Integrating cfDNA liquid biopsy and organoid-based drug screening reveals PI3K signaling as a promising therapeutic target in colorectal cancer.

BACKGROUND: The current precision medicine relies on biomarkers, which are mainly obtained through next-generation sequencing (NGS). However, this model failed to find effective drugs for most cancer patients. This study tried to combine liquid biopsy with functional drug tests using organoid models to find potential drugs for cancer patients. METHODS: Colorectal cancer (CRC) patients were prospectively enrolled and blood samples were collected from patients before the start of treatment. Targeted deep sequencing of cfDNA samples was performed using a 14-gene panel. Gastrointestinal (GI) cancer organoids were established and PI3K and mTOR inhibitors were evaluated on organoid models. RESULTS: A total of 195 mutations were detected across 58 cfDNA samples. The most frequently mutated genes were KRAS, TP53, PIK3CA, and BRAF, all of which exhibited higher mutation rates than tissue biopsy. Although 81% of variants had an allele frequency of less than 1%, certain mutations in KRAS, TP53, and SMAD4 had high allele frequencies exceeding 10%. Notably, among the seven patients with high allele frequency mutations, six had metastatic tumors, indicating that a high allele frequency of ctDNA could potentially serve as a biomarker of later-stage cancer. A high rate of PIK3CA mutation (31 out of 67, or 46.3%) was discovered in CRC patients, suggesting possible tumor progression mechanisms and targeted therapy opportunities. To evaluate the value of anti PI3K strategy in GI cancer, different lines of GI cancer organoids were established. The organoids recapitulated the morphologies of the original tumors. Organoids were generally insensitive to PI3K inhibitors. However, CRC-3 and GC-4 showed response to mTOR inhibitor Everolimus, and GC-3 was sensitive to PI3Kδ inhibitor Idelalisib. The CRC organoid with a PIK3CA mutation showed greater sensitivity to the PI3K inhibitor Alpelisib than wildtype organoids, suggesting potential treatment options for the corresponding patients. CONCLUSION: Liquid biopsy holds significant promise for improving precision treatment and tumor prognosis in colorectal cancer patients. The combination of biomarker-based drug prediction with organoid-based functional drug sensitivity assay may lead to more effective cancer treatment.

Liquid Biopsy of Lung Cancer Before Pathological Diagnosis Is Associated With Shorter Time to Treatment.

PURPOSE: Studies have investigated the early use of liquid biopsy (LBx) during the diagnostic workup of patients presenting with clinical evidence of advanced lung cancer, but real-world adoption and impact has not been characterized. The aim of this study was to determine whether the use of LBx before diagnosis (Dx; LBx-Dx) enables timely comprehensive genomic profiling (CGP) and shortens time until treatment initiation for advanced non-small-cell lung cancer (aNSCLC). MATERIALS AND METHODS: This study used the Flatiron Health-Foundation Medicine electronic health record-derived deidentified clinicogenomic database of patients with aNSCLC from approximately 280 US cancer clinics. RESULTS: Of 1,076 patients with LBx CGP ordered within 30 days prediagnosis/postdiagnosis, we focused on 56 (5.2%) patients who ordered LBx before diagnosis date (median 8 days between order and diagnosis, range, 1-28). Compared with 1,020 patients who ordered LBx after diagnosis (Dx-LBx), LBx-Dx patients had similar stage and ctDNA tumor fraction (TF). LBx-Dx patients received CGP results a median of 1 day after Dx versus 25 days for Dx-LBx patients. Forty-three percent of LBx-Dx were positive for an National Comprehensive Cancer Network driver, and 32% had ctDNA TF >1% but were driver negative (presumed true negatives). In 748 patients with previously untreated aNSCLC, median time from Dx to therapy was shorter in the LBx-Dx versus Dx-LBx group (21 v 35 days; P < .001). CONCLUSION: Early LBx in anticipation of pathologic diagnosis of aNSCLC was uncommon in this real-world cohort, yet this emerging paradigm was associated with an abbreviated time to CGP results and faster therapy initiation. Forthcoming prospective studies will clarify the utility of LBx in parallel with biopsy for diagnostic confirmation for patients presenting with suspected advanced lung cancer.

