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  • 1
    In: Clinical Chemistry, Oxford University Press (OUP), Vol. 69, No. 5 ( 2023-04-28), p. 510-518
    Abstract: Somatic copy number alterations (sCNAs) acquired during the evolution of breast cancer provide valuable prognostic and therapeutic information. Here we present a workflow for screening sCNAs using picogram amounts of cell-free DNA (cfDNA) and single circulating tumor cells (CTCs). Methods We repurposed the Ion ReproSeq PGS™ preimplantation genetic testing kit to perform shallow whole genome sequencing on 178 cfDNA samples (300 pg) and individual CTCs from 10 MBC patients with metastatic breast cancer (MBC) recovered by CellSearch®/DEPArray™. Results were analyzed using a tailored ichorCNA workflow. Results sCNAs were detected in cfDNA of 41/105 (39%) patients with MBC and 3/23 (13%) primary breast cancers on follow-up (PBC FU), all of whom subsequently relapsed. In 8 of 10 MBCs, individual CTCs had a higher copy number count than matched cfDNA. The median tumor fraction detected by ichorCNA was 0.34 (range 0.17–0.58) for MBC and 0.36 (range 0.31–0.37) for PBC FU. Patients with detectable tumor fraction (≥ 0.1) and TFx and OncomineTM variants had significantly lower overall survival rates (P values P = 0.002 and P & lt; 0.0001 for the log-rank test, respectively). Conclusions The ReproSeq PGS assay is rapid, at approximately $120 per sample, providing both a sCNA profile and estimation of the tumor DNA fraction from limiting cfDNA template (300pg) and individual CTCs. The approach could be used to examine the copy number landscape over time to guide treatment decisions, support future trial designs, and be applied to low volume blood spot samples enabling remote monitoring.
    Type of Medium: Online Resource
    ISSN: 0009-9147 , 1530-8561
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
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  • 2
    In: British Journal of Cancer, Springer Science and Business Media LLC, Vol. 127, No. 10 ( 2022-11-09), p. 1858-1864
    Abstract: We report copy-number profiling by low-pass WGS (LP-WGS) in individual circulating tumour cells (CTCs) for guiding treatment in patients with metastatic breast cancer (MBC), comparing CTC results with mutations detected in circulating tumour DNA (ctDNA) in the same blood samples. Methods Across 10 patients with MBC who were progressing at the time of blood sampling and that had 〉 20 CTCs detected by CellSearch ® , 63 single cells (50 CTCs and 13 WBCs) and 16 cell pools (8 CTC pools and 8 WBC pools) were recovered from peripheral blood by CellSearch ® /DEPArray™ and sequenced with Ampli1 LowPass technology (Menarini Silicon Biosystems). Copy-number aberrations were identified using the MSBiosuite software platform, and results were compared with mutations detected in matched plasma cfDNA analysed by targeted next-generation sequencing using the Oncomine™ Breast cfDNA Assay (Thermo Fisher). Results LP-WGS data demonstrated copy-number gains/losses in individual CTCs in regions including FGFR1, JAK2 and CDK6 in five patients, ERBB2 amplification in two HER2-negative patients and BRCA loss in two patients. Seven of eight matched plasmas also had mutations in ctDNA in PIK3CA, TP53, ESR1 and KRAS genes with mutant allele frequencies (MAF) ranging from 0.05 to 33.11%. Combining results from paired CTCs and ctDNA, clinically actionable targets were identified in all ten patients. Conclusion This combined analysis of CTCs and ctDNA may offer a new approach for monitoring of disease progression and to direct therapy in patients with advanced MBC, at a time when they are coming towards the end of other treatment options.
