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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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Tamura D, Abe M, Hiraki H, Sasaki N, Yashima‐Abo A, Ikarashi D, Kato R, Kato Y, Maekawa S, Kanehira M, Takata R, Maejima K, Sasagawa S, Fujita M, Suzuki Y, Nakagawa H, Iwaya T, Nishizuka SS, Obara W. Postoperative recurrence detection using individualized circulating tumor DNA in upper tract urothelial carcinoma. Cancer Sci 2024; 115:529-539. [PMID: 38083992 PMCID: PMC10859621 DOI: 10.1111/cas.16025] [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: 07/28/2023] [Revised: 10/13/2023] [Accepted: 11/06/2023] [Indexed: 02/13/2024] Open
Abstract
Biomarkers that could detect the postoperative recurrence of upper tract urothelial carcinoma (UTUC) have not been established. In this prospective study, we aim to evaluate the utility of individualized circulating tumor DNA (ctDNA) monitoring using digital PCR (dPCR) as a tumor recurrence biomarker for UTUC in the perioperative period. Twenty-three patients who underwent radical nephroureterectomy (RNU) were included. In each patient, whole exome sequencing by next-generation sequencing and TERT promoter sequencing of tumor DNA were carried out. Case-specific gene mutations were selected from sequencing analysis to examine ctDNA by dPCR analysis. We also prospectively collected plasma and urine ctDNA from each patient. The longitudinal variant allele frequencies of ctDNA during the perioperative period were plotted. Case-specific gene mutations were detected in 22 cases (96%) from ctDNA in the preoperative samples. Frequently detected genes were TERT (39%), FGFR3 (26%), TP53 (22%), and HRAS (13%). In all cases, we obtained plasma and urine samples for 241 time points and undertook individualized ctDNA monitoring for 2 years after RNU. Ten patients with intravesical recurrence had case-specific ctDNA detected in urine at the time of recurrence. The mean lead time of urinary ctDNA in intravesical recurrence was 60 days (range, 0-202 days). Two patients with distal metastasis had case-specific ctDNA in plasma at the time of metastasis. In UTUC, tumor-specific gene mutations can be monitored postoperatively as ctDNA in plasma and urine. Individualized ctDNA might be a minimally invasive biomarker for the early detection of postoperative recurrence.
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Affiliation(s)
- Daichi Tamura
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Masakazu Abe
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Hayato Hiraki
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Noriyuki Sasaki
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Akiko Yashima‐Abo
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Daiki Ikarashi
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Renpei Kato
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Yoichiro Kato
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Shigekatsu Maekawa
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Mitsugu Kanehira
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Ryo Takata
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Kazuhiro Maejima
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Shota Sasagawa
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Masashi Fujita
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical SciencesThe University of TokyoKashiwaJapan
| | - Hidewaki Nakagawa
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Takeshi Iwaya
- Department of Clinical OncologyIwate Medical University School of MedicineYahabaJapan
| | - Satoshi S. Nishizuka
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Wataru Obara
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
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Boutin M, Topham JT, Feilotter H, Kennecke HF, Couture F, Harb M, Kavan P, Berry S, Lim HJ, Goffin JR, Ahmad C, Lott A, Renouf DJ, Jonker DJ, Tu D, O’Callaghan CJ, Chen EX, Loree JM. Optimizing the number of variants tracked to follow disease burden with circulating tumor DNA assays in metastatic colorectal cancer. Ther Adv Med Oncol 2023; 15:17588359231183682. [PMID: 37389190 PMCID: PMC10302520 DOI: 10.1177/17588359231183682] [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: 02/21/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Background The number of somatic mutations detectable in circulating tumor DNA (ctDNA) is highly heterogeneous in metastatic colorectal cancer (mCRC). The optimal number of mutations required to assess disease kinetics is relevant and remains poorly understood. Objectives To determine whether increasing panel breadth (the number of tracked variants in a ctDNA assay) would alter the sensitivity in detecting ctDNA in patients with mCRC. Design We used archival tissue sequencing to perform an in silico assessment of the optimal number of tracked mutations to detect and monitor disease kinetics in mCRC using sequencing data from the Canadian Cancer Trials Group CO.26 trial. Methods For each patient, 1, 2, 4, 8, 12, or 16 of the most clonal (highest variant allele frequency) somatic variants were selected from archival tissue-based whole-exome sequencing and assessed for the proportion of variants detected in matched ctDNA at baseline, week 8, and progression timepoints. Results Data from 110 patients were analyzed. Genes most frequently encountered among the top four highest VAF variants in archival tissue were TP53 (51.9% of patients), APC (43.3%), KRAS (42.3%), and SMAD4 (9.6%). While the frequency of detecting at least one tracked variant increased when expanding beyond variant pool sizes of 1 and 2 in baseline (p = 0.0030) and progression (p = 0.0030) ctDNA samples, we observed no significant benefit to increases in variant pool size past four variants in any of the ctDNA timepoints (p < 0.05). Conclusion While increasing panel breadth beyond two tracked variants improved variant re-detection in ctDNA samples from patients with treatment refractory mCRC, increases beyond four tracked variants yielded no significant improvement in variant re-detection.