Tumor Fraction Correlates With Detection of Actionable Variants Across > 23,000 Circulating Tumor DNA Samples.

PURPOSE: Profiling of circulating tumor DNA (ctDNA) is increasingly adopted in the management of solid tumors, concurrent with increased availability of more comprehensive ctDNA panels. However, variable ctDNA shed can result in variable assay sensitivity. We studied the relationship between ctDNA tumor fraction (TF) and detection of actionable alterations across cancer types. METHODS: A total of 23,482 liquid biopsies (LBx) submitted between September 2020 and October 2021 were sequenced using a hybrid capture panel that reports genomic alterations (GAs) and genomic biomarkers across 324 cancer-related genes. The primary end points were the prevalence of targetable GAs by cancer type and detection in relationship to ctDNA TF. Sensitivity of detection in LBx was assessed in 1,289 patients with available tissue results. RESULTS: 94% (n = 22,130) of LBx had detectable ctDNA, with a median TF of 2.2%. LBx profiling detected GAs in National Comprehensive Cancer Network category 1 genes in 37% of lung, 30% of prostate, 36% of breast, and 51% of colon cancer cases. Potential germline GAs flagged on clinical reports were detected in genes including BRCA1/2, PALB2, CHEK2, and ATM. Polyclonal mutations in genes associated with resistance such as AR, ESR1, RB1, and NF1 were detected. The sensitivity of LBx to detect driver alterations identified in tissue biopsy from the same patient ranged from 58% to 86% but was consistently at or near 100% in cases with TF ≥ 10%. CONCLUSION: Elevated ctDNA shed is associated with both high sensitivity and negative predictive value for detection of actionable GAs. The presence of elevated TF suggests adequate tumor profiling and may reduce the value of subsequent reflex to confirmatory tissue testing in patients with negative LBx results.

DEEP Surveillance of Brain Cancer Using Self-Functionalized 3D Nanoprobes for Noninvasive Liquid Biopsy.

Brain cancers, one of the most fatal malignancies, require accurate diagnosis for guided therapeutic intervention. However, conventional methods for brain cancer prognosis (imaging and tissue biopsy) face challenges due to the complex nature and inaccessible anatomy of the brain. Therefore, deep analysis of brain cancer is necessary to (i) detect the presence of a malignant tumor, (ii) identify primary or secondary origin, and (iii) find where the tumor is housed. In order to provide a diagnostic technique with such exhaustive information here, we attempted a liquid biopsy-based deep surveillance of brain cancer using a very minimal amount of blood serum (5 µL) in real time. We hypothesize that holistic analysis of serum can act as a reliable source for deep brain cancer surveillance. To identify minute amounts of tumor-derived material in circulation, we synthesized an ultrasensitive 3D nanosensor, adopted SERS as a diagnostic methodology, and undertook a DEEP neural network-based brain cancer surveillance. Detection of primary and secondary tumor achieved 100% accuracy. Prediction of intracranial tumor location achieved 96% accuracy. This modality of using patient sera for deep surveillance is a promising noninvasive liquid biopsy tool with the potential to complement current brain cancer diagnostic methodologies.

Détection de la mutation T790M de l'exon 20 du gène EGFR dans le cancer du poumon résistant aux inhibiteurs de l'EGFR sur ADN tumoral circulant (biopsie liquide) / Circulating tumour DNA (liquid biopsy)-based EGFR exon 20 T790M mutation detection in advanced non-small cell lung cancer after previous EGFR-directed therapy

