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Lee MR, Woo SM, Kim MK, Han S, Park S, Lee WJ, Lee D, Choi SI, Choi W, Yoon K, Chun JW, Kim Y, Kong S. Application of plasma circulating KRAS mutations as a predictive biomarker for targeted treatment of pancreatic cancer. Cancer Sci 2024; 115:1283-1295. [PMID: 38348576 PMCID: PMC11007020 DOI: 10.1111/cas.16104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/11/2024] [Accepted: 01/27/2024] [Indexed: 04/12/2024] Open
Abstract
Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations in circulating tumor deoxyribonucleic acid (ctDNA) have been reported as representative noninvasive prognostic markers for pancreatic ductal adenocarcinoma (PDAC). Here, we aimed to evaluate single KRAS mutations as prognostic and predictive biomarkers, with an emphasis on potential therapeutic approaches to PDAC. A total of 128 patients were analyzed for multiple or single KRAS mutations (G12A, G12C, G12D, G12R, G12S, G12V, and G13D) in their tumors and plasma using droplet digital polymerase chain reaction (ddPCR). Overall, KRAS mutations were detected by multiplex ddPCR in 119 (93%) of tumor DNA and 68 (53.1%) of ctDNA, with a concordance rate of 80% between plasma ctDNA and tumor DNA in the metastatic stage, which was higher than the 44% in the resectable stage. Moreover, the prognostic prediction of both overall survival (OS) and progression-free survival (PFS) was more relevant using plasma ctDNA than tumor DNA. Further, we evaluated the selective tumor-suppressive efficacy of the KRAS G12C inhibitor sotorasib in a patient-derived organoid (PDO) from a KRAS G12C-mutated patient using a patient-derived xenograft (PDX) model. Sotorasib showed selective inhibition in vitro and in vivo with altered tumor microenvironment, including fibroblasts and macrophages. Collectively, screening for KRAS single mutations in plasma ctDNA and the use of preclinical models of PDO and PDX with genetic mutations would impact precision medicine in the context of PDAC.
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Affiliation(s)
- Mi Rim Lee
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Molecular Imaging Branch, Division of Convergence TechnologyResearch Institute of National Cancer CenterGoyangKorea
| | - Sang Myung Woo
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer CenterGoyangKorea
- Immuno‐Oncology Branch, Division of Rare and Refractory CenterResearch Institute of National Cancer CenterGoyangKorea
| | - Min Kyeong Kim
- Targeted Therapy Branch, Division of Rare and Refractory CenterResearch Institute of National Cancer CenterGoyangKorea
| | - Sung‐Sik Han
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer CenterGoyangKorea
| | - Sang‐Jae Park
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer CenterGoyangKorea
| | - Woo Jin Lee
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer CenterGoyangKorea
- Interventional Medicine Branch, Division of Clinical ResearchResearch Institute of National Cancer CenterGoyangKorea
| | - Dong‐eun Lee
- Biostatistics Collaboration TeamResearch Core Center, National Cancer CenterGoyangKorea
| | - Sun Il Choi
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Molecular Imaging Branch, Division of Convergence TechnologyResearch Institute of National Cancer CenterGoyangKorea
- Henan Key Laboratory of Brain Targeted Bio‐Nanomedicine, School of Life Sciences & School of PharmacyHenan UniversityKaifengHenanChina
| | - Wonyoung Choi
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Center for Clinical Trials, Hospital, National Cancer CenterGoyangKorea
- Cancer Molecular Biology Branch, Division of Cancer BiologyResearch Institute of National Cancer CenterGoyangKorea
| | - Kyong‐Ah Yoon
- College of Veterinary MedicineKonkuk UniversitySeoulKorea
| | - Jung Won Chun
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer CenterGoyangKorea
- Interventional Medicine Branch, Division of Clinical ResearchResearch Institute of National Cancer CenterGoyangKorea
| | - Yun‐Hee Kim
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Molecular Imaging Branch, Division of Convergence TechnologyResearch Institute of National Cancer CenterGoyangKorea
| | - Sun‐Young Kong
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Targeted Therapy Branch, Division of Rare and Refractory CenterResearch Institute of National Cancer CenterGoyangKorea
- Department of Laboratory MedicineHospital, National Cancer CenterGoyangKorea
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2
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Lee JY, Jeon S, Jun HR, Sung CO, Jang SJ, Choi CM, Chun SM. Revolutionizing Non-Small Cell Lung Cancer Diagnosis: Ultra-High-Sensitive ctDNA Analysis for Detecting Hotspot Mutations with Long-term Stored Plasma. Cancer Res Treat 2024; 56:484-501. [PMID: 37871897 PMCID: PMC11016651 DOI: 10.4143/crt.2023.712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/22/2023] [Indexed: 10/25/2023] Open
Abstract
PURPOSE Circulating cell-free DNA (cfDNA) has great potential in clinical oncology. The prognostic and predictive values of cfDNA in non-small cell lung cancer (NSCLC) have been reported, with epidermal growth factor receptor (EGFR), KRAS, and BRAF mutations in tumor-derived cfDNAs acting as biomarkers during the early stages of tumor progression and recurrence. However, extremely low tumor-derived DNA rates hinder cfDNA application. We developed an ultra-high-sensitivity lung version 1 (ULV1) panel targeting BRAF, KRAS, and EGFR hotspot mutations using small amounts of cfDNA, allowing for semi-quantitative analysis with excellent limit-of-detection (0.05%). MATERIALS AND METHODS Mutation analysis was performed on cfDNAs extracted from the plasma of 104 patients with NSCLC by using the ULV1 panel and targeted next-generation sequencing (CT-ULTRA), followed by comparison analysis of mutation patterns previously screened using matched tumor tissue DNA. RESULTS The ULV1 panel demonstrated robust selective amplification of mutant alleles, enabling the detection of mutations with a high degree of analytical sensitivity (limit-of-detection, 0.025%-0.1%) and specificity (87.9%-100%). Applying ULV1 to NSCLC cfDNA revealed 51.1% (23/45) samples with EGFR mutations, increasing with tumor stage: 8.33% (stage I) to 78.26% (stage IV). Semi-quantitative analysis proved effective for low-mutation-fraction clinical samples. Comparative analysis with PANAMutyper EGFR exhibited substantial concordance (κ=0.84). CONCLUSION Good detection sensitivity (~80%) was observed despite the limited volume (1 mL) and long-term storage (12-50 months) of plasma used and is expected to increase with high cfDNA inputs. Thus, the ULV1 panel is a fast and cost-effective method for early diagnosis, treatment selection, and clinical follow-up of patients with NSCLC.
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Affiliation(s)
- Ji-Young Lee
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Seoul, Korea
| | - Seyeon Jeon
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Seoul, Korea
| | - Ha Ra Jun
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Seoul, Korea
| | - Chang Ohk Sung
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chang-Min Choi
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sung-Min Chun
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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3
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Efthymiou V, Queenan N, Haas M, Naegele S, Goss D, Faden DL. Circulating Tumor DNA in the Immediate Postoperative Setting. Ann Surg Oncol 2024; 31:2319-2325. [PMID: 38190058 DOI: 10.1245/s10434-023-14860-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/17/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as an accurate real-time biomarker of disease status across many solid tumor types. Most studies evaluating the utility of ctDNA have focused on time points weeks to months after surgery, which, for many cancer types, is significantly later than decision-making time points for adjuvant treatment. In this systematic review, we summarize the state of the literature on the feasibility of using ctDNA as a biomarker in the immediate postoperative period. METHODS We performed a systematic review evaluating the early kinetics, defined here as 3 days of ctDNA in patients who underwent curative-intent surgery. RESULTS Among the 2057 studies identified, eight cohort studies met the criteria for evaluation. Across six different cancer types, all studies showed an increased risk of cancer recurrence in patients with detectable ctDNA in the immediate postoperative period. CONCLUSION While ctDNA clearance kinetics appear to vary based on tumor type, across all studies detectable ctDNA after surgery was predictive of recurrence, suggesting early postoperative time points could be feasibly used for determining minimal residual disease. However, larger studies need to be performed to better understand the precise kinetics of ctDNA clearance across different cancer types as well as to determine optimal postoperative time points.
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Affiliation(s)
- Vasileios Efthymiou
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Natalia Queenan
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Markus Haas
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Saskia Naegele
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Deborah Goss
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Daniel L Faden
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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4
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Pomerantz T, Brooks R. Circulating Tumor DNA (ctDNA) and Its Role in Gynecologic Malignancies. Curr Treat Options Oncol 2024; 25:510-522. [PMID: 38472567 DOI: 10.1007/s11864-024-01180-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 03/14/2024]
Abstract
OPINION STATEMENT Circulating tumor DNA (ctDNA) refers to small fragments of DNA released into the bloodstream by cancer cells. It is obtained through "liquid biopsy;" which most commonly refers to plasma or blood samples, but can be obtained from a number of bodily fluids including ascitic fluid, saliva, and even urine and stool. ctDNA is detected via polymerase chain reaction (PCR) or next-generation sequencing (NGS). The DNA from these samples is analyzed for the detection of point mutations, copy-number alterations, gene fusion, and DNA methylation. These results have the potential for use in cancer diagnosis, determining prognosis, targeting gene-specific therapies, and monitoring for/predicting disease recurrence and response to treatment. ctDNA offers an alternative to tissue biopsy; it is less invasive and can be monitored serially over time without multiple procedures. Moreover it may have the ability to detect disease recurrence or predict behavior in a way that solid tissue biopsies, tumor marker surveillance, and imaging cannot. Recent explosion in interest in ctDNA shows promising developments for widespread adoption of these techniques in cancer care. However, the use of ctDNA in diagnosis and treatment of gynecologic malignancies is currently limited, compared to adoption in other solid-organ tumors such as breast and colorectal cancers. Compared to other cancer types, there appear to be fewer comprehensive studies and clinical validations specifically focusing on the use of ctDNA in gynecologic cancers. More research is needed in this area to advance the potential for use of ctDNA in ovarian, endometrial, and cervical cancers before this can be routinely adopted to improve care for patients with gynecologic malignancies.
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Affiliation(s)
- Tali Pomerantz
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA.
| | - Rebecca Brooks
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA
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5
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Northcott J, Bartha G, Harris J, Li C, Navarro FC, Pyke RM, Hong M, Zhang Q, Ma S, Chen TX, Lai J, Udar N, Saldivar JS, Ayash E, Anderson J, Li J, Cui T, Le T, Chow R, Velasco RJ, Mallo C, Santiago R, Bruce RC, Goodman LJ, Chen Y, Norton D, Chen RO, Lyle JM. Analytical validation of NeXT Personal®, an ultra-sensitive personalized circulating tumor DNA assay. Oncotarget 2024; 15:200-218. [PMID: 38484152 PMCID: PMC10939476 DOI: 10.18632/oncotarget.28565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
We describe the analytical validation of NeXT Personal®, an ultra-sensitive, tumor-informed circulating tumor DNA (ctDNA) assay for detecting residual disease, monitoring therapy response, and detecting recurrence in patients diagnosed with solid tumor cancers. NeXT Personal uses whole genome sequencing of tumor and matched normal samples combined with advanced analytics to accurately identify up to ~1,800 somatic variants specific to the patient's tumor. A personalized panel is created, targeting these variants and then used to sequence cell-free DNA extracted from patient plasma samples for ultra-sensitive detection of ctDNA. The NeXT Personal analytical validation is based on panels designed from tumor and matched normal samples from two cell lines, and from 123 patients across nine cancer types. Analytical measurements demonstrated a detection threshold of 1.67 parts per million (PPM) with a limit of detection at 95% (LOD95) of 3.45 PPM. NeXT Personal showed linearity over a range of 0.8 to 300,000 PPM (Pearson correlation coefficient = 0.9998). Precision varied from a coefficient of variation of 12.8% to 3.6% over a range of 25 to 25,000 PPM. The assay targets 99.9% specificity, with this validation study measuring 100% specificity and in silico methods giving us a confidence interval of 99.92 to 100%. In summary, this study demonstrates NeXT Personal as an ultra-sensitive, highly quantitative and robust ctDNA assay that can be used to detect residual disease, monitor treatment response, and detect recurrence in patients.
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Affiliation(s)
| | | | | | - Conan Li
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | - Qi Zhang
- Personalis, Inc., Fremont, CA 94555, USA
| | - Shuyuan Ma
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - Janet Lai
- Personalis, Inc., Fremont, CA 94555, USA
| | - Nitin Udar
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - Erin Ayash
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - Jiang Li
- Personalis, Inc., Fremont, CA 94555, USA
| | - Tiange Cui
- Personalis, Inc., Fremont, CA 94555, USA
| | - Tu Le
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | | | | | | | - Yi Chen
- Personalis, Inc., Fremont, CA 94555, USA
| | - Dan Norton
- Personalis, Inc., Fremont, CA 94555, USA
| | | | - John M. Lyle
- Personalis, Inc., Fremont, CA 94555, USA
- Co-last authors
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Li W, Huang X, Patel R, Schleifman E, Fu S, Shames DS, Zhang J. Analytical evaluation of circulating tumor DNA sequencing assays. Sci Rep 2024; 14:4973. [PMID: 38424110 PMCID: PMC10904763 DOI: 10.1038/s41598-024-54361-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
In China, circulating tumor DNA analysis is widely used and numerous assays are available. Systematic evaluation to help users make informed selections is needed. Nine circulating tumor DNA assays, including one benchmark assay, were evaluated using 23 contrived reference samples. There were two sample types (cell-free DNA and plasma samples), three circulating tumor DNA inputs (low, < 20 ng; medium, 20-50 ng; high, > 50 ng), two variant allele frequency ranges (low, 0.1-0.5%; intermediate, 0.5-2.5%), and four variant types (single nucleotide, insertion/deletion, structural, and copy number). Sensitivity, specificity, reproducibility, and all processes from cell-free DNA extraction to bioinformatics analysis were assessed. The test assays were generally comparable or superior to the benchmark assay, demonstrating high analytical sensitivity. Variations in circulating tumor DNA extraction and quantification efficiency, sensitivity, and reproducibility were observed, particularly at lower inputs. These findings will guide circulating tumor DNA assay choice for research and clinical studies, allowing consideration of multiple technical parameters.