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Affiliation(s)
- Mélina Boutin
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada Centre Intégré de Cancérologie de la Montérégie, Université de Sherbrooke, QC, Canada
| | | | - Harriet Feilotter
- Canadian Cancer Trials Group, Queen’s University, Kingston, ON, Canada
| | | | | | | | | | - Scott Berry
- Department of Oncology, Queen’s University, Kingston, ON, Canada
| | - Howard J. Lim
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | | | | | - Daniel J. Renouf
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada Pancreas Center BC, Vancouver, BC, Canada
| | - Derek J. Jonker
- The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
| | - Dongsheng Tu
- Canadian Cancer Trials Group, Queen’s University, Kingston, ON, Canada
| | | | - Eric X. Chen
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Jonathan M. Loree
- Division of Medical Oncology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
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Liu Y, Wu W, Cai C, Zhang H, Shen H, Han Y. Patient-derived xenograft models in cancer therapy: technologies and applications. Signal Transduct Target Ther 2023; 8:160. [PMID: 37045827 PMCID: PMC10097874 DOI: 10.1038/s41392-023-01419-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Patient-derived xenograft (PDX) models, in which tumor tissues from patients are implanted into immunocompromised or humanized mice, have shown superiority in recapitulating the characteristics of cancer, such as the spatial structure of cancer and the intratumor heterogeneity of cancer. Moreover, PDX models retain the genomic features of patients across different stages, subtypes, and diversified treatment backgrounds. Optimized PDX engraftment procedures and modern technologies such as multi-omics and deep learning have enabled a more comprehensive depiction of the PDX molecular landscape and boosted the utilization of PDX models. These irreplaceable advantages make PDX models an ideal choice in cancer treatment studies, such as preclinical trials of novel drugs, validating novel drug combinations, screening drug-sensitive patients, and exploring drug resistance mechanisms. In this review, we gave an overview of the history of PDX models and the process of PDX model establishment. Subsequently, the review presents the strengths and weaknesses of PDX models and highlights the integration of novel technologies in PDX model research. Finally, we delineated the broad application of PDX models in chemotherapy, targeted therapy, immunotherapy, and other novel therapies.
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Affiliation(s)
- Yihan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Wantao Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China.
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China.
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Sattar RSA, Verma R, Nimisha, Kumar A, Dar GM, Apurva, Sharma AK, Kumari I, Ahmad E, Ali A, Mahajan B, Saluja SS. Diagnostic and prognostic biomarkers in colorectal cancer and the potential role of exosomes in drug delivery. Cell Signal 2022; 99:110413. [PMID: 35907519 DOI: 10.1016/j.cellsig.2022.110413] [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: 04/14/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/03/2022]
Abstract
Colorectal cancer (CRC) is third most common cancer with second most common cause of death worldwide. One fourth to one fifth of the CRC cases are detected at advance stage. Early detection of colorectal cancer might help in decreasing mortality and morbidity worldwide. CRC being a heterogeneous disease, new non-invasive approaches are needed to complement and improve the screening and management of CRC. Reliable and early detectable biomarkers would improve diagnosis, prognosis, therapeutic responses, and will enable the prediction of drug response and recurrence risk. Over the past decades molecular research has demonstrated the potentials of CTCs, ctDNAs, circulating mRNA, ncRNAs, and exosomes as tumor biomarkers. Non-invasive screening approaches using fecal samples for identification of altered gut microbes in CRC is also gaining attention. Exosomes can be potential candidates that can be employed in the drug delivery system. Further, the integration of in vitro, in vivo and in silico models that involve CRC biomarkers will help to understand the interactions occurring at the cellular level. This review summarizes recent update on CRC biomarkers and their application along with the nanoparticles followed by the application of organoid culture in CRC.
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Affiliation(s)
- Real Sumayya Abdul Sattar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Renu Verma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Nimisha
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Arun Kumar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ghulam Mehdi Dar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Apurva
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Abhay Kumar Sharma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Indu Kumari
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ejaj Ahmad
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Asgar Ali
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Bhawna Mahajan
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of Biochemistry, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of GI Surgery, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India.
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Iwaya T, Nishizuka SS. Reply. Gastroenterology 2021; 161:367-368. [PMID: 33766565 DOI: 10.1053/j.gastro.2021.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 12/02/2022]
Affiliation(s)
- Takeshi Iwaya
- Department of Surgery, Iwate Medical University School of Medicine, Yahaba, Iwate, Japan
| | - Satoshi S Nishizuka
- Division of Biomedical Research and Development, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Iwate, Japan
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Huggett JF, Devonshire AS, Whale AS, Cowen S, Foy CA. Pushing the Envelope with Clinical Use of Digital PCR. Clin Chem 2021; 67:921-923. [PMID: 34120171 DOI: 10.1093/clinchem/hvab082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 11/12/2022]
Affiliation(s)
- Jim F Huggett
- Molecular & Cell Biology, National Measurement Laboratory, LGC, Teddington, UK
| | - Alison S Devonshire
- Molecular & Cell Biology, National Measurement Laboratory, LGC, Teddington, UK
| | - Alexandra S Whale
- Molecular & Cell Biology, National Measurement Laboratory, LGC, Teddington, UK
| | - Simon Cowen
- Molecular & Cell Biology, National Measurement Laboratory, LGC, Teddington, UK
| | - Carole A Foy
- Molecular & Cell Biology, National Measurement Laboratory, LGC, Teddington, UK
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