    Type of Medium: Online Resource
    ISSN: 0007-0920 , 1532-1827
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
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  • 3
    In: JAMA Network Open, American Medical Association (AMA), Vol. 6, No. 7 ( 2023-07-25), p. e2325332-
    Abstract: Liquid biopsy has emerged as a complement to tumor tissue profiling for advanced non–small cell lung cancer (NSCLC). The optimal way to integrate liquid biopsy into the diagnostic algorithm for patients with newly diagnosed advanced NSCLC remains unclear. Objective To evaluate the use of circulating tumor DNA (ctDNA) genotyping before tissue diagnosis among patients with suspected advanced NSCLC and its association with time to treatment. Design, Setting, and Participants This single-group nonrandomized clinical trial was conducted among 150 patients at the Princess Margaret Cancer Centre–University Health Network (Toronto, Ontario, Canada) between July 1, 2021, and November 30, 2022. Patients referred for investigation and diagnosis of lung cancer were eligible if they had radiologic evidence of advanced lung cancer prior to a tissue diagnosis. Interventions Patients underwent plasma ctDNA testing with a next-generation sequencing (NGS) assay before lung cancer diagnosis. Diagnostic biopsy and tissue NGS were performed per standard of care. Main Outcome and Measures The primary end point was time from referral to treatment initiation among patients with advanced nonsquamous NSCLC using ctDNA testing before diagnosis (ACCELERATE [Accelerating Lung Cancer Diagnosis Through Liquid Biopsy] cohort). This cohort was compared with a reference cohort using standard tissue genotyping after tissue diagnosis. Results Of the 150 patients (median age at diagnosis, 68 years [range, 33-91 years]; 80 men [53%] ) enrolled, 90 (60%) had advanced nonsquamous NSCLC. The median time to treatment was 39 days (IQR, 27-52 days) for the ACCELERATE cohort vs 62 days (IQR, 44-82 days) for the reference cohort ( P   & amp;lt; .001). Among the ACCELERATE cohort, the median turnaround time from sample collection to genotyping results was 7 days (IQR, 6-9 days) for plasma and 23 days (IQR, 18-28 days) for tissue NGS ( P   & amp;lt; .001). Of the 90 patients with advanced nonsquamous NSCLC, 21 (23%) started targeted therapy before tissue NGS results were available, and 11 (12%) had actionable alterations identified only through plasma testing. Conclusions and Relevance This nonrandomized clinical trial found that the use of plasma ctDNA genotyping before tissue diagnosis among patients with suspected advanced NSCLC was associated with accelerated time to treatment compared with a reference cohort undergoing standard tissue testing. Trial Registration ClinicalTrials.gov Identifier: NCT04863924
    Type of Medium: Online Resource
    ISSN: 2574-3805
    Language: English
    Publisher: American Medical Association (AMA)
    Publication Date: 2023
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  • 4
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 41, No. 16_suppl ( 2023-06-01), p. 9019-9019
    Abstract: 9019 Background: Timeliness of molecular testing is essential to minimize the time to appropriate 1 st line treatment initiation (TTI) in advanced NSCLC pts. We hypothesized that LB-based molecular testing performed at the patient's 1 st visit could reduce this TTI. Methods: LIBELULE is a multicenter, randomized, comparative, open-label study, enrolling pts with radiological suspicion of stage IV lung cancer, no prior biopsy or cytology for advanced NSCLC diagnosis. In Arm A, a LB was performed at the 1 st visit using the InVisionFirst-Lung assay, an amplicon-based NGS panel covering 37-NSCLC associated genes. When LB results were informative, treatment was initiated on the basis of: InVisionFirst-Lung alone for pts with EGFR, BRAF V600E mutation (mut), ALK or ROS1 rearrangement (category 1 alterations); InVisionFirst-Lung and pathological results for pts with ERBB2, MET exon 14, KRAS, BRAF non V600 and/or LKB1 mut, RET or NTRK rearrangement (category 2 alterations). In control Arm B, histological sampling was planned with genomic analysis when indicated (local LB allowed) and treatment was initiated according to ESMO guidelines. The primary endpoint was the time from randomization to initiation of appropriate treatment based on informative genomic and pathological results. 286 pts were needed to detect a 21% shortening in TTI (α = 0.05, 1-β = 90%). Results: 319 pts were randomized between Arm A (n = 161) and B (n = 158): median age 68 y (39-97), 56.1% male, 28.5% non-smokers, PS0-1 82%, PS≥2 18,1%; adenocarcinoma: 56.7%, squamous cell carcinoma: 11%, SCLC: 10%, other tumor types: 5%. 5.3% of pts had no cancer. In Arm A, 81% of pts had ctDNA findings; category 1 and category 2 alterations were identified on tissue and/or LB in 29.2% ( EGFR mut: 21.7%) and 24%, respectively, whereas in Arm B, 23.2% of pts had category 1 ( EGFR mut: 20.3%) and 20% had category 2 alterations detected. Systemic treatment was initiated in 74.5% and 65.8% of pts in Arm A and B, respectively. Main reasons for not initiating treatment were diagnosis other than cancer, local treatment and palliative care. The mean TTI was 29.0 days (d) (95%CI 25.9-32.1) in Arm A vs 33.9 d (95%CI 28.4-39.5) in Arm B in the intention-to-treat population (p = 0.28), but significantly shorter in Arm A 29.1 d vs 38.8 d in Arm B for pts receiving systemic treatment (p = 0.01). The mean TTI was significantly shorter (21 d vs 37.4 d) in pts with category 1 alterations (p = 0.004) as well as the time to contributive genomic analysis (17.9 d vs 25.6 d; p 〈 0.001) in Arm A and B, respectively. In Arm A, 7.4% of pts vs 13.3% in Arm B initiated a treatment without genomic analysis available. Conclusions: Early LB significantly reduces the time to contributive molecular analysis and the time to initiation of appropriate 1 st line therapy in pts eligible for systemic treatment, especially for pts with actionable alterations indicating targeted 1 st line therapy. Clinical trial information: NCT03721120 .
