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Di Federico A, Alden SL, Smithy JW, Ricciuti B, Alessi JV, Wang X, Pecci F, Lamberti G, Gandhi MM, Vaz VR, Spurr LF, Sholl LM, Pfaff KL, Rodig SJ, Li YY, Cherniack AD, Nishino M, Johnson BE, Awad MM. Intrapatient variation in PD-L1 expression and tumor mutational burden and the impact on outcomes to immune checkpoint inhibitor therapy in patients with non-small-cell lung cancer. Ann Oncol 2024; 35:902-913. [PMID: 38950679 DOI: 10.1016/j.annonc.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Programmed death receptor ligand 1 (PD-L1) tumor proportion score (TPS) and tumor mutational burden (TMB) are key predictive biomarkers for immune checkpoint inhibitor (ICI) efficacy in non-small-cell lung cancer (NSCLC). Data on their variation across multiple samples are limited. PATIENTS AND METHODS Patients with NSCLC and multiple PD-L1 TPS and/or TMB assessments were included. Clinicopathologic and genomic data were analyzed according to PD-L1 and TMB variation. RESULTS In total, 402 PD-L1 sample pairs and 413 TMB sample pairs were included. Concordance between pairs was moderate for PD-L1 (ρ = 0.53, P < 0.0001) and high for TMB (ρ = 0.80, P < 0.0001). Shorter time between biopsies correlated with higher concordance in PD-L1, but not in TMB. Major increases (ΔTPS ≥ +50%) and decreases (ΔTPS ≤ -50%) in PD-L1 were observed in 9.7% and 8.0% of cases, respectively. PD-L1, but not TMB, decreased with intervening ICI (P = 0.02). Acquired copy number loss of CD274, PDCD1LG2, and JAK2 were associated with major decrease in PD-L1 (q < 0.05). Among patients with multiple PD-L1 assessments before ICI, cases where all samples had a PD-L1 ≥1%, compared to cases with at least one sample with PD-L1 <1% and another with PD-L1 ≥1%, achieved improved objective response rate and progression-free survival (PFS). Among patients with at least one PD-L1 <1% and one ≥1% before ICI, cases where the most proximal sample was PD-L1 ≥1% had longer median PFS compared to cases where the most proximal PD-L1 was <1%. Among patients with multiple TMB assessments before ICI, patients with a TMB ≥10 mut/Mb based on the most recent assessment, as compared to those with a TMB <10 mut/Mb, achieved improved PFS and overall survival to ICI; instead, no differences were observed when patients were categorized using the oldest TMB assessment. CONCLUSIONS Despite intrapatient concordance in PD-L1 and TMB, variation in these biomarkers can influence ICI outcomes, warranting consideration for reassessment before ICI initiation when feasible.
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Affiliation(s)
- A Di Federico
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - S L Alden
- Johns Hopkins School of Medicine, Baltimore
| | - J W Smithy
- Memorial Sloan Kettering Cancer Center, New York
| | - B Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - J V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - X Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston
| | - F Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - G Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - M M Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - V R Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - L F Spurr
- Pritzker School of Medicine, University of Chicago, Chicago; Department of Radiation and Cellular Oncology, University of Chicago, Chicago
| | - L M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston
| | - K L Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston
| | - S J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston
| | - Y Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston; Cancer Program, Broad Institute of MIT and Harvard, Cambridge
| | - A D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston; Cancer Program, Broad Institute of MIT and Harvard, Cambridge
| | - M Nishino
- Department of Radiology, Brigham and Women's Hospital, Boston; Department of Imaging, Dana-Farber Cancer Institute, Boston, USA
| | - B E Johnson
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - M M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston.
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DeSimone MS, Odintsov I, Tsai HK, Dickson BC, Alomari AK, Hornick JL, Fletcher CDM, Papke DJ. Epithelioid Fibrous Histiocytoma Is on a Continuum With Superficial ALK-rearranged Myxoid Spindle Cell Neoplasm: A Clinicopathologic Series of 35 Cases Including Alternate RET and NTRK3 Fusions. Am J Surg Pathol 2024:00000478-990000000-00421. [PMID: 39329254 DOI: 10.1097/pas.0000000000002315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
Anaplastic lymphoma kinase (ALK) rearrangements drive most examples of epithelioid fibrous histiocytoma (EFH) and have been reported in an emerging family of receptor tyrosine kinase (RTK) fusion-positive mesenchymal neoplasms, including superficial ones described under the rubric of "superficial ALK-rearranged myxoid spindle cell neoplasm" (SAMS). Here, we describe 35 superficial tumors with SAMS morphology, which occurred in 18 females (51%) and 17 males at a median age at presentation of 39 years (range: 6 to 82 y). Most tumors occurred on the lower extremity (25 tumors; 71%), followed by upper extremity (5; 14%), trunk (3; 9%), and face (2; 6%). Nine tumors were reported to have grown slowly before presentation, including >10 years in 2 cases. Tumors occurred primarily in the dermis (32 tumors; 91%) or subcutis (3; 9%); 8 dermal tumors extended into the subcutis. Median tumor size was 1.3 cm (range: 0.5 to 8.0 cm). Clinical follow-up was available for 12 patients (34%; range: 2 mo to 21 y; median: 2.7 y), none of whom experienced metastasis. One incompletely resected tumor recurred locally at 19 months, and no other patients experienced recurrence. Histologically, tumors were characterized by bland spindle-to-ovoid cells showing whorled growth and myxoid-to-collagenous stroma. Recurrent features included an epidermal collarette (19/30; 63%), perivascular hyalinization (20/35; 57%), amianthoid collagen (14/35; 40%), and metaplastic ossification (2/35; 6%). Immunohistochemistry (IHC) demonstrated expression of ALK (24/31; 77%), CD34 (15/21; 71%), EMA (17/28; 61%), and S-100 (9/32; 28%). Eleven tumors showed hybrid morphologic features between EFH and SAMS; 9 of them (82%) showed cytomorphology typical of EFH but with whorled growth, myxoid stroma, and/or regions of spindle cell morphology. Two hybrid tumors showed sharp transitions between a region characteristic of EFH and a region characteristic of SAMS, with a concomitant sharp transition in EMA, CD34, and S-100 expression by IHC. Sequencing revealed ALK fusions in 15 of 19 tumors: 2 each with fusion partners FLNA, SQSTM1, and VCL, and 1 each with COL1A2, DCTN1, EML4, FXR1, MPRIP, PLEKHH2, PRKAR1A, SPECC1L, and TLN2. Thirteen of 14 ALK-rearranged tumors expressed ALK by IHC. Three tumors negative for ALK fusions instead harbored alternate RTK fusions (NCOA4::RET, TRIM27::RET, and VIM::NTRK3), and 1 tumor was negative for RTK alterations. CDKN2A/B deletions were found in 2 tumors with ALK fusions and both tumors with RET fusions. SAMS is on a morphologic and molecular genetic spectrum with EFH, with a similar body site distribution, frequent clinical presentation as an exophytic skin tumor, and invariably benign outcomes; we conclude that SAMS should be considered a histologic variant of EFH. Some morphologically typical examples harbor alternate RET and NTRK3 fusions, such that SAMS is not an appropriate designation for this morphologic class; instead, to highlight the clinicopathologic similarities to EFH, we propose the diagnostic term "myxoid spindle cell variant of epithelioid fibrous histiocytoma."
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Affiliation(s)
- Mia S DeSimone
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
| | - Igor Odintsov
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
| | - Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
| | - Brendan C Dickson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ahmed K Alomari
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
| | | | - David J Papke
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
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3
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Fischer GM, Mahadevan NR, Hornick JL, Fletcher CD, Russell-Goldman E. A Comparative Genomic Study of Conventional and Undifferentiated Melanoma. Mod Pathol 2024:100626. [PMID: 39332711 DOI: 10.1016/j.modpat.2024.100626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 08/05/2024] [Accepted: 09/13/2024] [Indexed: 09/29/2024]
Abstract
Undifferentiated melanoma, defined as melanoma which has lost all usual phenotypic and immunohistochemical characteristics of conventional melanoma, can pose significant diagnostic challenges. Molecular studies have advanced our understanding of undifferentiated melanoma by demonstrating that a subset of these tumors harbor known melanoma driver alterations in genes such as BRAF, NRAS, and NF1. However, there is a paucity of data describing genetic alterations which may distinguish undifferentiated melanoma from conventional melanoma. In this study, we directly compared the genomic profiles of undifferentiated melanoma to a cohort of conventional melanomas, including 14 undifferentiated melanoma cases (comprised of two primary cases, two cutaneous recurrences and 10 metastases) and a cohort of 127 conventional melanomas including primary, recurrent, and metastatic cases. Targeted sequencing of 447 cancer-associated genes was performed, including identification of mutations and copy number alterations (CNAs). NRAS was the most frequent melanoma driver in undifferentiated melanoma (8/14 cases, 57%), although notably only one undifferentiated melanoma harbored an NRAS Q61R mutation. Compared to the conventional melanoma cohort, undifferentiated melanoma demonstrated statistically significant enrichment of pathogenic activating RAC1 mutations (6/14 total cases, 43%), including P29S (4/6 cases), P29L (1/6 cases) and D11E (1/6 cases). In addition to providing insight into the molecular pathogenesis of undifferentiated melanoma, these findings also suggest that RAS Q61R immunohistochemistry may have limited utility for its diagnosis. The presence of recurrent RAC1 mutations in undifferentiated melanoma is also notable as these alterations may contribute to mitogen-activated protein (MAP) kinase pathway targeted therapy resistance. Furthermore, the RAC1 alterations identified in this cohort have been shown to drive a melanocytic to mesenchymal switch in melanocytes, offering a possible explanation for the undifferentiated phenotype of these melanomas.
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Affiliation(s)
- Grant M Fischer
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Navin R Mahadevan
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher Dm Fletcher
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Eleanor Russell-Goldman
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts..
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4
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Hanrahan GB, Tsibris HC. Mutational landscape and tumour mutational burden in adults with malignant melanoma arising from congenital naevi. Br J Dermatol 2024; 191:627-630. [PMID: 38770634 DOI: 10.1093/bjd/ljae214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/13/2024] [Accepted: 06/02/2024] [Indexed: 05/22/2024]
Abstract
We evaluated the genetic mutations, tumour mutational burden (TMB) and ultraviolet (UV) signature pattern in melanomas arising in congenital melanocytic naevi (CMN) in adults treated at the Dana–Farber Cancer Institute. Whereas paediatric CMN melanomas are characterized by NRAS mutations and reportedly lack BRAF and PTEN mutations, analysis showed that adult CMN melanomas contain BRAF, PTEN and TERT promotor mutations. Adult CMN melanomas showed low average TMB and an absent UV signature, suggesting lower UV damage in adult CMN melanoma than in other subtypes. Patients treated with immune checkpoint inhibition showed refractory disease progression, potentially attributable to low TMB. Findings suggest adult CMN melanoma may have distinct genetic properties from paediatric CMN melanoma and show immunotherapy resistance.
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Affiliation(s)
- Grace B Hanrahan
- Center for Melanoma Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- University of Massachusetts T.H. Chan School of Medicine, Worcester, MA, USA
| | - Hillary C Tsibris
- Center for Melanoma Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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5
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Al Shihabi A, Tebon PJ, Nguyen HTL, Chantharasamee J, Sartini S, Davarifar A, Jensen AY, Diaz-Infante M, Cox H, Gonzalez AE, Norris S, Sperry J, Nakashima J, Tavanaie N, Winata H, Fitz-Gibbon ST, Yamaguchi TN, Jeong JH, Dry S, Singh AS, Chmielowski B, Crompton JG, Kalbasi AK, Eilber FC, Hornicek F, Bernthal NM, Nelson SD, Boutros PC, Federman NC, Yanagawa J, Soragni A. The landscape of drug sensitivity and resistance in sarcoma. Cell Stem Cell 2024:S1934-5909(24)00296-0. [PMID: 39305899 DOI: 10.1016/j.stem.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 06/14/2024] [Accepted: 08/21/2024] [Indexed: 09/25/2024]
Abstract
Sarcomas are rare malignancies with over 100 distinct histological subtypes. Their rarity and heterogeneity pose significant challenges to identifying effective therapies, and approved regimens show varied responses. Novel, personalized approaches to therapy are needed to improve patient outcomes. Patient-derived tumor organoids (PDTOs) model tumor behavior across an array of malignancies. We leverage PDTOs to characterize the landscape of drug resistance and sensitivity in sarcoma, collecting 194 specimens from 126 patients spanning 24 distinct sarcoma subtypes. Our high-throughput organoid screening pipeline tested single agents and combinations, with results available within a week from surgery. Drug sensitivity correlated with clinical features such as tumor subtype, treatment history, and disease trajectory. PDTO screening can facilitate optimal drug selection and mirror patient outcomes in sarcoma. We could identify at least one FDA-approved or NCCN-recommended effective regimen for 59% of the specimens, demonstrating the potential of our pipeline to provide actionable treatment information.
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Affiliation(s)
- Ahmad Al Shihabi
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peyton J Tebon
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Huyen Thi Lam Nguyen
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jomjit Chantharasamee
- Division of Hematology-Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sara Sartini
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ardalan Davarifar
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Division of Hematology-Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexandra Y Jensen
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Miranda Diaz-Infante
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hannah Cox
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Summer Norris
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | - Nasrin Tavanaie
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Helena Winata
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sorel T Fitz-Gibbon
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Takafumi N Yamaguchi
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jae H Jeong
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarah Dry
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Arun S Singh
- Division of Hematology-Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bartosz Chmielowski
- Division of Hematology-Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joseph G Crompton
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Division of Surgical Oncology David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anusha K Kalbasi
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Fritz C Eilber
- Division of Surgical Oncology David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Francis Hornicek
- Department of Orthopedic Surgery, University of Miami, Miami, FL, USA
| | - Nicholas M Bernthal
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Scott D Nelson
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Noah C Federman
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jane Yanagawa
- Department of Surgery, Division of Thoracic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alice Soragni
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
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Boiarsky D, Tewari AK, Gulhan DC, Bakouny Z, Ananda G, Savignano H, Lakshminarayanan G, McClure HM, Silver R, Choueiri TK, Taplin ME, Park PJ, Berchuck JE. A panel-based mutational signature of homologous recombination deficiency associates with response to PARP inhibition in metastatic castration-resistant prostate cancer. Prostate 2024. [PMID: 39252459 DOI: 10.1002/pros.24788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 09/11/2024]
Abstract
BACKGROUND The PARP inhibitor (PARPi) olaparib is approved for homologous recombination repair (HRR) gene-altered metastatic castration-resistant prostate cancer (mCRPC). However, there is significant heterogeneity in response to PARPi in patients with mCRPC. Better clinical biomarkers are needed to identify patients likely to benefit from PARPi. METHODS Patients with prostate adenocarcinoma and panel sequencing at Dana-Farber Cancer Institute were identified. Mutational signature analysis was performed using SigMA to characterize tumors as HRR deficient (HRD). The validity of SigMA to identify patients likely to benefit from olaparib was compared to the current FDA label (presence of a deleterious alteration in one of 14 HRR genes). RESULTS 546 patients were identified, of which 34% were HRD. Among patients with HRR gene alterations, only patients with BRCA2 two-copy loss (2CL) were more likely to be HRD compared to patients without HRR gene alterations (74% vs 31%; P = 9.1 × 10-7). 28 patients with mCRPC received olaparib, of which 13 were HRD and 9 had BRCA2 2CL. SigMA improved upon the current FDA label for predicting PSA50 (sensitivity: 100% vs 90%; specificity: 83% vs 44%; PPV: 77% vs 47%; NPV: 100% vs 89%) and rPFS > 6 months (sensitivity: both 92%; specificity: 93% vs 53%; PPV: 92% vs 63%; NPV: 93% vs 89%). On multivariate analysis, incorporating prognostic clinical factors and HR gene alterations, SigMA-predicted HRD independently associated with improved PSA-PFS (HR = 0.086, p = 0.00082) and rPFS (HR = 0.078, p = 0.0070). CONCLUSIONS SigMA-predicted HRD may better identify patients likely to benefit from olaparib as compared to the current FDA label. Larger studies are needed for further validation.