DEMANDEUR: Institut universitaire de cardiologie et de pneumologie de Québec Université Laval. OBJECTIF DE L'ANALYSE: L'analyse proposée vise à effectuer la détection de la mutation T790M du gène EGFR (EGFR-T790M) responsable de la résistance aux inhibiteurs de tyrosine kinase (ITK) à partir de l'ADN tumoral circulant d'un patient atteint d'un cancer du poumon non à petites cellules (CPNPC). CONTEXTE DE LA DEMANDE: Approximativement 60 % des patients atteints d'un CPNPC et traités avec un ITK de 1re ou de 2e génération vont développer la mutation de résistance EGFR-T790M et avoir besoin d'un changement thérapeutique. Bien qu'une analyse permettant notamment de détecter cette mutation à partir d'une biopsie tissulaire soit consignée dans le Répertoire québécois et système de mesure des procédures de biologie médicale (ci-après nommé « Répertoire ¼), la présente demande vise à détecter la mutation EGFR-T790M à partir d'échantillons de biopsie liquide, une autre méthode de prélèvement qui permet au patient d'éviter la biopsie tissulaire, les risques qui y sont associés et d'obtenir un changement thérapeutique plus rapidement. NOMBRE D'ANALYSES PRÉVUES: Le demandeur avait originalement prévu que, annuellement, entre 160 et 250 tests seraient nécessaires pour servir la population locale et 2 000 pour l'ensemble du Québec. Or, l'inscription de l'osimertinib en 1re intention de traitement des CPNPC avec mutations activatrices de l'EGFR entraîne une réduction importante du nombre de patients dont l'état nécessitera éventuellement une détection de la mutation EGFRT790M par biopsie liquide selon l'utilisation prévue par le demandeur. Les données de la RAMQ ont révélé que quelques patients continuent de recevoir des ITK de 1re et de 2e génération et sont susceptibles de tirer avantage de cette analyse. MÉTHODOLOGIE: La démarche d'évaluation comprend une revue rapide de la littérature scientifique et grise de même que des consultations menées auprès d'experts et d'autres parties prenantes. Un rapport d'évaluation portant sur la pertinence de recourir à la biopsie liquide dans le même contexte que la présente demande a été publié par Health Quality Ontario (HQO) en mars 2020. Ce rapport comporte une évaluation de la performance diagnostique, de l'utilité clinique, de la sécurité, de l'efficience et de l'impact budgétaire de même qu'une analyse des préférences et des valeurs selon la perspective du patient. Le rapport de HQO a été jugé de bonne qualité méthodologique et constitue la principale source de données de la présente évaluation. L'ensemble des données scientifiques, contextuelles et expérientielles a été interprété et apprécié à l'aide d'une grille-synthèse pour guider le processus de délibération du Comité scientifique des analyses de biologie médicale (CSABM). DONNÉES PUBLIÉES: Performance diagnostique: Selon le rapport d'évaluation de Health Quality Ontario publié en 2020, la concordance des résultats d'une détection de la mutation EGFRT790M entre la biopsie liquide et la biopsie tissulaire varierait de 50 % à 96 %. La sensibilité et la spécificité, la valeur prédictive négative (VPN) et la valeur prédictive positive (VPP) sont respectivement de 68 % [46 % - 88 %], 86 % [62 % - 99 %], 61 % et 89 %. L'utilisation de la droplet digital PCR (ddPCR) augmenterait la fréquence de détection positive de la mutation EGFR-T790M par biopsie liquide. Utilité clinique: HQO n'a repéré aucune donnée sur l'utilisation de la biopsie liquide comme méthode de triage (biopsie liquide + biopsie tissulaire) comparativement à la biopsie tissulaire seule. Toutefois, les études consultées soulignent qu'une fraction des porteurs de la mutation EGFR-T790M (17,8 %) sont identifiés grâce à l'utilisation