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Vranic S, Gatalica Z. Tumor-type agnostic, targeted therapies make a new step forward: The first tumor-agnostic approval of a HER2-targeted therapy. Biomol Biomed 2024. [PMID: 38656302 DOI: 10.17305/bb.2024.10641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Indexed: 04/26/2024]
Abstract
Oncologic treatment has recently undergone substantial therapeutic paradigm shifts, from classical tumor-specific and biomarker-agnostic approaches to more molecular, biomarker-specific, and tumor-agnostic. Tumor-type (histology) agnostic drugs work across cancer types and present a novel shift in precision oncology. Compared with traditional cancer therapies, this novel approach implies molecularly informed treatment strategies and enables targeted treatment regardless of tumor histology (type). Such drugs are usually utilized in small clinical cohorts with diverse tumor types sharing a common genomic event (molecular biomarker). One of the key elements of this approach is the presence of a common biomarker across many tumor types. Biomarker predicts response to the targeted drugs, as well as deciphers potential resistance mechanisms. Read more in the PDF.
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Affiliation(s)
- Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Zoran Gatalica
- Reference Medicine, Phoenix, AZ, United States of America
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Gatalica Z, Kuzmova N, Rose I, Ulamec M, Peric-Balja M, Skenderi F, Vranic S. The assessment of tumor-infiltrating lymphocytes in invasive apocrine carcinoma of the breast in relation to the HER2 status. Biomol Biomed 2024; 24:256-261. [PMID: 37782562 PMCID: PMC10950344 DOI: 10.17305/bb.2023.9868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/04/2023]
Abstract
In the current study, we assessed the prevalence and molecular features of HER2-low phenotype in the apocrine carcinomas of the breast (ApoCa) and its relationship with tumor-infiltrating lymphocytes (TILs). A cohort of 64 well-characterized therapy-naïve ApoCa was used. The TIL distribution was assessed using the hematoxylin and eosin whole slide/scanned images following the international TILs working group recommendations. Next-generation sequencing (NGS) was performed in a subset of HER2-low ApoCa. All patients were women, with a mean age of 62 years. Forty-three carcinomas were pure apocrine carcinoma (PAC; ER-/AR+), and the remaining 21 were classified as apocrine-like carcinomas (ALCs; ER+/-, AR+/-). HER2/neu was positive (score 3+ by IHC and/or amplified by FISH) in 20/43 (47%) PAC and 4/21 (19%) ALC. The prevalence of HER2-low expression (scores 1+ or 2+ without HER2 amplification) in ApoCa was 39% without significant differences between PAC and ALC (P = 0.14); however, the HER2-low phenotype was more prevalent in triple-negative PAC than in ALC (P < 0.001). Levels of TILs were low (≤10%) in 74% of ApoCa (median 5%, range 0%-50%). TIL levels were significantly higher in ALC than in PAC (P = 0.02). HER2 status had no impact on TIL distribution (P = 0.45). The genomic profile of HER2-low ApoCa was similar to other subtypes of ApoCa. ApoCa has predominantly low TIL, particularly PAC. The prevalence of the HER2-low phenotype in ApoCa is high, which should have therapeutic and clinical implications given the recently approved therapies with antibody-drug conjugates (ADCs) for HER2-low breast cancers.
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Affiliation(s)
- Zoran Gatalica
- Reference Medicine, Phoenix, Arizona, USA
- The University of Oklahoma Health Sciences Center, Oklahoma, USA
| | | | - Inga Rose
- Reference Medicine, Phoenix, Arizona, USA
| | - Monika Ulamec
- Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
- Department of Pathology and Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Melita Peric-Balja
- Oncological Pathology Department, Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
| | - Faruk Skenderi
- Department of Pathology, Sarajevo School of Science and Technology, Sarajevo, Bosnia and Herzegovina
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar
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Chong AL, Thorner P, Ellis M, Swensen J, Benlimame N, Fiset PO, Gatalica Z, Evans MG, Foulkes WD. Fetal Type Morphologies Suggest the Presence of DICER1 Hotspot Mutations in Non-small Cell Lung Cancer. Am J Surg Pathol 2024; 48:221-229. [PMID: 38050371 DOI: 10.1097/pas.0000000000002162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Germline and somatic pathogenic variants (PVs) in DICER1 , encoding a miRNA biogenesis protein, are associated with a wide variety of highly specific pathologic entities. The lung tumors pleuropulmonary blastoma, pulmonary blastoma (PB), and well-differentiated fetal lung adenocarcinoma (WDFLAC) are all known to harbor DICER1 biallelic variants (loss of function and/or somatic hotspot missense mutations), and all share pathologic features reminiscent of the immature lung. However, the role of DICER1 PVs in non-small cell lung cancer (NSCLC) is relatively unknown. Here, we aimed to establish the spectrum of lung pathologies associated with DICER1 hotspot PVs and to compare the mutational landscape of DICER1 -mutated NSCLC with and without hotspots. We queried DNA sequencing data from 12,146 NSCLCs featuring somatic DICER1 variants. 235 (1.9%) cases harboring ≥ 1 DICER1 PV were found and 9/235 (3.8%) were DICER1 hotspot-positive cases. Histologic review of DICER1 hotspot-positive cases showed that all but one tumor were classified as within the histologic spectrum of PB/WDFLAC, whereas all the DICER1 non-hotspot double variants were classified as lung adenocarcinomas, not otherwise specified. Comparison between the mutational landscape of DICER1 hotspot-positive and hotspot-negative cases revealed a higher frequency of CTNNB1 mutations in the hotspot-positive cases (5/9 vs. 2/225; P <0.00001). We conclude that DICER1 somatic hotspots are not implicated in the most common forms of NSCLC but rather select for morphologic features of lung tumor types such as PB and WDFLAC. As a corollary, cases showing this tumor morphology should undergo testing for DICER1 variants, and if positive, genetic counseling should be considered.
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Affiliation(s)
- Anne-Laure Chong
- Department of Human Genetics
- Cancer Axis, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital
| | - Paul Thorner
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
| | | | | | - Naciba Benlimame
- Research Pathology Facility, Lady Davis Institute, Jewish General Hospital, Montreal
| | | | - Zoran Gatalica
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | | | - William D Foulkes
- Department of Human Genetics
- Gerald Bronfman Department of Oncology, McGill University
- Cancer Axis, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC
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Fojnica A, Ljuca K, Akhtar S, Gatalica Z, Vranic S. An Updated Review of the Biomarkers of Response to Immune Checkpoint Inhibitors in Merkel Cell Carcinoma: Merkel Cell Carcinoma and Immunotherapy. Cancers (Basel) 2023; 15:5084. [PMID: 37894451 PMCID: PMC10605355 DOI: 10.3390/cancers15205084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/08/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Merkel cell carcinoma (MCC) is primarily a disease of the elderly Caucasian, with most cases occurring in individuals over 50. Immune checkpoint inhibitors (ICI) treatment has shown promising results in MCC patients. Although ~34% of MCC patients are expected to exhibit at least one of the predictive biomarkers (PD-L1, high tumor mutational burden/TMB-H/, and microsatellite instability), their clinical significance in MCC is not fully understood. PD-L1 expression has been variably described in MCC, but its predictive value has not been established yet. Our literature survey indicates conflicting results regarding the predictive value of TMB in ICI therapy for MCC. Avelumab therapy has shown promising results in Merkel cell polyomavirus (MCPyV)-negative MCC patients with TMB-H, while pembrolizumab therapy has shown better response in patients with low TMB. A study evaluating neoadjuvant nivolumab therapy found no significant difference in treatment response between the tumor etiologies and TMB levels. In addition to ICI therapy, other treatments that induce apoptosis, such as milademetan, have demonstrated positive responses in MCPyV-positive MCC, with few somatic mutations and wild-type TP53. This review summarizes current knowledge and discusses emerging and potentially predictive biomarkers for MCC therapy with ICI.
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Affiliation(s)
- Adnan Fojnica
- Institute of Virology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany;
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria
| | - Kenana Ljuca
- Health Center of Sarajevo Canton, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Saghir Akhtar
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha 2713, Qatar;
| | - Zoran Gatalica
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73019, USA;
- Reference Medicine, Phoenix, AZ 85040, USA
| | - Semir Vranic
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha 2713, Qatar;
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Ziegler C, Mir A, Anandakrishnan S, Martin P, Contreras E, Slemons I, Witkowski B, DeSilva C, Farmer A, Vranic S, Gatalica Z, Richardson D, Derkach DN. Assay-agnostic spatial profiling detects tumor microenvironment signatures: new diagnostic insights for triple-negative breast cancer. Mol Oncol 2023; 17:1953-1961. [PMID: 37666492 PMCID: PMC10552887 DOI: 10.1002/1878-0261.13515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 09/06/2023] Open
Abstract
The role of the tumor microenvironment (TME) in immuno-oncology has driven demand for technologies that deliver in situ, or spatial, molecular information. Compartmentalized heterogeneity that traditional methods miss is becoming key to predicting both acquired drug resistance to targeted therapies and patient response to immunotherapy. Here, we describe a novel method for assay-agnostic spatial profiling and demonstrate its ability to detect immune microenvironment signatures in breast cancer patients that are unresolved by the immunohistochemical (IHC) assessment of programmed cell death ligand-1 (PD-L1) on immune cells, which represents the only FDA microenvironment-based companion diagnostic test that has been approved for triple-negative breast cancer (TNBC). Two distinct physiological states were found that are uncorrelated to tumor mutational burden (TMB), microsatellite instability (MSI), PD-L1 expression, and intrinsic cancer subtypes.
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Affiliation(s)
| | - Alain Mir
- Takara Bio USASan FranciscoCaliforniaUSA
| | | | | | | | | | | | | | | | - Semir Vranic
- College of Medicine, QU HealthQatar UniversityDohaQatar
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Tomic K, Karan Krizanac D, Skenderi F, Krpina K, Carapina Bilic A, Galic K, Gatalica Z, Vranic S. Comprehensive genomic profiling of a metastatic small cell lung carcinoma with a complete and long-term response to atezolizumab: A case report. Respir Med Case Rep 2023; 45:101920. [PMID: 37810185 PMCID: PMC10558768 DOI: 10.1016/j.rmcr.2023.101920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/10/2023] Open
Abstract
Small cell lung cancer (SCLC) is a highly aggressive malignancy with a poor outcome. We present the case of a 57-year-old male patient with extensive-stage (ES-SCLC) treated with chemotherapy and atezolizumab. A complete response was achieved with a long remission of ∼three years. Comprehensive genomic profiling (CGP) of the tumor revealed high tumor mutation burden (13 mutations/Mb) and mutations of TP53, RB1 and ERCC4 genes. This case study confirms that a complete response to chemoimmunotherapy may be achieved in the case of ES-SCLC. It further provides the additional value of CGP and predictive testing in the management of ES-SCLC.
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Affiliation(s)
- Kresimir Tomic
- Department of Oncology, University Clinical Hospital Mostar, Mostar, Bosnia and Herzegovina
| | - Dragana Karan Krizanac
- Department of Pathology, Cytology and Forensic Medicine, University Clinical Hospital Mostar, Mostar, Bosnia and Herzegovina
| | - Faruk Skenderi
- Department of Pathology, UniMed Clinic, Sarajevo School of Science and Technology, Sarajevo, Bosnia and Herzegovina
| | - Kristina Krpina
- Clinic for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Andrea Carapina Bilic
- Department of Family Medicine, Health Care Center Mostar, Mostar, Bosnia and Herzegovina
| | - Kristina Galic
- Department for Lung Diseases, University Clinical Hospital Mostar, Mostar, Bosnia and Herzegovina
| | | | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar
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Price P, Ganugapati U, Gatalica Z, Kakadekar A, Macpherson J, Quenneville L, Rees H, Slodkowska E, Suresh J, Yu D, Lim HJ, Torlakovic EE. Reinventing Nuclear Histo-score Utilizing Inherent Morphologic Cutoffs: Blue-brown Color H-score (BBC-HS). Appl Immunohistochem Mol Morphol 2023; 31:500-506. [PMID: 36625446 PMCID: PMC10396076 DOI: 10.1097/pai.0000000000001095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/07/2022] [Indexed: 01/11/2023]
Abstract
Immunohistochemistry (IHC) is a testing methodology that is widely used for large number of diagnostic, prognostic, and predictive biomarkers. Although IHC is a qualitative methodology, in addition to threshold-based stratification (positive vs. negative), the increasing levels of expression of some of these biomarkers often lead to more intense staining, which published evidence linked to specific diagnosis, prognosis, and responses to therapy. It is essential that the descriptive thresholds between positive and negative staining, as well as between frequently used graded categories of staining intensity (eg, 1+, 2+, 3+) are standardized and reproducible. Histo-score (H-score) is a frequently used scoring system that utilizes these categories. Our study introduces categorization of the cutoff points between positive and negative results and graded categories of staining intensity for nuclear IHC biomarker assays based on color interaction between hematoxylin and diaminobenzidine (DAB); the Blue-brown Color H-score (BBC-HS). Six cases of diffuse large B-cell lymphoma were stained for a nuclear marker MUM1. The staining was assessed by H-score by 12 readers. Short tutorial and illustrated instructions were provided to readers. The novel scoring system in this study uses the interaction between DAB (DAB, brown stain) and hematoxylin (blue counterstain) to set thresholds between "0" (negative nuclei), "1+" (weakly positive nuclei), "2+" (moderately positive nuclei), and "3+" (strongly positive nuclei). The readers recorded scores for 300 cells. Krippendorff alpha (K-alpha) and intraclass correlation coefficient (ICC) were calculated. We have also assessed if reliability improved when counting the first 100 cells, first 200 cells, and for the total 300 cells using K-alpha and ICC. To assess the performance of each individual reader, the mean H-score and percent positive score (PPS) for each case was calculated, and the bias was calculated between each reader's score and the mean. K-alpha was 0.86 for H-score and 0.76 for PPS. ICC was 0.96 for H-score and 0.92 for PPS. The biases for H-score ranged from -58 to 41, whereas for PPS it ranged from -27% to 33%. Overall, most readers showed very low bias. Two readers were consistently underscoring and 2 were consistently overscoring compared with the mean. For nuclear IHC biomarker assays, our newly proposed cutoffs provide highly reliable/reproducible results between readers for positive and negative results and graded categories of staining intensity using existing morphologic parameters. BBC-HS is easy to teach and is applicable to both human eye and image analysis. BBC-HS application should facilitate the development of new reliable/reproducible scoring schemes for IHC biomarkers.
