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Mahmood U, Muhamad Faizul E, Howlett S, Amin Z, Hochhauser D, Shiu KK, Bridgewater J, Khan K. Comprehensive Examination of Cholangiocarcinoma Patients Treated with Novel Targeted Therapies after Extended Molecular Profiling on Liquid Biopsies. Cancers (Basel) 2024; 16:697. [PMID: 38398088 PMCID: PMC10886944 DOI: 10.3390/cancers16040697] [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: 12/23/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is associated with poor outcomes and limited treatment options, leading to increased use of targeted therapies for its management. Here, we performed one of the largest single-centre reviews evaluating outcomes following personalised targeted agents in CCA patients. METHODS All consecutive CCA patients receiving systemic therapy between January 2010 and April 2023 at UCLH were included. The primary objective of this study was to evaluate treatment response, survival outcomes and predictors of clinical benefit in CCA patients treated with molecularly guided therapies. Patient demographic factors, disease characteristics and survival outcomes were evaluated using the Kaplan-Meier method and Cox proportional-hazards models. RESULTS Of the 227 consecutive CCA patients, 162 (71%) had molecular profiling, of whom 56 (35%) were eligible and 55 received molecular-targeted treatment. CCA histological classifications comprised intrahepatic (N = 32), extrahepatic (N = 11), hilar (N = 4) and unknown (N = 9) subtypes. Most patients received targeted agents based on genomic profiling in a second treatment line setting (N = 34). Frequently observed genomic alterations occurred in the FGFR2 (N = 21), IDH1 (N = 7) and BRCA2 (N = 6) genes. Median progression-free survival (PFS) following first-, second- and third-line systemic therapy and overall survival (OS) were 8.44 (95% CI, 7.49-12.78), 5.65 (95% CI, 3.71-7.13), 5.55 (2.79-12.58) and 29.01 (24.21-42.91) months, respectively. CCA subtype and FGFR/BRCA molecular aberration status were not associated with PFS or OS. However, a prior CCA-related surgical history was predictive of OS (p = 0.02). Stratification by best overall response to second-line targeted agents demonstrated an association with PFS (p = 0.002) and OS (p = 0.02). Duration of treatment with second-line targeted therapy was associated with OS (p < 0.001). CONCLUSIONS Patients receiving targeted therapeutics achieved promising outcomes, especially those attaining a favourable treatment response and those receiving targeted agents for longer periods. Liquid biopsies can reliably provide information on extended molecular profiling to aid patient selection for personalised therapies.
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Affiliation(s)
- Umair Mahmood
- Department of Gastrointestinal Oncology, University College Hospital NHS Foundation Trust (UCLH), London NW1 2BU, UK
| | | | - Sarah Howlett
- Department of Gastrointestinal Oncology, University College Hospital NHS Foundation Trust (UCLH), London NW1 2BU, UK
| | - Zahir Amin
- Department of Radiology, University College Hospital NHS Foundation Trust (UCLH), London NW1 2BU, UK
| | - Daniel Hochhauser
- Department of Gastrointestinal Oncology, University College Hospital NHS Foundation Trust (UCLH), London NW1 2BU, UK
- University College London Cancer Institute, London WC1E 6DD, UK
| | - Kai-Keen Shiu
- Department of Gastrointestinal Oncology, University College Hospital NHS Foundation Trust (UCLH), London NW1 2BU, UK
- University College London Cancer Institute, London WC1E 6DD, UK
| | - John Bridgewater
- Department of Gastrointestinal Oncology, University College Hospital NHS Foundation Trust (UCLH), London NW1 2BU, UK
- University College London Cancer Institute, London WC1E 6DD, UK
| | - Khurum Khan
- Department of Gastrointestinal Oncology, University College Hospital NHS Foundation Trust (UCLH), London NW1 2BU, UK
- University College London Cancer Institute, London WC1E 6DD, UK