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Affiliation(s)
- Daniel Boiarsky
- Department of Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ziad Bakouny
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Guruprasad Ananda
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Hunter Savignano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Heather M McClure
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Rebecca Silver
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Rosalind Franklin University of Medicine and Science, Chicago, Illinois, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jacob E Berchuck
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
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7
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Young AN, Lin LH, Abel MK, Badhey MO, Lechner A, Horowitz NS, Berkowitz RS, Parra-Herran C, Elias KM. Atypical placental site nodules: Clinicopathologic features, management and patient outcomes in an institutional series. Gynecol Oncol 2024; 190:215-221. [PMID: 39236483 DOI: 10.1016/j.ygyno.2024.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/14/2024] [Accepted: 08/20/2024] [Indexed: 09/07/2024]
Abstract
OBJECTIVE To report the New England Trophoblastic Disease Center (NETDC) experience with atypical placental site nodules (APSN). METHODS The NETDC registry was reviewed from 2005 to 2022 and clinical data abstracted. Expert pathologists in GTD reviewed available slides with concurrent immunohistochemical analysis. Targeted deep sequencing was performed for four cases. RESULTS Among 35 cases of APSN identified, 29 had clinical and demographic data available. Abnormal uterine bleeding (59.3%) was the most common presenting symptom. Most women (79.3%) had an antecedent live birth. Two cases were incidentally diagnosed after hysterectomy for other indications, and one case lost to follow-up. Among the remaining 26 cases, 11 (42.3%) opted for hysterectomy and 15 for re-sampling (57.7%), among whom 3 later underwent hysterectomy for persistent APSN. Subsequent obstetrical outcomes included 3 spontaneous abortions, 1 therapeutic abortion, 1 ectopic pregnancy, 2 cesarean sections, 1 cesarean hysterectomy, and 1 spontaneous vaginal delivery. Subsequent pathology was available for 26 cases: 4 epithelioid trophoblastic tumors (15.4%), 9 APSN (34.6%), 3 PSN (11.5%), and 10 without abnormalities (38.4%). Histopathologic characteristics of APSN included moderate to severe cytologic atypia, median Ki-67 proliferation index of 8%, and typical immunohistochemical profiles (diffuse or multifocal positivity for p63 and GATA-3 and absent or focal CD146). No histopathologic feature predicted ETT. Among 4 sequenced cases, no recurrent genomic features were identified. CONCLUSIONS APSN is a rare form of gestational trophoblastic proliferation with uncertain malignant potential. While normal obstetric outcomes are possible, the persistence rate is high, and definitive management remains hysterectomy.
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Affiliation(s)
- Alexandria N Young
- Division of Gynecologic Oncology, New England Trophoblastic Disease Center, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Lawrence H Lin
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary Kathryn Abel
- Division of Gynecologic Oncology, New England Trophoblastic Disease Center, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marika Osterbur Badhey
- Division of Gynecologic Oncology, New England Trophoblastic Disease Center, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Adam Lechner
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Neil S Horowitz
- Division of Gynecologic Oncology, New England Trophoblastic Disease Center, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ross S Berkowitz
- Division of Gynecologic Oncology, New England Trophoblastic Disease Center, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlos Parra-Herran
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kevin M Elias
- Division of Gynecologic Oncology, New England Trophoblastic Disease Center, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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8
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Sabbagh MF, Janovitz T, Dias-Santagata D, Siegmund S, Nardi V, Wirth LJ, Randolph GW, Lennerz JK, Decker B, Nose V, Alzumaili BA, Faquin WC, Barletta JA, Le LP, Iafrate AJ, Sadow PM, Fisch AS. FGFR Alterations in Thyroid Carcinoma: A Novel Class of Primary Drivers with Significant Therapeutic Implications and Secondary Molecular Events Potentially Mediating Resistance in Thyroid Malignancy. Thyroid 2024; 34:1137-1149. [PMID: 39003525 DOI: 10.1089/thy.2024.0216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Background: Diagnostic classification of thyroid malignancy is primarily accomplished through examination of histomorphological features and may be substantiated and clarified by molecular data. Individual molecular drivers show relatively robust and specific associations with histological subtypes of thyroid malignancy, including BRAF sequence variants and kinase gene fusions in papillary thyroid carcinoma, predominantly RAS variants in follicular-patterned neoplasia, and additional "late" mutations affecting TERT promoter, TP53, and the PI3K/AKT/PTEN pathway in high-grade malignancies. Given the oncogenic role of FGFR, particularly FGFR1-3, the goal of this study was to explore the role of FGFR in thyroid carcinoma biology. Methods: We completed a multicenter retrospective observational study for thyroid carcinomas with pathogenic alterations in the FGFR gene family. We performed this study by querying the molecular data accumulated for thyroid carcinomas from each center. Results: Overall, 5030 sequenced thyroid malignancies were reviewed, yielding 17 tumors with FGFR alterations, including 11 where FGFR was the primary molecular driver and 6 where FGFR was a secondary pathogenic alteration, with a subset for which there was available clinical follow-up data. Of the 11 carcinomas with an FGFR driver, 9 were gene fusions involving FGFR2:VCL (4 tumors), TG::FGFR1 (3 tumors), FGFR2::CIT, and FGFR2::SHTN1, and the remaining 2 were driven by FGFR1 amplification. In the 6 tumors where a canonical driver of thyroid neoplasia was present (5 cases) or no clear primary driver was detected (1 case), sequencing detected secondary FGFR2 p.W290C, p.Y375C, and p.N549K, as well as FGFR1 p.N546K in the respective tyrosine kinase domains, some at subclonal variant allele frequencies. Conclusions: This study presents the first description of a collection of thyroid carcinomas grouped by primary driver alterations in FGFR, as well as a cohort of thyroid tumors with secondary alterations that potentially lead to tumor progression or resistance to targeted therapy. Given the availability of small molecular inhibitors targeting oncogenic FGFR, this study emphasizes the significant implications for patients from identification of FGFR alterations as they are currently under-recognized in the literature and, most importantly, have potential novel treatment options.
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Affiliation(s)
- Mark F Sabbagh
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Tyler Janovitz
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephanie Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lori J Wirth
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Gregory W Randolph
- Departments of Otolaryngology - Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, USA
| | | | - Brennan Decker
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Vania Nose
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Bayan A Alzumaili
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Justine A Barletta
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Long P Le
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter M Sadow
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Adam S Fisch
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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9
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Padmanabha N, Weinstock MJ, Xu S, Lepe M, Garrett LA, Kappes UP, Michaels PD. Transdifferentiation of diffuse large B-cell lymphoma to a poorly differentiated neoplasm following CAR T-cell therapy. J Hematop 2024; 17:149-153. [PMID: 38878262 DOI: 10.1007/s12308-024-00592-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/06/2024] [Indexed: 08/15/2024] Open
Abstract
Chimeric antigen receptor T-cell (CAR-T) therapy is a recent advancement in precision medicine with promising results for patients with relapsed or refractory B-cell malignancies. However, rare post-therapy morphologic, immunophenotypic, and genomic alterations can occur. This study is to present a case of a patient with diffuse large B-cell lymphoma (DLBCL) who underwent anti-CD19 CAR-T therapy with disease in the uterus that showed transdifferentiation to a poorly differentiated malignant neoplasm that failed to express any lineage specific markers. In immunohistochemistry, fluorescence in situ hybridization (FISH) and targeted next-generation sequencing (NGS) were utilized to fully characterize the diagnostic DLBCL sample in comparison to the poorly differentiated neoplasm of the uterus. Analysis of the diagnostic DLBCL and the poorly differentiated neoplasm demonstrated evidence of a clonal relationship as well as revealing acquisition of mutations associated with CAR-T resistance. Furthermore, downregulation of B-cell associated antigens was observed, underscoring a mechanistic link to CAR-T evasion as well as demonstrating diagnostic confusion. This case illustrates the utility of employing multiple diagnostic modalities in elucidating a pathologic link between a B-cell lymphoma and poorly differentiated neoplasm following targeted therapy.
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MESH Headings
- Humans
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Female
- Immunotherapy, Adoptive/methods
- Cell Transdifferentiation
- Middle Aged
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/genetics
- Uterine Neoplasms/pathology
- Uterine Neoplasms/therapy
- Uterine Neoplasms/genetics
- Uterine Neoplasms/diagnosis
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Affiliation(s)
- Nandan Padmanabha
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Matthew J Weinstock
- Department of Hematology and Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Sean Xu
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Marcos Lepe
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Leslie A Garrett
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ulrike P Kappes
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Phillip D Michaels
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Thorn 613A, 75 Francis St., Boston, MA, 02115, USA.
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10
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Ruiz-Esteves KN, Shank KR, Deutsch AJ, Gunturi A, Chamorro-Pareja N, Colling CA, Zubiri L, Perlman K, Ouyang T, Villani AC, Florez JC, Gusev A, Reynolds KL, Miller KK, Udler MS, Sise ME, Rengarajan M. Identification of Immune Checkpoint Inhibitor-Induced Diabetes. JAMA Oncol 2024:2822927. [PMID: 39207773 PMCID: PMC11362970 DOI: 10.1001/jamaoncol.2024.3104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/15/2024] [Indexed: 09/04/2024]
Abstract
Importance Immune checkpoint inhibitors (ICIs) have revolutionized cancer care; however, accompanying immune-related adverse events (irAEs) confer substantial morbidity and occasional mortality. Life-threatening irAEs may require permanent cessation of ICI, even in patients with positive tumor response. Therefore, it is imperative to comprehensively define the spectrum of irAEs to aid individualized decision-making around the initiation of ICI therapy. Objective To define incidence, risk factors, and clinical spectrum of an irreversible and life-threatening irAE: ICI-induced diabetes. Design, Setting, and Participants This cohort study, conducted at an academic integrated health care system examined 14 328 adult patients treated with ICIs, including 64 patients who developed ICI-induced diabetes, from July 2010 to January 2022. The data were analyzed from 2022 to 2023. Cases of ICI-induced diabetes were manually confirmed; detailed clinical phenotyping was performed at diagnosis and 1-year follow-up. For 862 patients, genotyping data were available, and polygenic risk for type 1 diabetes was determined. Main Outcomes and Measures For ICI-induced diabetes cases and controls, demographic characteristics, comorbidities, tumor category, and ICI category were compared. Among ICI-induced diabetes cases, markers of glycemic physiology were examined at diagnosis and 1-year follow-up. For patients with available genotyping, a published type 1 diabetes polygenic score (T1D GRS2) was calculated. Results Of 14 328 participants, 6571 (45.9%) were women, and the median (range) age was 66 (8-106) years. The prevalence of ICI-induced diabetes among ICI-treated patients was 0.45% (64 of 14 328), with an incidence of 124.8 per 100 000 person-years. Preexisting type 2 diabetes (odds ratio [OR], 5.91; 95% CI, 3.34-10.45) and treatment with combination ICI (OR, 2.57; 95% CI, 1.44-4.59) were significant clinical risk factors of ICI-induced diabetes. T1D GRS2 was associated with ICI-induced diabetes risk, with an OR of 4.4 (95% CI, 1.8-10.5) for patients in the top decile of T1D GRS2, demonstrating a genetic association between spontaneous autoimmunity and irAEs. Patients with ICI-induced diabetes were in 3 distinct phenotypic categories based on autoantibodies and residual pancreatic function, with varying severity of initial presentation. Conclusions and Relevance The results of this analysis of 14 328 ICI-treated patients followed up from ICI initiation determined the incidence, risk factors and clinical spectrum of ICI-induced diabetes. Widespread implementation of this approach across organ-specific irAEs may enhance diagnosis and management of these conditions, and this becomes especially pertinent as ICI treatment rapidly expands to treat a wide spectrum of cancers and is used at earlier stages of treatment.
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Affiliation(s)
- Karina N. Ruiz-Esteves
- Department of Medicine, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston
| | - Kaitlyn R. Shank
- Department of Medicine, Massachusetts General Hospital and Department of Medicine, Brigham and Women’s Hospital, Boston
| | - Aaron J. Deutsch
- Department of Medicine and Center for Genomic Medicine, Massachusetts General Hospital, Programs in Metabolism and Medical and Population Genetics, Broad Institute, Cambridge
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Alekhya Gunturi
- Department of Medicine, Massachusetts General Hospital and Boston University School of Medicine, Boston
| | - Natalia Chamorro-Pareja
- Department of Medicine, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston
| | - Caitlin A. Colling
- Department of Medicine, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston
| | - Leyre Zubiri
- Department of Medicine, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston
| | | | - Tianqi Ouyang
- Department of Medicine, Massachusetts General Hospital, Boston
| | - Alexandra-Chloé Villani
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jose C. Florez
- Department of Medicine and Center for Genomic Medicine, Massachusetts General Hospital, Programs in Metabolism and Medical and Population Genetics, Broad Institute, Cambridge
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Broad Institute, Cambridge, Massachusetts
- Division of Genetics, Brigham and Women’s Hospital and Harvard Medical School, Boston
| | - Kerry L. Reynolds
- Department of Medicine, Mass General Cancer Center, Massachusetts General Hospital, Boston
| | - Karen K. Miller
- Neuroendocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Miriam S. Udler
- Department of Medicine and Center for Genomic Medicine, Massachusetts General Hospital, Programs in Metabolism and Medical and Population Genetics, Broad Institute, Cambridge
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Meghan E. Sise
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston
| | - Michelle Rengarajan
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Broad Institute of Massachusetts Institute of Technology and Harvard University, Boston
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11
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Patel RV, Yao S, Aguilar Murillo E, Huang RY, Bi WL. Spatial Distribution of Meningiomas: A Magnetic Resonance Image Atlas. Neurosurgery 2024:00006123-990000000-01325. [PMID: 39194267 DOI: 10.1227/neu.0000000000003149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/13/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND AND OBJECTIVES The size and anatomic location of meningiomas have been shown to correlate with distinct clinical manifestations, histopathological subtypes, and surgical risk. However, meningioma anatomic origin sites can be obscured in large tumors and those crossing compartments. We therefore sought to apply unbiased lesion mapping to localize intracranial meningioma distributions and their association with biology and grade. METHODS MRI scans, World Health Organization (WHO) grade, and a molecularly Integrated Grade (IG) derived from cytogenetics were analyzed from adult patients with intracranial meningiomas. Semi-automated tumor segmentation was performed on T1-weighted contrast-enhanced MRI. We used the voxel-based lesion mapping technique to generate a meningioma atlas, mapping spatial frequency and correlating with tumor grades. RESULTS Of 881 patients with meningioma (median age: 57 years, 68.8% female), 589 were WHO grade 1 (66.8%), 265 WHO grade 2 (30.1%), and 27 WHO grade 3 (3.1%) with a median tumor volume of 14.6 cm3. After molecular reclassification, 585 were IG-1 (66.4%), 160 IG-2 (18.2%), and 136 IG-3 (15.4%). Benign tumors were concentrated in and around the midline anterior skull base while malignant meningiomas were enriched in the falcine/parasagittal region and the sphenoid wing, similar to the distribution when stratified by chromosome 1p loss. Meningiomas exhibited sharper spatial clustering when stratified by the molecular IG than by WHO grade. WHO grade 2 meningiomas divided equally across IG 1-3, with corresponding partition of spatial distribution in the midline anterior skull base (in WHO grade 2, IG-1) and falcine/parasagittal and sphenoid regions (WHO grade 2, IG-3). Meningioma volumes significantly varied across age, sex, and WHO/IG grades. CONCLUSION We demonstrate the utility of voxel-based lesion mapping for intracranial tumors, characterizing distinct meningioma distribution patterns across histopathological and molecularly defined grades. Molecular grading associated with sharper tumor spatial clusters, supporting a phenotype-genotype association in meningiomas.
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Affiliation(s)
- Ruchit V Patel
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Shun Yao
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Neurosurgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | - Raymond Y Huang
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Neuroradiology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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12
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Dehghani A, Sharma AE, Siegmund SE, Carreon CK, Stewart CJR, Medeiros F, Mirkovic J, Nucci MR, Crum CP, Hornick JL, Howitt BE, McCluggage WG, Kolin DL. STK11 (LKB1) immunohistochemistry is a sensitive and specific marker for STK11 adnexal tumours. Histopathology 2024. [PMID: 39169716 DOI: 10.1111/his.15303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/03/2024] [Accepted: 08/06/2024] [Indexed: 08/23/2024]
Abstract
AIMS ST11 adnexal tumour is a rare, recently described malignant neoplasm that is associated with Peutz-Jeghers syndrome. It predominantly originates from the para-adnexal soft tissues and often shows secondary involvement of the fallopian tube and ovary. STK11 adnexal tumours have a broad differential diagnosis due to their variable morphology and non-specific immunoprofile, and diagnostic confirmation currently requires sequencing to identify an STK11 mutation. We investigate the diagnostic utility of STK11 (LKB1) immunohistochemistry (IHC) in a cohort of STK11 adnexal tumours and morphological mimics. METHODS AND RESULTS IHC for STK11 was performed on 122 tumours, including 17 STK11 adnexal tumours and 105 morphological mimics (10 female adnexal tumours of Wolffian origin, 22 adult granulosa cell tumours, 10 juvenile granulosa cell tumours, four Sertoli-Leydig cell tumours, two Leydig cell tumours, one Sertoli cell tumour, one steroid cell tumour, four extra-ovarian sex cord-stromal tumours, 16 ovarian endometrioid carcinomas, eight tubo-ovarian high-grade serous carcinomas, five ovarian mesonephric-like adenocarcinomas, 14 ovarian carcinosarcomas, five peritoneal malignant mesotheliomas, two pelvic plexiform leiomyomata and one ovarian solid pseudopapillary tumour). All STK11 adnexal tumours showed complete loss of cytoplasmic staining for STK11. All other tumour types showed retained cytoplasmic staining, except for one endometrioid carcinoma with mucinous differentiation which showed complete loss of STK11 expression and a high-grade serous carcinoma with subclonal loss. CONCLUSIONS STK11 is a highly sensitive and specific immunohistochemical marker for distinguishing STK11 adnexal tumour from its histological mimics, and can obviate the need for confirmatory molecular studies in the appropriate morphological context.