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Affiliation(s)
- Phillipe Price
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
| | - Usharani Ganugapati
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
- Department of Pathology and Laboratory Medicine, Saskatchewan Health Authority, Saskatoon
| | - Zoran Gatalica
- Department of Pathology, Oklahoma University Medical Center, Oklahoma City, OK
| | - Archan Kakadekar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
| | - James Macpherson
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa
| | - Louise Quenneville
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
- Department of Pathology and Laboratory Medicine, Saskatchewan Health Authority, Saskatoon
| | - Henrike Rees
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
- Department of Pathology and Laboratory Medicine, Saskatchewan Health Authority, Saskatoon
| | - Elzbieta Slodkowska
- Department of Laboratory Medicine and Pathobiology, University of Toronto
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Janarthanee Suresh
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
| | - Darryl Yu
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
- Department of Pathology and Laboratory Medicine, Saskatchewan Health Authority, Saskatoon
| | - Hyun J. Lim
- College of Medicine, University of Saskatchewan
| | - Emina E. Torlakovic
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
- Department of Pathology and Laboratory Medicine, Saskatchewan Health Authority, Saskatoon
- Canadian Biomarker Quality Assurance, University of Saskatchewan, Saskatoon, SK
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Gatalica Z, Hoag J, Hall DW, Alyaqoub FS, Dombrowski S, Noel P, Szelinger S, Udhane S, Min W, Thakkar SG, Basu G. CGE23-072: The Frequency of Androgen Receptor Splice Variant 7 (AR-V7) in Solid Tumors. J Natl Compr Canc Netw 2023. [DOI: 10.6004/jnccn.2022.7215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Gatalica Z, Dogruluk TW, Noel P, Dombrowski SM, Hong L, Barbi M, Chandrasekaran T, Basu GD, Hall DW, Hoag JR, Kundranda MN. The Wnt signaling pathway in gastrointestinal cancers. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
807 Background: Activation of the Wnt signaling pathway leads to increases in β-catenin levels, which subsequently increases transcription of various genes, including those involved in cell proliferation. Dysregulation of the Wnt signaling pathway has been observed in numerous gastrointestinal (GI) cancers. Here we examine Wnt pathway activation across all GI cancers by investigating alterations in certain genes of the Wnt pathway, which may identify patients eligible for clinical trials. Methods: The Oncomap ExTra genomic profiling assay utilizes tumor-normal, whole-exome, whole-transcriptome DNA and RNA sequencing to identify somatic alterations in tumors. The assay detects single-nucleotide substitutions, indels, copy number alterations, alternative transcripts, and gene fusions. Alterations in genes that activate Wnt signaling and their frequency across all GI cancers was determined. Results: A total of 1928 patients assayed April 2018 to July 2022 were included. The Wnt signaling pathway was activated in 922 (47.8%) patients. Wnt pathway activation varied substantially across GI cancers, from 81.1% in colorectal cancer (CRC) to 3.4% in anal cancer. APC was the most commonly altered gene in CRC, small bowel and biliary carcinomas. CTNNB1 was predominant in liver (41.2%), MEN1 in neuroendocrine (14.6%), and RNF43 in gastric (9.4%) cancer. Of 921 patients with alterations in the Wnt pathway, 5.2% had a co-mutation in another Wnt pathway-related gene. RSPO2/3 fusions were found in 4 CRC, 1 stomach, 1 biliary, and 1 small bowel cancer and were mutually exclusive with other alterations in the Wnt pathway. Conclusions: Wnt signaling is activated in about half of all GI cancers, and APC alterations are the most frequently observed. Whole transcriptome profiling allowed us to identify RSPO2/3 fusions, which also contribute to activation of the Wnt pathway. Wnt activation appears to be a particularly important in CRC, with 81.1% of CRC having a Wnt pathway alteration. Our results highlight the therapeutic potential of targeting the abnormal Wnt/β-catenin signaling pathway in GI malignancies. [Table: see text]
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Vranic S, Gatalica Z. PD-L1 testing by immunohistochemistry in immuno-oncology. Biomol Biomed 2023; 23:15-25. [PMID: 35964287 PMCID: PMC9901897 DOI: 10.17305/bjbms.2022.7953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 08/06/2022] [Indexed: 02/08/2023]
Abstract
Immunotherapy, based on immune checkpoint inhibitors targeting the Programmed cell death ligand 1 (PD-L1) and/or Programmed Death Receptor 1 (PD-1), has substantially improved the outcomes of patients with various cancers. However, only ~30% of patients benefit from immune checkpoint inhibitors. Tumor PD-L1 expression, assessed by immunohistochemistry, is the most widely validated and used predictive biomarker to guide the selection of patients for immune checkpoint inhibitors. PD-L1 assessment may be challenging due to the necessity for different companion diagnostic assays for required specific immune checkpoint inhibitors and a relatively high level of inter-assay variability in terms of performance and cutoff levels. In this review, we discuss the role of PD-L1 immunohistochemistry as a predictive test in immunotherapy (immuno-oncology), highlight the complexity of the PD-L1 testing landscape, discuss various preanalytical, analytical and clinical issues that are associated with PD-L1 assays, and provide some insights into optimization of PD-L1 as a predictive biomarker in immuno-oncology.
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Affiliation(s)
- Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar,Correspondence to Semir Vranic:
| | - Zoran Gatalica
- Department of Pathology, University of Oklahoma College of Medicine, Oklahoma City, OK, United States
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Bhattacharya U, Thavathiru E, Neizer-Ashun F, Xu C, Gatalica Z, Dwivedi SKD, Dey A, Mukherjee P, Bhattacharya R. The deubiquitinase USP10 protects pancreatic cancer cells from endoplasmic reticulum stress. NPJ Precis Oncol 2022; 6:93. [PMID: 36543867 PMCID: PMC9772324 DOI: 10.1038/s41698-022-00336-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The ubiquitin-specific peptidase 10 (USP10) plays a context-specific, pro or anti-tumorigenic role in different malignancies. However, the role of USP10 in pancreatic cancer remains unclear. Our protein and RNA level analysis from archived specimens and public databases show that USP10 is overexpressed in pancreatic ductal adenocarcinoma (PDAC) and expression correlates with poor overall patient survival. Phenotypically, silencing USP10 decreased viability, clonal growth and invasive properties of pancreatic cancer cells. Mechanistically, silencing USP10 upregulated BiP and induced endoplasmic reticulum (ER) stress that led to an unfolded protein response (UPR) and upregulation of PERK, IRE1α. Decreased cell viability of USP10 silenced cells could be rescued by a chemical chaperone that promotes protein folding. Our studies suggest that USP10 by protecting pancreatic cancer cells from ER stress may support tumor progression.
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Affiliation(s)
- Udayan Bhattacharya
- grid.266902.90000 0001 2179 3618Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Elangovan Thavathiru
- grid.266902.90000 0001 2179 3618Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Fiifi Neizer-Ashun
- grid.266902.90000 0001 2179 3618Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Chao Xu
- grid.266902.90000 0001 2179 3618Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Zoran Gatalica
- grid.266902.90000 0001 2179 3618Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Shailendra Kumar Dhar Dwivedi
- grid.266902.90000 0001 2179 3618Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Anindya Dey
- grid.266902.90000 0001 2179 3618Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Priyabrata Mukherjee
- grid.266902.90000 0001 2179 3618Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA ,grid.266902.90000 0001 2179 3618Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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Vranic S, Basu GD, Hall DW, Gatalica Z. Tumor-Type Agnostic, Targeted Therapies: BRAF Inhibitors Join the Group. Acta Med Acad 2022; 51:217-231. [PMID: 36799315 PMCID: PMC10116180 DOI: 10.5644/ama2006-124.392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/29/2022] [Indexed: 02/17/2023] Open
Abstract
In the present review, we briefly discuss the breakthrough advances in precision medicine using a tumor-agnostic approach and focus on BRAF treatment modalities, the mechanisms of resistance and the diagnostic approach in cancers with BRAF mutations. Tumor-type agnostic drug therapies work across cancer types and present a significant novel shift in precision cancer medicine. They are the consequence of carefully designed clinical trials that showed the value of tumor biomarkers, not just in diagnosis but in therapy guidance. Six tumor-agnostic drugs (with seven indications) have been approved through October 2022 by FDA. The first tumor-agnostic treatment modality was pembrolizumab for MSI-H/dMMR solid tumors, approved in 2017. This was followed by approvals of larotrectinib and entrectinib for cancers with NTRK fusions without a known acquired resistance mutation. In 2020, pembrolizumab was approved for all TMB-high solid cancers, while a PD-L1 inhibitor dostarlimab-gxly was approved for dMMR solid cancers in 2021. A combination of BRAF/MEK inhibitors (dabrafenib/trametinib) was approved as a tumor-agnostic therapy in June 2022 for all histologic types of solid metastatic cancers harboring BRAFV600E mutations. In September 2022, RET inhibitor selpercatinib was approved for solid cancers with RET gene fusions. CONCLUSION: Precision cancer medicine has substantially improved cancer diagnostics and treatment. Tissue type-agnostic drug therapies present a novel shift in precision cancer medicine. This approach rapidly expands to provide treatments for patients with different cancers harboring the same molecular alteration.
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Affiliation(s)
- Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar; Department of Medical Sciences, Academy of Sciences and Arts of Bosnia and Herzegovina, Sarajevo, Bosnia and Herzegovina. ;
| | - Gargi D Basu
- Exact Sciences, Phoenix, Arizona, United States of America
| | - David W Hall
- Exact Sciences, Phoenix, Arizona, United States of America
| | - Zoran Gatalica
- Exact Sciences, Phoenix, Arizona, United States of America; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
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13
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Gatalica Z, Stafford P, Vranic S. Alpha-methylacyl-CoA racemase (AMACR) protein is upregulated in early proliferative lesions of the breast irrespective of apocrine differentiation. Hum Pathol 2022; 129:40-46. [PMID: 35998819 DOI: 10.1016/j.humpath.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 12/14/2022]
Abstract
Alpha-methylacyl-CoA racemase (AMACR/P504S) is a mitochondrial and peroxisomal enzyme involved in the branched-chain fatty acid and bile acid metabolism. AMACR is a useful diagnostic biomarker for prostate carcinomas and several other malignancies. Its expression in apocrine breast lesions had been previously reported, but its role in breast cancer progression has not been fully investigated. One hundred fifty breast samples (80 with invasive carcinomas) were studied. The expression of AMACR protein was analyzed using the immunohistochemical method (IHC). Lesions were considered positive if AMACR was detected in ≥10% of the cells at any intensity comprising a histologically defined normal epithelial structure or a pathologic lesion. In addition, AMACR mRNA relative expression was calculated from the whole-transcript RNA-Seq performed on >20,000 diverse tumor samples using a 20,000+ hybrid-capture NGS assay with the transcript capture panel based on the Agilent SureSelect Human All ExonV7. Expression of AMACR protein was restricted to epithelia. It was uncommon in the normal breast (7/81 samples, 9%). Increasing AMACR expression was observed with proliferative epithelial lesions (18% of usual ductal hyperplasias/adenosis, 70% of atypical lesions and 72% of DCIS/LCIS). Invasive ductal carcinomas NST and invasive lobular carcinomas expressed AMACR in 64% and 46%, respectively. The highest AMACR expression was observed in luminal B and HER2-positive breast carcinomas (86-100%). Triple-negative breast carcinomas exhibited AMACR in 50% of the cases. Apocrine lesions showed strong, nearly uniform overexpression of AMACR (100% of metaplasias, hyperplasias and in situ carcinomas and 88% of invasive apocrine carcinomas were positive). RNA-Seq analysis also confirmed AMACR expression in breast carcinomas, although its median value was substantially lower with a lower standard deviation than in prostate carcinomas. Over-expression of AMACR characterizes various proliferative, preinvasive and invasive breast lesions and is not specific to the apocrine morphology. It points to altered lipid metabolism (branched fatty acids) as one of the general characteristics of breast carcinogenesis, like several other malignancies. Its early detection may represent a potential target for cancer progression intervention.
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Affiliation(s)
- Zoran Gatalica
- Department of Pathology, University of Oklahoma College of Medicine, Oklahoma City, OK 73104, United States
| | | | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, 2713, Qatar.
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14
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Ajkunic A, Skenderi F, Shaker N, Akhtar S, Lamovec J, Gatalica Z, Vranic S. Acinic cell carcinoma of the breast: A comprehensive review. Breast 2022; 66:208-216. [PMID: 36332545 PMCID: PMC9636467 DOI: 10.1016/j.breast.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/03/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Acinic cell carcinoma of the breast is a rare special subtype of breast cancer in the category of salivary gland-type tumors. It is morphologically similar to acinic cell carcinomas of salivary glands and pancreas and has a triple-negative phenotype (estrogen receptor-negative, progesterone receptor-negative, and Her-2/neu negative). Its molecular genomic features are more similar to triple-negative breast cancer of no special type than to its salivary gland counterpart. However, the clinical course of the mammary acinic cell carcinoma appears to be less aggressive than the usual triple-negative breast carcinomas. This review comprehensively summarizes the current literature on the clinicopathologic, immunohistochemical, and molecular features of this rare and distinct subtype of breast cancer.
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Affiliation(s)
- Azra Ajkunic
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Faruk Skenderi
- Sarajevo School of Science and Technology, Sarajevo, Bosnia and Herzegovina
| | - Nada Shaker
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Saghir Akhtar
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Janez Lamovec
- Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Zoran Gatalica
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar,Corresponding author. College of Medicine, QU Health, Qatar University, 2713, Doha, Qatar.
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15
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Burgess EF, Sanders JA, Livasy C, Symanowski J, Gatalica Z, Steuerwald NM, Arguello D, Brouwer CR, Korn WM, Grigg CM, Zhu J, Matulay JT, Clark PE, Heath EI, Raghavan D. Identification of potential biomarkers and novel therapeutic targets through genomic analysis of small cell bladder carcinoma and associated clinical outcomes. Urol Oncol 2022; 40:383.e1-383.e10. [DOI: 10.1016/j.urolonc.2022.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/09/2022] [Accepted: 04/28/2022] [Indexed: 11/27/2022]
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16
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Skenderi F, Alahmad MAM, Tahirovic E, Alahmad YM, Gatalica Z, Vranic S. HER2-positive apocrine carcinoma of the breast: a population-based analysis of treatment and outcome. Breast Cancer Res Treat 2022; 193:523-533. [PMID: 35355162 PMCID: PMC9090698 DOI: 10.1007/s10549-022-06578-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/17/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE Apocrine carcinoma of the breast (APO) expresses HER2 in 30-50% of cases. This study explored the clinicopathological features and outcome of HER2+/APO and matched HER2+/NST cohort. METHODS We used the SEER database to explore the cohorts. Univariate and multivariate analyses were used to assess the survival. Based on ER and PR [steroid receptors/SR/] and HER2 status, we divided the cohorts to match the intrinsic molecular subtypes for comparisons. RESULTS We retrieved 259 cases of HER2+/APO. Most HER2+/APO were SR negative (65%). HER2+/APO were more prevalent in the 80+ age group (24.7% vs. 15.7%, p < 0.001). HER2+/SR-/APO had a significantly lower histological grade than the HER2+/SR-/NST (p < 0.001). Breast cancer-related deaths were more prevalent in HER2+/NST (7.8% vs. 3.9%, p = 0.019). This was particularly evident between SR- subgroups (10.4% in HER2+/SR-/NST vs. 4.2% in HER2+/SR-/APO, p = 0.008) and was reaffirmed in breast cancer-specific survival in univariate analysis (p = 0.03). Other than race and SR status, HER2+/APO subgroups did not differ in clinicopathological parameters. CONCLUSIONS Our study confirms the rarity of the APO and reveals that SR status in APO does not affect these patients' prognosis. HER2+/APO tumors tend to have a less aggressive phenotype and a more favorable outcome despite a markedly lower ER/PR positivity.