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Affiliation(s)
- Wenjin Li
- Oncology Biomarker Development, Roche (China) Holding Ltd, Pudong, Shanghai, China
| | - Xiayu Huang
- Oncology Biomarker Development, Roche (China) Holding Ltd, Pudong, Shanghai, China
| | - Rajesh Patel
- Oncology Biomarker Development, Genentech, Ltd, South San Francisco, USA
| | - Erica Schleifman
- Oncology Biomarker Development, Genentech, Ltd, South San Francisco, USA
| | - Shijing Fu
- Oncology Biomarker Development, Roche (China) Holding Ltd, Pudong, Shanghai, China
| | - David S Shames
- Oncology Biomarker Development, Genentech, Ltd, South San Francisco, USA.
| | - Jingyu Zhang
- Oncology Biomarker Development, Roche (China) Holding Ltd, Pudong, Shanghai, China.
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ramírez-Maldonado E, López Gordo S, Major Branco RP, Pavel MC, Estalella L, Llàcer-Millán E, Guerrero MA, López-Gordo E, Memba R, Jorba R. Clinical Application of Liquid Biopsy in Pancreatic Cancer: A Narrative Review. Int J Mol Sci 2024; 25:1640. [PMID: 38338919 PMCID: PMC10855073 DOI: 10.3390/ijms25031640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma contributes significantly to global cancer-related deaths, featuring only a 10% survival rate over five years. The quest for novel tumor markers is critical to facilitate early diagnosis and tailor treatment strategies for this disease, which is key to improving patient outcomes. In pancreatic ductal adenocarcinoma, these markers have been demonstrated to play a crucial role in early identification, continuous monitoring, and prediction of its prognosis and have led to better patient outcomes. Nowadays, biopsy specimens serve to ascertain diagnosis and determine tumor type. However, liquid biopsies present distinct advantages over conventional biopsy techniques. They offer a noninvasive, easily administered procedure, delivering insights into the tumor's status and facilitating real-time monitoring. Liquid biopsies encompass a variety of elements, such as circulating tumor cells, circulating tumor DNA, extracellular vesicles, microRNAs, circulating RNA, tumor platelets, and tumor endothelial cells. This review aims to provide an overview of the clinical applications of liquid biopsy as a technique in the management of pancreatic cancer.
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Affiliation(s)
- Elena Ramírez-Maldonado
- HBP Unit, General Surgery Department, Joan XXIII University Hospital, 43005 Tarragona, Spain; (M.-C.P.); (L.E.); (M.A.G.); (R.M.); (R.J.)
- Medicine and Surgery Department, Rovira i Virgili University, 43204 Reus, Spain
| | - Sandra López Gordo
- General Surgery Department, Maresme Health Consortium, 08304 Mataro, Spain;
| | | | - Mihai-Calin Pavel
- HBP Unit, General Surgery Department, Joan XXIII University Hospital, 43005 Tarragona, Spain; (M.-C.P.); (L.E.); (M.A.G.); (R.M.); (R.J.)
- Medicine and Surgery Department, Rovira i Virgili University, 43204 Reus, Spain
| | - Laia Estalella
- HBP Unit, General Surgery Department, Joan XXIII University Hospital, 43005 Tarragona, Spain; (M.-C.P.); (L.E.); (M.A.G.); (R.M.); (R.J.)
- Medicine and Surgery Department, Rovira i Virgili University, 43204 Reus, Spain
| | - Erik Llàcer-Millán
- HBP Unit, General Surgery Department, Joan XXIII University Hospital, 43005 Tarragona, Spain; (M.-C.P.); (L.E.); (M.A.G.); (R.M.); (R.J.)
- Medicine and Surgery Department, Rovira i Virgili University, 43204 Reus, Spain
| | - María Alejandra Guerrero
- HBP Unit, General Surgery Department, Joan XXIII University Hospital, 43005 Tarragona, Spain; (M.-C.P.); (L.E.); (M.A.G.); (R.M.); (R.J.)
- Medicine and Surgery Department, Rovira i Virgili University, 43204 Reus, Spain
| | | | - Robert Memba
- HBP Unit, General Surgery Department, Joan XXIII University Hospital, 43005 Tarragona, Spain; (M.-C.P.); (L.E.); (M.A.G.); (R.M.); (R.J.)
- Medicine and Surgery Department, Rovira i Virgili University, 43204 Reus, Spain
| | - Rosa Jorba
- HBP Unit, General Surgery Department, Joan XXIII University Hospital, 43005 Tarragona, Spain; (M.-C.P.); (L.E.); (M.A.G.); (R.M.); (R.J.)
- Medicine and Surgery Department, Rovira i Virgili University, 43204 Reus, Spain
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9
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Emiloju OE, Storandt M, Zemla T, Tran N, Jethwa K, Mahipal A, Mitchell J, Thiels C, Mathis K, McWilliams R, Hubbard J, Sinicrope F, Shi Q, Jin Z. Tumor-Informed Circulating Tumor DNA for Minimal Residual Disease Detection in the Management of Colorectal Cancer. JCO Precis Oncol 2024; 8:e2300127. [PMID: 38237099 PMCID: PMC10805428 DOI: 10.1200/po.23.00127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/09/2023] [Accepted: 11/07/2023] [Indexed: 01/23/2024] Open
Abstract
PURPOSE Recurrence after curative-intent treatment occurs in 20%-50% of patients with stage II-IV colorectal cancer (CRC), underscoring the need for early detection of minimal residual disease (MRD) using circulating tumor DNA (ctDNA). Here, we examined the pattern of use of a tumor-informed ctDNA assay in CRC MRD monitoring in routine clinical practice at Mayo Clinic, Rochester. METHODS We conducted a retrospective analysis of health records of patients with CRC who had at least one tumor-informed ctDNA assay from May 2019 through July 1, 2022. Recurrence was defined as radiographic evidence of disease. Descriptive characteristics of the cohort, ctDNA results, and subsequent interventions were recorded. RESULTS Of the 120 patients included, the median age at diagnosis was 67 years, 46% were female, and 94% were White. At diagnosis, 10 patients had stage I, 23 stage II, 60 stage III, and 25 stage IV disease. Of 476 ctDNA assays performed, 70% were performed in patients who had recurrent disease most commonly to monitor the effectiveness of therapeutic interventions and 16% resulted in a change in clinical decision making. There were 110 recurrences identified in 62 patients, as some patients experienced more than one recurrence over time. Compared with serum carcinoembryonic antigen levels, ctDNA results correlated better with radiologic imaging. CONCLUSION Routine ctDNA monitoring for MRD detection has been adopted in clinical practice; however, 84% of ctDNA assays performed did not result in a change in clinical management. This suggests the need for further clinical research data to guide routine clinical use of ctDNA MRD testing in CRC.
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Affiliation(s)
| | | | - Tyler Zemla
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Nguyen Tran
- Division of Oncology, Mayo Clinic, Rochester, MN
| | - Krishan Jethwa
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - Amit Mahipal
- Department of Hematology and Oncology, University Hospitals, Cleveland, OH
| | | | | | | | | | | | - Frank Sinicrope
- Division of Oncology, Mayo Clinic, Rochester, MN
- Department of Medicine, Mayo Clinic, Rochester, MN
| | - Qian Shi
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Zhaohui Jin
- Division of Oncology, Mayo Clinic, Rochester, MN
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10
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Holdenrieder S, van Rossum HH, van den Heuvel M. Lung cancer biomarkers: Raising the clinical value of the classical and the new ones. Tumour Biol 2024; 46:S1-S7. [PMID: 38517827 DOI: 10.3233/tub-240004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Blood-based diagnostics for lung cancer support the diagnosis, estimation of prognosis, prediction, and monitoring of therapy response in lung cancer patients. The clinical utility of serum tumor markers has considerably increased due to developments in serum protein tumor markers analytics and clinical biomarker studies, the exploration of preanalytical and influencing conditions, the interpretation of biomarker combinations and individual biomarker kinetics, as well as the implementation of biostatistical models. In addition, circulating tumor DNA (ctDNA) and other liquid biopsy markers are playing an increasingly prominent role in the molecular tumor characterization and the monitoring of tumor evolution over time. Thus, modern lung cancer biomarkers may considerably contribute to an individualized companion diagnostics and provide a sensitive guidance for patients throughout the course of their disease. In this special edition on Tumor Markers in Lung Cancer, experts summarize recent developments in clinical laboratory diagnostics of lung cancer and give an outlook on future challenges and opportunities.
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Affiliation(s)
- Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Munich, Germany
| | - Huub H van Rossum
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michel van den Heuvel
- Department of Pulmonology, Radboud University Medical Center Nijmegen, Nijmegen, The Netherlands
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11
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Dong Q, Chen C, Hu Y, Zhang W, Yang X, Qi Y, Zhu C, Chen X, Shen X, Ji W. Clinical application of molecular residual disease detection by circulation tumor DNA in solid cancers and a comparison of technologies: review article. Cancer Biol Ther 2023; 24:2274123. [PMID: 37955635 PMCID: PMC10653633 DOI: 10.1080/15384047.2023.2274123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/04/2023] [Indexed: 11/14/2023] Open
Abstract
Molecular residual disease (MRD), detected by circulating tumor DNA (ctDNA) can be involved in the entire process of solid tumor management, including recurrence prediction, efficacy evaluation, and risk stratification. Currently, the detection technologies are divided into two main categories, as follows: tumor-agnostic and tumor informed. Tumor-informed assay obtains mutation information by sequencing tumor tissue samples before blood MRD monitoring, followed by formulation of a personalized MRD panel. Tumor-agnostic assays are carried out using a fixed panel without the mutation information from primary tumor tissue. The choice of testing strategy may depend on the level of evidence from ongoing randomized clinical trials, investigator preference, cost-effectiveness, patient economics, and availability of tumor tissue. The review describes the difference between tumor informed and tumor agnostic detection. In addition, the clinical application of ctDNA MRD in solid tumors was introduced, with emphasis on lung cancer, colorectal cancer, Urinary system cancer, and breast cancer.
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Affiliation(s)
- Qiantong Dong
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Chenbin Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yuanbo Hu
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiteng Zhang
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xinxin Yang
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yingxue Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Chan Zhu
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Xiaodong Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xian Shen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiping Ji
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
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12
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Gimeno-Valiente F, Martín-Arana J, Tébar-Martínez R, Gambardella V, Martínez-Ciarpaglini C, García-Micó B, Martínez-Castedo B, Palomar B, García-Bartolomé M, Seguí V, Huerta M, Moro-Valdezate D, Pla-Martí V, Pérez-Santiago L, Roselló S, Roda D, Cervantes A, Tarazona N. Sequencing paired tumor DNA and white blood cells improves circulating tumor DNA tracking and detects pathogenic germline variants in localized colon cancer. ESMO Open 2023; 8:102051. [PMID: 37951129 PMCID: PMC10774972 DOI: 10.1016/j.esmoop.2023.102051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/22/2023] [Indexed: 11/13/2023] Open
Abstract
BACKGROUND In the setting of localized colon cancer (CC), circulating tumor DNA (ctDNA) monitoring in plasma has shown potential for detecting minimal residual disease (MRD) and predicting a higher risk of recurrence. With the tumor-only sequencing approach, however, germline variants may be misidentified as somatic variations, precluding the possibility of tracking in up to 11% of patients due to a lack of known somatic mutations. In this study, we assess the potential value of adding white blood cells (WBCs) to tumor tissue sequencing to enhance the accuracy of sequencing results. PATIENTS AND METHODS A total of 148 patients diagnosed with localized CC were prospectively recruited at the Hospital Clínico Universitario in Valencia (Spain). Employing a custom 29-gene panel, sequencing was conducted on tumor tissue, plasma and corresponding WBCs. Droplet digital PCR and amplicon-based NGS were performed on plasma samples post-surgery to track MRD. Oncogenic somatic variants were identified by annotating with COSMIC, OncoKB and an internal repository of pathogenic mutations database. A variant prioritization analysis, mainly characterized by the match of oncogenic mutations with the evidence levels defined in OncoKB, was carried out to select specific targeted therapies. RESULTS Utilizing paired tumor and WBCs sequencing, we identified somatic mutations in all patients (100%) within our cohort, compared to 89% using only tumor tissue. Consequently, the top 10 most frequently mutated genes for plasma monitoring were altered. The sequencing of WBCs identified 9% of patients with pathogenic mutations in the germline, with APC and TP53 being the most frequently mutated genes. Additionally, mutations in genes related to clonal hematopoiesis of indeterminate potential were detected in 27% of the cohort, with TP53, KRAS, and KMT2C being the most frequently altered genes. There were no observed differences in the sensitivity of monitoring MRD using ddPCR or amplicon-based NGS (p = 1). Ultimately, 41% of the patients harbored potentially targetable alterations at diagnosis. CONCLUSION The germline testing method not only enhanced sequencing results and raised the proportion of patients eligible for plasma monitoring, but also uncovered the existence of pathogenic germline variations, thereby aiding in the identification of patients at a higher risk of hereditary cancer syndromes.
