Clinical verification of circulating tumor RNA (ctRNA) as novel pretreatment predictor and tool for quantitative monitoring of treatment response in metastatic colorectal cancer (mCRC): A biomarker study of the DEEPER trial.

TPS3621 Background: A randomized phase II trial, DEEPER (JACCRO CC-13) [NCT02515734], is on-going to evaluate FOLFOXIRI plus cetuximab (cet) vs. FOLFOXIRI plus bevacizumab (bev) in terms of depth of response as primary endpoint in 360 mCRC patients (pts) with RAS wild-type tumors, PS0-1, and no previous chemotherapy. This is a head-to-head comparative trial of 2 key monoclonal antibodies in mCRC treatment; therefore, it would be of interest to perform the biomarker study for developing novel predictors of cet or bev. The clinical utility of circulating tumor DNA (ctDNA) analysis has been largely validated for monitoring during treatment and companion diagnostics after chemotherapy. However, there are few published results regarding ctRNA in cancer treatment. Use of ctRNA from liquid biopsies would enhance tumor profiling through the trending of actionable biomarkers not found in ctDNA, and allow for patient monitoring by measuring dynamic changes in levels of gene expressions. Methods: This study will enroll pts with willing to undergo biopsies of both tissue and blood among participants of the DEEPER trial. The estimated number is 250. The main purpose is to find novel predictors for efficacy of cet or bev in mCRC using liquid biopsies, which are performed to obtain ctDNA and ctRNA at 6 time points: pre-treatment, 8 weeks after treatment start, beginning of maintenance phase in FOLFOXIRI-regimen, progression, before and 8 weeks after 2nd-line treatment. The tissue samples collected before chemotherapy will be used for analyzing intra-tumoral genetic alterations. Associations between analytes in blood/tissue and the clinical outcomes of each treatment (with cet or bev) will be assessed using Fisher’s exact test, Kaplan-Meier curves, and log-rank tests in univariate analyses. We will evaluate on whether transcriptomic analysis in ctRNA could predict treatment efficacy more accurately compared to genomic analysis in ctDNA, and verify the clinical utility of ctRNA testing in mCRC treatment. Accrual will continue until the DEEPER trial is completed. Clinical trial information: UMIN000018412.

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Towards Routine Implementation of Liquid Biopsies in Cancer Management: It Is Always Too Early, until Suddenly It Is Too Late

Diagnostics ◽

10.3390/diagnostics11010103 ◽

2021 ◽

Vol 11 (1) ◽

pp. 103

Author(s):

Maarten J. IJzerman ◽

Jasper de Boer ◽

Arun Azad ◽

Koen Degeling ◽

Joel Geoghegan ◽

...

Keyword(s):

Clinical Utility ◽

Clinical Laboratory ◽

Genomic Analysis ◽

Current Evidence ◽

Liquid Biopsies ◽

Blood Draw ◽

Minimum Quality Standards ◽

Cancer Management ◽

Alternative Funding ◽

And Performance

Blood-based liquid biopsies are considered a new and promising diagnostic and monitoring tool for cancer. As liquid biopsies only require a blood draw, they are non-invasive, potentially more rapid and assumed to be a less costly alternative to genomic analysis of tissue biopsies. A multi-disciplinary workshop (n = 98 registrations) was organized to discuss routine implementation of liquid biopsies in cancer management. Real-time polls were used to engage with experts’ about the current evidence of clinical utility and the barriers to implementation of liquid biopsies. Clinical, laboratory and health economics presentations were given to illustrate the opportunities and current levels of evidence, followed by three moderated break-out sessions to discuss applications. The workshop concluded that tumor-informed assays using next-generation sequencing (NGS) or PCR-based genotyping assays will most likely provide better clinical utility than tumor-agnostic assays, yet at a higher cost. For routine application, it will be essential to determine clinical utility, to define the minimum quality standards and performance of testing platforms and to ensure their use is integrated into current clinical workflows including how they complement tissue biopsies and imaging. Early health economic models may help identifying the most viable application of liquid biopsies. Alternative funding models for the translation of complex molecular diagnostics, such as liquid biopsies, may also be explored if clinical utility has been demonstrated and when their use is recommended in multi-disciplinary consensus guidelines.

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Circulating tumor DNA in patients with metastatic urothelial cancer: concordance of genomic findings with matched tissue biopsies.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.e16036 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. e16036-e16036 ◽

Cited By ~ 1

Author(s):

Jean-Michel Lavoie ◽

Gillian Vandekerkhove ◽

Matti Annala ◽

Nora Sundahl ◽

Takeshi Sano ◽

...

