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Deng X, Seguinot BO, Bradshaw G, Lee JS, Coy S, Kalocsay M, Santagata S, Mitchison T. STMND1 is a phylogenetically ancient stathmin which localizes to motile cilia and exhibits nuclear translocation that is inhibited when soluble tubulin concentration increases. Mol Biol Cell 2024; 35:ar82. [PMID: 38630521 DOI: 10.1091/mbc.e23-12-0514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
Stathmins are small, unstructured proteins that bind tubulin dimers and are implicated in several human diseases, but whose function remains unknown. We characterized a new stathmin, STMND1 (Stathmin Domain Containing 1) as the human representative of an ancient subfamily. STMND1 features a N-terminal myristoylated and palmitoylated motif which directs it to membranes and a tubulin-binding stathmin-like domain (SLD) that contains an internal nuclear localization signal. Biochemistry and proximity labeling showed that STMND1 binds tubulin, and live imaging showed that tubulin binding inhibits translocation from cellular membranes to the nucleus. STMND1 is highly expressed in multiciliated epithelial cells, where it localizes to motile cilia. Overexpression in a model system increased the length of primary cilia. Our study suggests that the most ancient stathmins have cilium-related functions that involve sensing soluble tubulin.
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Affiliation(s)
- Xiang Deng
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Bryan O Seguinot
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Gary Bradshaw
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Jong Suk Lee
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Shannon Coy
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Marian Kalocsay
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Sandro Santagata
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Timothy Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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Tobochnik S, Regan MS, Dorotan MKC, Reich D, Lapinskas E, Hossain MA, Stopka SA, Santagata S, Murphy MM, Arnaout O, Bi WL, Chiocca EA, Golby AJ, Mooney MA, Smith TR, Ligon KL, Wen PY, Agar NYR, Lee JW. Pilot trial of perampanel on peritumoral hyperexcitability and clinical outcomes in newly diagnosed high-grade glioma. medRxiv 2024:2024.04.11.24305666. [PMID: 38645003 PMCID: PMC11030478 DOI: 10.1101/2024.04.11.24305666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Glutamatergic neuron-glioma synaptogenesis and peritumoral hyperexcitability promote glioma growth in a positive feedback loop. The objective of this study was to evaluate the feasibility and estimated effect sizes of the AMPA-R antagonist, perampanel, on intraoperative electrophysiologic hyperexcitability and clinical outcomes. Methods An open-label trial was performed comparing perampanel to standard of care (SOC) in patients undergoing resection of newly-diagnosed radiologic high-grade glioma. Perampanel was administered as a pre-operative loading dose followed by maintenance therapy until progressive disease or up to 12-months. SOC treatment involved levetiracetam for 7-days or as clinically indicated. The primary outcome of hyperexcitability was defined by intra-operative electrocorticography high frequency oscillation (HFO) rates. Seizure-freedom and overall survival (OS) were estimated by the Kaplan-Meier method. Tissue concentrations of perampanel, levetiracetam, and metabolites were measured by mass spectrometry. Results HFO rates were similar between perampanel-treated and SOC cohorts. The trial was terminated early after interim analysis for futility, and outcomes assessed in 11 patients (7 perampanel-treated, 4 SOC). Over a median 281 days of post-enrollment follow-up, 27% of patients had seizures, including 14% treated with perampanel and 50% treated with SOC. OS in perampanel-treated patients was similar to a glioblastoma reference cohort (p=0.81). Glutamate concentrations in surface biopsies were positively correlated with HFO rates in adjacent electrode contacts and were not significantly associated with treatment assignment or drug concentrations. Conclusions A peri-operative loading regimen of perampanel was safe and well-tolerated, with similar peritumoral hyperexcitability as in levetiracetam-treated patients. Maintenance anti-glutamatergic therapy was not observed to impact survival outcomes.
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Ricciuti B, Lamberti G, Puchala SR, Mahadevan NR, Lin JR, Alessi JV, Chowdhury A, Li YY, Wang X, Spurr L, Pecci F, Di Federico A, Venkatraman D, Barrichello AP, Gandhi M, Vaz VR, Pangilinan AJ, Haradon D, Lee E, Gupta H, Pfaff KL, Welsh EL, Nishino M, Cherniack AD, Johnson BE, Weirather JL, Dryg ID, Rodig SJ, Sholl LM, Sorger P, Santagata S, Umeton R, Awad MM. Genomic and Immunophenotypic Landscape of Acquired Resistance to PD-(L)1 Blockade in Non-Small-Cell Lung Cancer. J Clin Oncol 2024; 42:1311-1321. [PMID: 38207230 PMCID: PMC11095860 DOI: 10.1200/jco.23.00580] [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: 03/15/2023] [Revised: 08/27/2023] [Accepted: 10/24/2023] [Indexed: 01/13/2024] Open
Abstract
PURPOSE Although immune checkpoint inhibitors (ICI) have extended survival in patients with non-small-cell lung cancer (NSCLC), acquired resistance (AR) to ICI frequently develops after an initial benefit. However, the mechanisms of AR to ICI in NSCLC are largely unknown. METHODS Comprehensive tumor genomic profiling, machine learning-based assessment of tumor-infiltrating lymphocytes, multiplexed immunofluorescence, and/or HLA-I immunohistochemistry (IHC) were performed on matched pre- and post-ICI tumor biopsies from patients with NSCLC treated with ICI at the Dana-Farber Cancer Institute who developed AR to ICI. Two additional cohorts of patients with intervening chemotherapy or targeted therapies between biopsies were included as controls. RESULTS We performed comprehensive genomic profiling and immunophenotypic characterization on samples from 82 patients with NSCLC and matched pre- and post-ICI biopsies and compared findings with a control cohort of patients with non-ICI intervening therapies between biopsies (chemotherapy, N = 32; targeted therapies, N = 89; both, N = 17). Putative resistance mutations were identified in 27.8% of immunotherapy-treated cases and included acquired loss-of-function mutations in STK11, B2M, APC, MTOR, KEAP1, and JAK1/2; these acquired alterations were not observed in the control groups. Immunophenotyping of matched pre- and post-ICI samples demonstrated significant decreases in intratumoral lymphocytes, CD3e+ and CD8a+ T cells, and PD-L1-PD1 engagement, as well as increased distance between tumor cells and CD8+PD-1+ T cells. There was a significant decrease in HLA class I expression in the immunotherapy cohort at the time of AR compared with the chemotherapy (P = .005) and the targeted therapy (P = .01) cohorts. CONCLUSION These findings highlight the genomic and immunophenotypic heterogeneity of ICI resistance in NSCLC, which will need to be considered when developing novel therapeutic strategies aimed at overcoming resistance.
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Affiliation(s)
- Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sreekar R. Puchala
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | | | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Joao V. Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Alexander Chowdhury
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Yvonne Y. Li
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Xinan Wang
- Harvard School of Public Health, Boston, MA
| | - Liam Spurr
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Deepti Venkatraman
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Malini Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Victor R. Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Andy J. Pangilinan
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Danielle Haradon
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Elinton Lee
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Hersh Gupta
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Kathleen L. Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Emma L. Welsh
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Boston, MA
| | - Andrew D. Cherniack
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Bruce E. Johnson
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jason L Weirather
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Ian D Dryg
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Scott J. Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Peter Sorger
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Renato Umeton
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Mark M. Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
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Haddox CL, Nathenson MJ, Mazzola E, Lin JR, Baginska J, Nau A, Weirather JL, Choy E, Marino-Enriquez A, Morgan JA, Cote GM, Merriam P, Wagner AJ, Sorger PK, Santagata S, George S. Phase II Study of Eribulin plus Pembrolizumab in Metastatic Soft-tissue Sarcomas: Clinical Outcomes and Biological Correlates. Clin Cancer Res 2024; 30:1281-1292. [PMID: 38236580 PMCID: PMC10982640 DOI: 10.1158/1078-0432.ccr-23-2250] [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: 08/02/2023] [Revised: 10/19/2023] [Accepted: 01/12/2024] [Indexed: 01/19/2024]
Abstract
PURPOSE Eribulin modulates the tumor-immune microenvironment via cGAS-STING signaling in preclinical models. This non-randomized phase II trial evaluated the combination of eribulin and pembrolizumab in patients with soft-tissue sarcomas (STS). PATIENTS AND METHODS Patients enrolled in one of three cohorts: leiomyosarcoma (LMS), liposarcomas (LPS), or other STS that may benefit from PD-1 inhibitors, including undifferentiated pleomorphic sarcoma (UPS). Eribulin was administered at 1.4 mg/m2 i.v. (days 1 and 8) with fixed-dose pembrolizumab 200 mg i.v. (day 1) of each 21-day cycle, until progression, unacceptable toxicity, or completion of 2 years of treatment. The primary endpoint was the 12-week progression-free survival rate (PFS-12) in each cohort. Secondary endpoints included the objective response rate, median PFS, safety profile, and overall survival (OS). Pretreatment and on-treatment blood specimens were evaluated in patients who achieved durable disease control (DDC) or progression within 12 weeks [early progression (EP)]. Multiplexed immunofluorescence was performed on archival LPS samples from patients with DDC or EP. RESULTS Fifty-seven patients enrolled (LMS, n = 19; LPS, n = 20; UPS/Other, n = 18). The PFS-12 was 36.8% (90% confidence interval: 22.5-60.4) for LMS, 69.6% (54.5-89.0) for LPS, and 52.6% (36.8-75.3) for UPS/Other cohorts. All 3 patients in the UPS/Other cohort with angiosarcoma achieved RECIST responses. Toxicity was manageable. Higher IFNα and IL4 serum levels were associated with clinical benefit. Immune aggregates expressing PD-1 and PD-L1 were observed in a patient that completed 2 years of treatment. CONCLUSIONS The combination of eribulin and pembrolizumab demonstrated promising activity in LPS and angiosarcoma.
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Affiliation(s)
- Candace L. Haddox
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael J. Nathenson
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Emanuele Mazzola
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jia-Ren Lin
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Joanna Baginska
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Allison Nau
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jason L. Weirather
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Edwin Choy
- Division of Hematology Oncology, Massachusetts General Cancer Center, Boston, Massachusetts
| | | | - Jeffrey A. Morgan
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gregory M. Cote
- Division of Hematology Oncology, Massachusetts General Cancer Center, Boston, Massachusetts
| | - Priscilla Merriam
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew J. Wagner
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Peter K. Sorger
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Sandro Santagata
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Suzanne George
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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Yapp C, Nirmal AJ, Zhou F, Maliga Z, Tefft JB, Llopis PM, Murphy GF, Lian CG, Danuser G, Santagata S, Sorger PK. Multiplexed 3D Analysis of Immune States and Niches in Human Tissue. bioRxiv 2024:2023.11.10.566670. [PMID: 38014052 PMCID: PMC10680601 DOI: 10.1101/2023.11.10.566670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Tissue homeostasis and the emergence of disease are controlled by changes in the proportions of resident and recruited cells, their organization into cellular neighbourhoods, and their interactions with acellular tissue components. Highly multiplexed tissue profiling (spatial omics)1 makes it possible to study this microenvironment in situ, usually in 4-5 micron thick sections (the standard histopathology format)2. Microscopy-based tissue profiling is commonly performed at a resolution sufficient to determine cell types but not to detect subtle morphological features associated with cytoskeletal reorganisation, juxtracrine signalling, or membrane trafficking3. Here we describe a high-resolution 3D imaging approach able to characterize a wide variety of organelles and structures at sub-micron scale while simultaneously quantifying millimetre-scale spatial features. This approach combines cyclic immunofluorescence (CyCIF) imaging4 of over 50 markers with confocal microscopy of archival human tissue thick enough (30-40 microns) to fully encompass two or more layers of intact cells. 3D imaging of entire cell volumes substantially improves the accuracy of cell phenotyping and allows cell proximity to be scored using plasma membrane apposition, not just nuclear position. In pre-invasive melanoma in situ5, precise phenotyping shows that adjacent melanocytic cells are plastic in state and participate in tightly localised niches of interferon signalling near sites of initial invasion into the underlying dermis. In this and metastatic melanoma, mature and precursor T cells engage in an unexpectedly diverse array of juxtracrine and membrane-membrane interactions as well as looser "neighbourhood" associations6 whose morphologies reveal functional states. These data provide new insight into the transitions occurring during early tumour formation and immunoediting and demonstrate the potential for phenotyping of tissues at a level of detail previously restricted to cultured cells and organoids.
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Affiliation(s)
- Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
| | - Ajit J. Nirmal
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Felix Zhou
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Juliann B. Tefft
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
| | - Paula Montero Llopis
- Microscopy Resources on the North Quad (MicRoN), Harvard Medical School, Boston, MA 02115, USA
| | - George F. Murphy
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Christine G. Lian
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Peter K. Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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6
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Eschbacher KL, Tran QT, Moskalev EA, Jenkins S, Fritchie K, Stoehr R, Caron A, Link MJ, Brown PD, Guajardo A, Brat DJ, Wu A, Santagata S, Louis DN, Brastianos PK, Kaplan AB, Alexander B, Rossi S, Ferrarese F, Raleigh DR, Nguyen MP, Gross J, Velazquez Vega J, Rodriguez F, Perry A, Martinez-Lage M, Orr BA, Haller F, Giannini C. NAB2::STAT6 fusions and genome-wide DNA methylation profiling: Predictors of patient outcomes in meningeal solitary fibrous tumors. Brain Pathol 2024:e13256. [PMID: 38523251 DOI: 10.1111/bpa.13256] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/01/2024] [Indexed: 03/26/2024] Open
Abstract
Meningeal solitary fibrous tumors (SFT) are rare and have a high frequency of local recurrence and distant metastasis. In a cohort of 126 patients (57 female, 69 male; mean age at surgery 53.0 years) with pathologically confirmed meningeal SFTs with extended clinical follow-up (median 9.9 years; range 15 days-43 years), we performed extensive molecular characterization including genome-wide DNA methylation profiling (n = 80) and targeted TERT promoter mutation testing (n = 98). Associations were examined with NAB2::STAT6 fusion status (n = 101 cases; 51 = ex5-7::ex16-17, 26 = ex4::ex2-3; 12 = ex2-3::exANY/other and 12 = no fusion) and placed in the context of 2021 Central Nervous System (CNS) WHO grade. NAB2::STAT6 fusion breakpoints (fusion type) were significantly associated with metastasis-free survival (MFS) (p = 0.03) and, on multivariate analysis, disease-specific survival (DSS) when adjusting for CNS WHO grade (p = 0.03). DNA methylation profiling revealed three distinct clusters: Cluster 1 (n = 38), Cluster 2 (n = 22), and Cluster 3 (n = 20). Methylation clusters were significantly associated with fusion type (p < 0.001), with Cluster 2 harboring ex4::ex2-3 fusion in 16 (of 20; 80.0%), nearly all TERT promoter mutations (7 of 8; 87.5%), and predominantly an "SFT" histologic phenotype (15 of 22; 68.2%). Clusters 1 and 3 were less distinct, both dominated by tumors having ex5-7::ex16-17 fusion (respectively, 25 of 33; 75.8%, and 12 of 18; 66.7%) and with variable histological phenotypes. Methylation clusters were significantly associated with MFS (p = 0.027), but not overall survival (OS). In summary, NAB2::STAT6 fusion type was significantly associated with MFS and DSS, suggesting that tumors with an ex5::ex16-17 fusion may have inferior patient outcomes. Methylation clusters were significantly associated with fusion type, TERT promoter mutation status, histologic phenotype, and MFS.
