Liquid Biopsy Testing Research Articles

Diagnosing and Prognosing Bone Metastasis in Prostate Cancer: Clinical Utility of Blood Biomarkers.

Bone metastasis (BM) may occur in any type of cancer. The diagnosis of patients with BM has increased due to improved imaging technologies and advances in cancer drug therapy that have prolonged the survival time of cancer patients. BM may be asymptomatic in the early stages; however, as the disease progresses, it causes pain, fracture, neurological symptoms associated with spinal cord compression, hypercalcemia, and other specific symptoms that significantly impair the patient's quality of life (QOL). Imaging modalities have disadvantages, such as high cost, radiation exposure, and bone pain associated with holding posture for imaging test; further, they are time-consuming. Hence, patients with BM require convenient and useful biomarkers. However, no blood biomarkers generally useful for diagnosis and therapeutic monitoring of BM are established. Prostate cancer (PC) and breast cancer, in particular, are among the most prone to BM because BM occurs in approximately 70% of patients with advanced disease. Herein, we reviewed various potential bone turnover markers and liquid biopsy for diagnosis and prognosis prediction in patients with BM of PC based on PubMed literature search. The usefulness of conventional bone turnover markers of BM in PC is limited, and cut-off values vary. In the future, the creation of algorithms using these conventional markers and multiple tests, such as liquid biopsy and imaging tests, will help to develop highly accurate techniques for the diagnosis of BM.

Factors Likely to Affect the Uptake of Genomic Approaches to Cancer Screening in Primary Care: A Scoping Review.

Genomic tests are being developed for use in cancer screening. As most screening is offered in primary care settings, primary care provider and patient perceptions of such tests are likely to affect uptake. We conducted a scoping review to synthesize information on factors likely to affect patient and provider use of biospecimen collection and analysis for cancer screening, methods referred to as liquid biopsy or multi-cancer early detection (MCED) testing when used to detect multiple cancers. We ultimately identified 7 articles for review and analyzed them for major themes. None reported on primary care provider perspectives. Six articles focused on patient perceptions about testing for a single cancer (colorectal), and 1 reported on patient views related to testing for multiple cancers. Factors favoring this type of testing included its non-invasiveness, and the perceived safety, convenience, and effectiveness of testing. There is a dearth of information in the literature on primary care provider perceptions about liquid biopsy and MCED testing. The limited information on patient perceptions suggests that they are receptive to such tests. Research on primary care provider and patient test-related knowledge, attitudes, and behavior is needed to guide future implementation in primary care settings.

Genomic Landscape of Circulating-Tumor DNA in a Diverse Cohort of Metastatic Breast Cancer Patients

Introduction: Breast cancer is the most prevalent cancer and the second leading cause of cancer death among women in the United States. Liquid biopsy is becoming a more commonly accepted method in clinical practice. Thus, there is a need to investigate ways to utilize circulating-tumor DNA (ctDNA) in metastatic breast cancer (mBC). The primary objective of this study was to characterize the genomic landscape of ctDNA in a diverse patient population and across different subtypes of mBC. Methods: We analyzed the ctDNA profile in patients (n = 45) with mBC who received a Guardant360 liquid biopsy test. Patient demographics, age at diagnosis, race, subtype, and mutations were included in the analysis. Results: The majority of patients (n = 39, 86.7%) had at least one gene alteration detected in their liquid biopsy. We found no statistically significant differences in genomic landscape according to race. However, there were differences seen in tumor genomics according to age and subtype. Postmenopausal patients were more likely to have detectable disease on liquid biopsy compared to premenopausal patients (p = 0.001). Mutations in ESR1 (n = 10) and PIK3CA (n = 8) were more commonly seen in hormone positive (HR+) mBC, where known tailored treatment options are available (i.e., fulvestrant and alpelisib respectively). The most common alterations detected include TP53 (n = 22) followed by PIK3CA (n = 15), ESR1 (n = 11), CCND1 (n = 7), and ERBB2 (n = 7). Conclusion: Liquid biopsies are effective tools that can reveal clinically relevant information including mutational status and therapeutic options.