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Affiliation(s)
- Faruk Skenderi
- Faculty of Health Sciences, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | | | - Emin Tahirovic
- Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Yaman M Alahmad
- College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar
- Medical Education, Hamad Medical Corporation, Doha, Qatar
| | - Zoran Gatalica
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar.
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17
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Farcaş M, Gatalica Z, Trpkov K, Swensen J, Zhou M, Alaghehbandan R, Williamson SR, Magi-Galluzzi C, Gill AJ, Tretiakova M, Lopez JI, Montiel DP, Sperga M, Comperat E, Brimo F, Yilmaz A, Siadat F, Sangoi A, Gao Y, Ptákova N, Kuthi L, Pivovarcikova K, Rogala J, Agaimy A, Hartmann A, Fraune C, Rychly B, Hurnik P, Durcansky D, Bonert M, Gakis G, Michal M, Hora M, Hes O. Eosinophilic vacuolated tumor (EVT) of kidney demonstrates sporadic TSC/MTOR mutations: next-generation sequencing multi-institutional study of 19 cases. Mod Pathol 2022; 35:344-351. [PMID: 34521993 DOI: 10.1038/s41379-021-00923-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 11/09/2022]
Abstract
A distinct renal tumor has recently been described as "high-grade oncocytic renal tumor" and "sporadic renal cell carcinoma with eosinophilic and vacuolated cytoplasm". The Genitourinary Pathology Society (GUPS) consensus proposed a unifying name "eosinophilic vacuolated tumor" (EVT) for this emerging entity. In this multi-institutional study, we evaluated 19 EVTs, particularly their molecular features and mutation profile, using next-generation sequencing. All cases were sporadic and none of the patients had a tuberous sclerosis complex. There were 8 men and 11 women, with a mean age of 47 years (median 50; range 15-72 years). Average tumor size was 4.3 cm (median 3.8 cm; range 1.5-11.5 cm). All patients with available follow-up data (18/19) were alive and without evidence of disease recurrence or progression during the follow-up, ranging from 12 to 198 months (mean 56.3, median 41.5 months). The tumors were well circumscribed, but lacked a well-formed capsule, had nested to solid growth, focal tubular architecture, and showed ubiquitous, large intracytoplasmic vacuoles, round to oval nuclei, and prominent nucleoli. Immunohistochemically, cathepsin K, CD117, CD10, and antimitochondrial antigen were expressed in all cases. Other positive stains included: PAX8, AE1/AE3 and CK18. CK7 was typically restricted only to rare scattered cells. Vimentin, HMB45, melan-A, and TFE3 were negative in all cases. All tumors showed retained SDHB. All cases (19/19) showed non-overlapping mutations of the mTOR pathway genes: TSC1 (4), TSC2 (7), and MTOR (8); one case with MTOR mutation showed a coexistent RICTOR missense mutation. Low mutational rates were found in all samples (ranged from 0 to 6 mutations/Mbp). Microsatellite instability and copy number variations were not found in any of the 17 analyzable cases. EVT represents an emerging renal entity that shows a characteristic and readily identifiable morphology, consistent immunohistochemical profile, indolent behavior, and mutations in either TSC1, TSC2, or MTOR genes.
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Affiliation(s)
- Mihaela Farcaş
- Department of Pathology, Colentina Clinical Hospital, Bucharest, Romania.,Onco Team Diagnostic, Bucharest, Romania
| | - Zoran Gatalica
- Department of Pathology, Oklahoma University School of Medicine, Oklahoma, USA
| | - Kiril Trpkov
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Ming Zhou
- Department of Pathology, Tufts Medical Center, Boston, MA, USA
| | | | - Sean R Williamson
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal; North Shore Hospital, St Leonards, NSW, Australia.,University of Sydney, Sydney NSW Australia 2006; NSW Health Pathology Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Maria Tretiakova
- Department of Pathology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Jose I Lopez
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Institute, Barakaldo, Spain
| | - Delia Perez Montiel
- Department of Pathology, Institute Nacional de Cancerologia, Mexico City, Mexico
| | - Maris Sperga
- Department of Pathology, Stradin´s University, Riga, Latvia
| | - Eva Comperat
- Department of Pathology, Sorbonne Université, Service d'Anatomie et Cytologie Pathologiques, Hôpital Tenon, Paris, France.,Department of Pathology, University of Vienna, Vienna, Austria
| | - Fadi Brimo
- Department of Pathology, McGill University, Montreál, QC, Canada
| | - Asli Yilmaz
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Farshid Siadat
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ankur Sangoi
- Department of Pathology, El Camino Hospital, Mountain View, CA, USA
| | - Yuan Gao
- Department of Pathology, Heath Science Centre, St. John's, NL, Canada
| | - Nikola Ptákova
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Levente Kuthi
- Department of Pathology, University of Szeged, Szeged, Hungary
| | - Kristyna Pivovarcikova
- Department of Pathology, Charles University, Medical Faculty and Charles University Hospital Plzen, Plzen, Czech Republic
| | - Joanna Rogala
- Department of Pathology, Charles University, Medical Faculty and Charles University Hospital Plzen, Plzen, Czech Republic
| | - Abbas Agaimy
- Department of Pathology, University of Erlangen, Erlangen, Germany
| | - Arndt Hartmann
- Department of Pathology, University of Erlangen, Erlangen, Germany
| | - Cristoph Fraune
- Department of Pathology, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Boris Rychly
- Department of Pathology, Alfa Medical, Bratislava, Slovakia
| | - Pavel Hurnik
- Department of Pathology, University Hospital Ostrava, Ostrava, Czech Republic
| | - Dušan Durcansky
- Department of Pathology, University Hospital Nitra, Nitra, Slovakia
| | - Michael Bonert
- Department of Pathology, University of Toronto, Toronto, ON, Canada
| | - Georgios Gakis
- Department of Urology, University of Erlangen, Erlangen, Germany
| | - Michal Michal
- Department of Pathology, Charles University, Medical Faculty and Charles University Hospital Plzen, Plzen, Czech Republic
| | - Milan Hora
- Department of Urology, Charles University, Medical Faculty and Charles University Hospital Plzen, Plzen, Czech Republic
| | - Ondrej Hes
- Department of Pathology, Charles University, Medical Faculty and Charles University Hospital Plzen, Plzen, Czech Republic.
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18
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Armstrong SA, Malley R, Wang H, Lenz HJ, Arguello D, El-Deiry WS, Xiu J, Gatalica Z, Hwang JJ, Philip PA, Shields AF, Marshall JL, Salem ME, Weinberg BA. Molecular characterization of squamous cell carcinoma of the anal canal. J Gastrointest Oncol 2021; 12:2423-2437. [PMID: 34790403 DOI: 10.21037/jgo-20-610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 09/06/2021] [Indexed: 12/24/2022] Open
Abstract
Background Squamous cell carcinoma of the anal canal (SCCA) is an uncommon malignancy with limited therapeutic options. Nivolumab and pembrolizumab show promising results in patients with SCCA. Human papillomavirus (HPV)-negative tumors are frequently TP53-mutated (TP53-MT) and often resistant to therapy. Methods We present a large molecularly-profiled cohort of SCCA, exploring the underlying biology of SCCA, differences between TP53-wild type (TP53-WT) and TP53-MT tumors, and differences between local and metastatic tumors. SCCA specimens (n=311) underwent multiplatform testing with immunohistochemistry (IHC), in situ hybridization (ISH) and next-generation sequencing (NGS). Tumor mutational burden (TMB) was calculated using only somatic nonsynonymous missense mutations. Chi-square testing was used for comparative analyses. Results The most frequently mutated genes included PIK3CA (28.1%), KMT2D (19.5%), FBXW7 (12%), TP53 (12%) and PTEN (10.8%). The expression of PD-1 was seen in 68.8% and PD-L1 in 40.5% of tumors. High TMB was present in 6.7% of specimens. HER2 IHC was positive in 0.9%, amplification by chromogenic in situ hybridization (CISH) was seen 1.3%, and mutations in ERBB2 were present in 1.8% of tumors. The latter mutation has not been previously described in SCCA. When compared with TP53-WT tumors, TP53-MT tumors had higher rates of CDKN2A, EWSR1, JAK1, FGFR1 and BRAF mutations. PD-1 and PD-L1 expression were similar, and high TMB did not correlate with PD-1 (P=0.50) or PD-L1 (P=0.52) expression. Conclusions Molecular profiling differences between TP53-MT and TP53-WT SCCA indicate different carcinogenic pathways which may influence response to therapy. Low frequency mutations in several druggable genes may provide therapeutic opportunities for patients with SCCA.
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Affiliation(s)
- Samantha A Armstrong
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Rita Malley
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Hongkun Wang
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA, USA
| | | | | | | | | | - Jimmy J Hwang
- Department of Hematology/Oncology, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Philip A Philip
- Department of Oncology, Wayne State University School of Medicine, Karmanos Cancer Institute, Detroit, MI, USA
| | - Anthony F Shields
- Department of Oncology, Wayne State University School of Medicine, Karmanos Cancer Institute, Detroit, MI, USA
| | - John L Marshall
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Mohamed E Salem
- Department of Hematology/Oncology, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
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19
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Jones A, Rapisardo S, Zhang L, Mellors T, Withers JB, Gatalica Z, Akmaev VR. Analytical and clinical validation of an RNA sequencing-based assay for quantitative, accurate evaluation of a molecular signature response classifier in rheumatoid arthritis. Expert Rev Mol Diagn 2021; 21:1235-1243. [PMID: 34727834 DOI: 10.1080/14737159.2021.2000394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVES This study reports analytical and clinical validation of a molecular signature response classifier (MSRC) that identifies rheumatoid arthritis (RA) patients who are non-responders to tumor necrosis factor-ɑ inhibitors (TNFi). METHODS The MSRC integrates patient-specific data from 19 gene expression features, anti-cyclic citrullinated protein serostatus, sex, body mass index, and patient global assessment into a single score. RESULTS The MSRC results stratified samples (N = 174) according to non-response prediction with a positive predictive value of 87.7% (95% CI: 78-94%), sensitivity of 60.2% (95% CI: 50-69%), and specificity of 77.3% (95% CI: 65-87%). The 25-point scale was subdivided into three thresholds: signal not detected (<10.6), high (≥10.6), and very high (≥18.5). The MSRC relies on sequencing of RNA extracted from blood; this assay displays high gene expression concordance between inter- and intra-assay sample (R2 > 0.977) and minimal variation in cumulative gene assignment diversity, read mapping location, or gene-body coverage. The MSRC accuracy was 95.8% (46/48) for threshold concordance (no signal, high, very high). Intra- and inter-assay precision studies demonstrated high repeatability (92.6%, 25/27) and reproducibility (100%, 35/35). CONCLUSION The MSRC is a robust assay that accurately and reproducibly detects an RA patient's molecular signature of non-response to TNFi therapies.
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Affiliation(s)
- Alex Jones
- Data Science, Scipher Medicine Corporation, Waltham, MA, USA
| | - Sarah Rapisardo
- Laboratory Operations, Scipher Medicine Corporation, Waltham, MA, USA
| | - Lixia Zhang
- Data Science, Scipher Medicine Corporation, Waltham, MA, USA
| | | | | | - Zoran Gatalica
- Laboratory Operations, Scipher Medicine Corporation, Waltham, MA, USA
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20
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Michal M, Rubin BP, Agaimy A, Kosemehmetoglu K, Rudzinski ER, Linos K, John I, Gatalica Z, Davis JL, Liu YJ, McKenney JK, Billings SD, Švajdler M, Koshyk O, Kinkor Z, Michalová K, Kalmykova AV, Yusifli Z, Ptáková N, Hájková V, Grossman P, Šteiner P, Michal M. Correction to: EWSR1-PATZ1-rearranged sarcoma: a report of nine cases of spindle and round cell neoplasms with predilection for thoracoabdominal soft tissues and frequent expression of neural and skeletal muscle markers. Mod Pathol 2021; 34:2092. [PMID: 34112958 DOI: 10.1038/s41379-021-00740-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael Michal
- Department of Pathology, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic. .,Department of Pathology and Molecular Genetics, Bioptical Laboratory, Ltd., Plzen, Czech Republic.
| | - Brian P Rubin
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander University ErlangenNürnberg, University Hospital, Erlangen, Germany
| | - Kemal Kosemehmetoglu
- Department of Pathology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Erin R Rudzinski
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA
| | - Konstantinos Linos
- Department of Pathology and Laboratory Medicine, DartmouthHitchcock Medical Center and Geisel School of Medicine, Lebanon, NH, USA
| | - Ivy John
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zoran Gatalica
- Department of Pathology, Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | - Jessica L Davis
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Yajuan J Liu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jesse K McKenney
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Steven D Billings
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Marián Švajdler
- Department of Pathology, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic.,Department of Pathology and Molecular Genetics, Bioptical Laboratory, Ltd., Plzen, Czech Republic
| | - Olena Koshyk
- Laboratory of Pathology, CSD Health Care, Ltd., Kyiv, Ukraine
| | - Zdeněk Kinkor
- Department of Pathology, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic.,Department of Pathology and Molecular Genetics, Bioptical Laboratory, Ltd., Plzen, Czech Republic
| | - Květoslava Michalová
- Department of Pathology, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic.,Department of Pathology and Molecular Genetics, Bioptical Laboratory, Ltd., Plzen, Czech Republic
| | | | | | - Nikola Ptáková
- Department of Pathology and Molecular Genetics, Bioptical Laboratory, Ltd., Plzen, Czech Republic
| | - Veronika Hájková
- Department of Pathology and Molecular Genetics, Bioptical Laboratory, Ltd., Plzen, Czech Republic
| | - Petr Grossman
- Department of Pathology and Molecular Genetics, Bioptical Laboratory, Ltd., Plzen, Czech Republic
| | - Petr Šteiner
- Department of Pathology and Molecular Genetics, Bioptical Laboratory, Ltd., Plzen, Czech Republic
| | - Michal Michal
- Department of Pathology, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic.,Department of Pathology and Molecular Genetics, Bioptical Laboratory, Ltd., Plzen, Czech Republic
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21
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Dardis C, Donner D, Sanai N, Xiu J, Mittal S, Michelhaugh SK, Pandey M, Kesari S, Heimberger AB, Gatalica Z, Korn MW, Sumrall AL, Phuphanich S. Correction to: Gliosarcoma vs. glioblastoma: a retrospective case series using molecular profiling. BMC Neurol 2021; 21:316. [PMID: 34391386 PMCID: PMC8364012 DOI: 10.1186/s12883-021-02326-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Christopher Dardis
- Department of Neurology, Barrow Neurological Institute, Phoenix, AZ, USA.