de la biopsie liquide pour trier les patients résistants aux inhibiteurs des ITK de 1re et 2e génération et pour lesquels la biopsie tissulaire est évitée. En cas de détection de la mutation EGFR-T790M, l'impact sur la prise en charge demeurerait le même quelle que soit la méthode employée car, lorsque la biopsie est positive, le traitement est amorcé. Un gain de survie sans progression de 9,7 mois a été rapporté pour ces deux méthodes. PERSPECTIVE DES PATIENTS: Selon le rapport de HQO, les patients percevraient la biopsie liquide comme une approche plus rapide et plus pratique du fait qu'ils n'auraient pas à attendre plusieurs semaines pour obtenir un rendezvous pour subir une biopsie tissulaire qui pourrait nécessiter un déplacement vers un centre spécialisé plus éloigné. Ils auraient aussi exprimé de la peur et même de la panique relativement au processus de prélèvement de l'échantillon tissulaire qui nécessite une aiguille de gros calibre. POSITIONS ET ORIENTATIONS D'ORGANISMES D'INTÉRÊ: Le National Comprehensive Cancer Network (NCCN) et plusieurs comités d'experts ont recommandé l'utilisation de la biopsie liquide chez un patient qui est médicalement incapable de supporter l'échantillonnage effractif que requiert la biopsie tissulaire. L'ensemble des sociétés savantes recommandent l'utilisation de la biopsie tissulaire lorsque le résultat de la biopsie liquide est négatif. Toutefois, ils soulignent que la biopsie liquide ne devrait pas remplacer la biopsie tissulaire. En revanche, un résultat positif de la biopsie liquide devrait obtenir la même attention qu'un résultat positif de la biopsie tissulaire. ÉVALUATION ÉCONOMIQUE: La biopsie liquide comme méthode de triage est moins coûteuse et plus efficace que la biopsie tissulaire pour détecter la mutation EGFRT790M. Toutefois, lorsqu'on tient compte des avantages cliniques et des coûts liés à l'usage des traitements subséquents, le ratio coûtutilité incrémental est élevé, en raison notamment de l'inefficience de l'osimertinib. Depuis l'inscription aux listes des médicaments de l'osimertinib comme traitement de 1re intention, la population admissible à une biopsie liquide décroît continuellement. Le nombre actuel de personnes qui recevraient des ITK de 1re et 2e génération a été estimé à 32 selon les données de la RAMQ et à 40 en incluant les patients couverts par une assurance privée. Ces analyses estiment les économies de laboratoire à 460 $, mais elles anticipent que 5 patients supplémentaires pourraient recevoir l'osimertinib pour un impact budgétaire net d'environ 537 000 $ au cours des trois prochaines années. POSITION DES EXPERTS CONSULTÉS: Les experts consultés sont favorables à l'utilisation de la biopsie liquide dans le contexte décrit par le demandeur. Ils n'ont pas soulevé d'enjeu en particulier en dehors de la pertinence restreinte de cette analyse étant donné l'inscription récente du traitement osimertinib en 1re intention. L'émergence rapide de nombreuses indications de la biopsie liquide serait imminente et constituerait une révolution technologique et oncologique. ENJEUX PARTICULIERS: Au Québec, l'analyse est principalement employée en contexte de recherche. Des enjeux éthiques et cliniques liés à la biopsie liquide tels que la présence de faux négatifs en raison d'une sensibilité plus faible et la nécessité d'évaluer la survie globale des patients atteints de CPNPC en appliquant cette technique ont également été rapportés dans la littérature. RECOMMANDATION: Suivant une délibération par les membres du CSABM sur l'ensemble de la preuve, y compris la perspective des experts consultés, l'INESSS recommande d'introduire la détection de la mutation EGFR-T790M sur ADN tumoral circulant au Répertoire.