Prospective Study of the Usefulness of Liquid Biopsy in Patients with Unknown Fever Suspected of Malignant Lymphoma

Background: Malignant lymphoma, represented by intravascular large B-cell lymphoma (IVLBCL), is an important differential disease in classical fever of unknown origin (FUO). Bone marrow aspiration (BMA) and random skin biopsy (RSB) are useful in IVLBCL diagnosis, but their positivity rates are clinically insufficient and the procedures are invasive. The molecular genetic analysis of lymphomas using cell-free tumor DNA (cfDNA) in plasma (liquid biopsy) may be effective for IVLBCL (Shimada et al., Blood. 2021 Mar 18;137(11):1491). We conducted a multicenter prospective clinical trial to investigate the usefulness of liquid biopsy for early lymphoma diagnosis among patients with classical FUO. Methods: Patients with the following criteria were enrolled: (1) clinically suspected malignant lymphoma, (2) persistent fever for >3 weeks, refractory to antibiotics, (3) higher than standard lactate dehydrogenase, (4) unbiopsiable lesions, and (5) age ≥20 years. Liquid biopsies were performed as follows: (1) MYD88 L265P/CD79 Y196 mutation analysis using droplet digital PCR (ddPCR), (2) B-cell receptor (BCR)/T-cell receptor (TCR) reconstruction analysis using next generation sequencing (NGS), and (3) comprehensive genetic analysis using the hematopoietic oncogene panel (426 genes) and NGS. Pathological malignant lymphoma was diagnosed at each institution; later, a central diagnosis was made by two additional lymphoma pathology specialists. Results: Fifty patients were enrolled from 15 centers from October 2019 to September 2021; one was excluded. The median age was 73.5 (21-89) years; 28 patients (57.1%) were male. There were 29 cases (59%), 28 (57.1%), and one (2%) of hematologic malignancy, malignant lymphoma, and MDS/AML, respectively (Fig. 1A). Twenty (71%) malignant lymphomas were B-cell lymphomas (17 of which were IVLBCL [61%]), and 8 (29%) were mature T/NK-cell lymphomas. Nonhematologic diseases were present in 20 (41%) patients (7 collagen diseases [4 adult-onset Still's disease, 3 others], 2 solid tumors, 2 infections [1 syphilis, 1 tuberculosis], and 9 FUO). FUO pathological investigations were performed in 47 (97.9%) and 43 (87.6%) patients with BMA and RSB, respectively. IVLBCL had a 53% positivity rate for initial BMA (9/17) and RSB (8/15; Fig. 1B). Only 65% patients tested positive for either initial BMA or RSB and a majority (15/17) of them were diagnosed based on repeated evaluations during their lifetime. The BMA positive rate in patients with mature T/NK-cell lymphoma (8 cases) was high (75%). The mean cfDNA concentration was 215 (5.6-1320) ng/mL, with no significant difference between patients with lymphoma and those with other diseases (279 vs. 130 ng/mL, p=0.073). In ddPCR analysis, 85% of B-cell lymphoma cases (N=20) had either MYD88 or CD79B mutations; the mutation detection rate in IVLBCL (N=17) was 94% (Fig.1B, 2). All patients with non-B-cell lymphoma tested negative. The positive rate of patients with B-cell lymphoma in the NGS-based BCR reconstruction analysis was 90% and negative in two patients with IVLBCL. BCR reconstitution was also observed in two patients with T/NK-cell lymphoma. Comprehensive panel analysis demonstrated that 19/20 (95%) B-cell lymphoma cases showed MYD88 or CD79B mutations; all IVLBCL cases showed mutations. LymphGen algorithm analysis showed that 15, 1, and 1 IVLBCL cases were categorized as MCD (with MYD88 or CD79b mutations), composite (including MCD), and other, respectively (Fig. 2). In T/NK-cell lymphomas, TCR reconstitution was positive in 3/8 T/NK-cell lymphomas. Panel analysis could hardly predict T/NK-cell lymphoma. DdPCR results were returned to the physician within a median time of 14 days. Of the six patients who were not diagnosed with initial BMA and RSB, five were positive for the MYD88/CD79B mutation, according to the ddPCR results. Three of them were diagnosed through additional liquid biopsy testing. Two patients were diagnosed with IVLBCL based on central diagnosis after death. Conclusions: In the classical FUO cases with suspected malignant lymphoma, 57% and 35% had malignant lymphoma and IVLBCL, respectively. Compared to the classical diagnostic methods, liquid biopsy can be used to detect lymphoma-specific genetic mutations at an earlier stage, being clinically useful for the early diagnosis of difficult-to-diagnose malignant B-cell lymphomas. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Analysis of Liquid Biopsy Performance for the Detection of Lymphoma in Dogs with a Focus on Recurrent Copy Number Variants in Matched Plasma and Lymph Node Aspirates: Implications for a Comparative Oncology Model