| | - David Donner
- School of Medicine, Creighton University, Phoenix, AZ, USA
| | - Nader Sanai
- Barrow Brain Tumor Research Center, Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Joanne Xiu
- Precision Oncology Alliance, Caris Life Sciences, Phoenix, AZ, USA
| | - Sandeep Mittal
- Fralin Biomedical Research Institute, Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Sharon K Michelhaugh
- Fralin Biomedical Research Institute, Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Manjari Pandey
- Department of Medical Oncology, West Cancer Center, University of Tennessee Health Science Center, Germantown, TN, USA
| | - Santosh Kesari
- Pacific Neuroscience Institute and Department of Translational Neurosciences and Neurotherapeutics, John Wayne Cancer Institute, Santa Monica, CA, USA
| | - Amy B Heimberger
- Simpson Querry Biomedical Research Center, Department of Neurosurgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Zoran Gatalica
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael W Korn
- Precision Oncology Alliance, Caris Life Sciences, Phoenix, AZ, USA
| | - Ashley L Sumrall
- Department of Medical Oncology, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Surasak Phuphanich
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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22
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Kruslin B, Gatalica Z, Hes O, Skenderi F, Miettinen M, Contreras E, Xiu J, Ellis M, Florento E, Vranic S, Swensen J. TERT Gene Fusions Characterize a Subset of Metastatic Leydig Cell Tumors. Clin Genitourin Cancer 2021; 19:333-338. [PMID: 33741265 PMCID: PMC9907364 DOI: 10.1016/j.clgc.2021.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/01/2021] [Accepted: 02/12/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Metastatic Leydig cell tumors (LCT) are rare, difficult-to-treat malignancies without known underlying molecular-genetic events. An index case of metastatic LCT showed an LDLR-TERT gene fusion upon routine genetic profiling for detection of therapeutic targets, which was then followed by an investigation into a cohort of additional LCTs. PATIENTS AND METHODS Twenty-nine LCT (27 male and 2 female patients) were profiled using next-generation sequencing and immunohistochemistry. RESULTS TERT gene fusions were detected only in testicular metastatic LCTs, in 3 of 7 successfully analyzed cases (RMST:TERT, LDLR:TERT, and B4GALT5:TERT). TOP1 and CCND3 amplifications were identified in the case with a B4GALT5:TERT fusion. A TP53 mutation was detected in 1 metastatic tumor without a TERT fusion. Five primary (4 testicular and 1 ovarian) LCTs showed multiple gene amplifications, without a consistent pattern. A single metastatic ovarian LCT showed BAP1 mutation and copy number amplifications affecting the NPM1, PCM1, and SS18 genes. At the protein level, 4 of 7 metastatic and 6 of 10 primary testicular LCTs overexpressed Topo1. Androgen receptor was overexpressed in 10 of 13 primary testicular tumors and 2 of 5 metastatic testicular LCTs (without detectable ARv7 messenger RNA or ARv7 protein). Only 1 metastatic testicular LCT exhibited a high tumor mutational burden; all tested cases were microsatellite instability stable and did not express programmed cell death ligand 1. CONCLUSIONS Our study for the first time identified TERT gene fusions as a main genetic alteration and a potential therapeutic target in metastatic LCTs. Topo1 and androgen receptor may guide decisions on chemotherapy and/or hormone therapy for selected individual patients.
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Affiliation(s)
- Bozo Kruslin
- Clinical Department of Pathology and Cytology “Ljudevit Jurak”, University Hospital Centre “Sestre milosrdnice”, Zagreb, Croatia,School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Zoran Gatalica
- Caris Life Sciences, Phoenix, Arizona,Department of Pathology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma
| | - Ondrej Hes
- Department of Pathology, Charles University, Medical Faculty and Charles University Hospital Plzen, Pilsen, Czech Republic
| | - Faruk Skenderi
- Department of Pathology, Clinical Center, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Markku Miettinen
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | | | | | | | | | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar; Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar.
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23
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Wang J, Xiu J, Baca Y, Battaglin F, Arai H, Kawanishi N, Soni S, Zhang W, Millstein J, Salhia B, Goldberg RM, Philip PA, Seeber A, Hwang JJ, Shields AF, Marshall JL, Astsaturov I, Craig Lockhart A, Gatalica Z, Michael Korn W, Lenz HJ. Large-scale analysis of KMT2 mutations defines a distinctive molecular subset with treatment implication in gastric cancer. Oncogene 2021; 40:4894-4905. [PMID: 34163031 DOI: 10.1038/s41388-021-01840-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/01/2021] [Accepted: 05/13/2021] [Indexed: 11/08/2022]
Abstract
Frequent mutations of genes in the histone-lysine N-methyltransferase 2 (KMT2) family members were identified in gastric cancers (GCs). Understanding how gene mutations of KMT2 family affect cancer progression and tumor immune microenvironment may provide new treatment strategies. A total of 1245 GCs were analyzed using next-generation sequencing, whole transcriptome sequencing, immunohistochemistry (Caris Life Sciences, Phoenix, AZ). The overall mutation rate of genes in the KMT2 family was 10.6%. Compared to KMT2-wild-type GCs, genes involved in epigenetic modification, receptor tyrosine kinases/MAPK/PI3K, and DNA damage repair (DDR) pathways had higher mutation rates in KMT2-mutant GCs (p < 0.05). Significantly higher rates of high tumor mutational burden, microsatellite instability-high/mismatch-repair deficiency (dMMR), and PD-L1 positivity were observed in KMT2-mutant GCs (p < 0.01), compared to KMT2-wild-type GCs. The association between PD-L1 positivity and KMT2 mutations remained significant in the proficient-MMR and microsatellite stable subgroup. Based on transcriptome data from the TCGA, cell cycle, metabolism, and interferon-α/β response pathways were significantly upregulated in KMT2-mutant GCs than in KMT2-wild-type GCs. Patients with KMT2 mutation treated with immune checkpoint inhibitors had longer median overall survival compared to KMT2-wild-type patients with metastatic solid tumors (35 vs. 16 months, HR = 0.73, 95% CI: 0.62-0.87, p = 0.0003). In conclusion, this is the largest study to investigate the distinct molecular features between KMT2-mutant and KMT2-wild-type GCs to date. Our data indicate that GC patients with KMT2 mutations may benefit from ICIs and drugs targeting DDR, MAPK/PI3K, metabolism, and cell cycle pathways.
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Affiliation(s)
- Jingyuan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hiroyuki Arai
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Natsuko Kawanishi
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joshua Millstein
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Bodour Salhia
- Department of Translational Genomics, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Philip A Philip
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Andreas Seeber
- Department of Hematology and Oncology, Innsbruck Medical University, Innsbruck, Austria
| | - Jimmy J Hwang
- Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | - Anthony F Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - John L Marshall
- Ruesch Center for The Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | | | - A Craig Lockhart
- University of Miami/Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | | | | | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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24
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Dardis C, Donner D, Sanai N, Xiu J, Mittal S, Michelhaugh SK, Pandey M, Kesari S, Heimberger AB, Gatalica Z, Korn MW, Sumrall AL, Phuphanich S. Gliosarcoma vs. glioblastoma: a retrospective case series using molecular profiling. BMC Neurol 2021; 21:231. [PMID: 34162346 PMCID: PMC8220715 DOI: 10.1186/s12883-021-02233-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/11/2021] [Indexed: 12/20/2022] Open
Abstract
Background Gliosarcoma (GS) refers to the presence of mesenchymal differentiation (as seen using light microscopy) in the setting of glioblastoma (GB, an astrocytoma, WHO Grade 4). Although the same approach to treatment is typically adopted for GS and GB, there remains some debate as to whether GS should be considered a discrete pathological entity. Differences between these tumors have not been clearly established at the molecular level. Methods Patients with GS (n=48) or GB (n=1229) underwent molecular profiling (MP) with a pan-cancer panel of tests as part of their clinical care. The methods employed included next-generation sequencing (NGS) of DNA and RNA, copy number variation (CNV) of DNA and immunohistochemistry (IHC). The MP comprised 1153 tests in total, although results for each test were not available for every tumor profiled. We analyzed this data retrospectively in order to determine if our results were in keeping with what is known about the pathogenesis of GS by contrast with GB. We also sought novel associations between the MP and GS vs. GB which might improve our understanding of pathogenesis of GS. Results Potentially meaningful associations (p<0.1, Fisher’s exact test (FET)) were found for 14 of these tests in GS vs. GB. A novel finding was higher levels of proteins mediating immuno-evasion (PD-1, PD-L1) in GS. All of the differences we observed have been associated with epithelial-to-mesenchymal transition (EMT) in other tumor types. Many of the changes we saw in GS are novel in the setting of glial tumors, including copy number amplification in LYL1 and mutations in PTPN11. Conclusions GS shows certain characteristics of EMT, by contrast with GB. Treatments targeting immuno-evasion may be of greater therapeutic value in GS relative to GB. Supplementary Information The online version contains supplementary material available at (10.1186/s12883-021-02233-5).
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Affiliation(s)
- Christopher Dardis
- Department of Neurology, Barrow Neurological Institute, Phoenix, AZ, USA.
| | - David Donner
- School of Medicine, Creighton University, Phoenix, AZ, USA
| | - Nader Sanai
- Barrow Brain Tumor Research Center, Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Joanne Xiu
- Precision Oncology Alliance, Caris Life Sciences, Phoenix, AZ, USA
| | - Sandeep Mittal
- Fralin Biomedical Research Institute, Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Sharon K Michelhaugh
- Fralin Biomedical Research Institute, Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Manjari Pandey
- Department of Medical Oncology, West Cancer Center, University of Tennessee Health Science Center, Germantown, TN, USA
| | - Santosh Kesari
- Pacific Neuroscience Institute and Department of Translational Neurosciences and Neurotherapeutics, John Wayne Cancer Institute, Santa Monica, CA, USA
| | - Amy B Heimberger
- Simpson Querry Biomedical Research Center, Department of Neurosurgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Zoran Gatalica
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael W Korn
- Precision Oncology Alliance, Caris Life Sciences, Phoenix, AZ, USA
| | - Ashley L Sumrall
- Department of Medical Oncology, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Surasak Phuphanich
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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25
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Vranic S, Gatalica Z. Trop-2 protein as a therapeutic target: A focused review on Trop-2-based antibody-drug conjugates and their predictive biomarkers. Bosn J Basic Med Sci 2021; 22:14-21. [PMID: 34181512 PMCID: PMC8860310 DOI: 10.17305/bjbms.2021.6100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Antibody-drug conjugates represent a new class of highly potent antineoplastic drugs built by attaching a small molecule of an anticancer drug (payload) or another therapeutic agent to an antibody recognizing an epitope on the targeted cells. Trophoblast cell-surface antigen-2 (Trop-2) was originally described in trophoblasts and fetal tissues, but subsequently its overexpression has been demonstrated in various solid malignancies. Sacituzumab govitecan (SG), a conjugate of anti-Trop-2 antibody and SN-38 payload (an active metabolite of irinotecan), is the first in the class that has been clinically validated and approved by the Food and Drug Administration for the treatment of metastatic triple-negative breast (2020) and urothelial carcinomas (2021). In the current review, we summarize and critically appraise the most recent advances with regard to SG, emphasizing the predictive biomarker analysis.
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Affiliation(s)
- Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar; Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
| | - Zoran Gatalica
- Department of Pathology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, United States
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26
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Vranic S, Gatalica Z. The Role of Pathology in the Era of Personalized (Precision) Medicine: A Brief Review. Acta Med Acad 2021; 50:47-57. [PMID: 34075763 DOI: 10.5644/ama2006-124.325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 11/09/2022] Open
Abstract
This review provides a brief overview of the state-of-the-art molecular pathology approaches emphasizing the increasingly important pathology role in clinical precision cancer medicine. Recent advances in molecular biology and genetics have tremendously affected the practice of anatomic pathology, gradually transforming it from a morphology-based into a molecularbased discipline. Molecular diagnostics has a long tradition in pathology, especially in clinical pathology. The improvement of methodology for genomic testing in recent years has made it one of the cornerstones of precision cancer medicine. The decisions related to cancer treatments are no longer solely based on the histopathological diagnosis. Various genomic analyses of human cancers are being incorporated into diagnostic and decision-making algorithms. CONCLUSION: The pathologists continue to play an essential role in developing and implementing molecular and genomic tests in practice and communicate the results and their relevance with clinicians. Such activities are of utmost importance for successfully translating scientific advancements into a benefit to patients ("next-generation pathologists").
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Affiliation(s)
- Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar; Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar. ORCID: http://orcid.org/0000-0001-9743-7265. ,
| | - Zoran Gatalica
- Department of Pathology, Oklahoma University Health Sciences Center, Oklahoma City, OK, United States
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27
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Cimic A, Vranic S, Arguello D, Contreras E, Gatalica Z, Swensen J. Molecular Profiling Reveals Limited Targetable Biomarkers in Neuroendocrine Carcinoma of the Cervix. Appl Immunohistochem Mol Morphol 2021; 29:299-304. [PMID: 33208671 PMCID: PMC8132903 DOI: 10.1097/pai.0000000000000884] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Neuroendocrine carcinoma of the cervix (NEC) is a rare and highly aggressive cervical malignancy. Given that no targeted therapy has been approved specifically to NEC, we investigated the presence of novel, potentially targetable biomarkers in a large cohort of NEC. Sixty-two NEC were molecularly profiled for biomarkers of targeted therapies including antibody-drug conjugates [delta-like canonical notch ligand 3 (DLL3), a trophoblast cell surface antigen 2 (TROP-2), and folate receptor 1 (FOLR1)], NTRK1-3 gene fusions, and immune checkpoint inhibitors [programmed death-ligand 1 (PD-L1), tumor mutational burden, and microsatellite instability] using immunohistochemistry and DNA/RNA next-generation sequencing assays. A cohort of squamous cell carcinomas of the cervix (n=599) was used for comparison for immune-oncology biomarkers. DLL3 expression was observed in 81% of the cases. DLL3 expression was inversely correlated with commonly observed pathogenic mutations in PIK3CA (17%) (P=0.018) and PTEN (10%) (P=0.006). Other more frequently seen pathogenic mutations (TP53 17%, KRAS 11%, and CTNNB1 5%) were not associated with DLL3 expression. TROP-2 expression was detected in only 1 case and no case expressed FOLR1. Although NTRK protein expression was observed in 21% of the cases, none of these had an NTRK gene fusion. PD-L1 expression (10%) and high tumor mutational burden (3%) were significantly less frequent in NEC compared with the squamous cell carcinoma cohort (79% and 11%, respectively). None of the NEC exhibited high microsatellite instability status. Despite frequent DLL3 expression in NEC, a potential therapeutic benefit of DLL3-targeted drugs remains uncertain given the recent failure of the Rova-T therapeutic trial in small cell lung carcinomas. Small cohorts of NEC enriched in PIK3CA/PTEN/AKT and programmed cell death protein 1/PD-L1 alterations indicate therapeutic roles for their respective inhibitors.