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Affiliation(s)
- F Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
| | - J Martín-Arana
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - R Tébar-Martínez
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - V Gambardella
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - C Martínez-Ciarpaglini
- CIBERONC, Instituto de Salud Carlos III, Madrid; Department of Pathology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - B García-Micó
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - B Martínez-Castedo
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - B Palomar
- Department of Pathology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - M García-Bartolomé
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - V Seguí
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - M Huerta
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - D Moro-Valdezate
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - V Pla-Martí
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - L Pérez-Santiago
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - S Roselló
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - D Roda
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - A Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid.
| | - N Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid.
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13
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Dobilas A, Chen Y, Brueffer C, Leandersson P, Saal LH, Borgfeldt C. Preoperative ctDNA Levels Are Associated With Poor Overall Survival in Patients With Ovarian Cancer. Cancer Genomics Proteomics 2023; 20:763-770. [PMID: 38035709 PMCID: PMC10687736 DOI: 10.21873/cgp.20423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND/AIM Circulating tumor DNA (ctDNA), which is shed from cancer cells into the bloodstream, offers a potential minimally invasive approach for cancer diagnosis and monitoring. This research aimed to assess the preoperative ctDNA levels in ovarian tumors patients' plasma and establish correlations with clinicopathological parameters and patient prognosis. PATIENTS AND METHODS Tumor DNA was extracted from ovarian tumor tissue from 41 patients. Targeted sequencing using a panel of 127 genes recurrently mutated in cancer was performed to identify candidate somatic mutations in the tumor DNA. SAGAsafe digital PCR (dPCR) assays targeting the candidate mutations were used to measure ctDNA levels in patient plasma samples, obtained prior to surgery, to evaluate ctDNA levels in terms of mutant copy number/ml and variant allele frequency. RESULTS Somatic mutations were found in 24 tumor samples, 17 of which were from ovarian cancer patients. The most frequently mutated gene was TP53. Preoperative plasma ctDNA levels were detected in 14 of the 24 patients. With higher stage, plasma ctDNA mutant concentration increased (p for trend <0.001). The overall survival of cancer patients with more than 10 ctDNA mutant copies/ml in plasma was significantly worse (p=0.008). CONCLUSION Pre-operative ctDNA measurement in ovarian cancer patients' plasma holds promise as a predictive biomarker for tumor staging and prognosis.
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Affiliation(s)
- Arturas Dobilas
- Department of Obstetrics and Gynecology, Skåne University Hospital, Lund University, Lund, Sweden;
| | - Yilun Chen
- SAGA Diagnostics AB, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Christian Brueffer
- SAGA Diagnostics AB, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Pia Leandersson
- Reproductive Medicine Center, Skåne University Hospital, Malmo, Sweden
| | - Lao H Saal
- SAGA Diagnostics AB, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Christer Borgfeldt
- Department of Obstetrics and Gynecology, Skåne University Hospital, Lund University, Lund, Sweden
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14
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Salimi M, Rastegarpouyani S. E74-like Factor 5 Promoter Methylation in Circulating Tumor DNA as a Potential Prognostic Marker in Breast Cancer Patients. Asian Pac J Cancer Prev 2023; 24:4035-4041. [PMID: 38156835 PMCID: PMC10909102 DOI: 10.31557/apjcp.2023.24.12.4035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Epigenetic alternations, such as DNA methylation, play a crucial role in breast tumor initiation and progression. The identification of noninvasive prognostic biomarkers has great importance in cancer management. Methylated cell-free DNA (cfDNA), circulating in the blood as a convenient tumor-associated DNA marker, can be used as a minimally invasive cancer biomarker. This study aimed to evaluate the promoter methylation status of E74-like factor 5 (ELF5) tumor suppressor gene in both tumors and plasma cell-free DNA of 80 breast cancer patients, compared with normal controls. METHODS Plasma cfDNA concentrations were measured using quantitative real-time PCR, and methylation pattern in the ELF5 gene promoter region was performed using methylation-specific polymerase chain reaction (MS-PCR) technique. RESULTS The data revealed a statistically significant increase in cfDNA concentrations in breast cancer patients, particularly in those with higher stages of the disease, triple-negative status, and metastasis (p<0.001). ELF5 promoter region hypermethylation was observed in 70% of breast cancer patients in both plasma cfDNA and tumor tissues. Notably, all patients with lymph node involvement and distant metastatic exhibited promoter hypermethylation in the ELF5 gene. CONCLUSION Our findings suggest that ELF5 promoter methylation in circulating DNA could serve as a potential non-invasive prognostic molecular marker in breast cancer patients. However, further studies are warranted to evaluate its diagnostic value.
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Affiliation(s)
- Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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15
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Xie J, Hu B, Gong Y, He S, Lin J, Huang Q, Cheng J. A comparative study on ctDNA and tumor DNA mutations in lung cancer and benign cases with a high number of CTCs and CTECs. J Transl Med 2023; 21:873. [PMID: 38041139 PMCID: PMC10691057 DOI: 10.1186/s12967-023-04746-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Liquid biopsy provides a non-invasive approach that enables detecting circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) using blood specimens and theoretically benefits early finding primary tumor or monitoring treatment response as well as tumor recurrence. Despite many studies on these novel biomarkers, their clinical relevance remains controversial. This study aims to investigate the correlation between ctDNA, CTCs, and circulating tumor-derived endothelial cells (CTECs) while also evaluating whether mutation profiling in ctDNA is consistent with that in tumor tissue from lung cancer patients. These findings will help the evaluation and utilization of these approaches in clinical practice. METHODS 104 participants (49 with lung cancer and 31 with benign lesions) underwent CTCs and CTECs detection using integrating subtraction enrichment and immunostaining-fluorescence in situ hybridization (SE-iFISH) strategy. The circulating cell-free DNA (cfDNA) concentration was measured and the mutational profiles of ctDNA were examined by Roche AVENIO ctDNA Expanded Kit (targeted total of 77 genes) by next generation sequencing (NGS) in 28 patients (20 with lung cancer and 8 with benign lesions) with highest numbers of CTCs and CTECs. Mutation validation in matched tumor tissue DNA was then performed in 9 patients with ctDNA mutations using a customized xGen pan-solid tumor kit (targeted total of 474 genes) by NGS. RESULTS The sensitivity and specificity of total number of CTCs and CTECs for the diagnosis of NSCLC were 67.3% and 77.6% [AUC (95%CI): 0.815 (0.722-0.907)], 83.9% and 77.4% [AUC (95%CI): 0.739 (0.618-0.860)]. The concentration of cfDNA in plasma was statistically correlated with the size of the primary tumor (r = 0.430, P = 0.022) and CYFRA 21-1 (r = 0.411, P = 0.041), but not with the numbers of CTCs and CTECs. In this study, mutations were found to be poorly consistent between ctDNA and tumor DNA (tDNA) in patients, even when numerous CTCs and CTECs were present. CONCLUSION Detection of CTCs and CTECs could be the potential adjunct tool for the early finding of lung cancer. The cfDNA levels are associated with the tumor burden, rather than the CTCs or CTECs counts. Moreover, the poorly consistent mutations between ctDNA and tDNA require further exploration.
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Affiliation(s)
- Jianzhu Xie
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Binjie Hu
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanping Gong
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sijia He
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Lin
- Department of Pathology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Huang
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jin Cheng
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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16
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Kolbinger FR, Bernard V, Lee JJ, Stephens BM, Branchi V, Raghav KPS, Maitra A, Guerrero PA, Semaan A. Significance of Distinct Liquid Biopsy Compartments in Evaluating Somatic Mutations for Targeted Therapy Selection in Cancer of Unknown Primary. J Gastrointest Cancer 2023; 54:1276-1285. [PMID: 36862364 DOI: 10.1007/s12029-023-00922-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Abstract
PURPOSE Cancer of unknown primary (CUP) accounts for 2-5% of all cancer diagnoses, wherein standard investigations fail to reveal the original tumor site. Basket trials allocate targeted therapeutics based on actionable somatic mutations, independent of tumor entity. These trials, however, mostly rely on variants identified in tissue biopsies. Since liquid biopsies (LB) represent the overall tumor genomic landscape, they may provide an ideal diagnostic source in CUP patients. To identify the most informative liquid biopsy compartment, we compared the utility of genomic variant analysis for therapy stratification in two LB compartments (circulating cell-free (cf) and extracellular vesicle (ev) DNA). METHODS CfDNA and evDNA from 23 CUP patients were analyzed using a targeted gene panel covering 151 genes. Identified genetic variants were interpreted regarding diagnostic and therapeutic relevance using the MetaKB knowledgebase. RESULTS LB revealed a total of 22 somatic mutations in evDNA and/or cfDNA in 11/23 patients. Out of the 22 identified somatic variants, 14 are classified as Tier I druggable somatic variants. Comparison of variants identified in evDNA and cfDNA revealed an overlap of 58% of somatic variants in both LB compartments, whereas over 40% of variants were only found in one or the other compartment. CONCLUSION We observed substantial overlap between somatic variants identified in evDNA and cfDNA of CUP patients. Nonetheless, interrogation of both LB compartments can potentially increase the rate of druggable alterations, stressing the significance of liquid biopsies for possible primary-independent basket and umbrella trial inclusion.
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Affiliation(s)
- Fiona R Kolbinger
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vincent Bernard
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaewon J Lee
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bret M Stephens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vittorio Branchi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kanwal P S Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paola A Guerrero
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Alexander Semaan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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17
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Nulsen J, Hussain N, Al-Deka A, Yap J, Uddin K, Yau C, Ahmed AA. Completing a genomic characterisation of microscopic tumour samples with copy number. BMC Bioinformatics 2023; 24:453. [PMID: 38036971 PMCID: PMC10688092 DOI: 10.1186/s12859-023-05576-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Genomic insights in settings where tumour sample sizes are limited to just hundreds or even tens of cells hold great clinical potential, but also present significant technical challenges. We previously developed the DigiPico sequencing platform to accurately identify somatic mutations from such samples. RESULTS Here, we complete this genomic characterisation with copy number. We present a novel protocol, PicoCNV, to call allele-specific somatic copy number alterations from picogram quantities of tumour DNA. We find that PicoCNV provides exactly accurate copy number in 84% of the genome for even the smallest samples, and demonstrate its clinical potential in maintenance therapy. CONCLUSIONS PicoCNV complements our existing platform, allowing for accurate and comprehensive genomic characterisations of cancers in settings where only microscopic samples are available.
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Affiliation(s)
- Joel Nulsen
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Singula Bio Ltd., Oxford, UK
| | - Nosheen Hussain
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Singula Bio Ltd., Oxford, UK
| | - Aws Al-Deka
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Singula Bio Ltd., Oxford, UK
| | - Jason Yap
- University of Birmingham, Birmingham, UK
| | | | - Christopher Yau
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK
- Health Data Research UK, London, UK
| | - Ahmed Ashour Ahmed
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK.
- Nuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK.
- Singula Bio Ltd., Oxford, UK.
- Oxford Biomedical Research Centre, National Institute of Health Research, Oxford, UK.
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18
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Shuai Y, Ma Z, Ju J, Wei T, Gao S, Kang Y, Yang Z, Wang X, Yue J, Yuan P. Liquid-based biomarkers in breast cancer: looking beyond the blood. J Transl Med 2023; 21:809. [PMID: 37957623 PMCID: PMC10644618 DOI: 10.1186/s12967-023-04660-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
In recent decades, using circulating tumor cell (CTC), circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), exosomes and etc. as liquid biomarkers has received enormous attention in various tumors, including breast cancer (BC). To date, efforts in the area of liquid biopsy predominantly focus on the analysis of blood-based markers. It is worth noting that the identifications of markers from non-blood sources provide unique advantages beyond the blood and these alternative sources may be of great significance in offering supplementary information in certain settings. Here, we outline the latest advances in the analysis of non-blood biomarkers, predominantly including urine, saliva, cerebrospinal fluid, pleural fluid, stool and etc. The unique advantages of such testings, their current limitations and the appropriate use of non-blood assays and blood assays in different settings are further discussed. Finally, we propose to highlight the challenges of these alternative assays from basic to clinical implementation and explore the areas where more investigations are warranted to elucidate its potential utility.