Keyword(s):

Urothelial Cancer ◽

Stage Iv ◽

Circulating Tumor Dna ◽

Blood Collection ◽

Liquid Biopsies ◽

Tissue Samples ◽

Metastatic Urothelial Cancer ◽

Platinum Based Chemotherapy ◽

Matched Tissue ◽

Tumor Dna

e16036 Background: Patients (pts) with metastatic urothelial cancer (mUC) now have access to many different treatment options. This creates an incentive for molecular profiling of their tumors, with the aim of developing biomarkers. Genomic profiling may leverage the presence of circulating tumor DNA (ctDNA), but it has not been shown whether this recapitulates the findings from tissue samples. Methods: Whole blood samples were collected for next-generation sequencing of leukocyte and cell-free DNA (cfDNA). Deep targeted sequencing was performed across a UC-specific custom 50-gene panel (median depth of 986x). Matched archival tissue was profiled using the same assay for 65 pts. Results: Between 11/2011 and 12/2017, 90 pts developed mUC (87 evaluable). Baseline characteristics: median age 67, 83% male, 14% upper-tract disease, 17% stage IV at initial presentation. Treatments delivered: 76% platinum-based chemotherapy, 47% PD-1/PD-L1 inhibitor. At a median follow-up of 12.8 mo., 45% remain alive. We found ctDNA fractions above 2% in at least one blood collection in 81% of cases. For 17 pts, matched metastatic biopsies and cfDNA collection were available; in those cases 82% of coding somatic mutations identified in tissue were independently detected in cfDNA. Half of discordant findings could be attributed to low ctDNA fraction. Most (89%) mutations detected in primary tissue (cystectomy or nephrectomy) were present in later cfDNA collections. ctDNA detected mutations in TP53 and ARID1A in 64% and 29% of pts, respectively. A tumor mutation burden ≥25 mutation per Mb was observed in 27% of cases. Conclusions: There is a high concordance between genomic findings from ctDNA and matched tissue of pts with mUC. This supports the use of liquid biopsies to study potential biomarkers in this disease.

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Clinical utility of circulating tumor DNA as a response and follow-up marker in cancer therapy

Cancer and Metastasis Reviews ◽

10.1007/s10555-020-09876-9 ◽

2020 ◽

Vol 39 (3) ◽

pp. 999-1013 ◽

Cited By ~ 1

Author(s):

Pieter A. Boonstra ◽

Thijs T. Wind ◽

Michel van Kruchten ◽

Ed Schuuring ◽

Geke A. P. Hospers ◽

...

Keyword(s):

Cancer Therapy ◽

Treatment Response ◽

Clinical Utility ◽

Tumor Response ◽

Circulating Tumor Dna ◽

Tumor Burden ◽

Liquid Biopsies ◽

Secondary Resistance ◽

Tumor Dna

Abstract Response evaluation for cancer treatment consists primarily of clinical and radiological assessments. In addition, a limited number of serum biomarkers that assess treatment response are available for a small subset of malignancies. Through recent technological innovations, new methods for measuring tumor burden and treatment response are becoming available. By utilization of highly sensitive techniques, tumor-specific mutations in circulating DNA can be detected and circulating tumor DNA (ctDNA) can be quantified. These so-called liquid biopsies provide both molecular information about the genomic composition of the tumor and opportunities to evaluate tumor response during therapy. Quantification of tumor-specific mutations in plasma correlates well with tumor burden. Moreover, with liquid biopsies, it is also possible to detect mutations causing secondary resistance during treatment. This review focuses on the clinical utility of ctDNA as a response and follow-up marker in patients with non-small cell lung cancer, melanoma, colorectal cancer, and breast cancer. Relevant studies were retrieved from a literature search using PubMed database. An overview of the available literature is provided and the relevance of ctDNA as a response marker in anti-cancer therapy for clinical practice is discussed. We conclude that the use of plasma-derived ctDNA is a promising tool for treatment decision-making based on predictive testing, detection of resistance mechanisms, and monitoring tumor response. Necessary steps for translation to daily practice and future perspectives are discussed.