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Affiliation(s)
- Adela Cimic
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | | | | | - Zoran Gatalica
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
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28
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Prieto-Granada C, Morlote D, Pavlidakey P, Rodriguez-Waitkus P, Ramirez C, Florento E, Swensen J, Gatalica Z, Stevens TM. Poroid adnexal skin tumors with YAP1 fusions exhibit similar histopathologic features: A series of six YAP1-rearranged adnexal skin tumors. J Cutan Pathol 2021; 48:1139-1149. [PMID: 33704800 DOI: 10.1111/cup.14008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Adnexal skin tumors are diagnostically challenging with few known molecular signatures. Recently, however, YAP1-MAML2 and YAP1-NUTM1 fusions were identified in poroid adnexal skin tumors. METHODS Herein, we subjected eight poroid adnexal skin tumors (three poromas and five porocarcinomas) to fusion gene analysis by whole transcriptome sequencing and next-generation DNA sequencing analysis. RESULTS YAP1 fusions were identified in six cases. YAP1-NUTM1 fusions were identified in two poromas and three porocarcinomas. A single case of porocarcinoma harbored a YAP1-MAML2 fusion. Two cases were negative for gene fusion. All cases that harbored YAP1-NUTM1 fusions showed nuclear protein in testis (NUT) expression by immunohistochemistry, with NUT being negative in the YAP1-MAML2-positive case. In this case series, we provide a detailed histopathologic description of six YAP1-fused poroid skin tumors, which we show harbor reproducible histopathologic features, to include broad, bulbous tumor tongues with admixtures of basaloid, poroid cells punctuated by squamatized cuticles and ductules, with uniform tumor nuclei featuring frequent grooves and pseudonuclear inclusions. CONCLUSIONS Awareness of the characteristic histopathologic features of YAP1-fused poroid adnexal skin tumor is a step toward a more reproducible classification of adnexal skin tumors as well as a step toward targeted therapy for metastatic and/or unresectable examples of this poroid group of neoplasms.
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Affiliation(s)
- Carlos Prieto-Granada
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Diana Morlote
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Peter Pavlidakey
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Paul Rodriguez-Waitkus
- Department of Dermatology and Cutaneous Surgery, University of South Florida Morsani College of Medicine, Tampa, Florida, USA
| | | | | | | | - Zoran Gatalica
- The Oklahoma University Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Todd M Stevens
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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29
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Vranić S, Bešlija S, Gatalica Z. Targeting HER2 expression in cancer: New drugs and new indications. Bosn J Basic Med Sci 2021; 21:1-4. [PMID: 32530388 PMCID: PMC7861626 DOI: 10.17305/bjbms.2020.4908] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 06/07/2020] [Indexed: 12/13/2022] Open
Abstract
Functional activation of human epidermal growth factor receptor 2 (HER2) has been shown to strongly promote carcinogenesis, leading to the investigation of HER2-directed agents in cancers with HER2 genomic alterations. This has been best documented in the context of HER2 gene amplification in breast and gastric/gastroesophageal junction carcinomas for which several HER2-directed agents are available and have become a part of standard treatment regimens. Somatic HER2 gene mutations have been recently described at low frequency in a variety of human cancers and have emerged as a novel predictive biomarker for HER2-directed therapies. Preclinical data also indicate that activating HER2 mutations are potent oncogenic drivers in a manner that is analogous to HER2 amplification. HER2 mutations may clinically confer sensitivity to HER2-directed agents as recently shown in a phase II clinical trial with antibody-drug conjugate against HER2 trastuzumab deruxtecan in patients with non-squamous non-small cell lung carcinoma.
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Affiliation(s)
- Semir Vranić
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Semir Bešlija
- Department of Oncology, Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Zoran Gatalica
- Creighton University School of Medicine, Phoenix, Arizona, United States and Oklahoma University College of Medicine, Oklahoma City, Oklahoma, United States
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30
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Naffar-Abu Amara S, Kuiken HJ, Selfors LM, Butler T, Leung ML, Leung CT, Kuhn EP, Kolarova T, Hage C, Ganesh K, Panayiotou R, Foster R, Rueda BR, Aktipis A, Spellman P, Ince TA, Xiu J, Oberley M, Gatalica Z, Navin N, Mills GB, Bronson RT, Brugge JS. Transient commensal clonal interactions can drive tumor metastasis. Nat Commun 2020; 11:5799. [PMID: 33199705 PMCID: PMC7669858 DOI: 10.1038/s41467-020-19584-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022] Open
Abstract
The extent and importance of functional heterogeneity and crosstalk between tumor cells is poorly understood. Here, we describe the generation of clonal populations from a patient-derived ovarian clear cell carcinoma model which forms malignant ascites and solid peritoneal tumors upon intraperitoneal transplantation in mice. The clonal populations are engineered with secreted Gaussia luciferase to monitor tumor growth dynamics and tagged with a unique DNA barcode to track their fate in multiclonal mixtures during tumor progression. Only one clone, CL31, grows robustly, generating exclusively malignant ascites. However, multiclonal mixtures form large solid peritoneal metastases, populated almost entirely by CL31, suggesting that transient cooperative interclonal interactions are sufficient to promote metastasis of CL31. CL31 uniquely harbors ERBB2 amplification, and its acquired metastatic activity in clonal mixtures is dependent on transient exposure to amphiregulin, which is exclusively secreted by non-tumorigenic clones. Amphiregulin enhances CL31 mesothelial clearance, a prerequisite for metastasis. These findings demonstrate that transient, ostensibly innocuous tumor subpopulations can promote metastases via “hit-and-run” commensal interactions. Cooperative interactions among tumor cells may have important implications for metastasis. Here, the authors examined the spatio-temporal nature of interactions among clonal populations of ovarian carcinoma cells and found that transient interactions cells can promote metastases via commensal interactions.
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Affiliation(s)
| | - Hendrik J Kuiken
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Laura M Selfors
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Timothy Butler
- Department of Molecular and Medical Genetics, Oregon Health & Science University Portland, Portland, OR, 97239-3098, USA.,Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Marco L Leung
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Center for Applied Genomics, Children's Hospital of Philadelphia, Pennsylvania, PA, 19104, USA
| | - Cheuk T Leung
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Pharmacology, Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Elaine P Kuhn
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03766, USA
| | - Teodora Kolarova
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, 98195, USA
| | - Carina Hage
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Roche Innovation Center Munich, Roche Pharmaceutical Research and Early Development, Nonnenwald 2, 82377, Penzberg, Germany
| | - Kripa Ganesh
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,The Biochemistry, Structural, Developmental, Cell and Molecular Biology Allied PhD Program, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Richard Panayiotou
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Rosemary Foster
- Vincent Center for Reproductive Biology and Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Bo R Rueda
- Vincent Center for Reproductive Biology and Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Athena Aktipis
- Arizona Cancer Evolution Center and Department of Psychology, Arizona State University, Tempe, AZ, 85281, USA
| | - Paul Spellman
- Department of Molecular and Medical Genetics, Oregon Health & Science University Portland, Portland, OR, 97239-3098, USA
| | - Tan A Ince
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,New York Presbyterian-Brooklyn Methodist Hospital, Brooklyn, NY, 11215, USA
| | - Joanne Xiu
- Caris Life Sciences, Phoenix, AZ, 85040, USA
| | | | - Zoran Gatalica
- Caris Life Sciences, Phoenix, AZ, 85040, USA.,Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Nicholas Navin
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Gordon B Mills
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University Knight Cancer Institute, Portland, OR, 97239-3098, USA
| | - Rodrick T Bronson
- Rodent Histopathology Core, Harvard Medical School, Boston, MA, 02115, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
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Saul M, Poorman K, Tae H, Vanderwalde A, Stafford P, Spetzler D, Korn WM, Gatalica Z, Swensen J. Population bias in somatic measurement of microsatellite instability status. Cancer Med 2020; 9:6452-6460. [PMID: 32644297 PMCID: PMC7476819 DOI: 10.1002/cam4.3294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/23/2022] Open
Abstract
Microsatellite instability (MSI) is a key secondary effect of a defective DNA mismatch repair mechanism resulting in incorrectly replicated microsatellites in many malignant tumors. Historically, MSI detection has been performed by fragment analysis (FA) on a panel of representative genomic markers. More recently, using next-generation sequencing (NGS) to analyze thousands of microsatellites has been shown to improve the robustness and sensitivity of MSI detection. However, NGS-based MSI tests can be prone to population biases if NGS results are aligned to a reference genome instead of patient-matched normal tissue. We observed an increased rate of false positives in patients of African ancestry with an NGS-based diagnostic for MSI status utilizing 7317 microsatellite loci. We then minimized this bias by training a modified calling model that utilized 2011 microsatellite loci. With these adjustments 100% (95% CI: 89.1% to 100%) of African ancestry patients in an independent validation test were called correctly using the updated model. This poses not only a significant technical improvement but also has an important clinical impact on directing immune checkpoint inhibitor therapy.
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Affiliation(s)
| | | | | | - Ari Vanderwalde
- The University of Tennessee Health Science Center and West Cancer CenterMemphisTNUSA
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Khoury K, Tan AR, Elliott A, Xiu J, Gatalica Z, Heeke AL, Isaacs C, Pohlmann PR, Schwartzberg LS, Simon M, Korn WM, Swain SM, Lynce F. Prevalence of Phosphatidylinositol-3-Kinase (PI3K) Pathway Alterations and Co-alteration of Other Molecular Markers in Breast Cancer. Front Oncol 2020; 10:1475. [PMID: 32983983 PMCID: PMC7489343 DOI: 10.3389/fonc.2020.01475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/10/2020] [Indexed: 01/06/2023] Open
Abstract
Background: PI3K/AKT signaling pathway is activated in breast cancer and associated with cell survival. We explored the prevalence of PI3K pathway alterations and co-expression with other markers in breast cancer subtypes. Methods: Samples of non-matched primary and metastatic breast cancer submitted to a CLIA-certified genomics laboratory were molecularly profiled to identify pathogenic or presumed pathogenic mutations in the PIK3CA-AKT1-PTEN pathway using next generation sequencing. Cases with loss of PTEN by IHC were also included. The frequency of co-alterations was examined, including DNA damage response pathways and markers of response to immuno-oncology agents. Results: Of 4,895 tumors profiled, 3,558 (72.7%) had at least one alteration in the PIK3CA-AKT1-PTEN pathway: 1,472 (30.1%) harbored a PIK3CA mutation, 174 (3.6%) an AKT1 mutation, 2,682 (54.8%) had PTEN alterations (PTEN mutation in 7.0% and/or PTEN loss by IHC in 51.4% of cases), 81 (1.7%) harbored a PIK3R1 mutation, and 4 (0.08%) a PIK3R2 mutation. Most of the cohort consisted of metastatic sites (n = 2974, 60.8%), with PIK3CA mutation frequency increased in metastatic (32.1%) compared to primary sites (26.9%), p < 0.001. Other PIK3CA mutations were identified in 388 (7.9%) specimens, classified as "off-label," as they were not included in the FDA-approved companion test for PIK3CA mutations. Notable co-alterations included increased PD-L1 expression and high tumor mutational burden in PIK3CA-AKT1-PTEN mutated cohorts. Novel concurrent mutations were identified including CDH1 mutations. Conclusions: Findings from this cohort support further exploration of the clinical benefit of PI3K inhibitors for "off-label" PIK3CA mutations and combination strategies with potential clinical benefit for patients with breast cancer.
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Affiliation(s)
- Katia Khoury
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC, United States
| | | | | | - Joanne Xiu
- Caris Life Sciences, Phoenix, AZ, United States
| | - Zoran Gatalica
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Arielle L. Heeke
- Levine Cancer Institute, Charlotte, NC, United States
- Caris Life Sciences, Phoenix, AZ, United States
| | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC, United States
| | - Paula R. Pohlmann
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC, United States
| | | | - Michael Simon
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
| | | | - Sandra M. Swain
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC, United States
| | - Filipa Lynce
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC, United States
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Elliott A, Stafford P, Zhang J, Zhang Q, Swensen J, Martin D, Xiu J, Gatalica Z, Vaena D, Heath E, Korn WM. Abstract 3639: Fusion-associated neoantigen burden and predicted immunogenicity of CDK12 biallelic loss-of-function tumors vary substantially across cancer types. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Biallelic inactivation of CDK12 is associated with a distinct genomic signature of focal tandem duplications (FTDs). Gene fusions resulting from CDK12-associated FTDs increase neoantigen load, raising interest in CDK12 as a biomarker of response to immune checkpoint inhibitors (ICIs). Although FTDs have been detected at higher rates in CDK12-altered tumors compared to CDK12 WT tumors for multiple cancer types, fusion-associated neoantigen burden has only been evaluated in metastatic castration-resistant prostate cancer.
Methods: By retrospective review of molecular profiles, we identified tumors with CDK12 biallelic loss-of-function (LOF) in a primary cohort of over 9000 patient tumors, representing 39 cancer types, and assessed fusions detected by whole transcriptome sequencing for immune epitopes. Biomarker and fusion results for a second cohort of over 13,000 patient tumors were reviewed for validation of the initial findings.
Results: Tumors with CDK12 biallelic LOF (bLOF) (n=29) had significantly higher mean fusion rates (11.7 fusions/tumor) than CDK12 monoallelic LOF (mLOF) and WT tumors (4.1 and 2.6, respectively). Analysis of fusion topologies and breakpoints indicated a predominance of duplication events for CDK12 bLOF tumors and a bimodal distribution of breakpoint distances (modes at ~250-500 kb and ~1.0-2.5 Mb), consistent with prior reports. Fusion rates correlated with the rate of predicted neoantigens with high, intermediate, and low affinity for MHC class I. Fusion-associated neoantigen burden was significantly higher in CDK12 bLOF tumors (145.0 high affinity peptides/tumor) than mLOF (49.7) and WT (26.6) tumors. Among CDK12-altered tumors, fusion rates were significantly higher in prostate (16.4 fusions/tumor, n=11) and ovarian (19.7, n=6) than other cancer types (3.4 overall, n=12), potentially reflecting cancer type-specific roles for CDK12. Co-occurrence of mismatch repair deficiency (dMMR)/high microsatellite instability (MSI-High) with CDK12 bLOF (n=5), most often in colorectal tumors (n=4), correlated with a lower fusion rate (0.2 fusions/tumor); recurrent CDK12 frameshift mutations in these cases (G1461fs, T1463fs, and Q1291fs) coincide with poly-nucleotide tracts, suggesting CDK12 mutations are a secondary effect. In a separate cohort of over 13,000 patient tumors, additional CDK12 bLOF tumors (n=47) were identified, showing a similar distribution and association with high fusion rate (11.0 fusions/tumor).