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Affiliation(s)
- You Shuai
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhonghua Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Endoscopy, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jie Ju
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tong Wei
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Songlin Gao
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yikun Kang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zixuan Yang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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19
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Giacomini P, Valenti F, Allegretti M, Pallocca M, De Nicola F, Ciuffreda L, Fanciulli M, Scalera S, Buglioni S, Melucci E, Casini B, Carosi M, Pescarmona E, Giordani E, Sperati F, Jannitti N, Betti M, Maugeri-Saccà M, Cecere FL, Villani V, Pace A, Appetecchia M, Vici P, Savarese A, Krasniqi E, Ferraresi V, Russillo M, Fabi A, Landi L, Minuti G, Cappuzzo F, Zeuli M, Ciliberto G. The Molecular Tumor Board of the Regina Elena National Cancer Institute: from accrual to treatment in real-world. J Transl Med 2023; 21:725. [PMID: 37845764 PMCID: PMC10577953 DOI: 10.1186/s12967-023-04595-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Molecular Tumor Boards (MTB) operating in real-world have generated limited consensus on good practices for accrual, actionable alteration mapping, and outcome metrics. These topics are addressed herein in 124 MTB patients, all real-world accrued at progression, and lacking approved therapy options. METHODS Actionable genomic alterations identified by tumor DNA (tDNA) and circulating tumor DNA (ctDNA) profiling were mapped by customized OncoKB criteria to reflect diagnostic/therapeutic indications as approved in Europe. Alterations were considered non-SoC when mapped at either OncoKB level 3, regardless of tDNA/ctDNA origin, or at OncoKB levels 1/2, provided they were undetectable in matched tDNA, and had not been exploited in previous therapy lines. RESULTS Altogether, actionable alterations were detected in 54/124 (43.5%) MTB patients, but only in 39 cases (31%) were these alterations (25 from tDNA, 14 from ctDNA) actionable/unexploited, e.g. they had not resulted in the assignment of pre-MTB treatments. Interestingly, actionable and actionable/unexploited alterations both decreased (37.5% and 22.7% respectively) in a subset of 88 MTB patients profiled by tDNA-only, but increased considerably (77.7% and 66.7%) in 18 distinct patients undergoing combined tDNA/ctDNA testing, approaching the potential treatment opportunities (76.9%) in 147 treatment-naïve patients undergoing routine tDNA profiling for the first time. Non-SoC therapy was MTB-recommended to all 39 patients with actionable/unexploited alterations, but only 22 (56%) accessed the applicable drug, mainly due to clinical deterioration, lengthy drug-gathering procedures, and geographical distance from recruiting clinical trials. Partial response and stable disease were recorded in 8 and 7 of 19 evaluable patients, respectively. The time to progression (TTP) ratio (MTB-recommended treatment vs last pre-MTB treatment) exceeded the conventional Von Hoff 1.3 cut-off in 9/19 cases, high absolute TTP and Von Hoff values coinciding in 3 cases. Retrospectively, 8 patients receiving post-MTB treatment(s) as per physician's choice were noted to have a much longer overall survival from MTB accrual than 11 patients who had received no further treatment (35.09 vs 6.67 months, p = 0.006). CONCLUSIONS MTB-recommended/non-SoC treatments are effective, including those assigned by ctDNA-only alterations. However, real-world MTBs may inadvertently recruit patients electively susceptible to diverse and/or multiple treatments.
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Affiliation(s)
- Patrizio Giacomini
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy.
| | - Fabio Valenti
- UOC Translational Oncology Research, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Matteo Allegretti
- UOC Translational Oncology Research, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Matteo Pallocca
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Francesca De Nicola
- SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Ludovica Ciuffreda
- SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Maurizio Fanciulli
- SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Stefano Scalera
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Simonetta Buglioni
- Department of Pathology, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Elisa Melucci
- Department of Pathology, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Beatrice Casini
- Department of Pathology, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Mariantonia Carosi
- Department of Pathology, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Edoardo Pescarmona
- Department of Pathology, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Elena Giordani
- UOC Translational Oncology Research, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Francesca Sperati
- Clinical Trial Center, Biostatistics and Bioinformatics, San Gallicano Dermatological Institute IRCCS, 00144, Rome, Italy
| | - Nicoletta Jannitti
- Pharmacy Unit, Medical Direction, IRCCS-Regina Elena National Cancer Institute and San Gallicano Institute, 00144, Rome, Italy
| | - Martina Betti
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Marcello Maugeri-Saccà
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
- Medical Oncology 2, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | | | - Veronica Villani
- Neuro-Oncology Unit, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Andrea Pace
- Neuro-Oncology Unit, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Marialuisa Appetecchia
- Oncological Endocrinology Unit, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Patrizia Vici
- Phase IV Studies, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Antonella Savarese
- Medical Oncology 1, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Eriseld Krasniqi
- Phase IV Studies, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Virginia Ferraresi
- Sarcomas and Rare Tumors Departmental Unit, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Michelangelo Russillo
- Sarcomas and Rare Tumors Departmental Unit, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Alessandra Fabi
- Precision Medicine Unit in Senology, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Lorenza Landi
- Clinical Trial Center: Phase 1 and Precision Medicine, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Gabriele Minuti
- Clinical Trial Center: Phase 1 and Precision Medicine, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Federico Cappuzzo
- Medical Oncology 2, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Massimo Zeuli
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
- Medical Oncology 1, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS-Regina Elena National Cancer Institute, 00144, Rome, Italy
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20
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Nguyen VTC, Nguyen TH, Doan NNT, Pham TMQ, Nguyen GTH, Nguyen TD, Tran TTT, Vo DL, Phan TH, Jasmine TX, Nguyen VC, Nguyen HT, Nguyen TV, Nguyen THH, Huynh LAK, Tran TH, Dang QT, Doan TN, Tran AM, Nguyen VH, Nguyen VTA, Ho LMQ, Tran QD, Pham TTT, Ho TD, Nguyen BT, Nguyen TNV, Nguyen TD, Phu DTB, Phan BHH, Vo TL, Nai THT, Tran TT, Truong MH, Tran NC, Le TK, Tran THT, Duong ML, Bach HPT, Kim VV, Pham TA, Tran DH, Le TNA, Pham TVN, Le MT, Vo DH, Tran TMT, Nguyen MN, Van TTV, Nguyen AN, Tran TT, Tran VU, Le MP, Do TT, Phan TV, Nguyen HDL, Nguyen DS, Cao VT, Do TTT, Truong DK, Tang HS, Giang H, Nguyen HN, Phan MD, Tran LS. Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization. eLife 2023; 12:RP89083. [PMID: 37819044 PMCID: PMC10567114 DOI: 10.7554/elife.89083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (screening for the presence of tumor by methylation and size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (~0.55×) of cell-free DNA. We applied SPOT-MAS to 738 non-metastatic patients with breast, colorectal, gastric, lung, and liver cancer, and 1550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 73.9% and 62.3% for stages I and II, respectively, increasing to 88.3% for non-metastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening.
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21
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Mattox AK, Douville C, Wang Y, Popoli M, Ptak J, Silliman N, Dobbyn L, Schaefer J, Lu S, Pearlman AH, Cohen JD, Tie J, Gibbs P, Lahouel K, Bettegowda C, Hruban RH, Tomasetti C, Jiang P, Chan KA, Lo YMD, Papadopoulos N, Kinzler KW, Vogelstein B. The Origin of Highly Elevated Cell-Free DNA in Healthy Individuals and Patients with Pancreatic, Colorectal, Lung, or Ovarian Cancer. Cancer Discov 2023; 13:2166-2179. [PMID: 37565753 PMCID: PMC10592331 DOI: 10.1158/2159-8290.cd-21-1252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/16/2022] [Accepted: 08/09/2023] [Indexed: 08/12/2023]
Abstract
Cell-free DNA (cfDNA) concentrations from patients with cancer are often elevated compared with those of healthy controls, but the sources of this extra cfDNA have never been determined. To address this issue, we assessed cfDNA methylation patterns in 178 patients with cancers of the colon, pancreas, lung, or ovary and 64 patients without cancer. Eighty-three of these individuals had cfDNA concentrations much greater than those generally observed in healthy subjects. The major contributor of cfDNA in all samples was leukocytes, accounting for ∼76% of cfDNA, with neutrophils predominating. This was true regardless of whether the samples were derived from patients with cancer or the total plasma cfDNA concentration. High levels of cfDNA observed in patients with cancer did not come from either neoplastic cells or surrounding normal epithelial cells from the tumor's tissue of origin. These data suggest that cancers may have a systemic effect on cell turnover or DNA clearance. SIGNIFICANCE The origin of excess cfDNA in patients with cancer is unknown. Using cfDNA methylation patterns, we determined that neither the tumor nor the surrounding normal tissue contributes this excess cfDNA-rather it comes from leukocytes. This finding suggests that cancers have a systemic impact on cell turnover or DNA clearance. See related commentary by Thierry and Pisareva, p. 2122. This article is featured in Selected Articles from This Issue, p. 2109.
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Affiliation(s)
- Austin K. Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Janine Ptak
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Natalie Silliman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Lisa Dobbyn
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Joy Schaefer
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Steve Lu
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Alexander H. Pearlman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Joshua D. Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Jeanne Tie
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria 3021, Australia
- Department of Medical Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter Gibbs
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria 3021, Australia
- Department of Medical Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kamel Lahouel
- Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287
| | - Ralph H. Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Cristian Tomasetti
- Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010
| | - Peiyong Jiang
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - K.C. Allen Chan
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Yuk Ming Dennis Lo
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
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22
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Kim V, Guberina M, Bechrakis NE, Lohmann DR, Zeschnigk M, Le Guin CHD. Release of Cell-Free Tumor DNA in the Plasma of Uveal Melanoma Patients Under Radiotherapy. Invest Ophthalmol Vis Sci 2023; 64:35. [PMID: 37862025 PMCID: PMC10599159 DOI: 10.1167/iovs.64.13.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/01/2023] [Indexed: 10/21/2023] Open
Abstract
Purpose Uveal melanoma (UM) is a tumor of the eye that metastasizes in approximately half of cases. Prognostic testing requires accessibility to tumor tissue, which is usually not available with eye-preserving therapies. Noninvasive approaches to prognostic testing that provide valuable information for patient care are therefore needed. The aim of this study was to evaluate the use of circulating cell-free plasma DNA analysis in UM patients undergoing brachytherapy. Methods The study recruited 26 uveal melanoma patients referred to the department between February and October 2020. Blood samples were collected at various time points before, during, and after treatment, and deep amplicon sequencing was used to identify oncogenic variant alleles of the GNAQ and GNA11 genes, which serve as indicators for the presence of circulating tumor DNA (ctDNA). Results The results showed that all patients were ctDNA negative before brachytherapy. In 31% of patients, ctDNA was detected during therapy. The variant allele fraction of GNAQ or GNA11 alleles in ctDNA positive samples ranged from 0.24% to 2% and correlates with the largest basal diameter and thickness of the tumor. Conclusions The findings suggest that brachytherapy increases the presence of tumor DNA in the plasma of UM patients. Thus ctDNA analysis may offer a noninvasive approach for prognostic testing. However, efforts are still required to lower the limit of detection for tumor-specific genetic alterations.
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Affiliation(s)
- Viktoria Kim
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Maja Guberina
- Department of Radiotherapy, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nikolaos E Bechrakis
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Dietmar R Lohmann
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Michael Zeschnigk
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Claudia H D Le Guin
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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23
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Johnson JA, Moore BJ, Syrnioti G, Eden CM, Wright D, Newman LA. Landmark Series: The Cancer Genome Atlas and the Study of Breast Cancer Disparities. Ann Surg Oncol 2023; 30:6427-6440. [PMID: 37587359 DOI: 10.1245/s10434-023-13866-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/24/2023] [Indexed: 08/18/2023]
Abstract
Race-related variation in breast cancer incidence and mortality are well-documented in the United States. The effect of genetic ancestry on disparities in tumor genomics, risk factors, treatment, and outcomes of breast cancer is less understood. The Cancer Genome Atlas (TCGA) is a publicly available resource that has allowed for the recent emergence of genome analysis research seeking to characterize tumor DNA and protein expression by ancestry as well as the social construction of race and ethnicity. Results from TCGA based studies support previous clinical evidence that demonstrates that American women with African ancestry are more likely to be afflicted with breast cancers featuring aggressive biology and poorer outcomes compared with women with other backgrounds. Data from TCGA based studies suggest that Asian women have tumors with favorable immune microenvironments and may experience better disease-free survival compared with white Americans. TCGA contains limited data on Hispanic/Latinx patients due to small sample size. Overall, TCGA provides important opportunities to define the molecular, biologic, and germline genetic factors that contribute to breast cancer disparities.
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Affiliation(s)
- Josh A Johnson
- Department of Surgery, New York Presbyterian, Weill Cornell Medicine, New York, NY, USA
| | | | - Georgia Syrnioti
- Department of Surgery, New York Presbyterian, Weill Cornell Medicine, New York, NY, USA
| | - Claire M Eden
- Department of Surgery, New York Presbyterian Queens, Weill Cornell Medicine, Flushing, NY, USA
| | - Drew Wright
- Samuel J. Wood Library, Weill Cornell Medicine, New York, NY, USA
| | - Lisa A Newman
- Department of Surgery, New York Presbyterian, Weill Cornell Medicine, New York, NY, USA.
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24
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Zhang M, Yang H, Fu T, Meng M, Feng Y, Qu C, Li Z, Xing X, Li W, Ye M, Li S, Bu Z, Jia S. Liquid biopsy: circulating tumor DNA monitors neoadjuvant chemotherapy response and prognosis in stage II/III gastric cancer. Mol Oncol 2023; 17:1930-1942. [PMID: 37356061 PMCID: PMC10483607 DOI: 10.1002/1878-0261.13481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/09/2023] [Accepted: 06/23/2023] [Indexed: 06/27/2023] Open
Abstract
A good response to neoadjuvant chemotherapy (NACT) is strongly associated with a higher curative resection rate and favorable outcomes for patients with gastric cancer (GC). We examined the utility of serial circulating tumor DNA (ctDNA) testing for monitoring NACT response and prognosis in stage II-III GC. Seventy-nine patients were enrolled to receive two cycles of NACT following gastrectomy with D2-lymphadenectomy. Plasma at baseline, post-NACT, and after surgery, and tissue at pretreatment and surgery were collected. We used a 425-gene panel to detect genomic alterations (GAs). Results show that the mean cell-free DNA concentration of patients with clinical stage III was significantly higher than patients with stage II (15.43 ng·mL-1 vs 14.40 ng·mL-1 ). After receiving NACT and surgery, the overall detection rate of ctDNA gradually reduced (59.5%, 50.8%, and 47.4% for baseline, post-NACT, and postsurgery). The maximum variant allele frequency (max-VAF) and the number of GAs decreased from 0.50% to 0.08% and from 2.9 to 1.7 after NACT. For patients with a partial response after NACT, the max-VAF and the number of GAs declined significantly, but they increased for patients with progressive disease. Patients with detectable ctDNA at baseline, after NACT, or after surgery have a worse overall survival (OS) than patients with undetectable ctDNA. The estimated 3-year OS was 73% for the post-NACT ctDNA-negative patients and 34% for ctDNA-positive. Patients with perpetual negative ctDNA before and after NACT have the best prognosis. In conclusion, ctDNA was proposed as a potential biomarker to predict prognosis and monitor the NACT response for stage II-III GC patients.