Introduction Liquid biopsy has shown great promise for the detection and monitoring of lymphoma in humans. Recently, similar technology has been developed and made commercially available for dogs. Because the canine and human cancer genomes share such high homology (>90%), and certain lymphoma subtypes are highly similar in terms of their biologic and molecular features between the two species, the study of lymphoma in dogs affords unique opportunities for the genomic characterization of the disease, comparative oncology studies, and the development and assessment of novel therapies. The current study describes the performance of a next-generation sequencing-based liquid biopsy assay for the detection of canine lymphoma, and in a subset of patients, analyzes concordance for prognostic copy number variants between matched plasma samples and lymph node aspirate specimens. Methods As part of a larger clinical research collection program for the CANcer Detection in Dogs (CANDiD) study (Flory, 2022), blood samples were collected following diagnosis but prior to undergoing therapy from a cohort of 116 client-owned dogs with lymphoma (63 intermediate to large B-cell, 21 intermediate to large T-cell, 6 T-zone, and 26 unphenotyped). Lymphomas with inconclusive immunophenotype or other types of indolent lymphomas were excluded. A subset of dogs analyzed for the current study also had matched cytology specimens available from lymph node fine needle aspirates (FNA). Blood samples and FNA specimens were subjected to DNA extraction, library preparation, and next-generation sequencing. Sequencing data were analyzed using an internally developed bioinformatics pipeline to detect genomic alterations associated with the presence of cancer. Specific analysis focused on FNA-plasma concordance for recurrent copy number variants that have been previously identified in canine lymphoma patients and have prognostic potential (i.e., gains in chromosomes 13 and 31 and losses in chromosome 14) (Richards, 2015; Thomas, 2003). Results The overall detection rate for lymphoma by liquid biopsy was 92.2% (107/116); with detection rates of 57% for localized/regional disease (Stages I and II) and 95% for disseminated disease (Stages III, IV, and V). By immunophenotype, the detection rate for B-cell lymphoma was 97%, T-cell 91%, T-zone 50%, and unphenotyped 92%. In the subset of lymphoma-diagnosed dogs with matched plasma and FNA samples, the majority of cases had at least one of the prognostic copy number alterations previously reported in canine lymphoma patients (13G, 14L, 31G), demonstrating the potential of liquid biopsy to noninvasively detect clinically important biomarkers. A variety of genomic alterations were identified in patients with positive liquid biopsy results, including single nucleotide variants in common oncogenes and tumor suppressor genes (e.g., TP53 mutations), and copy number variants across the genome. Some of these variants are also important biomarkers in human lymphoma, in particular TP53 mutations (Chakravarty, 2017), highlighting the potential for canine liquid biopsy testing to support comparative oncology studies for the benefit of both species. Conclusion A novel next-generation sequencing-based liquid biopsy tool has demonstrated the ability to identify genomic alterations in blood samples of dogs with lymphoma, including recurrent CNVs previously described in canine lymphoma patients, and variants in genes previously described in human and canine lymphoma tissue. These findings, along with the high degree of homology between human and canine lymphomas, support the utility of liquid biopsy for the study of lymphoma in dogs as a comparative oncology model for accelerated biomarker discovery and therapeutic development in both species.

CTNI-64. FOCUSED ULTRASOUND MEDIATED BLOOD-BRAIN BARRIER PENETRANCE TO ENABLE CELL-FREE DNA (CFDNA) AS A LIQUID BIOPSY IN RECURRENT PRIMARY BRAIN TUMORS