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Affiliation(s)
- Amir Dehghani
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Aarti E Sharma
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie E Siegmund
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chrystalle K Carreon
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Colin J R Stewart
- Department of Histopathology, King Edward Memorial Hospital, Perth, WA, Australia
| | - Fabiola Medeiros
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jelena Mirkovic
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Marisa R Nucci
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher P Crum
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brooke E Howitt
- Department of Pathology, Stanford University Medical Center, Stanford, CA, USA
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - David L Kolin
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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13
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Moran JMT, Hoang MP, Mariño-Enríquez A, DeSimone MS. Malignant Proliferating Pilar Tumor With Sarcomatous Transformation ("Carcinosarcoma"): Case Report With Molecular Profile. Am J Dermatopathol 2024:00000372-990000000-00405. [PMID: 39141750 DOI: 10.1097/dad.0000000000002831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
ABSTRACT Malignant proliferating pilar tumors (MPPTs) are rare, unique cutaneous adnexal tumors. Sarcomatous transformation in MPPTs is even rarer (4 previous cases reported). Here, we report an extraordinary case of a MPPT with sarcomatous transformation occurring on the scalp of a 63-year-old man with an in-depth molecular profile along with histologic, immunohistochemical, and follow-up data. Shared mutations in the epithelial and sarcomatous components included a loss-of-function TP53 mutation. An inactivating TP53 mutation was only identified in the epithelial component, and an inactivating CDKN2A mutation was only identified in the sarcomatous component. Copy number variations previously reported in MPPT were also identified, including 6p21.1 loss, 6q arm loss, and 15q21.1-q26.3 gain [epithelial], and 6p22.2-p22.3 loss [sarcoma]. Histologically, the tumor demonstrated juxtaposed areas of proliferating pilar tumor, carcinoma with clear cell change, and sarcomatous areas that did not stain for AE1/AE3, p40, CD34, S100 protein, and smooth muscle actin by immunohistochemistry. The patient is alive at 2 years without evidence of recurrence or metastasis.
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Affiliation(s)
- Jakob M T Moran
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA; and
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA; and
| | - Adrian Mariño-Enríquez
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Mia S DeSimone
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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14
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Pecci F, Nakazawa S, Ricciuti B, Harada G, Lee JK, Alessi JV, Barrichello A, Vaz VR, Lamberti G, Di Federico A, Gandhi MM, Gazgalis D, Feng WW, Jiang J, Baldacci S, Locquet MA, Gottlieb FH, Chen MF, Lee E, Haradon D, Smokovich A, Voligny E, Nguyen T, Goel VK, Zimmerman Z, Atwal S, Wang X, Bahcall M, Heist RS, Iqbal S, Gandhi N, Elliott A, Vanderwalde AM, Ma PC, Halmos B, Liu SV, Che J, Schrock AB, Drilon A, Jänne PA, Awad MM. Activating Point Mutations in the MET Kinase Domain Represent a Unique Molecular Subset of Lung Cancer and Other Malignancies Targetable with MET Inhibitors. Cancer Discov 2024; 14:1440-1456. [PMID: 38564707 PMCID: PMC11294820 DOI: 10.1158/2159-8290.cd-23-1217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/23/2024] [Accepted: 04/01/2024] [Indexed: 04/04/2024]
Abstract
Activating point mutations in the MET tyrosine kinase domain (TKD) are oncogenic in a subset of papillary renal cell carcinomas. Here, using comprehensive genomic profiling among >600,000 patients, we identify activating MET TKD point mutations as putative oncogenic driver across diverse cancers, with a frequency of ∼0.5%. The most common mutations in the MET TKD defined as oncogenic or likely oncogenic according to OncoKB resulted in amino acid substitutions at positions H1094, L1195, F1200, D1228, Y1230, M1250, and others. Preclinical modeling of these alterations confirmed their oncogenic potential and also demonstrated differential patterns of sensitivity to type I and type II MET inhibitors. Two patients with metastatic lung adenocarcinoma harboring MET TKD mutations (H1094Y, F1200I) and no other known oncogenic drivers achieved confirmed partial responses to a type I MET inhibitor. Activating MET TKD mutations occur in multiple malignancies and may confer clinical sensitivity to currently available MET inhibitors. Significance: The identification of targetable genomic subsets of cancer has revolutionized precision oncology and offers patients treatments with more selective and effective agents. Here, we demonstrate that activating, oncogenic MET tyrosine kinase domain mutations are found across a diversity of cancer types and are responsive to MET tyrosine kinase inhibitors.
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Affiliation(s)
- Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Seshiru Nakazawa
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Guilherme Harada
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | | | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Adriana Barrichello
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Victor R Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Malini M Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Dimitris Gazgalis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William W Feng
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jie Jiang
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Simon Baldacci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marie-Anaïs Locquet
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Felix H Gottlieb
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Monica F Chen
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Elinton Lee
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Danielle Haradon
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Anna Smokovich
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Emma Voligny
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tom Nguyen
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vikas K Goel
- Turning Point Therapeutics, Bristol Myers Squibb Company, San Diego, California
| | - Zachary Zimmerman
- Turning Point Therapeutics, Bristol Myers Squibb Company, San Diego, California
| | - Sumandeep Atwal
- Turning Point Therapeutics, Bristol Myers Squibb Company, San Diego, California
| | - Xinan Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Magda Bahcall
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Sumaiya Iqbal
- The Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
| | | | | | | | - Patrick C Ma
- Penn State Cancer Institute, Penn State College of Medicine, Penn State University, Hershey, Pennsylvania
| | | | | | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Alexander Drilon
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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15
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Papke DJ, Odintsov I, Dickson BC, Nucci MR, Agaimy A, Fletcher CDM. Myxoid Inflammatory Myofibroblastic Sarcoma: Clinicopathologic Analysis of 25 Cases of a Distinctive Sarcoma With Deceptively Bland Morphology and Aggressive Clinical Behavior. Am J Surg Pathol 2024; 48:1005-1016. [PMID: 38717131 DOI: 10.1097/pas.0000000000002231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The number of recognized sarcoma types harboring targetable molecular alterations continues to increase. Here we present 25 examples of a distinctive myofibroblastic tumor, provisionally termed "myxoid inflammatory myofibroblastic sarcoma," which might be related to inflammatory myofibroblastic tumor, and which occurred in 13 males (52%) and 12 females at a median age of 37 years (range: 7 to 79 years). Primary tumor sites were peritoneum (18 patients; 72%), paratesticular (2; 8%), chest wall (1), upper extremity (1), esophagus (1), retroperitoneum (1), and uterus (1). Nine peritoneal tumors (50%) were multifocal at presentation; all other tumors were unifocal. Tumors showed bland-to-mildly-atypical neoplastic myofibroblasts in a myxoid stroma, with prominent inflammatory infiltrates in 22 cases (88%). Most tumors showed delicate branching stromal vessels like those of myxoid liposarcoma, and most showed infiltrative growth through non-neoplastic tissue. Immunohistochemistry demonstrated expression of SMA (19/25 tumors; 76%), desmin (13/22; 59%), and CD30 (5/11; 45%), while ALK was expressed in 1 tumor (of 25; 4%) that was negative for ALK rearrangement. Sequencing of 11 tumors showed seven to harbor tyrosine kinase fusions (4 PDGFRB , 2 PML :: JAK1 , 1 SEC31A :: PDGFRA ). Two instead harbored hot spot KRAS mutations (G12V and Q61H), and 2 were negative for known driving alterations. Clinical follow-up was available for 18 patients (72%; median: 2.7 years; range: 4 mo-12.3 years). Nine patients (50%) were alive with no evidence of disease, 5 (28%) died of disease, and 4 (22%) were alive with disease. Seven patients (39%) experienced peritoneal relapse or distant metastasis. Two patients showed disease progression on conventional, nontargeted chemotherapy. The patient whose tumor harbored SEC31A :: PDGFRA was treated after multiple relapses with imatinib and sunitinib therapy, with progression-free periods of 5 and 2 years, respectively. Despite its bland appearance, myxoid inflammatory myofibroblastic sarcoma harbors a significant risk for disseminated disease, particularly when it occurs in the peritoneum. Targeted therapy could be considered for patients with disseminated disease.
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Affiliation(s)
- David J Papke
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
| | - Igor Odintsov
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
| | | | - Marisa R Nucci
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
| | - Abbas Agaimy
- Institute of Pathology, Erlangen University Hospital, Friedrich Alexander University of Erlangen-Nuremberg, Erlangen, Germany
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16
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Nicoletti A, Paratore M, Vitale F, Negri M, Quero G, Esposto G, Mignini I, Alfieri S, Gasbarrini A, Zocco MA, Zileri Dal Verme L. Understanding the Conundrum of Pancreatic Cancer in the Omics Sciences Era. Int J Mol Sci 2024; 25:7623. [PMID: 39062863 PMCID: PMC11276793 DOI: 10.3390/ijms25147623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Pancreatic cancer (PC) is an increasing cause of cancer-related death, with a dismal prognosis caused by its aggressive biology, the lack of clinical symptoms in the early phases of the disease, and the inefficacy of treatments. PC is characterized by a complex tumor microenvironment. The interaction of its cellular components plays a crucial role in tumor development and progression, contributing to the alteration of metabolism and cellular hyperproliferation, as well as to metastatic evolution and abnormal tumor-associated immunity. Furthermore, in response to intrinsic oncogenic alterations and the influence of the tumor microenvironment, cancer cells undergo a complex oncogene-directed metabolic reprogramming that includes changes in glucose utilization, lipid and amino acid metabolism, redox balance, and activation of recycling and scavenging pathways. The advent of omics sciences is revolutionizing the comprehension of the pathogenetic conundrum of pancreatic carcinogenesis. In particular, metabolomics and genomics has led to a more precise classification of PC into subtypes that show different biological behaviors and responses to treatments. The identification of molecular targets through the pharmacogenomic approach may help to personalize treatments. Novel specific biomarkers have been discovered using proteomics and metabolomics analyses. Radiomics allows for an earlier diagnosis through the computational analysis of imaging. However, the complexity, high expertise required, and costs of the omics approach are the main limitations for its use in clinical practice at present. In addition, the studies of extracellular vesicles (EVs), the use of organoids, the understanding of host-microbiota interactions, and more recently the advent of artificial intelligence are helping to make further steps towards precision and personalized medicine. This present review summarizes the main evidence for the application of omics sciences to the study of PC and the identification of future perspectives.
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Affiliation(s)
- Alberto Nicoletti
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (A.N.); (M.P.); (F.V.); (M.N.); (G.E.); (I.M.); (A.G.); (L.Z.D.V.)
| | - Mattia Paratore
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (A.N.); (M.P.); (F.V.); (M.N.); (G.E.); (I.M.); (A.G.); (L.Z.D.V.)
| | - Federica Vitale
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (A.N.); (M.P.); (F.V.); (M.N.); (G.E.); (I.M.); (A.G.); (L.Z.D.V.)
| | - Marcantonio Negri
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (A.N.); (M.P.); (F.V.); (M.N.); (G.E.); (I.M.); (A.G.); (L.Z.D.V.)
| | - Giuseppe Quero
- Centro Pancreas, Chirurgia Digestiva, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (G.Q.); (S.A.)
| | - Giorgio Esposto
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (A.N.); (M.P.); (F.V.); (M.N.); (G.E.); (I.M.); (A.G.); (L.Z.D.V.)
| | - Irene Mignini
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (A.N.); (M.P.); (F.V.); (M.N.); (G.E.); (I.M.); (A.G.); (L.Z.D.V.)
| | - Sergio Alfieri
- Centro Pancreas, Chirurgia Digestiva, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (G.Q.); (S.A.)
| | - Antonio Gasbarrini
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (A.N.); (M.P.); (F.V.); (M.N.); (G.E.); (I.M.); (A.G.); (L.Z.D.V.)
| | - Maria Assunta Zocco
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (A.N.); (M.P.); (F.V.); (M.N.); (G.E.); (I.M.); (A.G.); (L.Z.D.V.)
| | - Lorenzo Zileri Dal Verme
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (A.N.); (M.P.); (F.V.); (M.N.); (G.E.); (I.M.); (A.G.); (L.Z.D.V.)
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17
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Forrest SJ, Gupta H, Ward A, Li YY, Doan D, Al-Ibraheemi A, Alexandrescu S, Bandopadhayay P, Shusterman S, Mullen EA, Collins NB, Chi SN, Wright KD, Kumari P, Mazor T, Ligon KL, Shivdasani P, Manam M, MacConaill LE, Ceca E, Benich SN, London WB, Schilsky RL, Bruinooge SS, Guidry Auvil JM, Cerami E, Rollins BJ, Meyerson ML, Lindeman NI, Johnson BE, Cherniack AD, Church AJ, Janeway KA. Molecular profiling of 888 pediatric tumors informs future precision trials and data-sharing initiatives in pediatric cancer. Nat Commun 2024; 15:5837. [PMID: 38992034 PMCID: PMC11239876 DOI: 10.1038/s41467-024-49944-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 06/18/2024] [Indexed: 07/13/2024] Open
Abstract
To inform clinical trial design and real-world precision pediatric oncology practice, we classified diagnoses, assessed the landscape of mutations, and identified genomic variants matching trials in a large unselected institutional cohort of solid tumors patients sequenced at Dana-Farber / Boston Children's Cancer and Blood Disorders Center. Tumors were sequenced with OncoPanel, a targeted next-generation DNA sequencing panel. Diagnoses were classified according to the International Classification of Diseases for Oncology (ICD-O-3.2). Over 6.5 years, 888 pediatric cancer patients with 95 distinct diagnoses had successful tumor sequencing. Overall, 33% (n = 289/888) of patients had at least 1 variant matching a precision oncology trial protocol, and 14% (41/289) were treated with molecularly targeted therapy. This study highlights opportunities to use genomic data from hospital-based sequencing performed either for research or clinical care to inform ongoing and future precision oncology clinical trials. Furthermore, the study results emphasize the importance of data sharing to define the genomic landscape and targeted treatment opportunities for the large group of rare pediatric cancers we encounter in clinical practice.
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Affiliation(s)
- Suzanne J Forrest
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Hersh Gupta
- Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abigail Ward
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Yvonne Y Li
- Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Duong Doan
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Alyaa Al-Ibraheemi
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Sanda Alexandrescu
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Pratiti Bandopadhayay
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Suzanne Shusterman
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Mullen
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Natalie B Collins
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Susan N Chi
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Karen D Wright
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Tali Mazor
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Evelina Ceca
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Sidney N Benich
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Wendy B London
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Barrett J Rollins
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew L Meyerson
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Bruce E Johnson
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Andrew D Cherniack
- Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alanna J Church
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Katherine A Janeway
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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18
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Kapp FG, Bazgir F, Mahammadzade N, Mehrabipour M, Vassella E, Bernhard SM, Döring Y, Holm A, Karow A, Seebauer C, Platz Batista da Silva N, Wohlgemuth WA, Oppenheimer A, Kröning P, Niemeyer CM, Schanze D, Zenker M, Eng W, Ahmadian MR, Baumgartner I, Rössler J. Somatic RIT1 delins in arteriovenous malformations hyperactivate RAS-MAPK signaling amenable to MEK inhibition. Angiogenesis 2024:10.1007/s10456-024-09934-8. [PMID: 38969873 DOI: 10.1007/s10456-024-09934-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/18/2024] [Indexed: 07/07/2024]
Abstract
Arteriovenous malformations (AVM) are benign vascular anomalies prone to pain, bleeding, and progressive growth. AVM are mainly caused by mosaic pathogenic variants of the RAS-MAPK pathway. However, a causative variant is not identified in all patients. Using ultra-deep sequencing, we identified novel somatic RIT1 delins variants in lesional tissue of three AVM patients. RIT1 encodes a RAS-like protein that can modulate RAS-MAPK signaling. We expressed RIT1 variants in HEK293T cells, which led to a strong increase in ERK1/2 phosphorylation. Endothelial-specific mosaic overexpression of RIT1 delins in zebrafish embryos induced AVM formation, highlighting their functional importance in vascular development. Both ERK1/2 hyperactivation in vitro and AVM formation in vivo could be suppressed by pharmacological MEK inhibition. Treatment with the MEK inhibitor trametinib led to a significant decrease in bleeding episodes and AVM size in one patient. Our findings implicate RIT1 in AVM formation and provide a rationale for clinical trials with targeted treatments.
