 29%); most were grade 1 or grade 2. Ten patients (29%) reported a grade 3 or grade 4 TRAE; no grade 5 events occurred. Exploratory analyses show that the presence of dysfunctional (CD8+PD-1+) or terminally dysfunctional (CD8+PD-1+TOX+) T cells and their interaction with programmed death ligand-1 (PD-L1)+ cells were independently associated with PFS24. PFS24 was associated with presence of MEGF8 or SETD1B somatic mutations. This trial met its co-primary endpoints (ORR and PFS24) early, and our findings highlight several genetic and tumor microenvironment parameters associated with response to PD-1 blockade in dMMR cancers, generating rationale for their validation in larger cohorts.ClinicalTrials.gov identifier: NCT03241745 .
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Affiliation(s)
- Claire F Friedman
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Beryl L Manning-Geist
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qin Zhou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tara Soumerai
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aliya Holland
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hunter Green
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melih Arda Ozsoy
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexia Iasonos
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis Hollmann
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mario M Leitao
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Jennifer J Mueller
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Vicky Makker
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - William P Tew
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Roisin E O'Cearbhaill
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Ying L Liu
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Maria M Rubinstein
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Tiffany Troso-Sandoval
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Stuart M Lichtman
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Alison Schram
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Chrisann Kyi
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Rachel N Grisham
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Pamela Causa Andrieu
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E John Wherry
- Institute of Immunology,University of Pennsylvania, Philadelphia, PA, USA
| | - Carol Aghajanian
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martee L Hensley
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Dmitriy Zamarin
- Tisch Cancer Institute,Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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4
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Garmezy B, Borad MJ, Bahleda R, Perez CA, Chen LT, Kato S, Oh DY, Severson P, Tam BY, Quah CS, Harding JJ. A Phase I Study of KIN-3248, an Irreversible Small-molecule Pan-FGFR Inhibitor, in Patients with Advanced FGFR2/3-driven Solid Tumors. Cancer Res Commun 2024; 4:1165-1173. [PMID: 38602417 PMCID: PMC11060137 DOI: 10.1158/2767-9764.crc-24-0137] [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] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/12/2024]
Abstract
PURPOSE Despite efficacy of approved FGFR inhibitors, emergence of polyclonal secondary mutations in the FGFR kinase domain leads to acquired resistance. KIN-3248 is a selective, irreversible, orally bioavailable, small-molecule inhibitor of FGFR1-4 that blocks both primary oncogenic and secondary kinase domain resistance FGFR alterations. EXPERIMENTAL DESIGN A first-in-human, phase I study of KIN-3248 was conducted in patients with advanced solid tumors harboring FGFR2 and/or FGFR3 gene alterations (NCT05242822). The primary objective was determination of MTD/recommended phase II dose (RP2D). Secondary and exploratory objectives included antitumor activity, pharmacokinetics, pharmacodynamics, and molecular response by circulating tumor DNA (ctDNA) clearance. RESULTS Fifty-four patients received doses ranging from 5 to 50 mg orally daily across six cohorts. Intrahepatic cholangiocarcinoma (48.1%), gastric (9.3%), and urothelial (7.4%) were the most common tumors. Tumors harbored FGFR2 (68.5%) or FGFR3 (31.5%) alterations-23 (42.6%) received prior FGFR inhibitors. One dose-limiting toxicity (hypersensitivity) occurred in cohort 1 (5 mg). Treatment-related, adverse events included hyperphosphatemia, diarrhea, and stomatitis. The MTD/RP2D was not established. Exposure was dose proportional and concordant with hyperphosphatemia. Five partial responses were observed; 4 in FGFR inhibitor naïve and 1 in FGFR pretreated patients. Pretreatment ctDNA profiling confirmed FGFR2/3 alterations in 63.3% of cases and clearance at cycle 2 associated with radiographic response. CONCLUSION The trial was terminated early for commercial considerations; therefore, RP2D was not established. Preliminary clinical data suggest that KIN-3248 is a safe, oral FGFR1-4 inhibitor with favorable pharmacokinetic parameters, though further dose escalation was required to nominate the MTD/RP2D. SIGNIFICANCE KIN-3248 was a rationally designed, next generation selective FGFR inhibitor, that was effective in interfering with both FGFR wild-type and mutant signaling. Clinical data indicate that KIN-3248 is safe with a signal of antitumor activity. Translational science support the mechanism of action in that serum phosphate was proportional with exposure, paired biopsies suggested phospho-ERK inhibition (a downstream target of FGFR2/3), and ctDNA clearance may act as a RECIST response surrogate.
