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Keshavarz F, Soltanshahi M, Khosravani F, Bakhshiyan F, Ghanbari A, Hassanzadeh S, Amirpour M, Ghalamfarsa G. Thymol-loaded liposomes effectively induced apoptosis and decreased EGFR expression in colorectal cancer cells. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:5157-5165. [PMID: 38240780 DOI: 10.1007/s00210-024-02945-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common and deadly cancers worldwide. Different factors, such as environmental and genetic factors and lifestyle, affect it. Owing to the presence of phenolic, alkaloid, antioxidant, and terpenoid compounds, herbal compounds can be effective in the treatment of various cancers. Thymol is a natural monoterpene phenol that is abundant in some plants and exerts several biological effects. The aim of this study was to investigate the apoptotic, anti-proliferative effect and EGFR gene expression under the influence of thymol-loaded nanoliposome in SW84 and SW111 cell lines derived from colorectal cancer. MATERIALS AND METHODS The lipid thin-film hydration method was used to synthesize thymol-loaded liposomes, and their characterization was performed using TEM, DLS, and HPLC analyses. SW84 and SW1111 cells were treated with thymol- and thymol-loaded liposomes at different doses, the inhibition of cell proliferation was evaluated using an MTT assay, the rate of apoptosis induction was assessed using flow cytometry, and EGFR gene expression was measured using real-time PCR. RESULTS The nanoparticles produced were spherical, uniform, and 200 ± 10 nm in size. HPLC analysis showed that approximately 98% thymol was loaded into the nanoliposome. The results of the MTT assay showed that thymol and thymol-nanoliposomes decreased the proliferation of SW84 and SW1111 cells in a concentration-dependent manner. The IC50 of thymol and thymol-nanoliposomes were 18 and 14.2 µg/ml for the SW48 cell line (P = 0.04) and 10.5 and 6.4 µg/ml for the SW1116 cell line (P = 0.001). Thymol-nanoliposomes significantly inhibited the proliferation of cancer cells compared to free thymol. Flow cytometry showed an increase in the percentage of apoptotic cells, especially in the thymol-nanoliposome group in the treated cells. Real-time PCR results also showed that thymol and thymol-nanoliposome both caused a decrease in the expression of EGFR genes in both cell lines, but this effect of decreasing gene expression was significantly higher in the thymol-nanoliposome group. CONCLUSIONS Our results showed that thymol-nanoliposomes reduced proliferation, increased apoptosis, and decreased EGFR expression in colorectal cancer-derived cell lines.
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Affiliation(s)
- Fatemeh Keshavarz
- Department of Immunology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Soltanshahi
- Department of Immunology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Khosravani
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Farzaneh Bakhshiyan
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Amir Ghanbari
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Sajad Hassanzadeh
- Department of Internal Medicine, School of Medicine, Yasuj University of Medical Sciences, Shahid Dr. Ghorban Ali Jalil Street, Yasuj, Iran
| | - Mozhgan Amirpour
- Department of Hematology and Blood Banking, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghasem Ghalamfarsa
- Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.
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2
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Hompe ED, Sachdeva UM. Updates in Translational Science for Esophageal and Gastric Cancers. Surg Oncol Clin N Am 2024; 33:571-581. [PMID: 38789199 DOI: 10.1016/j.soc.2023.12.022] [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] [Indexed: 05/26/2024]
Abstract
In this article, the authors summarize the current state of translational science for esophageal and gastric cancers. The available targeted therapies, immunotherapies, and recently discovered molecular targets are reviewed. The authors introduce circulating tumor deoxyribonucleic acid and its promise as a biomarker to detect disease recurrence. The authors present patient-derived organoids as a new model for studying carcinogenesis and treatment responses. Finally, we discuss the implications of organoid models for precision oncology and describe exciting new work applying gene editing technology to organoids and studying tumor-microenvironment interactions using 3-dimensional co-culture systems.
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Affiliation(s)
- Eliza D Hompe
- Division of Thoracic Surgery, Massachusetts General Hospital, 55 Fruit Street, Austen 7, Boston, MA 02114, ISA
| | - Uma M Sachdeva
- Division of Thoracic Surgery, Massachusetts General Hospital, 55 Fruit Street, Austen 7, Boston, MA 02114, ISA; Department of Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.
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Gottschalk Z, Cohen SA. Use of Circulating Tumor DNA to Guide Decision-making in Adjuvant Colon Cancer. Curr Oncol Rep 2024:10.1007/s11912-024-01565-y. [PMID: 38842605 DOI: 10.1007/s11912-024-01565-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2024] [Indexed: 06/07/2024]
Abstract
PURPOSE OF REVIEW The use of circulating tumor DNA (ctDNA) assays to guide clinical decision-making in early-stage colon cancer is an area of rapidly advancing active research. With assays clinically available, clinicians must be informed how to best use this novel tool to treat patients. RECENT FINDINGS Recent observational and prospective studies have suggested that ctDNA has potential to guide clinical decision-making in early-stage colon cancer by detecting minimal residual disease (MRD) and predicting recurrence risks. MRD-negative patients may be able to de-escalate or forgo adjuvant chemotherapy (ACT) without compromising disease-free survival or overall survival, while MRD-positive patients may benefit significantly from ACT. Recent and ongoing studies have given reason for optimism about the future of ctDNA as a useful biomarker for clinicians treating early-stage colon cancer. Data thus far are mostly limited to observational studies; inconsistent results highlight the need for caution. As more evidence emerges, ctDNA may become standard of care for colon cancer patients.
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Affiliation(s)
- Zachary Gottschalk
- Fred Hutchinson Cancer Center, 825 Eastlake Ave E, LG-465, Seattle, WA, 98177, USA
| | - Stacey A Cohen
- Fred Hutchinson Cancer Center, 825 Eastlake Ave E, LG-465, Seattle, WA, 98177, USA.
- University of Washington, Seattle, WA, USA.
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Capella MP, Fallah P, Basik M. Personalized circulating tumor DNA response to local radiotherapy in a patient with an early lobular breast cancer: A case report. Oncol Lett 2024; 27:282. [PMID: 38736743 PMCID: PMC11082640 DOI: 10.3892/ol.2024.14415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/26/2024] [Indexed: 05/14/2024] Open
Abstract
The detection of circulating tumor DNA (ctDNA) in the plasma of cancer patients is emerging as a very sensitive and specific prognostic biomarker. Previous studies with ctDNA have focused on the ability of ctDNA detection to predict micrometastatic and eventual clinical metastatic relapse. There are few data on the role of ctDNA in monitoring response to local therapy. The present study reports the case of a patient with early-stage lobular breast cancer, with a detectable ctDNA test which resolved with local radiotherapy to the breast. This case suggests that ctDNA is sensitive enough to detect the response of minimal residual disease, localized in the breast, to radiation therapy, and thus may assist in providing indications for local breast cancer treatment.
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Affiliation(s)
- Mariana Pilon Capella
- Department of Medicine and Oncology, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University Montreal, Montreal, QC H3T 1E2, Canada
| | - Parvaneh Fallah
- Department of Medicine and Oncology, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University Montreal, Montreal, QC H3T 1E2, Canada
| | - Mark Basik
- Division of Oncology, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University Montreal, Montreal, QC H3T 1E2, Canada
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Chen J, Gale RP, Hu Y, Yan W, Wang T, Zhang W. Measurable residual disease (MRD)-testing in haematological and solid cancers. Leukemia 2024; 38:1202-1212. [PMID: 38637690 PMCID: PMC11147778 DOI: 10.1038/s41375-024-02252-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024]
Affiliation(s)
- Junren Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
- Tianjin Institutes of Health Science, Tianjin, China.
| | - Robert Peter Gale
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College of Science, Technology and Medicine, London, UK
| | - Yu Hu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Wen Yan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Tiantian Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Wei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
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Pathak PS, Chan G, Deming DA, Chee CE. State-of-the-Art Management of Colorectal Cancer: Treatment Advances and Innovation. Am Soc Clin Oncol Educ Book 2024; 44:e438466. [PMID: 38768405 DOI: 10.1200/edbk_438466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Colorectal cancer (CRC) remains a significant global health challenge, ranking among the leading causes of cancer-related morbidity and mortality worldwide. Recent advancements in molecular characterization have revolutionized our understanding of the heterogeneity within colorectal tumors, particularly in the context of tumor sidedness. Tumor sidedness, referring to the location of the primary tumor in either the right or left colon, has emerged as a critical factor influencing prognosis and treatment responses in metastatic CRC. Molecular underpinnings of CRC, the impact of tumor sidedness, and how this knowledge guides therapeutic decisions in the era of precision medicine have led to improved outcomes and better quality of life in patients. The emergence of circulating tumor DNA as a prognostic and predictive tool in CRC heralds promising advancements in the diagnosis and monitoring of the disease. This innovation facilitates better patient selection for exploration of additional treatment options. As the field progresses, with investigational agents demonstrating potential as future treatments for refractory metastatic CRC, new avenues for enhancing outcomes in this challenging disease are emerging.
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Affiliation(s)
- Priyadarshini S Pathak
- Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Gloria Chan
- Department of Hematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore
| | - Dustin A Deming
- Division of Hematology, Medical Oncology, and Palliative Care, Department of Medicine, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
- University of Wisconsin Carbone Cancer Center, Madison, WI
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Cheng Ean Chee
- Department of Hematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Nordentoft I, Lindskrog SV, Birkenkamp-Demtröder K, Gonzalez S, Kuzman M, Levatic J, Glavas D, Ptashkin R, Smadbeck J, Afterman D, Lauterman T, Cohen Y, Donenhirsh Z, Tavassoly I, Alon U, Frydendahl A, Rasmussen MH, Andersen CL, Lamy P, Knudsen M, Polak P, Zviran A, Oklander B, Agerbæk M, Jensen JB, Dyrskjøt L. Whole-genome Mutational Analysis for Tumor-informed Detection of Circulating Tumor DNA in Patients with Urothelial Carcinoma. Eur Urol 2024:S0302-2838(24)02384-4. [PMID: 38811314 DOI: 10.1016/j.eururo.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/25/2024] [Accepted: 05/16/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND AND OBJECTIVE Circulating tumor DNA (ctDNA) can be used for sensitive detection of minimal residual disease (MRD). However, the probability of detecting ctDNA in settings of low tumor burden is limited by the number of mutations analyzed and the plasma volume available. We used a whole-genome sequencing (WGS) approach for ctDNA detection in patients with urothelial carcinoma. METHODS We used a tumor-informed WGS approach for ctDNA-based detection of MRD and evaluation of treatment responses. We analyzed 916 longitudinally collected plasma samples from 112 patients with localized muscle-invasive bladder cancer who received neoadjuvant chemotherapy (NAC) before radical cystectomy. Recurrence-free survival (primary endpoint), overall survival, and ctDNA dynamics during NAC were assessed. KEY FINDINGS AND LIMITATIONS We found that WGS-based ctDNA detection is prognostic for patient outcomes with a median lead time of 131 d over radiographic imaging. WGS-based ctDNA assessment after radical cystectomy identified recurrence with sensitivity of 91% and specificity of 92%. In addition, genomic characterization of post-treatment plasma samples with a high ctDNA level revealed acquisition of platinum therapy-associated mutational signatures and copy number variations not present in the primary tumors. The sequencing depth is a limitation for studying tumor evolution. CONCLUSIONS AND CLINICAL IMPLICATIONS Our results support the use of WGS for ultrasensitive ctDNA detection and highlight the possibility of plasma-based tracking of tumor evolution. WGS-based ctDNA detection represents a promising option for clinical use owing to the low volume of plasma needed and the ease of performing WGS, eliminating the need for personalized assay design. PATIENT SUMMARY Detection of tumor DNA in blood samples from patients with cancer of the urinary tract is associated with poorer outcomes. Disease recurrence after surgery can be identified by the presence of tumor DNA in blood before it can be detected on radiography scans.
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Affiliation(s)
- Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
| | - Sia Viborg Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | - Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | - Mads Agerbæk
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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8
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Wilson BE, Wright K, Koven R, Booth CM. Surveillance Imaging After Curative-Intent Treatment for Cancer: Benefits, Harms, and Evidence. J Clin Oncol 2024:JCO2302475. [PMID: 38805665 DOI: 10.1200/jco.23.02475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/23/2024] [Accepted: 03/29/2024] [Indexed: 05/30/2024] Open
Affiliation(s)
- Brooke E Wilson
- Department of Oncology, Queen's University, Kingston, ON, Canada
- Division of Cancer Care and Epidemiology, Queen's Cancer Research Institute, Kingston, ON, Canada
- School of Population Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Kristin Wright
- Department of Oncology, Queen's University, Kingston, ON, Canada
- Division of Cancer Care and Epidemiology, Queen's Cancer Research Institute, Kingston, ON, Canada
| | - Rachel Koven
- Division of Cancer Care and Epidemiology, Queen's Cancer Research Institute, Kingston, ON, Canada
| | - Christopher M Booth
- Department of Oncology, Queen's University, Kingston, ON, Canada
- Division of Cancer Care and Epidemiology, Queen's Cancer Research Institute, Kingston, ON, Canada
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Iguchi K, Shiozawa M, Uchiyama M, Asari M, Numata K, Rino Y, Saito A. Temporal dynamics of RAS mutations in circulating tumor DNA in metastatic colorectal cancer: clinical significance of mutation loss during treatment. J Cancer Res Clin Oncol 2024; 150:281. [PMID: 38805050 PMCID: PMC11133214 DOI: 10.1007/s00432-024-05805-3] [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: 04/16/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
PURPOSE In metastatic colorectal cancer (mCRC), RAS mutation loss may occur during the standard-of-care regimen. In this study, we aimed to investigate the temporal dynamics of the RAS gene and its clinical significance. METHODS This was a retrospective, single-center study that included 82 patients with tissue RAS-mutant (RAS-MT) mCRC who underwent circulating tumor DNA (ctDNA) RAS monitoring between January, 2013-April, 2023. Patients were analyzed for the rate of change over time to acquired RAS mutation loss (aRAS-ML) and clinicopathological factors. The prognostic relevance of mutation loss was assessed. RESULTS aRAS-ML was detected in 33 (40.2%) patients, 32 of whom had a mutation loss in the first ctDNA RAS assay. Patients with a RAS mutation detected in the first assay had a median time of 8 months until the second ctDNA RAS assay, with 4.5% cases newly converted to aRAS-ML; no new conversions were detected at the third assay. The aRAS-ML group exhibited more single-organ metastases in the target organ during ctDNA measurement (aRAS-ML: 84.8% vs. RAS-MT: 59.2%, p = 0.02). Of the 33 patients with aRAS-ML, seven (21.2%) received anti-epidermal growth factor receptor (EGFR) therapy, with a median progression-free survival of 8 months. Multivariate analysis revealed that persistent ctDNA RAS mutation was an independent prognostic factor for overall survival (hazard ratio: 2.7, 95% confidence interval: 1.1-6.3, p = 0.02). CONCLUSION The rate of ctDNA mutation loss in patients with RAS-MT mCRC decreases over time. Therefore, using a ctDNA RAS assay early in treatment will assist in challenging the use of EGFR regimens.