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Zhang Y, Du H, Wang N, Wang L, Huang Y. An update of clinical value of circulating tumor DNA in esophageal cancer: a systematic review and meta-analysis. BMC Cancer 2024; 24:129. [PMID: 38267901 PMCID: PMC10809487 DOI: 10.1186/s12885-024-11879-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/13/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Esophageal cancer (EC) is a deadly disease with limited therapeutic options. Although circulating tumor DNA (ctDNA) could be a promising tool in this regard, the availiable evidence is limited. We performed a systematic review and meta-analysis to summarize the clinical applicability of the next-generation sequencing (NGS) and droplet digital polymerase chain reaction (ddPCR) technology on the ctDNA detection of the EC and listed the current challenges. METHODS We systematically searched MEDLINE (via PubMed), Embase (via OVID), ISI Web of Science database and Cochrane Library from January, 2000 to April, 2023. Progression-free survival (PFS) and overall survival (OS) were set as primary outcome endpoints. Pathologic response was evaluated by tumor regression grade (TRG), according to the eighth edition of the American Joint Committee on Cancer (AJCC). Major pathologic regression (MPR) was defined as TRG 1 and 2. The MPR was set as secondary endpoint. Hazard rate (HR) and associated 95% CI were used as the effect indicators the association between ctDNA and prognosis of EC. MPR rates were also calculated. Fixed-effect model (Inverse Variance) or random-effect model (Mantel-Haenszel method) was performed depending on the statistically heterogeneity. RESULTS Twenty-two studies, containing 1144 patients with EC, were included in this meta-analysis. The results showed that OS (HR = 3.87; 95% CI, 2.86-5.23) and PFS (HR = 4.28; 95% CI, 3.34-5.48) were shorter in ctDNA-positive patients. In the neoadjuvant therapy, the sensitivity analysis showed the clarified HR of ctDNA-positive was 1.13(95% CI, 1.01-1.28). We also found that TP53, NOTCH1, CCND1 and CNKN2A are the most frequent mutation genes. CONCLUSIONS Positive ctDNA is associated with poor prognosis, which demonstrated clinical value of ctDNA. Longitudinal ctDNA monitoring showed potential prognostic value in the neoadjuvant therapy. In an era of precision medicine, ctDNA could be a promising tool to individualize treatment planning and to improve outcomes in EC. PROSPERO REGISTRATION NUMBER CRD42023412465.
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Affiliation(s)
- Yaozhong Zhang
- Department of Infectious diseases, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Huazhen Du
- Department of Emergency, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Na Wang
- Department of Molecular Biology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lei Wang
- Department of Thoracic Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yajie Huang
- Department of Medical oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China.
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Mu N, Jylhä C, Axelsson T, Sydén F, Brehmer M, Tham E. Patient-specific targeted analysis of circulating tumour DNA in plasma is feasible and may be a potential biomarker in UTUC. World J Urol 2023; 41:3421-3427. [PMID: 37721600 PMCID: PMC10693512 DOI: 10.1007/s00345-023-04583-w] [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: 04/01/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
PURPOSE The prognosis of upper urinary tract urothelial carcinoma (UTUC) is associated with tumour grade (G) and stage. Despite preoperative risk stratification and radical treatment, recurrence and progression are common. Thus, prognostic and monitoring biomarkers are needed. This feasibility study aimed to investigate if targeted analyses on circulating tumour DNA (ctDNA) in plasma could identify tumour-specific gene variants, and thus have potential for further evaluation as a biomarker in UTUC. METHODS Nine UTUC patients with genetically characterised tumours were included in this prospective pilot study. Two tumour-specific variants were chosen for targeted analyses with multiplex droplet digital PCR on cell-free DNA (cfDNA) from plasma at diagnosis or from recurrence. RESULTS Of six patients with diagnostic plasma samples, ctDNA was detected in four with G2 or G3 tumours and tumours > 300m2 in size. Three of these patients progressed in their disease and the fourth had the largest G3 tumour at sampling. In contrast, the two patients with undetectable ctDNA in diagnostic plasma had a G1 tumour and G3 carcinoma in situ (CIS), respectively. The patient with G3 CIS had detectable ctDNA later during follow-up and progressed thereafter with aggressive intravesical recurrence and CT-scan-verified CIS progression in the upper urinary tract. In three patients with small recurrent G1 or G2 tumours, none had detectable ctDNA in plasma and all were progression free. CONCLUSION Our early findings demonstrate that ctDNA in plasma can be detected by targeted analysis in patients with UTUC. However, further studies are needed to determine its role as a potential biomarker.
