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Wei H, Wu C, Yuan Y, Lai L. Uncovering the Achilles heel of genetic heterogeneity: machine learning-based classification and immunological properties of necroptosis clusters in Alzheimer's disease. Front Aging Neurosci 2023; 15:1249682. [PMID: 37799623 PMCID: PMC10548137 DOI: 10.3389/fnagi.2023.1249682] [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: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023] Open
Abstract
Background Alzheimer's disease (AD) is an age-associated neurodegenerative disease, and the currently available diagnostic modalities and therapeutic agents are unsatisfactory due to its high clinical heterogeneity. Necroptosis is a common type of programmed cell death that has been shown to be activated in AD. Methods In this study, we first investigated the expression profiles of necroptosis-related genes (NRGs) and the immune landscape of AD based on GSE33000 dataset. Next, the AD samples in the GSE33000 dataset were extracted and subjected to consensus clustering based upon the differentially expressed NRGs. Key genes associated with necroptosis clusters were identified using Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm, and then intersected with the key gene related to AD. Finally, we developed a diagnostic model for AD by comparing four different machine learning approaches. The discrimination performance and clinical relevance of the diagnostic model were assessed using various evaluation metrics, including the nomogram, calibration plot, decision curve analysis (DCA), and independent validation datasets. Results Aberrant expression patterns of NRGs and specific immune landscape were identified in the AD samples. Consensus clustering revealed that patients in the GSE33000 dataset could be classified into two necroptosis clusters, each with distinct immune landscapes and enriched pathways. The Extreme Gradient Boosting (XGB) was found to be the most optimal diagnostic model for the AD based on the predictive ability and reliability of the models constructed by four machine learning approaches. The five most important variables, including ACAA2, BHLHB4, CACNA2D3, NRN1, and TAC1, were used to construct a five-gene diagnostic model. The constructed nomogram, calibration plot, DCA, and external independent validation datasets exhibited outstanding diagnostic performance for AD and were closely related with the pathologic hallmarks of AD. Conclusion This work presents a novel diagnostic model that may serve as a framework to study disease heterogeneity and provide a plausible mechanism underlying neuronal loss in AD.
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Affiliation(s)
- Huangwei Wei
- Department of Neurology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Chunle Wu
- Department of Blood Transfusion, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yulin Yuan
- Department of Laboratory, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Lichuan Lai
- Department of Laboratory, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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Nel AE, Mei KC, Liao YP, Lu X. Multifunctional Lipid Bilayer Nanocarriers for Cancer Immunotherapy in Heterogeneous Tumor Microenvironments, Combining Immunogenic Cell Death Stimuli with Immune Modulatory Drugs. ACS Nano 2022; 16:5184-5232. [PMID: 35348320 PMCID: PMC9519818 DOI: 10.1021/acsnano.2c01252] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In addition to the contribution of cancer cells, the solid tumor microenvironment (TME) has a critical role in determining tumor expansion, antitumor immunity, and the response to immunotherapy. Understanding the details of the complex interplay between cancer cells and components of the TME provides an unprecedented opportunity to explore combination therapy for intervening in the immune landscape to improve immunotherapy outcome. One approach is the introduction of multifunctional nanocarriers, capable of delivering drug combinations that provide immunogenic stimuli for improvement of tumor antigen presentation, contemporaneous with the delivery of coformulated drug or synthetic molecules that provide immune danger signals or interfere in immune-escape, immune-suppressive, and T-cell exclusion pathways. This forward-looking review will discuss the use of lipid-bilayer-encapsulated liposomes and mesoporous silica nanoparticles for combination immunotherapy of the heterogeneous immune landscapes in pancreatic ductal adenocarcinoma and triple-negative breast cancer. We describe how the combination of remote drug loading and lipid bilayer encapsulation is used for the synthesis of synergistic drug combinations that induce immunogenic cell death, interfere in the PD-1/PD-L1 axis, inhibit the indoleamine-pyrrole 2,3-dioxygenase (IDO-1) immune metabolic pathway, restore spatial access to activated T-cells to the cancer site, or reduce the impact of immunosuppressive stromal components. We show how an integration of current knowledge and future discovery can be used for a rational approach to nanoenabled cancer immunotherapy.