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Affiliation(s)
- Kenta Iguchi
- Department of Colorectal Surgery, Kanagawa Cancer Center, 2-3-2, Nakao, Asahi-ku, Yokohama, 241-8515, Japan.
| | - Manabu Shiozawa
- Department of Colorectal Surgery, Kanagawa Cancer Center, 2-3-2, Nakao, Asahi-ku, Yokohama, 241-8515, Japan
| | - Mamoru Uchiyama
- Department of Colorectal Surgery, Kanagawa Cancer Center, 2-3-2, Nakao, Asahi-ku, Yokohama, 241-8515, Japan
| | - Masahiro Asari
- Department of Colorectal Surgery, Kanagawa Cancer Center, 2-3-2, Nakao, Asahi-ku, Yokohama, 241-8515, Japan
| | - Koji Numata
- Department of Colorectal Surgery, Kanagawa Cancer Center, 2-3-2, Nakao, Asahi-ku, Yokohama, 241-8515, Japan
| | - Yasushi Rino
- Department of Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
| | - Aya Saito
- Department of Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
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Fu R, Xiong Y, Cai M, Li F, Chen R, Wu Y, Zhong W. Evaluation of molecular residual disease in operable non-small cell lung cancer with gene fusions, MET exon skipping or de novo MET amplification. Front Med 2024:10.1007/s11684-024-1060-z. [PMID: 38805102 DOI: 10.1007/s11684-024-1060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/17/2024] [Indexed: 05/29/2024]
Abstract
Gene fusions and MET alterations are rare and difficult to detect in plasma samples. The clinical detection efficacy of molecular residual disease (MRD) based on circulating tumor DNA (ctDNA) in patients with non-small cell lung cancer (NSCLC) with these mutations remains unknown. This prospective, non-intervention study recruited 49 patients with operable NSCLC with actionable gene fusions (ALK, ROS1, RET, and FGFR1), MET exon 14 skipping or de novo MET amplification. We analyzed 43 tumor tissues and 111 serial perioperative plasma samples using 1021- and 338-gene panels, respectively. Detectable MRD correlated with a significantly higher recurrence rate (P < 0.001), yielding positive predictive values of 100% and 90.9%, and negative predictive values of 82.4% and 86.4% at landmark and longitudinal time points, respectively. Patients with detectable MRD showed reduced disease-free survival (DFS) compared to those with undetectable MRD (P < 0.001). Patients who harbored tissue-derived fusion/MET alterations in their MRD had reduced DFS compared to those who did not (P = 0.05). To our knowledge, this is the first comprehensive study on ctDNA-MRD clinical detection efficacy in operable NSCLC patients with gene fusions and MET alterations. Patients with detectable tissue-derived fusion/MET alterations in postoperative MRD had worse clinical outcomes.
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Affiliation(s)
- Rui Fu
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | | | - Miao Cai
- Geneplus-Beijing, Beijing, 102206, China
| | - Fang Li
- Geneplus-Beijing, Beijing, 102206, China
| | | | - Yilong Wu
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Wenzhao Zhong
- School of Medicine, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
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Zollinger DR, Rivers E, Fine A, Huang Y, Son J, Kalyan A, Gray W, Baharian G, Hammond C, Ram R, Ringman L, Hafez D, Savel D, Patel V, Dantone M, Guo C, Childress M, Xu C, Johng D, Wallden B, Pokharel P, Camara W, Hegde PS, Hughes J, Carter C, Davarpanah N, Degaonkar V, Gupta P, Mariathasan S, Powles T, Ferree S, Dennis L, Young A. Analytical validation of a novel comprehensive genomic profiling informed circulating tumor DNA monitoring assay for solid tumors. PLoS One 2024; 19:e0302129. [PMID: 38753705 PMCID: PMC11098318 DOI: 10.1371/journal.pone.0302129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/28/2024] [Indexed: 05/18/2024] Open
Abstract
Emerging technologies focused on the detection and quantification of circulating tumor DNA (ctDNA) in blood show extensive potential for managing patient treatment decisions, informing risk of recurrence, and predicting response to therapy. Currently available tissue-informed approaches are often limited by the need for additional sequencing of normal tissue or peripheral mononuclear cells to identify non-tumor-derived alterations while tissue-naïve approaches are often limited in sensitivity. Here we present the analytical validation for a novel ctDNA monitoring assay, FoundationOne®Tracker. The assay utilizes somatic alterations from comprehensive genomic profiling (CGP) of tumor tissue. A novel algorithm identifies monitorable alterations with a high probability of being somatic and computationally filters non-tumor-derived alterations such as germline or clonal hematopoiesis variants without the need for sequencing of additional samples. Monitorable alterations identified from tissue CGP are then quantified in blood using a multiplex polymerase chain reaction assay based on the validated SignateraTM assay. The analytical specificity of the plasma workflow is shown to be 99.6% at the sample level. Analytical sensitivity is shown to be >97.3% at ≥5 mean tumor molecules per mL of plasma (MTM/mL) when tested with the most conservative configuration using only two monitorable alterations. The assay also demonstrates high analytical accuracy when compared to liquid biopsy-based CGP as well as high qualitative (measured 100% PPA) and quantitative precision (<11.2% coefficient of variation).
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Affiliation(s)
| | | | - Alexander Fine
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | - Yanmei Huang
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | - Joseph Son
- Natera, Austin, TX, United States of America
| | | | - Wren Gray
- Natera, Austin, TX, United States of America
| | | | | | - Rosalyn Ram
- Natera, Austin, TX, United States of America
| | | | - Dina Hafez
- Natera, Austin, TX, United States of America
| | | | - Vipul Patel
- Natera, Austin, TX, United States of America
| | | | - Cui Guo
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | | | - Chang Xu
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | - Dorhyun Johng
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | - Brett Wallden
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | - Prapti Pokharel
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | - William Camara
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | - Priti S. Hegde
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | - Jason Hughes
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | - Corey Carter
- Roche/Genentech, South San Francisco, CA, United States of America
| | | | - Viraj Degaonkar
- Roche/Genentech, South San Francisco, CA, United States of America
| | - Pratyush Gupta
- Roche/Genentech, South San Francisco, CA, United States of America
| | | | - Thomas Powles
- Barts Cancer Institute, Barts Experimental Cancer Medicine Centre, Queen Mary University of London, Barts Health, London, United Kingdom
| | - Sean Ferree
- Natera, Austin, TX, United States of America
| | - Lucas Dennis
- Foundation Medicine Inc, Cambridge, MA, United States of America
| | - Amanda Young
- Foundation Medicine Inc, Cambridge, MA, United States of America
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ShilinLi, Hu Y. Identification of four mitochondria-related genes in sepsis based on RNA sequencing technology. BMC Immunol 2024; 25:32. [PMID: 38755528 PMCID: PMC11097488 DOI: 10.1186/s12865-024-00623-1] [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: 11/26/2023] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
OBJECTIVES The purpose of this study was to identify and analyze the mitochondrial genes associated with sepsis patients in order to elucidate the underlying mechanism of sepsis immunity and provide new ideas for the clinical treatment of sepsis. METHODS The hospitalized cases of sepsis (n = 20) and systemic inflammatory response syndrome (SIRS) (n = 12) admitted to the Emergency Intensive Care Unit (EICU) of the Affiliated Hospital of Southwest Medical University from January 2019 to December 2019 were collected consecutively. RNA-seq was used to sequence the RNA (mRNA) of peripheral blood cells. Bioinformatics techniques were used to screen and identify differentially expressed RNAs, with an absolute value of fold change (FC) greater than or equal to 1.2 and a false discovery rate (FDR) less than 0.05. At the same time, mitochondrial genes were obtained from the MitoCarta 3.0 database. Differential genes were then intersected with mitochondrial genes. The resulting crossover genes were subjected to GO, KEGG, and PPI analysis. Subsequently, the GSE65682 dataset was downloaded from the GEO database for survival analysis to assess the prognostic value of core genes, and GSE67652 was downloaded for ROC curve analysis to validate the diagnostic value of core genes. Finally, the localization of core genes was clarified through 10X single-cell sequencing. RESULTS The crossing of 314 sepsis differential genes and 1136 mitochondrial genes yielded 28 genes. GO and KEGG analysis showed that the crossover genes were mainly involved in the mitochondrion, mitochondrial matrix, and mitochondrial inner membrane. Survival analysis screened four genes that were significantly negatively associated with the prognosis of sepsis, namely FIS1, FKBP8, GLRX5, and GUK1. A comparison of peripheral blood RNA-seq results between the sepsis group and the SIRS group showed that the expression levels of these four genes were significantly decreased in the sepsis group compared to the SIRS group. ROC curve analysis based on GSE67652 indicates these four genes' high sensitivity and specificity for sepsis detection. Additionally, single-cell RNA sequencing found that the core genes were mainly expressed in macrophages, T cells, and B cells. CONCLUSIONS Mitochondria-related genes (FIS1, FKBP8, GLRX5, GUK1) were underexpressed in the sepsis group, negatively correlated with survival, and mainly distributed in immune cells. This finding may guide studying the immune-related mechanisms of sepsis. This study protocol was reviewed by the Ethics Committee of the Affiliated Hospital of Southwest Medical University (ethics number: KY2018029), the clinical trial registration number is ChiCTR1900021261, and the registration date is February 4, 2019.
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Affiliation(s)
- ShilinLi
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, Luzhou, Sichuan, China
| | - Yingchun Hu
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, Luzhou, Sichuan, China.
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Tan AC, Lai GGY, Saw SPL, Chua KLM, Takano A, Ong BH, Koh TPT, Jain A, Tan WL, Ng QS, Kanesvaran R, Rajasekaran T, Kalashnikova E, Renner D, Sudhaman S, Malhotra M, Sethi H, Liu MC, Aleshin A, Lim WT, Tan EH, Skanderup AJ, Ang MK, Tan DSW. Detection of circulating tumor DNA with ultradeep sequencing of plasma cell-free DNA for monitoring minimal residual disease and early detection of recurrence in early-stage lung cancer. Cancer 2024; 130:1758-1765. [PMID: 38422026 DOI: 10.1002/cncr.35263] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/03/2023] [Accepted: 12/13/2023] [Indexed: 03/02/2024]
Abstract
BACKGROUND In early-stage non-small cell lung cancer (NSCLC), recurrence is frequently observed. Circulating tumor DNA (ctDNA) has emerged as a noninvasive tool to risk stratify patients for recurrence after curative intent therapy. This study aimed to risk stratify patients with early-stage NSCLC via a personalized, tumor-informed multiplex polymerase chain reaction (mPCR) next-generation sequencing assay. METHODS This retrospective cohort study included patients with stage I-III NSCLC. Recruited patients received standard-of-care management (surgical resection with or without adjuvant chemotherapy, followed by surveillance). Whole-exome sequencing of NSCLC resected tissue and matched germline DNA was used to design patient-specific mPCR assays (Signatera, Natera, Inc) to track up to 16 single-nucleotide variants in plasma samples. RESULTS The overall cohort with analyzed plasma samples consisted of 57 patients. Stage distribution was 68% for stage I and 16% each for stages II and III. Presurgery (i.e., at baseline), ctDNA was detected in 15 of 57 patients (26%). ctDNA detection presurgery was significantly associated with shorter recurrence-free survival (RFS; hazard ratio [HR], 3.54; 95% confidence interval [CI], 1.00-12.62; p = .009). In the postsurgery setting, ctDNA was detected in seven patients, of whom 100% experienced radiological recurrence. ctDNA positivity preceded radiological findings by a median lead time of 2.8 months (range, 0-12.9 months). Longitudinally, ctDNA detection at any time point was associated with shorter RFS (HR, 16.1; 95% CI, 1.63-158.9; p < .0001). CONCLUSIONS ctDNA detection before surgical resection was strongly associated with a high risk of relapse in early-stage NSCLC in a large unique Asian cohort. Prospective studies are needed to assess the clinical utility of ctDNA status in this setting.
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MESH Headings
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/blood
- Lung Neoplasms/pathology
- Male
- Circulating Tumor DNA/blood
- Circulating Tumor DNA/genetics
- Female
- Middle Aged
- Aged
- Retrospective Studies
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/diagnosis
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/pathology
- High-Throughput Nucleotide Sequencing/methods
- Neoplasm, Residual/genetics
- Neoplasm, Residual/diagnosis
- Neoplasm Staging
- Early Detection of Cancer/methods
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/blood
- Adult
- Aged, 80 and over
- Multiplex Polymerase Chain Reaction/methods
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Affiliation(s)
- Aaron C Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Gillianne G Y Lai
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Stephanie P L Saw
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Kevin L M Chua
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Angela Takano
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Boon-Hean Ong
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- Department of Cardiothoracic Surgery, National Heart Centre Singapore, Singapore, Singapore
| | - Tina P T Koh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Amit Jain
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Wan Ling Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Quan Sing Ng
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Ravindran Kanesvaran
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Tanujaa Rajasekaran
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | | | | | | | | | | | | | | | - Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Eng-Huat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | | | - Mei-Kim Ang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Daniel S W Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Singapore, Singapore
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Conca V, Ciracì P, Boccaccio C, Minelli A, Antoniotti C, Cremolini C. Waiting for the "liquid revolution" in the adjuvant treatment of colon cancer patients: a review of ongoing trials. Cancer Treat Rev 2024; 126:102735. [PMID: 38613871 DOI: 10.1016/j.ctrv.2024.102735] [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: 12/01/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/15/2024]
Abstract
Since colon cancer has a high rate of shedding of tumour fragments into the blood, several research efforts are now focused on the investigation of the minimal residual disease through the detection of ctDNA to tailor the adjuvant therapy of colon cancer patients and optimize its cost/effectiveness balance. The negative prognostic impact of detectable ctDNA in patients' blood after radical surgery for colon cancer is well established. Several clinical trials adopting heterogeneous designs and techniques are now ongoing to translate promises into daily practice by answering five general questions: i) is a ctDNA-guided decision making efficacious in the post-operative management of colon cancer patients? ii) are de-escalation strategies possible in ctDNA-negative cases? iii) are escalation strategies useful to improve the prognosis of ctDNA-positive patients? iv) when MRD is identified at the end of the adjuvant chemotherapy, is another post-adjuvant systemic therapy efficacious? v) can we exploit ctDNA technologies in the follow up of colon cancer patients? This review focuses on currently ongoing trials and how their results may affect the ctDNA "liquid revolution" of early colon cancer.
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Affiliation(s)
- V Conca
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - P Ciracì
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C Boccaccio
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A Minelli
- Division of Medical Oncology, Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - C Antoniotti
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C Cremolini
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.