Conclusion: Fusion rates and predicted neoantigen load varied significantly between CDK12 biallelic tumors across cancer types, highlighting the value of biomarkers with a quantitative immunogenic/phenotypic readout. We propose that fusion rates are linked to CDK12 alterations and may serve as useful biomarker to enhance our ability to identify responders of ICI therapy.
Citation Format: Andrew Elliott, Phillip Stafford, Jian Zhang, Qing Zhang, Jeff Swensen, Daniel Martin, Joanne Xiu, Zoran Gatalica, Daniel Vaena, Elisabeth Heath, W. Michael Korn. Fusion-associated neoantigen burden and predicted immunogenicity of CDK12 biallelic loss-of-function tumors vary substantially across cancer types [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3639.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Elisabeth Heath
- 3Wayne State University/Karmanos Cancer Institute, Detroit, MI
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Ginwala R, Macfarlane A, Liu D, Alpaugh RK, Xiu J, Gatalica Z, Korn WM, Van Allen EM, Campbell KS, Kutikov A, Plimack E, Abbosh PH. Abstract 6624: Immune correlates of response to neoadjuvant chemotherapy in muscle-invasive bladder cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Neoadjuvant chemotherapy followed by radical cystectomy is the optimal treatment for patients with muscle invasive bladder cancer. Between 30 and 40% of patients receiving neoadjuvant chemotherapy will have pathological complete response at the time of radical cystectomy. Presence of somatic mutations in DNA damage repair genes correlate with chemoresponse, likely stemming from a loss-of-function in the ability to repair DNA damage brought on by cytotoxic chemotherapy. However, many chemoresponders have WT DNA repair status. As such, there is a keen interest to identify additional mechanisms associated with chemoresponse.
Results: A higher tumor mutation/neoantigen burden is associated with response to immune checkpoint blockade, so we sought to investigate a correlation between mutation burden and chemoresponse. We found that responders had a higher neoantigen burden and higher signature of tumor infiltrating CD8+ T cells (TILs). We interrogated a database of tumors that underwent clinical tumor sequencing (NextGen SEQ, Caris Life Sciences; 592 genes; n=897) and PD-L1 staining (Combined Positive Score [CPS] using 22C3 antibody) and found that mutation burden was directly proportional to CPS. In addition, we found that CPS was positively associated with KRAS and TP53 mutation, whereas it was negatively associated with FGFR3 activating alterations, MDM2 amplification and GATA3 amplification after correction for multiple comparisons. There was an overall increase in the proportional representation of TIL-derived T cell receptors (TCR) repertoire in the periphery after chemotherapy independent of responder status. This implies that the presence of immune response even in patients without pathologic response. Additionally, TIL-derived TCRs were also found in perivesical lymph nodes in both responders and non-responders, however, there was a distinct profile of activation/exhaustion associated with either patient group. Responders showed a unique CD69+/PD1−(activated/non-exhausted) population amongst the nodal CD8+ T cells suggesting that this population is required to achieve pathologic complete response.
Conclusions: These results further our understanding of immune responses to chemotherapy in bladder cancer and may enable the development of chemo-immunotherapy regimens to improve response rates to neoadjuvant chemotherapy.
Citation Format: Rashida Ginwala, Alexander Macfarlane, IV, David Liu, R K. Alpaugh, Joanne Xiu, Zoran Gatalica, W M. Korn, Eliezer M. Van Allen, Kerry S. Campbell, Alexander Kutikov, Elizabeth Plimack, Philip H. Abbosh. Immune correlates of response to neoadjuvant chemotherapy in muscle-invasive bladder cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6624.
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Affiliation(s)
| | | | - David Liu
- 2Dana Farber Cancer Center, Boston, MA
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Skenderi F, Palazzo J, Swensen J, Feldman R, Contreras E, Florento E, Gatalica Z, Vranic S. Novel targetable biomarkers in clear cell carcinoma of the breast uncovered by molecular profiling: A study of nine cases. Breast J 2020; 26:1781-1783. [PMID: 32279409 PMCID: PMC7586831 DOI: 10.1111/tbj.13842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 03/27/2020] [Indexed: 12/22/2022]
Abstract
We profiled nine pure clear cell carcinomas of the breast using massively parallel DNA and RNA sequencing (NGS), in situ hybridization (ISH), and immunohistochemistry (IHC). All cases were primary mammary clear cell carcinomas that were diagnosed in female patients (mean age: 53.4 years; range: 31‐69 years). Based on our findings, we conclude that the majority of clear cell carcinomas are ER/PR positive and consequently amenable to anti‐ER treatment modalities. A subset of clear cell carcinomas also harbored alterations in PIK3CA/PTEN/AKT pathway, particularly PTEN, indicating a potential benefit of PI3K/Akt/mTOR inhibitors. The status of I‐O biomarkers in clear cell carcinomas indicates a limited therapeutic benefit of immune checkpoint inhibitors (against PD‐1/PD‐L1).
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Affiliation(s)
- Faruk Skenderi
- Department of Pathology, Clinical Center, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | | | | | | | | | | | - Zoran Gatalica
- Caris Life Sciences, Phoenix, AZ, USA.,Creighton University School of Medicine, Phoenix, AZ, USA
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar
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36
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Dawson NA, Zibelman M, Lindsay T, Feldman RA, Saul M, Gatalica Z, Korn WM, Heath EI. An Emerging Landscape for Canonical and Actionable Molecular Alterations in Primary and Metastatic Prostate Cancer. Mol Cancer Ther 2020; 19:1373-1382. [DOI: 10.1158/1535-7163.mct-19-0531] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/03/2019] [Accepted: 03/18/2020] [Indexed: 11/16/2022]
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Burgess EF, Steuerwald N, Symanowski JT, Livasy C, Farhangfar CJ, Gatalica Z, Arguello D, Zhu J, Grigg C, Clark PE, Raghavan D. Pathogenic variants in PTEN to predict for increased risk of relapse and death in patients with limited stage small cell bladder cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.6_suppl.526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
526 Background: Small cell bladder cancer (SCBC) is a rare histologic subtype with insufficient genomic characterization. Patients with limited stage (LS) SCBC have a poor prognosis, and no biomarker exists to optimize treatment selection. We sought to identify genomic aberrations in patients with LS-SCBC using a comprehensive next generation sequencing (NGS) platform. Mutations in the PTEN/AKT pathway are important in urothelial tumor biology but have an undefined role in SCBC. Methods: 23 LS-SCBC cases were identified. NGS was performed on diagnostic transurethral bladder tumor resection or cystectomy specimens containing SCBC. Detected variants were filtered by in silico algorithms predicting for a deleterious impact on protein function. Variant allele frequencies (VAF) greater than 2% were permitted in this analysis. Variants in the PTEN gene were assessed for association with relapse-free survival (RFS) and overall survival (OS) using Kaplan-Meier techniques and Cox proportional hazards models. Results: Median follow up for the cohort was 4.02 years. 14/23 (60.9%) patients have died. Six unique deleterious PTEN mutations were observed in 9/23 (39.1%) patients. p.W274C was the most common PTEN variant and was detected in 5 (21.7%) patients. Three variants were detected at > 10% VAF. All 9 patients with a deleterious PTEN variant died. The presence of deleterious PTEN variants [HR = 4.68 [(1.54, 14.27), p = 0.003]] predicted for inferior OS. In the 19 patients with known relapse history, 6/7 (85.7%) with and 3/12 (25%) without any deleterious PTEN mutation relapsed. The presence of deleterious PTEN variants [HR = 9.41 [(2.32, 38.23), p < 0.001]] also predicted for inferior RFS. Conclusions: Pathogenic variants in tumor suppressor PTEN were associated with inferior RFS and OS in this pilot cohort of patients with LS-SCBC, suggesting that disruption of PTEN function may be a critical genomic event underlying the progression of small cell bladder cancer. Our findings also support prior reports that pathogenic gene variants detected at low allele frequencies may be clinically important.
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Affiliation(s)
| | | | | | - Chad Livasy
- Levine Cancer Institute, Atrium Health, Charlotte, NC
| | | | | | | | - Jason Zhu
- Levine Cancer Institute, Atrium Health, Charlotte, NC
| | - Claud Grigg
- Levine Cancer Institute, Atrium Health, Charlotte, NC
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Ou A, Sumrall A, Phuphanich S, Spetzler D, Gatalica Z, Xiu J, Michelhaugh S, Brenner A, Pandey M, Kesari S, Korn WM, Mittal S, Westin J, Heimberger AB. Primary CNS lymphoma commonly expresses immune response biomarkers. Neurooncol Adv 2020; 2:vdaa018. [PMID: 32201861 PMCID: PMC7067145 DOI: 10.1093/noajnl/vdaa018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Primary central nervous system lymphoma (PCNSL) is rare and there is limited genomic and immunological information available. Incidental clinical and radiographic responses have been reported in PCNSL patients treated with immune checkpoint inhibitors. Materials and Methods To genetically characterize and ascertain if the majority of PCNSL patients may potentially benefit from immune checkpoint inhibitors, we profiled 48 subjects with PCNSL from 2013 to 2018 with (1) next-generation sequencing to detect mutations, gene amplifications, and microsatellite instability (MSI); (2) RNA sequencing to detect gene fusions; and (3) immunohistochemistry to ascertain PD-1 and PD-L1 expression. Tumor mutational burden (TMB) was calculated using somatic nonsynonymous missense mutations. Results High PD-L1 expression (>5% staining) was seen in 18 patients (37.5%), and intermediate expression (1-5% staining) was noted in 14 patients (29.2%). Sixteen patients (33.3%) lacked PD-L1 expression. PD-1 expression (>1 cell/high-power field) was seen in 12/14 tumors (85.7%), uncorrelated with PD-L1 expression. TMB of greater than or equal to 5 mutations per megabase (mt/Mb) occurred in 41/42 tumors, with 19% (n = 8) exhibiting high TMB (≥17 mt/Mb), 71.4% (n = 30) exhibiting intermediate TMB (7-16 mt/Mb), and 9.5% (n = 4) exhibiting low TMB (≤6 mt/Mb). No samples had MSI. Twenty-six genes showed mutations, most frequently in MYD88 (34/42, 81%), CD79B (23/42, 55%), and PIM1 (23/42, 55%). Among 7 cases tested with RNA sequencing, an ETV6-IGH fusion was found. Overall, 18/48 samples expressed high PD-L1 and 38/42 samples expressed intermediate to high TMB. Conclusions Based on TMB biomarker expression, over 90% of PCNSL patients may benefit from the use of immune checkpoint inhibitors.
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Affiliation(s)
- Alexander Ou
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | | | | | - Joanne Xiu
- Caris Life Sciences, Phoenix, Arizona, USA
| | - Sharon Michelhaugh
- Fralin Biomedical Research Institute, Virginia Tech Carilion School of Medicine and Carilion Clinic, Roanoke, Virginia, USA
| | - Andrew Brenner
- University of Texas at San Antonio, San Antonio, Texas, USA
| | - Manjari Pandey
- Department of Medical Oncology, West Cancer Center and Research Institute, Memphis, Tennessee, USA
| | - Santosh Kesari
- John Wayne Cancer Institute, Santa Monica, California, USA
| | - W Michael Korn
- Caris Life Sciences, Phoenix, Arizona, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Sandeep Mittal
- Fralin Biomedical Research Institute, Virginia Tech Carilion School of Medicine and Carilion Clinic, Roanoke, Virginia, USA
| | - Jason Westin
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amy B Heimberger
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Khoury K, Tan A, Elliott A, Xiu J, Gatalica Z, Heeke AL, Isaacs C, Pohlmann PR, Schwartzberg LS, Simon M, Korn MW, Swain SM, Lynce F. Abstract P4-09-04: Prevalence of phosphatidylinositol-3-kinase (PI3K) pathway alterations and co-alteration of other markers in breast cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p4-09-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: PI3K/AKT signaling pathway is often activated in breast cancer (BC), through mutations in PIK3CA or AKT1, and alterations in PTEN, thus promoting cell survival. PI3K and AKT inhibitors have been shown to have significant activity against tumor progression and to overcome resistance in BC. We aim to explore the prevalence of PI3K pathway alterations and co-expression with other markers in different BC subtypes. This approach could allow identification of novel drug combinations that have the potential to elicit synergistic growth inhibition and be further explored in the clinical trial setting.
Methods: Molecular profiles of 4895 female and male BC cases submitted to Caris Life Sciences were reviewed to identify pathogenic or presumed pathogenic mutations in PIK3CA, AKT1, PTEN, PIK3R1 and PIK3R2 using 592-gene next generation sequencing (NGS; average read depth 500 ×). Cases with loss of PTEN by IHC were also included. Co-mutation frequency with PIK3CA-AKT1-PTEN alterations were examined, including homologous recombination deficiency (HRD) genes and DNA damage response (DDR) pathways, markers of response to immune-oncology (IO) agents and RAS signaling pathway. Cases were classified in BC subtypes according to the ASCO-CAP guidelines.
Results: The median age was 58 (range: 17-90). Gender frequency and primary/ metastatic site frequency were similar across BC subtypes. 3558 (72.7%) cases had at least one alteration in the PIK3CA-AKT1-PTEN pathway: 1472 (30.1%) cases harbored a PIK3CA mutation, 174 (3.6%) harbored an AKT1 mutation, and 2682 (54.8%) had PTEN alterations (PTEN mutation in 344, 7.0% and/or PTEN loss by IHC in 2516, 51.4% of cases). The most common hotspot mutations in PIK3CA were in the kinase domain (H1047R in 567 cases, 38.5% of all PIK3CA alterations) and in the helical domain (E545K in 304 cases, 20.7% of all PIK3CA alterations). Uncommon activating PIK3CA mutations were seen in 8.4% of breast tumors. The single hotspot mutation, E17K, was the most common AKT1 mutation (n=164, 94.3% of all AKT1 mutations). 81 (1.7%) tumors harbored a PIK3R1 mutation, with 66 unique alterations identified (4 pathogenic, 55 presumed pathogenic), and 4 (0.08%) cases harbored a PIK3R2 mutation (G373R mutation). With respect to the different BC subtypes, PIK3CA was the most frequent alteration in HER2 positive BC (present in 96.2% of mutated cases). Within HER2 negative subtypes, PTEN was most frequently altered and PTEN mutation or PTEN loss by IHC was present in 79.3% of mutated cases. Triple negative breast cancer (TNBC) was the subtype with the lowest frequency of PIK3CA mutations (18.0% in TNBC vs. 37% in other subtypes). The frequency of selected co-mutations with PIK3CA-AKT1-PTEN alterations is illustrated in table 1. Notable co-alterations in this cohort include increased PD-L1 expression and high tumor mutational burden (TMB). There were no significant increases in the frequency of mutations in DDR pathway mutations (not shown) in the PIK3CA-AKT1-PTEN altered cohort.