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Affiliation(s)
- Friedrich G Kapp
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, VASCERN VASCA European Reference Centre, 79106, Freiburg, Germany.
| | - Farhad Bazgir
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital, Heinrich-Heine University, Düsseldorf, Germany
| | - Nagi Mahammadzade
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, VASCERN VASCA European Reference Centre, 79106, Freiburg, Germany
| | - Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital, Heinrich-Heine University, Düsseldorf, Germany
| | - Erik Vassella
- Institute of Pathology and Tissue Medicine, University of Bern, Bern, Switzerland
| | - Sarah M Bernhard
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Yvonne Döring
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Pettenkoferstr 9, 80336, Munich, Germany
| | - Annegret Holm
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, VASCERN VASCA European Reference Centre, 79106, Freiburg, Germany
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Axel Karow
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Caroline Seebauer
- Department of Otorhinolaryngology, Regensburg University Medical Center, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | | | - Walter A Wohlgemuth
- University Clinic and Policlinic of Radiology at the Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Aviv Oppenheimer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, VASCERN VASCA European Reference Centre, 79106, Freiburg, Germany
| | - Pia Kröning
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, VASCERN VASCA European Reference Centre, 79106, Freiburg, Germany
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Whitney Eng
- Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital, Heinrich-Heine University, Düsseldorf, Germany
| | - Iris Baumgartner
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Jochen Rössler
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, VASCERN VASCA European Reference Centre, 79106, Freiburg, Germany.
- Department of Vascular Medicine, National Reference Center of Rare Lymphatic and Vascular Diseases, UA11 INSERM - UM IDESP, Campus Santé, Montpellier Cedex 5, France.
- Division of Paediatric Hematology and Oncology, Department of Paediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
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19
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Rolando JC, Melkonian AV, Walt DR. The Present and Future Landscapes of Molecular Diagnostics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:459-474. [PMID: 38360553 DOI: 10.1146/annurev-anchem-061622-015112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Nucleic acid testing is the cornerstone of modern molecular diagnostics. This review describes the current status and future directions of molecular diagnostics, focusing on four major techniques: polymerase chain reaction (PCR), next-generation sequencing (NGS), isothermal amplification methods such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR)-based detection methods. We explore the advantages and limitations of each technique, describe how each overlaps with or complements other techniques, and examine current clinical offerings. This review provides a broad perspective into the landscape of molecular diagnostics and highlights potential future directions in this rapidly evolving field.
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Affiliation(s)
- Justin C Rolando
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - Arek V Melkonian
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - David R Walt
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
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20
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Bauer AH, Alkhateeb KJ, Agoston AT, Odze RD, Joshi MG, Huffman BM, Enzinger P, Perez K, Deshpande V, Cleary JM, Wee JO, Dong F, Zhao L. Transcriptionally Active Human Papillomavirus Infection in a Minority of Esophageal Squamous Cell Carcinomas in North America. Am J Surg Pathol 2024; 48:883-889. [PMID: 38726899 DOI: 10.1097/pas.0000000000002235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The role of Human papillomavirus (HPV) infection in esophageal squamous cell carcinoma (ESCC) is a topic of ongoing debate. This study used two screening approaches to look for evidence of HPV infection in esophageal squamous cell carcinoma. We initially checked for HPV infection in a randomly selected group of 53 ESCC cases. We did not detect any tumors positive for high-risk HPV. However, during clinical practice, we identified an HPV-positive ESCC in the distal esophagus, which tested positive for HPV16. This index case was TP53 wild-type, as determined by next-generation DNA sequencing (NGS). Since TP53 mutations are rare in other HPV-driven cancers, we improved our screening method by limiting our screen to a subset of ESCC cases without TP53 mutations. A second screen of 95 ESCCs (from 93 patients) sequenced by NGS revealed an additional 7 ESCCs with TP53 wild-type status (7.3% of the total). Of the 7 cases, 2 cases were found to be high-risk HPV positive. Both patients also tested positive for circulating cell-free HPV DNA and had a complete response to neoadjuvant chemoradiation. The index patient had microscopic residual tumor following neoadjuvant therapy. The patient underwent adjuvant immunotherapy and remained disease free after 22 months of surveillance. This study affirms the transcriptionally active status of high-risk HPV in a minority of ESCC patients in North America.
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Affiliation(s)
- Anna H Bauer
- Department of Pathology, Brigham and Women's Hospital
- Division of Thoracic Surgery, Brigham and Women's Hospital
| | | | - Agoston T Agoston
- Department of Pathology, Brigham and Women's Hospital
- Harvard Medical School
| | | | - Megha G Joshi
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston
| | - Brandon M Huffman
- Beth-Israel Lahey Health, Winchester Hospital, Winchester, MA
- University of Missouri School of Medicine, Columbia, MO
| | - Peter Enzinger
- Beth-Israel Lahey Health, Winchester Hospital, Winchester, MA
- University of Missouri School of Medicine, Columbia, MO
| | - Kimberly Perez
- Beth-Israel Lahey Health, Winchester Hospital, Winchester, MA
- University of Missouri School of Medicine, Columbia, MO
| | - Vikram Deshpande
- University of Missouri School of Medicine, Columbia, MO
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - James M Cleary
- Beth-Israel Lahey Health, Winchester Hospital, Winchester, MA
- University of Missouri School of Medicine, Columbia, MO
| | - Jon O Wee
- University of Missouri School of Medicine, Columbia, MO
- Department of Pathology, Stanford Medicine, Stanford, CA
| | - Fei Dong
- Division of Gastrointestinal Oncology, Dana-Farber Cancer Institute
| | - Lei Zhao
- Department of Pathology, Brigham and Women's Hospital
- University of Missouri School of Medicine, Columbia, MO
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21
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Christakis A, Nowak J, Hamilton MJ, Goldblum JR, Parrack P, Lindeman NI, Odze R, Patil DT. Molecular profiling of visible polypoid and invisible conventional intestinal-type low-grade dysplasia in patients with idiopathic inflammatory bowel disease. J Clin Pathol 2024:jcp-2024-209601. [PMID: 38886044 DOI: 10.1136/jcp-2024-209601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
AIMS Little is known about the molecular features of visible polyps with low-grade intestinal-type dysplasia in patients with inflammatory bowel disease (IBD). To better understand their origins and biological potential, we sought to genomically profile these lesions and compare them with invisible low-grade dysplasia and sporadic adenomas from non-IBD patients. METHODS 22 polyps within areas of colitis, 13 polyps outside areas of colitis, 10 foci of invisible dysplasia from patients with IBD and 6 sporadic tubular adenomas from non-IBD patients were analysed using the OncoPanel assay. RESULTS Polyps arising in areas of colitis showed a greater spectrum of mutations, including APC, KRAS, FBXW7, TP53, ARID1A and TCF7L2. Polyps outside colitis and non-IBD sporadic adenomas showed a limited mutational profile, with APC and CTNNB1 mutations. Invisible dysplasia was characterised by TP53, CTNNB1 and KRAS alterations. Compared with dysplastic polyps, none of the invisible dysplastic foci showed APC alterations (73%-within colitis; p=0.0001, 92%-outside colitis; p<0.0001, 83%-sporadic adenomas; p=0.001). TP53 mutations were significantly higher in invisible dysplasia (50%) compared with polyps within colitis (9%; p=0.02) and outside colitis (8%; p=0.03). CONCLUSIONS Molecular alterations in visible low-grade dysplastic polyps with conventional intestinal-type dysplasia from patients with IBD and sporadic adenomas from non-IBD patients overlap significantly. APC alterations appear to play a major role in the development of visible low-grade dysplastic lesions in patients with IBD, regardless of background colitis. As with IBD-associated colorectal cancers, TP53 mutations are an early event in the development of invisible, low-grade conventional intestinal-type dysplasia in patients with IBD.
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Affiliation(s)
| | - Jonathan Nowak
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew J Hamilton
- Department of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - John R Goldblum
- Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Paige Parrack
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert Odze
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Deepa T Patil
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
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22
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Cheong TC, Jang A, Wang Q, Leonardi GC, Ricciuti B, Alessi JV, Di Federico A, Awad MM, Lehtinen MK, Harris MH, Chiarle R. Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers. Nat Commun 2024; 15:5110. [PMID: 38877018 PMCID: PMC11178778 DOI: 10.1038/s41467-024-49499-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are followed typical recurrent patterns, but the underlying mechanisms and clinical implications of these patterns are poorly understood. By developing Functionally Active Chromosomal Translocation Sequencing (FACTS), we discover that typical TK fusions involving ALK, ROS1, RET and NTRK1 are selected from pools of chromosomal rearrangements by two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies. Our findings highlight the principles of oncogenic TK fusion formation and selection in cancers, with clinical implications for guiding targeted therapy.
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Affiliation(s)
- Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ahram Jang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Qi Wang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Giulia C Leonardi
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | | | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
- Division of Hematopathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy.
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23
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Darmofal M, Suman S, Atwal G, Toomey M, Chen JF, Chang JC, Vakiani E, Varghese AM, Balakrishnan Rema A, Syed A, Schultz N, Berger MF, Morris Q. Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data. Cancer Discov 2024; 14:1064-1081. [PMID: 38416134 PMCID: PMC11145170 DOI: 10.1158/2159-8290.cd-23-0996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/07/2023] [Accepted: 02/23/2024] [Indexed: 02/29/2024]
Abstract
Tumor type guides clinical treatment decisions in cancer, but histology-based diagnosis remains challenging. Genomic alterations are highly diagnostic of tumor type, and tumor-type classifiers trained on genomic features have been explored, but the most accurate methods are not clinically feasible, relying on features derived from whole-genome sequencing (WGS), or predicting across limited cancer types. We use genomic features from a data set of 39,787 solid tumors sequenced using a clinically targeted cancer gene panel to develop Genome-Derived-Diagnosis Ensemble (GDD-ENS): a hyperparameter ensemble for classifying tumor type using deep neural networks. GDD-ENS achieves 93% accuracy for high-confidence predictions across 38 cancer types, rivaling the performance of WGS-based methods. GDD-ENS can also guide diagnoses of rare type and cancers of unknown primary and incorporate patient-specific clinical information for improved predictions. Overall, integrating GDD-ENS into prospective clinical sequencing workflows could provide clinically relevant tumor-type predictions to guide treatment decisions in real time. SIGNIFICANCE We describe a highly accurate tumor-type prediction model, designed specifically for clinical implementation. Our model relies only on widely used cancer gene panel sequencing data, predicts across 38 distinct cancer types, and supports integration of patient-specific nongenomic information for enhanced decision support in challenging diagnostic situations. See related commentary by Garg, p. 906. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Madison Darmofal
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, New York
| | - Shalabh Suman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gurnit Atwal
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Michael Toomey
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, New York
| | - Jie-Fu Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason C. Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anna M. Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Quaid Morris
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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24
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O'Neill AF, Church AJ, Feraco A, Spidle J, Wall CB, Kim HB, Elisofon S, Vakili K, Pimkin M, Dharia NV, Shelman NR, Perez-Atayde AR, Rodriguez-Galindo C. Clinical and immunophenotype correlating with response to immunotherapy in paediatric patients with primary liver carcinoma. A case series. EBioMedicine 2024; 104:105147. [PMID: 38749302 PMCID: PMC11108818 DOI: 10.1016/j.ebiom.2024.105147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Paediatric hepatocellular carcinomas (HCC) traditionally arise in the context of a normal structural and functional liver and carry a dismal prognosis. While chemotherapy is the frontline standard, there is emerging interest in the study of immunotherapies for paediatric patients with relapsed/refractory disease. There is limited data to support whether immunotherapies will be of utility in this patient population. METHODS Six paediatric patients (median age:16 years, range: 12-17 at the time of treatment) with advanced hepatocellular neosplams, either conventional hepatocellular or fibrolamellar carcinoma, were treated with immunotherapy. Patients were consented to institutional genomic profiling and biobanking protocols. Baseline samples and serial tissue samples, when available, were evaluated for somatic mutation rate, actionable gene mutations, and pan-immune bulk RNA expression profiling. Results were correlated with clinical course. FINDINGS Three patients responded to checkpoint inhibition: one achieved a complete, durable response and the other two, prolonged stable disease. Three additional patients progressed. Diagnostic tissue from the complete responder demonstrated a higher relative mutational burden and robust immune infiltrate. Pre-treatment samples from the three responders demonstrated decreased expression of genes associated with T-cell dysfunction. INTERPRETATION A subset of patients with primary paediatric hepatocellular tumours will respond to immunotherapy. Immunotherapies are currently under prospective study for relapsed/refractory liver tumours in paediatric patients. Results from this report support the prospective collection of serial serum and tissue samples which may further identify genomic and immunophenotypic patterns predictive of response. FUNDING This work was supported by Philanthropic funds (Pan Mass Challenge, Team Angus and Team Perspective).
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Affiliation(s)
- Allison F O'Neill
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA.
| | - Alanna J Church
- Boston Children's Hospital and Harvard Medical School, Department of Pathology, Boston, MA, USA
| | - Angela Feraco
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA
| | - Jennifer Spidle
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA
| | - Catherine B Wall
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA
| | - Heung Bae Kim
- Boston Children's Hospital and Harvard Medical School, Department of Surgery, Boston, MA, USA
| | - Scott Elisofon
- Boston Children's Hospital and Harvard Medical School, Department of Hepatology, Boston, MA, USA
| | - Khashayar Vakili
- Boston Children's Hospital and Harvard Medical School, Department of Surgery, Boston, MA, USA
| | - Max Pimkin
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA
| | | | - Nathan R Shelman
- University of Kentucky, Department of Pathology, Lexington, KY, USA
| | - Antonio R Perez-Atayde
- Boston Children's Hospital and Harvard Medical School, Department of Pathology, Boston, MA, USA
| | - Carlos Rodriguez-Galindo
- St. Jude Children's Research Hospital, Departments of Global Pediatric Medicine and Oncology, Memphis, TN, USA
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25
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Luo Q, Raulston EG, Prado MA, Wu X, Gritsman K, Whalen KS, Yan K, Booth CAG, Xu R, van Galen P, Doench JG, Shimony S, Long HW, Neuberg DS, Paulo JA, Lane AA. Targetable leukaemia dependency on noncanonical PI3Kγ signalling. Nature 2024; 630:198-205. [PMID: 38720074 DOI: 10.1038/s41586-024-07410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Phosphoinositide-3-kinase-γ (PI3Kγ) is implicated as a target to repolarize tumour-associated macrophages and promote antitumour immune responses in solid cancers1-4. However, cancer cell-intrinsic roles of PI3Kγ are unclear. Here, by integrating unbiased genome-wide CRISPR interference screening with functional analyses across acute leukaemias, we define a selective dependency on the PI3Kγ complex in a high-risk subset that includes myeloid, lymphoid and dendritic lineages. This dependency is characterized by innate inflammatory signalling and activation of phosphoinositide 3-kinase regulatory subunit 5 (PIK3R5), which encodes a regulatory subunit of PI3Kγ5 and stabilizes the active enzymatic complex. We identify p21 (RAC1)-activated kinase 1 (PAK1) as a noncanonical substrate of PI3Kγ that mediates this cell-intrinsic dependency and find that dephosphorylation of PAK1 by PI3Kγ inhibition impairs mitochondrial oxidative phosphorylation. Treatment with the selective PI3Kγ inhibitor eganelisib is effective in leukaemias with activated PIK3R5. In addition, the combination of eganelisib and cytarabine prolongs survival over either agent alone, even in patient-derived leukaemia xenografts with low baseline PIK3R5 expression, as residual leukaemia cells after cytarabine treatment have elevated G protein-coupled purinergic receptor activity and PAK1 phosphorylation. Together, our study reveals a targetable dependency on PI3Kγ-PAK1 signalling that is amenable to near-term evaluation in patients with acute leukaemia.