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Affiliation(s)
- André E. Nel
- Division of NanoMedicine, Department of Medicine, David Geffen School of Medicine University of California, Los Angeles, California, 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California 90095, United States
- Correspondence should be addressed to: André E. Nel, Division of NanoMedicine, Department of Medicine, University of California, Los Angeles, 52-175 CHS, Los Angeles, California 90095, USA. Phone: 310.825.6620;
| | - Kuo-Ching Mei
- Division of NanoMedicine, Department of Medicine, David Geffen School of Medicine University of California, Los Angeles, California, 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Yu-Pei Liao
- Division of NanoMedicine, Department of Medicine, David Geffen School of Medicine University of California, Los Angeles, California, 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Xiangsheng Lu
- Division of NanoMedicine, Department of Medicine, David Geffen School of Medicine University of California, Los Angeles, California, 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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De Mattos-Arruda L, Sammut SJ, Ross EM, Bashford-Rogers R, Greenstein E, Markus H, Morganella S, Teng Y, Maruvka Y, Pereira B, Rueda OM, Chin SF, Contente-Cuomo T, Mayor R, Arias A, Ali HR, Cope W, Tiezzi D, Dariush A, Dias Amarante T, Reshef D, Ciriaco N, Martinez-Saez E, Peg V, Ramon Y Cajal S, Cortes J, Vassiliou G, Getz G, Nik-Zainal S, Murtaza M, Friedman N, Markowetz F, Seoane J, Caldas C. The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer. Cell Rep 2019; 27:2690-2708.e10. [PMID: 31141692 PMCID: PMC6546974 DOI: 10.1016/j.celrep.2019.04.098] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [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: 01/22/2018] [Revised: 12/13/2018] [Accepted: 04/22/2019] [Indexed: 02/07/2023] Open
Abstract
The detailed molecular characterization of lethal cancers is a prerequisite to understanding resistance to therapy and escape from cancer immunoediting. We performed extensive multi-platform profiling of multi-regional metastases in autopsies from 10 patients with therapy-resistant breast cancer. The integrated genomic and immune landscapes show that metastases propagate and evolve as communities of clones, reveal their predicted neo-antigen landscapes, and show that they can accumulate HLA loss of heterozygosity (LOH). The data further identify variable tumor microenvironments and reveal, through analyses of T cell receptor repertoires, that adaptive immune responses appear to co-evolve with the metastatic genomes. These findings reveal in fine detail the landscapes of lethal metastatic breast cancer.
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Affiliation(s)
- Leticia De Mattos-Arruda
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain
| | - Stephen-John Sammut
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Edith M Ross
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Erez Greenstein
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Havell Markus
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; Mayo Clinic Center for Individualized Medicine, Scottsdale, AZ, USA
| | - Sandro Morganella
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yvonne Teng
- Cancer Molecular Diagnosis Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Yosef Maruvka
- The Broad Institute, Cambridge, MA 02142, USA; Massachusetts General Hospital Cancer Center and Department of Pathology, Charlestown, MA 02129, USA
| | - Bernard Pereira
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Oscar M Rueda
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Suet-Feung Chin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Tania Contente-Cuomo
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; Mayo Clinic Center for Individualized Medicine, Scottsdale, AZ, USA
| | - Regina Mayor
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - Alexandra Arias
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - H Raza Ali
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Wei Cope
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Daniel Tiezzi
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Aliakbar Dariush
- Institute of Astronomy, University of Cambridge, Cambridge CB3 0HA, UK
| | - Tauanne Dias Amarante
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Dan Reshef
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nikaoly Ciriaco
- Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Elena Martinez-Saez
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Vicente Peg
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain; Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Santiago Ramon Y Cajal
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain; Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Javier Cortes
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Ramon y Cajal Hospital, 28034 Madrid, Spain
| | - George Vassiliou
- Cancer Molecular Diagnosis Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Wellcome Trust/MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Gad Getz
- The Broad Institute, Cambridge, MA 02142, USA; Massachusetts General Hospital Cancer Center and Department of Pathology, Charlestown, MA 02129, USA
| | - Serena Nik-Zainal
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Muhammed Murtaza
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; Mayo Clinic Center for Individualized Medicine, Scottsdale, AZ, USA
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Florian Markowetz
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 2QQ, UK.
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