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Affiliation(s)
| | - Quynh T Tran
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | | | | | | | | | | | | | | | - Daniel J Brat
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ashley Wu
- University of California, San Francisco, California, USA
| | | | - David N Louis
- Brigham and Women's Hospital, Boston, Massachusetts, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | | | | | | | | | - Minh P Nguyen
- University of California, San Francisco, California, USA
| | | | | | - Fausto Rodriguez
- University of California Los Angeles, Los Angeles, California, USA
| | - Arie Perry
- University of California, San Francisco, California, USA
| | | | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Caterina Giannini
- Mayo Clinic, Rochester, Minnesota, USA
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
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Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin JR, Muhlich JL, Mittendorf EA, Santagata S, Guerriero JL, Sorger PK. Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter. bioRxiv 2024:2023.11.01.565120. [PMID: 37961235 PMCID: PMC10634977 DOI: 10.1101/2023.11.01.565120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Tumors are complex assemblies of cellular and acellular structures patterned on spatial scales from microns to centimeters. Study of these assemblies has advanced dramatically with the introduction of high-plex spatial profiling. Image-based profiling methods reveal the intensities and spatial distributions of 20-100 proteins at subcellular resolution in 103-107 cells per specimen. Despite extensive work on methods for extracting single-cell data from these images, all tissue images contain artefacts such as folds, debris, antibody aggregates, optical aberrations and image processing errors that arise from imperfections in specimen preparation, data acquisition, image assembly, and feature extraction. We show that these artefacts dramatically impact single-cell data analysis, obscuring meaningful biological interpretation. We describe an interactive quality control software tool, CyLinter, that identifies and removes data associated with imaging artefacts. CyLinter greatly improves single-cell analysis, especially for archival specimens sectioned many years prior to data collection, such as those from clinical trials.
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Affiliation(s)
- Gregory J. Baker
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Edward Novikov
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Ziyuan Zhao
- Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA
| | - Tuulia Vallius
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | - Janae A. Davis
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | - Jeremy L. Muhlich
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | - Elizabeth A. Mittendorf
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber/Brigham and Women’s Cancer Center, Boston, MA
- Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Sandro Santagata
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
- Department of Systems Biology, Harvard Medical School, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Jennifer L. Guerriero
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber/Brigham and Women’s Cancer Center, Boston, MA
- Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Peter K. Sorger
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
- Department of Systems Biology, Harvard Medical School, Boston, MA
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8
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Coy S, Lee JS, Chan SJ, Woo T, Jones J, Alexandrescu S, Wen PY, Sorger PK, Ligon KL, Santagata S. Systematic characterization of antibody-drug conjugate targets in central nervous system tumors. Neuro Oncol 2024; 26:458-472. [PMID: 37870091 PMCID: PMC10912007 DOI: 10.1093/neuonc/noad205] [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: 06/10/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Antibody-drug conjugates (ADCs) enhance the specificity of cytotoxic drugs by directing them to cells expressing target antigens. Multiple ADCs are FDA-approved for solid and hematologic malignancies, including those expressing HER2, TROP2, and NECTIN4. Recently, an ADC targeting HER2 (Trastuzumab-Deruxtecan) increased survival and reduced growth of brain metastases in treatment-refractory metastatic breast cancer, even in tumors with low HER2 expression. Thus, low-level expression of ADC targets may be sufficient for treatment responsiveness. However, ADC target expression is poorly characterized in many central nervous system (CNS) tumors. METHODS We analyzed publicly available RNA-sequencing and proteomic data from the children's brain tumor network (N = 188 tumors) and gene-expression-omnibus RNA-expression datasets (N = 356) to evaluate expression of 14 potential ADC targets that are FDA-approved or under investigation in solid cancers. We also used immunohistochemistry to measure the levels of HER2, HER3, NECTIN4, TROP2, CLDN6, CLDN18.2, and CD276/B7-H3 protein in glioblastoma, oligodendroglioma, meningioma, ependymoma, pilocytic astrocytoma, medulloblastoma, atypical teratoid/rhabdoid tumor (AT/RT), adamantinomatous craniopharyngioma (ACP), papillary craniopharyngioma (PCP), and primary CNS lymphoma (N = 575). RESULTS Pan-CNS analysis showed subtype-specific expression of ADC target proteins. Most tumors expressed HER3, B7-H3, and NECTIN4. Ependymomas strongly expressed HER2, while meningiomas showed weak-moderate HER2 expression. ACP and PCP strongly expressed B7-H3, with TROP2 expression in whorled ACP epithelium. AT/RT strongly expressed CLDN6. Glioblastoma showed little subtype-specific marker expression, suggesting a need for further target development. CONCLUSIONS CNS tumors exhibit subtype-specific expression of ADC targets including several FDA-approved for other indications. Clinical trials of ADCs in CNS tumors may therefore be warranted.
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Affiliation(s)
- Shannon Coy
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, Massachusetts, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, USA
| | - Jong Suk Lee
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, Massachusetts, USA
| | - Sabrina J Chan
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, Massachusetts, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Terri Woo
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jacquelyn Jones
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, Massachusetts, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, Massachusetts, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, USA
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9
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Gritsch D, Santagata S, Brastianos PK. Integrating Systemic Therapies into the Multimodality Therapy of Patients with Craniopharyngioma. Curr Treat Options Oncol 2024; 25:261-273. [PMID: 38300480 DOI: 10.1007/s11864-023-01156-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 02/02/2024]
Abstract
OPINION STATEMENT The integration of targeted therapy into the multimodal management of craniopharyngiomas represents a significant advancement in the field of neuro-oncology. Historically, the management of these tumors has been challenging due to their proximity to vital brain structures, necessitating a delicate balance between tumor control and the preservation of neurological function. Traditional treatment modalities, such as surgical resection and radiation, while effective, carry their own set of risks, including potential damage to surrounding healthy tissues and the potential for long-term side effects. Recent insights into the molecular biology of craniopharyngiomas, particularly the discovery of the BRAF V600E mutation in nearly all papillary craniopharyngiomas, have paved the way for a targeted systemic treatment approach. However, advances have been limited for adamantinomatous craniopharyngiomas. The success of BRAF/MEK inhibitors in clinical trials underscores the potential of these targeted therapies not only to control tumor growth but also to reduce the need for more invasive treatments, potentially minimizing treatment-related complications. However, the introduction of these novel therapies also brings forth new challenges, such as determining the optimal timing, sequencing, and duration of targeted treatments. Furthermore, there are open questions regarding which specific BRAF/MEK inhibitors to use, the potential need for combination therapy, and the strategies for managing intolerable adverse events. Finally, ensuring equitable access to these therapies, especially in healthcare systems with limited resources, is crucial to prevent widening healthcare disparities. In conclusion, targeted therapy with BRAF/MEK inhibitors holds great promise for improving outcomes and quality of life for patients with BRAF-mutated craniopharyngiomas. However, additional research is needed to address the questions that remain about its optimal use and integration into comprehensive treatment plans.
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Affiliation(s)
- David Gritsch
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 55 Fruit Street, Boston, MA, 02114, USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Priscilla K Brastianos
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 55 Fruit Street, Boston, MA, 02114, USA.
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10
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Zhang X, Pant SM, Ritch CC, Tang HY, Shao H, Dweep H, Gong YY, Brooks R, Brafford P, Wolpaw AJ, Lee Y, Weeraratna A, Sehgal A, Herlyn M, Kossenkov A, Speicher D, Sorger PK, Santagata S, Dang CV. Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity. Nat Commun 2024; 15:633. [PMID: 38245503 PMCID: PMC10799901 DOI: 10.1038/s41467-024-44778-2] [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: 11/04/2022] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
The circadian clock regulator Bmal1 modulates tumorigenesis, but its reported effects are inconsistent. Here, we show that Bmal1 has a context-dependent role in mouse melanoma tumor growth. Loss of Bmal1 in YUMM2.1 or B16-F10 melanoma cells eliminates clock function and diminishes hypoxic gene expression and tumorigenesis, which could be rescued by ectopic expression of HIF1α in YUMM2.1 cells. By contrast, over-expressed wild-type or a transcriptionally inactive mutant Bmal1 non-canonically sequester myosin heavy chain 9 (Myh9) to increase MRTF-SRF activity and AP-1 transcriptional signature, and shift YUMM2.1 cells from a Sox10high to a Sox9high immune resistant, mesenchymal cell state that is found in human melanomas. Our work describes a link between Bmal1, Myh9, mouse melanoma cell plasticity, and tumor immunity. This connection may underlie cancer therapeutic resistance and underpin the link between the circadian clock, MRTF-SRF and the cytoskeleton.
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Affiliation(s)
- Xue Zhang
- The Wistar Institute, Philadelphia, PA, USA.
- Ludwig Institute for Cancer Research, New York, NY, USA.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Shishir M Pant
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Cecily C Ritch
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Yao-Yu Gong
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Rebekah Brooks
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Patricia Brafford
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Adam J Wolpaw
- The Wistar Institute, Philadelphia, PA, USA
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yool Lee
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Ashani Weeraratna
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Amita Sehgal
- Howard Hughes Medical Institute, Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chi V Dang
- The Wistar Institute, Philadelphia, PA, USA.
- Ludwig Institute for Cancer Research, New York, NY, USA.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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11
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Guerriero JL, Lin JR, Pastorello RG, Du Z, Chen YA, Townsend MG, Shimada K, Hughes ME, Ren S, Tayob N, Zheng K, Mei S, Patterson A, Taneja KL, Metzger O, Tolaney SM, Lin NU, Dillon DA, Schnitt SJ, Sorger PK, Mittendorf EA, Santagata S. Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer. NPJ Breast Cancer 2024; 10:2. [PMID: 38167908 PMCID: PMC10761880 DOI: 10.1038/s41523-023-00605-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/02/2023] [Indexed: 01/05/2024] Open
Abstract
Emerging data suggests that HER2 intratumoral heterogeneity (ITH) is associated with therapy resistance, highlighting the need for new strategies to assess HER2 ITH. A promising approach is leveraging multiplexed tissue analysis techniques such as cyclic immunofluorescence (CyCIF), which enable visualization and quantification of 10-60 antigens at single-cell resolution from individual tissue sections. In this study, we qualified a breast cancer-specific antibody panel, including HER2, ER, and PR, for multiplexed tissue imaging. We then compared the performance of these antibodies against established clinical standards using pixel-, cell- and tissue-level analyses, utilizing 866 tissue cores (representing 294 patients). To ensure reliability, the CyCIF antibodies were qualified against HER2 immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) data from the same samples. Our findings demonstrate the successful qualification of a breast cancer antibody panel for CyCIF, showing high concordance with established clinical antibodies. Subsequently, we employed the qualified antibodies, along with antibodies for CD45, CD68, PD-L1, p53, Ki67, pRB, and AR, to characterize 567 HER2+ invasive breast cancer samples from 189 patients. Through single-cell analysis, we identified four distinct cell clusters within HER2+ breast cancer exhibiting heterogeneous HER2 expression. Furthermore, these clusters displayed variations in ER, PR, p53, AR, and PD-L1 expression. To quantify the extent of heterogeneity, we calculated heterogeneity scores based on the diversity among these clusters. Our analysis revealed expression patterns that are relevant to breast cancer biology, with correlations to HER2 ITH and potential relevance to clinical outcomes.
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Affiliation(s)
- Jennifer L Guerriero
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA.
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA.
| | - Jia-Ren Lin
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Ricardo G Pastorello
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Pathology, Hospital Sírio Libanês, São Paulo, SP, 01308-050, Brazil
| | - Ziming Du
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Madeline G Townsend
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kenichi Shimada
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Melissa E Hughes
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Siyang Ren
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Nabihah Tayob
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kelly Zheng
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Shaolin Mei
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Alyssa Patterson
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Krishan L Taneja
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Otto Metzger
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Sara M Tolaney
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Nancy U Lin
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Stuart J Schnitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Peter K Sorger
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Elizabeth A Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Sandro Santagata
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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12
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Rahman R, Trippa L, Lee EQ, Arrillaga-Romany I, Fell G, Touat M, McCluskey C, Wiley J, Gaffey S, Drappatz J, Welch MR, Galanis E, Ahluwalia MS, Colman H, Nabors LB, Hepel J, Elinzano H, Schiff D, Chukwueke UN, Beroukhim R, Nayak L, McFaline-Figueroa JR, Batchelor TT, Rinne ML, Kaley TJ, Lu-Emerson C, Mellinghoff IK, Bi WL, Arnaout O, Peruzzi PP, Haas-Kogan D, Tanguturi S, Cagney D, Aizer A, Doherty L, Lavallee M, Fisher-Longden B, Dowling S, Geduldig J, Watkinson F, Pisano W, Malinowski S, Ramkissoon S, Santagata S, Meredith DM, Chiocca EA, Reardon DA, Alexander BM, Ligon KL, Wen PY. Inaugural Results of the Individualized Screening Trial of Innovative Glioblastoma Therapy: A Phase II Platform Trial for Newly Diagnosed Glioblastoma Using Bayesian Adaptive Randomization. J Clin Oncol 2023; 41:5524-5535. [PMID: 37722087 DOI: 10.1200/jco.23.00493] [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: 03/03/2023] [Revised: 05/17/2023] [Accepted: 07/24/2023] [Indexed: 09/20/2023] Open
Abstract
PURPOSE The Individualized Screening Trial of Innovative Glioblastoma Therapy (INSIGhT) is a phase II platform trial that uses response adaptive randomization and genomic profiling to efficiently identify novel therapies for phase III testing. Three initial experimental arms (abemaciclib [a cyclin-dependent kinase [CDK]4/6 inhibitor], neratinib [an epidermal growth factor receptor [EGFR]/human epidermal growth factor receptor 2 inhibitor], and CC-115 [a deoxyribonucleic acid-dependent protein kinase/mammalian target of rapamycin inhibitor]) were simultaneously evaluated against a common control arm. We report the results for each arm and examine the feasibility and conduct of the adaptive platform design. PATIENTS AND METHODS Patients with newly diagnosed O6-methylguanine-DNA methyltransferase-unmethylated glioblastoma were eligible if they had tumor genotyping to identify prespecified biomarker subpopulations of dominant glioblastoma signaling pathways (EGFR, phosphatidylinositol 3-kinase, and CDK). Initial random assignment was 1:1:1:1 between control (radiation therapy and temozolomide) and the experimental arms. Subsequent Bayesian adaptive randomization was incorporated on the basis of biomarker-specific progression-free survival (PFS) data. The primary end point was overall survival (OS), and one-sided P values are reported. The trial is registered with ClinicalTrials.gov (identifier: NCT02977780). RESULTS Two hundred thirty-seven patients were treated (71 control; 73 abemaciclib; 81 neratinib; 12 CC-115) in years 2017-2021. Abemaciclib and neratinib were well tolerated, but CC-115 was associated with ≥ grade 3 treatment-related toxicity in 58% of patients. PFS was significantly longer with abemaciclib (hazard ratio [HR], 0.72; 95% CI, 0.49 to 1.06; one-sided P = .046) and neratinib (HR, 0.72; 95% CI, 0.50 to 1.02; one-sided P = .033) relative to the control arm but there was no PFS benefit with CC-115 (one-sided P = .523). None of the experimental therapies demonstrated a significant OS benefit (P > .05). CONCLUSION The INSIGhT design enabled efficient simultaneous testing of three experimental agents using a shared control arm and adaptive randomization. Two investigational arms had superior PFS compared with the control arm, but none demonstrated an OS benefit. The INSIGhT design may promote improved and more efficient therapeutic discovery in glioblastoma. New arms have been added to the trial.