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Affiliation(s)
| | | | - Rastilav Bahleda
- Drug Development Department (DITEP), Gustave Roussy, Villejuif, France
| | - Cesar A. Perez
- Sarah Cannon Research Institute at Florida Cancer Specialists, Orlando, Florida
| | - Li-Tzong Chen
- Kaohsiung Medical University Hospital and Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shumei Kato
- Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
| | - Do-Youn Oh
- Seoul National University Hospital, Cancer Research Institute, Seoul National University College of Medicine, Integrated Major in Innovative Medical Science, Seoul National University Graduate School, Seoul, Republic of South Korea
| | | | - Betty Y. Tam
- Formerly Kinnate Biopharma, San Francisco, California
| | | | - James J. Harding
- Gastrointestinal Oncology and Early Drug Development Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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5
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Varkaris A, Pazolli E, Gunaydin H, Wang Q, Pierce L, Boezio AA, Bulku A, DiPietro L, Fridrich C, Frost A, Giordanetto F, Hamilton EP, Harris K, Holliday M, Hunter TL, Iskandar A, Ji Y, Larivée A, LaRochelle JR, Lescarbeau A, Llambi F, Lormil B, Mader MM, Mar BG, Martin I, McLean TH, Michelsen K, Pechersky Y, Puente-Poushnejad E, Raynor K, Rogala D, Samadani R, Schram AM, Shortsleeves K, Swaminathan S, Tajmir S, Tan G, Tang Y, Valverde R, Wehrenberg B, Wilbur J, Williams BR, Zeng H, Zhang H, Walters WP, Wolf BB, Shaw DE, Bergstrom DA, Watters J, Fraser JS, Fortin PD, Kipp DR. Discovery and Clinical Proof-of-Concept of RLY-2608, a First-in-Class Mutant-Selective Allosteric PI3Kα Inhibitor That Decouples Antitumor Activity from Hyperinsulinemia. Cancer Discov 2024; 14:240-257. [PMID: 37916956 PMCID: PMC10850943 DOI: 10.1158/2159-8290.cd-23-0944] [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: 08/16/2023] [Revised: 10/21/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
PIK3CA (PI3Kα) is a lipid kinase commonly mutated in cancer, including ∼40% of hormone receptor-positive breast cancer. The most frequently observed mutants occur in the kinase and helical domains. Orthosteric PI3Kα inhibitors suffer from poor selectivity leading to undesirable side effects, most prominently hyperglycemia due to inhibition of wild-type (WT) PI3Kα. Here, we used molecular dynamics simulations and cryo-electron microscopy to identify an allosteric network that provides an explanation for how mutations favor PI3Kα activation. A DNA-encoded library screen leveraging electron microscopy-optimized constructs, differential enrichment, and an orthosteric-blocking compound led to the identification of RLY-2608, a first-in-class allosteric mutant-selective inhibitor of PI3Kα. RLY-2608 inhibited tumor growth in PIK3CA-mutant xenograft models with minimal impact on insulin, a marker of dysregulated glucose homeostasis. RLY-2608 elicited objective tumor responses in two patients diagnosed with advanced hormone receptor-positive breast cancer with kinase or helical domain PIK3CA mutations, with no observed WT PI3Kα-related toxicities. SIGNIFICANCE Treatments for PIK3CA-mutant cancers are limited by toxicities associated with the inhibition of WT PI3Kα. Molecular dynamics, cryo-electron microscopy, and DNA-encoded libraries were used to develop RLY-2608, a first-in-class inhibitor that demonstrates mutant selectivity in patients. This marks the advance of clinical mutant-selective inhibition that overcomes limitations of orthosteric PI3Kα inhibitors. See related commentary by Gong and Vanhaesebroeck, p. 204 . See related article by Varkaris et al., p. 227 . This article is featured in Selected Articles from This Issue, p. 201.
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Affiliation(s)
- Andreas Varkaris
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | | | - Qi Wang
- D. E. Shaw Research, New York, New York
| | - Levi Pierce
- Relay Therapeutics, Inc., Cambridge, Massachusetts
| | | | | | | | | | - Adam Frost
- Altos Labs, Institute of Science, San Francisco, California
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California
- California Institute of Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California
| | | | - Erika P. Hamilton
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, Tennessee
| | - Katherine Harris
- MGH/Mass General Cancer Center at Danvers, Danvers, Massachusetts
| | | | | | | | - Yongli Ji
- Hematology/Oncology, Exeter Hospital, Exeter, New Hampshire
| | | | | | | | | | - Brenda Lormil
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | | | - Iain Martin
- Relay Therapeutics, Inc., Cambridge, Massachusetts
| | | | | | | | | | - Kevin Raynor
- Relay Therapeutics, Inc., Cambridge, Massachusetts
| | | | | | - Alison M. Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Shahein Tajmir
- MGH Radiology, Harvard Medical School, Boston, Massachusetts
| | - Gege Tan
- Relay Therapeutics, Inc., Cambridge, Massachusetts
| | - Yong Tang
- Relay Therapeutics, Inc., Cambridge, Massachusetts
| | | | | | | | | | - Hongtao Zeng
- Relay Therapeutics, Inc., Cambridge, Massachusetts
| | - Hanmo Zhang
- Relay Therapeutics, Inc., Cambridge, Massachusetts
| | - W. Patrick Walters
- Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Beni B. Wolf
- Relay Therapeutics, Inc., Cambridge, Massachusetts
| | - David E. Shaw
- D. E. Shaw Research, New York, New York
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York
| | | | | | - James S. Fraser
- California Institute of Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California
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6
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Guercio BJ, Sarfaty M, Teo MY, Ratna N, Duzgol C, Funt SA, Lee CH, Aggen DH, Regazzi AM, Chen Z, Lattanzi M, Al-Ahmadie HA, Brannon AR, Shah R, Chu C, Lenis AT, Pietzak E, Bochner BH, Berger MF, Solit DB, Rosenberg JE, Bajorin DF, Iyer G. Clinical and Genomic Landscape of FGFR3-Altered Urothelial Carcinoma and Treatment Outcomes with Erdafitinib: A Real-World Experience. Clin Cancer Res 2023; 29:4586-4595. [PMID: 37682528 DOI: 10.1158/1078-0432.ccr-23-1283] [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: 05/04/2023] [Revised: 07/02/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023]
Abstract
PURPOSE Erdafitinib is the only FDA-approved targeted therapy for FGFR2/3-altered metastatic urothelial cancer. We characterized the genetic landscape of FGFR-altered urothelial carcinoma and real-world clinical outcomes with erdafitinib, including on-treatment genomic evolution. EXPERIMENTAL DESIGN Prospectively collected clinical data were integrated with institutional genomic data to define the landscape of FGFR2/3-altered urothelial carcinoma. To identify mechanisms of erdafitinib resistance, a subset of patients underwent prospective cell-free (cf) DNA assessment. RESULTS FGFR3 alterations predictive of erdafitinib sensitivity were identified in 39% (199/504) of patients with non-muscle invasive, 14% (75/526) with muscle-invasive, 43% (81/187) with localized upper tract, and 26% (59/228) with metastatic specimens. One patient had a potentially sensitizing FGFR2 fusion. Among 27 FGFR3-altered cases with a primary tumor and metachronous metastasis, 7 paired specimens (26%) displayed discordant FGFR3 status. Erdafitinib achieved a response rate of 40% but median progression-free and overall survival of only 2.8 and 6.6 months, respectively (n = 32). Dose reductions (38%, 12/32) and interruptions (50%, 16/32) were common. Putative resistance mutations detected in cfDNA involved TP53 (n = 5), AKT1 (n = 1), and second-site FGFR3 mutations (n = 2). CONCLUSIONS FGFR3 mutations are common in urothelial carcinoma, whereas FGFR2 alterations are rare. Discordance of FGFR3 mutational status between primary and metastatic tumors occurs frequently and raises concern over sequencing archival primary tumors to guide patient selection for erdafitinib therapy. Erdafitinib responses were typically brief and dosing was limited by toxicity. FGFR3, AKT1, and TP53 mutations detected in cfDNA represent putative mechanisms of acquired erdafitinib resistance.