Conclusions: We observed a high prevalence of expected hotspot mutations in PIK3CA and AKT1 across BC subtypes. There was a significant increase in PD-L1 expression in tumor cells, and high TMB in PIK3CA-AKT1-PTEN mutated cohorts. A similar association was seen with RAS signaling pathways. Further development of drugs that affect the PIK3CA-AKT1-PTEN pathway in all BC subtypes and combination with drugs that target the immune system may be of interest.
Table 1. Selected co-alterations based on statistical significancePathwayGene/ ProteinAll subtypes (%)HR+ HER2+ (%)HR- HER2+ (%)HR+HER2- (%)TNBC (%)MTWTMTWTMTWTMTWTMTWTHomologous recombinationBRCA13.02.71.00.60.00.80.8*1.8*6.16.0BRCA24.15.41.02.53.62.34.1*7.9*4.43.0PALB20.7*1.3*0.00.00.00.00.5*2.5*0.90.3Possible predictors of IO benefitPD-149.850.038.552.266.766.737.541.766.058.1PD-L1 (SP142)6.9*4.2*3.30.78.14.93.33.011.68.1(Tumor Cells)PD-L1 (SP142)29.226.650.018.825.027.312.916.742.140.4(Immune Cells)MSI0.70.60.00.01.20.80.80.40.71.2TMB-High (≥ 10 mut/Mb)22.9*18.8*36.0*17.2*29.825.921.2*16.6*23.621.3Chromatin remodelingARID1A12.4*18.6*19.423.87.118.917.121.55.89.6ARID20.70.80.01.90.00.70.80.60.60.9RAS-RAF-MEK-ERK HRAS0.7*0.1*0.00.00.00.00.20.11.40.3KRAS2.0*1.1*1.00.00.00.01.91.22.22.0NRAS0.20.00.00.00.00.00.20.00.30.0BRAF0.50.11.00.01.20.00.60.30.40.0OthersTP5360.9*53.1*66.360.885.586.738.4*25.6*84.786.4CDH110.3*6.1*9.1*2.5*4.82.215.1*9.6*4.9*2.3*NF16.2*2.1*9.5*0.8*2.73.65.8*1.8*6.7*2.8*RB15.5*2.6*2.21.33.63.03.9*1.7*7.85.0ERBB22.3*3.4*3.03.13.56.73.23.51.0*2.3*Notes: MT = at least 1 pathogenic mutation in PIK3CA, AKT1, or PTEN or PTEN loss by IHC. WT = no pathogenic mutations in PIK3CA, AKT1, and PTEN.*statistically significant difference between MT and WT
Citation Format: Katia Khoury, Antoinette Tan, Andrew Elliott, Joanne Xiu, Zoran Gatalica, Arielle L Heeke, Claudine Isaacs, Paula R Pohlmann, Lee S Schwartzberg, Michael Simon, Michael W Korn, Sandra M Swain, Filipa Lynce. Prevalence of phosphatidylinositol-3-kinase (PI3K) pathway alterations and co-alteration of other markers in breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-09-04.
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Affiliation(s)
- Katia Khoury
- 1Medstar Georgetown University Hospital, Washington, DC
| | | | | | | | | | | | | | | | | | | | | | | | - Filipa Lynce
- 1Medstar Georgetown University Hospital, Washington, DC
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Wang J, Xiu J, Baca Y, Goldberg RM, Philip PA, Seeber A, Battaglin F, Arai H, Soni S, Tokunaga R, Zhang W, Hwang JJ, Shields AF, Marshall J, Astsaturov IA, Lockhart AC, Gatalica Z, Korn WM, Lenz HJ. Molecular landscape of gastric cancer (GC) harboring mutations of histone methyltransferases. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.4_suppl.418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
418 Background: Alteration of histone modifications participating in transcription and genomic instability, has been recognized as an important role in tumorigenesis. Aberrant expression of histone-lysine N-methyltransferase 2 ( KMT2) family, which methylate histone H3 on lysine 4, is significantly correlated with poor survival in GC. Understanding how gene mutations of KMT2 family interact to affect cancer progression could lead to new treatment strategies. Methods: A total of 1,245 GC were analyzed using next-generation sequencing (NGS) and immunohistochemistry (IHC; Caris Life Sciences, Phoenix, AZ). Tumor mutational burden (TMB) was calculated based on somatic nonsynonymous mutations, and MSI status was evaluated by a combination of IHC, fragment analysis and NGS. PD-L1 status was analyzed by IHC (SP142). Gene fusions were detected by Archer (N = 59) or whole-transcriptome sequencing (N = 129). Results: The overall mutation rate of genes in KMT2 family was 10.6% ( KMT2A: 1.7 %, KMT2C: 4.7%, KMT2D: 7.1%). Overall, the mutation rates were significantly higher in KMT2-mutated (MT) GC than KMT2-wild type (WT) GC, except for TP53 (43% vs 63%, p < .0001). Interestingly, among the genes with significant higher mutation rates in KMT2-MT GC, 28% (21/76) of them were related to DNA damage repair (including BRCA1/ 2, RAD50) and 33% (25/76) of them were related to chromatin remodeling (including ARID1A/ 2, SMARCA4). Overexpression of HER2, amplifications of KRAS, CDK6 and HER2 were significant lower, while PCM1 and BCL3 amplifications were significant higher in KMT2-MT, compared to KMT2-WT GC ( p < .05). Significantly higher prevalence of TMB-high ( > 17mut/MB) (49% vs 3%), MSI-H (53% vs 2%), and PD-L1 overexpression (20% vs 7%) were present in KMT2-MT GC, compared to KMT2-WT GC ( p < .001). The rates of fusions involving ARHGAP26 (19% vs 3%, p < .01)and RELA (29% vs 0%, p < .0001) were significantly higher in KMT2-MT than those in KMT2-WT GC. Conclusions: This is the largest study to investigate the distinct genomic landscape between KMT2-MT and WT GC. Our data indicates that KMT2-MT GC patients could potentially benefit from agents targeting DNA damage repair and immunotherapy, which warrants further in-vitro and in-vivo investigation.
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Affiliation(s)
- Jingyuan Wang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | | | | | | | - Andreas Seeber
- Department of Internal Medicine V (Hematology and Oncology), Innsbruck, Austria
| | - Francesca Battaglin
- Division of Medical Oncology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA
| | | | | | - Ryuma Tokunaga
- Division of Medical Oncology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA
| | - Wu Zhang
- USC Keck School of Medicine, Los Angeles, CA
| | | | | | | | | | | | | | | | - Heinz-Josef Lenz
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
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Patel SP, Othus M, Chae YK, Giles FJ, Hansel DE, Singh PP, Fontaine A, Shah MH, Kasi A, Baghdadi TA, Matrana M, Gatalica Z, Korn WM, Hayward J, McLeod C, Chen HX, Sharon E, Mayerson E, Ryan CW, Plets M, Blanke CD, Kurzrock R. A Phase II Basket Trial of Dual Anti-CTLA-4 and Anti-PD-1 Blockade in Rare Tumors (DART SWOG 1609) in Patients with Nonpancreatic Neuroendocrine Tumors. Clin Cancer Res 2020; 26:2290-2296. [PMID: 31969335 DOI: 10.1158/1078-0432.ccr-19-3356] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/22/2019] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE Immune checkpoint blockade has improved outcomes across tumor types; little is known about the efficacy of these agents in rare tumors. We report the results of the (nonpancreatic) neuroendocrine neoplasm cohort of SWOG S1609 dual anti-CTLA-4 and anti-PD-1 blockade in rare tumors (DART). PATIENTS AND METHODS We performed a prospective, open-label, multicenter phase II clinical trial of ipilimumab plus nivolumab across multiple rare tumor cohorts, with the (nonpancreatic) neuroendocrine cohort reported here. Response assessment by grade was not prespecified. The primary endpoint was overall response rate [ORR; RECIST v1.1; complete response (CR) and partial response (PR)]; secondary endpoints included progression-free survival (PFS), overall survival (OS), stable disease >6 months, and toxicity. RESULTS Thirty-two eligible patients received therapy; 18 (56%) had high-grade disease. Most common primary sites were gastrointestinal (47%; N = 15) and lung (19%; N = 6). The overall ORR was 25% [95% confidence interval (CI) 13-64%; CR, 3%, N = 1; PR, 22%, N = 7]. Patients with high-grade neuroendocrine carcinoma had an ORR of 44% (8/18 patients) versus 0% in low/intermediate grade tumors (0/14 patients; P = 0.004). The 6-month PFS was 31% (95% CI, 19%-52%); median OS was 11 months (95% CI, 6-∞). The most common toxicities were hypothyroidism (31%), fatigue (28%), and nausea (28%), with alanine aminotransferase elevation (9%) as the most common grade 3/4 immune-related adverse event, and no grade 5 events. CONCLUSIONS Ipilimumab plus nivolumab demonstrated a 44% ORR in patients with nonpancreatic high-grade neuroendocrine carcinoma, with 0% ORR in low/intermediate grade disease.
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Affiliation(s)
- Sandip P Patel
- University of California at San Diego Moores Cancer Center, La Jolla, California.
| | - Megan Othus
- SWOG Statistical Center, Seattle, Washington
| | | | - Francis J Giles
- Northwestern University, Chicago, Illinois.,Developmental Therapeutics Consortium, Chicago, Illinois
| | - Donna E Hansel
- University of California at San Diego, La Jolla, California
| | | | - Annette Fontaine
- New Mexico MU-NCORP/New Mexico Cancer Center, Albuquerque, New Mexico
| | - Manisha H Shah
- Ohio State University Comprehensive Cancer Center (Alliance for Clinical Trials in Oncology), Columbus, Ohio
| | - Anup Kasi
- University of Kansas Medical Center, Westwood, Kansas
| | - Tareq Al Baghdadi
- Michigan CRC NCORP/IHA Hematology Oncology Consultants, Ypsilanti, Michigan
| | - Marc Matrana
- Ochsner Clinic Foundation (ECOG-ACRIN), New Orleans, Louisiana
| | | | - W Michael Korn
- Caris Life Sciences, Tempe, Arizona.,University of California San Francisco, San Francisco, California
| | | | | | - Helen X Chen
- National Cancer Institute, Investigational Drug Branch, Cancer Therapy Evaluation Program, Bethesda, Maryland
| | - Elad Sharon
- National Cancer Institute, Investigational Drug Branch, Cancer Therapy Evaluation Program, Bethesda, Maryland
| | | | | | | | - Charles D Blanke
- SWOG Group Chair's Office, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon
| | - Razelle Kurzrock
- University of California at San Diego Moores Cancer Center, La Jolla, California.
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Gatalica Z, Vranic S, Krušlin B, Poorman K, Stafford P, Kacerovska D, Senarathne W, Florento E, Contreras E, Leary A, Choi A, In GK. Comparison of the biomarkers for targeted therapies in primary extra-mammary and mammary Paget's disease. Cancer Med 2020; 9:1441-1450. [PMID: 31899853 PMCID: PMC7013075 DOI: 10.1002/cam4.2820] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 12/14/2022] Open
Abstract
Background Primary Extra‐mammary Paget's disease (EMPD) is a very rare cutaneous adenocarcinoma affecting anogenital or axillary regions. It is characterized by a prolonged course with recurrences and eventually distant metastatic spread for which no specific therapy is known. Methods Eighteen EMPD (13 vulvar and five scrotal) and ten mammary Paget's disease (MPD) cases were comprehensively profiled for gene mutations, fusions and copy number alterations, and for therapy‐relevant protein biomarkers). Results Mutations in TP53 and PIK3CA were the most frequent in both cohorts: 7/15 and 5/15 in EMPD; 1/6 and 4/7 in MPD HER2 gene amplification was detected in 4/18 EMPD (3 vulvar and 1 scrotal case) in contrast to MPD where it was detected in the majority (7/8) of cases. TOP2A gene amplification was seen in 2/12 EMPD and 1/6 MPD, respectively. Similarly, no difference in estrogen receptor expression was seen between the EMPD (4/15) and MPD (3/10). Androgen receptor was also expressed in the majority of both cohorts (12/16 EMPD) and (7/8 MPD).Here ARv7 splice variant was detected in 1/7 EMPD and 1/4 MPD cases, respectively. PD‐L1 expression on immune cells was exclusively observed in three vulvar EMPD. In contrast to MPD, six EMPDs harbored a “high” tumor mutation burden (≥10 mutations/Mb). All tested cases from both cohorts were MSI stable. Conclusions EMPD shares some targetable biomarkers with its mammary counterpart (steroid receptors, PIK3CA signaling pathways, TOP2A amplification). HER2 positivity is notably lower in EMPD while biomarkers to immune checkpoint inhibitors (high TMB and PD‐L1) were observed in some EMPD. Given that no consistent molecular alteration characterizes EMPD, comprehensive theranostic profiling is required to identify individual patients with targetable molecular alterations.
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Affiliation(s)
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Božo Krušlin
- Ljudevit Jurak Department of Pathology and Cytology, Clinical Hospital Center Sestre Milosrdnice, Zagreb, Croatia.,School of Medicine, University of Zagreb, Zagreb, Croatia
| | | | | | - Denisa Kacerovska
- Medical Faculty in Pilsen, Sikl's Department of Pathology, Charles University in Prague, Pilsen, Czech Republic.,Bioptical Laboratory, Pilsen, Czech Republic
| | | | | | | | | | - April Choi
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Gino K In
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
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Vranic S, Cyprian FS, Gatalica Z, Palazzo J. PD-L1 status in breast cancer: Current view and perspectives. Semin Cancer Biol 2019; 72:146-154. [PMID: 31883913 DOI: 10.1016/j.semcancer.2019.12.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/21/2022]
Abstract
Breast cancer was traditionally not considered a particularly immunogenic tumor. However, recent developments have shown that some aggressive triple-negative breast cancers are immunogenic, exhibit a resistance to chemotherapy and have a poor prognosis. These cancers have been shown to express molecules identified as targets for immunotherapy. Despite the advances, the challenges are many, and include identifying the patients that may benefit from immunotherapy. The best methods to analyze these samples and to evaluate immunogenicity are also major challenges. Therefore, the most accurate and reliable assessment of immune cells as potential targets is one of the most important aims in the current research in breast immunotherapy. In the present review, we briefly discuss the mechanisms of the regulation of checkpoint inhibitors (PD-1/PD-L1) in breast cancer and explore the predictive aspects in the PD-L1 testing.