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Affiliation(s)
- Meng Zhang
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Heli Yang
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Tao Fu
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Meizhu Meng
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Yi Feng
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Changda Qu
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Zhongwu Li
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Xiaofang Xing
- Department of Gastrointestinal Translational Research, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Wenmei Li
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Meiying Ye
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Sisi Li
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Zhaode Bu
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Shuqin Jia
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
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Rosenberg S, Ben Cohen G, Kato S, Okamura R, Lippman SM, Kurzrock R. Concordance between cancer gene alterations in tumor and circulating tumor DNA correlates with poor survival in a real-world precision-medicine population. Mol Oncol 2023; 17:1844-1856. [PMID: 36694946 PMCID: PMC10483598 DOI: 10.1002/1878-0261.13383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/01/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Genomic analysis, performed on tumoral tissue DNA and on circulating tumor DNA (ctDNA) from blood, is the cornerstone of precision cancer medicine. Herein, we characterized the clinical prognostic implications of the concordance of alterations in major cancer genes between tissue- and blood-derived DNA in a pan-cancer cohort. The molecular profiles of both liquid (Guardant Health) and tissue (Foundation Medicine) biopsies from 433 patients were analyzed. Mutations and amplifications of cancer genes scored by these two tests were assessed. In 184 (42.5%) patients, there was at least one mutual gene alteration. The mean number of mutual gene-level alterations in the samples was 0.67 per patient (range: 0-5). A higher mutual gene-level alteration number correlated with shorter overall survival (OS). As confirmed in multivariable analysis, patients with ≥2 mutual gene-level alterations in blood and tissue had a hazard ratio (HR) of death of 1.49 (95% confidence interval [CI]=1-2.2; P=0.047), whereas patients with ≥3 mutual gene-level alterations had an HR of death 2.38 (95% CI=1.47-3.87; P=0.0005). Together, our results show that gene-level concordance between tissue DNA and ctDNA analysis is prevalent and is an independent factor predicting significantly shorter patient survival.
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Affiliation(s)
- Shai Rosenberg
- Gaffin Center for Neuro‐Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of MedicineHebrew University of JerusalemIsrael
- The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of MedicineHebrew University of JerusalemIsrael
| | - Gil Ben Cohen
- Gaffin Center for Neuro‐Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of MedicineHebrew University of JerusalemIsrael
- The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of MedicineHebrew University of JerusalemIsrael
| | - Shumei Kato
- Center for Personalized Cancer Therapy, Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | | | - Scott M. Lippman
- Center for Personalized Cancer Therapy, Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
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Doerr A. A biosensor detects tumor DNA in vivo. Nat Biotechnol 2023; 41:1201. [PMID: 37699980 DOI: 10.1038/s41587-023-01960-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
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Loft M, To YH, Gibbs P, Tie J. Clinical application of circulating tumour DNA in colorectal cancer. Lancet Gastroenterol Hepatol 2023; 8:837-852. [PMID: 37499673 DOI: 10.1016/s2468-1253(23)00146-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 07/29/2023]
Abstract
Liquid biopsies that detect circulating tumour DNA (ctDNA) have the potential to revolutionise the personalised management of colorectal cancer. For patients with early-stage disease, emerging clinical applications include the assessment of molecular residual disease after surgery, the monitoring of adjuvant chemotherapy efficacy, and early detection of recurrence during surveillance. In the advanced disease setting, data highlight the potential of ctDNA levels as a prognostic marker and as an early indicator of treatment response. ctDNA assessment can complement standard tissue-based testing for molecular characterisation, with the added ability to monitor emerging mutations under the selective pressure of targeted therapy. Here we provide an overview of the evidence supporting the use of ctDNA in colorectal cancer, the studies underway to address some of the outstanding questions, and the barriers to widespread clinical uptake.
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Affiliation(s)
- Matthew Loft
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Medical Oncology, Western Health, Footscray, VIC, Australia
| | - Yat Hang To
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC, Australia
| | - Peter Gibbs
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Medical Oncology, Western Health, Footscray, VIC, Australia
| | - Jeanne Tie
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia.
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Mullins KE, Seneviratne C, Shetty AC, Jiang F, Christenson R, Stass S. Proof of concept: Detection of cell free RNA from EDTA plasma in patients with lung cancer and non-cancer patients. Clin Biochem 2023; 118:110583. [PMID: 37182637 DOI: 10.1016/j.clinbiochem.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/16/2023]
Abstract
INTRODUCTION Nucleic acid sequencing technologies have advanced significantly in recent years, thereby allowing for the development of liquid biopsies as new means to detect cancer biomarkers and cancer heterogenicity. Most of the assays available, clinically, focus on cell free DNA (cfDNA), however, cell free RNA (cfRNA) is also present. cfRNA has the potential to complement and improve cancer detection especially in cancers like lung cancer, which are usually only diagnosed at late stages and therefore have poor long-term survival outcomes. METHODS Remnant EDTA plasma was collected from lung cancer patients and non-cancer individuals at the University of Maryland Medical Center. RNA was extracted and processed for next generation sequencing with a tagmentation-based library preparation approach. RESULTS cfRNA was successfully extracted and sequenced from 52 EDTA-treated plasma samples with volumes as low as 1.5 mL. This quantity was sufficient to prepare libraries with the length of libraries averaging from 264 bp to 381 bp and resulted in over 2.2 to 3.6 million total sequence reads respectively. Sequential dilution of cfRNA samples from healthy individuals indicated that the starting cfRNA concentration influenced the detection of differentially expressed genes. CONCLUSIONS This proof-of-concept study provides a framework for screening cfRNA for identifying biomarkers for early detection of lung cancer (and other cancers), using minimal amounts of samples (1.5 mL) from standard EDTA 3-mL collection tubes routinely used for patient care. Further studies in large populations are required to establish limit of detection and other parameters including precision, accuracy, sensitivity, and specificity, to standardize this method.
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Affiliation(s)
- Kristin E Mullins
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA; Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD, USA.
| | - Chamindi Seneviratne
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA; The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amol C Shetty
- The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Feng Jiang
- Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD, USA
| | - Robert Christenson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA; Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD, USA
| | - Sanford Stass
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA; Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD, USA
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29
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Chaudhuri AA. Cell-Free DNA Liquid Biopsy: The Epitome of Personalized Precision Oncology. Radiat Res 2023; 200:92-95. [PMID: 37084268 PMCID: PMC10425279 DOI: 10.1667/rade-23-00044.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 04/23/2023]
Affiliation(s)
- Aadel A. Chaudhuri
- Department of Radiation Oncology, Division of Biology and Biomedical Sciences, Department of Genetics, Department of Biomedical Engineering, Department of Computer Science and Engineering, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
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30
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Rose KM, Huelster HL, Meeks JJ, Faltas BM, Sonpavde GP, Lerner SP, Ross JS, Spiess PE, Grass GD, Jain RK, Kamat AM, Vosoughi A, Wang L, Wang X, Li R. Circulating and urinary tumour DNA in urothelial carcinoma - upper tract, lower tract and metastatic disease. Nat Rev Urol 2023; 20:406-419. [PMID: 36977797 DOI: 10.1038/s41585-023-00725-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 03/30/2023]
Abstract
Precision medicine has transformed the way urothelial carcinoma is managed. However, current practices are limited by the availability of tissue samples for genomic profiling and the spatial and temporal molecular heterogeneity observed in many studies. Among rapidly advancing genomic sequencing technologies, non-invasive liquid biopsy has emerged as a promising diagnostic tool to reproduce tumour genomics, and has shown potential to be integrated in several aspects of clinical care. In urothelial carcinoma, liquid biopsies such as plasma circulating tumour DNA (ctDNA) and urinary tumour DNA (utDNA) have been investigated as a surrogates for tumour biopsies and might bridge many shortfalls currently faced by clinicians. Both ctDNA and utDNA seem really promising in urothelial carcinoma diagnosis, staging and prognosis, response to therapy monitoring, detection of minimal residual disease and surveillance. The use of liquid biopsies in patients with urothelial carcinoma could further advance precision medicine in this population, facilitating personalized patient monitoring through non-invasive assays.
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Affiliation(s)
- Kyle M Rose
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Heather L Huelster
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Joshua J Meeks
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Bishoy M Faltas
- Department of Hematology/Oncology, Weill-Cornell Medicine, New York, NY, USA
| | - Guru P Sonpavde
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Seth P Lerner
- Department of Urology, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc, Cambridge, MA, USA
- Departments of Urology and Pathology, Upstate Medical University, Syracuse, NY, USA
| | - Philippe E Spiess
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - G Daniel Grass
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Rohit K Jain
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Ashish M Kamat
- Department of Urology, MD Anderson Cancer Center, Houston, TX, USA
| | - Aram Vosoughi
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Liang Wang
- Department of Tumour Biology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Xuefeng Wang
- Department of Biostatistics/Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Roger Li
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA.
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL, USA.
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Xue R, Yang L, Yang M, Xue F, Li L, Liu M, Ren Y, Qi Y, Zhao J. Circulating cell-free DNA sequencing for early detection of lung cancer. Expert Rev Mol Diagn 2023; 23:589-606. [PMID: 37318381 DOI: 10.1080/14737159.2023.2224504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
INTRODUCTION Lung cancer is a leading cause of death in patients with cancer. Early diagnosis is crucial to improve the prognosis of patients with lung cancer. Plasma circulating cell-free DNA (cfDNA) contains comprehensive genetic and epigenetic information from tissues throughout the body, suggesting that early detection of lung cancer can be done non-invasively, conveniently, and cost-effectively using high-sensitivity techniques such as sequencing. AREAS COVERED In this review, we summarize the latest technological innovations, coupled with next-generation sequencing (NGS), regarding genomic alterations, methylation, and fragmentomic features of cfDNA for the early detection of lung cancer, as well as their clinical advances. Additionally, we discuss the suitability of study designs for diagnostic accuracy evaluation for different target populations and clinical questions. EXPERT OPINION Currently, cfDNA-based early screening and diagnosis of lung cancer faces many challenges, such as unsatisfactory performance, lack of quality control standards, and poor repeatability. However, the progress of several large prospective studies employing epigenetic features has shown promising predictive performance, which has inspired cfDNA sequencing for future clinical applications. Furthermore, the development of multi-omics markers for lung cancer, including genome-wide methylation and fragmentomics, is expected to play an increasingly important role in the future.
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Affiliation(s)
- Ruyue Xue
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lu Yang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Meijia Yang
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Fangfang Xue
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Lifeng Li
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Manjiao Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Yong Ren
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Yu Qi
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Zhao
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Raei N, Safaralizadeh R, Latifi-Navid S. Clinical application of circulating tumor DNA in metastatic cancers. Expert Rev Mol Diagn 2023; 23:1209-1220. [PMID: 37797209 DOI: 10.1080/14737159.2023.2268008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023]
Abstract
INTRODUCTION Advances in genomics have facilitated the application of cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) in phase II and phase III clinical trials. The various mutations of cfDNA/ctDNA have been correlated with clinical features. Advances in next-generation sequencing (NGS) and digital droplet PCR have paved the way for identifying cfDNA/ctDNA mutations. AREAS COVERED Herein, the biology of ctDNA and its function in clinical application in metastasis, which may lead to improved clinical management of metastatic cancer patients, are comprehensively reviewed. EXPERT OPINION Metastatic cancer ctDNA shows the greatest frequency of mutations in TP53, HER-2, KRAS, and EGFR genes (alteration frequency of > 50%). Therefore, identifying key mutations frequently present in metastatic cancers can help identify patients with pre-malignant tumors before cancer progression. Studying ctDNA can help determine the prognosis and select appropriate treatments for affected patients. Nevertheless, the obstacles to detecting and analyzing ctDNA should be addressed before translation into routine practice. Also, more clinical trials should be conducted to study the significance of ctDNA in commonly diagnosed malignancies. Given the recent advances in personalized anti-neoplastic treatments, further studies are needed to detect a panel of ctDNA and patient-specific ctDNA for various cancers.
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Affiliation(s)
- Negin Raei
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
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Cohen R, Platell CF, McCoy MJ, Meehan K, Fuller K. Circulating tumour DNA in colorectal cancer management. Br J Surg 2023; 110:773-783. [PMID: 37190784 PMCID: PMC10364542 DOI: 10.1093/bjs/znad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/17/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023]
Abstract
Circulating tumour DNA analysis can be performed using two opposing paradigms: tumour-informed and tumour-agnostic approaches. The first requires sequencing data from the primary tumour sample to identify tumour DNA in circulation, whereas the latter occurs without previous primary tumour genetic profiling.
Several preanalytical and laboratory considerations need to be taken into account before proceeding with in-house circulating tumour DNA analysis.
Detection of circulating tumour DNA after curative resection is associated with a significant risk of recurrence. For those with stage II disease and detectable postoperative circulating tumour DNA, administration of adjuvant chemotherapy results in a reduction in the number of patients receiving chemotherapy while providing non-inferior recurrence-free survival compared with standard histopathological decision-making algorithms.
Monitoring circulating tumour DNA during post-treatment surveillance may provide a significantly earlier diagnosis of recurrence.