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Affiliation(s)
- Qingyu Luo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Evangeline G Raulston
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Miguel A Prado
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Xiaowei Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kira Gritsman
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Karley S Whalen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kezhi Yan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Christopher A G Booth
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ran Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Peter van Galen
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shai Shimony
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Hematology, Rabin Medical Center, Tel Aviv Faculty of Medicine, Tel Aviv, Israel
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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26
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Collins K, Galea LA, Foroughi F, Siegmund SE, Anderson WJ, Appu S, Idrees MT, Ulbright TM, Acosta AM. Genomic analysis of primary epithelial neoplasms of the seminal vesicle identifies a subset of mucinous cystic tumours driven by KRAS mutations. Histopathology 2024; 84:1192-1198. [PMID: 38409850 DOI: 10.1111/his.15167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Carcinomas of the seminal vesicle are exceedingly rare, with a limited number of cases described in the literature. Reported cases span a relatively wide morphological spectrum, and their genomic features remain unexplored. DESIGN In this study, we interrogated five primary epithelial neoplasms of the seminal vesicle using a targeted DNA sequencing platform (OncoPanel, 447 genes). RESULTS The tumours included one adenocarcinoma with intestinal phenotype presenting after external beam radiation (for prostatic adenocarcinoma), one carcinoma with Müllerian-type clear cell phenotype, two mucinous tumours resembling low-grade mucinous neoplasms of the appendix (LAMN) and one mucinous cystadenoma. The post-radiation mucinous adenocarcinoma had genomic findings consistent with bi-allelic inactivation of TP53, as well as multiple copy-number changes with regional and chromosomal arm-level copy-number losses. The Müllerian-type clear cell carcinoma exhibited a complex copy-number profile with numerous regional and arm-level copy-number changes, as well as focal amplification events, including copy-number gain of 8q and amplification of a region within 20q13. Both low-grade mucinous tumours resembling LAMN harboured hot-spot gain-of-function KRAS variants (p.G12V and p.G13D) as the only genomic alteration. No genomic alterations were detected inthe lesion diagnosed as mucinous cystadenoma. CONCLUSION Our results suggest that primary low-grade mucinous neoplasms of the seminal vesicle may represent a distinct entity equivalent to appendiceal counterparts, driven by gain-of-function variants of RAS GTPases. The remaining tumours showed genomic features that closely resembled those of neoplasms with comparable phenotypes and/or biological characteristics arising in other sites, suggesting that they could be managed similarly, with special considerations related to their anatomical location.
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MESH Headings
- Humans
- Male
- Adult
- Aged
- Young Adult
- Middle Aged
- Proto-Oncogene Proteins p21(ras)/genetics
- Seminal Vesicles/pathology
- Neoplasms, Glandular and Epithelial/genetics
- Neoplasms, Glandular and Epithelial/pathology
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Cystadenoma, Mucinous/genetics
- Cystadenoma, Mucinous/pathology
- Neoplasms, Cystic, Mucinous, and Serous/genetics
- Neoplasms, Cystic, Mucinous, and Serous/pathology
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Affiliation(s)
- Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Laurence A Galea
- Department of Anatomical Pathology, Melbourne Pathology, Sonic Healthcare, Melbourne, VIC, Australia
| | - Forough Foroughi
- Department of Anatomical Pathology, QML Pathology, Brisbane, QLD, Australia
| | - Stephanie E Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - William J Anderson
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sree Appu
- Department of Surgery, Monash University, Melbourne, VIC, Australia
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomas M Ulbright
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andres M Acosta
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
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27
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Kim EY, Liu M, Giobbie-Hurder A, Bahar F, Khaddour K, Silk AW, Thakuria M. Patterns of initial distant metastases in 151 patients undergoing surveillance for treated Merkel cell carcinoma. J Eur Acad Dermatol Venereol 2024; 38:1202-1212. [PMID: 38433521 DOI: 10.1111/jdv.19907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/19/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Merkel cell carcinoma (MCC) is associated with high rates of recurrence and distant metastatic progression. Current guidelines for surveillance imaging are not evidence based. Better characterization of the pattern of distant metastatic spread will better inform surveillance and facilitate earlier detection of metastases. OBJECTIVES This retrospective study aimed to assess potential relationships between primary tumour site and site of initial distant metastasis, time to distant metastasis, overall survival (OS) and MCC-specific death (MSD). METHODS Patients with local or regional (Stage I-III) disease who were treated with curative intent and progressed to Stage IV were included in this study (n = 151). Fisher's exact test was used to assess differences in patterns of initial distant metastases based on primary tumour site. Time to initial distant metastasis was calculated from date of MCC diagnosis. OS and MSD were calculated from date of initial distant metastasis to date of death from any or MCC-related causes, respectively. RESULTS Of 151 patients included in analysis, 89 (58.9%) had a single initial distant metastatic site, and 62 (41.1%) had multiple sites. Patients with upper limb primary tumours were significantly less likely to develop distant lymph node or liver metastases (p = 0.02 and 0.04, respectively). Median time to distant metastasis was 11 months (IQR 6.7-17.9 months). Median OS was 15.3 months, and was shorter for patients with liver (7.0 months, p = 0.0004) or bone metastases (8.9 months, p < 0.0001). Using skin/soft tissue metastasis as a reference group, patients with multiple metastatic sites had significantly higher hazards of MSD (HR = 3.46 univariate, 3.77 multivariate analysis). Time to distant metastasis, OS and MSD did not differ by viral status. CONCLUSION Sites of initial distant metastasis are related to primary tumour sites and survival outcomes. Because patients often have multiple initial metastases, full-body cross-sectional rather than region-specific imaging may facilitate earlier detection of metastatic disease.
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Affiliation(s)
- Emily Y Kim
- Brigham and Women's Hospital, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mofei Liu
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Furkan Bahar
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Karam Khaddour
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Ann W Silk
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Manisha Thakuria
- Brigham and Women's Hospital, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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28
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Sangoi AR, Tsai H, Harik L, Mahlow J, Tretiakova M, Williamson SR, Hirsch MS. Vascular, adipose tissue, and/or calyceal invasion in clear cell tubulopapillary renal cell tumour: potentially problematic diagnostic scenarios. Histopathology 2024; 84:1167-1177. [PMID: 38422612 DOI: 10.1111/his.15166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024]
Abstract
AIMS The 2022 WHO classification for kidney tumours recently downgraded clear cell tubulopapillary (also known as clear cell papillary) renal cell carcinoma (RCC) to a benign neoplasm (i.e. clear cell tubulopapillary renal cell tumour) based on the overwhelmingly banal nature of this neoplasm. However, it has been recognized that some clear cell tubulopapillary renal cell tumours demonstrate vascular, adipose or pelvicalyceal invasion, raising the possibility of more aggressive behaviour. The goal of this study was to determine if these 'high stage' features have an effect on tumour prognosis, warranting a carcinoma designation. METHODS AND RESULTS After excluding cases with tissue artefact (i.e. prior core biopsy track changes) and other RCC subtypes with next-generation sequencing, nine clear cell tubulopapillary renal cell tumours with these so-called 'high stage' features, and otherwise classic morphologic and immunophenotypic findings, including low-grade cytology and 'cup-like' CA9 expression, were evaluated. Median tumour size was 2.2 cm with a range of 0.8 to 6.7 cm. Eight cases (89%) demonstrated perinephric or hilar adipose tissue invasion, although most of these cases showed a bulging (in contrast to an infiltrative) growth pattern. One case demonstrated renal vascular invasion in addition to hilar adipose tissue invasion, and one case demonstrated extension into the pelvicalyceal system. There were no recurrences or evidence of metastatic disease. CONCLUSION These overall findings continue to support the benign designation for clear cell tubulopapillary renal cell tumours, despite morphologic features that might raise the possibility of a 'higher stage' neoplasm.
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Affiliation(s)
- Ankur R Sangoi
- Department of Pathology, Stanford Medical Center, Stanford, CA, USA
| | - Harrison Tsai
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Advanced Molecular Diagnostics, Brigham and Womens Hospital, Boston, MA, USA
| | - Lara Harik
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Jonathan Mahlow
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Maria Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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29
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Dong F. Pan-Cancer Molecular Biomarkers: A Paradigm Shift in Diagnostic Pathology. Clin Lab Med 2024; 44:325-337. [PMID: 38821647 DOI: 10.1016/j.cll.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
The rapid adoption of next-generation sequencing in clinical oncology has enabled the detection of molecular biomarkers shared between multiple tumor types. These pan-cancer biomarkers include sequence-altering mutations, copy number changes, gene rearrangements, and mutational signatures and have been demonstrated to predict response to targeted therapy. This article reviews issues surrounding current and emerging pan-cancer molecular biomarkers in clinical oncology: technological advances that enable the broad detection of cancer mutations across hundreds of genes, the spectrum of driver and passenger mutations derived from human cancer genomes, and implications for patient care now and in the near future.
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Affiliation(s)
- Fei Dong
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Ave, Palo Alto, CA 94304, USA.
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30
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Priedigkeit N, Harrison B, Shue R, Hughes M, Li Y, Kirkner GJ, Spurr LF, Remolano MC, Strauss S, Files J, Feeney AM, Grant L, Mohammed-Abreu A, Garrido-Castro A, Sousa RB, Bychkovsky B, Nakhlis F, Bellon JR, King TA, Winer EP, Lindeman N, Johnson BE, Sholl L, Dillon D, Overmoyer B, Tolaney SM, Cherniack A, Lin NU, Lynce F. Clinicogenomic characterization of inflammatory breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592972. [PMID: 38766070 PMCID: PMC11100693 DOI: 10.1101/2024.05.07.592972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background Inflammatory breast cancer (IBC) is a rare and poorly characterized type of breast cancer with an aggressive clinical presentation. The biological mechanisms driving the IBC phenotype are relatively undefined-partially due to a lack of comprehensive, large-scale genomic studies and limited clinical cohorts. Patients and Methods A retrospective analysis of 2457 patients with metastatic breast cancer who underwent targeted tumor-only DNA-sequencing was performed at Dana-Farber Cancer Institute. Clinicopathologic, single nucleotide variant (SNV), copy number variant (CNV) and tumor mutational burden (TMB) comparisons were made between clinically confirmed IBC cases within a dedicated IBC center versus non-IBC cases. Results Clinicopathologic differences between IBC and non-IBC cases were consistent with prior reports-including IBC being associated with younger age at diagnosis, higher grade, and enrichment with hormone receptor (HR)-negative and HER2-positive tumors. The most frequent somatic alterations in IBC involved TP53 (72%), ERBB2 (32%), PIK3CA (24%), CCND1 (12%), MYC (9%), FGFR1 (8%) and GATA3 (8%). A multivariate logistic regression analysis revealed a significant enrichment in TP53 SNVs in IBC; particularly in HER2-positive and HR-positive disease which was associated with worse outcomes. Tumor mutational burden (TMB) did not differ substantially between IBC and non-IBC cases and a pathway analysis revealed an enrichment in NOTCH pathway alterations in HER2-positive disease. Conclusion Taken together, this study provides a comprehensive, clinically informed landscape of somatic alterations in a large cohort of patients with IBC. Our data support higher frequency of TP53 mutations and a potential enrichment in NOTCH pathway activation-but overall; a lack of major genomic differences. These results both reinforce the importance of TP53 alterations in IBC pathogenesis as well as their influence on clinical outcomes; but also suggest additional analyses beyond somatic DNA-level changes are warranted.
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Affiliation(s)
- Nolan Priedigkeit
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Beth Harrison
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Robert Shue
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Melissa Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | - Yvonne Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Gregory J. Kirkner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Liam F. Spurr
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | | | - Sarah Strauss
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Janet Files
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anne-Marie Feeney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Libby Grant
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Ana Garrido-Castro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | | | - Brittany Bychkovsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Faina Nakhlis
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jennifer R. Bellon
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Department of Radiation Oncology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Tari A. King
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Eric P. Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | - Neal Lindeman
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Bruce E. Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Lynette Sholl
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Deborah Dillon
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Beth Overmoyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | - Sara M. Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | - Andrew Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Nancy U. Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | - Filipa Lynce
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
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31
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Laguna JC, Pastor B, Nalda I, Hijazo-Pechero S, Teixido C, Potrony M, Puig-Butillé JA, Mezquita L. Incidental pathogenic germline alterations detected through liquid biopsy in patients with solid tumors: prevalence, clinical utility and implications. Br J Cancer 2024; 130:1420-1431. [PMID: 38532104 PMCID: PMC11059286 DOI: 10.1038/s41416-024-02607-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/25/2024] [Indexed: 03/28/2024] Open
Abstract
Liquid biopsy, a minimally invasive approach for detecting tumor biomarkers in blood, has emerged as a leading-edge technique in cancer precision medicine. New evidence has shown that liquid biopsies can incidentally detect pathogenic germline variants (PGVs) associated with cancer predisposition, including in patients with a cancer for which genetic testing is not recommended. The ability to detect these incidental PGV in cancer patients through liquid biopsy raises important questions regarding the management of this information and its clinical implications. This incidental identification of PGVs raises concerns about cancer predisposition and the potential impact on patient management, not only in terms of providing access to treatment based on the tumor molecular profiling, but also the management of revealing genetic predisposition in patients and families. Understanding how to interpret this information is essential to ensure proper decision-making and to optimize cancer treatment and prevention strategies. In this review we provide a comprehensive summary of current evidence of incidental PGVs in cancer predisposition genes identified by liquid biopsy in patients with cancer. We critically review the methodological considerations of liquid biopsy as a tool for germline diagnosis, clinical utility and potential implications for cancer prevention, treatment, and research.
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Affiliation(s)
- Juan Carlos Laguna
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Belén Pastor
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Irene Nalda
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Sara Hijazo-Pechero
- Preclinical and Experimental Research in Thoracic Tumors (PRETT), Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), l'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Teixido
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Miriam Potrony
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, IDIBAPS, Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), Barcelona, Spain
| | - Joan Antón Puig-Butillé
- CIBER of Rare Diseases (CIBERER), Barcelona, Spain
- Molecular Biology CORE, Hospital Clínic of Barcelona, IDIBAPS, Barcelona, Spain
| | - Laura Mezquita
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain.
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain.
- Department of Medicine, University of Barcelona, Barcelona, Spain.
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32
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Odintsov I, Makarem M, Nishino M, Bachert SE, Zhang T, LoPiccolo J, Paweletz CP, Gokhale PC, Ivanova E, Saldanha A, Rudin CM, Lockwood WW, Ladanyi M, Somwar R, Jänne PA, Sholl LM. Prevalence and Therapeutic Targeting of High-Level ERBB2 Amplification in NSCLC. J Thorac Oncol 2024; 19:732-748. [PMID: 38154514 DOI: 10.1016/j.jtho.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 12/30/2023]
Abstract
INTRODUCTION ERBB2 amplification in lung cancer remains poorly characterized. HER2 (encoded by ERBB2) is a transmembrane tyrosine kinase capable of ligand-independent dimerization and signaling when overexpressed, and a common cause of HER2 overexpression is ERBB2 amplification. Here, we evaluated the clinicopathologic and genomic characteristics of ERBB2-amplified NSCLC and explored a HER2 antibody-drug conjugate (ADC) therapeutic strategy. METHODS Our institutional next-generation DNA sequencing data (OncoPanel) from 5769 NSCLC samples (5075 patients) were queried for cases having high-level ERBB2 amplification (≥6 copies). Clinical and demographic characteristics were extracted from the electronic medical records. Efficacy of the pan-ERBB inhibitor afatinib or HER2 ADCs (trastuzumab deruxtecan and trastuzumab emtansine) was evaluated in NSCLC preclinical models and patients with ERBB2 amplification. RESULTS High-level ERBB2 amplification was identified in 0.9% of lung adenocarcinomas and reliably predicted overexpression of HER2. ERBB2 amplification events are detected in two distinct clinicopathologic and genomic subsets of NSCLC: as the sole mitogenic driver in tumors arising in patients with a smoking history or as a concomitant alteration with other mitogenic drivers in patients with a light or never smoking history. We further reveal that trastuzumab deruxtecan is effective therapy in in vitro and in vivo preclinical models of NSCLC harboring ERBB2 amplification and report two cases of clinical activity of an anti-HER2 ADC in patients who acquired ERBB2 amplification after previous targeted therapy. CONCLUSIONS High-level ERBB2 amplification reliably predicts HER2 overexpression in patients with NSCLC, and HER2 ADC is effective therapy in this population.