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Affiliation(s)
- Rifaquat Rahman
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | | | - Eudocia Q Lee
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | | | | | - Mehdi Touat
- Brigham and Women's Hospital, Boston, MA
- Sorbonne Universite, Hôpitaux Universitaires La Pitié Salpêtrière, Paris, France
| | | | | | | | | | - Mary R Welch
- Division of Neuro-Oncology, Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, NewYork-Presbyterian, New York, NY
| | | | | | - Howard Colman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | | | | | | | | | - Ugonma N Chukwueke
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | - Lakshmi Nayak
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | | | - Tracy T Batchelor
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | | | | | | | | | - Wenya Linda Bi
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | | | | | - Daphne Haas-Kogan
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | - Shyam Tanguturi
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | | | - Ayal Aizer
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | - David A Reardon
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | - Brian M Alexander
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | - Keith L Ligon
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
| | - Patrick Y Wen
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
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13
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Driver J, Santagata S, Bi WL, Chi JH. Genomic analysis of spinal meningiomas: correlation with histopathological grade. J Neurosurg Spine 2023; 39:729-733. [PMID: 37728381 DOI: 10.3171/2023.6.spine23425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/29/2023] [Indexed: 09/21/2023]
Abstract
OBJECTIVE Spinal meningiomas are one of the most common primary intradural tumors of the adult spine. Spinal meningiomas typically have a benign course with low rates of recurrence. Recent advances in genomic profiling have provided valuable information on meningioma biology and natural history, but these studies have focused primarily on cranial meningiomas. Chromosomal copy number analysis of meningiomas has been shown to be a valuable molecular profiling technique for distinguishing benign from aggressive tumors. The Integrated Grade for Meningioma is a novel grading scheme that uses mitotic index and copy-number profile to identify aggressive tumors at high risk for recurrence. The integrated grade has been shown to be a better predictor of tumor behavior than WHO grade alone. The objective of this study was to evaluate the chromosomal copy-number profile of spinal meningiomas, and to correlate these findings with the assigned WHO grades. METHODS The authors evaluated 94 spinal meningiomas treated surgically at their institution between 2002 and 2022. The histopathological results including WHO grade, mitotic index, presence of atypical features, and MIB-1 index were recorded. Chromosomal copy number as determined by institutional whole-genome DNA copy-number profiling was available for 57 tumors. RESULTS The WHO grades of the cohort consisted of 81 (86%) WHO grade 1 tumors and 13 (14%) WHO grade 2 tumors. In tumors for which copy-number profiling was available, 44 (77%) of 57 demonstrated loss of 22q/NF2. Notably absent were frequent high-risk copy number alterations including loss of 1p, 3p, 4p/q, 6p/q, 10p/q, 14q, 18p/q, 19p/q, and focal loss of CDKN2A on 9p. Of the 9 WHO grade 2 tumors for which copy-number profiling was available, 6 tumors were reclassified to a lower risk profile (integrated grade 1). CONCLUSIONS This analysis suggests that spinal meningiomas exhibit overwhelmingly indolent biology, as supported by their benign integrated grade. These findings have implications in the surgical management of these patients in relation to the need for complete Simpson grade I resection, as well as the potential avoidance of adjuvant therapy following surgery in the setting of otherwise frequently benign pathology.
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Affiliation(s)
| | - Sandro Santagata
- 2Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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14
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Chen WC, Choudhury A, Youngblood MW, Polley MYC, Lucas CHG, Mirchia K, Maas SLN, Suwala AK, Won M, Bayley JC, Harmanci AS, Harmanci AO, Klisch TJ, Nguyen MP, Vasudevan HN, McCortney K, Yu TJ, Bhave V, Lam TC, Pu JKS, Li LF, Leung GKK, Chan JW, Perlow HK, Palmer JD, Haberler C, Berghoff AS, Preusser M, Nicolaides TP, Mawrin C, Agnihotri S, Resnick A, Rood BR, Chew J, Young JS, Boreta L, Braunstein SE, Schulte J, Butowski N, Santagata S, Spetzler D, Bush NAO, Villanueva-Meyer JE, Chandler JP, Solomon DA, Rogers CL, Pugh SL, Mehta MP, Sneed PK, Berger MS, Horbinski CM, McDermott MW, Perry A, Bi WL, Patel AJ, Sahm F, Magill ST, Raleigh DR. Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses. Nat Med 2023; 29:3067-3076. [PMID: 37944590 PMCID: PMC11073469 DOI: 10.1038/s41591-023-02586-z] [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: 03/07/2023] [Accepted: 09/11/2023] [Indexed: 11/12/2023]
Abstract
Surgery is the mainstay of treatment for meningioma, the most common primary intracranial tumor, but improvements in meningioma risk stratification are needed and indications for postoperative radiotherapy are controversial. Here we develop a targeted gene expression biomarker that predicts meningioma outcomes and radiotherapy responses. Using a discovery cohort of 173 meningiomas, we developed a 34-gene expression risk score and performed clinical and analytical validation of this biomarker on independent meningiomas from 12 institutions across 3 continents (N = 1,856), including 103 meningiomas from a prospective clinical trial. The gene expression biomarker improved discrimination of outcomes compared with all other systems tested (N = 9) in the clinical validation cohort for local recurrence (5-year area under the curve (AUC) 0.81) and overall survival (5-year AUC 0.80). The increase in AUC compared with the standard of care, World Health Organization 2021 grade, was 0.11 for local recurrence (95% confidence interval 0.07 to 0.17, P < 0.001). The gene expression biomarker identified meningiomas benefiting from postoperative radiotherapy (hazard ratio 0.54, 95% confidence interval 0.37 to 0.78, P = 0.0001) and suggested postoperative management could be refined for 29.8% of patients. In sum, our results identify a targeted gene expression biomarker that improves discrimination of meningioma outcomes, including prediction of postoperative radiotherapy responses.
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Affiliation(s)
- William C Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
| | - Abrar Choudhury
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Mark W Youngblood
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Mei-Yin C Polley
- NRG Statistics and Data Management Center, NRG Oncology, Philadelphia, PA, USA
| | | | - Kanish Mirchia
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sybren L N Maas
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Abigail K Suwala
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research, German Cancer Research Center, Heidelberg, Germany
| | - Minhee Won
- NRG Statistics and Data Management Center, NRG Oncology, Philadelphia, PA, USA
| | - James C Bayley
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Akdes S Harmanci
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Arif O Harmanci
- Center for Secure Artificial Intelligence for Healthcare, Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, USA
| | - Tiemo J Klisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, and Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Minh P Nguyen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen McCortney
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Theresa J Yu
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Varun Bhave
- Department of Neurosurgery, Brigham and Women's Hospital, and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tai-Chung Lam
- Department of Clinical Oncology, The University of Hong Kong, Pokfulam, China
| | - Jenny Kan-Suen Pu
- Division of Neurosurgery, Department of Surgery, The University of Hong Kong, Pokfulam, China
| | - Lai-Fung Li
- Division of Neurosurgery, Department of Surgery, The University of Hong Kong, Pokfulam, China
| | - Gilberto Ka-Kit Leung
- Division of Neurosurgery, Department of Surgery, The University of Hong Kong, Pokfulam, China
| | - Jason W Chan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Haley K Perlow
- Department of Radiation Oncology, Ohio State University, Columbus, OH, USA
| | - Joshua D Palmer
- Department of Radiation Oncology, Ohio State University, Columbus, OH, USA
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Anna S Berghoff
- Division of Oncology, Department of Medicine, Medical University of Vienna, Vienna, Austria
| | - Matthias Preusser
- Division of Oncology, Department of Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Christian Mawrin
- Department of Neuropathology, University of Magdeburg, Magdeburg, Germany
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adam Resnick
- Department of Neurological Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brian R Rood
- Brain Tumor Institute, Children's National Hospital, Washington, DC, USA
| | - Jessica Chew
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Jacob S Young
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Lauren Boreta
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Schulte
- Neurosciences Department, University of California San Diego, La Jolla, CA, USA
| | - Nicholas Butowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - James P Chandler
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - David A Solomon
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - C Leland Rogers
- NRG Statistics and Data Management Center, NRG Oncology, Philadelphia, PA, USA
| | - Stephanie L Pugh
- NRG Statistics and Data Management Center, NRG Oncology, Philadelphia, PA, USA
| | - Minesh P Mehta
- NRG Statistics and Data Management Center, NRG Oncology, Philadelphia, PA, USA
- Miami Neuroscience Institute, Baptist Health, Miami, FL, USA
| | - Penny K Sneed
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Craig M Horbinski
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
- Department of Pathology, Northwestern University, Chicago, IL, USA
| | | | - Arie Perry
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Akash J Patel
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research, German Cancer Research Center, Heidelberg, Germany
| | - Stephen T Magill
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA.
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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15
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Zhang R, Yang Y, Hu C, Huang M, Cen W, Ling D, Long Y, Yang XH, Xu B, Peng J, Wang S, Zhu W, Wei M, Yang J, Xu Y, Zhang X, Ma J, Wang F, Zhang H, Ma P, Zhu X, Song G, Sun LY, Wang DS, Wang FH, Li YH, Santagata S, Li Q, Feng YF, Du Z. Comprehensive analysis reveals potential therapeutic targets and an integrated risk stratification model for solitary fibrous tumors. Nat Commun 2023; 14:7479. [PMID: 37980418 PMCID: PMC10657378 DOI: 10.1038/s41467-023-43249-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/03/2023] [Indexed: 11/20/2023] Open
Abstract
Solitary fibrous tumors (SFTs) are rare mesenchymal tumors with unpredictable evolution and with a recurrence or metastasis rate of 10-40%. Current medical treatments for relapsed SFTs remain ineffective. Here, we identify potential therapeutic targets and risk factors, including IDH1 p.R132S, high PD-L1 expression, and predominant macrophage infiltration, suggesting the potential benefits of combinational immune therapy and targeted therapy for SFTs. An integrated risk model incorporating mitotic count, density of Ki-67+ cells and CD163+ cells, MTOR mutation is developed, applying a discovery cohort of 101 primary non-CNS patients with negative tumor margins (NTM) and validated in three independent cohorts of 210 SFTs with the same criteria, and in 36 primary CNS SFTs with NTM. Compared with the existing models, our model shows significantly improved efficacy in identifying high-risk primary non-CNS and CNS SFTs with NTM for tumor progression.Our findings hold promise for advancing therapeutic strategies and refining risk prediction in SFTs.
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Affiliation(s)
- Renjing Zhang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yang Yang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Chunfang Hu
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Mayan Huang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Wenjian Cen
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Dongyi Ling
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yakang Long
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xin-Hua Yang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Boheng Xu
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Junling Peng
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Sujie Wang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Weijie Zhu
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Mingbiao Wei
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jiaojiao Yang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yuxia Xu
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xu Zhang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jiangjun Ma
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Fang Wang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Hongtu Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peiqing Ma
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaojun Zhu
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Musculoskeletal Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Guohui Song
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Musculoskeletal Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Li-Yue Sun
- Second Department of Oncology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - De-Shen Wang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Feng-Hua Wang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yu-Hong Li
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Qin Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
| | - Yan-Fen Feng
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Ziming Du
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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16
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Nirmal AJ, Yapp C, Santagata S, Sorger PK. Cell Spotter (CSPOT): A machine-learning approach to automated cell spotting and quantification of highly multiplexed tissue images. bioRxiv 2023:2023.11.15.567196. [PMID: 38014110 PMCID: PMC10680730 DOI: 10.1101/2023.11.15.567196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Highly multiplexed tissue imaging and in situ spatial profiling aim to extract single-cell data from specimens containing closely packed cells of diverse morphology. This is challenging due to the difficulty of accurately assigning boundaries between cells (segmentation) and then generating per-cell staining intensities. Existing methods use gating to convert per-cell intensity data to positive and negative scores; this is a common approach in flow cytometry, but one that is problematic in imaging. In contrast, human experts identify cells in crowded environments using morphological, neighborhood, and intensity information. Here we describe a computational approach (Cell Spotter or CSPOT) that uses supervised machine learning in combination with classical segmentation to perform automated cell type calling. CSPOT is robust to artifacts that commonly afflict tissue imaging and can replace conventional gating. The end-to-end Python implementation of CSPOT can be integrated into cloud-based image processing pipelines to substantially improve the speed, accuracy, and reproducibility of single-cell spatial data.
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Affiliation(s)
- Ajit J. Nirmal
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Clarence Yapp
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sandro Santagata
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K. Sorger
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
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17
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Coy S, Cheng B, Lee JS, Rashid R, Browning L, Xu Y, Chakrabarty SS, Yapp C, Chan S, Tefft JB, Scott E, Spektor A, Ligon KL, Baker GJ, Pellman D, Sorger PK, Santagata S. 2D and 3D multiplexed subcellular profiling of nuclear instability in human cancer. bioRxiv 2023:2023.11.07.566063. [PMID: 37986801 PMCID: PMC10659270 DOI: 10.1101/2023.11.07.566063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Nuclear atypia, including altered nuclear size, contour, and chromatin organization, is ubiquitous in cancer cells. Atypical primary nuclei and micronuclei can rupture during interphase; however, the frequency, causes, and consequences of nuclear rupture are unknown in most cancers. We demonstrate that nuclear envelope rupture is surprisingly common in many human cancers, particularly glioblastoma. Using highly-multiplexed 2D and super-resolution 3D-imaging of glioblastoma tissues and patient-derived xenografts and cells, we link primary nuclear rupture with reduced lamin A/C and micronuclear rupture with reduced lamin B1. Moreover, ruptured glioblastoma cells activate cGAS-STING-signaling involved in innate immunity. We observe that local patterning of cell states influences tumor spatial organization and is linked to both lamin expression and rupture frequency, with neural-progenitor-cell-like states exhibiting the lowest lamin A/C levels and greatest susceptibility to primary nuclear rupture. Our study reveals that nuclear instability is a core feature of cancer, and links nuclear integrity, cell state, and immune signaling.