REQUESTER: Institut universitaire de cardiologie et de pneumologie de QuébecUniversité Laval. PURPOSE OF TEST: The test is designed to detect the EGFR gene T790M mutation (EGFRT790M), which is responsible for resistance to tyrosine kinase inhibitors (TKIs), in circulating tumour DNA in non-small cell lung cancer (NSCLC) patients. BACKGROUND TO THE REQUEST: Approximately 60% of NSCLC patients treated with a 1st- or 2ndgeneration TKI will develop the EGFR-T790M resistance mutation and require a change in therapy. Although a test used to detect this mutation from a tissue biopsy is listed in the Répertoire québécois et système de mesure des procédures de biologie médicale (hereinafter the "Répertoire"), the present request concerns the detection of the EGFRT790M mutation in samples obtained by liquid biopsy, an alternative specimen collection method that enables the patient to avoid a tissue biopsy and the associated risks, and to obtain a change in therapy more quickly. EXPECTED NUMBER OF TESTS: The requester had originally anticipated that between 160 and 250 tests would be required annually to serve the local population and 2000 for all of Québec. However, the listing of osimertinib as a 1st-line therapy for NSCLC with EGFR-activating mutations is resulting in a significant reduction in the number of patients who will possibly require EGFRT790M mutation testing by liquid biopsy, based on the use anticipated by the requester. RAMQ data show that a few patients continue to receive 1st- or 2nd-generation TKIs and are likely to benefit from this test. METHODOLOGY: The assessment process included a rapid review of the scientific and grey literature, and consultations with experts and other stakeholders. An assessment report on the relevance of using liquid biopsy in the same context as this request was published by Health Quality Ontario (HQO) in March 2020. The report includes an assessment of its diagnostic performance, clinical utility, safety, cost-effectiveness and budget impact, and an assessment of patient preferences and values. The HQO report was deemed to be of good methodological quality and is the main source of data for the present assessment. All the scientific, contextual and experiential data were interpreted and assessed using a synthesis grid to guide the Comité scientifique des analyses de biologie médicale (CSABM)'s deliberation process. PUBLISHED DATA: Diagnostic performance: According to the Health Quality Ontario assessment report published in 2020, the concordance rate for EGFR-T790M mutation detection results between liquid biopsy and tissue biopsy ranges from 50% to 96%. The sensitivity and specificity, negative predictive value (NPV) and positive predictive value (PPV) are 68% [46%-88%], 86% [62%-99%], 61% and 89%, respectively. The use of droplet digital PCR (ddPCR) appears to increase the rate of positive detection of the EGFR-T790M mutation by liquid biopsy. Clinical utility: HQO did not find any data on the use of liquid biopsy as a triage test (liquid biopsy + tissue biopsy) versus tissue biopsy alone. However, the studies examined note that a proportion of EGFR-T790M mutation carriers (17.8%) are identified through the use of liquid biopsy to detect 1st- or 2nd-generation TKI-resistant patients, who thus avoid a tissue biopsy. If the EGFR-T790M mutation is detected, the impact on management would remain the same, regardless of the method used, because when the biopsy is positive, treatment is initiated. A 9.7-month gain in progression-free survival was reported for both methods. PATIENT PERSPECTIVE: According to the HQO report, patients perceived liquid biopsy as a faster and more convenient approach because they would not have to wait several weeks to get an appointment for a tissue biopsy, which could require a trip to a specialized centre that might be further away. They also expressed fear and even panic about the tissue sample collection procedure, in which a large-gauge needle is used. POSITIONS AND PERSPECTIVES OF ORGANIZATIONS OF INTEREST: The National Comprehensive Cancer Network (NCCN) and a number of expert panels have recommended the use of liquid biopsy in patients who are medically unable to tolerate the invasive specimen collection involved in a tissue biopsy. All the learned societies recommend the use of tissue biopsy when the liquid biopsy result is negative. However, they stress that liquid biopsy should not replace tissue biopsy. In any event, a positive liquid biopsy result should be given the same attention as a positive tissue biopsy result. ECONOMIC EVALUATION: Liquid biopsy as a triage test is less expensive and more effective than tissue biopsy in detecting the EGFR-T790M mutation. However, when the clinical benefits and costs of the subsequent treatments are factored. in, the incremental cost-utility ratio is high, in part because of osimertinib's non-cost-effectiveness. Since the listing of this drug as a 1st-line therapy in the formularies, the liquid biopsy-eligible population has been steadily decreasing. The current number of people receiving 1st- or 2nd-generation TKIs was estimated to be 32, based on RAMQ data, and 40 if patients with private insurance are included. These analyses estimate the laboratory savings at $460, but they anticipate that 5 additional patients could receive osimertinib, for a net budget impact of approximately $537,000 over the next 3 years. POSITION OF THE EXPERTS CONSULTED: The experts consulted support the use of liquid biopsy in the context defined by the requester. They did not raise any specific issues, apart from the limited relevance of this test, given the recent listing of osimertinib as a 1st-line therapy. The rapid emergence of a large number of indications for liquid biopsy appears to be imminent and would constitute a technological and oncologic revolution. SPECIFIC ISSUES: In Québec, liquid biopsy is used primarily in research settings. Ethical and clinical issues associated with this test, such as false negatives due to lower sensitivity and the need to assess overall survival in NSCLC patients in whom this technique is used, have also been reported in the literature. RECOMMENDATION: Based on the deliberation, by the CSABM's members, of all the evidence, including the perspective of the experts consulted, INESSS recommends that circulating tumour DNA-based EGFR-T790M mutation detection be included in the Répertoire