Abstract The WHO recommends molecular characterization of CNS tumors. (Louis et al., 2021, 2016). However, many patients at diagnosis and recurrence, do not have tissue accessible for genomics. Blood-based liquid biopsy tests, provide a non-invasive means to obtain genomic data. Liquid biopsy tests are widely adopted to avoid side effects related to invasive biopsies in other solid tumors. However, for primary brain tumors, most patients have cfDNA concentrations below the Limit-of-Detection (LOD) of the tests. The primary contributor to low yield is the blood-brain barrier (BBB) which prevents free passage of tumor analytes into the circulatory system. BBB opening mediated by Focused Ultrasound (FUS) oscillation of microbubbles (MB) has led to an increase of tumor-derived circulating biomarkers in pre-clinical models and in human GBM (Zhu et al 2018, Meng et al 2021). Cordance Medical is developing a non-invasive, portable FUS platform that can enable clinic-based BBB opening treatments. The Cordance device utilizes three transducer types, a Type 1 transducer for non-invasive BBB opening localization obtains Doppler images of the Circle-of-Willis through the temporal lobe. The Doppler images align to the existing MRI using CoW as the fiducial. An array of Type 2 transducers for BBB opening to generate sufficient acoustic pressure to safely oscillate MBs to open the BBB. Finally, Type 3 transducers for safety monitoring receive echo signals from the MBs. Signals are analyzed for harmonic content which enables safety monitoring. The primary endpoint, we will be examining the Cordance platform's ability to increase the concentration of circulating biomarkers following a safe BBB opening. We will recruit patients with recurrent GBM. Patients will receive a baseline blood draw, a BBB opening treatment with the Cordance device, followed by a blood draw after the treatment. Liquid biopsy tests to be examined include the MSK ACCESS test and tumor-informed ddPCR MRD test.

Clinical utility of liquid biopsy-based companion diagnostics in the non-small-cell lung cancer treatment

Recently, technological advances in the detection and biological characterization of circulating tumor DNA (ctDNA) have enabled the implementation of liquid biopsy testing into clinical practice. Methods for analysis of liquid biopsies have rapidly evolved over the past few years and have continued to advance, thus providing details about tumor biological characteristics such as tumor progression, metastasis, tumor heterogeneity, genomic mutation profile, clonal evolution, etc. In tandem with technological advances, the implementation of liquid biopsy in routine clinical settings has proceeded. In 2016, the Food and Drug Administration (FDA) approved the first ctDNA liquid biopsy test to detect epidermal growth factor receptor (EGFR) gene mutations in patients with non-small-cell lung cancer (NSCLC) as a companion diagnostic for molecular targeted drug of EGFR-tyrosine kinase inhibitor (TKI, EGFR-TKI). More recently, multigene panel assays of liquid biopsy have been approved as companion diagnostics and have been used in routine clinical settings. The estimation of blood tumor mutation burden (bTMB) to predict the efficacy of immune checkpoint inhibitor (ICI) treatment can be one of the promising approaches to liquid biopsy. The next stage of implementation of liquid biopsy for routine clinical settings is for monitoring of ctDNA after surgical treatment to predict prognosis and to detect disease relapse earlier than conventional imaging diagnosis. Its clinical utility is under assessment in several clinical trials. This review introduces recent advances in liquid biopsy methodology, the development of biomarkers, and its clinical utility in the treatment of NSCLC patients.

WIN Symposium 2022 - Abstract Poster Presentations.

WIN Symposium 2022 - Abstract Poster Presentations.

BLOODPAC: Collaborating to chart a path towards blood-based screening for early cancer detection.

BLOODPAC: Collaborating to chart a path towards blood-based screening for early cancer detection.

Prognostic value of plasma circulating tumor DNA fraction across four common cancer types: a real-world outcomes study

Genomic analysis of circulating tumor DNA (ctDNA) is increasingly incorporated into the clinical management of patients with advanced cancer. Beyond tumor profiling, ctDNA analysis also can enable calculation of circulating tumor fraction (TF), which has previously been found to be prognostic. While most prognostic models in metastatic cancer are tumor type specific and require significant patient-level data, quantification of TF in ctDNA has the potential to serve as a pragmatic, tumor-agnostic prognostic tool. This study utilized a cohort of patients in a nationwide de-identified clinico-genomic database with metastatic castration-resistant prostate cancer (mCRPC), metastatic breast cancer (mBC), advanced non-small-cell lung cancer (aNSCLC), or metastatic colorectal cancer (mCRC) undergoing liquid biopsy testing as part of routine care. TF was calculated based on single-nucleotide polymorphism aneuploidy across the genome. Clinical, disease, laboratory, and treatment data were captured from the electronic health record. Overall survival (OS) was evaluated by TF level while controlling for relevant covariables. A total of 1725 patients were included: 198 mCRPC, 402 mBC, 902 aNSCLC, and 223 mCRC. TF ≥10% was highly correlated with OS in univariable analyses for all cancer types: mCRPC [hazard ratio (HR) 3.3, 95% confidence interval (CI) 2.04-5.34, P < 0.001], mBC (HR 2.4, 95% CI 1.71-3.37, P < 0.001), aNSCLC (HR 1.68, 95% CI 1.34-2.1, P < 0.001), and mCRC (HR 2.11, 95% CI 1.39-3.2, P < 0.001). Multivariable assessments of TF had similar point estimates and CIs, suggesting a consistent and independent association with survival. Exploratory analysis showed that TF remained consistently prognostic across a wide range of cutpoints. Plasma ctDNA TF is a pragmatic, independent prognostic biomarker across four advanced cancers with potential to guide clinical conversations around expected treatment outcomes. With further prospective validation, ctDNA TF could be incorporated into care paradigms to enable precision escalation and de-escalation of cancer therapy based on patient-level tumor biology.