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Affiliation(s)
- Shannon Coy
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian Cheng
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jong Suk Lee
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rumana Rashid
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lindsay Browning
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yilin Xu
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sankha S. Chakrabarty
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarence Yapp
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sabrina Chan
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Juliann B. Tefft
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Emily Scott
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Alexander Spektor
- Department of Radiation Oncology, Brigham and Women’s Hospital and Dana Farber Cancer Institute, Boston, MA, USA
| | - Keith L. Ligon
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory J. Baker
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Peter K. Sorger
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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18
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Hermida-Prado F, Xie Y, Sherman S, Nagy Z, Russo D, Akhshi T, Chu Z, Feit A, Campisi M, Chen M, Nardone A, Guarducci C, Lim K, Font-Tello A, Lee I, García-Pedrero J, Cañadas I, Agudo J, Huang Y, Sella T, Jin Q, Tayob N, Mittendorf EA, Tolaney SM, Qiu X, Long H, Symmans WF, Lin JR, Santagata S, Bedrosian I, Yardley DA, Mayer IA, Richardson ET, Oliveira G, Wu CJ, Schuster EF, Dowsett M, Welm AL, Barbie D, Metzger O, Jeselsohn R. Endocrine Therapy Synergizes with SMAC Mimetics to Potentiate Antigen Presentation and Tumor Regression in Hormone Receptor-Positive Breast Cancer. Cancer Res 2023; 83:3284-3304. [PMID: 37450351 PMCID: PMC10543960 DOI: 10.1158/0008-5472.can-23-1711] [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: 06/09/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Immunotherapies have yet to demonstrate significant efficacy in the treatment of hormone receptor-positive (HR+) breast cancer. Given that endocrine therapy (ET) is the primary approach for treating HR+ breast cancer, we investigated the effects of ET on the tumor immune microenvironment (TME) in HR+ breast cancer. Spatial proteomics of primary HR+ breast cancer samples obtained at baseline and after ET from patients enrolled in a neoadjuvant clinical trial (NCT02764541) indicated that ET upregulated β2-microglobulin and influenced the TME in a manner that promotes enhanced immunogenicity. To gain a deeper understanding of the underlying mechanisms, the intrinsic effects of ET on cancer cells were explored, which revealed that ET plays a crucial role in facilitating the chromatin binding of RelA, a key component of the NF-κB complex. Consequently, heightened NF-κB signaling enhanced the response to interferon-gamma, leading to the upregulation of β2-microglobulin and other antigen presentation-related genes. Further, modulation of NF-κB signaling using a SMAC mimetic in conjunction with ET augmented T-cell migration and enhanced MHC-I-specific T-cell-mediated cytotoxicity. Remarkably, the combination of ET and SMAC mimetics, which also blocks prosurvival effects of NF-κB signaling through the degradation of inhibitors of apoptosis proteins, elicited tumor regression through cell autonomous mechanisms, providing additional support for their combined use in HR+ breast cancer. SIGNIFICANCE Adding SMAC mimetics to endocrine therapy enhances tumor regression in a cell autonomous manner while increasing tumor immunogenicity, indicating that this combination could be an effective treatment for HR+ patients with breast cancer.
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Affiliation(s)
- Francisco Hermida-Prado
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- University of Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), IUOPA, Oviedo, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shira Sherman
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zsuzsanna Nagy
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Douglas Russo
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tara Akhshi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zhengtao Chu
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
| | - Avery Feit
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marco Campisi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Minyue Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Agostina Nardone
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cristina Guarducci
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Irene Lee
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Juana García-Pedrero
- University of Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), IUOPA, Oviedo, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Israel Cañadas
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Judith Agudo
- Harvard Medical School, Boston, Massachusetts
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ying Huang
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tal Sella
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Qingchun Jin
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nabihah Tayob
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Elizabeth A. Mittendorf
- Harvard Medical School, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Sara M. Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Jia-Ren Lin
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Sandro Santagata
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Isabelle Bedrosian
- Department of Breast Surgical Oncology, Division of Surgery, MD Anderson Cancer Center, Houston, Texas
| | - Denise A. Yardley
- Department of Medical Oncology, Sarah Cannon Cancer Center, Nashville, Tennessee
- Tennessee Oncology, Nashville, Tennessee
| | - Ingrid A. Mayer
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Edward T. Richardson
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Catherine J. Wu
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Eugene F. Schuster
- The BC Now Toby Robins Research Centre at the Institute of Cancer Research, London, United Kingdom
- Ralph Lauren Centre for BC Research, Royal Marsden Hospital, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Mitch Dowsett
- The BC Now Toby Robins Research Centre at the Institute of Cancer Research, London, United Kingdom
- Ralph Lauren Centre for BC Research, Royal Marsden Hospital, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Alana L. Welm
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
| | - David Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Otto Metzger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Rinath Jeselsohn
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
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19
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Williams EA, Brastianos PK, Wakimoto H, Zolal A, Filbin MG, Cahill DP, Santagata S, Juratli TA. A comprehensive genomic study of 390 H3F3A-mutant pediatric and adult diffuse high-grade gliomas, CNS WHO grade 4. Acta Neuropathol 2023; 146:515-525. [PMID: 37524847 PMCID: PMC10412483 DOI: 10.1007/s00401-023-02609-6] [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: 04/18/2023] [Revised: 05/30/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
Malignant brain tumors, known as H3K27-altered diffuse midline glioma (DMG) and H3G34-mutant diffuse hemispheric glioma (DHG), can affect individuals of all ages and are classified as CNS WHO grade 4. We comprehensively characterized 390 H3F3A-mutant diffuse gliomas (201 females, 189 males) arising in pediatric patients (under 20 years old) and adults (20 years and older) evaluated by the CGP program at Foundation Medicine between 2013 and 2020. We assessed information from pathology reports, histopathology review, and clinical data. The cohort included 304 H3K27M-mutant DMG (156 females, 148 males) and 86 H3G34-mutant DHG (45 females, 41 males). Median patient age was 20 years (1-74 years). The frequency of H3K27M-mutant DMG was similar in both pediatric and adult patients in our cohort-48.6% of the patients were over 20 years old, 31.5% over 30, and 18% over 40 at initial diagnosis. FGFR1 hotspot point mutations (N546K and K656E) were exclusively identified in H3K27M-mutant DMG tumors (64/304, 21%; p = 0.0001); these tend to occur in older patients (median age: 32.5 years) and mainly arose in the diencephalon. H3K27M-mutant DMG had higher rates of mutations in NF1 (31.0 vs 8.1%; p = 0.0001) and PIK3CA/PIK3R1 (27.9% vs 15.1%; p = 0.016) compared to H3G34-mutant DHG. However, H3G34-mutant DHG had higher rates of targetable alterations in cell-cycle pathway genes (CDK4 and CDK6 amplification; CDKN2A/B deletion) (27.0 vs 9.0%). Potentially targetable PDGFRA alterations were identified in ~ 20% of both H3G34-mutant DHG and H3K27M-mutant DMG. Overall, in the present study H3K27M-mutant DMG occurred at similar rates in both adult and patient patients. Through our analysis, we were able to identify molecular features characteristic of DMG and DHG. By identifying the recurrent co-mutations including actionable FGFR1 point mutations found in nearly one-third of H3K27M-mutant DMG in young adults, our findings can inform clinical translational studies, patient diagnosis, and clinical trial design.
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Affiliation(s)
- Erik A Williams
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center, and Jackson Memorial Hospitals, Miami, USA
- Foundation Medicine Inc, Cambridge, USA
| | - Priscilla K Brastianos
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Laboratory of Translational Neuro-Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - Amir Zolal
- Department of Neurosurgery, Division of Neuro-Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Laboratory of Translational Neuro-Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
- Department of Systems Biology, Harvard Medical School, Boston, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
| | - Tareq A Juratli
- Department of Neurosurgery, Laboratory of Translational Neuro-Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA.
- Department of Neurosurgery, Division of Neuro-Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany.
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.
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20
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Stopka SA, Ruiz D, Baquer G, Bodineau C, Hossain MA, Pellens VT, Regan MS, Pourquié O, Haigis MC, Bi WL, Coy SM, Santagata S, Agar NYR, Basu SS. Chemical QuantArray: A Quantitative Tool for Mass Spectrometry Imaging. Anal Chem 2023; 95:11243-11253. [PMID: 37469028 PMCID: PMC10445330 DOI: 10.1021/acs.analchem.3c00803] [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] [Indexed: 07/21/2023]
Abstract
Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) is a powerful analytical technique that provides spatially preserved detection and quantification of analytes in tissue specimens. However, clinical translation still requires improved throughput, precision, and accuracy. To accomplish this, we created "Chemical QuantArray", a gelatin tissue microarray (TMA) mold filled with serial dilutions of isotopically labeled endogenous metabolite standards. The mold is then cryo-sectioned onto a tissue homogenate to produce calibration curves. To improve precision and accuracy, we automatically remove pixels outside of each TMA well and investigated several intensity normalizations, including the utilization of a second stable isotope internal standard (IS). Chemical QuantArray enables the quantification of several endogenous metabolites over a wide dynamic range and significantly improve over current approaches. The technique reduces the space needed on the MALDI slides for calibration standards by approximately 80%. Furthermore, removal of empty pixels and normalization to an internal standard or matrix peak provided precision (<20% RSD) and accuracy (<20% DEV). Finally, we demonstrate the applicability of Chemical QuantArray by quantifying multiple purine metabolites in 14 clinical tumor specimens using a single MALDI slide. Chemical QuantArray improves the analytical characteristics and practical feasibility of MALDI-MSI metabolite quantification in clinical and translational applications.
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Affiliation(s)
- Sylwia A Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniela Ruiz
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts 02115, United States
| | - Gerard Baquer
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Clément Bodineau
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Md Amin Hossain
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Valentina T Pellens
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Olivier Pourquié
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Marcia C Haigis
- Department of Cell Biology, Blavatnik Institute, Ludwig Center, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wenya L Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Shannon M Coy
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts 02115, United States
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, Massachusetts 02115, United States
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Sankha S Basu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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21
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Cello G, Patel RV, McMahon JT, Santagata S, Bi WL. Impact of H3K27 trimethylation loss in meningiomas: a meta-analysis. Acta Neuropathol Commun 2023; 11:122. [PMID: 37491289 PMCID: PMC10369842 DOI: 10.1186/s40478-023-01615-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/06/2023] [Indexed: 07/27/2023] Open
Abstract
Trimethylation of lysine 27 on histone 3 (H3K27me3) loss has been implicated in worse prognoses for patients with meningiomas. However, there have been challenges in measuring H3K27me3 loss, quantifying its impact, and interpreting its clinical utility. We conducted a systematic review across Pubmed, Embase, and Web of Science to identify studies examining H3K27me3 loss in meningioma. Clinical, histopathological, and immunohistochemistry (IHC) characteristics were aggregated. A meta-analysis was performed using a random-effects model to assess prevalence of H3K27me3 loss and meningioma recurrence risk. Study bias was characterized using the NIH Quality Assessment Tool and funnel plots. Nine publications met inclusion criteria with a total of 2376 meningioma cases. The prevalence of H3K27me3 loss was 16% (95% CI 0.09-0.27), with higher grade tumors associated with a significantly greater proportion of loss. H3K27me3 loss was more common in patients who were male, had recurrent meningiomas, or required adjuvant radiation therapy. Patients were 1.70 times more likely to have tumor recurrence with H3K27me3 loss (95% CI 1.35-2.15). The prevalence of H3K27me3 loss in WHO grade 2 and 3 meningiomas was found to be significantly greater in tissue samples less than five years old versus tissue of all ages and when a broader definition of IHC staining loss was applied. This analysis demonstrates that H3K27me3 loss significantly associates with more aggressive meningiomas. While differences in IHC and tumor tissue age have led to heterogeneity in studying H3K27me3 loss, a robust prognostic signal is present. Our findings suggest an opportunity to improve study design and standardize tissue processing to optimize clinical viability of this epigenetic marker.
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Affiliation(s)
- Gregory Cello
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Ruchit V Patel
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - James Tanner McMahon
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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22
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Brastianos PK, Twohy E, Geyer S, Gerstner ER, Kaufmann TJ, Tabrizi S, Kabat B, Thierauf J, Ruff MW, Bota DA, Reardon DA, Cohen AL, De La Fuente MI, Lesser GJ, Campian J, Agarwalla PK, Kumthekar P, Mann B, Vora S, Knopp M, Iafrate AJ, Curry WT, Cahill DP, Shih HA, Brown PD, Santagata S, Barker FG, Galanis E. BRAF-MEK Inhibition in Newly Diagnosed Papillary Craniopharyngiomas. N Engl J Med 2023; 389:118-126. [PMID: 37437144 PMCID: PMC10464854 DOI: 10.1056/nejmoa2213329] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
BACKGROUND Craniopharyngiomas, primary brain tumors of the pituitary-hypothalamic axis, can cause clinically significant sequelae. Treatment with the use of surgery, radiation, or both is often associated with substantial morbidity related to vision loss, neuroendocrine dysfunction, and memory loss. Genotyping has shown that more than 90% of papillary craniopharyngiomas carry BRAF V600E mutations, but data are lacking with regard to the safety and efficacy of BRAF-MEK inhibition in patients with papillary craniopharyngiomas who have not undergone previous radiation therapy. METHODS Eligible patients who had papillary craniopharyngiomas that tested positive for BRAF mutations, had not undergone radiation therapy previously, and had measurable disease received the BRAF-MEK inhibitor combination vemurafenib-cobimetinib in 28-day cycles. The primary end point of this single-group, phase 2 study was objective response at 4 months as determined with the use of centrally determined volumetric data. RESULTS Of the 16 patients in the study, 15 (94%; 95% confidence interval [CI], 70 to 100) had a durable objective partial response or better to therapy. The median reduction in the volume of the tumor was 91% (range, 68 to 99). The median follow-up was 22 months (95% CI, 19 to 30) and the median number of treatment cycles was 8. Progression-free survival was 87% (95% CI, 57 to 98) at 12 months and 58% (95% CI, 10 to 89) at 24 months. Three patients had disease progression during follow-up after therapy had been discontinued; none have died. The sole patient who did not have a response stopped treatment after 8 days owing to toxic effects. Grade 3 adverse events that were at least possibly related to treatment occurred in 12 patients, including rash in 6 patients. In 2 patients, grade 4 adverse events (hyperglycemia in 1 patient and increased creatine kinase levels in 1 patient) were reported; 3 patients discontinued treatment owing to adverse events. CONCLUSIONS In this small, single-group study involving patients with papillary craniopharyngiomas, 15 of 16 patients had a partial response or better to the BRAF-MEK inhibitor combination vemurafenib-cobimetinib. (Funded by the National Cancer Institute and others; ClinicalTrials.gov number, NCT03224767.).
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Affiliation(s)
- Priscilla K Brastianos
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Erin Twohy
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Susan Geyer
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Elizabeth R Gerstner
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Timothy J Kaufmann
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Shervin Tabrizi
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Brian Kabat
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Julia Thierauf
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Michael W Ruff
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Daniela A Bota
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - David A Reardon
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Adam L Cohen
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Macarena I De La Fuente
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Glenn J Lesser
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Jian Campian
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Pankaj K Agarwalla
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Priya Kumthekar
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Bhupinder Mann
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Shivangi Vora
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Michael Knopp
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - A John Iafrate
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - William T Curry
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Daniel P Cahill
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Helen A Shih
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Paul D Brown
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Sandro Santagata
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Fred G Barker
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
| | - Evanthia Galanis
- From Massachusetts General Hospital Cancer Center, Harvard Medical School (P.K.B., E.R.G., S.T., J.T., A.J.I., W.T.C., D.P.C., H.A.S., F.G.B.), Dana-Farber Cancer Institute (D.A.R.), and Brigham and Women's Hospital, Harvard Program in Therapeutic Science, Dana-Farber Partners CancerCare (S.S.) - all in Boston; Alliance Statistics and Data Management Center (E.T., S.G., B.K.), Mayo Clinic (T.J.K., M.W.R., P.D.B., E.G.), Rochester, MN; UC Irvine-Chao Family Comprehensive Cancer Center, Orange, CA (D.A.B.); Huntsman Cancer Institute, University of Utah, Salt Lake City (A.L.C.); Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami (M.I.D.L.F.); Wake Forest University School of Medicine, Winston-Salem, NC (G.J.L.); Washington University School of Medicine, St. Louis (J.C.); Rutgers Cancer Institute, New Brunswick, NJ (P.K.A.); Northwestern University, Chicago (P.K.); the Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD (B.M.); and Ohio State University Comprehensive Cancer Center, Columbus (S.V., M.K.)