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15
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Li Y, Xu J, Hu X, Chen Y, Liu F, Chen Y, Ma X, Dong Q, Sun L, Mo S, Zhang L, He X, Tong S, Wu H, Li W, Cai S, Zhu S, Pan Q, Peng J. Personalized circulating tumor DNA monitoring improves recurrence surveillance and management after curative resection of colorectal liver metastases: a prospective cohort study. Int J Surg 2024; 110:2776-2787. [PMID: 38445460 DOI: 10.1097/js9.0000000000001236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Approximately 60% of patients with colorectal liver metastases (CRLM) experience relapse within 2 years after radical resection, previous studies have proven that repeat local treatment (LT) could prolong survival, however, it is difficult to seize the window for LT due to the lack of a high-sensitive surveillance method. In this study, the authors aim to examine the value of longitudinal circulating tumor DNA (ctDNA) in guiding adjuvant chemotherapy, optimizing clinical surveillance strategy, and thereby improving CRLM outcomes. MATERIALS AND METHODS The authors conducted a prospective clinical trial using a personalized, tumor-informed ctDNA assay to monitor 60 CRLM patients undergoing resection with curative intent. Formalin-fixed paraffin-embedded tumor samples were collected after surgery. Blood samples were collected before surgery, 30 days after surgery (post-OP), and every third month until relapse or up to 2 years. RESULTS A total of 394 plasma samples from 60 eligible patients were analyzed, with a median follow-up time of 31.3 months. Landmark analyses revealed that detectable ctDNA at post-OP (HR, 4.8), postadjuvant chemotherapy (HR, 6.0), and end-of-treatment (HR, 5.6) were associated with higher recurrence risk ( P <0.001). Post-OP ctDNA positivity served as the only independent prognostic marker in the multivariant analysis (HR, 5.1; P <0.001). Longitudinal ctDNA analysis identified relapsed patients at both sensitivity and specificity of 100%. Most (75%) patients were found with radiological relapse within 6 months after the first detectable ctDNA with a median lead time of 3.5 months. In relapsed patients, 73.2% had oligometastatic disease and 61% were liver-restricted, of which 72.0% received repeat LTs, and 60.0% achieved a secondary no evidence of disease status. CONCLUSIONS Longitudinal ctDNA monitoring assists in early prediction of relapse, and thereby improves survival of CRLM patients by increased secondary resection rate and secondary no evidence of disease rate.
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Affiliation(s)
- Yaqi Li
- Department of Colorectal Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Jing Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Xiang Hu
- Department of Colorectal Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Yikuan Chen
- Department of Colorectal Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Fangqi Liu
- Department of Colorectal Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Yun Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Xiaoji Ma
- Department of Colorectal Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Qiduo Dong
- BGI Genomics, BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Lei Sun
- Tianjin Medical Laboratory BGI, BGI-Tianjin, Tianjin
| | - Shaobo Mo
- Department of Colorectal Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Long Zhang
- Department of Colorectal Surgery
- Cancer Institute, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Xingfeng He
- Department of Colorectal Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Shanyou Tong
- Department of Colorectal Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Huizi Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Wenhua Li
- Department of Medical Oncology
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Sanjun Cai
- Department of Colorectal Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Shida Zhu
- Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics
- BGI Genomics, BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Qi Pan
- Department of Hepatic Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Junjie Peng
- Department of Colorectal Surgery
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
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16
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Belmont E, Bansal VV, Yousef MMG, Zeineddine MA, Su D, Dhiman A, Liao CY, Polite B, Eng OS, Fournier KF, White MG, Turaga KK, Shen JP, Shergill A. Multi-Institutional Study Evaluating the Role of Circulating Tumor DNA in the Management of Appendiceal Cancers. JCO Precis Oncol 2024; 8:e2300531. [PMID: 38723230 DOI: 10.1200/po.23.00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/06/2024] [Accepted: 04/01/2024] [Indexed: 06/09/2024] Open
Abstract
PURPOSE Conventional surveillance methods are poorly sensitive for monitoring appendiceal cancers (AC). This study investigated the utility of circulating tumor DNA (ctDNA) in evaluating systemic therapy response and recurrence after surgery for AC. METHODS Patients from two specialized centers who underwent tumor-informed ctDNA testing (Signatera) were evaluated to determine the association between systemic therapy and ctDNA detection. In addition, the accuracy of ctDNA detection during surveillance for the diagnosis of recurrence after complete cytoreductive surgery (CRS) for grade 2-3 ACs with peritoneal metastases (PM) was investigated. RESULTS In this cohort of 94 patients with AC, most had grade 2-3 tumors (84.0%) and PM (84.0%). Fifty patients completed the assay in the presence of identifiable disease, among which ctDNA was detected in 4 of 7 (57.1%), 10 of 16 (62.5%), and 19 of 27 (70.4%) patients with grade 1, 2, and 3 diseases, respectively. Patients who had recently received systemic chemotherapy had ctDNA detected less frequently (7 of 16 [43.8%] v 26 of 34 [76.5%]; odds ratio, 0.22 [95% CI, 0.06 to 0.82]; P = .02). Among 36 patients with complete CRS for grade 2-3 AC-PM, 16 (44.4%) developed recurrence (median follow-up, 19.6 months). ctDNA detection was associated with shorter recurrence-free survival (median 11.3 months v not reached; hazard ratio, 14.1 [95% CI, 1.7 to 113.8]; P = .01) and showed high accuracy for the detection of recurrence (sensitivity 93.8%, specificity 85.0%). ctDNA was more sensitive than carcinoembryonic antigen (62.5%), CA19-9 (25.0%), and CA125 (18.8%) and was the only elevated biomarker in four (25%) patients with recurrence. CONCLUSION This study revealed a reduced ctDNA detection frequency after systemic therapy and accurate recurrence assessment after CRS. These findings underscore the role of ctDNA as a predictive and prognostic biomarker for grade 2-3 AC-PM management.
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Affiliation(s)
- Erika Belmont
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, Chicago, IL
| | - Varun V Bansal
- Division of Surgical Oncology, Yale School of Medicine, New Haven, CT
| | - Mahmoud M G Yousef
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mohammad A Zeineddine
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David Su
- Division of Surgical Oncology, Yale School of Medicine, New Haven, CT
| | - Ankit Dhiman
- Department of Surgery, Medical College of Georgia, Augusta, GA
| | - Chih-Yi Liao
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, Chicago, IL
| | - Blasé Polite
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, Chicago, IL
| | - Oliver S Eng
- Department of Surgery, University of California, Irvine, Orange, CA
| | - Keith F Fournier
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael G White
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kiran K Turaga
- Division of Surgical Oncology, Yale School of Medicine, New Haven, CT
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ardaman Shergill
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, Chicago, IL
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Hashimoto T, Nakamura Y, Oki E, Kobayashi S, Yuda J, Shibuki T, Bando H, Yoshino T. Bridging horizons beyond CIRCULATE-Japan: a new paradigm in molecular residual disease detection via whole genome sequencing-based circulating tumor DNA assay. Int J Clin Oncol 2024; 29:495-511. [PMID: 38551727 PMCID: PMC11043144 DOI: 10.1007/s10147-024-02493-4] [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: 01/28/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
Circulating tumor DNA (ctDNA) is the fraction of cell-free DNA in patient blood that originates from a tumor. Advances in DNA sequencing technologies and our understanding of the molecular biology of tumors have increased interest in exploiting ctDNA to facilitate detection of molecular residual disease (MRD). Analysis of ctDNA as a promising MRD biomarker of solid malignancies has a central role in precision medicine initiatives exemplified by our CIRCULATE-Japan project involving patients with resectable colorectal cancer. Notably, the project underscores the prognostic significance of the ctDNA status at 4 weeks post-surgery and its correlation to adjuvant therapy efficacy at interim analysis. This substantiates the hypothesis that MRD is a critical prognostic indicator of relapse in patients with colorectal cancer. Despite remarkable advancements, challenges endure, primarily attributable to the exceedingly low ctDNA concentration in peripheral blood, particularly in scenarios involving low tumor shedding and the intrinsic error rates of current sequencing technologies. These complications necessitate more sensitive and sophisticated assays to verify the clinical utility of MRD across all solid tumors. Whole genome sequencing (WGS)-based tumor-informed MRD assays have recently demonstrated the ability to detect ctDNA in the parts-per-million range. This review delineates the current landscape of MRD assays, highlighting WGS-based approaches as the forefront technique in ctDNA analysis. Additionally, it introduces our upcoming endeavor, WGS-based pan-cancer MRD detection via ctDNA, in our forthcoming project, SCRUM-Japan MONSTAR-SCREEN-3.
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Affiliation(s)
- Tadayoshi Hashimoto
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Yoshiaki Nakamura
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shin Kobayashi
- Department of Hepatobiliary and Pancreatic Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Junichiro Yuda
- Department of Hematology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Taro Shibuki
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hideaki Bando
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
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Zheng J, Qin C, Wang Q, Tian D, Chen Z. Circulating tumour DNA-Based molecular residual disease detection in resectable cancers: a systematic review and meta-analysis. EBioMedicine 2024; 103:105109. [PMID: 38614009 PMCID: PMC11021841 DOI: 10.1016/j.ebiom.2024.105109] [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: 09/23/2023] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND Circulating tumour DNA (ctDNA)-based molecular residual disease (MRD) detection technology has been widely used for recurrence evaluation, but there is no agreement on the efficacy of assessing recurrence and overall survival (OS) prognosis, as well as the sensitivity and specificity of landmark detection and longitudinal detection. METHODS We systematically searched Pubmed, Embase, Cochrane, and Scopus for prospective studies or randomized controlled trials that collected blood samples prospectively. The search period was from Jan 1, 2013, to Sept 10, 2023. We excluded retrospective studies. The primary endpoint was to assess the hazard ratio (HR) between circulating tumour DNA positive (ctDNA+) and negative (ctDNA-) for recurrence-free survival incidence (RFS), disease-free survival (DFS), progression-free survival (PFS), event-free survival (EFS), time to recurrence (TTR), distant metastasis-free survival (DMFS) or OS in patients with resectable cancers. We calculated the pooled HR of recurrence and OS and 95% confidence interval (CI) in patients with resected cancers using a random-effects model. Pooled sensitivity and specificity were estimated using the bivariate random effects model. FINDINGS This systematic review and meta-analysis returned 7578 records, yielding 80 included studies after exclusion. We found that the HR of recurrence across all included cancers between patients with ctDNA+ and ctDNA- was 7.48 (95% CI 6.39-8.77), and the OS was 5.58 (95% CI 4.17-7.48). We also found that the sensitivity, area under the summary receiver operating characteristic curve (AUSROC) and diagnostic odds ratio (DOR) of longitudinal tests were higher than that of landmark tests between patients with ctDNA+ and ctDNA- (0.74, 95% CI 0.68-0.80 vs 0.50, 95% CI 0.46-0.55; 0.88 vs. 0.80; 25.70, 95% CI 13.20-45.40 vs. 9.90, 95% CI 7.77-12.40). INTERPRETATION Postoperative ctDNA testing was a significant prognosis factor for recurrence and OS in patients with resectable cancers. However, the overall sensitivity of ctDNA-MRD detection could be better. Longitudinal monitoring can improve the sensitivity, AUSROC, and DOR. FUNDING Special fund project for clinical research of Qingyuan People's Hospital (QYRYCRC2023006), plan on enhancing scientific research in GMU (GZMU-SH-301).
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Affiliation(s)
- Jiachun Zheng
- Department of Respiratory and Critical Care Medicine, Affiliated Qingyuan Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Chuling Qin
- Guangzhou Medical University, Guangzhou, 511436, China
| | - Qianxi Wang
- Guangzhou Medical University, Guangzhou, 511436, China
| | - Dongbo Tian
- Department of Respiratory and Critical Care Medicine, Affiliated Qingyuan Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China.
| | - Zisheng Chen
- Department of Respiratory and Critical Care Medicine, Affiliated Qingyuan Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China.
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Oh Y, Yoon SM, Lee J, Park JH, Lee S, Hong T, Chung LI, Sudhaman S, Riddell T, Palsuledesai CC, Krainock M, Liu MC, Chae YK. Personalized, tumor-informed, circulating tumor DNA assay for detecting minimal residual disease in non-small cell lung cancer patients receiving curative treatments. Thorac Cancer 2024; 15:1095-1102. [PMID: 38558374 PMCID: PMC11062881 DOI: 10.1111/1759-7714.15281] [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: 01/07/2024] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a prognostic and predictive biomarker for detection of minimal residual disease (MRD), monitoring treatment response, and early detection of recurrence in cancer patients. In this study, we explored the utility of ctDNA-based MRD detection to predict recurrence in a real-world cohort of primarily early-stage non-small cell lung cancer (NSCLC) patients treated with curative intent. METHODS Longitudinal plasma samples were collected post curative-intent treatment from 36 patients with stage I-IV NSCLC. A personalized, tumor-informed assay was used to detect and quantify ctDNA in plasma samples. RESULTS Of the 24 patients with plasma samples available during the MRD window (within 6 months of curative surgery and before adjuvant therapy), ctDNA was detectable in two patients. Patients with ctDNA-positivity during the MRD window were 15 times more likely to recur compared to ctDNA-negative patients (HR: 15.0, 95% CI: 1.0-253.0, p = 0.010). At any time post-curative intent treatment, ctDNA-positivity was associated with significantly poorer recurrence-free survival compared to persistently ctDNA-negative patients (p < 0.0001). CONCLUSION Our real-world data indicate that longitudinal, personalized, tumor-informed ctDNA monitoring is a valuable tool in patients with NSCLC receiving curative treatment to identify patients at high risk for recurrence.