Real-world utilization of liquid biopsy for epidermal growth factor receptor (EGFR) testing in patients with metastatic non-small cell lung cancer (mNSCLC).

402 Background: Tissue biopsy (TB) testing is the standard of care to guide the selection of targeted therapy in EGFRm patients with mNSCLC. However, liquid biopsy (LB) tests are increasingly important in assessing tumor genomics at mNSCLC diagnosis. This study assessed real-world utilization of LB for EGFR testing in 1L setting and its influence on 1L treatment decisions in mNSCLC patients. Methods: Adults newly diagnosed with mNSCLC from January 1, 2019 to May 31, 2021 and treated with 1L were identified from the Flatiron EMR database. LB utilization and patterns (either used alone or in combination with TB) were evaluated. “Concurrent” (TB &amp; LB) testing was defined as patients with both test order dates prior to result dates for either test, while “sequential” (TB &amp; LB) testing was defined as patients having one test’s result date before the other test’s order date. As patients could have multiple biomarker tests, the first two EGFR tests following diagnosis were evaluated. Results: Of 5,036 patients that met the study criteria, 89.2% (N = 4,494) had EGFR testing following diagnosis. Among those tested for EGFRm, 63.7% (N = 2,864) had TB only, while 36.3% (N = 1,630) had LB (LB only: 37.9%; concurrent: 36.1%; sequential: 26.0%). Around 90% of patients with LB had NGS testing (87.7% received LB testing within 90 days of diagnosis). Among patients who initiated 1L after EGFR testing, the median (IQR) time in days from testing to 1L initiation varied by testing patterns: LB only: 18 (12-30); concurrent: 29 (22-39); sequential: 28 (18-41). Disagreement in test results was 10.6% for patients who had conclusive test results for both TB and LB tests. Among concurrent EGFRm patients (N = 130), 21.5% initiated 1L after receiving LB results (and before TB results) and 60.0% after receiving both test results. Among patients with sequential LB followed by TB (N = 10), 80.0% of them initiated 1L after receiving LB results and before TB results (Table). Conclusions: In this real-world study among mNSCLC patients in a 1L setting, more than one-third used LB for EGFR testing, either alone or in combination with TB. Among LB patients, majority had NGS testing.[Table: see text]

Development and Analytical Validation of a 6-Plex Reverse Transcription Droplet Digital PCR Assay for the Absolute Quantification of Prostate Cancer Biomarkers in Circulating Tumor Cells of Patients with Metastatic Castration-Resistant Prostate Cancer.

Gene expression in circulating tumor cells (CTCs) can be used as a predictive liquid biopsy test in metastatic castration-resistant prostate cancer (mCRPC). We developed a novel 6-plex reverse transcription droplet digital PCR (RT-ddPCR) assay for the absolute quantification of 4 prostate cancer biomarkers, a reference gene, and a synthetic DNA external control (DNA-EC) in CTCs isolated from mCRPC patients. A novel 6-plex RT-ddPCR assay was developed for the simultaneous absolute quantification of AR-FL, AR-V7, PSA, and PSMA, HPRT (used as a reference gene), and a synthetic DNA-EC that was included for quality control. The assay was optimized and analytically validated using DNA synthetic standards for each transcript as positive controls. Epithelial cellular adhesion molecule (EpCAM)-positive CTC fractions isolated from 90 mCRPC patients and 11 healthy male donors were analyzed, and results were directly compared with reverse transcription quantitative PCR (RT-qPCR) for all markers in all samples. Linear dynamic range, limit of detection, limit of quantification, intra- and interassay precision, and analytical specificity were determined for each marker. Application of the assay in EpCAM-positive CTC showed positivity for AR-FL (71/90; 78.9%), AR-V7 (28/90; 31.1%), PSA (41/90; 45.6%), PSMA (38/90; 42.2%), and HPRT (90/90; 100%); DNA-EC concentration was constant across all samples. Direct comparison with RT-qPCR for the same markers in the same samples revealed RT-ddPCR to have superior diagnostic sensitivity. Our 6-plex RT-ddPCR assay was highly sensitive, specific, and reproducible, and enabled simultaneous and absolute quantification of 5 gene transcripts in minute amounts of CTC-derived cDNA. Application of this assay in clinical samples gave diagnostic sensitivity and specificity comparable to, or better than, RT-qPCR.