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Liquid Biopsies: Genotyping Circulating Tumor DNA

Journal of Clinical Oncology ◽

10.1200/jco.2012.45.2011 ◽

2014 ◽

Vol 32 (6) ◽

pp. 579-586 ◽

Cited By ~ 1096

Author(s):

Luis A. Diaz ◽

Alberto Bardelli

Keyword(s):

Tumor Heterogeneity ◽

Dna Analysis ◽

Tumor Tissue ◽

Tumor Staging ◽

Circulating Tumor Dna ◽

Genetic Alterations ◽

Routine Practice ◽

Liquid Biopsies ◽

Tumor Dna ◽

Single Snapshot

Genotyping tumor tissue in search of somatic genetic alterations for actionable information has become routine practice in clinical oncology. Although these sequence alterations are highly informative, sampling tumor tissue has significant inherent limitations; tumor tissue is a single snapshot in time, is subject to selection bias resulting from tumor heterogeneity, and can be difficult to obtain. Cell-free fragments of DNA are shed into the bloodstream by cells undergoing apoptosis or necrosis, and the load of circulating cell-free DNA (cfDNA) correlates with tumor staging and prognosis. Moreover, recent advances in the sensitivity and accuracy of DNA analysis have allowed for genotyping of cfDNA for somatic genomic alterations found in tumors. The ability to detect and quantify tumor mutations has proven effective in tracking tumor dynamics in real time as well as serving as a liquid biopsy that can be used for a variety of clinical and investigational applications not previously possible.

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The detection of specific hypermethylated WIF1 and NPY genes in circulating DNA by crystal digital PCR™ is a powerful new tool for colorectal cancer diagnosis and screening

BMC Cancer ◽

10.1186/s12885-021-08816-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Alexis Overs ◽

Mylène Flammang ◽

Eric Hervouet ◽

Laurent Bermont ◽

Jean-Luc Pretet ◽

...

Keyword(s):

Liquid Biopsy ◽

Digital Pcr ◽

Circulating Tumor Dna ◽

Point Of View ◽

University Hospital ◽

Liquid Biopsies ◽

Tissue Samples ◽

Mutation Status ◽

Tumor Tissues ◽

Tumor Stages

Abstract Background In oncology, liquid biopsy is of major relevance from theranostic point of view. The searching for mutations in circulating tumor DNA (ctDNA) in case of colorectal cancers (CRCs) allows the optimization of patient care. In this context, independent of mutation status biomarkers are required for its detection to confirm the presence of ctDNA in liquid biopsies. Indeed, the hypermethylation of NPY and WIF1 genes appear to be an ideal biomarker for the specific detection of ctDNA in CRCs. The objective of this work is to develop the research of hypermethylation of NPY and WIF1 by Crystal Digital PCR™ for the detection of ctDNA in CRCs. Methods Detection of hypermethylated NPY and WIF1 was developed on Cristal digital PCR™. Biological validation was performed from a local cohort of 22 liquid biopsies and 23 tissue samples from patients with CRC. These patients were treated at the University Hospital of Besancon (France). Results The local cohort study confirmed that NPY and WIF1 were significantly hypermethylated in tumor tissues compared to adjacent non-tumor tissues (WIF1 p < 0.001; NPY p < 0.001; non-parametric Wilcoxon paired-series test). Histological characteristics, tumor stages or mutation status were not correlated to the methylation profiles. On the other hand, hypermethylation of NPY or WIF1 in liquid biopsy had a 95.5% [95%CI 77–100%] sensitivity and 100% [95%CI 69–100%] specificity. Conclusion Using Crystal digital PCR™, this study shows that hypermethylation of NPY and WIF1 are constant specific biomarkers of CRCs regardless of a potential role in carcinogenesis.

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Genomic Profiling of Uterine Aspirates and cfDNA as an Integrative Liquid Biopsy Strategy in Endometrial Cancer

Journal of Clinical Medicine ◽

10.3390/jcm9020585 ◽

2020 ◽

Vol 9 (2) ◽

pp. 585 ◽

Cited By ~ 3

Author(s):

Carlos Casas-Arozamena ◽

Eva Díaz ◽

Cristian Pablo Moiola ◽

Lorena Alonso-Alconada ◽

Alba Ferreiros ◽

...