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Affiliation(s)
- Youjin Oh
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
- Department of internal medicineJohn H. Stroger Hospital of Cook CountyChicagoIllinoisUSA
| | - Sung Mi Yoon
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
- North Central Bronx Hospital, Albert Einstein College of MedicineBronxNew YorkUSA
| | - Jeeyeon Lee
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
- Kyungpook National University School of Medicine, Kyungpook National University Chilgok HospitalDaeguRepublic of Korea
| | - Joo Hee Park
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
| | - Soowon Lee
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
- Baylor UniversityWacoTexasUSA
| | - Timothy Hong
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
| | | | | | | | | | | | | | - Young Kwang Chae
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
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Alvarez J, Shi Q, Dasari A, Garcia-Aguilar J, Sanoff H, George TJ, Hong TS, Yothers G, Philip PA, Nelson GD, Al Baghdadi T, Alese O, Zambare W, Omer DM, Verheij FS, Buckley J, Williams H, George M, Garcia R, O'Reilly EM, Meyerhardt JA, Shergill A, Horvat N, Romesser PB, Hall WA, Smith JJ. ALLIANCE A022104/NRG-GI010: The Janus Rectal Cancer Trial: a randomized phase II/III trial testing the efficacy of triplet versus doublet chemotherapy regarding clinical complete response and disease-free survival in patients with locally advanced rectal cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.25.24306396. [PMID: 38712176 PMCID: PMC11071544 DOI: 10.1101/2024.04.25.24306396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Background Recent data have demonstrated that in locally advanced rectal cancer (LARC), a total neoadjuvant therapy (TNT) approach improves compliance with chemotherapy and increases rates of tumor response compared to neoadjuvant chemoradiation (CRT) alone. They further indicate that the optimal sequencing of TNT involves consolidation (rather than induction) chemotherapy to optimize complete response rates. Data, largely from retrospective studies, have also shown that patients with clinical complete response (cCR) after neoadjuvant therapy may be managed safely with the watch and wait approach (WW) instead of preemptive total mesorectal resection (TME). However, the optimal consolidation chemotherapy regimen to achieve cCR has not been established, and a randomized clinical trial has not robustly evaluated cCR as a primary endpoint. Collaborating with a multidisciplinary oncology team and patient groups, we designed this NCI-sponsored study of chemotherapy intensification to address these issues and to drive up cCR rates, to provide opportunity for organ preservation, improve quality of life for patients and improve survival outcomes. Methods In this NCI-sponsored multi-group randomized, seamless phase II/III trial (1:1), up to 760 patients with LARC, T4N0, any T with node positive disease (any T, N+) or T3N0 requiring abdominoperineal resection or coloanal anastomosis and distal margin within 12 cm of anal verge will be enrolled. Stratification factors include tumor stage (T4 vs T1-3), nodal stage (N+ vs N0) and distance from anal verge (0-4; 4-8; 8-12 cm). Patients will be randomized to receive neoadjuvant long course chemoradiation (LCRT) followed by consolidation doublet (mFOLFOX6 or CAPOX) or triplet chemotherapy (mFOLFIRINOX) for 3-4 months. LCRT in both arms involves 4500 cGy in 25 fractions over 5 weeks + 900 cGy boost in 5 fractions with a fluoropyrimidine (capecitabine preferred). Patients will undergo assessment 8-12 (+/- 4) weeks post-TNT completion. The primary endpoint for the phase II portion will compare cCR between treatment arms. A total number of 296 evaluable patients (148 per arm) will provide statistical power of 90.5% to detect an 17% increase in cCR rate, at a one-sided alpha=0.048. The primary endpoint for the phase III portion will compare disease-free survival (DFS) between treatment arms. A total of 285 DFS events will provide 85% power to detect an effect size of hazard ratio 0.70 at a one-sided alpha of 0.025, requiring enrollment of 760 patients (380 per arm). Secondary objectives include time-to event outcomes (overall survival, organ preservation time and time to distant metastasis) and adverse effects. Biospecimens including archival tumor tissue, plasma and buffy coat in EDTA tubes, and serial rectal MRIs will be collected for exploratory correlative research. This study, activated in late 2022, is open across the NCTN and has a current accrual of 312. Support: U10CA180821, U10CA180882, U24 CA196171; https://acknowledgments.alliancefound.org . Discussion Building off of data from modern day rectal cancer trials and patient input from national advocacy groups, we have designed the current trial studying chemotherapy intensification via a consolidation chemotherapy approach with the intent to enhance cCR and DFS rates, increase organ preservation rates, and improve quality of life for patients with rectal cancer. Trial Registration Clinicaltrials.gov ID: NCT05610163 ; Support includes U10CA180868 (NRG) and U10CA180888 (SWOG).
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Sullo FG, Passardi A, Gallio C, Molinari C, Marisi G, Pozzi E, Solaini L, Bittoni A. Advancing Personalized Medicine in the Treatment of Locally Advanced Rectal Cancer. J Clin Med 2024; 13:2562. [PMID: 38731090 PMCID: PMC11084727 DOI: 10.3390/jcm13092562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/12/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Rectal cancer presents a significant burden globally, often requiring multimodal therapy for locally advanced cases. Long-course chemoradiotherapy (LCRT) and short-course radiotherapy (SCRT) followed by surgery have been conventional neoadjuvant approaches. Recent trials favor LCRT due to improved local control. However, distant tumor recurrence remains a concern, prompting the exploration of total neoadjuvant therapy (TNT) as a comprehensive treatment strategy. Immune checkpoint inhibitors (ICIs) show promise, particularly in mismatch repair-deficient (dMMR) or microsatellite instability-high (MSI-H) tumors, potentially revolutionizing neoadjuvant regimens. Nonoperative management (NOM) represents a viable alternative post-neoadjuvant therapy for selected patients achieving complete clinical response (cCR). Additionally, monitoring minimal residual disease (MRD) using circulating tumor DNA (ctDNA) emerges as a non-invasive method for the assessment of treatment response. This review synthesizes current evidence on TNT, ICIs, NOM, and ctDNA, elucidating their implications for rectal cancer management and highlighting avenues for future research and clinical application.
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Affiliation(s)
- Francesco Giulio Sullo
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, via P. Maroncelli 40, 47014 Meldola, Italy; (F.G.S.); (C.G.); (A.B.)
| | - Alessandro Passardi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, via P. Maroncelli 40, 47014 Meldola, Italy; (F.G.S.); (C.G.); (A.B.)
| | - Chiara Gallio
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, via P. Maroncelli 40, 47014 Meldola, Italy; (F.G.S.); (C.G.); (A.B.)
| | - Chiara Molinari
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, via P. Maroncelli 40, 47014 Meldola, Italy; (C.M.); (G.M.)
| | - Giorgia Marisi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, via P. Maroncelli 40, 47014 Meldola, Italy; (C.M.); (G.M.)
| | - Eleonora Pozzi
- Department of Medical and Surgical Science, University of Bologna, 47121 Forlì, Italy (L.S.)
| | - Leonardo Solaini
- Department of Medical and Surgical Science, University of Bologna, 47121 Forlì, Italy (L.S.)
| | - Alessandro Bittoni
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, via P. Maroncelli 40, 47014 Meldola, Italy; (F.G.S.); (C.G.); (A.B.)
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22
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Zarkavelis G, Amylidi AL, Torounidou N, Yerolatsite M, Keravasili A, Keramisanou V, Mauri D. Exploring RAS mutation incidence and temporal heterogeneity in metastatic colorectal cancer patients - a single-institution experience utilising circulating tumour DNA. Contemp Oncol (Pozn) 2024; 28:45-50. [PMID: 38800532 PMCID: PMC11117156 DOI: 10.5114/wo.2024.138899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/25/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Colorectal cancer (CRC) remains a significant global health challenge, ranking among the leading causes of neoplastic mortality. Despite transformative therapeutic advances, a considerable proportion of patients are diagnosed with metastatic disease, and 15-30% of those initially presenting with early-stage CRC eventually experience recurrence. Comprehensive molecular testing, especially the evaluation of microsatellite instability and mutations in KRAS/NRAS or BRAF genes, is essential upon diagnosis of stage IV disease, guiding treatment decisions. Material and methods This manuscript explores the mutational landscape of KRAS and NRAS in patients with CRC, employing digital polymerase chain reaction (PCR) BEAMing for the detection of mutations in liquid biopsy. Our study enrolled patients with histologically confirmed CRC and stage IV disease, focusing on identifying mutations in KRAS and NRAS genes during various stages of therapy. Results Evaluating baseline, midline, and progression samples, we found that 66.6% maintained consistent mutational status post-disease progression, while 33.3% exhibited a shift in mutational status. The application of techniques with high sensitivity, such as BEAMing Digital PCR, is pivotal for accurate circulating tumour DNA (ctDNA) mutation detection. The study underscores the significance of continuous molecular monitoring in guiding therapeutic decisions for patients with metastatic CRC. Conclusions Our findings contribute to our understanding of the evolving mutational landscape and the potential clinical implications of ctDNA ana- lysis in the era of personalised cancer medicine.
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Affiliation(s)
- George Zarkavelis
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | - Anna Lea Amylidi
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | - Nanteznta Torounidou
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina, Greece
| | - Melina Yerolatsite
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina, Greece
| | - Athanasia Keravasili
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina, Greece
| | - Varvara Keramisanou
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina, Greece
| | - Davide Mauri
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
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23
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Nesic M, Rasmussen MH, Henriksen TV, Demuth C, Frydendahl A, Nordentoft I, Dyrskjøt L, Andersen CL. Beyond basics: Key mutation selection features for successful tumor-informed ctDNA detection. Int J Cancer 2024. [PMID: 38623608 DOI: 10.1002/ijc.34964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
Tumor-informed mutation-based approaches are frequently used for detection of circulating tumor DNA (ctDNA). Not all mutations make equally effective ctDNA markers. The objective was to explore if prioritizing mutations using mutational features-such as cancer cell fraction (CCF), multiplicity, and error rate-would improve the success rate of tumor-informed ctDNA analysis. Additionally, we aimed to develop a practical and easily implementable analysis pipeline for identifying and prioritizing candidate mutations from whole-exome sequencing (WES) data. We analyzed WES and ctDNA data from three tumor-informed ctDNA studies, one on bladder cancer (Cohort A) and two on colorectal cancer (Cohorts I and N). The studies included 390 patients. For each patient, a unique set of mutations (median mutations/patient: 6, interquartile 13, range: 1-46, total n = 4023) were used as markers of ctDNA. The tool PureCN was used to assess the CCF and multiplicity of each mutation. High-CCF mutations were detected more frequently than low-CCF mutations (Cohort A: odds ratio [OR] 20.6, 95% confidence interval [CI] 5.72-173, p = 1.73e-12; Cohort I: OR 2.24, 95% CI 1.44-3.52, p = 1.66e-04; and Cohort N: OR 1.78, 95% CI 1.14-2.79, p = 7.86e-03). The detection-likelihood was additionally improved by selecting mutations with multiplicity of two or above (Cohort A: OR 1.55, 95% CI 1. 14-2.11, p = 3.85e-03; Cohort I: OR 1.78, 95% CI 1.23-2.56, p = 1.34e-03; and Cohort N: OR 1.94, 95% CI 1.63-2.31, p = 2.83e-14). Furthermore, selecting the mutations for which the ctDNA detection method had the lowest error rates, additionally improved the detection-likelihood, particularly evident when plasma cell-free DNA tumor fractions were below 0.1% (p = 2.1e-07). Selecting mutational markers with high CCF, high multiplicity, and low error rate significantly improve ctDNA detection likelihood. We provide free access to the analysis pipeline enabling others to perform qualified prioritization of mutations for tumor-informed ctDNA analysis.
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Affiliation(s)
- Marijana Nesic
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Tenna V Henriksen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christina Demuth
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Amanda Frydendahl
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Claus L Andersen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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24
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Frydendahl A, Rasmussen MH, Jensen SØ, Henriksen TV, Demuth C, Diekema M, Ditzel HJ, Wen SWC, Pedersen JS, Dyrskjøt L, Andersen CL. Error-Corrected Deep Targeted Sequencing of Circulating Cell-Free DNA from Colorectal Cancer Patients for Sensitive Detection of Circulating Tumor DNA. Int J Mol Sci 2024; 25:4252. [PMID: 38673836 PMCID: PMC11049993 DOI: 10.3390/ijms25084252] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Circulating tumor DNA (ctDNA) is a promising biomarker, reflecting the presence of tumor cells. Sequencing-based detection of ctDNA at low tumor fractions is challenging due to the crude error rate of sequencing. To mitigate this challenge, we developed ultra-deep mutation-integrated sequencing (UMIseq), a fixed-panel deep targeted sequencing approach, which is universally applicable to all colorectal cancer (CRC) patients. UMIseq features UMI-mediated error correction, the exclusion of mutations related to clonal hematopoiesis, a panel of normal samples for error modeling, and signal integration from single-nucleotide variations, insertions, deletions, and phased mutations. UMIseq was trained and independently validated on pre-operative (pre-OP) plasma from CRC patients (n = 364) and healthy individuals (n = 61). UMIseq displayed an area under the curve surpassing 0.95 for allele frequencies (AFs) down to 0.05%. In the training cohort, the pre-OP detection rate reached 80% at 95% specificity, while it was 70% in the validation cohort. UMIseq enabled the detection of AFs down to 0.004%. To assess the potential for detection of residual disease, 26 post-operative plasma samples from stage III CRC patients were analyzed. From this we found that the detection of ctDNA was associated with recurrence. In conclusion, UMIseq demonstrated robust performance with high sensitivity and specificity, enabling the detection of ctDNA at low allele frequencies.
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Affiliation(s)
- Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Sarah Østrup Jensen
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Tenna Vesterman Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Mathilde Diekema
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Henrik Jørn Ditzel
- Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark;
- Department of Oncology, Odense University Hospital, 5000 Odense, Denmark
| | | | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Bioinformatics Research Center, Faculty of Science, Aarhus University, 8000 Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
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Lele SJ, Adilbay D, Lewis E, Pang J, Asarkar AA, Nathan CAO. ctDNA as an Adjunct to Posttreatment PET for Head and Neck Cancer Recurrence Risk Assessment. Otolaryngol Head Neck Surg 2024. [PMID: 38591659 DOI: 10.1002/ohn.760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/21/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVE Circulating tumor DNA (ctDNA) detection is an emerging technique that identifies minimal residual disease in patients with solid tumors. ctDNA can act as an adjunct method to help overcome the limitations of positron emission tomography (PET) and select patients who are at high risk for recurrence. STUDY DESIGN Retrospective Single Institutional Study. SETTING University Hospital Setting. METHODS Twenty-nine patients who underwent definitive treatment for squamous cell carcinoma of the head and neck (HNSCC) from 8/2021 to 01/2023 had ctDNA levels analyzed at 1 to 3, 6, 9, and 12 months after definitive treatment. A personalized, tumor-informed, multiplex polymerase chain reaction (PCR) next-generation sequencing (NGS) assay was used to detect the ctDNA levels. The primary outcome was recurrence-free probability (RFP), and the secondary outcomes were overall survival (OS), sensitivity, specificity, and the test's negative (NPV) and positive predictive values (PPV). RESULTS The median age of patients was 65 years (interquartile range: 56-69), with majority being males (n = 22, 76%). The primary sites were larynx (n = 12), oropharynx (n = 10), and oral cavity (n = 6). Posttreatment ctDNA was detected in 7 patients, all of whom had disease recurrence. ctDNA detection after definitive treatment was associated with a higher risk of disease recurrence (hazard ratio: 9.94, 95% confidence interval: 1.56-63.3, P = .015). ctDNA identified recurrence with 100% specificity and 78% sensitivity. The NPV and PPV were 91% and 100%. PET had 78% sensitivity but only 68% specificity with 86% NPV, and 54% PPV. CONCLUSION Based on our data, ctDNA can be an excellent adjunct test for posttreatment PET and can help guide physicians in cases where PET results are inconclusive and difficult to interpret.
