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Lorkowski SW, Dermawan JK, Rubin BP. The practical utility of AI-assisted molecular profiling in the diagnosis and management of cancer of unknown primary: an updated review. Virchows Arch 2024; 484:369-375. [PMID: 37999736 DOI: 10.1007/s00428-023-03708-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023]
Abstract
Cancer of unknown primary (CUP) presents a complex diagnostic challenge, characterized by metastatic tumors of unknown tissue origin and a dismal prognosis. This review delves into the emerging significance of artificial intelligence (AI) and machine learning (ML) in transforming the landscape of CUP diagnosis, classification, and treatment. ML approaches, trained on extensive molecular profiling data, have shown promise in accurately predicting tissue of origin. Genomic profiling, encompassing driver mutations and copy number variations, plays a pivotal role in CUP diagnosis by providing insights into tumor type-specific oncogenic alterations. Mutational signatures (MS), reflecting somatic mutation patterns, offer further insights into CUP diagnosis. Known MS with established etiology, such as ultraviolet (UV) light-induced DNA damage and tobacco exposure, have been identified in cases of dedifferentiated/transdifferentiated melanoma and carcinoma. Deep learning models that integrate gene expression data and DNA methylation patterns offer insights into tissue lineage and tumor classification. In digital pathology, machine learning algorithms analyze whole-slide images to aid in CUP classification. Finally, precision oncology, guided by molecular profiling, offers targeted therapies independent of primary tissue identification. Clinical trials assigning CUP patients to molecularly guided therapies, including targetable alterations and tumor mutation burden as an immunotherapy biomarker, have resulted in improved overall survival in a subset of patients. In conclusion, AI- and ML-driven approaches are revolutionizing CUP management by enhancing diagnostic accuracy. Precision oncology utilizing enhanced molecular profiling facilitates the identification of targeted therapies that transcend the need to identify the tissue of origin, ultimately improving patient outcomes.
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Affiliation(s)
- Shuhui Wang Lorkowski
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
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van Mourik A, Tonkin-Hill G, O'Farrell J, Waller S, Tan L, Tothill RW, Bowtell D, Fox S, Fellowes A, Fedele C, Schofield P, Sivakumaran T, Wong HL, Mileshkin L. Six-year experience of Australia's first dedicated cancer of unknown primary clinic. Br J Cancer 2023; 129:301-308. [PMID: 37225894 PMCID: PMC10338450 DOI: 10.1038/s41416-023-02254-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Diagnosis and management of cancers of unknown primary (CUP) remain challenging. This study examines the referral patterns, management and outcomes of patients referred to Australia's first dedicated CUP clinic. METHODS Retrospective medical record review was conducted for patients seen at the Peter MacCallum Cancer Centre CUP clinic between July 2014 and August 2020. Overall survival (OS) was analysed for patients with a CUP diagnosis where treatment information was available. RESULTS Of 361 patients referred, fewer than half had completed diagnostic work-up at the time of referral. A diagnosis of CUP was established in 137 (38%), malignancy other than CUP in 177 (49%) and benign pathology in 36 (10%) patients. Genomic testing was successfully completed in 62% of patients with initial provisional CUP and impacted management in 32% by identifying a tissue of origin or actionable genomic alteration. The use of site-specific, targeted therapy or immunotherapy was independently associated with longer OS compared to empirical chemotherapy. CONCLUSION Our specialised CUP clinic facilitated diagnostic work-up among patients with suspected malignancy and provided access to genomic testing and clinical trials for patients with a CUP diagnosis, all of which are important to improve outcomes in this patient population.
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Affiliation(s)
- Arielle van Mourik
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Gina Tonkin-Hill
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - John O'Farrell
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Shohei Waller
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Lavinia Tan
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Richard W Tothill
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Clinical Pathology and Centre for Cancer Research, The University of Melbourne, Parkville, VIC, Australia
| | - David Bowtell
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Stephen Fox
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Clinical Pathology and Centre for Cancer Research, The University of Melbourne, Parkville, VIC, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Andrew Fellowes
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | - Penelope Schofield
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Psychology, and Iverson Health Innovation Research Institute Swinburne University, Melbourne, VIC, Australia
- Behavioural Sciences Unit, Health Services Research and Implementation Sciences, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Tharani Sivakumaran
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Hui-Li Wong
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.
| | - Linda Mileshkin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
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Seligson ND, Kolesar JM, Alam B, Baker L, Lamba JK, Fridley BL, Salahudeen AA, Hertz DL, Hicks JK. Integrating pharmacogenomic testing into paired germline and somatic genomic testing in patients with cancer. Pharmacogenomics 2023; 24:731-738. [PMID: 37702060 DOI: 10.2217/pgs-2023-0125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
Precision medicine has revolutionized clinical care for patients with cancer through the development of targeted therapy, identification of inherited cancer predisposition syndromes and the use of pharmacogenetics to optimize pharmacotherapy for anticancer drugs and supportive care medications. While germline (patient) and somatic (tumor) genomic testing have evolved separately, recent interest in paired germline/somatic testing has led to an increase in integrated genomic testing workflows. However, paired germline/somatic testing has generally lacked the incorporation of germline pharmacogenomics. Integrating pharmacogenomics into paired germline/somatic genomic testing would be an efficient method for increasing access to pharmacogenomic testing. In this perspective, the authors argue for the benefits of implementing a comprehensive approach integrating somatic and germline testing that is inclusive of pharmacogenomics in clinical practice.
