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Bhinder B, Ferguson A, Sigouros M, Uppal M, Elsaeed AG, Bareja R, Alnajar H, Eng KW, Conteduca V, Sboner A, Mosquera JM, Elemento O, Beltran H. Immunogenomic Landscape of Neuroendocrine Prostate Cancer. Clin Cancer Res 2023; 29:2933-2943. [PMID: 37223924 PMCID: PMC10524949 DOI: 10.1158/1078-0432.ccr-22-3743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/29/2023] [Accepted: 05/16/2023] [Indexed: 05/25/2023]
Abstract
PURPOSE Patients with neuroendocrine prostate cancer (NEPC) are often managed with immunotherapy regimens extrapolated from small-cell lung cancer (SCLC). We sought to evaluate the tumor immune landscape of NEPC compared with other prostate cancer types and SCLC. EXPERIMENTAL DESIGN In this retrospective study, a cohort of 170 patients with 230 RNA-sequencing and 104 matched whole-exome sequencing data were analyzed. Differences in immune and stromal constituents, frequency of genomic alterations, and associations with outcomes were evaluated. RESULTS In our cohort, 36% of the prostate tumors were identified as CD8+ T-cell inflamed, whereas the remaining 64% were T-cell depleted. T-cell-inflamed tumors were enriched in anti-inflammatory M2 macrophages and exhausted T cells and associated with shorter overall survival relative to T-cell-depleted tumors (HR, 2.62; P < 0.05). Among all prostate cancer types in the cohort, NEPC was identified to be the most immune depleted, wherein only 9 out of the 36 total NEPC tumors were classified as T-cell inflamed. These inflamed NEPC cases were enriched in IFN gamma signaling and PD-1 signaling compared with other NEPC tumors. Comparison of NEPC with SCLC revealed that NEPC had poor immune content and less mutations compared with SCLC, but expression of checkpoint genes PD-L1 and CTLA-4 was comparable between NEPC and SCLC. CONCLUSIONS NEPC is characterized by a relatively immune-depleted tumor immune microenvironment compared with other primary and metastatic prostate adenocarcinoma except in a minority of cases. These findings may inform development of immunotherapy strategies for patients with advanced prostate cancer.
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Affiliation(s)
- Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alison Ferguson
- Department for BioMedical Research, University of Bern, 3012 Bern, Switzerland
| | - Michael Sigouros
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Manik Uppal
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ahmed G. Elsaeed
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rohan Bareja
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Hussein Alnajar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Kenneth Wha Eng
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Vincenza Conteduca
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medical and Surgical Sciences, Unit of Medical Oncology and Biomolecular Therapy, University of Foggia, Policlinico Riuniti, 71122 Foggia, Italy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 USA
| | - Andrea Sboner
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Juan Miguel Mosquera
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Himisha Beltran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 USA
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Amgad M, Atteya LA, Hussein H, Mohammed KH, Hafiz E, Elsebaie MAT, Alhusseiny AM, AlMoslemany MA, Elmatboly AM, Pappalardo PA, Sakr RA, Mobadersany P, Rachid A, Saad AM, Alkashash AM, Ruhban IA, Alrefai A, Elgazar NM, Abdulkarim A, Farag AA, Etman A, Elsaeed AG, Alagha Y, Amer YA, Raslan AM, Nadim MK, Elsebaie MAT, Ayad A, Hanna LE, Gadallah A, Elkady M, Drumheller B, Jaye D, Manthey D, Gutman DA, Elfandy H, Cooper LAD. NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer. Gigascience 2022; 11:6586817. [PMID: 35579553 PMCID: PMC9112766 DOI: 10.1093/gigascience/giac037] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 10/28/2021] [Revised: 12/24/2021] [Accepted: 03/18/2022] [Indexed: 01/20/2023] Open
Abstract
Background Deep learning enables accurate high-resolution mapping of cells and tissue structures that can serve as the foundation of interpretable machine-learning models for computational pathology. However, generating adequate labels for these structures is a critical barrier, given the time and effort required from pathologists. Results This article describes a novel collaborative framework for engaging crowds of medical students and pathologists to produce quality labels for cell nuclei. We used this approach to produce the NuCLS dataset, containing >220,000 annotations of cell nuclei in breast cancers. This builds on prior work labeling tissue regions to produce an integrated tissue region- and cell-level annotation dataset for training that is the largest such resource for multi-scale analysis of breast cancer histology. This article presents data and analysis results for single and multi-rater annotations from both non-experts and pathologists. We present a novel workflow that uses algorithmic suggestions to collect accurate segmentation data without the need for laborious manual tracing of nuclei. Our results indicate that even noisy algorithmic suggestions do not adversely affect pathologist accuracy and can help non-experts improve annotation quality. We also present a new approach for inferring truth from multiple raters and show that non-experts can produce accurate annotations for visually distinctive classes. Conclusions This study is the most extensive systematic exploration of the large-scale use of wisdom-of-the-crowd approaches to generate data for computational pathology applications.