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Affiliation(s)
- Saudamini J Lele
- Department of Otolaryngology and Head Neck Surgery, Louisiana State University of Health Sciences, Shreveport, Louisiana, USA
| | - Dauren Adilbay
- Department of Otolaryngology and Head Neck Surgery, Louisiana State University of Health Sciences, Shreveport, Louisiana, USA
| | - Ellen Lewis
- Department of Otolaryngology and Head Neck Surgery, Louisiana State University of Health Sciences, Shreveport, Louisiana, USA
- Feist Weiller Cancer Center, Shreveport, Louisiana, USA
| | - John Pang
- Department of Otolaryngology and Head Neck Surgery, Louisiana State University of Health Sciences, Shreveport, Louisiana, USA
- Feist Weiller Cancer Center, Shreveport, Louisiana, USA
| | - Ameya A Asarkar
- Department of Otolaryngology and Head Neck Surgery, Louisiana State University of Health Sciences, Shreveport, Louisiana, USA
- Feist Weiller Cancer Center, Shreveport, Louisiana, USA
| | - Cherie-Ann O Nathan
- Department of Otolaryngology and Head Neck Surgery, Louisiana State University of Health Sciences, Shreveport, Louisiana, USA
- Feist Weiller Cancer Center, Shreveport, Louisiana, USA
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Saito T, Kurokawa Y, Fujitani K, Kawabata R, Takeno A, Mikami J, Endo S, Matsuyama J, Akamaru Y, Hirota M, Kishi K, Urakawa S, Yamamoto K, Tanaka K, Takahashi T, Oka M, Wada H, Eguchi H, Doki Y. Serum NY-ESO-1 antibody as a predictive biomarker for postoperative recurrence of gastric cancer: a multicenter prospective observational study. Br J Cancer 2024; 130:1157-1165. [PMID: 38326601 PMCID: PMC10991393 DOI: 10.1038/s41416-023-02540-3] [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: 04/11/2023] [Revised: 11/18/2023] [Accepted: 12/01/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND No reliable marker has been identified to predict postoperative recurrence of gastric cancer. We designed a clinical trial to investigate the utility of serum NY-ESO-1 antibody responses as a predictive marker for postoperative recurrence in gastric cancer. METHODS A multicenter prospective study was conducted between 2012 and 2021. Patients with resectable cT3-4 gastric cancer were included. Postoperative NY-ESO-1 and p53 antibody responses were serially evaluated every 3 months for 1 year in patients with positive preoperative antibody responses. The recurrence rate was assessed by the positivity of antibody responses at 3 and 12 months postoperatively. RESULTS Among 1001 patients, preoperative NY-ESO-1 and p53 antibody responses were positive in 12.6% and 18.1% of patients, respectively. NY-ESO-1 antibody responses became negative postoperatively in non-recurrent patients (negativity rates; 45% and 78% at 3 and 12 months, respectively), but remained positive in recurrent patients (negativity rates; 9% and 8%, respectively). p53 antibody responses remained positive in non-recurrent patients. In multivariate analysis, NY-ESO-1 antibody positivity at 3 months (P < 0.03) and 12 months (P < 0.001) were independent prognostic factors for a shorter recurrence-free interval. CONCLUSIONS Serum NY-ESO-1 antibodies may be a useful predictive marker for postoperative recurrence in gastric cancer. CLINICAL TRIAL REGISTRATION UMIN000007925.
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Affiliation(s)
- Takuro Saito
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Japan.
| | - Yukinori Kurokawa
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kazumasa Fujitani
- Department of Gastroenterological Surgery, Osaka General Medical Center, Osaka, Japan
| | | | - Atsushi Takeno
- Department of Surgery, Kansai Rosai Hospital, Amagasaki, Japan
| | - Jota Mikami
- Department of Surgery, Sakai City Medical Center, Sakai, Japan
| | - Shunji Endo
- Department of Surgery, Higashi-Osaka Medical Center, Higashi-Osaka, Japan
| | - Jin Matsuyama
- Department of Surgery, Yao Municipal Hospital, Yao, Japan
| | - Yusuke Akamaru
- Department of Surgery, Ikeda City Hospital, Osaka, Japan
| | - Masashi Hirota
- Department of Surgery, Toyonaka Municipal Hospital, Toyonaka, Japan
| | - Kentaro Kishi
- Department of Surgery, Osaka Police Hospital, Osaka, Japan
| | - Shinya Urakawa
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kei Yamamoto
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Koji Tanaka
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tsuyoshi Takahashi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Mikio Oka
- Department of Immuno-Oncology, Kawasaki Medical School, Okayama, Japan
| | - Hisashi Wada
- Department of Clinical Research in Tumor Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Japan
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Abe M, Hiraki H, Tsuyukubo T, Ono S, Maekawa S, Tamura D, Yashima-Abo A, Kato R, Fujisawa H, Iwaya T, Park WY, Idogawa M, Tokino T, Obara W, Nishizuka SS. The Clinical Validity of Urinary Pellet DNA Monitoring for the Diagnosis of Recurrent Bladder Cancer. J Mol Diagn 2024; 26:278-291. [PMID: 38301868 DOI: 10.1016/j.jmoldx.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/07/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
The aim of this study was to evaluate the clinical validity of monitoring urine pellet DNA (upDNA) of bladder cancer (BC) by digital PCR (dPCR) as a biomarker for early recurrence prediction, treatment efficacy evaluation, and no-recurrence corroboration. Tumor panel sequencing was first performed to select patient-unique somatic mutations to monitor both upDNA and circulating tumor DNA (ctDNA) by dPCR. For longitudinal monitoring using upDNA as well as plasma ctDNA, an average of 7.2 (range, 2 to 12) time points per case were performed with the dPCR assay for 32 previously treated and untreated patients with BC. Clinical recurrence based on imaging and urine cytology was compared using upDNA variant allele frequency (VAF) dynamics. A continuous increasing trend of upDNA VAF ≥1% was considered to indicate molecular recurrence. Most (30/32; 93.8%) cases showed at least one traceable somatic mutation. In 5 of 7 cases (71.4%) with clinical recurrence, upDNA VAF >1% was detected 7 to 15 months earlier than the imaging diagnosis. The upDNA VAF remained high after initial treatment for locally recurrent cases. The clinical validity of upDNA monitoring was confirmed with the observation that 26 of 30 cases (86.7%) were traceable. Local recurrences were not indicated by ctDNA alone. The results support the clinical validity of upDNA monitoring in the management of recurrent BC.
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Affiliation(s)
- Masakazu Abe
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan; Department of Urology, Iwate Medical University School of Medicine, Yahaba, Japan
| | - Hayato Hiraki
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
| | - Takashi Tsuyukubo
- Department of Urology, Iwate Prefectural Central Hospital, Morioka, Japan
| | - Sadahide Ono
- Department of Diagnostic Pathology, Iwate Prefectural Central Hospital, Morioka, Japan
| | - Shigekatsu Maekawa
- Department of Urology, Iwate Medical University School of Medicine, Yahaba, Japan
| | - Daichi Tamura
- Department of Urology, Iwate Medical University School of Medicine, Yahaba, Japan
| | - Akiko Yashima-Abo
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
| | - Renpei Kato
- Department of Urology, Iwate Medical University School of Medicine, Yahaba, Japan
| | - Hiromitsu Fujisawa
- Department of Urology, Iwate Prefectural Central Hospital, Morioka, Japan
| | - Takeshi Iwaya
- Department of Clinical Oncology, Iwate Medical University School of Medicine, Yahaba, Japan
| | - Woong-Yang Park
- Geninus Inc., Seoul, Republic of Korea; Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Masashi Idogawa
- Department of Medical Genome Sciences, Cancer Research Institute, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takashi Tokino
- Department of Medical Genome Sciences, Cancer Research Institute, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Wataru Obara
- Department of Urology, Iwate Medical University School of Medicine, Yahaba, Japan
| | - Satoshi S Nishizuka
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan.
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Ren F, Fei Q, Qiu K, Zhang Y, Zhang H, Sun L. Liquid biopsy techniques and lung cancer: diagnosis, monitoring and evaluation. J Exp Clin Cancer Res 2024; 43:96. [PMID: 38561776 PMCID: PMC10985944 DOI: 10.1186/s13046-024-03026-7] [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: 01/12/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024] Open
Abstract
Lung cancer stands as the most prevalent form of cancer globally, posing a significant threat to human well-being. Due to the lack of effective and accurate early diagnostic methods, many patients are diagnosed with advanced lung cancer. Although surgical resection is still a potential means of eradicating lung cancer, patients with advanced lung cancer usually miss the best chance for surgical treatment, and even after surgical resection patients may still experience tumor recurrence. Additionally, chemotherapy, the mainstay of treatment for patients with advanced lung cancer, has the potential to be chemo-resistant, resulting in poor clinical outcomes. The emergence of liquid biopsies has garnered considerable attention owing to their noninvasive nature and the ability for continuous sampling. Technological advancements have propelled circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), extracellular vesicles (EVs), tumor metabolites, tumor-educated platelets (TEPs), and tumor-associated antigens (TAA) to the forefront as key liquid biopsy biomarkers, demonstrating intriguing and encouraging results for early diagnosis and prognostic evaluation of lung cancer. This review provides an overview of molecular biomarkers and assays utilized in liquid biopsies for lung cancer, encompassing CTCs, ctDNA, non-coding RNA (ncRNA), EVs, tumor metabolites, TAAs and TEPs. Furthermore, we expound on the practical applications of liquid biopsies, including early diagnosis, treatment response monitoring, prognostic evaluation, and recurrence monitoring in the context of lung cancer.
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Affiliation(s)
- Fei Ren
- Department of Geriatrics, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Qian Fei
- Department of Oncology, Shengjing Hospital of China Medical University, Shen Yang, 110000, China
| | - Kun Qiu
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Yuanjie Zhang
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Heyang Zhang
- Department of Hematology, The First Hospital of China Medical University, Shen Yang, 110000, China.
| | - Lei Sun
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China.
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Tian X, Liu X, Wang K, Wang R, Li Y, Qian K, Wang T, Zhao X, Liu L, Zhang PL, Xiong Y, Rui J, Chen R, Zhang Y. Postoperative ctDNA in indicating the recurrence risk and monitoring the effect of adjuvant therapy in surgical non-small cell lung cancer. Thorac Cancer 2024; 15:797-807. [PMID: 38409945 PMCID: PMC10995713 DOI: 10.1111/1759-7714.15251] [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: 10/12/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a potential novel biomarker to predict molecular residual disease (MRD) in lung cancer after definitive treatment. Herein, we investigated the value of ctDNA in prognosing risk of relapse and monitoring the effect of adjuvant therapy in surgical non-small cell lung cancer (NSCLC). METHODS We enrolled 58 NSCLC patients in a real-world setting, and 58 tumor tissues and 325 plasma samples were analyzed. Tumor tissues and plasma samples were subjected to targeted next-generation sequencing (NGS) of 1021 cancer-related and ultra-deep targeted NGS covering 338 genes, respectively. RESULTS ctDNA was detected in 31.0% of cases at the first postoperative time, which was associated with advanced tumor stage, T stage and KEAP1 or GRIN2A mutations in tissues. ctDNA positivity at landmark and longitudinal indicated the shorter disease-free survival. For patients with ctDNA positivity at the first postoperative time, regardless of adjuvant therapy, all patients who were persistently ctDNA positive during postoperative surveillance had disease recurrence. Among the patients who were ctDNA negative, only two patients (15.4%, 2/13) receiving adjuvant therapy relapsed, while one patient (50.0%, 1/2) without adjuvant therapy relapsed. For the first postoperative ctDNA negative patients, the recurrence rate of patients with adjuvant therapy was and higher than without adjuvant therapy (22.6% [7/31] vs. 11.1% [1/9]). The patients who became ctDNA positive may also benefit from intervention therapy. CONCLUSION Postoperative ctDNA is a prognostic marker, and ctDNA-detection may facilitate personalized adjuvant therapy, and applying adjuvant therapy to the patients with detectable ctDNA could bring clinical benefits for them.
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Affiliation(s)
- Xiaoru Tian
- Department of Thoracic SurgeryXuanwu Hospital Capital Medical UniversityBeijingChina
| | - Xingsheng Liu
- Department of Thoracic SurgeryXuanwu Hospital Capital Medical UniversityBeijingChina
| | - Kai Wang
- Medical CenterGeneplus‐BeijingBeijingChina
| | - Ruotian Wang
- Department of Thoracic SurgeryXuanwu Hospital Capital Medical UniversityBeijingChina
| | - Yuanbo Li
- Department of Thoracic SurgeryXuanwu Hospital Capital Medical UniversityBeijingChina
| | - Kun Qian
- Department of Thoracic SurgeryXuanwu Hospital Capital Medical UniversityBeijingChina
| | - Tengteng Wang
- Department of Thoracic SurgeryXuanwu Hospital Capital Medical UniversityBeijingChina
| | - Xin Zhao
- Department of Thoracic SurgeryXuanwu Hospital Capital Medical UniversityBeijingChina
| | - Lei Liu
- Department of Thoracic SurgeryXuanwu Hospital Capital Medical UniversityBeijingChina
| | - Pei Long Zhang
- Department of Thoracic SurgeryXuanwu Hospital Capital Medical UniversityBeijingChina
| | | | - Jinqiu Rui
- Medical CenterGeneplus‐BeijingBeijingChina
| | | | - Yi Zhang
- Department of Thoracic SurgeryXuanwu Hospital Capital Medical UniversityBeijingChina
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Shaw JA, Page K, Wren E, de Bruin EC, Kalashnikova E, Hastings R, McEwen R, Zhang E, Wadsley M, Acheampong E, Renner D, Gleason KL, Ambasager B, Stetson D, Fernandez-Garcia D, Guttery D, Allsopp RC, Rodriguez A, Zimmermann B, Sethi H, Aleshin A, Liu MC, Richards C, Stebbing J, Ali S, Rehman F, Cleator S, Kenny L, Ahmed S, Armstrong AC, Coombes RC. Serial Postoperative Circulating Tumor DNA Assessment Has Strong Prognostic Value During Long-Term Follow-Up in Patients With Breast Cancer. JCO Precis Oncol 2024; 8:e2300456. [PMID: 38691816 PMCID: PMC11161241 DOI: 10.1200/po.23.00456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/09/2023] [Accepted: 01/18/2024] [Indexed: 05/03/2024] Open
Abstract
PURPOSE Here, we report the sensitivity of a personalized, tumor-informed circulating tumor DNA (ctDNA) assay (Signatera) for detection of molecular relapse during long-term follow-up of patients with breast cancer. METHODS A total of 156 patients with primary breast cancer were monitored clinically for up to 12 years after surgery and adjuvant chemotherapy. Semiannual blood samples were prospectively collected, and analyzed retrospectively to detect residual disease by ultradeep sequencing using ctDNA assays, developed from primary tumor whole-exome sequencing data. RESULTS Personalized Signatera assays detected ctDNA ahead of clinical or radiologic relapse in 30 of the 34 patients who relapsed (patient-level sensitivity of 88.2%). Relapse was predicted with a lead interval of up to 38 months (median, 10.5 months; range, 0-38 months), and ctDNA positivity was associated with shorter relapse-free survival (P < .0001) and overall survival (P < .0001). All relapsing triple-negative patients (n = 7/23) had a ctDNA-positive test within a median of 8 months (range, 0-19 months), while the 16 nonrelapsed patients with triple-negative breast cancer remained ctDNA-negative during a median follow-up of 58 months (range, 8-99 months). The four patients who had negative tests before relapse all had hormone receptor-positive (HR+) disease and conversely, five of the 122 nonrelapsed patients (all HR+) had an occasional positive test. CONCLUSION Serial postoperative ctDNA assessment has strong prognostic value, provides a potential window for earlier therapeutic intervention, and may enable more effective monitoring than current clinical tests such as cancer antigen 15-3. Our study provides evidence that those with serially negative ctDNA tests have superior clinical outcomes, providing reassurance to patients with breast cancer. For select cases with HR+ disease, decisions about treatment management might require serial monitoring despite the ctDNA-positive result.