Platinum-resistant ovarian cancer: From drug resistance mechanisms to liquid biopsy-based biomarkers for disease management.

Resistance to platinum-based chemotherapy is a major clinical challenge in ovarian cancer, contributing to the high mortality-to-incidence ratio. Management of the platinum-resistant disease has been difficult due to diverse underlying molecular mechanisms. Over the past several years, research has revealed several novel molecular targets that are being explored as biomarkers for treatment planning and monitoring of response. The therapeutic landscape of ovarian cancer is also rapidly evolving, and alternative therapies are becoming available for the recurrent platinum-resistant disease. This review provides a snapshot of platinum resistance mechanisms and discusses liquid-based biomarkers and their potential utility in effective management of platinum-resistant ovarian cancer.

PIVKA-II serves as a potential biomarker that complements AFP for the diagnosis of hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors of the digestive system and has high morbidity and mortality rates. It is essential to search new biomarkers to improve the accuracy of early HCC diagnosis. Therefore, we evaluated the diagnostic value of prothrombin induced by vitamin K deficiency or antagonist- II (PIVKA-II) as a potential biomarker that complements α-fetoprotein (AFP) in HCC by detecting the serum PIVKA-II levels. METHODS: Serum PIVKA-II levels were compared in 168 HCC patients, 150 benign liver disease patients and 153 healthy controls to investigate the PIVKA-II potential to be a HCC biomarker. Receiver operating characteristic curve (ROC) analysis was used to evaluate the value of PIVKA-II in the diagnosis of HCC and its complementary role of AFP. The correlation between serum PIVKA-II levels and clinicopathological characteristics was analyzed to study the value of PIVKA-II in assessing HCC progression and prognosis. Finally, the ability of PIVKA-II in assessing the surgical treatment effects of HCC was studied by comparing the pre- and post-operative serum PIVKA-II levels in 89 HCC patients. RESULTS: Serum PIVKA-II levels in HCC patients were significantly higher than that in patients with benign liver disease and healthy controls. The PIVKA-II performance in the diagnosing HCC as an individual biomarker was remarkable. The combined detection of PIVKA-II and AFP improved the diagnostic efficiency of HCC. PIVKA-II retained significant diagnosis capabilities for AFP-negative HCC patients. Significant correlations were found between PIVKA-II expression levels and some clinicopathological characteristics, including tumor size, tumor stage, tumor metastasis, differentiation degree and complications. PIVKA-II expression obviously decreased after surgical resection. CONCLUSIONS: PIVKA-II is a promising serum biomarker for the HCC diagnosis that can be used as a supplement for AFP. The combined diagnosis of the two markers greatly improved the diagnostic efficiency of HCC. The PIVKA-II levels in HCC patients were widely associated with clinicopathological characteristics representing tumor cell dissemination and/or poor prognosis. PIVKA-II can be used to evaluate the curative effects of HCC resection.

Exosome-based liquid biopsies in cancer: opportunities and challenges.