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Affiliation(s)
- Ninni Mu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Jylhä
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas Axelsson
- Division of Urology, Danderyd Hospital, Stockholm, Sweden
| | - Filip Sydén
- Department of Urology, Stockholm South General Hospital, Stockholm, Sweden
| | - Marianne Brehmer
- Department of Urology, Stockholm South General Hospital, Stockholm, Sweden
- Department of Clinical Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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Haider Z, Wästerlid T, Spångberg LD, Rabbani L, Jylhä C, Thorvaldsdottir B, Skaftason A, Awier HN, Krstic A, Gellerbring A, Lyander A, Hägglund M, Jeggari A, Rassidakis G, Sonnevi K, Sander B, Rosenquist R, Tham E, Smedby KE. Whole-genome informed circulating tumor DNA analysis by multiplex digital PCR for disease monitoring in B-cell lymphomas: a proof-of-concept study. Front Oncol 2023; 13:1176698. [PMID: 37333831 PMCID: PMC10272573 DOI: 10.3389/fonc.2023.1176698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/02/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction Analyzing liquid biopsies for tumor-specific aberrations can facilitate detection of measurable residual disease (MRD) during treatment and at follow-up. In this study, we assessed the clinical potential of using whole-genome sequencing (WGS) of lymphomas at diagnosis to identify patient-specific structural (SVs) and single nucleotide variants (SNVs) to enable longitudinal, multi-targeted droplet digital PCR analysis (ddPCR) of cell-free DNA (cfDNA). Methods In 9 patients with B-cell lymphoma (diffuse large B-cell lymphoma and follicular lymphoma), comprehensive genomic profiling at diagnosis was performed by 30X WGS of paired tumor and normal specimens. Patient-specific multiplex ddPCR (m-ddPCR) assays were designed for simultaneous detection of multiple SNVs, indels and/or SVs, with a detection sensitivity of 0.0025% for SV assays and 0.02% for SNVs/indel assays. M-ddPCR was applied to analyze cfDNA isolated from serially collected plasma at clinically critical timepoints during primary and/or relapse treatment and at follow-up. Results A total of 164 SNVs/indels were identified by WGS including 30 variants known to be functionally relevant in lymphoma pathogenesis. The most frequently mutated genes included KMT2D, PIM1, SOCS1 and BCL2. WGS analysis further identified recurrent SVs including t(14;18)(q32;q21) (IGH::BCL2), and t(6;14)(p25;q32) (IGH::IRF4). Plasma analysis at diagnosis showed positive circulating tumor DNA (ctDNA) levels in 88% of patients and the ctDNA burden correlated with baseline clinical parameters (LDH and sedimentation rate, p-value <0.01). While clearance of ctDNA levels after primary treatment cycle 1 was observed in 3/6 patients, all patients analyzed at final evaluation of primary treatment showed negative ctDNA, hence correlating with PET-CT imaging. One patient with positive ctDNA at interim also displayed detectable ctDNA (average variant allele frequency (VAF) 6.9%) in the follow-up plasma sample collected 2 years after final evaluation of primary treatment and 25 weeks before clinical manifestation of relapse. Conclusion In summary, we demonstrate that multi-targeted cfDNA analysis, using a combination of SNVs/indels and SVs candidates identified by WGS analysis, provides a sensitive tool for MRD monitoring and can detect lymphoma relapse earlier than clinical manifestation.
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Affiliation(s)
- Zahra Haider
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Tove Wästerlid
- Department of Medicine, Division of Clinical Epidemiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Linn Deleskog Spångberg
- Department of Medicine, Division of Clinical Epidemiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Leily Rabbani
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Jylhä
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Birna Thorvaldsdottir
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aron Skaftason
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Hero Nikdin Awier
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Aleksandra Krstic
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Gellerbring
- Clinical Genomics Stockholm, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Anna Lyander
- Clinical Genomics Stockholm, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Moa Hägglund
- Clinical Genomics Stockholm, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Ashwini Jeggari
- Clinical Genomics Stockholm, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Georgios Rassidakis
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Laboratory, Stockholm, Sweden
| | - Kristina Sonnevi
- Department of Medicine, Division of Clinical Epidemiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine, Division of Pathology and Cancer Diagnostics, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Karin E. Smedby
- Department of Medicine, Division of Clinical Epidemiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
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Earl J, Kataki A, Smolkova B. Liquid Biopsy in Gastrointestinal Cancers: How Close Are We to Reaching the Clinic? Cancers (Basel) 2023; 15:2831. [PMID: 37345168 DOI: 10.3390/cancers15102831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Gastrointestinal (GI) cancers are malignancies that develop within the digestive system and account for one in four cancer cases according to WHO data [...].
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Affiliation(s)
- Julie Earl
- Molecular Epidemiology and Predictive Tumor Markers Group, Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9100, CIBERONC, 28034 Madrid, Spain
| | - Agapi Kataki
- 1st Department of Propaedeutic Surgery, National and Kapodistrian University of Athens, Vasilissis Sofias 114, 11527 Athens, Greece
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, 845-05 Bratislava, Slovakia
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