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Lin JR, Chen YA, Campton D, Cooper J, Coy S, Yapp C, Tefft JB, McCarty E, Ligon KL, Rodig SJ, Reese S, George T, Santagata S, Sorger PK. High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers. Nat Cancer 2023; 4:1036-1052. [PMID: 37349501 PMCID: PMC10368530 DOI: 10.1038/s43018-023-00576-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/08/2023] [Indexed: 06/24/2023]
Abstract
Precision medicine is critically dependent on better methods for diagnosing and staging disease and predicting drug response. Histopathology using hematoxylin and eosin (H&E)-stained tissue (not genomics) remains the primary diagnostic method in cancer. Recently developed highly multiplexed tissue imaging methods promise to enhance research studies and clinical practice with precise, spatially resolved single-cell data. Here, we describe the 'Orion' platform for collecting H&E and high-plex immunofluorescence images from the same cells in a whole-slide format suitable for diagnosis. Using a retrospective cohort of 74 colorectal cancer resections, we show that immunofluorescence and H&E images provide human experts and machine learning algorithms with complementary information that can be used to generate interpretable, multiplexed image-based models predictive of progression-free survival. Combining models of immune infiltration and tumor-intrinsic features achieves a 10- to 20-fold discrimination between rapid and slow (or no) progression, demonstrating the ability of multimodal tissue imaging to generate high-performance biomarkers.
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Affiliation(s)
- Jia-Ren Lin
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | | | | | - Shannon Coy
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Juliann B Tefft
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | | | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Sandro Santagata
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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Allen C, Santagata S. Meet the authors: Dr. Clint Allen and Dr. Sandro Santagata. Cancer Cell 2023; 41:834-836. [PMID: 37160103 DOI: 10.1016/j.ccell.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In this Q&A, Cell Press Community Review Scientific Editor Leia Judge talks to Dr. Clint Allen and Dr. Sandro Santagata about their new papers "Phenotypic plasticity and reduced tissue retention of exhausted tumor-infiltrating T cells following neoadjuvant immunotherapy in head and neck cancer" and "Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma" and their experiences with publishing through Cell Press Community Review.
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25
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Gaglia G, Burger ML, Ritch CC, Rammos D, Dai Y, Crossland GE, Tavana SZ, Warchol S, Jaeger AM, Naranjo S, Coy S, Nirmal AJ, Krueger R, Lin JR, Pfister H, Sorger PK, Jacks T, Santagata S. Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma. Cancer Cell 2023; 41:871-886.e10. [PMID: 37059105 PMCID: PMC10193529 DOI: 10.1016/j.ccell.2023.03.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 01/31/2023] [Accepted: 03/22/2023] [Indexed: 04/16/2023]
Abstract
Lymphocytes are key for immune surveillance of tumors, but our understanding of the spatial organization and physical interactions that facilitate lymphocyte anti-cancer functions is limited. We used multiplexed imaging, quantitative spatial analysis, and machine learning to create high-definition maps of lung tumors from a Kras/Trp53-mutant mouse model and human resections. Networks of interacting lymphocytes ("lymphonets") emerged as a distinctive feature of the anti-cancer immune response. Lymphonets nucleated from small T cell clusters and incorporated B cells with increasing size. CXCR3-mediated trafficking modulated lymphonet size and number, but T cell antigen expression directed intratumoral localization. Lymphonets preferentially harbored TCF1+ PD-1+ progenitor CD8+ T cells involved in responses to immune checkpoint blockade (ICB) therapy. Upon treatment of mice with ICB or an antigen-targeted vaccine, lymphonets retained progenitor and gained cytotoxic CD8+ T cell populations, likely via progenitor differentiation. These data show that lymphonets create a spatial environment supportive of CD8+ T cell anti-tumor responses.
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Affiliation(s)
- Giorgio Gaglia
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Megan L Burger
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR 97212, USA; School of Medicine, Division of Hematology and Oncology, Oregon Health & Science University, Portland, OR 97212, USA
| | - Cecily C Ritch
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Danae Rammos
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yang Dai
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Grace E Crossland
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sara Z Tavana
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Simon Warchol
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; School of Engineering and Applied Sciences, Harvard University, Boston, MA 02134, USA
| | - Alex M Jaeger
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Santiago Naranjo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shannon Coy
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ajit J Nirmal
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Krueger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; School of Engineering and Applied Sciences, Harvard University, Boston, MA 02134, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Hanspeter Pfister
- School of Engineering and Applied Sciences, Harvard University, Boston, MA 02134, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Perurena N, Lock R, Davis RA, Raghavan S, Pilla NF, Ng R, Loi P, Guild CJ, Miller AL, Sicinska E, Cleary JM, Rubinson DA, Wolpin BM, Gray NS, Santagata S, Hahn WC, Morton JP, Sansom OJ, Aguirre AJ, Cichowski K. USP9X mediates an acute adaptive response to MAPK suppression in pancreatic cancer but creates multiple actionable therapeutic vulnerabilities. Cell Rep Med 2023; 4:101007. [PMID: 37030295 PMCID: PMC10140597 DOI: 10.1016/j.xcrm.2023.101007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/18/2022] [Accepted: 03/17/2023] [Indexed: 04/10/2023]
Abstract
Pancreatic ductal adenocarcinomas (PDACs) frequently harbor KRAS mutations. Although MEK inhibitors represent a plausible therapeutic option, most PDACs are innately resistant to these agents. Here, we identify a critical adaptive response that mediates resistance. Specifically, we show that MEK inhibitors upregulate the anti-apoptotic protein Mcl-1 by triggering an association with its deubiquitinase, USP9X, resulting in acute Mcl-1 stabilization and protection from apoptosis. Notably, these findings contrast the canonical positive regulation of Mcl-1 by RAS/ERK. We further show that Mcl-1 inhibitors and cyclin-dependent kinase (CDK) inhibitors, which suppress Mcl-1 transcription, prevent this protective response and induce tumor regression when combined with MEK inhibitors. Finally, we identify USP9X as an additional potential therapeutic target. Together, these studies (1) demonstrate that USP9X regulates a critical mechanism of resistance in PDAC, (2) reveal an unexpected mechanism of Mcl-1 regulation in response to RAS pathway suppression, and (3) provide multiple distinct promising therapeutic strategies for this deadly malignancy.
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Affiliation(s)
- Naiara Perurena
- Genetics Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Rebecca Lock
- Genetics Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Rachel A Davis
- Genetics Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Srivatsan Raghavan
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Natalie F Pilla
- Genetics Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Raymond Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrick Loi
- Genetics Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Caroline J Guild
- Genetics Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Abigail L Miller
- Genetics Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - James M Cleary
- Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Douglas A Rubinson
- Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Brian M Wolpin
- Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Sandro Santagata
- Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - William C Hahn
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer P Morton
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G11 1QH, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G11 1QH, UK
| | - Andrew J Aguirre
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karen Cichowski
- Genetics Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA.
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Raleigh D, Chen W, Choudhury A, Youngblood M, Polley MY, Lucas CH, Mirchia K, Maas S, Suwala A, Won M, Bayley J, Harmanci A, Harmanci A, Klisch T, Nguyen M, Vasudevan H, McCortney K, Yu T, Bhave V, Lam TC, Pu J, Leung G, Chang J, Perlow H, Palmer J, Haberler C, Berghoff A, Preusser M, Nicolaides T, Mawrin C, Agnihotri S, Resnick A, Rood B, Chew J, Young J, Boreta L, Braunstein S, Schulte J, Butowski N, Santagata S, Spetzler D, Bush NAO, Villanueva-Meyer J, Chandler J, Solomon D, Rogers C, Pugh S, Mehta M, Sneed P, Berger M, Horbinski C, McDermott M, Perry A, Bi W, Patel A, Sahm F, Magill S. Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses. Res Sq 2023:rs.3.rs-2663611. [PMID: 36993741 PMCID: PMC10055655 DOI: 10.21203/rs.3.rs-2663611/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background Surgery is the mainstay of treatment for meningioma, the most common primary intracranial tumor, but improvements in meningioma risk stratification are needed and current indications for postoperative radiotherapy are controversial. Recent studies have proposed prognostic meningioma classification systems using DNA methylation profiling, copy number variants, DNA sequencing, RNA sequencing, histology, or integrated models based on multiple combined features. Targeted gene expression profiling has generated robust biomarkers integrating multiple molecular features for other cancers, but is understudied for meningiomas. Methods Targeted gene expression profiling was performed on 173 meningiomas and an optimized gene expression biomarker (34 genes) and risk score (0 to 1) was developed to predict clinical outcomes. Clinical and analytical validation was performed on independent meningiomas from 12 institutions across 3 continents (N = 1856), including 103 meningiomas from a prospective clinical trial. Gene expression biomarker performance was compared to 9 other classification systems. Results The gene expression biomarker improved discrimination of postoperative meningioma outcomes compared to all other classification systems tested in the independent clinical validation cohort for local recurrence (5-year area under the curve [AUC] 0.81) and overall survival (5-year AUC 0.80). The increase in area under the curve compared to the current standard of care, World Health Organization 2021 grade, was 0.11 for local recurrence (95% confidence interval [CI] 0.07-0.17, P < 0.001). The gene expression biomarker identified meningiomas benefiting from postoperative radiotherapy (hazard ratio 0.54, 95% CI 0.37-0.78, P = 0.0001) and re-classified up to 52.0% meningiomas compared to conventional clinical criteria, suggesting postoperative management could be refined for 29.8% of patients. Conclusions A targeted gene expression biomarker improves discrimination of meningioma outcomes compared to recent classification systems and predicts postoperative radiotherapy responses.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Minhee Won
- NRG Statistics and Data Management Center
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Joshua Palmer
- The Ohios State University James Comprehensive Cancer Center
| | | | | | | | | | | | | | | | - Brian Rood
- Center for Cancer and Immunology Research, Children's National Research Institute
| | | | | | | | - Steve Braunstein
- Department of Radiation Oncology, University of California San Francisco, San Francisco California
| | | | | | | | | | | | | | | | | | - C Rogers
- NRG Statistics and Data Management Center
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Choudhury A, Chen WC, Lucas CHG, Bayley JC, Harmanci AS, Maas SLN, Santagata S, Klisch T, Perry A, Bi WL, Sahm F, Patel AJ, Magill ST, Raleigh DR. Hypermitotic meningiomas harbor DNA methylation subgroups with distinct biological and clinical features. Neuro Oncol 2023; 25:520-530. [PMID: 36227281 PMCID: PMC10013643 DOI: 10.1093/neuonc/noac224] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Meningiomas, the most common primary intracranial tumors, can be separated into 3 DNA methylation groups with distinct biological drivers, clinical outcomes, and therapeutic vulnerabilities. Alternative meningioma grouping schemes using copy number variants, gene expression profiles, somatic short variants, or integrated molecular models have been proposed. These data suggest meningioma DNA methylation groups may harbor subgroups unifying contrasting theories of meningioma biology. METHODS A total of 565 meningioma DNA methylation profiles from patients with comprehensive clinical follow-up at independent discovery (n = 200) or validation (n = 365) institutions were reanalyzed and classified into Merlin-intact, Immune-enriched, or Hypermitotic DNA methylation groups. RNA sequencing from the discovery (n = 200) or validation (n = 302) cohort were analyzed in the context of DNA methylation groups to identify subgroups. Biological features and clinical outcomes were analyzed across meningioma grouping schemes. RESULTS RNA sequencing revealed differential enrichment of FOXM1 target genes across two subgroups of Hypermitotic meningiomas. Differential expression and ontology analyses showed the subgroup of Hypermitotic meningiomas without FOXM1 target gene enrichment was distinguished by gene expression programs driving macromolecular metabolism. Analysis of genetic, epigenetic, gene expression, or cellular features revealed Hypermitotic meningioma subgroups were concordant with Proliferative or Hypermetabolic meningiomas, which were previously reported alongside Merlin-intact and Immune-enriched tumors using an integrated molecular model. The addition of DNA methylation subgroups to clinical models refined the prediction of postoperative outcomes compared to the addition of DNA methylation groups. CONCLUSIONS Meningiomas can be separated into three DNA methylation groups and Hypermitotic meningiomas can be subdivided into Proliferative and Hypermetabolic subgroups, each with distinct biological and clinical features.
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Affiliation(s)
- Abrar Choudhury
- Departments of Radiation Oncology and Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - William C Chen
- Departments of Radiation Oncology and Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Calixto-Hope G Lucas
- Departments of Radiation Oncology and Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - James C Bayley
- Department of Neurosurgery, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Akdes S Harmanci
- Department of Neurosurgery, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Sybren L N Maas
- Departments of Pathology, Leiden University Medical Center, Leiden, and Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Tiemo Klisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Arie Perry
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Wenya Linda Bi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Akash J Patel
- Department of Neurosurgery, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Stephen T Magill
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - David R Raleigh
- Departments of Radiation Oncology and Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
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Brastianos PK, Twohy EL, Gerstner ER, Kaufmann TJ, Iafrate AJ, Lennerz J, Jeyapalan S, Piccioni DE, Monga V, Fadul CE, Schiff D, Taylor JW, Chowdhary SA, Bettegowda C, Ansstas G, De La Fuente M, Anderson MD, Shonka N, Damek D, Carrillo J, Kunschner-Ronan LJ, Chaudhary R, Jaeckle KA, Senecal FM, Kaley T, Morrison T, Thomas AA, Welch MR, Iwamoto F, Cachia D, Cohen AL, Vora S, Knopp M, Dunn IF, Kumthekar P, Sarkaria J, Geyer S, Carrero XW, Martinez-Lage M, Cahill DP, Brown PD, Giannini C, Santagata S, Barker FG, Galanis E. Alliance A071401: Phase II Trial of Focal Adhesion Kinase Inhibition in Meningiomas With Somatic NF2 Mutations. J Clin Oncol 2023; 41:618-628. [PMID: 36288512 PMCID: PMC9870228 DOI: 10.1200/jco.21.02371] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [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: 10/05/2021] [Revised: 07/14/2022] [Accepted: 09/09/2022] [Indexed: 01/27/2023] Open
Abstract
PURPOSE Patients with progressive or recurrent meningiomas have limited systemic therapy options. Focal adhesion kinase (FAK) inhibition has a synthetic lethal relationship with NF2 loss. Given the predominance of NF2 mutations in meningiomas, we evaluated the efficacy of GSK2256098, a FAK inhibitor, as part of the first genomically driven phase II study in recurrent or progressive grade 1-3 meningiomas. PATIENTS AND METHODS Eligible patients whose tumors screened positively for NF2 mutations were treated with GSK2256098, 750 mg orally twice daily, until progressive disease. Efficacy was evaluated using two coprimary end points: progression-free survival at 6 months (PFS6) and response rate by Macdonald criteria, where PFS6 was evaluated separately within grade-based subgroups: grade 1 versus 2/3 meningiomas. Per study design, the FAK inhibitor would be considered promising in this patient population if either end point met the corresponding decision criteria for efficacy. RESULTS Of 322 patients screened for all mutation cohorts of the study, 36 eligible and evaluable patients with NF2 mutations were enrolled and treated: 12 grade 1 and 24 grade 2/3 patients. Across all grades, one patient had a partial response and 24 had stable disease as their best response to treatment. In grade 1 patients, the observed PFS6 rate was 83% (10/12 patients; 95% CI, 52 to 98). In grade 2/3 patients, the observed PFS6 rate was 33% (8/24 patients; 95% CI, 16 to 55). The study met the PFS6 efficacy end point both for the grade 1 and the grade 2/3 cohorts. Treatment was well tolerated; seven patients had a maximum grade 3 adverse event that was at least possibly related to treatment with no grade 4 or 5 events. CONCLUSION GSK2256098 was well tolerated and resulted in an improved PFS6 rate in patients with recurrent or progressive NF2-mutated meningiomas, compared with historical controls. The criteria for promising activity were met, and FAK inhibition warrants further evaluation for this patient population.