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Affiliation(s)
- Ryan Cohen
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
| | - Cameron F Platell
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Melanie J McCoy
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Katie Meehan
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kathy Fuller
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
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Rhrissorrakrai K, Utro F, Levovitz C, Parida L. Lesion Shedding Model: unraveling site-specific contributions to ctDNA. Brief Bioinform 2023; 24:7068948. [PMID: 36869848 PMCID: PMC10025438 DOI: 10.1093/bib/bbad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/09/2023] [Accepted: 02/01/2023] [Indexed: 03/05/2023] Open
Abstract
Sampling circulating tumor DNA (ctDNA) using liquid biopsies offers clinically important benefits for monitoring cancer progression. A single ctDNA sample represents a mixture of shed tumor DNA from all known and unknown lesions within a patient. Although shedding levels have been suggested to hold the key to identifying targetable lesions and uncovering treatment resistance mechanisms, the amount of DNA shed by any one specific lesion is still not well characterized. We designed the Lesion Shedding Model (LSM) to order lesions from the strongest to the poorest shedding for a given patient. By characterizing the lesion-specific ctDNA shedding levels, we can better understand the mechanisms of shedding and more accurately interpret ctDNA assays to improve their clinical impact. We verified the accuracy of the LSM under controlled conditions using a simulation approach as well as testing the model on three cancer patients. The LSM obtained an accurate partial order of the lesions according to their assigned shedding levels in simulations and its accuracy in identifying the top shedding lesion was not significantly impacted by number of lesions. Applying LSM to three cancer patients, we found that indeed there were lesions that consistently shed more than others into the patients' blood. In two of the patients, the top shedding lesion was one of the only clinically progressing lesions at the time of biopsy suggesting a connection between high ctDNA shedding and clinical progression. The LSM provides a much needed framework with which to understand ctDNA shedding and to accelerate discovery of ctDNA biomarkers. The LSM source code has been available in the IBM BioMedSciAI Github (https://github.com/BiomedSciAI/Geno4SD).
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Affiliation(s)
| | - Filippo Utro
- IBM Research, IBM, 1101 Kitchawan Road, 10598, NY, USA
| | | | - Laxmi Parida
- IBM Research, IBM, 1101 Kitchawan Road, 10598, NY, USA
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35
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Romagnoli D, Nardone A, Galardi F, Paoli M, De Luca F, Biagioni C, Franceschini GM, Pestrin M, Sanna G, Moretti E, Demichelis F, Migliaccio I, Biganzoli L, Malorni L, Benelli M. MIMESIS: minimal DNA-methylation signatures to quantify and classify tumor signals in tissue and cell-free DNA samples. Brief Bioinform 2023; 24:6991124. [PMID: 36653909 DOI: 10.1093/bib/bbad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/17/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
DNA-methylation alterations are common in cancer and display unique characteristics that make them ideal markers for tumor quantification and classification. Here we present MIMESIS, a computational framework exploiting minimal DNA-methylation signatures composed by a few dozen informative DNA-methylation sites to quantify and classify tumor signals in tissue and cell-free DNA samples. Extensive analyses of multiple independent and heterogenous datasets including >7200 samples demonstrate the capability of MIMESIS to provide precise estimations of tumor content and to enable accurate classification of tumor type and molecular subtype. To assess our framework for clinical applications, we designed a MIMESIS-informed assay incorporating the minimal signatures for breast cancer. Using both artificial samples and clinical serial cell-free DNA samples from patients with metastatic breast cancer, we show that our approach provides accurate estimations of tumor content, sensitive detection of tumor signal and the ability to capture clinically relevant molecular subtype in patients' circulation. This study provides evidence that our extremely parsimonious approach can be used to develop cost-effective and highly scalable DNA-methylation assays that could support and facilitate the implementation of precision oncology in clinical practice.
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Affiliation(s)
| | - Agostina Nardone
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Francesca Galardi
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Marta Paoli
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca De Luca
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Chiara Biagioni
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Gian Marco Franceschini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Marta Pestrin
- Medical Oncology Unit, Azienda Sanitaria Universitaria Giuliano Isontina, 34170 Gorizia, Italy
| | - Giuseppina Sanna
- Medical Oncology, Ospedale Civile SS Annunziata, 07100 Sassari, Italy
| | - Erica Moretti
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Ilenia Migliaccio
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Laura Biganzoli
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Luca Malorni
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Matteo Benelli
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
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Azzi G, Tavallai M, Aushev VN, Koyen Malashevich A, Botta GP, Tejani MA, Hanna D, Krinshpun S, Malhotra M, Jurdi A, Aleshin A, Kasi PM. Using Tumor-Informed Circulating Tumor DNA (ctDNA)-Based Testing for Patients with Anal Squamous Cell Carcinoma. Oncologist 2023; 28:220-229. [PMID: 36562592 PMCID: PMC10020810 DOI: 10.1093/oncolo/oyac249] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/27/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Anal squamous cell carcinoma (SCCA) is an uncommon malignancy with a rising incidence that has a high cure rate in its early stages. There is an unmet need for a reliable method to monitor response to treatment and assist in surveillance. Circulating tumor DNA (ctDNA) testing has shown great promise in other solid tumors for monitoring disease progression and detecting relapse in real time. This study aimed to determine the feasibility and use of personalized and tumor-informed ctDNA testing in SCCA. PATIENTS AND METHODS We analyzed real-world data from 251 patients (817 plasma samples) with stages I-IV SCCA, collected between 11/5/19 and 5/31/22. The tumor genomic landscape and feasibility of ctDNA testing was examined for all patients. The prognostic value of longitudinal ctDNA testing was assessed in patients with clinical follow-up (N = 37). RESULTS Whole-exome sequencing analysis revealed PIK3CA as the most commonly mutated gene, and no associations between mutations and stage. Anytime ctDNA positivity and higher ctDNA levels (MTM/mL) were associated with metastatic disease (P = .004). For 37 patients with clinical follow-up, median follow-up time was 21.0 months (range: 4.1-67.3) post-diagnosis. For patients with stages I-III disease, anytime ctDNA-positivity after definitive treatment was associated with reduced DFS (HR: 28.0; P = .005). CONCLUSIONS Our study demonstrates the feasibility of personalized and tumor-informed ctDNA testing as an adjunctive tool in patients with SCCA as well as potential use for detection of molecular/minuteimal residual disease, and relapse during surveillance. Prospective studies are needed to better evaluate the use of ctDNA testing in this indication.
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Affiliation(s)
- Georges Azzi
- HolyCross Medical Group, Ft. Lauderdale, FL, USA
| | | | | | | | | | | | - Diana Hanna
- USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | | | | | | | | | - Pashtoon M Kasi
- Corresponding author: Pashtoon M. Kasi, MD, MS, Department of Medical Oncology and Hematology, Weill Cornell Medicine, Englander Institute of Precision Medicine, Meyer Cancer Center, NewYork-Presbyterian Hospital, New York, NY 10021, USA. E-mail:
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37
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Bayle A, Belcaid L, Aldea M, Vasseur D, Peyraud F, Nicotra C, Geraud A, Sakkal M, Seknazi L, Cerbone L, Blanc-Durand F, Hadoux J, Mosele F, Tagliamento M, Bernard-Tessier A, Verret B, Smolenschi C, Clodion R, Auger N, Romano PM, Gazzah A, Camus MN, Micol J, Caron O, Hollebecque A, Loriot Y, Besse B, Lacroix L, Rouleau E, Ponce S, Soria JC, Barlesi F, Andre F, Italiano A. Clinical utility of circulating tumor DNA sequencing with a large panel: a National Center for Precision Medicine (PRISM) study. Ann Oncol 2023; 34:389-396. [PMID: 36709039 DOI: 10.1016/j.annonc.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/10/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) sequencing is a promising approach for tailoring therapy in patients with cancer. We report hereby the results from a prospective study where we investigated the impact of comprehensive molecular profiling of ctDNA in patients with advanced solid tumors. PATIENTS AND METHODS Genomic analysis was performed using the FoundationOne Liquid CDx Assay [324 genes, tumor mutational burden (TMB), microsatellite instability status]. Each individual genomic report was reviewed and discussed weekly by a multidisciplinary tumor board (MTB). Actionable targets were classified by ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT) tier leading to molecular-based treatment suggestions wherever it was possible. RESULTS Between December 2020 and November 2021, 1772 patients with metastatic solid tumors underwent molecular profiling. Median time to assay results was 12 days. Results were contributive for 1658 patients (94%). At least one actionable target was detected in 1059 patients (64%) with a total of 1825 actionable alterations including alteration of the DNA damage repair response pathway (n = 336, 18%), high TMB (>16 mutations/Mb; n = 243, 13%), PIK3CA mutations (n = 150, 8%), ERBB family pathway alterations (n = 127, 7%), PTEN alterations (n = 95, 5%), FGFR alterations (n = 67, 4%) and MET activations (n = 13, 0.7%). The MTB recommended a matched therapy for 597 patients (56%) with a total of 819 therapeutic orientations: clinical trials (n = 639, 78%), off-label/compassionate use (n = 81, 10%), approved drug (n = 51, 6%), and early access program (n = 48, 6%). In total, 122 patients (21%) were treated. Among the assessable patients (n = 107), 4 (4%) had complete response, 35 (33%) had partial response, 27 (25%) had stable disease, and 41 (38%) a progressive disease as best response. The median progression-free survival and median overall survival were 4.7 months (95% confidence interval 2.7-6.7 months) and 8.3 months (95% confidence interval 4.7-11.9 months) respectively. CONCLUSIONS ctDNA sequencing with a large panel is an efficient approach to match patients with advanced cancer with targeted therapies.
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Affiliation(s)
- A Bayle
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif; Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Oncostat U1018, Inserm, Paris-Saclay University, labeled Ligue Contre le Cancer, Villejuif, France
| | - L Belcaid
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif; Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - M Aldea
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - D Vasseur
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - F Peyraud
- Department of Early Phase Trial Unit, Institut Bergonié Comprehensive Cancer Centre, Bordeaux
| | - C Nicotra
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - A Geraud
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - M Sakkal
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - L Seknazi
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - L Cerbone
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - F Blanc-Durand
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - J Hadoux
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - F Mosele
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - M Tagliamento
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | | | - B Verret
- Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - C Smolenschi
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - R Clodion
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - N Auger
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - P M Romano
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - A Gazzah
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - M N Camus
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - J Micol
- Department of Hematology, Gustave Roussy, Villejuif
| | - O Caron
- Department of Genetics, Gustave Roussy, Villejuif
| | - A Hollebecque
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - Y Loriot
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - B Besse
- Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - L Lacroix
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - E Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - S Ponce
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - J C Soria
- Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - F Barlesi
- Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - F Andre
- Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - A Italiano
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif; Department of Early Phase Trial Unit, Institut Bergonié Comprehensive Cancer Centre, Bordeaux; Faculty of Medicine, University of Bordeaux, Bordeaux, France.
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Li H, Lu S, Zhou Z, Zhu X, Shao Y. Role of Circulating Tumor DNA in Colorectal Cancer. Methods Mol Biol 2023; 2695:227-236. [PMID: 37450122 DOI: 10.1007/978-1-0716-3346-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Colorectal cancer (CRC) is a very common gastrointestinal tumor, ranking second in the global cause of cancer death. Because of the invasive nature of biopsy and cannot reflect the heterogeneity of tumor or monitor the dynamic progress of tumor, it is necessary to induce a novel noninvasive method to improve the current treatment strategies of colorectal cancer. Among all the components of liquid biopsy, circulating tumor DNA (ctDNA) may have the best future. CtDNA maintains the same genomic characteristics as those in matched tumor tissues, so it allows quantitative evaluation and analysis of mutation load in body fluid. Furthermore, because the half-life of ctDNA is from 16 min to several hours in circulation, the circulating ctDNA can be measured repeatedly within a certain period to monitor the response of CRC to treatment, the occurrence of drug resistance, and the diagnosis of recurrence.
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Affiliation(s)
- Haotian Li
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Sheng Lu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zidong Zhou
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiaocheng Zhu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yong Shao
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
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Liu B, Hu Z, Ran J, Xie N, Tian C, Tang Y, Ouyang Q. The circulating tumor DNA (ctDNA) alteration level predicts therapeutic response in metastatic breast cancer: Novel prognostic indexes based on ctDNA. Breast 2022; 65:116-123. [PMID: 35926241 PMCID: PMC9356206 DOI: 10.1016/j.breast.2022.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/18/2022] Open
Abstract
Purpose Circulating tumor DNA (ctDNA) has good clinical guiding value for metastatic breast cancer (MBC) patients. This study aimed to apply a novel genetic analysis approach for therapeutic prediction based on ctDNA alterations. Method This nonrandomized, multicenter study recruited 223 MBC patients (NCT05079074). Plasma samples were collected for target-capture deep sequencing of ctDNA at baseline, after the 2nd cycle of treatment, and when progressive disease (PD) was evaluated. Samples were categorized into four levels according to the number of ctDNA alterations: level 1 (no alterations), level 2 (1–2 alterations), level 3 (3–4 alterations) and level 4 (≥5 alterations). According to ctDNA alteration level and variant allele frequency (VAF), a novel ctDNA-level Response Evaluation Criterion in Solid Tumors (ctle-RECIST) was established to assess treatment response and predict progression-free survival (PFS). Results The median PFS in level 1 (6.63 months) patients was significantly longer than that in level 2–4 patients (level 2: 5.70 months; level 3–4: 4.90 months, p < 0.05). After 2 cycles of treatment, based on ctle-RECIST, the median PFS of level-based disease control rate (lev-DCR) patients was significantly longer than that of level-based PD (lev-PD) patients [HR 2.42 (1.52–3.85), p < 0.001]. In addition, we found that ctDNA level assessment could be a good supplement to radiologic assessment. The median PFS in the dual-DCR group tended to be longer than that in the single-DCR group [HR 1.41 (0.93–2.13), p = 0.107]. Conclusion The ctDNA alteration level and ctle-RECIST could be novel biomarkers of prognosis and could complement radiologic assessment in MBC. Based on the number of ctDNA alterations, samples were categorized into four levels: level 1 to level 4. ctDNA alterations differed in different alteration level groups. Higher ctDNA alteration levels (levels 3–4) were associated with a higher probability of liver metastasis. According to ctDNA alteration level and variant allele frequency, a novel ctDNA-level RECIST (ctle-RECIST) was established to assess treatment response. ctle-RECIST can not only independently predict PFS, but also assist radiologic assessment and improve the clinical application value of prediction.