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Affiliation(s)
- Mohamed Amgad
- Department of Pathology, Northwestern University, 750 N Lake Shore Dr., Chicago, IL 60611, USA
| | - Lamees A Atteya
- Cairo Health Care Administration, Egyptian Ministry of Health, 3 Magles El Shaab Street, Cairo, Postal code 222, Egypt
| | - Hagar Hussein
- Department of Pathology, Nasser institute for research and treatment, 3 Magles El Shaab Street, Cairo, Postal code 222, Egypt
| | - Kareem Hosny Mohammed
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3620 Hamilton Walk M163, Philadelphia, PA 19104, USA
| | - Ehab Hafiz
- Department of Clinical Laboratory Research, Theodor Bilharz Research Institute, 1 El-Nile Street, Imbaba Warrak El-Hadar, Giza, Postal code 12411, Egypt
| | - Maha A T Elsebaie
- Department of Medicine, Cook County Hospital, 1969 W Ogden Ave, Chicago, IL 60612, USA
| | - Ahmed M Alhusseiny
- Department of Pathology, Baystate Medical Center, University of Massachusetts, 759 Chestnut St, Springfield, MA 01199, USA
| | - Mohamed Atef AlMoslemany
- Faculty of Medicine, Menoufia University, Gamal Abd El-Nasir, Qism Shebeen El-Kom, Shibin el Kom, Menofia Governorate, Postal code: 32511, Egypt
| | - Abdelmagid M Elmatboly
- Faculty of Medicine, Al-Azhar University, 15 Mohammed Abdou, El-Darb El-Ahmar, Cairo Governorate, Postal code 11651, Egypt
| | - Philip A Pappalardo
- Consultant for The Center for Applied Proteomics and Molecular Medicine (CAPMM), George Mason University, 10920 George Mason Circle Institute for Advanced Biomedical Research Room 2008, MS1A9 Manassas, Virginia 20110, USA
| | - Rokia Adel Sakr
- Department of Pathology, National Liver Institute, Gamal Abd El-Nasir, Qism Shebeen El-Kom, Shibin el Kom, Menofia Governorate, Postal code: 32511, Egypt
| | - Pooya Mobadersany
- Department of Pathology, Northwestern University, 750 N Lake Shore Dr., Chicago, IL 60611, USA
| | - Ahmad Rachid
- Faculty of Medicine, Ain Shams University, 38 Abbassia, Next to the Al-Nour Mosque, Cairo, Postal code: 1181, Egypt
| | - Anas M Saad
- Cleveland Clinic Foundation, 9500 Euclid Ave. Cleveland, Ohio 44195, USA
| | - Ahmad M Alkashash
- Department of Pathology, Indiana University, 635 Barnhill Drive Medical Science Building A-128 Indianapolis, IN 46202, USA
| | - Inas A Ruhban
- Faculty of Medicine, Damascus University, Damascus, Damaskus, PO Box 30621, Syria
| | - Anas Alrefai
- Faculty of Medicine, Ain Shams University, 38 Abbassia, Next to the Al-Nour Mosque, Cairo, Postal code: 1181, Egypt
| | - Nada M Elgazar
- Faculty of Medicine, Mansoura University, 1 El Gomhouria St, Dakahlia Governorate 35516, Egypt
| | - Ali Abdulkarim
- Faculty of Medicine, Cairo University, Kasr Al Ainy Hospitals, Kasr Al Ainy St., Cairo, Postal code: 11562, Egypt
| | - Abo-Alela Farag