340P Prediction of relapse in colon cancer patients by machine learning models combining radiomics and deep features extracted from baseline computed tomography

Up to 40% of localized colon cancer (CC) patients relapse despite optimal initial treatment. Circulating tumor DNA has emerged as a new prognostic biomarker in this setting. However, liquid biopsy tests provide a limited accuracy in the early prediction of relapse. On this basis, radiomics and artificial intelligence (AI) are posed to provide relevant insights in the prediction of relapse and patient outcome. Here we propose a predictive model of CC recurrence using clinical data in combination with radiomics and deep features extracted from baseline computed tomography (CT) images. A single-center retrospective observational study was designed. Real-world clinical data and CT examinations were collected from 2015 to 2017. Manual segmentation of the tumor was performed slice by slice by a radiologist with 10+ years of experience in CC using ITK-SNAP. Feature extraction techniques were applied to the tumor voxels through an analysis pipeline in Python adapted from Quibim Precision® software (Quibim, Valencia, ES). Feature reduction techniques were applied to select the characteristics providing independent information. The types of features extracted were: Radiomics, Deep features and fractal dimension. Several classifiers were trained with the clinical and image features as the input, to predict relapse from CC. Relapse and non-relapse classes were balanced to the number of slices containing tumor. Train-validation data ratio was 70:30. Baseline CT exams from 60 localized CC patients were included. 48% and 20% of them had stage III and high-risk stage II, respectively. The remaining patients were diagnosed with low-risk CC. 36.7% of patients relapsed. Merging the clinical data with the radiomics, fractal and deep features provided a high and increased accuracy 95% (CI 95%: 85 – 100) when compared to clinical variables alone (55%, CI 95%: 32 – 78). Random Forest and cross validation model provided the best performance. The extraction of radiomics and deep features from CT exams in CC patients and their combination in an AI model provide promising insights towards the early prediction of relapse, leading to identify new and accurate prognostic imaging panels.

Liquid Biopsies in Colorectal Liver Metastases: Towards the Era of Precision Oncologic Surgery.

Simple SummaryLiquid biopsies are increasingly gaining attention in the field of cancer therapeutics and, in particular, in the field of oncologic surgery. Liquid biopsy testing could help improve prognostication, detect recurrences early and monitor tumor evolution in the context of cancer therapies. This review aimed to provide an overview of liquid biopsies and focused on their utility among patients with CRLM.Tumor mutational analysis has been incorporated into the management of patients with CRLM since it can provide valuable prognostic information as well as guide peri-operative systemic treatment. Unlike tumor biopsy, liquid biopsy has emerged as a promising, non-invasive alternative that can detect cell-derived markers from a variety of body fluids and might better characterize all subclones present at a specific time point and allow sequential monitoring of disease evolution. Although not currently considered standard of care, an increasing number of cancer centers are nowadays routinely using liquid biopsies in the treatment of CRLM patients with promising results. The current review provides an overview of liquid biopsies in cancer therapeutics and focuses on the application of this relatively new approach on patients with CRLM.

The Prognostic Value of Liquid Biopsies for Benefit of Salvage Radiotherapy in Relapsed Oligometastatic Prostate Cancer.