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Affiliation(s)
| | - Erin L. Twohy
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | | | | | - A. John Iafrate
- Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Jochen Lennerz
- Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | | | | | | | | | - David Schiff
- University of Virginia Medical Center, Charlottesville, VA
| | - Jennie W. Taylor
- University of California, San Francisco Brain Tumor Center, San Francisco, CA
| | - Sajeel A. Chowdhary
- Lynn Cancer Institute, Boca Raton Regional Hospital/Baptist Hospital South Florida, Boca Raton, FL
| | | | | | | | | | | | | | | | | | | | | | | | - Thomas Kaley
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Mary R. Welch
- Columbia University Irving Medical Center, New York, NY
| | - Fabio Iwamoto
- Columbia University Irving Medical Center, New York, NY
| | | | | | - Shivangi Vora
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Michael Knopp
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Ian F. Dunn
- College of Medicine, University of Oklahoma, Oklahoma City, OK
| | | | | | - Susan Geyer
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | - Xiomara W. Carrero
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | | | - Daniel P. Cahill
- Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | | | | | - Sandro Santagata
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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30
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Lin JR, Wang S, Coy S, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell 2023; 186:363-381.e19. [PMID: 36669472 PMCID: PMC10019067 DOI: 10.1016/j.cell.2022.12.028] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [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: 04/01/2021] [Revised: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/20/2023]
Abstract
Advanced solid cancers are complex assemblies of tumor, immune, and stromal cells characterized by high intratumoral variation. We use highly multiplexed tissue imaging, 3D reconstruction, spatial statistics, and machine learning to identify cell types and states underlying morphological features of known diagnostic and prognostic significance in colorectal cancer. Quantitation of these features in high-plex marker space reveals recurrent transitions from one tumor morphology to the next, some of which are coincident with long-range gradients in the expression of oncogenes and epigenetic regulators. At the tumor invasive margin, where tumor, normal, and immune cells compete, T cell suppression involves multiple cell types and 3D imaging shows that seemingly localized 2D features such as tertiary lymphoid structures are commonly interconnected and have graded molecular properties. Thus, while cancer genetics emphasizes the importance of discrete changes in tumor state, whole-specimen imaging reveals large-scale morphological and molecular gradients analogous to those in developing tissues.
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Affiliation(s)
- Jia-Ren Lin
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shu Wang
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Shannon Coy
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Yu-An Chen
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Clarence Yapp
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Madison Tyler
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Maulik K Nariya
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Cody N Heiser
- Program in Chemical & Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sandro Santagata
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K Sorger
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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31
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Warchol S, Krueger R, Nirmal AJ, Gaglia G, Jessup J, Ritch CC, Hoffer J, Muhlich J, Burger ML, Jacks T, Santagata S, Sorger PK, Pfister H. Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data. IEEE Trans Vis Comput Graph 2023; 29:106-116. [PMID: 36170403 PMCID: PMC10043053 DOI: 10.1109/tvcg.2022.3209378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
New highly-multiplexed imaging technologies have enabled the study of tissues in unprecedented detail. These methods are increasingly being applied to understand how cancer cells and immune response change during tumor development, progression, and metastasis, as well as following treatment. Yet, existing analysis approaches focus on investigating small tissue samples on a per-cell basis, not taking into account the spatial proximity of cells, which indicates cell-cell interaction and specific biological processes in the larger cancer microenvironment. We present Visinity, a scalable visual analytics system to analyze cell interaction patterns across cohorts of whole-slide multiplexed tissue images. Our approach is based on a fast regional neighborhood computation, leveraging unsupervised learning to quantify, compare, and group cells by their surrounding cellular neighborhood. These neighborhoods can be visually analyzed in an exploratory and confirmatory workflow. Users can explore spatial patterns present across tissues through a scalable image viewer and coordinated views highlighting the neighborhood composition and spatial arrangements of cells. To verify or refine existing hypotheses, users can query for specific patterns to determine their presence and statistical significance. Findings can be interactively annotated, ranked, and compared in the form of small multiples. In two case studies with biomedical experts, we demonstrate that Visinity can identify common biological processes within a human tonsil and uncover novel white-blood cell networks and immune-tumor interactions.
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32
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Woods JK, Lidov HG, Ligon KL, Santagata S, Chi SN, Yeo KK, Alexandrescu S. PD-L1 and PD-1 expression in pediatric central nervous system germ cell tumors. Mod Pathol 2022; 35:1770-1774. [PMID: 36057740 DOI: 10.1038/s41379-022-01142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 12/24/2022]
Abstract
Central nervous system (CNS) germ cell tumors (GCTs) represent 2-3% of all primary CNS tumors. The majority are germinomas, which are radiosensitive and have an excellent prognosis. Contrarily, CNS non-germinomatous GCTs (NGGCTs) have less favorable prognosis and require more aggressive treatment. The expression of checkpoint/immune markers in CNS GCTs, particularly NGGCTs, is unknown. We previously reported a case of a patient whose intracranial NGGCT (predominantly choriocarcinoma) responded to immune checkpoint inhibition therapy. This case led us to evaluate our archive of intracranial GCTs for expression of PD-L1 and PD-1. With IRB approval, we searched the pathology archives at our institution for CNS GCTs. Demographic, radiologic, clinical, and histologic information was extracted from the medical records. Immunohistochemistry for lymphocytic markers (CD4, CD8, CD20), PD-1, and PD-L1 was performed. PD-L1 was considered positive if greater than 1% of tumor cells were positive and PD-1 was reported as a percentage of positive inflammatory cells. Fifty cases were identified, including 28 germinomas (mean age at diagnosis: 15.5 years; 17 males, 11 females), and 22 NGGCTs (mean age at diagnosis: 12.0 years, 21 males, 1 female). Germinomas were mostly suprasellar (17/28) and NGGCTs were predominantly pineal (17/22). Twenty-two germinomas (79%) were positive for PD-L1 expression, and 13 NGGCTs (57%) were positive for PD-L1. Cases of choriocarcinoma showed the most diffuse PD-L1 expression. PD-1 expression was seen in lymphocytes among 27/28 of the germinomas and 20/23 of the NGGCTs (ranging from 1-40% of lymphocytes). As expected, larger quantities of inflammatory cells were present in cases of germinoma. We demonstrate immune activity in CNS GCTs, and our results suggest that immune checkpoint inhibitors may be efficacious in the treatment of intracranial GCTs. Among NGGCTs, cases of choriocarcinoma showed the highest expression of PD-L1 in tumor cells, suggesting that this subtype may have the greatest benefit from checkpoint blockade.
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Affiliation(s)
- Jared K Woods
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Hart G Lidov
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Susan N Chi
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Kee Kiat Yeo
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
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33
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Williams E, Brastianos P, Wakimoto H, Santagata S, Cahill D, Juratli T. PATH-08. A COMPREHENSIVE GENOMIC STUDY OF 390 H3F3A-MUTANT PEDIATRIC-TYPE DIFFUSE HIGH-GRADE GLIOMAS WHO CNS GRADE 4. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
OBJECTIVES
Histone gene mutant malignant gliomas - H3K27-altered diffuse midline glioma (DMG) and diffuse hemispheric glioma (DHG) H3G34-mutant - occur in all age groups and can have significant variation in clinical outcomes. Here, we report comprehensive genomic profiling from one of the largest collections of H3F3A-mutant gliomas analyzed to date, identifying subsets defined by recurrently co-mutated genes.
METHODS
We identified 390 H3F3A-mutant diffuse gliomas WHO grade 4 (201 females and 189 males) that were profiled in the comprehensive genomic profiling program at Foundation Medicine between 2013-2020. Information from pathology reports, histopathology reviews, and clinical data was assessed.
RESULTS
Our cohort comprised 304 (77.9%) H3K27M-mutant DMG WHO grade 4 (156 females and 148 males) and 86 H3G34-mutant DHG (45 females and 41 males) with a median age of 20 years (1-74 years). H3K27M-mutant DMG distributed equally between pediatric and adult patients, with 52% of the patients older than 20 years, 30% older than 30 years, and 18% older than 40 years at the time of first diagnosis. Clonal FGFR1 hotspot mutations were exclusively detected in K27M-mutant DMG (n = 64/304, 21%; p=0.0001), with a significant association with a higher age at first diagnosis (median 32.5 years), and with a wide tumor distribution across the diencephalon. Additional genes which were significantly more frequently altered in K27M-mutant compared to G34-mutant diffuse gliomas included NF1 (31% vs. 8.1%; p=0.0001) and PIK3CA/PIK3R1 (27.9% vs. 15.1%; p=0.016). Conversely, targetable alterations of the cell-cycle pathway (CDK4/6 amplifications and CDKN2A/B deletions) were enriched in H3G34-mutant DHG (26%) compared to H3K27M-mutant DMG (7%). Potentially targetable PDGFR alterations were present in 32.5% of H3G34-mutant DHG and in 18% of H3K27M-mutant DMG.
CONCLUSIONS
These data expand our understanding of the tumor-specific molecular features of pediatric-type high-grade gliomas, identifying cohort sub-structure by recurrent co-mutations, which can inform diagnosis and clinical trial design.
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Affiliation(s)
| | - Priscilla Brastianos
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School , Boston, MA , USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School , Boston , USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA , USA
| | - Daniel Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA , USA
| | - Tareq Juratli
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School , Boston, MA , USA
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Eschbacher K, Jenkins S, Fritchie K, Moskalev E, Caron A, Link M, Brown P, Guajardo A, Brat D, Wu A, Santagata S, Louis D, Brastianos P, Kaplan A, Alexander B, Rossi S, Ferrarese F, Raleigh D, Nguyen M, Gross J, Vega JV, Rodriguez F, Perry A, Alverez MML, Haller F, Giannini C. PATH-34. SOLITARY FIBROUS TUMOR: NATURAL HISTORY AND PROGNOSIS IN ACCORDANCE WITH THE WHO 2021 CLASSIFICATION OF CNS TUMORS. Neuro Oncol 2022. [PMCID: PMC9660918 DOI: 10.1093/neuonc/noac209.607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Meningeal solitary fibrous tumor (SFT) is a rare tumor with high propensity to recur and metastasize, even late in the course of disease. The WHO 2021 classification of CNS tumors divides SFT in 3 grades, based on mitotic index and necrosis. We re-examined our cohort of 126 patients (57 F, 69 M; mean age 53.0 years) with SFT, confirmed by STAT6 nuclear positivity and/or NAB2::STAT6 fusion, with extended follow-up (median 7.6 years; range 4 days-26.6 years). Tumors included 76 grade 1, 36 grade 2 and 14 grade 3 according to 2021 WHO criteria, evaluated at primary resection (n=90), recurrence (n=35), or metastasis (n=1). Fifty-six patients had one or more post-surgical events, the earliest event being local recurrence (n=41) or metastasis (n=15). Forty patients died (29 of disease; 9 of other causes; 2 unknown). Overall survival (OS), and progression-free survival (PFS, recurrence and/or metastasis) from time of primary resection (n=90) were not significantly associated with grade; however, risk of metastasis differed significantly (5-year estimates: 4.1%, 15.3%, and 37.8% for grades 1, 2, and 3 SFT, respectively; p=0.005). NAB2::STAT6 fusion status was known in 101 cases (51 = ex5-7-ex16-17, 26 = ex4_ex2-3; 12 = ex2-3_exANY/other and 12 =no fusion). Disease specific 5-year survival in primary tumors with molecular data (n = 75) was 80.0% in patients whose tumors harbored ex5-7_ex16-17 compared to 93.3% in all others combined (p=0.014). Targeted TERT promoter mutation testing was performed in 98 patients, revealing patients with tumors lacking TERT promoter mutation (n = 88) were younger at time of surgery than those harboring a mutation (n=10; p = 0.022), and none with a mutation harboring concurrent ex5-7_ex16-17 fusion (p = 0.0009). In summary, WHO 2021 grade is associated with risk of metastasis. Patients whose tumors harbor ex5-7_ex16-17 fusion have a higher risk of dying from the disease.
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Affiliation(s)
- Kathryn Eschbacher
- Department of Laboratory Medicine & Pathology, Mayo Clinic , Rochester, MN , USA
| | - Sarah Jenkins
- Department of Biomedical Statistics and Informatics, Mayo Clinic , Rochester, MN , USA
| | - Karen Fritchie
- Department of Pathology, Cleveland Clinic , Cleveland, OH , USA
| | - Evgeny Moskalev
- Institute of Pathology, University Hospital Erlangen , Erlangen , Germany
| | - Alissa Caron
- Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester, MN , USA
| | - Michael Link
- Department of Neurosurgery, Mayo Clinic , Rochester, MN , USA
| | - Paul Brown
- Department of Radiation Oncology, Mayo Clinic , Rochester, MN , USA
| | | | - Daniel Brat
- Department of Pathology, Northwestern University , Chicago, IL , USA
| | - Ashely Wu
- Department of Pathology, University of California, San Francisco , San Francisco, CA , USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA , USA
| | - David Louis
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School , Boston, MA , USA
| | - Priscilla Brastianos
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School , Boston, MA , USA
| | - Alexander Kaplan
- Department of Neuro-oncology, Massachusetts General Hospital and Harvard Medical School , Boston, MA , USA
| | - Brian Alexander
- Department of Radiation Oncology, Dana-Farber Cancer Institute , Boston , USA
| | - Sabrina Rossi
- Department of Pathology and Molecular Genetics, Ospedale Ca'Foncello , Treviso , Italy
| | - Fabio Ferrarese
- Department of Radiation Oncology, Ospedale Ca'Foncello , Treviso , Italy
| | - David Raleigh
- Department of Pathology, University of California, San Francisco , San Francisco , USA
| | - Minh Nguyen
- University of California, San Francisco , San Francisco, CA , USA
| | - John Gross
- Department of Pathology, John Hopkins , Boston, MD , USA
| | - Jose Velazquez Vega
- Department of Pathology, Children's Healthcare of Atlanta , Atlanta, GA , USA
| | - Fausto Rodriguez
- Department of Pathology, University of California, Los Angeles , Los Angeles, CA , USA
| | - Arie Perry
- Department of Pathology, University of California, San Francisco , San Francisco, CA , USA
| | | | - Florian Haller
- Institute of Pathology, University Hospital Erlangen , Erlangen , Germany
| | - Caterina Giannini
- Department of Pathology and Laboratory Medicine, Mayo Clinic , Rochester, MN , USA
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Williams E, Brastianos P, Wakimoto H, Cahill D, Santagata S, Juratli T. PATH-17. DISTINCT MOLECULAR SUBCLASSES OF H3F3A-WILDTYPE, EGFR-ALTERED PEDIATRIC-TYPE DIFFUSE MIDLINE GLIOMAS WHO CNS GRADE 4. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
OBJECTIVES
Histone gene H3K27-altered diffuse midline glioma (DMG) are malignant tumors that occur in all age groups. In this study, we report comprehensive genomic profiling from H3F3A-wildtype, EGFR-altered DMG, as a distinct and newly recognized subset of pediatric-type DMG.
METHODS
Tumors were profiled in the comprehensive genomic profiling (CGP) program at Foundation Medicine between 2013-2020. Information from pathology reports, histopathology review, and patient clinical data was assessed.