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Affiliation(s)
- Brendan J Guercio
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York
| | - Michal Sarfaty
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Min Yuen Teo
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Neha Ratna
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cihan Duzgol
- Commonwealth Radiology Associates, Andover, Massachusetts
| | - Samuel A Funt
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Chung-Han Lee
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - David H Aggen
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Ashley M Regazzi
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ziyu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Hikmat A Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - A Rose Brannon
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronak Shah
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carissa Chu
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew T Lenis
- Department of Urology, Columbia University Irving Medical Center, New York, New York
| | - Eugene Pietzak
- Weill Cornell Medical College, New York, New York
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bernard H Bochner
- Weill Cornell Medical College, New York, New York
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan E Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Dean F Bajorin
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Gopa Iyer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
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7
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Friedman CF, Ravichandran V, Miller K, Vanderbilt C, Zhou Q, Iasonos A, Vivek M, Mishra P, Leitao MM, Broach V, Sonoda Y, Kyi C, Zamarin D, O'Cearbhaill RE, Konner J, Berger MF, Weigelt B, Momeni Boroujeni A, Park KJ, Aghajanian C, Solit DB, Donoghue MT. Assessing the Genomic Landscape of Cervical Cancers: Clinical Opportunities and Therapeutic Targets. Clin Cancer Res 2023; 29:4660-4668. [PMID: 37643132 PMCID: PMC10644000 DOI: 10.1158/1078-0432.ccr-23-1078] [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: 04/12/2023] [Revised: 06/29/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
Abstract
PURPOSE Tumor genomic profiling is increasingly used to guide treatment strategy in patients with cancer. We integrated tumor genomic, clinical demographic, and treatment response data to assess how prospective tumor-normal sequencing impacted treatment selection in patients with cervical cancer. EXPERIMENTAL DESIGN Cervical cancers were prospectively analyzed using the MSK-IMPACT (Memorial Sloan Kettering Cancer Center - Integrated Mutation Profiling of Actionable Cancer Targets) next-generation sequencing panel. Clinical data, including histology, stage at diagnosis, treatment history, clinical trial enrollment and outcomes, date of last follow-up, and survival status were obtained from medical records. RESULTS A total of 177 patients with cervical cancer (squamous, 69; endocervical adenocarcinoma, 50; gastric type, 22; adenosquamous, 21; and other, 15) underwent MSK-IMPACT testing. The most prevalent genomic alterations were somatic mutations or amplifications in PIK3CA (25%), ERBB2 (12%), KMT2C (10%), and KMT2D (9%). Furthermore, 13% of patients had high tumor mutational burden (TMB >10 mut/Mb), 3 of which were also microsatellite instability-high (MSI-H). Thirty-seven percent of cases had at least one potentially actionable alteration designated as a level 3B mutational event according to the FDA-recognized OncoKB tumor mutation database and treatment classification system. A total of 30 patients (17%) were enrolled on a therapeutic clinical trial, including 18 (10%) who were matched with a study based on their MSK-IMPACT results. Twenty patients (11%) participated in an immune checkpoint inhibition study for metastatic disease; 2 remain progression free at >5 years follow-up. CONCLUSIONS Tumor genomic profiling can facilitate the selection of targeted/immunotherapies, as well as clinical trial enrollment, for patients with cervical cancer.