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Affiliation(s)
- Jacqueline A. Shaw
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Karen Page
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Evie Wren
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Elza C. de Bruin
- Oncology R&D, Research & Early Development, AstraZeneca, Cambridge, United Kingdom
| | | | - Robert Hastings
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Rob McEwen
- Oncology R&D, Research & Early Development, AstraZeneca, Cambridge, United Kingdom
| | - Eddie Zhang
- Oncology R&D, Research & Early Development, AstraZeneca, Waltham, MA
| | - Marc Wadsley
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Emmanuel Acheampong
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | | | - Kelly L.T. Gleason
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Bana Ambasager
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Daniel Stetson
- Oncology R&D, Research & Early Development, AstraZeneca, Waltham, MA
| | | | - David Guttery
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Rebecca C. Allsopp
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | | | | | | | | | | | - Cathy Richards
- University Hospitals Leicester NHS Trust, Leicester, United Kingdom
| | - Justin Stebbing
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Farah Rehman
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Susan Cleator
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Laura Kenny
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Samreen Ahmed
- University Hospitals Leicester NHS Trust, Leicester, United Kingdom
| | - Anne C. Armstrong
- Division of Cancer Sciences, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - R. Charles Coombes
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
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Fu X, Luo Z, Deng Y, LaFramboise W, Bartlett D, Schwartz R. Marker selection strategies for circulating tumor DNA guided by phylogenetic inference. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585352. [PMID: 38586041 PMCID: PMC10996527 DOI: 10.1101/2024.03.21.585352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Motivation Blood-based profiling of tumor DNA ("liquid biopsy") has offered great prospects for non-invasive early cancer diagnosis, treatment monitoring, and clinical guidance, but require further advances in computational methods to become a robust quantitative assay of tumor clonal evolution. We propose new methods to better characterize tumor clonal dynamics from circulating tumor DNA (ctDNA), through application to two specific questions: 1) How to apply longitudinal ctDNA data to refine phylogeny models of clonal evolution, and 2) how to quantify changes in clonal frequencies that may be indicative of treatment response or tumor progression. We pose these questions through a probabilistic framework for optimally identifying maximum likelihood markers and applying them to characterizing clonal evolution. Results We first estimate a distribution over plausible clonal lineage models, using bootstrap samples over pre-treatment tissue-based sequence data. We then refine these lineage models and the clonal frequencies they imply over successive longitudinal samples. We use the resulting framework for modeling and refining tree distributions to pose a set of optimization problems to select ctDNA markers to maximize measures of utility capturing ability to solve the two questions of reducing uncertain in phylogeny models or quantifying clonal frequencies given the models. We tested our methods on synthetic data and showed them to be effective at refining distributions of tree models and clonal frequencies so as to minimize measures of tree distance relative to the ground truth. Application of the tree refinement methods to real tumor data further demonstrated their effectiveness in refining a clonal lineage model and assessing its clonal frequencies. The work shows the power of computational methods to improve marker selection, clonal lineage reconstruction, and clonal dynamics profiling for more precise and quantitative assays of tumor progression. Availability https://github.com/CMUSchwartzLab/Mase-phi.git. Contact russells@andrew.cmu.edu.
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Affiliation(s)
- Xuecong Fu
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
| | - Zhicheng Luo
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
| | - Yueqian Deng
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
| | - William LaFramboise
- Allegheny Health Network Cancer Institute, Allegheny Health Network, 320 East North Avenue, 15212, Pittsburgh, PA, USA
| | - David Bartlett
- Allegheny Health Network Cancer Institute, Allegheny Health Network, 320 East North Avenue, 15212, Pittsburgh, PA, USA
| | - Russell Schwartz
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
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32
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Norton EJ, Bateman AC. Risk assessment in pT1 colorectal cancer. J Clin Pathol 2024; 77:225-232. [PMID: 37985141 DOI: 10.1136/jcp-2023-208803] [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: 10/02/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023]
Abstract
Colorectal cancer (CRC) is a common malignancy worldwide and tumour stage is closely related to clinical outcome. A small but significant proportion of submucosal-invasive (ie, pT1) CRC are associated with regional lymph node metastases (LNM) and a worse prognosis. The likelihood of LNM in pT1 CRC needs to be balanced against the operative risk and costs of surgical resection when determining the best patient management. A wide range of histopathological and clinical factors may affect LNM risk in this setting. This script provides a comprehensive overview of the tumour and patient-associated features that have been linked to LNM risk in pT1 CRC. Some of the features are well established within the literature and are included in published guidelines, while others are novel and emerging in nature. Odds ratios for LNM that are associated with key predictive features are provided where appropriate, and published models developed as an aid to the calculation of LNM risk are discussed.
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Affiliation(s)
- Emma Jane Norton
- Cellular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Adrian C Bateman
- Cellular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
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Ohmura H, Hanamura F, Okumura Y, Ando Y, Masuda T, Mimori K, Akashi K, Baba E. Liquid biopsy for breast cancer and other solid tumors: a review of recent advances. Breast Cancer 2024:10.1007/s12282-024-01556-8. [PMID: 38492205 DOI: 10.1007/s12282-024-01556-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/13/2024] [Indexed: 03/18/2024]
Abstract
Liquid biopsy using circulating tumor DNA (ctDNA) has been reported to be less invasive and effective for comprehensive genetic analysis of heterogeneous solid tumors, including decision-making for therapeutic strategies, predicting recurrence, and detecting genetic factors related to treatment resistance in various types of cancers. Breast cancer, colorectal cancer, and lung cancer are among the most prevalent malignancies worldwide, and clinical studies of liquid biopsy for these cancers are ongoing. Liquid biopsy has been used as a companion diagnostic tool in clinical settings, and research findings have accumulated, especially in cases of colorectal cancer after curative resection and non-small cell lung cancer (NSCLC) after curative chemoradiotherapy, in which ctDNA detection helps predict eligibility for adjuvant chemotherapy. Liquid biopsy using ctDNA shows promise across a wide range of cancer types, including breast cancer, and its clinical applications are expected to expand further through ongoing research. In this article, studies on liquid biopsy in breast cancer, colorectal cancer, and NSCLC are compared focusing on ctDNA.
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Affiliation(s)
- Hirofumi Ohmura
- Department of Oncology and Social Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
- Department of Internal Medicine, Kyushu University Beppu Hospital, Oita, Japan
| | - Fumiyasu Hanamura
- Department of Internal Medicine, Kyushu University Beppu Hospital, Oita, Japan
| | - Yuta Okumura
- Department of Internal Medicine, Kyushu University Beppu Hospital, Oita, Japan
- Department of Gastrointestinal and Medical Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Yuki Ando
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Eishi Baba
- Department of Oncology and Social Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan.
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Hosoda K, Umemura K, Shimizu A, Kubota K, Notake T, Kitagawa N, Sakai H, Hayashi H, Yasukawa K, Soejima Y. The platelet-to-lymphocyte ratio is a complementary prognostic factor to tumor markers in predicting early recurrence of hepatocellular carcinoma after hepatectomy. J Surg Oncol 2024; 129:765-774. [PMID: 38105473 DOI: 10.1002/jso.27564] [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: 08/24/2023] [Accepted: 12/03/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND The usefulness of inflammation-based prognostic scores for early recurrence (ER) after hepatectomy for hepatocellular carcinoma has rarely been reported. This study aimed to evaluate the potential of inflammation-based prognostic scores as predictors of ER and their relationship with tumor markers. METHODS We enrolled 338 patients who underwent hepatectomy for hepatocellular carcinoma between January 2007 and December 2021. Clinicopathological factors were compared between patients who developed ER (ER group) and those who did not develop ER (non-ER group). The association between inflammation-based prognostic scores and ER status was evaluated. These scores were compared with those of well-established tumor markers. RESULTS The platelet-to-lymphocyte ratio (PLR) correlated with ER of hepatocellular carcinoma, with an area under the curve (AUC) value of 0.70, sensitivity of 68.1%, and specificity of 67.7%. In patients with low tumor marker levels, the PLR showed a strong correlation with ER of hepatocellular carcinoma, with an AUC value of 0.851, sensitivity of 100%, and specificity of 76.2%. Multivariate analysis revealed that the PLR was an independent prognostic factor for ER. CONCLUSIONS The PLR is useful and complementary to tumor markers for predicting ER after hepatectomy for hepatocellular carcinoma.
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Affiliation(s)
- Kiyotaka Hosoda
- Department of Surgery, Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kentaro Umemura
- Department of Surgery, Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Akira Shimizu
- Department of Surgery, Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Koji Kubota
- Department of Surgery, Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Tsuyoshi Notake
- Department of Surgery, Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Noriyuki Kitagawa
- Department of Surgery, Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hiroki Sakai
- Department of Surgery, Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hikaru Hayashi
- Department of Surgery, Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Koya Yasukawa
- Department of Surgery, Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yuji Soejima
- Department of Surgery, Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
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Naegele S, Ruiz-Torres DA, Zhao Y, Goss D, Faden DL. Comparing the Diagnostic Performance of Quantitative PCR, Digital Droplet PCR, and Next-Generation Sequencing Liquid Biopsies for Human Papillomavirus-Associated Cancers. J Mol Diagn 2024; 26:179-190. [PMID: 38103593 PMCID: PMC10918646 DOI: 10.1016/j.jmoldx.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/29/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Human papillomavirus (HPV)-associated cancers, including oropharyngeal squamous cell carcinoma (HPV + OPSCC), cervical cancer, and squamous cell carcinoma of the anus (HPV + SCCA), release circulating tumor HPV DNA (ctHPVDNA) into the blood. The diagnostic performance of ctHPVDNA detection depends on the approaches used and the individual assay metrics. A comparison of these approaches has not been systematically performed to inform expected performance, which in turn affects clinical interpretation. A meta-analysis was performed using Ovid MEDLINE, Embase, and Web of Science Core Collection databases to assess the diagnostic accuracy of ctHPVDNA detection across cancer anatomic sites, detection platforms, and blood components. The population included patients with HPV + OPSCC, HPV-associated cervical cancer, and HPV + SCCA with pretreatment samples analyzed by quantitative PCR (qPCR), digital droplet PCR (ddPCR), or next-generation sequencing (NGS). Thirty-six studies involving 2986 patients met the inclusion criteria. The sensitivity, specificity, and quality of each study were assessed and pooled for each analysis. The sensitivity of ctHPVDNA detection was greatest with NGS, followed by ddPCR and then qPCR when pooling all studies, whereas specificity was similar (sensitivity: ddPCR > qPCR, P < 0.001; NGS > ddPCR, P = 0.014). ctHPVDNA from OPSCC was more easily detected compared with cervical cancer and SCCA, overall (P = 0.044). In conclusion, detection platform, anatomic site of the cancer, and blood component used affects ctHPVDNA detection and must be considered when interpreting results. Plasma NGS-based testing may be the most sensitive approach for ctHPVDNA overall.
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Affiliation(s)
- Saskia Naegele
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts
| | - Daniel A Ruiz-Torres
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts
| | - Yan Zhao
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts
| | - Deborah Goss
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts
| | - Daniel L Faden
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
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36
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Monroe G, Malla M. Post-operative Surveillance and Management of Intrahepatic Cholangiocarcinoma Using Circulating Tumor DNA: A Case Report. Cureus 2024; 16:e55914. [PMID: 38601368 PMCID: PMC11003875 DOI: 10.7759/cureus.55914] [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] [Accepted: 03/10/2024] [Indexed: 04/12/2024] Open
Abstract
Cholangiocarcinomas (CCAs) are a subclass of biliary tract tumors that arise from the epithelial lining of bile ducts. They are subdivided broadly into intra- and extrahepatic CCA, with extrahepatic being the more common. Circulating tumor DNA (ctDNA) is a form of liquid biopsy obtained from dying tumor cells in the peripheral blood. Assays may be tumor-informed or tumor-agnostic, with the former requiring tissue sampling to evaluate detectable mutations present in an individual patient's tumor. Here we present a case of intrahepatic CCA managed with hepatectomy followed by adjuvant chemotherapy, with subsequent surveillance and management guided by tumor-informed ctDNA. A 79-year-old female presented to our hospital in December 2019 with three months of postprandial epigastric abdominal pain. Computed tomography (CT) revealed a 5.7 x 5.2 cm left hepatic lobe mass, and surgical pathology confirmed invasive CCA. She underwent left hepatectomy with hepaticojejunostomy one month after presentation and started adjuvant chemotherapy thereafter. She followed us to our cancer center for standard surveillance along with ctDNA. Her tumor markers were within normal limits, and ctDNA was negative until May 2022, when ctDNA was detected, while CA 19-9 remained normal; CT imaging was without evidence of disease. Positron emission tomography-computed tomography (PET-CT) performed in July 2022 revealed local recurrence at the surgical margin, which was confirmed by an endoscopic biopsy. She began gemcitabine-capecitabine chemotherapy in October 2022, completed four cycles followed by chemoradiation therapy, and is currently at her baseline functional status with no detectable radiologic or molecular evidence of disease.
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Affiliation(s)
- Gary Monroe
- Department of Medicine, West Virginia University School of Medicine, Morgantown, USA
| | - Midhun Malla
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, USA
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Baumgartner JM, Botta GP. Role of Circulating Tumor DNA Among Patients with Colorectal Peritoneal Metastases. J Gastrointest Cancer 2024; 55:41-46. [PMID: 37436640 PMCID: PMC11096195 DOI: 10.1007/s12029-023-00959-8] [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] [Accepted: 07/01/2023] [Indexed: 07/13/2023]
Abstract
PURPOSE This was a review of circulating tumor DNA (ctDNA) in patients with peritoneal metastases from colorectal cancer. METHODS We searched the PubMed database for studies reporting detection of ctDNA in patients with colorectal cancer (CRC) and with peritoneal metastases (PM) from colorectal cancer (CRPM). We extracted data on the population included, number of subjects, study design, type of ctDNA assay used and schedule, and the major findings from these publications. RESULTS We identified 13 studies for review investigating ctDNA, using a variety of ctDNA assays, among 1787 patients with CRC without PM, as well as four eligible published and one unpublished (in press) studies, which included 255 patients with PM from any primary site and 61 patients with CRPM. Among the 13 studies investigating ctDNA among CRC without PM, posttreatment surveillance ctDNA was associated with recurrence and was generally more sensitive than imaging or tumor markers. Among the five studies including patients with PM, ctDNA was not universally able to detect the presence of PM, but when present, ctDNA predicted worse outcomes. CONCLUSION Circulating-tumor DNA is a potentially useful surveillance tool for patients with CRC. However, the sensitivity of ctDNA to detect CRPM is variable and warrants further inquiry.