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Affiliation(s)
- Igor Odintsov
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Maisam Makarem
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sara Emily Bachert
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky
| | - Tom Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; School of Medicine, New York Medical College, Valhalla, New York
| | - Jaclyn LoPiccolo
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cloud P Paweletz
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Prafulla C Gokhale
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elena Ivanova
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aisha Saldanha
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William W Lockwood
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Romel Somwar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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33
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Wasko UN, Jiang J, Dalton TC, Curiel-Garcia A, Edwards AC, Wang Y, Lee B, Orlen M, Tian S, Stalnecker CA, Drizyte-Miller K, Menard M, Dilly J, Sastra SA, Palermo CF, Hasselluhn MC, Decker-Farrell AR, Chang S, Jiang L, Wei X, Yang YC, Helland C, Courtney H, Gindin Y, Muonio K, Zhao R, Kemp SB, Clendenin C, Sor R, Vostrejs WP, Hibshman PS, Amparo AM, Hennessey C, Rees MG, Ronan MM, Roth JA, Brodbeck J, Tomassoni L, Bakir B, Socci ND, Herring LE, Barker NK, Wang J, Cleary JM, Wolpin BM, Chabot JA, Kluger MD, Manji GA, Tsai KY, Sekulic M, Lagana SM, Califano A, Quintana E, Wang Z, Smith JAM, Holderfield M, Wildes D, Lowe SW, Badgley MA, Aguirre AJ, Vonderheide RH, Stanger BZ, Baslan T, Der CJ, Singh M, Olive KP. Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer. Nature 2024; 629:927-936. [PMID: 38588697 PMCID: PMC11111406 DOI: 10.1038/s41586-024-07379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/02/2024] [Indexed: 04/10/2024]
Abstract
Broad-spectrum RAS inhibition has the potential to benefit roughly a quarter of human patients with cancer whose tumours are driven by RAS mutations1,2. RMC-7977 is a highly selective inhibitor of the active GTP-bound forms of KRAS, HRAS and NRAS, with affinity for both mutant and wild-type variants3. More than 90% of cases of human pancreatic ductal adenocarcinoma (PDAC) are driven by activating mutations in KRAS4. Here we assessed the therapeutic potential of RMC-7977 in a comprehensive range of PDAC models. We observed broad and pronounced anti-tumour activity across models following direct RAS inhibition at exposures that were well-tolerated in vivo. Pharmacological analyses revealed divergent responses to RMC-7977 in tumour versus normal tissues. Treated tumours exhibited waves of apoptosis along with sustained proliferative arrest, whereas normal tissues underwent only transient decreases in proliferation, with no evidence of apoptosis. In the autochthonous KPC mouse model, RMC-7977 treatment resulted in a profound extension of survival followed by on-treatment relapse. Analysis of relapsed tumours identified Myc copy number gain as a prevalent candidate resistance mechanism, which could be overcome by combinatorial TEAD inhibition in vitro. Together, these data establish a strong preclinical rationale for the use of broad-spectrum RAS-GTP inhibition in the setting of PDAC and identify a promising candidate combination therapeutic regimen to overcome monotherapy resistance.
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MESH Headings
- Animals
- Female
- Humans
- Mice
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Apoptosis/drug effects
- Carcinoma, Pancreatic Ductal/drug therapy
- Carcinoma, Pancreatic Ductal/pathology
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/metabolism
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Disease Models, Animal
- DNA Copy Number Variations
- Drug Resistance, Neoplasm/drug effects
- Genes, myc
- Guanosine Triphosphate/metabolism
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/genetics
- Pancreatic Neoplasms/drug therapy
- Pancreatic Neoplasms/pathology
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/metabolism
- Proto-Oncogene Proteins p21(ras)/genetics
- Proto-Oncogene Proteins p21(ras)/metabolism
- Proto-Oncogene Proteins p21(ras)/antagonists & inhibitors
- Treatment Outcome
- Xenograft Model Antitumor Assays
- Mutation
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Affiliation(s)
- Urszula N Wasko
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Tanner C Dalton
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Alvaro Curiel-Garcia
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - A Cole Edwards
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Bianca Lee
- Revolution Medicines, Redwood City, CA, USA
| | - Margo Orlen
- University of Pennsylvania Perelman School of Medicine, Department of Medicine, Philadelphia, PA, USA
| | - Sha Tian
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Clint A Stalnecker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kristina Drizyte-Miller
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Julien Dilly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Stephen A Sastra
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Carmine F Palermo
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Marie C Hasselluhn
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Amanda R Decker-Farrell
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | - Xing Wei
- Revolution Medicines, Redwood City, CA, USA
| | - Yu C Yang
- Revolution Medicines, Redwood City, CA, USA
| | | | | | | | | | | | - Samantha B Kemp
- University of Pennsylvania Perelman School of Medicine, Department of Medicine, Philadelphia, PA, USA
| | - Cynthia Clendenin
- University of Pennsylvania Perelman School of Medicine, Abramson Cancer Center, Philadelphia, PA, USA
| | - Rina Sor
- University of Pennsylvania Perelman School of Medicine, Abramson Cancer Center, Philadelphia, PA, USA
| | - William P Vostrejs
- University of Pennsylvania Perelman School of Medicine, Department of Medicine, Philadelphia, PA, USA
| | - Priya S Hibshman
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amber M Amparo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Connor Hennessey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Matthew G Rees
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | | | - Lorenzo Tomassoni
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Basil Bakir
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura E Herring
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie K Barker
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Junning Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - James M Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - John A Chabot
- Department of Surgery, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael D Kluger
- Department of Surgery, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Gulam A Manji
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Kenneth Y Tsai
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Miroslav Sekulic
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Stephen M Lagana
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Andrea Califano
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- J. P. Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Chan Zuckerberg Biohub New York, New York, NY, USA
| | | | | | | | | | | | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael A Badgley
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert H Vonderheide
- University of Pennsylvania Perelman School of Medicine, Department of Medicine, Philadelphia, PA, USA
- University of Pennsylvania Perelman School of Medicine, Abramson Cancer Center, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Ben Z Stanger
- University of Pennsylvania Perelman School of Medicine, Department of Medicine, Philadelphia, PA, USA
- University of Pennsylvania Perelman School of Medicine, Abramson Cancer Center, Philadelphia, PA, USA
| | - Timour Baslan
- Department of Biomedical Sciences, School of Veterinary Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Channing J Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Kenneth P Olive
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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34
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Lechner A, Rai A, Rojas-Rudilla V, Kuang Y, Paweletz CP, Sholl LM, Dong F. Atypical Droplet Digital Polymerase Chain Reaction Patterns That Indicate Uncommon but Clinically Actionable EGFR Mutations in Lung Cancer. Arch Pathol Lab Med 2024; 148:553-558. [PMID: 37639432 DOI: 10.5858/arpa.2023-0088-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2023] [Indexed: 08/31/2023]
Abstract
CONTEXT Droplet digital polymerase chain reaction (ddPCR) is a sensitive method to detect common pathogenic EGFR mutations in non-small cell lung cancer. Although targeted assays have not been specifically designed to detect them, uncommon EGFR mutations have been linked to response to targeted therapy. OBJECTIVE To describe atypical ddPCR patterns that correspond to uncommon but clinically actionable EGFR mutations. DESIGN A cohort of 1134 consecutive non-small cell lung cancers that underwent targeted next-generation sequencing was reviewed. Uncommon EGFR mutations involving probe binding sites were evaluated by ddPCR. RESULTS Two hundred fifty-five of 1134 cancers (22.5%) harbored pathogenic EGFR mutations. One hundred eighty-six of 255 (72.9%) had canonical EGFR exon 19 deletion or exon 21 p.L858R variants designed for detection by ddPCR. An additional 25 of 255 cases (9.8%) had uncommon EGFR mutations within the probe-binding site, including 1 case with concurrent uncommon mutations in both exon 19 and exon 21. These mutations included uncommon EGFR exon 19 deletions (n = 6), EGFR exon 19 substitutions p.L747P (n = 3) and p.L747A (n = 1), dinucleotide substitutions leading to EGFR p.L858R (n = 5), EGFR exon 21 substitutions p.K860I (n = 1) and p.L861Q (n = 9), and EGFR p.[L858R;K860I] (n = 1). Droplet digital polymerase chain reaction generated atypical but reproducible signal for each of these uncommon variants. CONCLUSIONS Droplet digital polymerase chain reaction analysis of uncommon pathogenic EGFR variants can yield unique and reproducible results. Recognition of atypical patterns in EGFR ddPCR testing can prompt confirmatory molecular testing and aid appropriate targeted therapy selection for patients with non-small cell lung cancer.
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Affiliation(s)
- Adam Lechner
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
- the University of Missouri School of Medicine, Columbia (Lechner)
| | - Anooja Rai
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
| | - Vanesa Rojas-Rudilla
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
| | - Yanan Kuang
- the Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, Massachusetts(Kuang)
- the Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts(Kuang, Paweletz)
| | - Cloud P Paweletz
- the Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts(Kuang, Paweletz)
| | - Lynette M Sholl
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
| | - Fei Dong
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
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Singh H, Sahgal P, Kapner K, Corsello SM, Gupta H, Gujrathi R, Li YY, Cherniack AD, El Alam R, Kerfoot J, Andrews E, Lee A, Nambiar C, Hannigan AM, Remland J, Brais L, Leahy ME, Rubinson DA, Schlechter BL, Meyerson M, Kuang Y, Paweletz CP, Lee JK, Quintanilha JC, Aguirre AJ, Perez KJ, Huffman BM, Rossi H, Abrams TA, Kabraji S, Trusolino L, Bertotti A, Sicinska ET, Parikh AR, Wolpin BM, Schrock AB, Giannakis M, Ng K, Meyerhardt JA, Hornick JL, Sethi NS, Cleary JM. RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer. Clin Cancer Res 2024; 30:1669-1684. [PMID: 38345769 PMCID: PMC11018475 DOI: 10.1158/1078-0432.ccr-23-2581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/17/2023] [Accepted: 02/06/2024] [Indexed: 04/16/2024]
Abstract
PURPOSE ERBB2-amplified colorectal cancer is a distinct molecular subtype with expanding treatments. Implications of concurrent oncogenic RAS/RAF alterations are not known. EXPERIMENTAL DESIGN Dana-Farber and Foundation Medicine Inc. Colorectal cancer cohorts with genomic profiling were used to identify ERBB2-amplified cases [Dana-Farber, n = 47/2,729 (1.7%); FMI, n = 1857/49,839 (3.7%)]. Outcomes of patients receiving HER2-directed therapies are reported (Dana-Farber, n = 9; Flatiron Health-Foundation Medicine clinicogenomic database, FH-FMI CGDB, n = 38). Multisite HER2 IHC and genomic profiling were performed to understand HER2 intratumoral and interlesional heterogeneity. The impact of concurrent RAS comutations on the effectiveness of HER2-directed therapies were studied in isogenic colorectal cancer cell lines and xenografts. RESULTS ERBB2 amplifications are enriched in left-sided colorectal cancer. Twenty percent of ERBB2-amplified colorectal cancers have co-occurring oncogenic RAS/RAF alterations. While RAS/RAF WT colorectal cancers typically have clonal ERBB2 amplification, colorectal cancers with co-occurring RAS/RAF alterations have lower level ERRB2 amplification, higher intratumoral heterogeneity, and interlesional ERBB2 discordance. These distinct genomic patterns lead to differential responsiveness and patterns of resistance to HER2-directed therapy. ERBB2-amplified colorectal cancer with RAS/RAF alterations are resistant to trastuzumab-based combinations, such as trastuzumab/tucatinib, but retain sensitivity to trastuzumab deruxtecan in in vitro and murine models. Trastuzumab deruxtecan shows clinical efficacy in cases with high-level ERBB2-amplified RAS/RAF coaltered colorectal cancer. CONCLUSIONS Co-occurring RAS/RAF alterations define a unique subtype of ERBB2-amplified colorectal cancer that has increased intratumoral heterogeneity, interlesional discordance, and resistance to trastuzumab-based combinations. Further examination of trastuzumab deruxtecan in this previously understudied cohort of ERBB2-amplified colorectal cancer is warranted.
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Affiliation(s)
- Harshabad Singh
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Pranshu Sahgal
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
- Broad Institute of Harvard and MIT, Cambridge MA, USA
| | - Kevin Kapner
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | | | - Hersh Gupta
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
- Broad Institute of Harvard and MIT, Cambridge MA, USA
| | - Rahul Gujrathi
- Department of Radiology, Boston Medical Center and Boston University, Boston, MA USA
| | - Yvonne Y. Li
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
- Broad Institute of Harvard and MIT, Cambridge MA, USA
| | - Andrew D. Cherniack
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
- Broad Institute of Harvard and MIT, Cambridge MA, USA
| | - Raquelle El Alam
- Department of Radiology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Joseph Kerfoot
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Elizabeth Andrews
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Annette Lee
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Chetan Nambiar
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Alison M. Hannigan
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Joshua Remland
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Lauren Brais
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Meghan E. Leahy
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Douglas A. Rubinson
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Benjamin L. Schlechter
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Matthew Meyerson
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
- Broad Institute of Harvard and MIT, Cambridge MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
| | - Yanan Kuang
- Belfer Center for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Cloud P. Paweletz
- Belfer Center for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | | | | | - Andrew J. Aguirre
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
- Broad Institute of Harvard and MIT, Cambridge MA, USA
| | - Kimberly J. Perez
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Brandon M. Huffman
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Humberto Rossi
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Thomas A. Abrams
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Sheheryar Kabraji
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Livio Trusolino
- Candiolo Cancer Institute FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Andrea Bertotti
- Candiolo Cancer Institute FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Ewa T. Sicinska
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Aparna R. Parikh
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Brian M. Wolpin
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | | | - Marios Giannakis
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Kimmie Ng
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Jeffrey A. Meyerhardt
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - Jason L. Hornick
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Nilay S. Sethi
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
| | - James M. Cleary
- Dana-Farber Brigham and Women’s Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA
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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] [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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Gikandi A, Chi SN, Yeo KK, O'Neill AF, Shulman DS, DuBois SG, Collins NB. Off-label prescribing of immune checkpoint inhibitor therapy at a single pediatric cancer center. Cancer Med 2024; 13:e7154. [PMID: 38629258 PMCID: PMC11022150 DOI: 10.1002/cam4.7154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/26/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICI) have improved outcomes in a variety of adult cancers and are prescribed with increasing frequency across oncology. However, patterns of off-label use of ICI in pediatrics remain unclear. METHODS This is a single-institution, retrospective cohort study evaluating off-label ICI use in pediatric and young adult patients with cancer treated at our institution from 2014 to 2022. Response was based on clinician assessment derived from clinical records. Immune-related adverse events (iRAEs) were classified according to CTCAE v5.0. RESULTS We identified 50 unique patients treated with off-label ICI (28 with solid tumors, 20 with central nervous system (CNS) tumors, 2 with hematologic malignancies). At time of ICI initiation, only five patients (10%) had localized disease, and all but one patient was treated in the relapsed/refractory setting. All patients were treated with the FDA-approved weight-based dosing recommendations. Overall, there was disease control in 21 patients (42%), with best response including one complete response (melanoma), two partial responses (high-grade glioma, CNS nongerminomatous germ cell tumor), and 18 patients with stable disease. Forty-four patients (88%) eventually experienced disease progression. Among 22 patients (44%) experiencing iRAEs, 10 (20%) had a grade ≥3 irAE, 12 (24%) required corticosteroids, and 14 (28%) required ICI discontinuation. irAE occurrence was associated with significantly improved progression-free survival (HR 0.35; 95% CI: 0.18 to 0.68; p = 0.002) and overall survival (HR 0.33; 95% CI: 0.17 to 0.66; p = 0.002). CONCLUSIONS At our institution, ICI was most commonly prescribed in the relapsed/refractory setting to patients with metastatic disease. The treatment was generally well-tolerated in the pediatric population. The overall response rate was low, and the majority of patients eventually experienced disease progression. A few patients, however, had durable treatment responses. Further studies are needed to identify which pediatric patients are most likely to benefit from ICI.