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Affiliation(s)
- Claire F. Friedman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Vignesh Ravichandran
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kathryn Miller
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Qin Zhou
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexia Iasonos
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Malavika Vivek
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pamela Mishra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mario M. Leitao
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of OB/GYN, Weill Cornell Medical College, New York, New York
| | - Vance Broach
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of OB/GYN, Weill Cornell Medical College, New York, New York
| | - Yukio Sonoda
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of OB/GYN, Weill Cornell Medical College, New York, New York
| | - Chrisann Kyi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Dmitriy Zamarin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Roisin E. O'Cearbhaill
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Jason Konner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amir Momeni Boroujeni
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kay J. Park
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - David B. Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark T.A. Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
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8
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Robinson TM, Bowman RL, Persaud S, Liu Y, Neigenfind R, Gao Q, Zhang J, Sun X, Miles LA, Cai SF, Sciambi A, Llanso A, Famulare C, Goldberg A, Dogan A, Roshal M, Levine RL, Xiao W. Single-cell genotypic and phenotypic analysis of measurable residual disease in acute myeloid leukemia. Sci Adv 2023; 9:eadg0488. [PMID: 37729414 PMCID: PMC10881057 DOI: 10.1126/sciadv.adg0488] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/21/2023] [Indexed: 09/22/2023]
Abstract
Measurable residual disease (MRD), defined as the population of cancer cells that persist following therapy, serves as the critical reservoir for disease relapse in acute myeloid leukemia and other malignancies. Understanding the biology enabling MRD clones to resist therapy is necessary to guide the development of more effective curative treatments. Discriminating between residual leukemic clones, preleukemic clones, and normal precursors remains a challenge with current MRD tools. Here, we developed a single-cell MRD (scMRD) assay by combining flow cytometric enrichment of the targeted precursor/blast population with integrated single-cell DNA sequencing and immunophenotyping. Our scMRD assay shows high sensitivity of approximately 0.01%, deconvolutes clonal architecture, and provides clone-specific immunophenotypic data. In summary, our scMRD assay enhances MRD detection and simultaneously illuminates the clonal architecture of clonal hematopoiesis/preleukemic and leukemic cells surviving acute myeloid leukemia therapy.
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Affiliation(s)
- Troy M. Robinson
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sonali Persaud
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Liu
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rosemary Neigenfind
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qi Gao
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jingping Zhang
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaotian Sun
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Linde A. Miles
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sheng F. Cai
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Christopher Famulare
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aaron Goldberg
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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9
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Maron SB, Chatila W, Walch H, Chou JF, Ceglia N, Ptashkin R, Do RKG, Paroder V, Pandit-Taskar N, Lewis JS, Biachi De Castria T, Sabwa S, Socolow F, Feder L, Thomas J, Schulze I, Kim K, Elzein A, Bojilova V, Zatzman M, Bhanot U, Nagy RJ, Lee J, Simmons M, Segal M, Ku GY, Ilson DH, Capanu M, Hechtman JF, Merghoub T, Shah S, Schultz N, Solit DB, Janjigian YY. Determinants of Survival with Combined HER2 and PD-1 Blockade in Metastatic Esophagogastric Cancer. Clin Cancer Res 2023; 29:3633-3640. [PMID: 37406106 PMCID: PMC10502449 DOI: 10.1158/1078-0432.ccr-22-3769] [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: 12/09/2022] [Revised: 02/21/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
PURPOSE We report updated clinical outcomes from a phase II study of pembrolizumab, trastuzumab, and chemotherapy (PTC) in metastatic esophagogastric cancer in conjunction with outcomes from an independent Memorial Sloan Kettering (MSK) cohort. PATIENTS AND METHODS The significance of pretreatment 89Zr-trastuzumab PET, plasma circulating tumor DNA (ctDNA) dynamics, and tumor HER2 expression and whole exome sequencing was evaluated to identify prognostic biomarkers and mechanisms of resistance in patients treated on-protocol with PTC. Additional prognostic features were evaluated using a multivariable Cox regression model of trastuzumab-treated MSK patients (n = 226). Single-cell RNA sequencing (scRNA-seq) data from MSK and Samsung were evaluated for mechanisms of therapy resistance. RESULTS 89Zr-trastuzumab PET, scRNA-seq, and serial ctDNA with CT imaging identified how pre-treatment intrapatient genomic heterogeneity contributes to inferior progression-free survival (PFS). We demonstrated that the presence of intensely avid lesions by 89Zr-trastuzumab PET declines in tumor-matched ctDNA by 3 weeks, and clearance of tumor-matched ctDNA by 9 weeks were minimally invasive biomarkers of durable PFS. Paired pre- and on-treatment scRNA-seq identified rapid clearance of HER2-expressing tumor clones with expansion of clones expressing a transcriptional resistance program, which was associated with MT1H, MT1E, MT2A, and MSMB expression. Among trastuzumab-treated patients at MSK, ERBB2 amplification was associated with improved PFS, while alterations in MYC and CDKN2A/B were associated with inferior PFS. CONCLUSIONS These findings highlight the clinical relevance of identifying baseline intrapatient heterogeneity and serial ctDNA monitoring of HER2-positive esophagogastric cancer patients to identify early evidence of treatment resistance, which could guide proactive therapy escalation or deescalation.