Simple SummaryAround 30% of patients with oligometastatic prostate cancer relapse will benefit from local PET/CT-guided ablative radiotherapy (RT) with improved progression-free and ADT (Androgene Deprivation Therapy)-free survivals. Therefore, there is an urgent need for predictive testing for therapeutic benefits prior to initiation. Various tests have already been established on tumor specimens for the prediction of prostate cancer’s behavior or therapy outcome. However, in imaging-proven relapse tumor tissue from the local recurrence or metastases is often not available. Hence, there is a need for a liquid biopsy-based testing. We aimed to assess the prognostic value of CTCs- associated mRNA and blood-derived RNA for the benefit of PSMA PET-guided salvage RT in oligometastatic prostate cancer relapses. Significant correlations were found between the relative transcript levels of several investigated genes and clinicopathological parameters. Furthermore, distinct “transcriptional signatures” were found in patients with temporary and long-term benefits from RT.To assess the prognostic value of “liquid biopsies” for the benefit of salvage RT in oligometastatic prostate cancer relapse, we enrolled 44 patients in the study between the years 2016 and 2020. All the patients were diagnosed as having an oligometastatic prostate cancer relapse on prostate-specific membrane antigen (PSMA)-targeted PET-CT and underwent irradiation at the Department of Radiotherapy at the Hannover Medical School. Tumor cells and total RNA, enriched from the liquid biopsies of patients, were processed for the subsequent quantification analysis of relative transcript levels in real-time PCR. In total, 54 gene transcripts known or suggested to be associated with prostate cancer or treatment outcome were prioritized for analysis. We found significant correlations between the relative transcript levels of several investigated genes and the Gleason score, PSA (prostate-specific antigen) value, or UICC stage (tumor node metastasis -TNM classification of malignant tumors from Union for International Cancer Control). Furthermore, a significant association of MTCO2, FOXM1, SREBF1, HOXB7, FDXR, and MTRNR transcript profiles was found with a temporary and/or long-term benefit from RT. Further studies on larger patients cohorts are necessary to prove our preliminary findings for establishing liquid biopsy tests as a predictive examination method prior to salvage RT.

Complementary Roles for Tissue- and Blood-Based Comprehensive Genomic Profiling for Detection of Actionable Driver Alterations in Advanced NSCLC

IntroductionWhereas tumor biopsy is the reference standard for genomic profiling of advanced NSCLC, there are now multiple assays approved by the Food and Drug Administration for liquid biopsy testing of circulating tumor DNA. Here, we study the incremental value that liquid biopsy comprehensive genomic profiling (CGP) adds to tissue molecular testing. MethodsPatients with metastatic NSCLC were enrolled in a prospective diagnostic study to receive circulating tumor DNA CGP; tissue CGP was optional in addition to their standard tissue testing. Focusing on nine genes listed per the National Comprehensive Cancer Network (NCCN) guidelines, liquid CGP was compared with available tissue testing results across three subcohorts: tissue CGP, standard-of-care testing of up to five biomarkers, or no tissue testing. ResultsA total of 515 patients with advanced nonsquamous NSCLC received liquid CGP. Among 131 with tissue CGP results, NCCN biomarkers were detected in 86 (66%) with tissue CGP and 56 (43%) with liquid CGP (p < 0.001). Adding liquid CGP to tissue CGP detected no additional patients with NCCN biomarkers, whereas tissue CGP detected NCCN biomarkers in 30 patients (23%) missed by liquid CGP. Studying 264 patients receiving tissue testing of up to five genes, 102 (39%) had NCCN biomarkers detected in tissue, with an additional 48 (18%) detected using liquid CGP, including 18 with RET, MET, or ERBB2 drivers not studied in tissue. ConclusionsFor the detection of patients with advanced nonsquamous NSCLC harboring 9 NCCN biomarkers, liquid CGP increases detection in patients with limited tissue results, but does not increase detection in patients with tissue CGP results available. In contrast, tissue CGP can add meaningfully to liquid CGP for detection of NCCN biomarkers and should be considered as a follow-up when an oncogenic driver is not identified by liquid biopsy.

Partial advances in the diagnosis and treatment of gastrointestinal cancer.

Partial advances in the diagnosis and treatment of gastrointestinal cancer.

Extracellular vesicles expressing CEACAM proteins in the urine of bladder cancer patients.