- Faculty of Medicine, Ain Shams University, 38 Abbassia, Next to the Al-Nour Mosque, Cairo, Postal code: 1181, Egypt
| | - Amira Etman
- Faculty of Medicine, Menoufia University, Gamal Abd El-Nasir, Qism Shebeen El-Kom, Shibin el Kom, Menofia Governorate, Postal code: 32511, Egypt
| | - Ahmed G Elsaeed
- Faculty of Medicine, Mansoura University, 1 El Gomhouria St, Dakahlia Governorate 35516, Egypt
| | - Yahya Alagha
- Faculty of Medicine, Cairo University, Kasr Al Ainy Hospitals, Kasr Al Ainy St., Cairo, Postal code: 11562, Egypt
| | - Yomna A Amer
- Faculty of Medicine, Menoufia University, Gamal Abd El-Nasir, Qism Shebeen El-Kom, Shibin el Kom, Menofia Governorate, Postal code: 32511, Egypt
| | - Ahmed M Raslan
- Department of Anaesthesia and Critical Care, Menoufia University Hospital, Gamal Abd El-Nasir, Qism Shebeen El-Kom, Shibin el Kom, Menofia Governorate, Postal code: 32511, Egypt
| | - Menatalla K Nadim
- Department of Clinical Pathology, Ain Shams University, 38 Abbassia, Next to the Al-Nour Mosque, Cairo, Postal code: 1181, Egypt
| | - Mai A T Elsebaie
- Faculty of Medicine, Ain Shams University, 38 Abbassia, Next to the Al-Nour Mosque, Cairo, Postal code: 1181, Egypt
| | - Ahmed Ayad
- Research Department, Oncology Consultants, 2130 W. Holcombe Blvd, 10th Floor, Houston, Texas 77030, USA
| | - Liza E Hanna
- Department of Pathology, Nasser institute for research and treatment, 3 Magles El Shaab Street, Cairo, Postal code 222, Egypt
| | - Ahmed Gadallah
- Faculty of Medicine, Ain Shams University, 38 Abbassia, Next to the Al-Nour Mosque, Cairo, Postal code: 1181, Egypt
| | - Mohamed Elkady
- Siparadigm Diagnostic Informatics, 25 Riverside Dr no. 2, Pine Brook, NJ 07058, USA
| | - Bradley Drumheller
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 201 Dowman Dr, Atlanta, GA 30322, USA
| | - David Jaye
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 201 Dowman Dr, Atlanta, GA 30322, USA
| | - David Manthey
- Kitware Inc., 1712 Route 9. Suite 300. Clifton Park, New York 12065, USA
| | - David A Gutman
- Department of Neurology, Emory University School of Medicine, 201 Dowman Dr, Atlanta, GA 30322, USA
| | - Habiba Elfandy
- Department of Pathology, National Cancer Institute, Kasr Al Eini Street, Fom El Khalig, Cairo, Postal code: 11562, Egypt.,Department of Pathology, Children's Cancer Hospital Egypt (CCHE 57357), 1 Seket Al-Emam Street, El-Madbah El-Kadeem Yard, El-Saida Zenab, Cairo, Postal code: 11562, Egypt
| | - Lee A D Cooper
- Department of Pathology, Northwestern University, 750 N Lake Shore Dr., Chicago, IL 60611, USA.,Lurie Cancer Center, Northwestern University, 675 N St Clair St Fl 21 Ste 100, Chicago, IL 60611, USA.,Center for Computational Imaging and Signal Analytics, Northwestern University Feinberg School of Medicine, 750 N Lake Shore Dr., Chicago, IL 60611, USA
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