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Affiliation(s)
- Steven B. Maron
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Walid Chatila
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Henry Walch
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joanne F. Chou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryan Ptashkin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard Kinh Gian Do
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Viktoriya Paroder
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neeta Pandit-Taskar
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason S. Lewis
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tiago Biachi De Castria
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shalom Sabwa
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fiona Socolow
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lara Feder
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jasmine Thomas
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Isabell Schulze
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kwanghee Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arijh Elzein
- Department of Pharmacology, Weill Cornell Medicine Graduate School of Medical Sciences, New York, New York
| | - Viktoria Bojilova
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew Zatzman
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Umesh Bhanot
- Precision Pathology Center, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Marc Simmons
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michal Segal
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Yuyat Ku
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - David H. Ilson
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Marinela Capanu
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F. Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Taha Merghoub
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sohrab Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B. Solit
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y. Janjigian
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
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10
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Yang N, Wang Y, Liu S, Tariq SB, Luna JM, Mazo G, Tan A, Zhang T, Wang J, Yan W, Choi J, Rossi A, Xiang JZ, Rice CM, Merghoub T, Wolchok JD, Deng L. OX40L-expressing recombinant modified vaccinia virus Ankara induces potent antitumor immunity via reprogramming Tregs. J Exp Med 2023; 220:e20221166. [PMID: 37145142 PMCID: PMC10165539 DOI: 10.1084/jem.20221166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 07/06/2022] [Revised: 03/05/2023] [Accepted: 04/06/2023] [Indexed: 05/06/2023] Open
Abstract
Effective depletion of immune suppressive regulatory T cells (Tregs) in the tumor microenvironment without triggering systemic autoimmunity is an important strategy for cancer immunotherapy. Modified vaccinia virus Ankara (MVA) is a highly attenuated, non-replicative vaccinia virus with a long history of human use. Here, we report rational engineering of an immune-activating recombinant MVA (rMVA, MVA∆E5R-Flt3L-OX40L) with deletion of the vaccinia E5R gene (encoding an inhibitor of the DNA sensor cyclic GMP-AMP synthase, cGAS) and expression of two membrane-anchored transgenes, Flt3L and OX40L. Intratumoral (IT) delivery of rMVA (MVA∆E5R-Flt3L-OX40L) generates potent antitumor immunity, dependent on CD8+ T cells, the cGAS/STING-mediated cytosolic DNA-sensing pathway, and type I IFN signaling. Remarkably, IT rMVA (MVA∆E5R-Flt3L-OX40L) depletes OX40hi regulatory T cells via OX40L/OX40 interaction and IFNAR signaling. Single-cell RNA-seq analyses of tumors treated with rMVA showed the depletion of OX40hiCCR8hi Tregs and expansion of IFN-responsive Tregs. Taken together, our study provides a proof-of-concept for depleting and reprogramming intratumoral Tregs via an immune-activating rMVA.
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Affiliation(s)
- Ning Yang
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Wang
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shuaitong Liu
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shanza Baseer Tariq
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph M. Luna
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Gregory Mazo
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adrian Tan
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, USA
| | - Tuo Zhang
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, USA
| | | | - Wei Yan
- IMVAQ Therapeutics, Sammamish, WA, USA
| | - John Choi
- IMVAQ Therapeutics, Sammamish, WA, USA
| | - Anthony Rossi
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenny Zhaoying Xiang
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, USA
| | - Charles M. Rice
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Taha Merghoub
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Jedd D. Wolchok
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Liang Deng
- Department of Medicine, Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Dermatology, Weill Cornell Medical College, New York, NY, USA
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11
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Bolton KL, Chen D, Corona de la Fuente R, Fu Z, Murali R, Köbel M, Tazi Y, Cunningham JM, Chan IC, Wiley BJ, Moukarzel LA, Winham SJ, Armasu SM, Lester J, Elishaev E, Laslavic A, Kennedy CJ, Piskorz A, Sekowska M, Brand AH, Chiew YE, Pharoah P, Elias KM, Drapkin R, Churchman M, Gourley C, DeFazio A, Karlan B, Brenton JD, Weigelt B, Anglesio MS, Huntsman D, Gayther S, Konner J, Modugno F, Lawrenson K, Goode EL, Papaemmanuil E. Molecular Subclasses of Clear Cell Ovarian Carcinoma and Their Impact on Disease Behavior and Outcomes. Clin Cancer Res 2022; 28:4947-4956. [PMID: 35816189 PMCID: PMC9777703 DOI: 10.1158/1078-0432.ccr-21-3817] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/24/2022] [Accepted: 07/07/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE To identify molecular subclasses of clear cell ovarian carcinoma (CCOC) and assess their impact on clinical presentation and outcomes. EXPERIMENTAL DESIGN We profiled 421 primary CCOCs that passed quality control using a targeted deep sequencing panel of 163 putative CCOC driver genes and whole transcriptome sequencing of 211 of these tumors. Molecularly defined subgroups were identified and tested for association with clinical characteristics and overall survival. RESULTS We detected a putative somatic driver mutation in at least one candidate gene in 95% (401/421) of CCOC tumors including ARID1A (in 49% of tumors), PIK3CA (49%), TERT (20%), and TP53 (16%). Clustering of cancer driver mutations and RNA expression converged upon two distinct subclasses of CCOC. The first was dominated by ARID1A-mutated tumors with enriched expression of canonical CCOC genes and markers of platinum resistance; the second was largely comprised of tumors with TP53 mutations and enriched for the expression of genes involved in extracellular matrix organization and mesenchymal differentiation. Compared with the ARID1A-mutated group, women with TP53-mutated tumors were more likely to have advanced-stage disease, no antecedent history of endometriosis, and poorer survival, driven by their advanced stage at presentation. In women with ARID1A-mutated tumors, there was a trend toward a lower rate of response to first-line platinum-based therapy. CONCLUSIONS Our study suggests that CCOC consists of two distinct molecular subclasses with distinct clinical presentation and outcomes, with potential relevance to both traditional and experimental therapy responsiveness. See related commentary by Lheureux, p. 4838.