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Affiliation(s)
- Joel M Baumgartner
- Division of Surgical Oncology, Department of Surgery, University of California, San Diego, La Jolla, CA, USA.
| | - Gregory P Botta
- Division of Hematology-Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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Recio F, Scalise CB, Loar P, Lumish M, Berman T, Peddada A, Kalashnikova E, Rivero-Hinojosa S, Beisch T, Nicosia B, Farmer T, Dutta P, Malhotra M, ElNaggar AC, Liu MC, Vaccarello L, Holloway RW. Post-surgical ctDNA-based molecular residual disease detection in patients with stage I uterine malignancies. Gynecol Oncol 2024; 182:63-69. [PMID: 38262240 DOI: 10.1016/j.ygyno.2023.12.025] [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: 08/15/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Among uterine malignancies, endometrial cancer (EC) is the most common cancer of the female reproductive tract. Traditionally, risk stratification in EC is determined by standard clinicopathological risk factors. Although circulating tumor DNA (ctDNA) has emerged as a prognostic biomarker in various malignancies, its clinical validity in EC remains to be established. METHODS In this analysis of real-world data, 267 plasma samples from 101 patients with stage I EC were analyzed using a tumor-informed ctDNA assay (Signatera™ bespoke mPCR-NGS). Patients were followed post-surgically and monitored with ctDNA testing for a median of 6.8 months (range: 0.37-19.1). RESULTS Patients who tested ctDNA-positive at both their first time point and longitudinally experienced inferior recurrence-free survival (RFS) (HR = 6.2; p = 0.0006 and HR = 15.5; p < 0.0001, respectively), and showed a recurrence rate of 58% and 52%, vs. 6% and 0%, respectively for the ctDNA-negative patients. Most ctDNA-positive patients had high-risk histologies or sarcoma, versus low-risk and high-intermediate risk (H-IR) EC. Furthermore, patients with high-risk histologies who were ctDNA-positive showed shorter RFS compared to those who tested negative (HR = 9.5; p = 0.007), and those who tested positive in the low/H-IR cohort (HR = 0.25; p = 0.04). Post-surgically, detectable ctDNA was highly prognostic of clinical outcome and remained the only significant risk factor for recurrence when adjusted for clinicopathological risk factors, such as histologic risk group, mismatch repair (MMR), and p53 status. CONCLUSION Incorporating ctDNA monitoring along with traditional known risk factors may aid in identifying patients with stage I EC who are at highest risk of recurrence, and possibly aid in treatment stratification.
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Affiliation(s)
- Fernando Recio
- AdventHealth Orlando Gynecologic Oncology, Orlando, FL, USA
| | | | | | | | - Tara Berman
- Inova Schar Cancer Institute, Fairfax, VA, USA
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Chen ZG, Ji XM, Xu YX, Fong WP, Liu XY, Liang JY, Tan Q, Wen L, Cai YY, Wang DS, Li YH. Methylated ctDNA predicts early recurrence risk in patients undergoing resection of initially unresectable colorectal cancer liver metastases. Ther Adv Med Oncol 2024; 16:17588359241230752. [PMID: 38425989 PMCID: PMC10903215 DOI: 10.1177/17588359241230752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024] Open
Abstract
Background Patients with initially unresectable colorectal cancer liver metastases (IU-CRLM) might benefit from using an effective systemic treatment followed by resection of liver metastases but the curative success rate is quite low. Indeed, nearly one-third of patients exhibit early recurrence within the first 6 months after surgery, and these individuals often have poor overall survival. Objectives This study aims to clarify the application value of serial circulating tumor DNA (ctDNA) analysis in predicting the clinical outcome of IU-CRLM patients following liver metastasectomy. Design A retrospective study was conducted on a cohort of patients with IU-CRLM between February 2018 and April 2021. Methods Plasma samples at different time points during CRLM treatment [baseline (BL), preoperation (PRE), postoperation (POST), end-of-treatment (EOT), and progressive disease (PD)] were retrospectively collected from patients with initially unresectable CRLM enrolled at the Sun Yat-sen University Cancer Center. Dynamic changes of SEPTIN 9 (SEPT9) and Neuropeptide Y (NPY) methylated circulating tumor DNA (MetctDNA) levels in serial plasma samples were detected using droplet-digital PCR (ddPCR). Results SEPT9 and NPY genes were hypermethylated in colon cancer cell lines and tissues while no difference was observed between primary and metastatic tumors. Patients with MetctDNA positive at POST or EOT had significantly lower recurrence-free survival (RFS) compared to patients with MetctDNA negative at these time points [POST: Hazard ratio (HR) 9.44, 95% confidence interval (CI) 5.15-17.30, p < 0.001; EOT: HR 11.48, 95% CI 3.27-40.31, p < 0.001]. Multivariate analysis demonstrated that POST (OR 33.96, 95% CI 4.03-286.10, p = 0.001) and EOT (OR 18.36, 95% CI 1.14-295.71, p = 0.04) MetctDNA was an independent risk factor for early recurrence. Time-dependent receiver operating characteristic curve (T-ROC) analysis revealed that area under the curve (AUC) value was greatest at the relapse time point of 6 months post-intervention, with POST-AUC and EOT-AUC values of 0.74 (95% CI 0.66-0.81) and 0.73 (95% CI 0.53-0.94), respectively. Serial MetctDNA analysis showed that RFS was significantly lower in patients with no MetctDNA clearance compared with those with MetctDNA clearance (HR 26.05, 95% CI 4.92-137.81, p < 0.001). Conclusion Our study confirmed that serial ctDNA analysis of NPY and SEPT9 gene methylation could effectively predict early recurrence in IU-CRLM patients, especially at POST and EOT.
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Affiliation(s)
- Zhi-Gang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Xiao-Meng Ji
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Yu-Xia Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Molecular Diagnostics Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - William Pat Fong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Xiao-Yun Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Molecular Diagnostics Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Jie-Ying Liang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Qiong Tan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Lei Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Yan-Yu Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - De-Shen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, P.R. China
| | - Yu-Hong Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, P.R. China
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Rachman T, Bartlett D, LaFramboise W, Wagner P, Schwartz R, Carja O. Modeling the Effect of Spatial Structure on Solid Tumor Evolution and Circulating Tumor DNA Composition. Cancers (Basel) 2024; 16:844. [PMID: 38473206 PMCID: PMC10930890 DOI: 10.3390/cancers16050844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating tumor DNA (ctDNA) monitoring, while sufficiently advanced to reflect tumor evolution in real time and inform cancer diagnosis, treatment, and prognosis, mainly relies on DNA that originates from cell death via apoptosis or necrosis. In solid tumors, chemotherapy and immune infiltration can induce spatially variable rates of cell death, with the potential to bias and distort the clonal composition of ctDNA. Using a stochastic evolutionary model of boundary-driven growth, we study how elevated cell death on the edge of a tumor can simultaneously impact driver mutation accumulation and the representation of tumor clones and mutation detectability in ctDNA. We describe conditions in which invasive clones are over-represented in ctDNA, clonal diversity can appear elevated in the blood, and spatial bias in shedding can inflate subclonal variant allele frequencies (VAFs). Additionally, we find that tumors that are mostly quiescent can display similar biases but are far less detectable, and the extent of perceptible spatial bias strongly depends on sequence detection limits. Overall, we show that spatially structured shedding might cause liquid biopsies to provide highly biased profiles of tumor state. While this may enable more sensitive detection of expanding clones, it could also increase the risk of targeting a subclonal variant for treatment. Our results indicate that the effects and clinical consequences of spatially variable cell death on ctDNA composition present an important area for future work.
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Affiliation(s)
- Thomas Rachman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA 15213, USA
| | - David Bartlett
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - William LaFramboise
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - Patrick Wagner
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - Russell Schwartz
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Oana Carja
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Torresan S, de Scordilli M, Bortolot M, Di Nardo P, Foltran L, Fumagalli A, Guardascione M, Ongaro E, Puglisi F. Liquid biopsy in colorectal cancer: Onward and upward. Crit Rev Oncol Hematol 2024; 194:104242. [PMID: 38128627 DOI: 10.1016/j.critrevonc.2023.104242] [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: 10/05/2023] [Revised: 11/20/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Colorectal cancer (CRC) remains a leading cause of cancer-related deaths worldwide. In recent years, liquid biopsy has emerged as one of the most interesting areas of research in oncology, leading to innovative trials and practical changes in all aspects of CRC management. RNAs and cell free DNA (cfDNA) methylation are emerging as promising biomarkers for early diagnosis. Post-surgical circulating tumour DNA (ctDNA) can aid in evaluating minimal residual disease and personalising adjuvant treatment. In rectal cancer, ctDNA could improve response assessment to neoadjuvant therapy and risk stratification, especially in the era of organ-preservation trials. In the advanced setting, ctDNA analysis offers the opportunity to monitor treatment response and identify driver and resistance mutations more comprehensively than traditional tissue analysis, providing prognostic and predictive information. The aim of this review is to provide a detailed overview of the clinical applications and future perspectives of liquid biopsy in CRC.
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Affiliation(s)
- Sara Torresan
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Marco de Scordilli
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy.
| | - Martina Bortolot
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Paola Di Nardo
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Luisa Foltran
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Arianna Fumagalli
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Michela Guardascione
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Elena Ongaro
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Fabio Puglisi
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy
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Warren EAK, Maithel SK. Molecular pathology for cholangiocarcinoma: a review of actionable genetic targets and their relevance to adjuvant & neoadjuvant therapy, staging, follow-up, and determination of minimal residual disease. Hepatobiliary Surg Nutr 2024; 13:29-38. [PMID: 38322206 PMCID: PMC10839719 DOI: 10.21037/hbsn-22-563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 02/08/2024]
Abstract
Cholangiocarcinoma (CCA) represents a group of epithelial cell tumors classified based on their anatomic location along the biliary tree. This rare malignancy is often diagnosed at an advanced stage and deemed unresectable. Even for those patients who are surgical candidates, recurrence rates are high and survival rates low. The mainstay of therapy for advanced CCA remains cisplatin plus gemcitabine, with a median overall survival (mOS) under 12 months, although the TOPAZ-1 trial showed a survival benefit with the addition of programmed cell death ligand 1 (PD-L1) blockade. In recent years, molecular profiling has revealed a wealth of potentially targetable genetic alterations, including fibroblast growth factor receptor (FGFR) fusions, isocitrate dehydrogenase 1 (IDH1) mutations, human epidermal growth factor receptor 2 (HER2) amplification and overexpression, and microsatellite instability (MSI). These discoveries have prompted numerous clinical trials employing drugs against these specific genetic changes. The foundation laid by early clinical studies and the landscape of ongoing trials are both summarized here. While the role of adjuvant therapy has yet to be defined in this disease, we emphasize the importance of employing targeted therapies in trials in the adjuvant and neoadjuvant spaces and discuss ways to overcome challenges due to low incidence of targetable mutations. Personalized medicine for this disease promises significant clinical benefit to patients, but further investigation is needed.
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Affiliation(s)
- Emilie A K Warren
- Division of Surgical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Shishir K Maithel
- Division of Surgical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
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Henriksen TV, Demuth C, Frydendahl A, Nors J, Nesic M, Rasmussen MH, Reinert T, Larsen OH, Jaensch C, Løve US, Andersen PV, Kolbro T, Thorlacius-Ussing O, Monti A, Gögenur M, Kildsig J, Bondeven P, Schlesinger NH, Iversen LH, Gotschalck KA, Andersen CL. Unraveling the potential clinical utility of circulating tumor DNA detection in colorectal cancer-evaluation in a nationwide Danish cohort. Ann Oncol 2024; 35:229-239. [PMID: 37992872 DOI: 10.1016/j.annonc.2023.11.009] [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: 06/19/2023] [Revised: 09/29/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Increasingly, circulating tumor DNA (ctDNA) is proposed as a tool for minimal residual disease (MRD) assessment. Digital PCR (dPCR) offers low analysis costs and turnaround times of less than a day, making it ripe for clinical implementation. Here, we used tumor-informed dPCR for ctDNA detection in a large colorectal cancer (CRC) cohort to evaluate the potential for post-operative risk assessment and serial monitoring, and how the metastatic site may impact ctDNA detection. Additionally, we assessed how altering the ctDNA-calling algorithm could customize performance for different clinical settings. PATIENTS AND METHODS Stage II-III CRC patients (N = 851) treated with a curative intent were recruited. Based on whole-exome sequencing on matched tumor and germline DNA, a mutational target was selected for dPCR analysis. Plasma samples (8 ml) were collected within 60 days after operation and-for a patient subset (n = 246)-every 3-4 months for up to 36 months. Single-target dPCR was used for ctDNA detection. RESULTS Both post-operative and serial ctDNA detection were prognostic of recurrence [hazard ratio (HR) = 11.3, 95% confidence interval (CI) 7.8-16.4, P < 0.001; HR = 30.7, 95% CI 20.2-46.7, P < 0.001], with a cumulative ctDNA detection rate of 87% at the end of sample collection in recurrence patients. The ctDNA growth rate was prognostic of survival (HR = 2.6, 95% CI 1.5-4.4, P = 0.001). In recurrence patients, post-operative ctDNA detection was challenging for lung metastases (4/21 detected) and peritoneal metastases (2/10 detected). By modifying the cut-off for calling a sample ctDNA positive, we were able to adjust the sensitivity and specificity of our test for different clinical contexts. CONCLUSIONS The presented results from 851 stage II-III CRC patients demonstrate that our personalized dPCR approach effectively detects MRD after operation and shows promise for serial ctDNA detection for recurrence surveillance. The ability to adjust sensitivity and specificity shows exciting potential to customize the ctDNA caller for specific clinical settings.
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Affiliation(s)
- T V Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - C Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - A Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - J Nors
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - M Nesic
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - M H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - T Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - O H Larsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - C Jaensch
- Department of Surgery, Regional Hospital Gødstrup, Herning
| | - U S Løve
- Department of Surgery, Regional Hospital Viborg, Viborg
| | - P V Andersen
- Department of Surgery, Odense University Hospital, Odense
| | - T Kolbro
- Department of Surgery, Odense University Hospital, Svendborg
| | | | - A Monti
- Department of Surgery, North Denmark Regional Hospital Hjørring, Hjørring
| | - M Gögenur
- Center for Surgical Sciences, Zealand University Hospital, Køge
| | - J Kildsig
- Department of Surgery, Copenhagen University Hospital, Herlev
| | - P Bondeven
- Department of Surgery, Regional Hospital Randers, Randers
| | - N H Schlesinger
- Department of Surgery, Copenhagen University Hospital, Bispebjerg
| | - L H Iversen
- Department of Surgery, Aarhus University Hospital, Aarhus
| | - K A Gotschalck
- Department of Surgery, Regional Hospital Horsens, Horsens, Denmark
| | - C L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus.
