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Yang Z, Guan F, Bronk L, Zhao L. Multi-omics approaches for biomarker discovery in predicting the response of esophageal cancer to neoadjuvant therapy: A multidimensional perspective. Pharmacol Ther 2024; 254:108591. [PMID: 38286161 DOI: 10.1016/j.pharmthera.2024.108591] [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: 08/23/2023] [Revised: 12/02/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024]
Abstract
Neoadjuvant chemoradiotherapy (NCRT) followed by surgery has been established as the standard treatment strategy for operable locally advanced esophageal cancer (EC). However, achieving pathologic complete response (pCR) or near pCR to NCRT is significantly associated with a considerable improvement in survival outcomes, while pCR patients may help organ preservation for patients by active surveillance to avoid planned surgery. Thus, there is an urgent need for improved biomarkers to predict EC chemoradiation response in research and clinical settings. Advances in multiple high-throughput technologies such as next-generation sequencing have facilitated the discovery of novel predictive biomarkers, specifically based on multi-omics data, including genomic/transcriptomic sequencings and proteomic/metabolomic mass spectra. The application of multi-omics data has shown the benefits in improving the understanding of underlying mechanisms of NCRT sensitivity/resistance in EC. Particularly, the prominent development of artificial intelligence (AI) has introduced a new direction in cancer research. The integration of multi-omics data has significantly advanced our knowledge of the disease and enabled the identification of valuable biomarkers for predicting treatment response from diverse dimension levels, especially with rapid advances in biotechnological and AI methodologies. Herein, we summarize the current status of research on the use of multi-omics technologies in predicting NCRT response for EC patients. Current limitations, challenges, and future perspectives of these multi-omics platforms will be addressed to assist in experimental designs and clinical use for further integrated analysis.
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Affiliation(s)
- Zhi Yang
- Department of Radiation Oncology, Xijing Hospital, Fourth Military Medical University, 15 West Changle Road, Xi'an, China
| | - Fada Guan
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510, United States of America
| | - Lawrence Bronk
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Lina Zhao
- Department of Radiation Oncology, Xijing Hospital, Fourth Military Medical University, 15 West Changle Road, Xi'an, China.
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2
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Addala V, Newell F, Pearson JV, Redwood A, Robinson BW, Creaney J, Waddell N. Computational immunogenomic approaches to predict response to cancer immunotherapies. Nat Rev Clin Oncol 2024; 21:28-46. [PMID: 37907723 DOI: 10.1038/s41571-023-00830-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The establishment of large-scale genomic collaborative efforts along with the development of new single-cell transcriptomic techniques and multi-omics approaches have enabled characterization of the mutational and transcriptional profiles of many cancer types and helped to identify clinically actionable alterations as well as predictive and prognostic biomarkers. Researchers have developed computational approaches and machine learning algorithms to accurately obtain clinically useful information from genomic and transcriptomic sequencing data from bulk tissue or single cells and explore tumours and their microenvironment. The rapid growth in sequencing and computational approaches has resulted in the unmet need to understand their true potential and limitations in enabling improvements in the management of patients with cancer who are receiving immunotherapies. In this Review, we describe the computational approaches currently available to analyse bulk tissue and single-cell sequencing data from cancer, stromal and immune cells, as well as how best to select the most appropriate tool to address various clinical questions and, ultimately, improve patient outcomes.