Early detection and long‐term monitoring are important for urothelial carcinoma of the bladder (UCB). Urine cytology and existing markers have insufficient diagnostic performance. Here, we examined medium‐sized extracellular vesicles (EVs) in urine to identify specific markers for UCB and evaluated their usefulness as diagnostic material. To identify specific markers in urinary EVs derived from UCB, we undertook shotgun proteomics using urine from four UCB patients and four healthy subjects. Next, 29 healthy specimens, 18 noncancer specimens, and 33 UCB specimens, all from men, were analyzed for urinary EVs by flow cytometry to evaluate the diagnostic performance of UCB‐specific EVs. Nanoparticle‐tracking analysis indicated that the size of EVs extracted from urine was mostly <400 nm. By shotgun proteomics, we detected several proteins characteristic of UCB and found that carcinoembryonic antigen‐related adhesion molecule (CEACAM) proteins were increased in patients. Flow cytometric analysis revealed that the degree of expression of CEACAM1, CEACAM5, and CEACAM6 proteins on the surface of EVs varied among patients. Extracellular vesicles expressing CEACAM proteins also expressed mucin 1, suggesting that they were derived from tumorigenic uroepithelial cells. The number of EVs expressing CEACAM1, 5, and 6 proteins was significantly increased in UCB (mean ± SD, 8.6 ± 13%) compared to non‐UCB (0.69 ± 0.46) and healthy (0.46 ± 0.34) by flow cytometry. The results of receiver operating characteristic (ROC) analysis showed a good score of area under the ROC curve of 0.907. We identified EVs that specifically express CEACAM proteins in urine and have potential for diagnostic applications. These EVs are potential targets in a new liquid biopsy test for UCB patients.

Integrating chromatin accessibility states in the design of targeted sequencing panels for liquid biopsy

Dying tumor cells shed DNA fragments into the circulation that are known as circulating tumor DNA (ctDNA). Liquid biopsy tests aim to detect cancer using known markers, including genetic alterations and epigenetic profiles of ctDNA. Despite various advantages, the major limitation remains the low fraction of tumor-originating DNA fragments in a high background of normal blood-cell originating fragments in the cell-free DNA (cfDNA) pool in plasma. Deep targeted sequencing of cfDNA allows for enrichment of fragments in known cancer marker-associated regions of the genome, thus increasing the chances of detecting the low fraction variant harboring fragments. Most targeted sequencing panels are designed to include known recurrent mutations or methylation markers of cancer. Here, we propose the integration of cancer-specific chromatin accessibility states into panel designs for liquid biopsy. Using machine learning approaches, we first identify accessible and inaccessible chromatin regions specific to each major human cancer type. We then introduce a score that quantifies local chromatin accessibility in tumor relative to blood cells and show that this metric can be useful for prioritizing marker regions with higher chances of being detected in cfDNA for inclusion in future panel designs.

Abstract 689: A randomized phase III study assessing the efficacy of liquid biopsy in early diagnosis of recurrence and second malignancies in lung cancer survivors

Abstract We designed a 6,000-patient prospective, multi-institutional randomized clinical trial to assess the efficacy of liquid biopsy in early diagnosis of recurrence and second malignancies in lung cancer survivors. To ensure over 25% of participants are of disadvantaged or minority status, we have recruited multiple community hospitals (Jamaica, Flushing, Wyckoff, and Staten Island/Bronx satellites of Northwell hospitals) to the study in partnership with Memorial Sloan Kettering Cancer Center. Patients included in this study are survivors of non-metastatic non-small cell lung cancer, status-post definitive treatment (surgery or radiation) with no evidence of disease for at least one year. These patients may be on maintenance therapy for their prior lung cancer but may not have any other active malignancy at the time of enrollment. Participants will be randomized 1:1 to standard surveillance at the discretion of the treating physician or standard surveillance plus six-monthly methylation-based liquid biopsy tests over a two-year study period, and strict guidelines on follow-up of positive liquid biopsy testing will be provided to reduce harms from false positives or overdiagnosis. The primary endpoint of this study is the incidence of late stage cancer (distant recurrence or new primary cancer of stage III/IV). Secondary endpoints include incidence of early cancers (locoregional recurrence or new primary cancer of stage I/II), metastasis-free survival, and utilization of liquid biopsy versus standard of care scans. We will stratify our results by minority and socioeconomic status to specifically ascertain the effect of this intervention on populations of need. This is the first randomized controlled trial of liquid biopsy in a survivor population and the first trial utilizing liquid biopsy in a large minority population. We will have preliminary experiences to report in April 2022. Citation Format: Sana Raoof. A randomized phase III study assessing the efficacy of liquid biopsy in early diagnosis of recurrence and second malignancies in lung cancer survivors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 689.