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Affiliation(s)
| | - Susan N Chi
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kee Kiat Yeo
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Allison F O'Neill
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - David S Shulman
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven G DuBois
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Natalie B Collins
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
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Siegmund SE, Al-Obaidy KI, Tsai HK, Idrees MT, Akgul M, Acosta AM, Hirsch MS. Concordance of MTOR Pathway Mutations and the Diagnosis of Renal Low-Grade Oncocytic Tumor (LOT). Int J Surg Pathol 2024; 32:316-330. [PMID: 37357748 DOI: 10.1177/10668969231178032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
The differential diagnosis for oncocytic renal tumors spans the spectrum from benign entities to more aggressive renal cell carcinomas (RCC). Recent work has characterized a provisional renal oncocytic neoplasm, namely the low-grade oncocytic tumor (LOT), which demonstrates overlapping morphologic features with oncocytoma and chromophobe RCC, but also has a unique immunoprofile (ie, diffusely positive for KRT7, negative for KIT) and a high rate (80% to 100%) of mTOR pathway gene alterations. Given the diagnostic overlap among oncocytic tumors, we looked for concordance between mTOR pathway mutations and LOT. Thirty low-grade renal oncocytic neoplasms underwent histologic review and immunohistochemistry for KRT7 and KIT. Tumors were classified as "determinate" (eg, LOT) for tumors with solid, nested or vaguely tubular growth and diffuse KRT7 staining and negative KIT, or "indeterminate" if the morphology and/or immunostains did not fully support a definitive LOT diagnosis. Next-generation sequencing was performed without any knowledge of the diagnoses, and identified mTOR pathway mutations in 80% (12/15) of the determinate tumors, compared with 7% (1/15) in the indeterminate group. One determinate tumor was reclassified as papillary RCC (MTOR mutation negative) and 6 indeterminate tumors were confirmed to be oncocytoma (N = 4), clear cell RCC or papillary RCC with reverse polarity, respectively. Overall, integration of morphology, immunohistochemistry, and molecular data enabled a final definitive diagnosis for 70% of tumors (21 of the total 30), with a high concordance (93%) for LOT specifically in the determinate group; the remaining 9 tumors (30%) were classified as renal oncocytic neoplasm, not otherwise specified.
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Affiliation(s)
- Stephanie E Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Khaleel I Al-Obaidy
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, MA, USA
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mahmut Akgul
- Department of Pathology, Albany Medical Center, Albany, NY, USA
| | - Andres M Acosta
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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Boiarsky D, Gulhan DC, Savignano H, Lakshminarayanan G, McClure HM, Silver R, Hirsch MS, Sholl LM, Choudhury AD, Ananda G, Park PJ, Tewari AK, Berchuck JE. A Panel-Based Mutational Signature of Mismatch Repair Deficiency is Associated With Durable Response to Pembrolizumab in Metastatic Castration-Resistant Prostate Cancer. Clin Genitourin Cancer 2024; 22:558-568.e3. [PMID: 38342659 PMCID: PMC10939759 DOI: 10.1016/j.clgc.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/13/2024]
Abstract
INTRODUCTION/BACKGROUND Immune checkpoint inhibitors (ICIs) have limited efficacy in prostate cancer (PCa). Better biomarkers are needed to predict responses to ICIs. We sought to demonstrate that a panel-based mutational signature identifies mismatch repair (MMR) deficient (MMRd) PCa and is a biomarker of response to pembrolizumab. PATIENTS AND METHODS Clinico-genomic data was obtained for 2664 patients with PCa sequenced at Dana-Farber Cancer Institute (DFCI) and Memorial Sloan Kettering (MSK). Clinical outcomes were collected for patients with metastatic castration-resistant PCa (mCRPC) treated with pembrolizumab at DFCI. SigMA was used to characterize tumors as MMRd or MMR proficient (MMRp). The concordance between MMRd with microsatellite instability (MSI-H) was assessed. Radiographic progression-free survival (rPFS) and overall survival (OS) were collected for patients treated with pembrolizumab. Event-time distributions were estimated using Kaplan-Meier methodology. RESULTS Across both cohorts, 100% (DFCI: 12/12; MSK: 43/43) of MSI-H tumors were MMRd. However, 14% (2/14) and 9.1% (6/66) of MMRd tumors in the DFCI and MSK cohorts respectively were microsatellite stable (MSS), and 26% (17/66) were MSI-indeterminate in the MSK cohort. Among patients treated with pembrolizumab, those with MMRd (n = 5) versus MMRp (n = 14) mCRPC experienced markedly improved rPFS (HR = 0.088, 95% CI: 0.011-0.70; P = .0064) and OS (HR = 0.11, 95% CI: 0.014-0.80; P = .010) from start of treatment. Four patients with MMRd experienced remissions of >= 2.5 years. CONCLUSION SigMA detects additional cases of MMRd as compared to MSI testing in PCa and identifies patients likely to experience durable response to pembrolizumab.
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Affiliation(s)
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Hunter Savignano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Heather M McClure
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Rebecca Silver
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Guruprasad Ananda
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.
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40
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Peterson M, Kolin DL, Konstantinopoulos PA. Case report: Response to everolimus in a patient with platinum resistant, high grade serous ovarian carcinoma with biallelic TSC2 inactivation. Front Oncol 2024; 14:1357980. [PMID: 38601768 PMCID: PMC11004469 DOI: 10.3389/fonc.2024.1357980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/15/2024] [Indexed: 04/12/2024] Open
Abstract
Background Patients with platinum-resistant recurrent high grade serous ovarian carcinoma have poor outcomes and limited treatment options. Case presentation We present a case of a 48-year-old woman with platinum-resistant high grade serous ovarian carcinoma harboring the pathogenic TSC2 R611Q variant with concomitant single copy loss of TSC2 (suggesting biallelic TSC2 inactivation) identified in targeted tumor sequencing. The patient was treated with the mTOR inhibitor everolimus, with an excellent response by imaging and a marked decrease in CA125; she remained on everolimus for 19 months until she developed progressive disease. Conclusions While mTOR inhibition is frequently used in tumors associated with tuberous sclerosis complex (TSC), such as lymphangioleiomyomatosis and malignant perivascular epithelioid cell tumors, this is the first case of a patient with ovarian cancer harboring TSC1/2 mutations who responded to mTOR inhibition. This case highlights the utility of targeted DNA sequencing in the management of ovarian carcinoma and demonstrates the value of tumor-agnostic targeted therapies.
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Affiliation(s)
- Mariko Peterson
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - David L. Kolin
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
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Wang X, Lamberti G, Di Federico A, Alessi J, Ferrara R, Sholl ML, Awad MM, Vokes N, Ricciuti B. Tumor mutational burden for the prediction of PD-(L)1 blockade efficacy in cancer: challenges and opportunities. Ann Oncol 2024:S0923-7534(24)00084-X. [PMID: 38537779 DOI: 10.1016/j.annonc.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/19/2024] [Accepted: 03/19/2024] [Indexed: 05/16/2024] Open
Abstract
Tumor mutational burden (TMB) is a biomarker that measures the number of somatic mutations in a tumor's genome. TMB has emerged as a predictor of response to immune checkpoint inhibitors (ICIs) in various cancer types, and several studies have shown that patients with high TMB have better outcomes when treated with programmed death-ligand 1-based therapies. Recently, the Food and Drug Administration has approved TMB as a companion diagnostic for the use of pembrolizumab in solid tumors. However, despite its potential, the use of TMB as a biomarker for immunotherapy efficacy is limited by several factors. Here we review the limitations of TMB in predicting immunotherapy outcomes in patients with cancer and discuss potential strategies to optimize its use in the clinic.
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Affiliation(s)
- X Wang
- Harvard T.H. Chan School of Public Health, Boston
| | - G Lamberti
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - A Di Federico
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - J Alessi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - R Ferrara
- University Vita-Salute San Raffaele, Milan; Department of Medical Oncology, IRCCS San Raffaele, Milan, Italy
| | - M L Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston
| | - M M Awad
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - N Vokes
- Department of Thoracic Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, USA
| | - B Ricciuti
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA.
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Gupta V, Vashisht V, Vashisht A, Mondal AK, Alptekin A, Singh H, Kolhe R. Comprehensive Analysis of Clinically Relevant Copy Number Alterations (CNAs) Using a 523-Gene Next-Generation Sequencing Panel and NxClinical Software in Solid Tumors. Genes (Basel) 2024; 15:396. [PMID: 38674331 PMCID: PMC11049607 DOI: 10.3390/genes15040396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Copy number alterations (CNAs) are significant in tumor initiation and progression. Identifying these aberrations is crucial for targeted therapies and personalized cancer diagnostics. Next-generation sequencing (NGS) methods present advantages in scalability and cost-effectiveness, surpassing limitations associated with reference assemblies and probe capacities in traditional laboratory approaches. This retrospective study evaluated CNAs in 50 FFPE tumor samples (breast cancer, ovarian carcinoma, pancreatic cancer, melanoma, and prostate carcinoma) using Illumina's TruSight Oncology 500 (TSO500) and the Affymetrix Oncoscan Molecular Inversion Probe (OS-MIP) (ThermoFisher Scientific, Waltham, MA, USA). NGS analysis with the NxClinical 6.2 software demonstrated a high sensitivity and specificity (100%) for CNA detection, with a complete concordance rate as compared to the OS-MIP. All 54 known CNAs were identified by NGS, with gains being the most prevalent (63%). Notable CNAs were observed in MYC (18%), TP53 (12%), BRAF (8%), PIK3CA, EGFR, and FGFR1 (6%) genes. The diagnostic parameters exhibited high accuracy, including a positive predictive value, negative predictive value, and overall diagnostic accuracy. This study underscores NxClinical as a reliable software for identifying clinically relevant gene alterations using NGS TSO500, offering valuable insights for personalized cancer treatment strategies based on CNA analysis.
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Affiliation(s)
- Vivek Gupta
- Department of Pathology, Government Institute of Medical Sciences, Greater Noida 201310, India;
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Vishakha Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ahmet Alptekin
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
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Gómez Tejeda Zañudo J, Barroso-Sousa R, Jain E, Jin Q, Li T, Buendia-Buendia JE, Pereslete A, Abravanel DL, Ferreira AR, Wrabel E, Helvie K, Hughes ME, Partridge AH, Overmoyer B, Lin NU, Tayob N, Tolaney SM, Wagle N. Exemestane plus everolimus and palbociclib in metastatic breast cancer: clinical response and genomic/transcriptomic determinants of resistance in a phase I/II trial. Nat Commun 2024; 15:2446. [PMID: 38503755 PMCID: PMC10951222 DOI: 10.1038/s41467-024-45835-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/02/2024] [Indexed: 03/21/2024] Open
Abstract
The landscape of cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) resistance is still being elucidated and the optimal subsequent therapy to overcome resistance remains uncertain. Here we present the final results of a phase Ib/IIa, open-label trial (NCT02871791) of exemestane plus everolimus and palbociclib for CDK4/6i-resistant metastatic breast cancer. The primary objective of phase Ib was to evaluate safety and tolerability and determine the maximum tolerated dose/recommended phase II dose (100 mg palbociclib, 5 mg everolimus, 25 mg exemestane). The primary objective of phase IIa was to determine the clinical benefit rate (18.8%, n = 6/32), which did not meet the predefined endpoint (65%). Secondary objectives included pharmacokinetic profiling (phase Ib), objective response rate, disease control rate, duration of response, and progression free survival (phase IIa), and correlative multi-omics analysis to investigate biomarkers of resistance to CDK4/6i. All participants were female. Multi-omics data from the phase IIa patients (n = 24 tumor/17 blood biopsy exomes; n = 27 tumor transcriptomes) showed potential mechanisms of resistance (convergent evolution of HER2 activation, BRAFV600E), identified joint genomic/transcriptomic resistance features (ESR1 mutations, high estrogen receptor pathway activity, and a Luminal A/B subtype; ERBB2/BRAF mutations, high RTK/MAPK pathway activity, and a HER2-E subtype), and provided hypothesis-generating results suggesting that mTOR pathway activation correlates with response to the trial's therapy. Our results illustrate how genome and transcriptome sequencing may help better identify patients likely to respond to CDK4/6i therapies.
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Affiliation(s)
- Jorge Gómez Tejeda Zañudo
- Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Romualdo Barroso-Sousa
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Oncology Center, Hospital Sírio-Libanês, Brasília, Brazil
| | - Esha Jain
- Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Repare Therapeutics, Cambridge, MA, USA
| | - Qingchun Jin
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, MA, USA
| | - Tianyu Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, MA, USA
| | - Jorge E Buendia-Buendia
- Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cellarity, Somerville, MA, USA
| | | | - Daniel L Abravanel
- Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Arlindo R Ferreira
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Unit, Champalimaud Clinical Centre, Champalimaud Foundation, Lisbon, Portugal
| | - Eileen Wrabel
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karla Helvie
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Ann H Partridge
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Beth Overmoyer
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nancy U Lin
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nabihah Tayob
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, MA, USA
| | - Sara M Tolaney
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nikhil Wagle
- Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Genentech, South San Francisco, CA, USA.
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Qin X, Lam A, Zhang X, Sengupta S, Iorgulescu JB, Ni H, Das S, Rager M, Zhou Z, Zuo T, Meara GK, Floru AE, Kemet C, Veerapaneni D, Kashy D, Lin L, Lloyd K, Kwok L, Smith KS, Nagaraju RT, Meijers R, Ceol C, Liu CT, Alexandrescu S, Wu CJ, Keskin DB, George RE, Feng H. CKLF instigates a "cold" microenvironment to promote MYCN-mediated tumor aggressiveness. SCIENCE ADVANCES 2024; 10:eadh9547. [PMID: 38489372 PMCID: PMC10942121 DOI: 10.1126/sciadv.adh9547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024]
Abstract
Solid tumors, especially those with aberrant MYCN activation, often harbor an immunosuppressive microenvironment to fuel malignant growth and trigger treatment resistance. Despite this knowledge, there are no effective strategies to tackle this problem. We found that chemokine-like factor (CKLF) is highly expressed by various solid tumor cells and transcriptionally up-regulated by MYCN. Using the MYCN-driven high-risk neuroblastoma as a model system, we demonstrated that as early as the premalignant stage, tumor cells secrete CKLF to attract CCR4-expressing CD4+ cells, inducing immunosuppression and tumor aggression. Genetic depletion of CD4+ T regulatory cells abolishes the immunorestrictive and protumorigenic effects of CKLF. Our work supports that disrupting CKLF-mediated cross-talk between tumor and CD4+ suppressor cells represents a promising immunotherapeutic approach to battling MYCN-driven tumors.
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Affiliation(s)
- Xiaodan Qin
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Andrew Lam
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Xu Zhang
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Satyaki Sengupta
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - J. Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Molecular Diagnostics Laboratory, Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hongru Ni
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Sanjukta Das
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- School of Biotechnology, KIIT University, Bhubanesw, India
| | - Madison Rager
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Zhenwei Zhou
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Tao Zuo
- Department of Pathology & Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Grace K. Meara
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Alexander E. Floru
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Chinyere Kemet
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Divya Veerapaneni
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Daniel Kashy
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Liang Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Lauren Kwok
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Kaylee S. Smith
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Raghavendar T. Nagaraju
- Faculty of Biology, Medicine and Health, Division of Cancer Sciences, University of Manchester, Manchester, UK
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK
| | - Rob Meijers
- Institute for Protein Innovation, Boston, MA, USA
| | - Craig Ceol
- Department of Molecular, Cell and Cancer Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Derin B. Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rani E. George
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Hui Feng
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
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Russell-Goldman E, Baranov E, Siegmund S, Yang CS, Laga AC, Hanna J. Epidermodysplasia verruciformis-associated eccrine neoplasm: a rare entity with distinctive clinical and histopathologic features. Virchows Arch 2024; 484:423-427. [PMID: 38483613 DOI: 10.1007/s00428-024-03785-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/04/2024] [Accepted: 03/10/2024] [Indexed: 04/17/2024]
Abstract
Most tumors are caused by inherited or acquired genetic changes. However, a subset of tumors is driven by viral infection including Kaposi sarcoma, nasopharyngeal carcinoma, and others. Human papillomavirus (HPV) is an especially common cause of epithelial cancers and hyperplasias. Epidermodysplasia verruciformis (EDV) is a rare type of HPV infection with characteristic histopathologic features and a unique spectrum of HPV subtypes. We report here a distinctive form of EDV-associated eccrine neoplasia. Seven tumors from two patients were analyzed and show highly uniform features including multiple clustered clinical lesions, multifocal epidermal origin, eccrine differentiation with close association with the acrosyringium, an anastomosing growth pattern, and a bland monotonous poroid-to-basaloid cytomorphology. Clinical follow-up for one patient has been benign to date. These tumors show strong similarity to two previously reported cases, suggesting that this type of EDV-associated eccrine neoplasia may represent a rare but reproducible form of skin adnexal tumor with distinctive clinicopathologic features.