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Affiliation(s)
- Kelly L. Bolton
- Washington University School of Medicine, St. Louis, Missouri
| | - Denise Chen
- Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania
| | | | - Zhuxuan Fu
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | | | - Martin Köbel
- The University of Calgary, Calgary, Alberta, Canada
| | - Yanis Tazi
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | | | - Brian J. Wiley
- Washington University School of Medicine, St. Louis, Missouri
| | | | | | | | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | - Esther Elishaev
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Angela Laslavic
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Catherine J. Kennedy
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Anna Piskorz
- University of Cambridge, Cambridge, United Kingdom
| | | | - Alison H. Brand
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Yoke-Eng Chiew
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Paul Pharoah
- University of Cambridge, Cambridge, United Kingdom
| | | | - Ronny Drapkin
- University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | - Anna DeFazio
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| | - Beth Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | | | - Britta Weigelt
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | - David Huntsman
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Simon Gayther
- Cedars-Sinai Medical Center, Los Angeles, California
| | - Jason Konner
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Francesmary Modugno
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
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12
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Vanguri RS, Luo J, Aukerman AT, Egger JV, Fong CJ, Horvat N, Pagano A, Araujo-Filho JDAB, Geneslaw L, Rizvi H, Sosa R, Boehm KM, Yang SR, Bodd FM, Ventura K, Hollmann TJ, Ginsberg MS, Gao J, Hellmann MD, Sauter JL, Shah SP. Multimodal integration of radiology, pathology and genomics for prediction of response to PD-(L)1 blockade in patients with non-small cell lung cancer. Nat Cancer 2022; 3:1151-1164. [PMID: 36038778 PMCID: PMC9586871 DOI: 10.1038/s43018-022-00416-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [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] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/29/2022] [Indexed: 11/23/2022]
Abstract
Immunotherapy is used to treat almost all patients with advanced non-small cell lung cancer (NSCLC); however, identifying robust predictive biomarkers remains challenging. Here we show the predictive capacity of integrating medical imaging, histopathologic and genomic features to predict immunotherapy response using a cohort of 247 patients with advanced NSCLC with multimodal baseline data obtained during diagnostic clinical workup, including computed tomography scan images, digitized programmed death ligand-1 immunohistochemistry slides and known outcomes to immunotherapy. Using domain expert annotations, we developed a computational workflow to extract patient-level features and used a machine-learning approach to integrate multimodal features into a risk prediction model. Our multimodal model (area under the curve (AUC) = 0.80, 95% confidence interval (CI) 0.74-0.86) outperformed unimodal measures, including tumor mutational burden (AUC = 0.61, 95% CI 0.52-0.70) and programmed death ligand-1 immunohistochemistry score (AUC = 0.73, 95% CI 0.65-0.81). Our study therefore provides a quantitative rationale for using multimodal features to improve prediction of immunotherapy response in patients with NSCLC using expert-guided machine learning.
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Affiliation(s)
- Rami S Vanguri
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jia Luo
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew T Aukerman
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacklynn V Egger
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher J Fong
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natally Horvat
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Pagano
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Luke Geneslaw
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hira Rizvi
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ramon Sosa
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin M Boehm
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francis M Bodd
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katia Ventura
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis J Hollmann
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Michelle S Ginsberg
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jianjiong Gao
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Hellmann
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Jennifer L Sauter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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13
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Ganly I, Liu EM, Kuo F, Makarov V, Dong Y, Park J, Gong Y, Gorelick AN, Knauf JA, Benedetti E, Tait-Mulder J, Morris LG, Fagin JA, Intlekofer AM, Krumsiek J, Gammage PA, Ghossein R, Xu B, Chan TA, Reznik E. Mitonuclear genotype remodels the metabolic and microenvironmental landscape of Hürthle cell carcinoma. Sci Adv 2022; 8:eabn9699. [PMID: 35731870 PMCID: PMC9216518 DOI: 10.1126/sciadv.abn9699] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Hürthle cell carcinomas (HCCs) display two exceptional genotypes: near-homoplasmic mutation of mitochondrial DNA (mtDNA) and genome-wide loss of heterozygosity (gLOH). To understand the phenotypic consequences of these genetic alterations, we analyzed genomic, metabolomic, and immunophenotypic data of HCC and other thyroid cancers. Both mtDNA mutations and profound depletion of citrate pools are common in HCC and other thyroid malignancies, suggesting that thyroid cancers are broadly equipped to survive tricarboxylic acid cycle impairment, whereas metabolites in the reduced form of NADH-dependent lysine degradation pathway were elevated exclusively in HCC. The presence of gLOH was not associated with metabolic phenotypes but rather with reduced immune infiltration, indicating that gLOH confers a selective advantage partially through immunosuppression. Unsupervised multimodal clustering revealed four clusters of HCC with distinct clinical, metabolomic, and microenvironmental phenotypes but overlapping genotypes. These findings chart the metabolic and microenvironmental landscape of HCC and shed light on the interaction between genotype, metabolism, and the microenvironment in cancer.
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Affiliation(s)
- Ian Ganly
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Minwei Liu
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fengshen Kuo
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yiyu Dong
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinsung Park
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yongxing Gong
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander N. Gorelick
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeffrey A Knauf
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Elisa Benedetti
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Luc G.T. Morris
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James A. Fagin
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew M Intlekofer
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jan Krumsiek
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Payam A. Gammage
- CRUK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A. Chan
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ed Reznik
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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14
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Schad SE, Chow A, Mangarin L, Pan H, Zhang J, Ceglia N, Caushi JX, Malandro N, Zappasodi R, Gigoux M, Hirschhorn D, Budhu S, Amisaki M, Arniella M, Redmond D, Chaft J, Forde PM, Gainor JF, Hellmann MD, Balachandran V, Shah S, Smith KN, Pardoll D, Elemento O, Wolchok JD, Merghoub T. Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions. J Exp Med 2022; 219:e20212169. [PMID: 35604411 PMCID: PMC9130031 DOI: 10.1084/jem.20212169] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 10/20/2021] [Revised: 01/04/2022] [Accepted: 03/08/2022] [Indexed: 11/04/2022] Open
Abstract
Transcription factors ThPOK and Runx3 regulate the differentiation of "helper" CD4+ and "cytotoxic" CD8+ T cell lineages respectively, inducing single positive (SP) T cells that enter the periphery with the expression of either the CD4 or CD8 co-receptor. Despite the expectation that these cell fates are mutually exclusive and that mature CD4+CD8+ double positive (DP) T cells are present in healthy individuals and augmented in the context of disease, yet their molecular features and pathophysiologic role are disputed. Here, we show DP T cells in murine and human tumors as a heterogenous population originating from SP T cells which re-express the opposite co-receptor and acquire features of the opposite cell type's phenotype and function following TCR stimulation. We identified distinct clonally expanded DP T cells in human melanoma and lung cancer by scRNA sequencing and demonstrated their tumor reactivity in cytotoxicity assays. Our findings indicate that antigen stimulation induces SP T cells to differentiate into DP T cell subsets gaining in polyfunctional characteristics.