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Affiliation(s)
- Binliang Liu
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Zheyu Hu
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Jialu Ran
- Department of Biostatistics and Bioinformatics, Rollins School of Public Heath, Emory University, Atlanta, GA 30322, USA
| | - Ning Xie
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Can Tian
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Yu Tang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
| | - Quchang Ouyang
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China.
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Jónás VZ, Paulik R, Kozlovszky M, Molnár B. Calibration-Aimed Comparison of Image-Cytometry- and Flow-Cytometry-Based Approaches of Ploidy Analysis. Sensors (Basel) 2022; 22:6952. [PMID: 36146303 PMCID: PMC9502733 DOI: 10.3390/s22186952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Ploidy analysis is the fundamental method of measuring DNA content. For decades, the principal way of conducting ploidy analysis was through flow cytometry. A flow cytometer is a specialized tool for analyzing cells in a solution. This is convenient in laboratory environments, but prohibits measurement reproducibility and the complete detachment of sample preparation from data acquisition and analysis, which seems to have become paramount with the constant decrease in the number of pathologists per capita all over the globe. As more open computer-aided systems emerge in medicine, the demand for overcoming these shortcomings, and opening access to even more (and more flexible) options, has also emerged. Image-based analysis systems can provide an alternative to these types of workloads, placing the abovementioned problems in a different light. Flow cytometry data can be used as a reference for calibrating an image-based system. This article aims to show an approach to constructing an image-based solution for ploidy analysis, take measurements for a basic comparison of the data produced by the two methods, and produce a workflow with the ultimate goal of calibrating the image-based system.
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Affiliation(s)
| | - Róbert Paulik
- Image Analysis Department, 3DHISTECH Ltd., 1141 Budapest, Hungary
| | - Miklós Kozlovszky
- Department of BioTech Research Center, Óbuda University, 1034 Budapest, Hungary
| | - Béla Molnár
- Image Analysis Department, 3DHISTECH Ltd., 1141 Budapest, Hungary
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Nair VS, Hui ABY, Chabon JJ, Esfahani MS, Stehr H, Nabet BY, Zhou L, Chaudhuri AA, Benson J, Ayers K, Bedi H, Ramsey M, Van Wert R, Antic S, Lui N, Backhus L, Berry M, Sung AW, Massion PP, Shrager JB, Alizadeh AA, Diehn M. Genomic Profiling of Bronchoalveolar Lavage Fluid in Lung Cancer. Cancer Res 2022; 82:2838-2847. [PMID: 35748739 PMCID: PMC9379362 DOI: 10.1158/0008-5472.can-22-0554] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/24/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Abstract
Genomic profiling of bronchoalveolar lavage (BAL) samples may be useful for tumor profiling and diagnosis in the clinic. Here, we compared tumor-derived mutations detected in BAL samples from subjects with non-small cell lung cancer (NSCLC) to those detected in matched plasma samples. Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) was used to genotype DNA purified from BAL, plasma, and tumor samples from patients with NSCLC. The characteristics of cell-free DNA (cfDNA) isolated from BAL fluid were first characterized to optimize the technical approach. Somatic mutations identified in tumor were then compared with those identified in BAL and plasma, and the potential of BAL cfDNA analysis to distinguish lung cancer patients from risk-matched controls was explored. In total, 200 biofluid and tumor samples from 38 cases and 21 controls undergoing BAL for lung cancer evaluation were profiled. More tumor variants were identified in BAL cfDNA than plasma cfDNA in all stages (P < 0.001) and in stage I to II disease only. Four of 21 controls harbored low levels of cancer-associated driver mutations in BAL cfDNA [mean variant allele frequency (VAF) = 0.5%], suggesting the presence of somatic mutations in nonmalignant airway cells. Finally, using a Random Forest model with leave-one-out cross-validation, an exploratory BAL genomic classifier identified lung cancer with 69% sensitivity and 100% specificity in this cohort and detected more cancers than BAL cytology. Detecting tumor-derived mutations by targeted sequencing of BAL cfDNA is technically feasible and appears to be more sensitive than plasma profiling. Further studies are required to define optimal diagnostic applications and clinical utility. SIGNIFICANCE Hybrid-capture, targeted deep sequencing of lung cancer mutational burden in cell-free BAL fluid identifies more tumor-derived mutations with increased allele frequencies compared with plasma cell-free DNA. See related commentary by Rolfo et al., p. 2826.
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Affiliation(s)
- Viswam S. Nair
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Division of Pulmonary, Critical Care & Sleep Medicine, University of Washington School of Medicine, Seattle, Washington
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Angela Bik-Yu Hui
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Jacob J. Chabon
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Mohammad S. Esfahani
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Barzin Y. Nabet
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Li Zhou
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Aadel A. Chaudhuri
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
| | - Jalen Benson
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Kelsey Ayers
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Harmeet Bedi
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Meghan Ramsey
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Ryan Van Wert
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Sanja Antic
- Division of Allergy, Pulmonary & Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Natalie Lui
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Leah Backhus
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Mark Berry
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Arthur W. Sung
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Pierre P. Massion
- Division of Allergy, Pulmonary & Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Joseph B. Shrager
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Ash A. Alizadeh
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
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Benesova L, Ptackova R, Halkova T, Semyakina A, Svaton M, Fiala O, Pesek M, Minarik M. Detection and Quantification of ctDNA for Longitudinal Monitoring of Treatment in Non-Small Cell Lung Cancer Patients Using a Universal Mutant Detection Assay by Denaturing Capillary Electrophoresis. Pathol Oncol Res 2022; 28:1610308. [PMID: 35837614 PMCID: PMC9274771 DOI: 10.3389/pore.2022.1610308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022]
Abstract
Background: Observation of anticancer therapy effect by monitoring of minimal residual disease (MRD) is becoming an important tool in management of non-small cell lung cancer (NSCLC). The approach is based on periodic detection and quantification of tumor-specific somatic DNA mutation in circulating tumor DNA (ctDNA) extracted from patient plasma. For such repetitive testing, complex liquid-biopsy techniques relying on ultra-deep NGS sequencing are impractical. There are other, cost-effective, methods for ctDNA analysis, typically based on quantitative PCR or digital PCR, which are applicable for detecting specific individual mutations in hotspots. While such methods are routinely used in NSCLC therapy prediction, however, extension to cover broader spectrum of mutations (e.g., in tumor suppressor genes) is required for universal longitudinal MRD monitoring. Methods: For a set of tissue samples from 81 NSCLC patients we have applied a denaturing capillary electrophoresis (DCE) for initial detection of somatic mutations within 8 predesigned PCR amplicons covering oncogenes and tumor suppressor genes. Mutation-negative samples were then subjected to a large panel NGS sequencing. For each patient mutation found in tissue was then traced over time in ctDNA by DCE. Results: In total we have detected a somatic mutation in tissue of 63 patients. For those we have then prospectively analyzed ctDNA from collected plasma samples over a period of up to 2 years. The dynamics of ctDNA during the initial chemotherapy therapy cycles as well as in the long-term follow-up matched the clinically observed response. Conclusion: Detection and quantification of tumor-specific mutations in ctDNA represents a viable complement to MRD monitoring during therapy of NSCLC patients. The presented approach relying on initial tissue mutation detection by DCE combined with NGS and a subsequent ctDNA mutation testing by DCE only represents a cost-effective approach for its routine implementation.
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Affiliation(s)
- Lucie Benesova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Renata Ptackova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Tereza Halkova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Anastasiya Semyakina
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Martin Svaton
- Department of Pneumology and Phtiseology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Ondrej Fiala
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Milos Pesek
- Department of Pneumology and Phtiseology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Marek Minarik
- Elphogene, Prague, Czechia
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czechia
- *Correspondence: Marek Minarik,
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43
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Beasley AB, Chen FK, Isaacs TW, Gray ES. Future perspectives of uveal melanoma blood based biomarkers. Br J Cancer 2022; 126:1511-1528. [PMID: 35190695 PMCID: PMC9130512 DOI: 10.1038/s41416-022-01723-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 01/15/2022] [Accepted: 01/27/2022] [Indexed: 01/06/2023] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy affecting adults. Despite successful local treatment of the primary tumour, metastatic disease develops in up to 50% of patients. Metastatic UM carries a particularly poor prognosis, with no effective therapeutic option available to date. Genetic studies of UM have demonstrated that cytogenetic features, including gene expression, somatic copy number alterations and specific gene mutations can allow more accurate assessment of metastatic risk. Pre-emptive therapies to avert metastasis are being tested in clinical trials in patients with high-risk UM. However, current prognostic methods require an intraocular tumour biopsy, which is a highly invasive procedure carrying a risk of vision-threatening complications and is limited by sampling variability. Recently, a new diagnostic concept known as "liquid biopsy" has emerged, heralding a substantial potential for minimally invasive genetic characterisation of tumours. Here, we examine the current evidence supporting the potential of blood circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), microRNA (miRNA) and exosomes as biomarkers for UM. In particular, we discuss the potential of these biomarkers to aid clinical decision making throughout the management of UM patients.
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Affiliation(s)
- Aaron B Beasley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Sciences (incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
- Department of Ophthalmology, Perth Children's Hospital, Perth, WA, Australia
| | - Timothy W Isaacs
- Centre for Ophthalmology and Visual Sciences (incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
- Perth Retina, West Leederville, WA, Australia
| | - Elin S Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.
- Centre for Ophthalmology and Visual Sciences (incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA, Australia.
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44
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Kaur H, Handa U, Kundu R, Bhagat R, Dalal U. Correlation of Morphological Features of Chromosomal Instability and Flow Cytometric DNA Ploidy Analysis in Aspirates of Breast Carcinoma. Acta Cytol 2022; 66:389-395. [PMID: 35462374 DOI: 10.1159/000524053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/06/2022] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Morphological indicators of chromosomal instability (CI), including multipolar mitoses, chromatin bridges (CB), strings, nuclear buds (NB), micronuclei (MN), and deoxyribonucleic acid (DNA) ploidy analysis help in prognostication of breast carcinoma. The present study was done to evaluate CI in breast carcinoma and correlate with DNA ploidy and tumor grade. STUDY DESIGN Fifty cases of carcinoma breast diagnosed by fine-needle aspiration cytology were included. Robinson's grading method was used on smears to grade breast carcinoma. To assess the morphological features of CI, the best May-Grünwald Giemsa stained smear was chosen. At least 1,000 epithelial cells on oil immersion magnification (×100 objective) were counted. DNA ploidy on the aspirates was done by flow cytometry. RESULTS All the patients were female, diagnosed as infiltrating ductal carcinoma on cytology. Eight tumors were grade I, 32 were grade II, and 10 were grade III. MN was seen in 48 cases, NB in 45, and CB in 12 cases. Mean MN, NB, and CB scores in aneuploid (24) cases were 9.96 ± 8.42, 5.29 ± 4.71, and 1.08 ± 1.84 while 6.19 ± 6.67, 1.92 ± 1.79, and 0.11 ± 0.33 were seen in diploid (26) cases. Statistically significant positive correlation was observed between CI and DNA ploidy. CONCLUSIONS Morphological evaluation of CI by light microscopy on routinely stained breast aspirates is feasible, although a meticulous search is required. Cytomorphological features of CI and ploidy have a positive correlation with increasing tumor grade.
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Affiliation(s)
- Harmeet Kaur
- Department of Pathology, Government Medical College and Hospital, Chandigarh, India
| | - Uma Handa
- Department of Pathology, Government Medical College and Hospital, Chandigarh, India
| | - Reetu Kundu
- Department of Cytology & Gynecological Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ranjeev Bhagat
- Department of Pathology, Government Medical College and Hospital, Chandigarh, India
| | - Usha Dalal
- Department of General Surgery, Government Medical College and Hospital, Chandigarh, India
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45
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Xiang C, Guo L, Zhao R, Teng H, Wang Y, Xiong L, Han Y. Identification and Validation of Noncanonical RET Fusions in Non-Small-Cell Lung Cancer through DNA and RNA Sequencing. J Mol Diagn 2022; 24:374-385. [PMID: 35063667 DOI: 10.1016/j.jmoldx.2021.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/14/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022] Open
Abstract
RET fusion has emerged as a targetable driver in non-small-cell lung cancer. A comparative analysis on RET fusions at DNA [DNA sequencing (DNA-seq)] and RNA [RNA sequencing (RNA-seq)] levels was performed in this study. Archived tumor samples from 54 non-small-cell lung cancer patients with DNA-level noncanonical RET fusions were selected for RNA-seq. RNA-seq identified RET fusion transcripts in 41 of 44 samples passing quality control. In the subset of cases harboring RET 3'-end fusions and predicted to produce in-frame proteins (group A; n = 33), RNA-seq identified the same 3'-end fusions in 32 (96.9%). A total of 26 of 32 also had a reciprocal RET 5'-end fusion detected by DNA-seq that was not transcribed. In the subset with DNA-level out-of-frame RET fusions (group B; n = 9), RNA-seq identified in-frame RET fusion transcripts in 8 cases (88.9%). In the subset only identified with a RET 5'-end fusion by DNA-seq (group C; n = 2), RNA-seq detected the corresponding 3'-end fusion in one case. The discordant DNA- and RNA-level fusions observed in group B may be mediated by complex genomic rearrangement events and transcriptional or post-transcriptional processes. In conclusion, DNA-seq demonstrates a high concordance of 96.9% on detecting in-frame RET fusion, but shows a low concordance on detecting out-of-frame RET fusion and RET 5'-end fusion compared with RNA-seq.