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2023
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  • 5
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2022
    In:  Cancer Research Vol. 82, No. 4_Supplement ( 2022-02-15), p. P2-01-14-P2-01-14
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 4_Supplement ( 2022-02-15), p. P2-01-14-P2-01-14
    Abstract: Neutrophils (Ns) influence cancer cell survival and metastasis through the release of chemokines, cytokines and interactions within the microenvironment and at distal sites from the primary tumour. Background: Patients with Breast Cancer (BC) often display elevated levels of circulating blood neutrophils and an elevated neutrophil: lymphocyte ratio (NLR) is associated with a shorter disease-free survival in patients with Early Breast Cancer (EBC). Evidence from mouse models of BC shows that Ns can either have a tumour-promoting or tumour-inhibitory role. CD62L (L-selectin) is a cell adhesion molecule found on the surface of leukocytes which is important for helping circulatory Ns bind to the endothelium and migrate into tissues and is rapidly shed upon N activation. Our laboratory has found a lower proportion of Ns expressing CD62L in pre-clinical models of BC, which implies that Ns from tumour-bearing mice have less endothelial- adhesive capacity and hence will remain in the circulation for a longer time. However, there is limited knowledge regarding whether different N subpopulations are present within the circulation of patients with BC, how early this occurs in the disease process and whether this is influenced by BC phenotype. In order to address these questions, we phenotyped Ns from BC patients. Objectives: Our primary objectives were to investigate changes in the surface marker CD62L expression via flow cytometry in neutrophils from patients and HVs to see if the changes seen in the pre-clinical mouse models were also seen in patients. Since kinases govern many aspects of intracellular signalling and functions, we also assessed the Serine Threonine Kinase (STK) and Phosphotyrosine Kinase (PK) activity within circulatory neutrophils in patients with Breast Cancer and paired HVs using a Pamgene kinase assay. This evaluated the activity of kinases (n = 340 kinases) in N lysates to compare N kinase activity in EBC patients and age-matched HVs. Methods: We recruited 28 patients with Early BC (EBC) (10 Node +, 18 node -; 10 T1 and 16 T2 and 2 T3) and paired healthy volunteers (HVs) who were age and sex-matched to compare phenotypical features of Ns isolated from the blood. 21 Patients with Oestrogen receptor positive (ER+) and 7 with Oestrogen receptor negative (ER -) EBC were recruited between June 2018 and June 2021. No patient had overt metastatic disease and all were screened for exclusion factors, such as infection, autoimmune conditions and certain medication known to influence neutrophils. Results: We found that ER+ patients had a lower level of the CD62Llow neutrophil subset compared to HVs (P & lt; 0.0375). In contrast there was a significant increase in the CD62Llow neutrophil subset (2-fold higher) for ER - patients compared to HVs (P & lt; 0.0316).The Pamgene kinase assay showed that there was a general upregulation in both STK and PK kinase activity, especially the tyrosine family of kinases for patients with ER positive breast cancer (Median kinase score which is the combined sensitivity score and specificity score & gt; 1.2) and a general downregulation in kinase activity, especially the CMGC family of kinases for patients with ER negative disease (Median kinase score & gt; 1.2) compared to paired HVs. The functional implications of these differences in kinase activity are being actively investigated. Conclusion: We have detected changes in CD62L expression and neutrophil kinase activity within the circulation of patients with EBC and the nature of these changes appear to be intrinsically linked to ER subtype. These findings may have important implications for use as part of an early diagnostic multi-omic platform. Citation Format: Anisha Ramessur, Bana Ambasager, Ilaria Malanchi, Raoul Charles Coombes. The multi switching activity of neutrophils in the circulation of patients with early breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-01-14.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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