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Affiliation(s)
- Sara E. Schad
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Andrew Chow
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Levi Mangarin
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Heng Pan
- Weill Cornell Medical College, New York, NY
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY
| | - Jiajia Zhang
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justina X. Caushi
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Nicole Malandro
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Roberta Zappasodi
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Mathieu Gigoux
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel Hirschhorn
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sadna Budhu
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Masataka Amisaki
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Jamie Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Patrick M. Forde
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Justin F. Gainor
- Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Matthew D. Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vinod Balachandran
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sohrab Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kellie N. Smith
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Drew Pardoll
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Olivier Elemento
- Weill Cornell Medical College, New York, NY
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY
| | - Jedd D. Wolchok
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Taha Merghoub
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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15
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Swinburne NC, Yadav V, Kim J, Choi YR, Gutman DC, Yang JT, Moss N, Stone J, Tisnado J, Hatzoglou V, Haque SS, Karimi S, Lyo J, Juluru K, Pichotta K, Gao J, Shah SP, Holodny AI, Young RJ. Semisupervised Training of a Brain MRI Tumor Detection Model Using Mined Annotations. Radiology 2022; 303:80-89. [PMID: 35040676 PMCID: PMC8962822 DOI: 10.1148/radiol.210817] [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: 03/30/2021] [Revised: 10/12/2021] [Accepted: 11/03/2021] [Indexed: 11/11/2022]
Abstract
Background Artificial intelligence (AI) applications for cancer imaging conceptually begin with automated tumor detection, which can provide the foundation for downstream AI tasks. However, supervised training requires many image annotations, and performing dedicated post hoc image labeling is burdensome and costly. Purpose To investigate whether clinically generated image annotations can be data mined from the picture archiving and communication system (PACS), automatically curated, and used for semisupervised training of a brain MRI tumor detection model. Materials and Methods In this retrospective study, the cancer center PACS was mined for brain MRI scans acquired between January 2012 and December 2017 and included all annotated axial T1 postcontrast images. Line annotations were converted to boxes, excluding boxes shorter than 1 cm or longer than 7 cm. The resulting boxes were used for supervised training of object detection models using RetinaNet and Mask region-based convolutional neural network (R-CNN) architectures. The best-performing model trained from the mined data set was used to detect unannotated tumors on training images themselves (self-labeling), automatically correcting many of the missing labels. After self-labeling, new models were trained using this expanded data set. Models were scored for precision, recall, and F1 using a held-out test data set comprising 754 manually labeled images from 100 patients (403 intra-axial and 56 extra-axial enhancing tumors). Model F1 scores were compared using bootstrap resampling. Results The PACS query extracted 31 150 line annotations, yielding 11 880 boxes that met inclusion criteria. This mined data set was used to train models, yielding F1 scores of 0.886 for RetinaNet and 0.908 for Mask R-CNN. Self-labeling added 18 562 training boxes, improving model F1 scores to 0.935 (P < .001) and 0.954 (P < .001), respectively. Conclusion The application of semisupervised learning to mined image annotations significantly improved tumor detection performance, achieving an excellent F1 score of 0.954. This development pipeline can be extended for other imaging modalities, repurposing unused data silos to potentially enable automated tumor detection across radiologic modalities. © RSNA, 2022 Online supplemental material is available for this article.
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Affiliation(s)
| | | | - Julie Kim
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Ye R. Choi
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - David C. Gutman
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Jonathan T. Yang
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Nelson Moss
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Jacqueline Stone
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Jamie Tisnado
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Vaios Hatzoglou
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Sofia S. Haque
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Sasan Karimi
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - John Lyo
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Krishna Juluru
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Karl Pichotta
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Jianjiong Gao
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Sohrab P. Shah
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Andrei I. Holodny
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
| | - Robert J. Young
- From the Departments of Radiology (N.C.S., V.Y., Y.R.C., D.C.G.,
J.T., V.H., S.S.H., S.K., J.L., K.J., A.I.H., R.J.Y.), Radiation Oncology
(J.T.Y.), Neurosurgery (N.M.), Neurology (J.S.), and Epidemiology and
Biostatistics, Division of Computational Oncology, (K.P., J.G., S.P.S.),
Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Weill
Cornell Medical College, New York, NY (J.K.)