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Affiliation(s)
- Chan Xiang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lianying Guo
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ruiying Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Haohua Teng
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yulu Wang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Liwen Xiong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
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46
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Tu E, McGlinchey K, Wang J, Martin P, Ching SL, Floc’h N, Kurasawa J, Starrett JH, Lazdun Y, Wetzel L, Nuttall B, Ng FS, Coffman KT, Smith PD, Politi K, Cooper ZA, Streicher K. Anti-PD-L1 and anti-CD73 combination therapy promotes T cell response to EGFR-mutated NSCLC. JCI Insight 2022; 7:e142843. [PMID: 35132961 PMCID: PMC8855814 DOI: 10.1172/jci.insight.142843] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
Treatment with anti-PD-1 and anti-PD-L1 therapies has shown durable clinical benefit in non-small cell lung cancer (NSCLC). However, patients with NSCLC with epidermal growth factor receptor (EGFR) mutations do not respond as well to treatment as patients without an EGFR mutation. We show that EGFR-mutated NSCLC expressed higher levels of CD73 compared with EGFR WT tumors and that CD73 expression was regulated by EGFR signaling. EGFR-mutated cell lines were significantly more resistant to T cell killing compared with WT cell lines through suppression of T cell proliferation and function. In a xenograft mouse model of EGFR-mutated NSCLC, neither anti-PD-L1 nor anti-CD73 antibody alone inhibited tumor growth compared with the isotype control. In contrast, the combination of both antibodies significantly inhibited tumor growth, increased the number of tumor-infiltrating CD8+ T cells, and enhanced IFN-γ and TNF-α production of these T cells. Consistently, there were increases in gene expression that corresponded to inflammation and T cell function in tumors treated with the combination of anti-PD-L1 and anti-CD73. Together, these results further support the combination of anti-CD73 and anti-PD-L1 therapies in treating EGFR-mutated NSCLC, while suggesting that increased T cell activity may play a role in response to therapy.
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Affiliation(s)
| | - Kelly McGlinchey
- Research Early Oncology, AstraZeneca, Gaithersburg, Maryland, USA
| | | | | | | | - Nicolas Floc’h
- Oncology R&D, Bioscience, AstraZeneca, Cambridge, United Kingdom
| | - James Kurasawa
- Biologics Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | | | | | - Leslie Wetzel
- Research Early Oncology, AstraZeneca, Gaithersburg, Maryland, USA
| | | | | | | | - Paul D. Smith
- Oncology R&D, Bioscience, AstraZeneca, Cambridge, United Kingdom
| | - Katerina Politi
- Department of Pathology and Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, Connecticut, USA
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Urazbakhtin S, Smirnova A, Volakhava A, Zerkalenkova E, Salyutina M, Doubek M, Jelinkova H, Khudainazarova N, Volchkov E, Belyaeva L, Komech E, Pavlova S, Lebedev Y, Plevova K, Olshanskaya Y, Komkov A, Mamedov I. The Absence of Retroelement Activity Is Characteristic for Childhood Acute Leukemias and Adult Acute Lymphoblastic Leukemia. Int J Mol Sci 2022; 23:ijms23031756. [PMID: 35163677 PMCID: PMC8835895 DOI: 10.3390/ijms23031756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 02/06/2023] Open
Abstract
Retroelements (RE) have been proposed as important players in cancerogenesis. Different cancer types are characterized by a different level of tumor-specific RE insertions. In previous studies, small cohorts of hematological malignancies, such as acute myeloid leukemia, multiple myeloma, and chronic lymphocytic leukemia have been characterized by a low level of RE insertional activity. Acute lymphoblastic leukemia (ALL) in adults and childhood acute leukemias have not been studied in this context. We performed a search for new RE insertions (Alu and L1) in 44 childhood ALL, 14 childhood acute myeloid leukemia, and 14 adult ALL samples using a highly sensitive NGS-based approach. First, we evaluated the method sensitivity revealing the 1% detection threshold for the proportion of cells with specific RE insertion. Following this result, we did not identify new tumor-specific RE insertions in the tested cohort of acute leukemia samples at the established level of sensitivity. Additionally, we analyzed the transcription levels of active L1 copies and found them increased. Thus, the increased transcription of active L1 copies is not sufficient for overt elevation of L1 retrotranspositional activity in leukemia.
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Affiliation(s)
- Shamil Urazbakhtin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
| | - Anastasia Smirnova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Anastasiya Volakhava
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (A.V.); (M.D.); (S.P.); (K.P.)
| | - Elena Zerkalenkova
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
| | - Maria Salyutina
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
| | - Michael Doubek
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (A.V.); (M.D.); (S.P.); (K.P.)
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
- Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
| | - Nelly Khudainazarova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
| | - Egor Volchkov
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
| | - Laima Belyaeva
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
| | - Ekaterina Komech
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
| | - Sarka Pavlova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (A.V.); (M.D.); (S.P.); (K.P.)
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
| | - Yuri Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (A.V.); (M.D.); (S.P.); (K.P.)
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
- Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
| | - Alexander Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
| | - Ilgar Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (A.V.); (M.D.); (S.P.); (K.P.)
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
- Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-910-4228-706
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48
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Lin YH, Lim SN, Chen CY, Chi HC, Yeh CT, Lin WR. Functional Role of Mitochondrial DNA in Cancer Progression. Int J Mol Sci 2022; 23:ijms23031659. [PMID: 35163579 PMCID: PMC8915179 DOI: 10.3390/ijms23031659] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/25/2022] Open
Abstract
Mitochondrial DNA (mtDNA) has been identified as a significant genetic biomarker in disease, cancer and evolution. Mitochondria function as modulators for regulating cellular metabolism. In the clinic, mtDNA variations (mutations/single nucleotide polymorphisms) and dysregulation of mitochondria-encoded genes are associated with survival outcomes among cancer patients. On the other hand, nuclear-encoded genes have been found to regulate mitochondria-encoded gene expression, in turn regulating mitochondrial homeostasis. These observations suggest that the crosstalk between the nuclear genome and mitochondrial genome is important for cellular function. Therefore, this review summarizes the significant mechanisms and functional roles of mtDNA variations (DNA level) and mtDNA-encoded genes (RNA and protein levels) in cancers and discusses new mechanisms of crosstalk between mtDNA and the nuclear genome.
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Affiliation(s)
- Yang-Hsiang Lin
- Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
| | - Siew-Na Lim
- Department of Neurology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Cheng-Yi Chen
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan;
| | - Hsiang-Cheng Chi
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 404, Taiwan;
- Chinese Medicine Research Center, China Medical University, Taichung 404, Taiwan
| | - Chau-Ting Yeh
- Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Hepatology and Gastroenterology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (C.-T.Y.); (W.-R.L.); Tel./Fax: +886-3-3281200 (ext. 8102) (W.-R.L.)
| | - Wey-Ran Lin
- Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Hepatology and Gastroenterology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Correspondence: (C.-T.Y.); (W.-R.L.); Tel./Fax: +886-3-3281200 (ext. 8102) (W.-R.L.)
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49
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Abstract
Cancer is often called a disease of aging. There are numerous ways in which cancer epidemiology and behaviour change with the age of the patient. The molecular bases for these relationships remain largely underexplored. To characterise them, we analyse age-associations in the nuclear and mitochondrial somatic mutational landscape of 20,033 tumours across 35 tumour-types. Age influences both the number of mutations in a tumour (0.077 mutations per megabase per year) and their evolutionary timing. Specific mutational signatures are associated with age, reflecting differences in exogenous and endogenous oncogenic processes such as a greater influence of tobacco use in the tumours of younger patients, but higher activity of DNA damage repair signatures in those of older patients. We find that known cancer driver genes such as CDKN2A and CREBBP are mutated in age-associated frequencies, and these alter the transcriptome and predict for clinical outcomes. These effects are most striking in brain cancers where alterations like SUFU loss and ATRX mutation are age-dependent prognostic biomarkers. Using three cancer datasets, we show that age shapes the somatic mutational landscape of cancer, with clinical implications.
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Affiliation(s)
- Constance H Li
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Department of Urology, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, CA, USA
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Department of Human Genetics, University of California, Los Angeles, CA, USA.
- Department of Urology, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, CA, USA.
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada.
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada.
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50
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Therizols G, Bash-Imam Z, Panthu B, Machon C, Vincent A, Ripoll J, Nait-Slimane S, Chalabi-Dchar M, Gaucherot A, Garcia M, Laforêts F, Marcel V, Boubaker-Vitre J, Monet MA, Bouclier C, Vanbelle C, Souahlia G, Berthel E, Albaret MA, Mertani HC, Prudhomme M, Bertrand M, David A, Saurin JC, Bouvet P, Rivals E, Ohlmann T, Guitton J, Dalla Venezia N, Pannequin J, Catez F, Diaz JJ. Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance. Nat Commun 2022; 13:173. [PMID: 35013311 PMCID: PMC8748862 DOI: 10.1038/s41467-021-27847-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/10/2021] [Indexed: 02/06/2023] Open
Abstract
Mechanisms of drug-tolerance remain poorly understood and have been linked to genomic but also to non-genomic processes. 5-fluorouracil (5-FU), the most widely used chemotherapy in oncology is associated with resistance. While prescribed as an inhibitor of DNA replication, 5-FU alters all RNA pathways. Here, we show that 5-FU treatment leads to the production of fluorinated ribosomes exhibiting altered translational activities. 5-FU is incorporated into ribosomal RNAs of mature ribosomes in cancer cell lines, colorectal xenografts, and human tumors. Fluorinated ribosomes appear to be functional, yet, they display a selective translational activity towards mRNAs depending on the nature of their 5'-untranslated region. As a result, we find that sustained translation of IGF-1R mRNA, which encodes one of the most potent cell survival effectors, promotes the survival of 5-FU-treated colorectal cancer cells. Altogether, our results demonstrate that "man-made" fluorinated ribosomes favor the drug-tolerant cellular phenotype by promoting translation of survival genes.
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MESH Headings
- Antimetabolites, Antineoplastic/pharmacology
- Cell Line, Tumor
- Cell Survival/drug effects
- Colorectal Neoplasms/drug therapy
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/metabolism
- Colorectal Neoplasms/pathology
- DNA Replication
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Drug Resistance, Neoplasm/genetics
- Drug Tolerance/genetics
- Fluorouracil/pharmacology
- HCT116 Cells
- Halogenation
- Humans
- Protein Biosynthesis/drug effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Receptor, IGF Type 1/agonists
- Receptor, IGF Type 1/genetics
- Receptor, IGF Type 1/metabolism
- Ribosomes/drug effects
- Ribosomes/genetics
- Ribosomes/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Gabriel Therizols
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Zeina Bash-Imam
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Baptiste Panthu
- CIRI-Inserm U1111, Ecole Normale Supérieure de Lyon, Lyon, F-693643, France
- Inserm U1060, CARMEN, F-69310, Pierre Bénite, France
| | - Christelle Machon
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
- Laboratoire de chimie analytique, Faculté de pharmacie de Lyon, 8 avenue Rockefeller, F-69373, Lyon, France
- Laboratoire de biochimie et de pharmaco-toxicologie, Centre hospitalier Lyon-Sud - HCL, F-69495, Pierre Bénite, France
| | - Anne Vincent
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Julie Ripoll
- LIRMM, UMR 5506, University of Montpellier, CNRS, Montpellier, France
| | - Sophie Nait-Slimane
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Mounira Chalabi-Dchar
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Angéline Gaucherot
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Maxime Garcia
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Florian Laforêts
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | | | - Marie-Ambre Monet
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | | | - Christophe Vanbelle
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Guillaume Souahlia
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Elise Berthel
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Marie Alexandra Albaret
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
- Department of Translational Research and Innovation, Centre Léon Bérard, 69373, Lyon, France
| | - Hichem C Mertani
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Michel Prudhomme
- Department of Digestive Surgery, CHU Nimes, Univ Montpellier, Nimes, France
| | - Martin Bertrand
- Department of Digestive Surgery, CHU Nimes, Univ Montpellier, Nimes, France
| | - Alexandre David
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, France
- IRMB-PPC, Univ Montpellier, INSERM, CHU Montpellier, CNRS, Montpellier, France
| | - Jean-Christophe Saurin
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
- Department of Endoscopy and Gastroenterology, Pavillon L, Edouard Herriot Hospital, Lyon, France
| | - Philippe Bouvet
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Eric Rivals
- LIRMM, UMR 5506, University of Montpellier, CNRS, Montpellier, France
- Institut Français de Bioinformatique, CNRS UMS 3601, Évry, France
| | - Théophile Ohlmann
- CIRI-Inserm U1111, Ecole Normale Supérieure de Lyon, Lyon, F-693643, France
| | - Jérôme Guitton
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
- Laboratoire de biochimie et de pharmaco-toxicologie, Centre hospitalier Lyon-Sud - HCL, F-69495, Pierre Bénite, France
- Laboratoire de toxicologie, Faculté de pharmacie de Lyon, Université de Lyon, 8 avenue Rockefeller, F-69373, Lyon, France
| | - Nicole Dalla Venezia
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | | | - Frédéric Catez
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France.
- Centre Léon Bérard, F-69008, Lyon, France.
- Université de Lyon 1, F-69000, Lyon, France.
- Institut Convergence PLAsCAN, F-69373, Lyon, France.
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France.
- Centre Léon Bérard, F-69008, Lyon, France.
- Université de Lyon 1, F-69000, Lyon, France.
- Institut Convergence PLAsCAN, F-69373, Lyon, France.
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