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Affiliation(s)
- Venkateswar Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Felicity Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alec Redwood
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Bruce W Robinson
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Medical School, University of Western Australia, Perth, Western Australia, Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
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Zhuang C, Chen B, Wu S, Xu L, Zhang X, Zheng X, Chen Y, Geng Y, Guan J, Lin Y, Wilman AH, Wu R. Repurposing of the PET Probe Prototype PiB for Label and Radiation-Free CEST MRI Molecular Imaging of Amyloid. ACS Chem Neurosci 2023; 14:4344-4351. [PMID: 38061891 PMCID: PMC10741654 DOI: 10.1021/acschemneuro.3c00539] [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: 08/16/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
Positron emission tomography (PET) probes are specific and sensitive while suffering from radiation risk. It is worthwhile to explore the chemical emission saturation transfer (CEST) effects of the probe prototypes and repurpose them for CEST imaging to avoid radiation. In this study, we used 11C-PiB as an example of a PET probe for detecting amyloid and tested the feasibility of repurposing this PET probe prototype, PiB, for CEST imaging. After optimizing the parameters through preliminary phantom experiments, we used APP/PS1 transgenic mice and age-matched C57 mice for in vivo CEST magnetic resonance imaging (MRI) of amyloid. Furthermore, the pathological assessment was conducted on the same brain slices to evaluate the correlation between the CEST MRI signal abnormality and β-amyloid deposition detected by immunohistochemical staining. In our results, the Z-spectra revealed an apparent CEST effect that peaked at approximately 6 ppm. APP/PS1 mice as young as 9 months injected with PiB showed a significantly higher CEST effect compared to the control groups. The hyperintense region was correlated with the Aβ deposition shown by pathological staining. In conclusion, repurposing the PET probe prototype for CEST MRI imaging is feasible and enables label- and radiation-free detection of the amyloid while maintaining the sensitivity and specificity of the ligand. This study opens the door to developing CEST probes based on PET probe prototypes.
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Affiliation(s)
- Caiyu Zhuang
- Department
of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, China
- Department
of Radiology, First Affiliated Hospital, Shantou University Medical College, Shantou 515041, China
| | - Beibei Chen
- Department
of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, China
| | - Shuohua Wu
- Department
of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, China
| | - Liang Xu
- Department
of Medical Imaging, Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
| | - Xiaolei Zhang
- Department
of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, China
| | - Xinhui Zheng
- Department
of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, China
| | - Yue Chen
- Department
of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, China
| | - Yiqun Geng
- Laboratory
of Molecular Pathology, Shantou University
Medical College, Shantou 515041, China
| | - Jitian Guan
- Department
of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, China
| | - Yan Lin
- Department
of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, China
- Provincial
Key Laboratory for Breast Cancer Diagnosis and Treatment, Shantou 515041, China
| | - Alan H. Wilman
- The Department
of Biomedical Engineering, University of
Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Renhua Wu
- Department
of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, China
- Provincial
Key Laboratory for Breast Cancer Diagnosis and Treatment, Shantou 515041, China
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Belle CJ, Lonie JM, Brosda S, Barbour AP. Tumour microenvironment influences response to treatment in oesophageal adenocarcinoma. Front Immunol 2023; 14:1330635. [PMID: 38155973 PMCID: PMC10753779 DOI: 10.3389/fimmu.2023.1330635] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/30/2023] [Indexed: 12/30/2023] Open
Abstract
The poor treatment response of oesophageal adenocarcinoma (OAC) leads to low survival rates. Its increasing incidence makes finding more effective treatment a priority. Recent treatment improvements can be attributed to the inclusion of the tumour microenvironment (TME) and immune infiltrates in treatment decisions. OAC TME is largely immunosuppressed and reflects treatment resistance as patients with inflamed TME have better outcomes. Priming the tumour with the appropriate neoadjuvant chemoradiotherapy treatment could lead to higher immune infiltrations and higher expression of immune checkpoints, such as PD-1/PDL-1, CTLA4 or emerging new targets: LAG-3, TIM-3, TIGIT or ICOS. Multiple trials support the addition of immune checkpoint inhibitors to the current standard of care. However, results vary, supporting the need for better response biomarkers based on TME composition. This review explores what is known about OAC TME, the clinical significance of the various cell populations infiltrating it and the emerging therapeutical combination with a focus on immune checkpoints inhibitors.