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Affiliation(s)
- Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar
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Gatalica Z, Stafford P, Contreras E, Swensen J, Feldman R. Abstract A035: Therapeutic targets in androgen deprivation therapy-resistant prostatic carcinoma. Mol Cancer Ther 2019. [DOI: 10.1158/1535-7163.targ-19-a035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Androgen deprivation therapy (ADT) for patients with metastatic prostate carcinoma eventually leads to development of castration-resistant prostate cancer (CRPC) with limited therapeutic options. ADT is characterized by the presence of ARv7 splice variant and several resistance mutations in AR gene. We explored potential therapeutic targets in CRPC. Methods: Biopsy samples from 80 patients with prostate carcinomas (39 primary and 41 metastatic samples) were analyzed for mutations using 592 gene NGS panel and a whole transcriptome sequencing (WTS). Tumor mutational burden (TMB) and microsatellite instability (MSI) were calculated from the NGS data. Protein expression of the full length AR and ARv7 variant, as well as mismatch repair (MMR) enzymes (MLH1, MSH2, MSH6 and PMS2) and tumor cells’ (TC) expression of PD-L1 were analyzed using IHC methods. Tests results were correlated with clinical history of androgen deprivation (ADT-Hx). Chi-square analysis was used to compare subgroups. Results: Clinical histories were available for 63 patients (26 with and 37 without ADT-Hx). The median age in this cohort was 67 (range: 45-88). Overall, ARv7 was detected in 20/80 cases. Two out of 15 cases had ARv7 present in biopsies without previous ADT-Hx (one primary prostate and one metastatic bone biopsy). Five patients with ADT-Hx harbored AR gene mutations (ARmut) in exon 8 which are known to confer ADT resistance were detected in the cohort (6% overall; 1 co-occurred with ARv7). Microsatellite instability (MSI-H) was detected in 6 cases (7.5% overall); of note, AR resistance mutation (ARv7 or ARmut) occurred at significantly higher rate in patients with MSI-H/MMRd compared to MSS/MMRp (83%; 5/6 vs. 26%; 19/72, p=0.001). Average total mutational burden (TMB) in microsatellite stable (MSS) cases was low (6/Mb); high TMB (>80th percentile for the prostate carcinoma cohort) was detected in one MSS CRPC. PD-L1 TC-expression was detected in 1 metastatic (ARv7 negative) case. Pathogenic gene fusions were detected in 33 cases, most commonly TMPRSS2:ERG (26/79; 7/17 in ARv7). The most commonly mutated gene was TP53 (30 cases; 9/17 in ARv7). BRCA 1/2 mutations were found in 7 cases (3 in ARv7) and CDK12 mutations in 4 (2 in ARv7) cases. Other DNA repair genes mutations (n=1, each) includied MUTYH, PRKDC, ATM, BRIP1, ERCC2, FANCA and FANCD2. Gene expression analysis identified numerous differently expressed genes between ARv7+/ADT+, ARv7-/ADT+ and ARv7-/ADT- tumor groups, requiring further analysis. Conclusion: Upon failure of ADT, tumor samples from men with CRPC (biopsy positive for ARv7 or ARmut) demonstrate molecular alterations that are potential targets for treatment. Immune-oncology agents in patients harboring evidence of genomic instability (e.g. high MSI or TMB) and PARP inhibitors in patients with alterations in DNA repair pathways (e.g. BRCA1/2, ATM, PRKDC, CDK12, etc.) should be investigated further. Comprehensive tumor profiling is necessary to detect targetable pathways.
Citation Format: Zoran Gatalica, Phillip Stafford, Elma Contreras, Jeff Swensen, Rebecca Feldman. Therapeutic targets in androgen deprivation therapy-resistant prostatic carcinoma [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A035. doi:10.1158/1535-7163.TARG-19-A035
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Ziegler C, Slemons I, DeSilva C, Witkowski B, Mir A, Anandakrishnan S, Farmer A, Contreras E, Richardson D, Vranic S, Gatalica Z, Derkach DN. Abstract B094: Novel method for patient stratification in breast carcinoma based upon spatial analysis of tumor microenvironment. Mol Cancer Ther 2019. [DOI: 10.1158/1535-7163.targ-19-b094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Breast cancer consists of several intrinsic molecular subtypes, providing the basis for clinical treatment decisions. Lately, it is becoming increasingly recognized that factors other than the intrinsic cancer characteristics, such as immune components’ activity in the tumor microenvironment, have important effects on treatment choices and efficacy. bioSyntagma has developed a method, the Molecular Fingerprint (mPrint®), that enables multiplexed analysis of spatially defined regions in formalin-fixed, paraffin-embedded (FFPE) tumor samples allowing for analysis of the gene signatures unique to the tumor microenvironment. This method was applied to molecularly defined sets of breast cancers and used to evaluate four different tumor regions of interest (ROIs): 1) viable carcinoma proper (>90% cancer cells), 2) fibrotic tumor center (sparse cellularity), 3) interface between viable tumor and inflammatory component (tumor and inflammatory microenvironment) and 4) tissue away from the tumor (normal breast tissue). This was compared to the whole tissue scrapes from each patient block. Each ROI and tissue scrape was analyzed by high throughput qPCR for a panel of 248 genes using SmartChip technology (Takara Bio, USA). Sequential tissue slices from each patient were also analyzed using immunohistochemistry (IHC) for three targets and investigated for correlation with qPCR results for validation of the method. Overall, reasonable concordance was observed in general expression trends between selected IHC and RNA expression. qPCR data were further analyzed using hierarchical clustering analysis and showed that morphologically defined ROI’s cluster completely differently than traditional clustering of entire tissue scrapes. Notably, patient clustering based on morphological regions was independent of the intrinsic cancer subtype, as determined by molecular profiling of whole tissue scrapes, as well as independent of trends in Tumor Mutational Burden (TMB) and Microsatellite Instability (MSI). These findings suggest that current methods of patient stratification based on whole tumor molecular subtyping may be inferior to stratification based on molecular characteristics of the tumor microenvironment.
Citation Format: Colleen Ziegler, Isaiah Slemons, Chris DeSilva, Barbara Witkowski, Alain Mir, Sangeetha Anandakrishnan, Andrew Farmer, Elma Contreras, David Richardson, Semir Vranic, Zoran Gatalica, Dmitry N. Derkach. Novel method for patient stratification in breast carcinoma based upon spatial analysis of tumor microenvironment [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B094. doi:10.1158/1535-7163.TARG-19-B094
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Affiliation(s)
| | | | | | | | - Alain Mir
- 2Takara Bio USA, Inc., Mountain View, CA
| | | | | | | | | | - Semir Vranic
- 4College of Medicine, QU Health, Qatar University, Doha
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Sumrall A, Mittal S, Phuphanich S, Heimberger A, Eschbacher J, Korn M, Gatalica Z, Pandey M, Xiu J. PATH-55. MUTATIONS OF H3.3 AND H3.1 IN A LARGE COHORT OF GLIOMAS. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Mutations in the histone genes H3.3 and H3.1 are driver events in pediatric and adult gliomas and carry diagnostic and prognostic importance for tumors originating from midline structures. Patients with tumors affected by these mutations are difficult to treat. We surveyed a large cohort of gliomas for H3-mutations, including H3K27m. Consecutive gliomas submitted for tumor profiling at Caris Life Sciences from 2015- 2019 were analyzed. NextGen sequencing was done on 592 genes; MGMT promoter methylation was tested by pyrosequencing; and EGFRvIII and gene fusions were tested by RNA-sequencing. Of nearly 1800 tumors analyzed, 41 harbored H3F3A alterations, including 33 with the K27M mutation (4 arose from the spinal cord, 1 from cerebellum, 1 from brain stem, 4 from thalamus, and 23 from brain, NOS). Eight G34R mutations were identified. A HIST1H3B-K27M was detected in a tumor from the brain stem. H3 mutations were more prevalent in pediatric tumors, and all H3 mutations seen in pediatric tumors were from grade IV tumors. Among the H3-mutated adult tumors, histology differed. There were 2 grade II tumors, 1 low grade glioma, 1 anaplastic ganglioglioma, and 2 anaplastic astrocytomas. In the investigated cohort, H3-mutations were mutually exclusive of IDH1/2 mutations and EGFR alterations. Significantly higher mutation rates were seen in H3-mutated tumors for TP53, ATRX, NF1, PDGFRA, FGFR1, FBXW7, BLM, and TSC2 compared with H3-WT. The H3-WT tumors were more enriched for MGMT-methylation and PTEN mutation. In H3-mutated tumors that were MGMT-methylated, most H3-mutations seen were G34R while K27M was largely exclusive. There was a heterogeneous distribution of H3 mutations, and the co-occurring molecular alterations seen in H3-mutated tumors further support the hypothesis that these tumors are a distinct molecular entity. By better characterizing these associations, we can develop insight into novel treatment strategies for a class of tumors with historically dismal prognosis.
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Affiliation(s)
| | | | | | - Amy Heimberger
- The University of Texas MD Anderson Cancer, Houston, TX, USA
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Gargano SM, Senarathne W, Feldman R, Florento E, Stafford P, Swensen J, Vranic S, Gatalica Z. Novel therapeutic targets in salivary duct carcinoma uncovered by comprehensive molecular profiling. Cancer Med 2019; 8:7322-7329. [PMID: 31609094 PMCID: PMC6885888 DOI: 10.1002/cam4.2602] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 01/01/2023] Open
Abstract
Salivary duct carcinoma (SDC) is a rare, aggressive salivary gland malignancy, which often presents at an advanced stage. A proportion of SDC are characterized by HER2 amplification and/or overexpression of androgen receptor (AR), which could be targeted in a subset of patients, but the presence of AR splice variant‐7 (AR‐V7) in some SDC cases could result in resistance to anti‐androgen therapy. We evaluated a cohort of 28 cases of SDC for potentially targetable biomarkers and pathways using immunohistochemistry (IHC) and next‐generation sequencing (DNA and RNA) assays. Pathogenic genetic aberrations were found in all but 1 case and affected TP53 (n = 19), HRAS (n = 7), PIK3CA, ERBB2 (HER2), and NF1 (n = 5 each); KMT2C (MLL3) and PTEN (n = 3 each); BRAF (p.V600E), KDM5C and NOTCH1 (n = 2 each). Androgen receptor was expressed in all cases and 13 of 27 harbored the AR‐V7 splice variant (including a case without any other detectable genetic alteration). HER2 IHC was expressed in 11 of 28 cases. The majority of SDC cases had no biomarkers predictive of immunotherapy response: 5 cases exhibited low (1%‐8%) programmed death ligand 1 (PD‐L1) expression in tumor cells, 2 cases exhibited elevated TMB, and no samples exhibited microsatellite instability. Notably, the pre‐treatment biopsies from 2 patients with metastatic disease, who demonstrated clinical responses to anti‐androgen therapy, showed AR expression and no AR splice variants. We conclude that comprehensive molecular profiling of SDCs can guide the selection of patients for targeted therapies involving AR, HER2, PD‐L1, mitogen‐activated protein kinase, and PIK3CA pathways.
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Affiliation(s)
- Stacey M Gargano
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, PA, USA
| | | | | | | | | | | | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar
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Vranic S, Arguello D, Contreras E, Cimic A, Gatalica Z. Molecular profiling reveals novel targetable biomarkers in neuroendocrine carcinoma of the uterine cervix. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz250.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Nikanjam M, Arguello D, Gatalica Z, Swensen J, Barkauskas DA, Kurzrock R. Relationship between protein biomarkers of chemotherapy response and microsatellite status, tumor mutational burden and PD-L1 expression in cancer patients. Int J Cancer 2019; 146:3087-3097. [PMID: 31479512 PMCID: PMC7051881 DOI: 10.1002/ijc.32661] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 12/12/2022]
Abstract
Chemotherapy and checkpoint inhibitor immunotherapies are increasingly used in combinations. We determined associations between the presence of anti‐PD‐1/PD‐L1 therapeutic biomarkers and protein markers of potential chemotherapy response. Data were extracted from a clinical‐grade testing database (Caris Life Sciences; February 2015 through November 2017): immunotherapy response markers (microsatellite instability‐high [MSI‐H], tumor mutational burden‐high [TMB‐H], and PD‐L1 protein expression) and protein chemotherapy response markers (excision repair complementation group 1 [ERCC1], topoisomerase 1 [TOPO1], topoisomerase 2 [TOP2A], thymidylate synthase [TS], tubulin beta 3 [TUBB3], ribonucleotide reductase regulatory subunit M1 [RRM1] and O‐6‐methyl guanine DNA methyltransferase [MGMT]). Relationships were determined by the Mantel‐Haenszel chi‐squared test or Fischer's exact tests. Overall, 28,034 patients representing a total of 40 tumor types were assessed. MSI‐H was found in 3.3% of patients (73% were also TMB‐H), TMB‐H, 8.4% (28.3% were also MSI‐H) and PD‐L1 expression in 11.0% of patients (5.1% were also MSI‐H; 16.4% were also TMB‐H). Based on concurrent biomarker expression, combinations of immunotherapy with platinum (ERCC1 negativity) or with doxorubicin, epirubicin or etoposide (TOP2A positivity) have a higher probability of response, whereas combinations with irinotecan or topotecan (TOPO1 positivity), with gemcitabine (RRM1 negativity), and fluorouracil, pemetrexed or capecitabine (TS negativity) may be of less benefit. The potential for immunotherapy and taxane (TUBB3 negativity) combinations is present for MSI‐H but not TMB‐H or PD‐L1‐expressing tumors; for temozolomide and dacarbazine (MGMT negative), PD‐L1 is frequently coexpressed, but MSI‐H and TMB‐H are not associated. Protein markers of potential chemotherapy response along with next‐generation sequencing for immunotherapy response markers can help support rational combinations as part of an individualized, precision oncology approach. What's new? With the emerging success of immunotherapy of cancers, combinations with conventional chemotherapies are increasingly being tested in clinical trials. Here the authors examined concurrent biomarker expression of checkpoint (PD‐1/PD‐L1) blockade immunotherapy and various cytotoxic chemotherapies to determine which chemotherapeutic agents will best synergize with immunotherapy. They predict that combining platinum or doxorubicin, epirubicin, or etoposide treatments with PD‐1/PD‐L1 inhibitors would have a higher probability of response than other treatments, supporting a rational combination strategy in a possibly individualized treatment approach.
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Affiliation(s)
- Mina Nikanjam
- Center for Personalized Cancer Therapy, Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, San Diego, CA
| | | | | | | | - Donald A Barkauskas
- Department of Preventive Medicine, Biostatistics Division, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, San Diego, CA
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Kruslin B, Gatalica Z, Hes O, Xiu J, Florento E, Swensen J. TERT gene fusions characterize a subset of metastatic Leydig cell tumours. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz249.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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