Keyword(s):

Endometrial Cancer ◽

Targeted Therapies ◽

Circulating Tumor Cell ◽

Circulating Tumor Dna ◽

Genetic Alterations ◽

Tumor Evolution ◽

Liquid Biopsies ◽

Post Surgery ◽

Incidence And Mortality ◽

Genetic Landscape

The incidence and mortality of endometrial cancer (EC) have risen in recent years, hence more precise management is needed. Therefore, we combined different types of liquid biopsies to better characterize the genetic landscape of EC in a non-invasive and dynamic manner. Uterine aspirates (UAs) from 60 patients with EC were obtained during surgery and analyzed by next-generation sequencing (NGS). Blood samples, collected at surgery, were used for cell-free DNA (cfDNA) and circulating tumor cell (CTC) analyses. Finally, personalized therapies were tested in patient-derived xenografts (PDXs) generated from the UAs. NGS analyses revealed the presence of genetic alterations in 93% of the tumors. Circulating tumor DNA (ctDNA) was present in 41.2% of cases, mainly in patients with high-risk tumors, thus indicating a clear association with a more aggressive disease. Accordingly, the results obtained during the post-surgery follow-up indicated the presence of ctDNA in three patients with progressive disease. Moreover, 38.9% of patients were positive for CTCs at surgery. Finally, the efficacy of targeted therapies based on the UA-specific mutational landscape was demonstrated in PDX models. Our study indicates the potential clinical applicability of a personalized strategy based on a combination of different liquid biopsies to characterize and monitor tumor evolution, and to identify targeted therapies.

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Evolving Clinical Utility of Liquid Biopsy in Gastrointestinal Cancers

Cancers ◽

10.3390/cancers11081164 ◽

2019 ◽

Vol 11 (8) ◽

pp. 1164 ◽

Cited By ~ 6

Author(s):

Jacobson ◽

Munding ◽

Hayden ◽

Levy ◽

Kuzel ◽

...

Keyword(s):

Liquid Biopsy ◽

Clinical Utility ◽

Clinical Evidence ◽

Circulating Tumor Dna ◽

Gastrointestinal Cancers ◽

Liquid Biopsies ◽

Colon And Rectum ◽

Increased Sensitivity ◽

Tumor Dna ◽

Genomic Material

Room for improvement exists regarding recommendations for screening, staging, therapy selection, and frequency of surveillance of gastrointestinal cancers. Screening is costly and invasive, improved staging demands increased sensitivity and specificity to better guide therapy selection. Surveillance requires increased sensitivity for earlier detection and precise management of recurrences. Peripherally collected blood-based liquid biopsies enrich and analyze circulating tumor cells and/or somatic genomic material, including circulating tumor DNA along with various subclasses of RNA. Such assays have the potential to impact clinical practice at multiple stages of management in gastrointestinal cancers. This review summarizes current basic and clinical evidence for the utilization of liquid biopsy in cancers of the esophagus, pancreas, stomach, colon, and rectum. Technical aspects of various liquid biopsy methodologies and targets are reviewed and evidence supporting current commercially available assays is examined. Finally, current clinical applicability, potential future uses, and pitfalls of applying liquid biopsy to the screening, staging and therapeutic management of these diseases are discussed.

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Diagnostic Accuracy of Liquid Biopsy in Endometrial Cancer

Cancers ◽

10.3390/cancers13225731 ◽

2021 ◽

Vol 13 (22) ◽

pp. 5731

Author(s):

Marta Łukasiewicz ◽

Krzysztof Pastuszak ◽

Sylwia Łapińska-Szumczyk ◽

Robert Różański ◽

Sjors G. J. G. In ‘t Veld ◽

...

Keyword(s):

Artificial Intelligence ◽

Endometrial Cancer ◽

Primary Tumor ◽

Liquid Biopsy ◽

Circulating Tumor Dna ◽

Sequencing Data ◽

Liquid Biopsies ◽

Tissue Samples ◽

Sample Classification ◽

Tumor Tissues

Background: Liquid biopsy is a minimally invasive collection of a patient body fluid sample. In oncology, they offer several advantages compared to traditional tissue biopsies. However, the potential of this method in endometrial cancer (EC) remains poorly explored. We studied the utility of tumor educated platelets (TEPs) and circulating tumor DNA (ctDNA) for preoperative EC diagnosis, including histology determination. Methods: TEPs from 295 subjects (53 EC patients, 38 patients with benign gynecologic conditions, and 204 healthy women) were RNA-sequenced. DNA sequencing data were obtained for 519 primary tumor tissues and 16 plasma samples. Artificial intelligence was applied to sample classification. Results: Platelet-dedicated classifier yielded AUC of 97.5% in the test set when discriminating between healthy subjects and cancer patients. However, the discrimination between endometrial cancer and benign gynecologic conditions was more challenging, with AUC of 84.1%. ctDNA-dedicated classifier discriminated primary tumor tissue samples with AUC of 96% and ctDNA blood samples with AUC of 69.8%. Conclusions: Liquid biopsies show potential in EC diagnosis. Both TEPs and ctDNA profiles coupled with artificial intelligence constitute a source of useful information. Further work involving more cases is warranted.

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