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Affiliation(s)
- Clemence J. Belle
- Surgical Oncology Group, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - James M. Lonie
- Surgical Oncology Group, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Sandra Brosda
- Surgical Oncology Group, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew P. Barbour
- Surgical Oncology Group, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
- Department of Surgery, Princess Alexandra Hospital, Brisbane, QLD, Australia
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Lonie JM, Brosda S, Bonazzi VF, Aoude LG, Patel K, Brown I, Sharma S, Lampe G, Addala V, Koufariotis LT, Wood S, Waddell N, Dolcetti R, Barbour AP. The oesophageal adenocarcinoma tumour immune microenvironment dictates outcomes with different modalities of neoadjuvant therapy - results from the AGITG DOCTOR trial and the cancer evolution biobank. Front Immunol 2023; 14:1220129. [PMID: 37965317 PMCID: PMC10642165 DOI: 10.3389/fimmu.2023.1220129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/14/2023] [Indexed: 11/16/2023] Open
Abstract
A plateau in treatment effect can be seen for the current 'one-size-fits-all' approach to oesophageal adenocarcinoma (OAC) management using neoadjuvant chemoradiotherapy (nCRT) or chemotherapy (nCT). In OAC, the tumour microenvironment (TME) is largely immunosuppressed, however a subgroup of patients with an immune-inflamed TME exist and show improved outcomes. We aimed to understand the overall immune-based mechanisms underlying treatment responses and patient outcomes in OAC, and in relation to neoadjuvant therapy modality. This study included 107 patients; 68 patients were enrolled in the Australian Gastro-Intestinal Trials Group sponsored DOCTOR Trial, and 38 patients were included from the Cancer Evolution Biobank. Matched pre-treatment and post-treatment tumour biopsies were used to perform multi-modality analysis of the OAC TME including NanoString mRNA expression analysis, multiplex and single colour immunohistochemistry (IHC), and peripheral blood mononuclear cell analysis of tumour-antigen specific T cell responses. Patients with the best clinicopathological outcomes and survival had an immune-inflamed TME enriched with anti-tumour immune cells and pathways. Those with the worst survival showed a myeloid T regulatory cell enriched TME, with decreased CD8+ cell infiltration and increased pro-tumour immune cells. Multiplex IHC analysis identified that high intra-tumoural infiltration of CD8+ cells, and low infiltration with CD163+ cells was associated with improved survival. High tumour core CD8+ T cell infiltration, and a low tumour margin infiltration of CD163+ cells was also associated with improved survival. nCRT showed improved survival compared with nCT for patients with low CD8+, or high CD163+ cell infiltration. Poly-functional T cell responses were seen with tumour-antigen specific T cells. Overall, our study supports the development of personalised therapeutic approaches based on the immune microenvironment in OAC. Patients with an immune-inflamed TME show favourable outcomes regardless of treatment modality. However, in those with an immunosuppressed TME with CD163+ cell infiltration, treatment with nCRT can improve outcomes. Our findings support previous studies into the TME of OAC and with more research, immune based biomarker selection of treatment modality may lead in improved outcomes in this deadly disease.
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Affiliation(s)
- James M. Lonie
- Surgical Oncology Group, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Sandra Brosda
- Surgical Oncology Group, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Vanessa F. Bonazzi
- Surgical Oncology Group, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Lauren G. Aoude
- Surgical Oncology Group, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Kalpana Patel
- Surgical Oncology Group, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Ian Brown
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Envoi Specialist Pathologists, Brisbane, QLD, Australia
- Department of Pathology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Sowmya Sharma
- Medlab Pathology, Sydney, NSW, Australia
- Medical Genomics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Guy Lampe
- Department of Anatomical Pathology, Central Laboratory Pathology Queensland, Brisbane, QLD, Australia
| | - Venkateswar Addala
- Medical Genomics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Scott Wood
- Medical Genomics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicola Waddell
- Medical Genomics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Riccardo Dolcetti
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Translational and Clinical Immunotherapy, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia
| | - Andrew P. Barbour
- Surgical Oncology Group, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
- Department of Surgery, Princess Alexandra Hospital, Brisbane, QLD, Australia
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6
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Davern M, Donlon NE. The future of combination immunotherapy in oesophageal adenocarcinoma. Front Immunol 2023; 14:1217132. [PMID: 37520544 PMCID: PMC10375285 DOI: 10.3389/fimmu.2023.1217132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/12/2023] [Indexed: 08/01/2023] Open
Affiliation(s)
- Maria Davern
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Noel E. Donlon
- Department of Surgery, Trinity St. James’s Cancer Institute, Trinity Translational Medicine Institute, St. James’s Hospital, Trinity College Dublin, Dublin, Ireland
- Department of Upper GI Surgery, Beaumont Hospital, Dublin, Ireland
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