RESULTS
We collected demographic and genomic data from 39 pediatric patients with H3F3A-wildtype, EGFR-altered HGG (17 females, 22 males; median age: 8.5 years, range 1-18 years). Female patients were younger at first diagnosis compared to male (median age 7 years vs. 10 years). All cases were microsatellite stable (MSS). The EGFR alterations consisted of 30 mutations and 9 amplifications. The mutations were distributed across the entire gene with no clear hotspot location. Our genomic data converged to identify three distinct molecular patterns. The first and most common group contained TP53 mutations (n = 17, 43.5%), showed no association with patient sex (8 females, 9 males), contained ATRX mutations (n = 3) and CDKN2A deletions (n = 5); these tumors did not harbor pathogenic mutations in TERTp, PIK3CA/PIK3R1, BCOR/BCORL1, STAG2, or SETD2. The second group featured TERTp-mutant tumors (n = 10), were more common in males (70%), and often demonstrated additional mutations in PIK3CA/PIK3R1 (n = 4), BCOR/BCORL1 (n = 4), CDKN2A/B (n = 4), and SETD2 (n = 2). The third group (n = 12) lacked TERTp and TP53 mutations and had a heterogeneous spectrum of non-recurrent mutations, including one CDKN2A/B deletion.
CONCLUSIONS
We have identified three distinct molecular subclasses that defined specific genomic tumor subgroups in pediatric-type EGFR altered DMG. Overall, these data increase our understanding of the pathobiology of this DMG subset and can guide the design of clinical trials.
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Affiliation(s)
| | - Priscilla Brastianos
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School , Boston, MA , USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School , Boston , USA
| | - Daniel Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA , USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA , USA
| | - Tareq Juratli
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center, Harvard Medical School , Boston, MA , USA
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36
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Meredith D, Gestrich C, Grieco K, Lidov H, Ligon K, Santagata S, Yeo KK, Alexandrescu S. 104. H3K27-altered diffuse midline gliomas with secondary driver molecular alterations. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Notarangelo G, Spinelli JB, Perez EM, Baker GJ, Kurmi K, Elia I, Stopka SA, Baquer G, Lin JR, Golby AJ, Joshi S, Baron HF, Drijvers JM, Georgiev P, Ringel AE, Zaganjor E, McBrayer SK, Sorger PK, Sharpe AH, Wucherpfennig KW, Santagata S, Agar NYR, Suvà ML, Haigis MC. Oncometabolite d-2HG alters T cell metabolism to impair CD8 + T cell function. Science 2022; 377:1519-1529. [PMID: 36173860 PMCID: PMC9629749 DOI: 10.1126/science.abj5104] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Gain-of-function mutations in isocitrate dehydrogenase (IDH) in human cancers result in the production of d-2-hydroxyglutarate (d-2HG), an oncometabolite that promotes tumorigenesis through epigenetic alterations. The cancer cell-intrinsic effects of d-2HG are well understood, but its tumor cell-nonautonomous roles remain poorly explored. We compared the oncometabolite d-2HG with its enantiomer, l-2HG, and found that tumor-derived d-2HG was taken up by CD8+ T cells and altered their metabolism and antitumor functions in an acute and reversible fashion. We identified the glycolytic enzyme lactate dehydrogenase (LDH) as a molecular target of d-2HG. d-2HG and inhibition of LDH drive a metabolic program and immune CD8+ T cell signature marked by decreased cytotoxicity and impaired interferon-γ signaling that was recapitulated in clinical samples from human patients with IDH1 mutant gliomas.
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Affiliation(s)
- Giulia Notarangelo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jessica B. Spinelli
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth M. Perez
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.,Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Gregory J. Baker
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Kiran Kurmi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Ilaria Elia
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sylwia A. Stopka
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Gerard Baquer
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.,Department of Electronic Engineering, Rovira i Virgili University, Tarragona, Spain
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Alexandra J. Golby
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Shakchhi Joshi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Heide F. Baron
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Departments of Psychiatry and Neurology, Harvard Medical School, Boston, MA, USA
| | - Jefte M. Drijvers
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Peter Georgiev
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Alison E. Ringel
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Elma Zaganjor
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Samuel K. McBrayer
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter K. Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Arlene H. Sharpe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kai W. Wucherpfennig
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nathalie Y. R. Agar
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mario L. Suvà
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Marcia C. Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Corresponding author.
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38
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Anderson AC, Yanai I, Yates LR, Wang L, Swarbrick A, Sorger P, Santagata S, Fridman WH, Gao Q, Jerby L, Izar B, Shang L, Zhou X. Spatial transcriptomics. Cancer Cell 2022; 40:895-900. [PMID: 36099884 DOI: 10.1016/j.ccell.2022.08.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spatial transcriptomics, with other spatial technologies, has enabled scientists to dissect the organization and interaction of different cell types within the tumor microenvironment. We asked experts to discuss some aspects of this technology from revealing the tumor microenvironment and heterogeneity, to tracking tumor evolution, to guiding tumor therapy, to current technical challenges.
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39
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Willimas EA, Brastianos PK, Wakimoto H, Santagata S, Cahill DP, Juratli TA. P04.04.A A comprehensive genomic study of 390 H3F3A-mutant pediatric-type diffuse high-grade gliomas WHO CNS grade 4. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac174.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Histone gene mutant malignant gliomas - H3K27-altered diffuse midline glioma (DMG) and diffuse hemispheric glioma (DHG) H3G34-mutant - occur in all age groups and can have significant variation in clinical outcomes. Here, we report comprehensive genomic profiling from one of the largest collections of H3F3A-mutant gliomas analyzed to date, identifying subsets defined by recurrently co-mutated genes.
Material and Methods
We identified 390 H3F3A-mutant diffuse gliomas WHO grade 4 (201 females and 189 males) that were profiled in the comprehensive genomic profiling program at Foundation Medicine between 2013-2020. Information from pathology reports, histopathology review, and patient clinical data was assessed
Results
Our cohort comprised 304 (77.9%) H3K27M-mutant DMG WHO grade 4 (156 females and 148 males) and 86 H3G34-mutant DHG (45 females and 41 males) with a median age of 20 years (1- 74 years). H3K27M-mutant DMG distributed equally between pediatric and adult patients, with 52% of the patients older than 20 years, 30% older than 30 years, and 18% older than 40 years at the time of first diagnosis. Clonal FGFR1 hotspot mutations were exclusively detected in K27M-mutant DMG (n = 64/304, 21%; p=0.0001), with a significant association with a higher age at first diagnosis (median 32.5 years), and with a wide tumor distribution across the diencephalon. Additional genes which were significantly more frequently altered in K27M-mutant compared to G34-mutant diffuse gliomas included NF1 (31% vs. 8.1%; p=0.0001) and PIK3CA/PIK3R1 (27.9% vs. 15.1%; p=0.016). Conversely, targetable alterations of the cell-cycle pathway (CDK4/6 amplifications and CDKN2A/B deletions) were enriched in H3G34-mutant DHG (26%) compared to H3K27M-mutant DMG (7%). Potentially targetable PDGFR alterations were present in 32.5% of H3G34-mutant DHG and in 18% of H3K27M-mutant DMG.
Conclusion
These data expand our understanding of the tumor-specific molecular features of pediatric-type high-grade gliomas, identifying cohort sub-structure by recurrent co-mutations, which can inform diagnosis and clinical trial design.
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Affiliation(s)
- E A Willimas
- Foundation Medicine Inc , Cambridge, MA , United States
| | - P K Brastianos
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical , Boston, MA , United States
| | - H Wakimoto
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory , Boston, MA , United States
| | - S Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA , United States
| | - D P Cahill
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory, Massachusetts General Hospital Cancer Center , Boston, MA , United States
| | - T A Juratli
- University Hospital Dresden , Dresden , Germany
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40
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Muhlich JL, Chen YA, Yapp C, Russell D, Santagata S, Sorger PK. Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. Bioinformatics 2022; 38:4613-4621. [PMID: 35972352 PMCID: PMC9525007 DOI: 10.1093/bioinformatics/btac544] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 04/04/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Stitching microscope images into a mosaic is an essential step in the analysis and visualization of large biological specimens, particularly human and animal tissues. Recent approaches to highly multiplexed imaging generate high-plex data from sequential rounds of lower-plex imaging. These multiplexed imaging methods promise to yield precise molecular single-cell data and information on cellular neighborhoods and tissue architecture. However, attaining mosaic images with single-cell accuracy requires robust image stitching and image registration capabilities that are not met by existing methods. RESULTS We describe the development and testing of ASHLAR, a Python tool for coordinated stitching and registration of 103 or more individual multiplexed images to generate accurate whole-slide mosaics. ASHLAR reads image formats from most commercial microscopes and slide scanners, and we show that it performs better than existing open-source and commercial software. ASHLAR outputs standard OME-TIFF images that are ready for analysis by other open-source tools and recently developed image analysis pipelines. AVAILABILITY AND IMPLEMENTATION ASHLAR is written in Python and is available under the MIT license at https://github.com/labsyspharm/ashlar. The newly published data underlying this article are available in Sage Synapse at https://dx.doi.org/10.7303/syn25826362; the availability of other previously published data re-analyzed in this article is described in Supplementary Table S4. An informational website with user guides and test data is available at https://labsyspharm.github.io/ashlar/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jeremy L Muhlich
- Human Tumor Atlas Network, Harvard Medical School, Boston, MA 02115, USA,Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yu-An Chen
- Human Tumor Atlas Network, Harvard Medical School, Boston, MA 02115, USA,Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Clarence Yapp
- Human Tumor Atlas Network, Harvard Medical School, Boston, MA 02115, USA,Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas Russell
- Human Tumor Atlas Network, Harvard Medical School, Boston, MA 02115, USA,Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sandro Santagata
- Human Tumor Atlas Network, Harvard Medical School, Boston, MA 02115, USA,Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
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41
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Coy S, Wang S, Stopka SA, Lin JR, Yapp C, Ritch CC, Salhi L, Baker GJ, Rashid R, Baquer G, Regan M, Khadka P, Cole KA, Hwang J, Wen PY, Bandopadhayay P, Santi M, De Raedt T, Ligon KL, Agar NYR, Sorger PK, Touat M, Santagata S. Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma. Nat Commun 2022; 13:4814. [PMID: 35973991 PMCID: PMC9381513 DOI: 10.1038/s41467-022-32430-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 07/29/2022] [Indexed: 12/11/2022] Open
Abstract
How the glioma immune microenvironment fosters tumorigenesis remains incompletely defined. Here, we use single-cell RNA-sequencing and multiplexed tissue-imaging to characterize the composition, spatial organization, and clinical significance of extracellular purinergic signaling in glioma. We show that microglia are the predominant source of CD39, while tumor cells principally express CD73. In glioblastoma, CD73 is associated with EGFR amplification, astrocyte-like differentiation, and increased adenosine, and is linked to hypoxia. Glioblastomas enriched for CD73 exhibit inflammatory microenvironments, suggesting that purinergic signaling regulates immune adaptation. Spatially-resolved single-cell analyses demonstrate a strong spatial correlation between tumor-CD73 and microglial-CD39, with proximity associated with poor outcomes. Similar spatial organization is present in pediatric high-grade gliomas including H3K27M-mutant diffuse midline glioma. These data reveal that purinergic signaling in gliomas is shaped by genotype, lineage, and functional state, and that core enzymes expressed by tumor and myeloid cells are organized to promote adenosine-rich microenvironments potentially amenable to therapeutic targeting.
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Affiliation(s)
- Shannon Coy
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Shu Wang
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Boston, MA, USA
| | - Sylwia A Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Cecily C Ritch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA
| | - Lisa Salhi
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle Epinière, and AP-HP Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Gregory J Baker
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Rumana Rashid
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA
- Pitt-CMU Medical Scientist Training Program, University of Pittsburgh-Carnegie Mellon, Pittsburgh, PA, USA
| | - Gerard Baquer
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Prasidda Khadka
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristina A Cole
- Children's Hospital of Philadelphia, University of Pennsylvania, Pennsylvania, PA, USA
| | - Jaeho Hwang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Patrick Y Wen
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pratiti Bandopadhayay
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Thomas De Raedt
- Children's Hospital of Philadelphia, University of Pennsylvania, Pennsylvania, PA, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Mehdi Touat
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle Epinière, and AP-HP Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France.
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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Lim-Fat MJ, Youssef GC, Touat M, Iorgulescu JB, Whorral S, Allen M, Rahman R, Chukwueke U, McFaline-Figueroa JR, Nayak L, Lee EQ, Batchelor TT, Arnaout O, Peruzzi PP, Chiocca EA, Reardon DA, Meredith D, Santagata S, Beroukhim R, Bi WL, Ligon KL, Wen PY. Clinical utility of targeted next-generation sequencing assay in IDH-wildtype glioblastoma for therapy decision-making. Neuro Oncol 2022; 24:1140-1149. [PMID: 34878541 PMCID: PMC9248387 DOI: 10.1093/neuonc/noab282] [Citation(s) in RCA: 14] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Targeted gene NGS testing is available through many academic institutions and commercial entities and is increasingly incorporated in practice guidelines for glioblastoma (GBM). This single-center retrospective study aimed to evaluate the clinical utility of incorporating NGS results in the management of GBM patients at a clinical trials-focused academic center. METHODS We identified 1011 consecutive adult patients with pathologically confirmed GBM (IDHwt or IDHmut) who had somatic tumor sequencing (Oncopanel, ~500 cancer gene panel) at DFCI from 2013-2019. Clinical records of all IDHwt GBM patients were reviewed to capture clinical trial enrollment and off-label targeted therapy use based on NGS results. RESULTS Of the 557 IDHwt GBM patients with sequencing, 182 entered clinical trials at diagnosis (32.7%) and 213 (38.2%) entered after recurrence. Sequencing results for 130 patients (23.3%) were utilized for clinical trial enrollment for either targeted therapy indications (6.9 % upfront and 27.7% at recurrent clinical trials and 3.1% for off-label targeted therapy) or exploratory studies (55.4% upfront and 6.9% recurrent clinical trials). Median overall survival was 20.1 months with no survival difference seen between patients enrolled in clinical trials compared to those who were not, in a posthoc analysis. CONCLUSIONS While NGS testing has become essential for improved molecular diagnostics, our study illustrates that targeted gene panels remain underutilized for selecting therapy in GBM-IDHwt. Targeted therapy and clinical trial design remain to be improved to help leverage the potential of NGS in clinical care.
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Affiliation(s)
- Mary Jane Lim-Fat
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Gilbert C Youssef
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Mehdi Touat
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - J Bryan Iorgulescu
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Sydney Whorral
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Marie Allen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Rifaquat Rahman
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ugonma Chukwueke
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - J Ricardo McFaline-Figueroa
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Lakshmi Nayak
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eudocia Q Lee
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Tracy T Batchelor
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Omar Arnaout
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pier Paolo Peruzzi
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - David Meredith
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Sandro Santagata
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Rameen Beroukhim
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Keith L Ligon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Gestrich C, Grieco K, Lidov H, Ligon K, Santagata S, Yeo KK, Alexandrescu S, Meredith D. DIPG-44. H3K27-altered diffuse midline gliomas with secondary driver molecular alterations. Neuro Oncol 2022. [PMCID: PMC9164861 DOI: 10.1093/neuonc/noac079.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
INTRODUCTION: Large-scale sequencing led to the identification of driver molecular alterations such as FGFR1 and BRAF in occasional diffuse midline gliomas (DMGs) H3K27-altered, but their significance is not completely explored. We evaluated these associations in our institutional cohorts. MATERIALS AND METHODS: We searched our sequencing data base (2013-2020) for H3K27M-mutant gliomas and analyzed the co-occurring genetic alterations. The demographics, clinical information, and pathology were reviewed. Copy number profiles were evaluated using BioDiscovery's Nexus Copy Number software package. Oncoplots and Kaplan-Meier survival curves were generated with the maftools R package. RESULTS: We identified 77 patients (age range 2-68, median 26). The diagnosis was DMG (n=55), anaplastic astrocytoma/glioblastoma (n=19), low-grade glioma (n=1), low-grade glioneuronal tumor (n=1), and ganglioglioma (n=1). Recurrent alterations were seen in TP53 (n=42), ATRX (n=17), NF1 (n=15), PDGFRA (n = 4). Five cases had BRAF V600E (1 ganglioglioma; 4 DMG); twelve had FGFR1 mutations (9 DMG; 3 anaplastic astrocytoma/glioblastoma). The most common location in the BRAF group was the brainstem and in the FGFR1 was the thalamus. Survival ranged from 0 to 97 months, median 12.9 months (28.8 months for FGFR1 and 22.8 for the BRAF V600E). This was not significantly different from OS reported in the literature for DMG.The BRAF V600E ganglioglioma patient is alive 37 months after diagnosis. CONCLUSION: There was no significant difference in outcomes for patients with secondary molecular drivers when compared with conventional H3K27M DMG. The outcome of the BRAF V600E tumors seemed to correlate with the histology. These findings and the possibility of targeted therapy argue for comprehensive sequencing of H3K27-altered gliomas.