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Affiliation(s)
- Eleanor Russell-Goldman
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Esther Baranov
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Stephanie Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Catherine S Yang
- Department of Dermatology, Brigham and Women's Hospital and, Harvard Medical School, Boston, MA, USA
| | - Alvaro C Laga
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - John Hanna
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
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Ravi P, Freeman D, Thomas J, Ravi A, Mantia C, McGregor BA, Berchuck JE, Epstein I, Budde P, Ahangarian Abhari B, Rupieper E, Gajewski J, Schubert AS, Kilian AL, Bräutigam M, Zucht HD, Sonpavde G. Comprehensive multiplexed autoantibody profiling of patients with advanced urothelial cancer. J Immunother Cancer 2024; 12:e008215. [PMID: 38309723 PMCID: PMC10840035 DOI: 10.1136/jitc-2023-008215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Comprehensive profiling of autoantibodies (AAbs) in metastatic urothelial cancer (mUC) has not been performed to date. This may aid in diagnosis of UC, uncover novel therapeutic targets in this disease as well as identify associations between AAbs and response and toxicity to systemic therapies. METHODS We used serum from patients with mUC collected prior to and after systemic therapy (immune checkpoint inhibitor (ICI) or platinum-based chemotherapy (PBC)) at Dana-Farber Cancer Institute. 38 age-matched and sex-matched healthy controls (HCs) from healthy blood donors were also evaluated. The SeroTag immuno-oncology discovery array (Oncimmune) was used, with quantification of the AAb reactivity toward 1132 antigens. Bound AAbs were detected using an anti-immunoglobulin G-specific detection antibody conjugated to the fluorescent reporter dye phycoerythrin. The AAb reactivity was reported as the median fluorescence intensity for each color and sample using a Luminex FlexMAP3D analyzer. Clinical outcomes of interest included radiographic response and development of immune-related adverse events (irAEs). Significance analysis of microarray was used to compare mUC versus HC and radiographic response. Associations with irAE were evaluated using a logistic regression model. P<0.05 was considered statistically significant. RESULTS 66 patients were included with a median age of 68 years; 54 patients (82%) received ICI and 12 patients (18%) received PBC. Compared with HCs, AAbs against the cancer/testis antigens (CTAG1B, CTAG2, MAGEB18), HSPA1A, TP53, KRAS, and FGFR3 were significantly elevated in patients with mUC. AAbs against BRCA2, TP53, and CTNBB1 were associated with response, and those against BICD2 and UACA were associated with resistance to ICI therapy. AAbs against MITF, CDH3, and KDM4A were associated with development of irAEs in patient who received an ICI. A higher variance in pre-to-post treatment fold change in AAb levels was seen in patients treated with ICI versus PBC and was associated with response to ICI. CONCLUSIONS This is the first report of comprehensive AAb profiling of patients with mUC and identified key AAbs that were elevated in patients with mUC versus HCs as well as AAbs associated with therapeutic response to ICI. These findings are hypothesis generating and further mechanistic studies evaluating humoral immunity in UC are required.
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Affiliation(s)
- Praful Ravi
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Dory Freeman
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Arvind Ravi
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | | | | | - Ilana Epstein
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | | | | | | | | | | | | | | | - Guru Sonpavde
- AdventHealth Cancer Institute, Orlando, Florida, USA
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Tobochnik S, Dorotan MKC, Ghosh HS, Lapinskas E, Vogelzang J, Reardon DA, Ligon KL, Bi WL, Smirnakis SM, Lee JW. Glioma genetic profiles associated with electrophysiologic hyperexcitability. Neuro Oncol 2024; 26:323-334. [PMID: 37713468 PMCID: PMC10836775 DOI: 10.1093/neuonc/noad176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Distinct genetic alterations determine glioma aggressiveness, however, the diversity of somatic mutations contributing to peritumoral hyperexcitability and seizures over the course of the disease is uncertain. This study aimed to identify tumor somatic mutation profiles associated with clinically significant hyperexcitability. METHODS A single center cohort of adults with WHO grades 1-4 glioma and targeted exome sequencing (n = 1716) was analyzed and cross-referenced with a validated EEG database to identify the subset of individuals who underwent continuous EEG monitoring (n = 206). Hyperexcitability was defined by the presence of lateralized periodic discharges and/or electrographic seizures. Cross-validated discriminant analysis models trained exclusively on recurrent somatic mutations were used to identify variants associated with hyperexcitability. RESULTS The distribution of WHO grades and tumor mutational burdens were similar between patients with and without hyperexcitability. Discriminant analysis models classified the presence or absence of EEG hyperexcitability with an overall accuracy of 70.9%, regardless of IDH1 R132H inclusion. Predictive variants included nonsense mutations in ATRX and TP53, indel mutations in RBBP8 and CREBBP, and nonsynonymous missense mutations with predicted damaging consequences in EGFR, KRAS, PIK3CA, TP53, and USP28. This profile improved estimates of hyperexcitability in a multivariate analysis controlling for age, sex, tumor location, integrated pathologic diagnosis, recurrence status, and preoperative epilepsy. Predicted somatic mutation variants were over-represented in patients with hyperexcitability compared to individuals without hyperexcitability and those who did not undergo continuous EEG. CONCLUSION These findings implicate diverse glioma somatic mutations in cancer genes associated with peritumoral hyperexcitability. Tumor genetic profiling may facilitate glioma-related epilepsy prognostication and management.
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Affiliation(s)
- Steven Tobochnik
- Department of Neurology, VA Boston Healthcare System, Boston, Massachusetts, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | | | - Hia S Ghosh
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Emily Lapinskas
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David A Reardon
- Department of Medical Oncology, Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Stelios M Smirnakis
- Department of Neurology, VA Boston Healthcare System, Boston, Massachusetts, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jong Woo Lee
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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48
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Taraszka K, Groha S, King D, Tell R, White K, Ziv E, Zaitlen N, Gusev A. A comprehensive analysis of clinical and polygenic germline influences on somatic mutational burden. Am J Hum Genet 2024; 111:242-258. [PMID: 38211585 PMCID: PMC10870141 DOI: 10.1016/j.ajhg.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 01/13/2024] Open
Abstract
Tumor mutational burden (TMB), the total number of somatic mutations in the tumor, and copy number burden (CNB), the corresponding measure of aneuploidy, are established fundamental somatic features and emerging biomarkers for immunotherapy. However, the genetic and non-genetic influences on TMB/CNB and, critically, the manner by which they influence patient outcomes remain poorly understood. Here, we present a large germline-somatic study of TMB/CNB with >23,000 individuals across 17 cancer types, of which 12,000 also have extensive clinical, treatment, and overall survival (OS) measurements available. We report dozens of clinical associations with TMB/CNB, observing older age and male sex to have a strong effect on TMB and weaker impact on CNB. We additionally identified significant germline influences on TMB/CNB, including fine-scale European ancestry and germline polygenic risk scores (PRSs) for smoking, tanning, white blood cell counts, and educational attainment. We quantify the causal effect of exposures on somatic mutational processes using Mendelian randomization. Many of the identified features associated with TMB/CNB were additionally associated with OS for individuals treated at a single tertiary cancer center. For individuals receiving immunotherapy, we observed a complex relationship between PRSs for educational attainment, self-reported college attainment, TMB, and survival, suggesting that the influence of this biomarker may be substantially modified by socioeconomic status. While the accumulation of somatic alterations is a stochastic process, our work demonstrates that it can be shaped by host characteristics including germline genetics.
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Affiliation(s)
- Kodi Taraszka
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA; Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA 02215, USA.
| | - Stefan Groha
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA 02215, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - David King
- Tempus Labs, Inc, Chicago, IL 60654, USA
| | | | | | - Elad Ziv
- Department of Medicine, University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Noah Zaitlen
- Department of Neurology, University of California, Los Angeles, CA 90095, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA 02215, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.
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49
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Collins K, Acosta AM, Siegmund SE, Cheng L, Hirsch MS, Idrees MT. Genetic Profiling Uncovers Genome-Wide Loss of Heterozygosity and Provides Insight into Mechanisms of Sarcomatoid Transformation in Chromophobe Renal Cell Carcinoma. Mod Pathol 2024; 37:100396. [PMID: 38043790 DOI: 10.1016/j.modpat.2023.100396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/07/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
Sarcomatoid transformation occurs in ∼8% of chromophobe renal cell carcinoma (chRCC) and is associated with aggressive clinical behavior. In recent years, several studies have identified genomic, transcriptomic, and epigenomic correlates of aggressive behavior in chRCC; however, the molecular mechanisms associated with sarcomatoid transformation remain incompletely understood. In this study, we analyzed paired conventional and sarcomatoid histologic components of individual chRCC to elucidate the genomic alterations that underlie sarcomatoid transformation in this tumor type. Massively parallel sequencing was performed on paired (conventional and sarcomatoid) components from 8 chRCCs. All cases harbored TP53 variants (87.5% showing TP53 variants in both components and 12.5% only in the sarcomatoid component). Intratumor comparisons revealed that TP53 variants were concordant in 71% and discordant in 29% of cases. Additional recurrent single-nucleotide variants were found in RB1 (37.5% of cases) and PTEN (25% of cases), with the remaining single-nucleotide variants detected in these tumors (PBRM1, NF1, and ASXL1) being nonrecurrent. Copy number variant analysis showed the characteristic pattern of chromosomal losses associated with chRCC (1, 2, 6, 10, 13, 17, and 21) in the conventional histologic components only. Interestingly, the sarcomatoid components of these tumors demonstrated widespread loss of heterozygosity but lacked the above chromosomal losses, likely as a consequence of whole-genome duplication/imbalanced chromosomal duplication events. Overall, the findings suggest that TP53 variants followed by whole-genome duplication/imbalanced chromosomal duplication events underlie sarcomatoid transformation in chRCC.
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Affiliation(s)
- Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Andres M Acosta
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Stephanie E Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Liang Cheng
- Department of Pathology, Warren Alpert Medical School of Brown University, Lifespan Academic Medical Center, Providence, Rhode Island
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
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50
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Xu B, Viswanathan K, Ahadi MS, Ahmadi S, Alzumaili B, Bani MA, Baudin E, Behrman DB, Capelletti M, Chau NG, Chiarucci F, Chou A, Clifton-Bligh R, Coluccelli S, de Biase D, De Leo A, Dogan S, Fagin JA, Fuchs TL, Glover AR, Hadoux J, Lacroix L, Lamartina L, Lubin DJ, Luxford C, Magliocca K, Maloberti T, Mohanty AS, Najdawi F, Nigam A, Papachristos AJ, Repaci A, Robinson B, Scoazec JY, Shi Q, Sidhu S, Solaroli E, Sywak M, Tuttle RM, Untch B, Barletta JA, Al Ghuzlan A, Gill AJ, Ghossein R, Tallini G, Ganly I. Association of the Genomic Profile of Medullary Thyroid Carcinoma with Tumor Characteristics and Clinical Outcomes in an International Multicenter Study. Thyroid 2024; 34:167-176. [PMID: 37842841 PMCID: PMC10884546 DOI: 10.1089/thy.2023.0279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Purpose: The prognostic importance of RET and RAS mutations and their relationship to clinicopathologic parameters and outcomes in medullary thyroid carcinoma (MTC) need to be clarified. Experimental Design: A multicenter retrospective cohort study was performed utilizing data from 290 patients with MTC. The molecular profile was determined and associations were examined with clinicopathologic data and outcomes. Results: RET germ line mutations were detected in 40 patients (16.3%). Somatic RET and RAS mutations occurred in 135 (46.9%) and 57 (19.8%) patients, respectively. RETM918T was the most common somatic RET mutation (n = 75). RET somatic mutations were associated with male sex, larger tumor size, advanced American Joint Committee Cancer (AJCC) stage, vascular invasion, and high International Medullary Thyroid Carcinoma Grading System (IMTCGS) grade. When compared with other RET somatic mutations, RETM918T was associated with younger age, AJCC (eighth edition) IV, vascular invasion, extrathyroidal extension, and positive margins. RET somatic or germ line mutations were significantly associated with reduced distant metastasis-free survival on univariate analysis, but there were no significant independent associations on multivariable analysis, after adjusting for tumor grade and stage. There were no significant differences in outcomes between RET somatic and RET germ line mutations, or between RETM918T and other RET mutations. Other recurrent molecular alterations included TP53 (4.2%), ARID2 (2.9%), SETD2 (2.9%), KMT2A (2.9%), and KMT2C (2.9%). Among them, TP53 mutations were associated with decreased overall survival (OS) and disease-specific survival (DSS), independently of tumor grade and AJCC stage. Conclusions: RET somatic mutations were associated with high-grade, aggressive primary tumor characteristics, and decreased distant metastatic-free survival but this relationship was not significant after accounting for tumor grade and disease stage. RETM918T was associated with aggressive primary tumors but was not independently associated with clinical outcomes. TP53 mutation may represent an adverse molecular event associated with decreased OS and DSS in MTC, but its prognostic value needs to be confirmed in future studies.
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Affiliation(s)
- Bin Xu
- Department of Pathology and Laboratory Medicine; New York, New York, USA
| | - Kartik Viswanathan
- Department of Pathology, Emory University Hospital Midtown, Atlanta, Georgia, USA
| | - Mahsa S Ahadi
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research; Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Sara Ahmadi
- Division of Endocrinology and Metabolism, Department of Medicine; Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Bayan Alzumaili
- Department of Pathology and Laboratory Medicine; New York, New York, USA
| | - Mohamed-Amine Bani
- Medical Pathology and Biology Department; Service d'oncologie endocrinienne; Gustave Roussy Campus Cancer, Villejuif, France
| | - Eric Baudin
- Département d'imagerie, Service d'oncologie endocrinienne; Gustave Roussy Campus Cancer, Villejuif, France
| | - David Blake Behrman
- Department of Pathology, Emory University Hospital Midtown, Atlanta, Georgia, USA
| | - Marzia Capelletti
- Department of Pathology; Brigham and Women's Hospital, Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicole G Chau
- Department of Pathology; Brigham and Women's Hospital, Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Federico Chiarucci
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna Medical Center; Bologna, Italy
| | - Angela Chou
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research; Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Roderick Clifton-Bligh
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research; Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Sara Coluccelli
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna Medical Center; Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology; Bologna, Italy
| | - Antonio De Leo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna Medical Center; Bologna, Italy
| | - Snjezana Dogan
- Department of Pathology and Laboratory Medicine; New York, New York, USA
| | - James A Fagin
- Division of Specialized Medicine; New York, New York, USA
| | - Talia L Fuchs
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research; Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Anthony Robert Glover
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Julien Hadoux
- Département d'imagerie, Service d'oncologie endocrinienne; Gustave Roussy Campus Cancer, Villejuif, France
| | - Ludovic Lacroix
- Medical Pathology and Biology Department; Service d'oncologie endocrinienne; Gustave Roussy Campus Cancer, Villejuif, France
| | - Livia Lamartina
- Département d'imagerie, Service d'oncologie endocrinienne; Gustave Roussy Campus Cancer, Villejuif, France
| | - Daniel J Lubin
- Department of Pathology, Emory University Hospital Midtown, Atlanta, Georgia, USA
| | - Catherine Luxford
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research; Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Kelly Magliocca
- Department of Pathology, Emory University Hospital Midtown, Atlanta, Georgia, USA
| | - Thais Maloberti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna Medical Center; Bologna, Italy
| | - Abhinita S Mohanty
- Department of Pathology and Laboratory Medicine; New York, New York, USA
| | - Fedaa Najdawi
- Department of Pathology; Brigham and Women's Hospital, Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Aradhya Nigam
- Department of Surgery; Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexander James Papachristos
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research; Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Andrea Repaci
- Division of Endocrinology and Diabetes Prevention and Care; IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Bruce Robinson
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research; Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Jean-Yves Scoazec
- Medical Pathology and Biology Department; Service d'oncologie endocrinienne; Gustave Roussy Campus Cancer, Villejuif, France
| | - Qiuying Shi
- Department of Pathology, Emory University Hospital Midtown, Atlanta, Georgia, USA
| | - Stan Sidhu
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research; Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Erica Solaroli
- Endocrinology Unit, Azienda USL di Bologna, Bologna, Italy
| | - Mark Sywak
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research; Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | | | - Brian Untch
- Department of Surgery; Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Justine A Barletta
- Department of Pathology; Brigham and Women's Hospital, Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Abir Al Ghuzlan
- Medical Pathology and Biology Department; Service d'oncologie endocrinienne; Gustave Roussy Campus Cancer, Villejuif, France
| | - Anthony J Gill
- Royal North Shore Hospital and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research; Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology; Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Ronald Ghossein
- Department of Pathology and Laboratory Medicine; New York, New York, USA
| | - Giovanni Tallini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna Medical Center; Bologna, Italy
| | - Ian Ganly
- Department of Surgery; Memorial Sloan Kettering Cancer Center, New York, New York, USA
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