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Affiliation(s)
- Nathan D Seligson
- Department of Pharmacotherapy & Translational Research, The University of Florida, Jacksonville, FL 32209, USA
- Center for Pharmacogenomics & Translational Research, Nemours Children's Health, Jacksonville, FL 32207, USA
| | - Jill M Kolesar
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Department of Pharmacy Practice & Science, University of Kentucky, Lexington, KY 40536, USA
| | - Benish Alam
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Laura Baker
- Nemours Center for Cancer & Blood Disorders, Nemours Children's Health, Wilmington, DE 19803, USA
| | - Jatinder K Lamba
- Department of Pharmacotherapy & Translational Research, The University of Florida, Gainesville, FL 32611, USA
| | - Brooke L Fridley
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Ameen A Salahudeen
- Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Tempus Labs Inc., Chicago, IL 60654, USA
| | - Daniel L Hertz
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - J Kevin Hicks
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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Hegde M, Girisa S, Kunnumakkara AB. A compilation of bioinformatic approaches to identify novel downstream targets for the detection and prophylaxis of cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 134:75-113. [PMID: 36858743 DOI: 10.1016/bs.apcsb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The paradigm of cancer genomics has been radically changed by the development in next-generation sequencing (NGS) technologies making it possible to envisage individualized treatment based on tumor and stromal cells genome in a clinical setting within a short timeframe. The abundance of data has led to new avenues for studying coordinated alterations that impair biological processes, which in turn has increased the demand for bioinformatic tools for pathway analysis. While most of this work has been concentrated on optimizing certain algorithms to obtain quicker and more accurate results. Large volumes of these existing algorithm-based data are difficult for the biologists and clinicians to access, download and reanalyze them. In the present study, we have listed the bioinformatics algorithms and user-friendly graphical user interface (GUI) tools that enable code-independent analysis of big data without compromising the quality and time. We have also described the advantages and drawbacks of each of these platforms. Additionally, we emphasize the importance of creating new, more user-friendly solutions to provide better access to open data and talk about relevant problems like data sharing and patient privacy.
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Affiliation(s)
- Mangala Hegde
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Sosmitha Girisa
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India
| | - Ajaikumar B Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam, India.
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Yu L, Lin J, Li H, Sun L, Wang S, Chen Y, Chen H, Lin L. Case Report: Clinical benefit from multi-target tyrosine kinase inhibitor and PARP inhibitor in a patient with cancer of unknown primary with BRCA1 large genomic rearrangement. Front Pharmacol 2023; 14:997760. [PMID: 36755949 PMCID: PMC9899799 DOI: 10.3389/fphar.2023.997760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Background: Cancer of unknown primary (CUP), which accounts for 3%-5% of new cancer cases every year, involves the presence of a type of histologically confirmed metastatic tumors whose primary site cannot be confirmed by conventional diagnostic methods. This difficulty in identifying the primary site means that CUP patients fail to receive precisely targeted therapy. Most patients are treated with empiric chemotherapy, with a median survival of 6 months and even poorer prognosis within an unfavorable subset of CUP. Case report: An 80-year-old woman presented with masses in the abdomen. Following comprehensive imagological and immunohistochemical examinations, she was diagnosed with CUP. She emphatically declined chemotherapy; thus, anlotinib has been administered with patient consent since 02/07/2019, and stable disease (SD) was observed for 2 years. During subsequent treatment, a large genomic rearrangement in BRCA1 was identified in the patient via NGS, and SD was observed for a further 6 months following olaparib treatment. The type of LGR identified in this patient was discovered to be BRCA1 exon 17-18 inversion (inv), which has never been previously reported. Conclusion: For CUP patients, a chemo-free regimen seems to be acceptable as a first-line treatment, and NGS-guided targeted treatment could improve patient outcomes.
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Affiliation(s)
- Ling Yu
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jietao Lin
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hanhan Li
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lingling Sun
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shubo Wang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Yaoxu Chen
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Hanrui Chen
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Hanrui Chen, ; Lizhu Lin,
| | - Lizhu Lin
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Hanrui Chen, ; Lizhu Lin,
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