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16
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Tsui DWY, Cheng ML, Shady M, Yang JL, Stephens D, Won H, Srinivasan P, Huberman K, Meng F, Jing X, Patel J, Hasan M, Johnson I, Gedvilaite E, Houck-Loomis B, Socci ND, Selcuklu SD, Seshan VE, Zhang H, Chakravarty D, Zehir A, Benayed R, Arcila M, Ladanyi M, Funt SA, Feldman DR, Li BT, Razavi P, Rosenberg J, Bajorin D, Iyer G, Abida W, Scher HI, Rathkopf D, Viale A, Berger MF, Solit DB. Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients. Genome Med 2021; 13:96. [PMID: 34059130 PMCID: PMC8165771 DOI: 10.1186/s13073-021-00898-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 03/02/2020] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) profiling is increasingly used to guide cancer care, yet mutations are not always identified. The ability to detect somatic mutations in plasma depends on both assay sensitivity and the fraction of circulating DNA in plasma that is tumor-derived (i.e., cfDNA tumor fraction). We hypothesized that cfDNA tumor fraction could inform the interpretation of negative cfDNA results and guide the choice of subsequent assays of greater genomic breadth or depth. METHODS Plasma samples collected from 118 metastatic cancer patients were analyzed with cf-IMPACT, a modified version of the FDA-authorized MSK-IMPACT tumor test that can detect genomic alterations in 410 cancer-associated genes. Shallow whole genome sequencing (sWGS) was also performed in the same samples to estimate cfDNA tumor fraction based on genome-wide copy number alterations using z-score statistics. Plasma samples with no somatic alterations detected by cf-IMPACT were triaged based on sWGS-estimated tumor fraction for analysis with either a less comprehensive but more sensitive assay (MSK-ACCESS) or broader whole exome sequencing (WES). RESULTS cfDNA profiling using cf-IMPACT identified somatic mutations in 55/76 (72%) patients for whom MSK-IMPACT tumor profiling data were available. A significantly higher concordance of mutational profiles and tumor mutational burden (TMB) was observed between plasma and tumor profiling for plasma samples with a high tumor fraction (z-score≥5). In the 42 patients from whom tumor data was not available, cf-IMPACT identified mutations in 16/42 (38%). In total, cf-IMPACT analysis of plasma revealed mutations in 71/118 (60%) patients, with clinically actionable alterations identified in 30 (25%), including therapeutic targets of FDA-approved drugs. Of the 47 samples without alterations detected and low tumor fraction (z-score<5), 29 had sufficient material to be re-analyzed using a less comprehensive but more sensitive assay, MSK-ACCESS, which revealed somatic mutations in 14/29 (48%). Conversely, 5 patients without alterations detected by cf-IMPACT and with high tumor fraction (z-score≥5) were analyzed by WES, which identified mutational signatures and alterations in potential oncogenic drivers not covered by the cf-IMPACT panel. Overall, we identified mutations in 90/118 (76%) patients in the entire cohort using the three complementary plasma profiling approaches. CONCLUSIONS cfDNA tumor fraction can inform the interpretation of negative cfDNA results and guide the selection of subsequent sequencing platforms that are most likely to identify clinically-relevant genomic alterations.
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Affiliation(s)
- Dana W Y Tsui
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Weill Cornell Medical College, Weill Cornell University, New York, USA.
- Present Address: PetDx, Inc., La Jolla, USA.
| | - Michael L Cheng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
- Present Address: Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Maha Shady
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Present Address: Graduate School of Arts and Sciences, Harvard University, Cambridge, USA
| | - Julie L Yang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Dennis Stephens
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Helen Won
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Kety Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Fanli Meng
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Xiaohong Jing
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Present Address: NYU Langone Health, New York, USA
| | - Juber Patel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Maysun Hasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ian Johnson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Brian Houck-Loomis
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - S Duygu Selcuklu
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Venkatraman E Seshan
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Maria Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Samuel A Funt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Jonathan Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dean Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dana Rathkopf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Cornell Medical College, Weill Cornell University, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA.
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17
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Allen A, Qin ACR, Raj N, Wang J, Uddin S, Yao Z, Tang L, Meyers PA, Taylor BS, Berger MF, Yaeger R, Reidy-Lagunes D, Pratilas CA. Rare BRAF mutations in pancreatic neuroendocrine tumors may predict response to RAF and MEK inhibition. PLoS One 2019; 14:e0217399. [PMID: 31158244 PMCID: PMC6546234 DOI: 10.1371/journal.pone.0217399] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 02/26/2019] [Accepted: 05/12/2019] [Indexed: 12/24/2022] Open
Abstract
The clinical significance of BRAF alterations in well-differentiated (WD) metastatic pancreatic neuroendocrine tumor (panNET) is unknown, but BRAF-mutated panNET could represent a subset characterized by an identifiable and clinically actionable driver. Following the identification of two patients with WD metastatic panNET whose tumors harbored BRAF mutations, we queried the MSK-IMPACT series of 80 patients with WD metastatic panNET for additional mutations in BRAF, and in other genes involved in RAS/ RTK/ PI3K signaling pathways. BRAF mutations were identified in six samples (7.5%): two tumors harbored V600E mutations, one tumor each expressed K601E, T599K, and T310I mutations, and one tumor expressed both G596D and E451K BRAF. Few additional actionable driver alterations were identified. To determine the ERK activating capability of four BRAF mutations not previously characterized, mutant constructs were tested in model systems. Biochemical characterization of BRAF mutations revealed both high and low activity mutants. Engineered cells expressing BRAF K601E and V600E were used for in vitro drug testing of RAF and MEK inhibitors currently in clinical use. BRAF K601E demonstrated reduced sensitivity to dabrafenib compared to BRAF V600E, but the combination of RAF plus MEK inhibition was effective in cells expressing this mutation. Herein, we describe the clinical course of a patient with BRAF K601E and a patient with BRAF V600E WD metastatic panNET, and the identification of four mutations in BRAF not previously characterized. The combined clinical and biochemical data support a potential role for RAF and MEK inhibitors, or a combination of these, in a selected panNET population.
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Affiliation(s)
- Amy Allen
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alice Can Ran Qin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nitya Raj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Jiawan Wang
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sharmeen Uddin
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Zhan Yao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Paul A. Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Barry S. Taylor
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Diane Reidy-Lagunes
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Christine A. Pratilas
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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