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Kim EY, Ruiz ES, Hanna GJ, Thakuria M, Silk AW. Sensitivity of personalized circulating tumor DNA assay in advanced cutaneous squamous cell carcinoma. J Am Acad Dermatol 2024; 90:427-429. [PMID: 37844691 DOI: 10.1016/j.jaad.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023]
Affiliation(s)
- Emily Y Kim
- Georgetown University School of Medicine, Washington, District of Columbia; Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts; Department of Dermatology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts
| | - Emily S Ruiz
- Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts; Department of Dermatology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Glenn J Hanna
- Harvard Medical School, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Manisha Thakuria
- Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts; Department of Dermatology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Ann W Silk
- Harvard Medical School, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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Verschoor YL, van de Haar J, van den Berg JG, van Sandick JW, Kodach LL, van Dieren JM, Balduzzi S, Grootscholten C, IJsselsteijn ME, Veenhof AAFA, Hartemink KJ, Vollebergh MA, Jurdi A, Sharma S, Spickard E, Owers EC, Bartels-Rutten A, den Hartog P, de Miranda NFCC, van Leerdam ME, Haanen JBAG, Schumacher TN, Voest EE, Chalabi M. Neoadjuvant atezolizumab plus chemotherapy in gastric and gastroesophageal junction adenocarcinoma: the phase 2 PANDA trial. Nat Med 2024; 30:519-530. [PMID: 38191613 PMCID: PMC10878980 DOI: 10.1038/s41591-023-02758-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024]
Abstract
Gastric and gastroesophageal junction (G/GEJ) cancers carry a poor prognosis, and despite recent advancements, most patients die of their disease. Although immune checkpoint blockade became part of the standard-of-care for patients with metastatic G/GEJ cancers, its efficacy and impact on the tumor microenvironment (TME) in early disease remain largely unknown. We hypothesized higher efficacy of neoadjuvant immunotherapy plus chemotherapy in patients with nonmetastatic G/GEJ cancer. In the phase 2 PANDA trial, patients with previously untreated resectable G/GEJ tumors (n = 21) received neoadjuvant treatment with one cycle of atezolizumab monotherapy followed by four cycles of atezolizumab plus docetaxel, oxaliplatin and capecitabine. Treatment was well tolerated. There were grade 3 immune-related adverse events in two of 20 patients (10%) but no grade 4 or 5 immune-related adverse events, and all patients underwent resection without treatment-related delays, meeting the primary endpoint of safety and feasibility. Tissue was obtained at multiple time points, allowing analysis of the effects of single-agent anti-programmed cell death ligand 1 (PD-L1) and the subsequent combination with chemotherapy on the TME. Twenty of 21 patients underwent surgery and were evaluable for secondary pathologic response and survival endpoints, and 19 were evaluable for exploratory translational analyses. A major pathologic response (≤10% residual viable tumor) was observed in 14 of 20 (70%, 95% confidence interval 46-88%) patients, including 9 (45%, 95% confidence interval 23-68%) pathologic complete responses. At a median follow-up of 47 months, 13 of 14 responders were alive and disease-free, and five of six nonresponders had died as a result of recurrence. Notably, baseline anti-programmed cell death protein 1 (PD-1)+CD8+ T cell infiltration was significantly higher in responders versus nonresponders, and comparison of TME alterations following anti-PD-L1 monotherapy versus the subsequent combination with chemotherapy showed an increased immune activation on single-agent PD-1/L1 axis blockade. On the basis of these data, monotherapy anti-PD-L1 before its combination with chemotherapy warrants further exploration and validation in a larger cohort of patients with nonmetastatic G/GEJ cancer. ClinicalTrials.gov registration: NCT03448835 .
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Affiliation(s)
- Yara L Verschoor
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Joris van de Haar
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - José G van den Berg
- Department of Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Johanna W van Sandick
- Department of Surgery, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Liudmila L Kodach
- Department of Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Jolanda M van Dieren
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Sara Balduzzi
- Biometrics department, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Cecile Grootscholten
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Alexander A F A Veenhof
- Department of Surgery, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Koen J Hartemink
- Department of Surgery, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Marieke A Vollebergh
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | | | | | - Emilia C Owers
- Department of Nuclear Medicine, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Annemarieke Bartels-Rutten
- Department of Radiology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Peggy den Hartog
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Monique E van Leerdam
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - John B A G Haanen
- Department of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
- Oncology Service, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Emile E Voest
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Myriam Chalabi
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.
- Department of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.
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Sun J, Karasaki KM, Farma JM. The Use of Gene Expression Profiling and Biomarkers in Melanoma Diagnosis and Predicting Recurrence: Implications for Surveillance and Treatment. Cancers (Basel) 2024; 16:583. [PMID: 38339333 PMCID: PMC10854922 DOI: 10.3390/cancers16030583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Cutaneous melanoma is becoming more prevalent in the United States and has the highest mortality among cutaneous malignancies. The majority of melanomas are diagnosed at an early stage and, as such, survival is generally favorable. However, there remains prognostic uncertainty among subsets of early- and intermediate-stage melanoma patients, some of whom go on to develop advanced disease while others remain disease-free. Melanoma gene expression profiling (GEP) has evolved with the notion to help bridge this gap and identify higher- or lower-risk patients to better tailor treatment and surveillance protocols. These tests seek to prognosticate melanomas independently of established AJCC 8 cancer staging and clinicopathologic features (sex, age, primary tumor location, thickness, ulceration, mitotic rate, lymphovascular invasion, microsatellites, and/or SLNB status). While there is a significant opportunity to improve the accuracy of melanoma prognostication and diagnosis, it is equally important to understand the current landscape of molecular profiling for melanoma treatment. Society guidelines currently do not recommend molecular testing outside of clinical trials for melanoma clinical decision making, citing insufficient high-quality evidence guiding indications for the testing and interpretation of results. The goal of this chapter is to review the available literature for GEP testing for melanoma diagnosis and prognostication and understand their place in current treatment paradigms.
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Affiliation(s)
- James Sun
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19002, USA;
| | | | - Jeffrey M. Farma
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19002, USA;
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Sandberg E, Nunes L, Edqvist PH, Mathot L, Chen L, Edgren T, Al Nassralla S, Glimelius B, Landegren U, Sjöblom T. Sensitive and Specific Analyses of Colorectal Cancer Recurrence through Multiplex superRCA Mutation Detection in Blood Plasma. Cancers (Basel) 2024; 16:549. [PMID: 38339300 PMCID: PMC10854605 DOI: 10.3390/cancers16030549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Mutation analysis of circulating tumor DNA (ctDNA) has applications in monitoring of colorectal cancer (CRC) patients for recurrence. Considering the low tumor fraction of ctDNA in cell-free DNA (cfDNA) isolated from blood plasma, the sensitivity of the detection method is important. Here, plasma DNA collected at diagnosis and follow-up from 25 CRC patients was analyzed using a multiplex superRCA mutation detection assay. The assay was also performed on genomic DNA (gDNA) from tumor and normal tissue from 20 of these patients. The lower limit of detection for most sequence variants was in the range of 10-5, while when analyzing cfDNA from plasma with a typical input of 33 ng, the practical detection limit was ~10-4 or 0.01% mutant allele frequency (MAF). In 17 of 19 patients with identified hotspot mutations in tumor gDNA, at least one hotspot mutation could be detected in plasma DNA at the time of diagnosis. The MAF increased at subsequent time points in four of the patients who experienced a clinical relapse. Multiplex superRCA analysis of the remaining six patients did not reveal any hotspot mutations. In conclusion, multiplex superRCA assays proved suitable for monitoring CRC patients by analyzing hotspot mutations in cfDNA, and dynamic changes in MAF were observed in patients with clinical relapse.
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Affiliation(s)
- Emma Sandberg
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Luís Nunes
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Per-Henrik Edqvist
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Lucy Mathot
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Lei Chen
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
- Rarity Bioscience AB, SE-752 37 Uppsala, Sweden;
| | - Tomas Edgren
- Rarity Bioscience AB, SE-752 37 Uppsala, Sweden;
| | - Shahed Al Nassralla
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Bengt Glimelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Ulf Landegren
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
| | - Tobias Sjöblom
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden; (E.S.); (L.N.); (P.-H.E.); (L.M.); (L.C.); (S.A.N.); (B.G.)
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Fan W, Xia Z, Chen R, Lin D, Li F, Zheng Y, Luo J, Xiong Y, Yu P, Gao W, Gong Y, Zhang F, Zhang S, Li L. Circulating tumor DNA analysis predicts recurrence and avoids unnecessary adjuvant chemotherapy in I-IV colorectal cancer. Ther Adv Med Oncol 2024; 16:17588359231220607. [PMID: 38282662 PMCID: PMC10822076 DOI: 10.1177/17588359231220607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/21/2023] [Indexed: 01/30/2024] Open
Abstract
Background Circulating tumor DNA (ctDNA) has emerged as a biomarker that can define the risk of recurrence after curative-intent surgery for patients with colorectal cancer (CRC). However, beyond the predictive power of postoperative ctDNA detection, the efficacy and potential limitations of ctDNA detection urgently need to be fully elucidated in a large cohort of CRC. Objectives To define potentially cured CRC patients through ctDNA monitoring following surgery. Design A prospective, multicenter, observational study. Methods We enrolled 309 patients with stages I-IV CRC who underwent definitive surgery. Tumor tissues were sequenced by a custom-designed next-generation sequencing panel to identify somatic mutations. Plasma was analyzed using a ctDNA-based molecular residual disease (MRD) assay which integrated tumor-genotype-informed and tumor-genotype-naïve ctDNA analysis. The turnaround time of the assay was 10-14 days. Results Postoperative ctDNA was detected in 5.4%, 13.8%, 15%, and 30% of patients with stage I, II, III, and IV disease, respectively, and in 17.5% of all longitudinal samples. Patients with positive postsurgery MRD had a higher recurrence rate than those with negative postsurgery MRD [hazard ratio (HR), 13.17; p < 0.0001], producing a sensitivity of 64.6%, a specificity of 94.8%, a positive predictive value (PPV) of 75.6%, and a negative predictive value (NPV) of 91.5%. Furthermore, patients with positive longitudinal MRD also had a significantly higher recurrence rate (HR, 14.44; p < 0.0001), with increased sensitivity (75.0%), specificity (94.9%), PPV (79.6%), and NPV (93.4%). Subgroup analyses revealed that adjuvant therapy did not confer superior survival for patients with undetectable or detectable MRD. In addition, MRD detection was less effective in identifying lung-only and peritoneal metastases. Conclusion Postoperative ctDNA status is a strong predictor of recurrence independent of stage and microsatellite instability status. Longitudinal undetectable MRD could be used to define the potentially cured population in CRC patients undergoing curative-intent surgery.
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Affiliation(s)
- Wenhua Fan
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Zhiyuan Xia
- Department of Colorectal & Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | | | - Dagui Lin
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Fang Li
- Geneplus-Beijing, Beijing, China
| | - Yang Zheng
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jiongyong Luo
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | | | | | - Wei Gao
- Geneplus-Beijing, Beijing, China
| | | | - Feiran Zhang
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Jinping District, Shantou, Guangdong 515041, China
| | - Sen Zhang
- Department of Colorectal & Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning 530021, China
| | - Liren Li
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou 510060, China
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Wang X, Wang L, Lin H, Zhu Y, Huang D, Lai M, Xi X, Huang J, Zhang W, Zhong T. Research progress of CTC, ctDNA, and EVs in cancer liquid biopsy. Front Oncol 2024; 14:1303335. [PMID: 38333685 PMCID: PMC10850354 DOI: 10.3389/fonc.2024.1303335] [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: 09/27/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024] Open
Abstract
Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and extracellular vehicles (EVs) have received significant attention in recent times as emerging biomarkers and subjects of transformational studies. The three main branches of liquid biopsy have evolved from the three primary tumor liquid biopsy detection targets-CTC, ctDNA, and EVs-each with distinct benefits. CTCs are derived from circulating cancer cells from the original tumor or metastases and may display global features of the tumor. ctDNA has been extensively analyzed and has been used to aid in the diagnosis, treatment, and prognosis of neoplastic diseases. EVs contain tumor-derived material such as DNA, RNA, proteins, lipids, sugar structures, and metabolites. The three provide different detection contents but have strong complementarity to a certain extent. Even though they have already been employed in several clinical trials, the clinical utility of three biomarkers is still being studied, with promising initial findings. This review thoroughly overviews established and emerging technologies for the isolation, characterization, and content detection of CTC, ctDNA, and EVs. Also discussed were the most recent developments in the study of potential liquid biopsy biomarkers for cancer diagnosis, therapeutic monitoring, and prognosis prediction. These included CTC, ctDNA, and EVs. Finally, the potential and challenges of employing liquid biopsy based on CTC, ctDNA, and EVs for precision medicine were evaluated.
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Affiliation(s)
- Xiaoling Wang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Lijuan Wang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Haihong Lin
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Yifan Zhu
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Defa Huang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Mi Lai
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xuxiang Xi
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Junyun Huang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Wenjuan Zhang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Tianyu Zhong
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
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50
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Housini M, Dariya B, Ahmed N, Stevens A, Fiadjoe H, Nagaraju GP, Basha R. Colorectal cancer: Genetic alterations, novel biomarkers, current therapeutic strategies and clinical trials. Gene 2024; 892:147857. [PMID: 37783294 DOI: 10.1016/j.gene.2023.147857] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023]
Abstract
Colorectal cancer (CRC) is the third most commonly detected cancer with a serious global health issue. The rates for incidence and mortality for CRC are alarming, especially since the prognosis is abysmal when the CRC is diagnosed at an advanced or metastatic stage. Both type of (modifiable/ non-modifiable) types of risk factors are established for CRC. Despite the advances in recent technology and sophisticated research, the survival rate is still meager due to delays in diagnosis. Therefore, there is urgently required to identify critical biomarkers aiming at early diagnosis and improving effective therapeutic strategies. Additionally, a complete understanding of the dysregulated pathways like PI3K/Akt, Notch, and Wnt associated with CRC progression and metastasis is very beneficial in designing a therapeutic regimen. This review article focused on the dysregulated signaling pathways, genetics and epigenetics alterations, and crucial biomarkers of CRC. This review also provided the list of clinical trials targeting signaling cascades and therapies involving small molecules. This review discusses up-to-date information on novel diagnostic and therapeutic strategies alongside specific clinical trials.
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Affiliation(s)
- Mohammad Housini
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX 76107, United States
| | - Begum Dariya
- Center for Drug Design, University of Minnesota, Minneapolis, MN 5545, United States
| | - Nadia Ahmed
- Department of Diagnostic Radiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Alyssa Stevens
- Missouri Southern State University, Joplin, MO 64801, United States
| | - Hope Fiadjoe
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, United States
| | - Ganji Purnachandra Nagaraju
- Division of Hematology & Oncology, The University of Alabama at Birmingham, Birmingham, AL 35233, United States.
| | - Riyaz Basha
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX 76107, United States; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, United States.
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