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Affiliation(s)
- Catherine Gestrich
- Department of Pathology, Boston Children's Hospital, Harvard Medical School , Boston, MA , USA
| | - Kristina Grieco
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA , USA
| | - Hart Lidov
- Department of Pathology, Boston Children's Hospital, Harvard Medical School , Boston, MA , USA
| | - Keith Ligon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA , USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA , USA
| | - Kee Kiat Yeo
- Department of Pediatric Oncology, Dana Farber Cancer Institute , Boston, MA , USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children's Hospital, Harvard Medical School , Boston, MA , USA
| | - David Meredith
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA , USA
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44
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Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AA, Jacobson CA, Pelletier RJ, Yapp C, Arias-Camison R, Chen YA, Lian CG, Murphy GF, Santagata S, Sorger PK. The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution. Cancer Discov 2022; 12:1518-1541. [PMID: 35404441 PMCID: PMC9167783 DOI: 10.1158/2159-8290.cd-21-1357] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [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: 10/13/2021] [Revised: 02/05/2022] [Accepted: 04/01/2022] [Indexed: 11/16/2022]
Abstract
Cutaneous melanoma is a highly immunogenic malignancy that is surgically curable at early stages but life-threatening when metastatic. Here we integrate high-plex imaging, 3D high-resolution microscopy, and spatially resolved microregion transcriptomics to study immune evasion and immunoediting in primary melanoma. We find that recurrent cellular neighborhoods involving tumor, immune, and stromal cells change significantly along a progression axis involving precursor states, melanoma in situ, and invasive tumor. Hallmarks of immunosuppression are already detectable in precursor regions. When tumors become locally invasive, a consolidated and spatially restricted suppressive environment forms along the tumor-stromal boundary. This environment is established by cytokine gradients that promote expression of MHC-II and IDO1, and by PD1-PDL1-mediated cell contacts involving macrophages, dendritic cells, and T cells. A few millimeters away, cytotoxic T cells synapse with melanoma cells in fields of tumor regression. Thus, invasion and immunoediting can coexist within a few millimeters of each other in a single specimen. SIGNIFICANCE The reorganization of the tumor ecosystem in primary melanoma is an excellent setting in which to study immunoediting and immune evasion. Guided by classic histopathology, spatial profiling of proteins and mRNA reveals recurrent morphologic and molecular features of tumor evolution that involve localized paracrine cytokine signaling and direct cell-cell contact. This article is highlighted in the In This Issue feature, p. 1397.
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Affiliation(s)
- Ajit J. Nirmal
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Tuulia Vallius
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Brian Quattrochi
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Alyce A. Chen
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Connor A. Jacobson
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Roxanne J. Pelletier
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Raquel Arias-Camison
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Christine G. Lian
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - George F. Murphy
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Peter K. Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
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45
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Gray GK, Li CMC, Rosenbluth JM, Selfors LM, Girnius N, Lin JR, Schackmann RCJ, Goh WL, Moore K, Shapiro HK, Mei S, D'Andrea K, Nathanson KL, Sorger PK, Santagata S, Regev A, Garber JE, Dillon DA, Brugge JS. A human breast atlas integrating single-cell proteomics and transcriptomics. Dev Cell 2022; 57:1400-1420.e7. [PMID: 35617956 DOI: 10.1016/j.devcel.2022.05.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/23/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022]
Abstract
The breast is a dynamic organ whose response to physiological and pathophysiological conditions alters its disease susceptibility, yet the specific effects of these clinical variables on cell state remain poorly annotated. We present a unified, high-resolution breast atlas by integrating single-cell RNA-seq, mass cytometry, and cyclic immunofluorescence, encompassing a myriad of states. We define cell subtypes within the alveolar, hormone-sensing, and basal epithelial lineages, delineating associations of several subtypes with cancer risk factors, including age, parity, and BRCA2 germline mutation. Of particular interest is a subset of alveolar cells termed basal-luminal (BL) cells, which exhibit poor transcriptional lineage fidelity, accumulate with age, and carry a gene signature associated with basal-like breast cancer. We further utilize a medium-depletion approach to identify molecular factors regulating cell-subtype proportion in organoids. Together, these data are a rich resource to elucidate diverse mammary cell states.
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Affiliation(s)
- G Kenneth Gray
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Carman Man-Chung Li
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Jennifer M Rosenbluth
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA 02115, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura M Selfors
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Nomeda Girnius
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA; The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Jia-Ren Lin
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Ron C J Schackmann
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Walter L Goh
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Kaitlin Moore
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Hana K Shapiro
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Shaolin Mei
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Kurt D'Andrea
- Department of Medicine, Division of Translation Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katherine L Nathanson
- Department of Medicine, Division of Translation Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter K Sorger
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Sandro Santagata
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital (BWH), Boston, MA 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA 02115, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital (BWH), Boston, MA 02115, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA.
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46
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Tsvetkov P, Coy S, Petrova B, Dreishpoon M, Verma A, Abdusamad M, Rossen J, Joesch-Cohen L, Humeidi R, Spangler RD, Eaton JK, Frenkel E, Kocak M, Corsello SM, Lutsenko S, Kanarek N, Santagata S, Golub TR. Copper induces cell death by targeting lipoylated TCA cycle proteins. Science 2022; 375:1254-1261. [PMID: 35298263 DOI: 10.1126/science.abf0529] [Citation(s) in RCA: 1376] [Impact Index Per Article: 688.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Copper is an essential cofactor for all organisms, and yet it becomes toxic if concentrations exceed a threshold maintained by evolutionarily conserved homeostatic mechanisms. How excess copper induces cell death, however, is unknown. Here, we show in human cells that copper-dependent, regulated cell death is distinct from known death mechanisms and is dependent on mitochondrial respiration. We show that copper-dependent death occurs by means of direct binding of copper to lipoylated components of the tricarboxylic acid (TCA) cycle. This results in lipoylated protein aggregation and subsequent iron-sulfur cluster protein loss, which leads to proteotoxic stress and ultimately cell death. These findings may explain the need for ancient copper homeostatic mechanisms.
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Affiliation(s)
| | - Shannon Coy
- Laboratory of Systems Pharmacology, Department of Systems Biology, Boston, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Boryana Petrova
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Boston Children's Hospital, Boston, MA USA
| | | | - Ana Verma
- Laboratory of Systems Pharmacology, Department of Systems Biology, Boston, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Mai Abdusamad
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jordan Rossen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Ranad Humeidi
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - John K Eaton
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evgeni Frenkel
- Whitehead Institute and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mustafa Kocak
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Steven M Corsello
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Svetlana Lutsenko
- Department of Physiology, Johns Hopkins Medical Institutes, Baltimore, MD, USA
| | - Naama Kanarek
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Pathology, Boston Children's Hospital, Boston, MA USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Department of Systems Biology, Boston, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Todd R Golub
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, MA, USA.,Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
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47
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Smith RS, Takagishi SR, Amici DR, Metz K, Gayatri S, Alasady MJ, Wu Y, Brockway S, Taiberg SL, Khalatyan N, Taipale M, Santagata S, Whitesell L, Lindquist S, Savas JN, Mendillo ML. HSF2 cooperates with HSF1 to drive a transcriptional program critical for the malignant state. Sci Adv 2022; 8:eabj6526. [PMID: 35294249 PMCID: PMC8926329 DOI: 10.1126/sciadv.abj6526] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/25/2022] [Indexed: 05/14/2023]
Abstract
Heat shock factor 1 (HSF1) is well known for its role in the heat shock response (HSR), where it drives a transcriptional program comprising heat shock protein (HSP) genes, and in tumorigenesis, where it drives a program comprising HSPs and many noncanonical target genes that support malignancy. Here, we find that HSF2, an HSF1 paralog with no substantial role in the HSR, physically and functionally interacts with HSF1 across diverse types of cancer. HSF1 and HSF2 have notably similar chromatin occupancy and regulate a common set of genes that include both HSPs and noncanonical transcriptional targets with roles critical in supporting malignancy. Loss of either HSF1 or HSF2 results in a dysregulated response to nutrient stresses in vitro and reduced tumor progression in cancer cell line xenografts. Together, these findings establish HSF2 as a critical cofactor of HSF1 in driving a cancer cell transcriptional program to support the anabolic malignant state.
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Affiliation(s)
- Roger S. Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Seesha R. Takagishi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94158, USA
- Tetrad Graduate Program, UCSF, San Francisco, CA 94143, USA
| | - David R. Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kyle Metz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sitaram Gayatri
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Milad J. Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yaqi Wu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Master of Biotechnology Program, Northwestern University, Evanston, IL 60208, USA
| | - Sonia Brockway
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Stephanie L. Taiberg
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Natalia Khalatyan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| | - Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Jeffrey N. Savas
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marc L. Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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48
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Brastianos PK, Kim AE, Giobbie-Hurder A, Lee EQ, Wang N, Eichler AF, Chukwueke U, Forst DA, Arrillaga-Romany IC, Dietrich J, Corbin Z, Moliterno J, Baehring J, White M, Lou KW, Larson J, de Sauvage MA, Evancic K, Mora J, Nayyar N, Loeffler J, Oh K, Shih HA, Curry WT, Cahill DP, Barker FG, Gerstner ER, Santagata S. Phase 2 study of pembrolizumab in patients with recurrent and residual high-grade meningiomas. Nat Commun 2022; 13:1325. [PMID: 35289329 PMCID: PMC8921328 DOI: 10.1038/s41467-022-29052-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 08/18/2021] [Accepted: 02/16/2022] [Indexed: 01/16/2023] Open
Abstract
High-grade meningiomas are associated with neuro-cognitive morbidity and have limited treatments. High-grade meningiomas harbor an immunosuppressive tumor microenvironment (TME) and programmed death-ligand 1 (PD-L1) expression may contribute to their aggressive phenotype. Here, we present the results of a single-arm, open-label phase 2 trial (NCT03279692) evaluating the efficacy of pembrolizumab, a PD-1 inhibitor, in a cohort of 25 evaluable patients with recurrent and progressive grade 2 and 3 meningiomas. The primary endpoint is the proportion of patients alive and progression-free at 6 months (PFS-6). Secondary endpoints include progression-free and overall survival, best intracranial response, and toxicity. Our study has met its primary endpoint and achieved a PFS-6 rate of 0.48 (90% exact CI: 0.31-0.66) and a median PFS of 7.6 months (90% CI: 3.4-12.9 months). Twenty percent of patients have experienced one (or more) grade-3 or higher treatment-related adverse events. These results suggest that pembrolizumab exerts promising efficacy on a subset of these tumors. Further studies are needed to identify the biological facets within the meningioma TME that may drive response to immune-based therapies.
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Affiliation(s)
| | - Albert E Kim
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | | | - Eudocia Quant Lee
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nancy Wang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - April F Eichler
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ugonma Chukwueke
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Deborah A Forst
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | | | - Jorg Dietrich
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Zachary Corbin
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Jennifer Moliterno
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Joachim Baehring
- The Chenevert Family Brain Tumor Center, Smilow Cancer Hospital and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Michael White
- Wilmot Cancer Center, University of Rochester, Division of Neuro-Oncology, Rochester, NY, USA
| | - Kevin W Lou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Juliana Larson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Magali A de Sauvage
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Kathryn Evancic
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Joana Mora
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Naema Nayyar
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jay Loeffler
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Kevin Oh
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Helen A Shih
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - William T Curry
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Daniel P Cahill
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Fred G Barker
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Elizabeth R Gerstner
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
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49
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Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods 2022; 19:311-315. [PMID: 34824477 PMCID: PMC8916956 DOI: 10.1038/s41592-021-01308-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/22/2021] [Indexed: 01/02/2023]
Abstract
Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.
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Affiliation(s)
- Denis Schapiro
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Computational Biomedicine and Institute of Pathology, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
| | - Artem Sokolov
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Clarence Yapp
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Yu-An Chen
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jeremy L Muhlich
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Joshua Hess
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Allison L Creason
- Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Ajit J Nirmal
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory J Baker
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Maulik K Nariya
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zoltan Maliga
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Connor A Jacobson
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Matthew W Hodgman
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Juha Ruokonen
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Samouil L Farhi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daniel Persson
- Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Courtney Betts
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Shamilene Sivagnanam
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Jeremy Goecks
- Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Robert J Coffey
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa M Coussens
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Sandro Santagata
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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50
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Abstract
Tumors that arise in and around the skull base comprise a wide range of common and rare entities. Recent studies have advanced our understanding of their pathogenesis, which in some cases, have significantly influenced clinical practice. The genotype of meningiomas is strongly associated with their phenotype, including histologic subtype and tumor location, and clinical outcome. A single molecular alteration, NAB2-STAT6 fusion, has redefined the category of solitary fibrous tumors to include the previous entity hemangiopericytomas. Schwannomas, both sporadic and familial, are characterized by near ubiquitous alterations in NF2 , with additional mutations in SMARCB1 or LZTR1 in schwannomatosis. In pituitary adenohypophyseal tumors, cell lineage transcription factors such as SF-1, T-PIT, and PIT-1 are now essential for classification, providing a more rigorous taxonomy for tumors that were previously considered null cell adenomas. The pituicyte lineage transcription factor TTF-1 defines neurohypophyseal tumors, which may represent a single nosological entity with a spectrum of morphologic manifestations (ie, granular cell tumor, pituicytoma, and spindle cell oncocytoma). Likewise, the notochord cell lineage transcription factor brachyury defines chordoma, discriminating them from chondrosarcomas. The identification of nonoverlapping genetic drivers of adamantinomatous craniopharyngiomas and papillary craniopharyngiomas indicates that these are distinct tumor entities and has led to successful targeted treatment of papillary craniopharyngiomas using BRAF and/or mitogen-activated protein kinase inhibitors. Similarly, dramatic therapeutic responses have been achieved in patients with Langerhans cell histiocytosis, both with BRAF -mutant and BRAF -wildtype tumors. Familiarity with the pathology of skull base tumors, their natural history, and molecular features is essential for optimizing patient care.
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Affiliation(s)
- Wenya Linda Bi
- Center for Skull Base and Pituitary Surgery, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School , Boston , Massachusetts , USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston , Massachusetts , USA
- Laboratory of Systems Pharmacology, Harvard Medical School , Boston , Massachusetts , USA
- Ludwig Center at Harvard, Harvard Medical School , Boston , Massachusetts , USA
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