Liquid biopsy in cancer has gained momentum in clinical research and is experiencing a boom for a variety of applications. There are significant efforts to utilize liquid biopsies in cancer for early detection and treatment stratification, as well as residual disease and recurrence monitoring. Although most efforts have used circulating tumor cells and circulating tumor DNA for this purpose, exosomes and other extracellular vesicles have emerged as a platform with potentially broader and complementary applications. Exosomes/extracellular vesicles are small vesicles released by cells, including cancer cells, into the surrounding biofluids. These exosomes contain tumor-derived materials such as DNA, RNA, protein, lipid, sugar structures, and metabolites. In addition, exosomes carry molecules on their surface that provides clues regarding their origin, making it possible to sort vesicle types and enrich signatures from tissue-specific origins. Exosomes are part of the intercellular communication system and cancer cells frequently use them as biological messengers to benefit their growth. Since exosomes are part of the disease process, they have become of tremendous interest in biomarker research. Exosomes are remarkably stable in biofluids, such as plasma and urine, and can be isolated for clinical evaluation even in the early stages of the disease. Exosome-based biomarkers have quickly become adopted in the clinical arena and the first exosome RNA-based prostate cancer test has already helped >50 000 patients in their decision process and is now included in the National Comprehensive Cancer Network guidelines for early prostate cancer detection. This review will discuss the advantages and challenges of exosome-based liquid biopsies for tumor biomarkers and clinical implementation in the context of circulating tumor DNA and circulating tumor cells.

PI3K mutations detected in liquid biopsy are associated to reduced sensitivity to CDK4/6 inhibitors in metastatic breast cancer patients.

BACKGROUND: PI3K pathway hyperactivation due to PIK3CA mutations contributes to endocrine resistance, and PIK3CA is one of the most frequently mutated genes in breast cancer (BC), occurring approximately 40 % of HR+, HER2- advanced BC (ABC). Cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6i) have changed the treatment landscape of HR+, HER2- ABC. Putative mechanisms of resistance to CDK4/6i have been identified, but limited data are available on PI3K deregulation. The present study evaluates the impact of PIK3CA mutations on CDK4/6i plus hormone therapy and evaluates potential characteristics that may suggest for a PI3K screening in patients with ABC. METHODS: ABC patients were enrolled, and 12 mL of blood were collected in EDTA tubes at baseline prior to CDK4/6i plus hormone therapy. Plasma was separated and circulating free DNA (cfDNA) was extracted. PIK3CA mutation analysis was performed on a ddPCR. Selected and analyzed mutations included: p.C420R, p.E542 K, p.E545A, p.E545D, p.E545G, p.E545K, p.Q546E, p.Q546R, p.H1047L, p.H1047R, p.H1047Y. Statistical analysis were performed to investigate the predictive power of such mutations and any association with clinical factors. RESULTS: Thirty patients were enrolled. PIK3CA mutation status at baseline was independently associated with shorter median PFS (7.44 vs 12.9 months, p = 0.01) in subject receiving CDK4/6i plus hormone therapy. PIK3CA mutations were found to be associated to Ki67 expression in primary lesions (p = 0.006). Moreover, the probability to find a PI3K mutation improved considering also the therapeutic management in previous lines of treatment (McFadden's R2 = 0.415, p = 0.004; AUC of the ROC curve = 0.914). CONCLUSION: The findings of this pilot study suggest that the presence of a PI3K mutation in liquid biopsy correlates with a worse PFS in patients with ABC receiving CDK4/6i, and that liquid biopsy is a useful tool to suggests a better tailored pharmacological intervention.

dPCR application in liquid biopsies: divide and conquer.

Introduction: Precision medicine is already a reality in oncology, since biomarker-driven therapies have clearly improved patient survival. Furthermore, a new, minimally invasive strategy termed 'liquid biopsy' (LB) has revolutionized the field by allowing comprehensive cancer genomic profiling through the analysis of circulating tumor DNA (ctDNA). However, its detection requires extremely sensitive and efficient technologies. A powerful molecular tool based on the principle of 'divide and conquer' has emerged to solve this problem. Thus, digital PCR (dPCR) allows absolute and accurate quantification of target molecules.Areas covered: In this review we will discuss the fundamentals of dPCR and the most common approaches used for partition of samples and quantification. The advantages and limitations of dPCR will be mentioned in the context of LB in oncology.Expert opinion: In our opinion, dPCR has proven to be one of the most sensitive methods available for LB analysis, albeit some aspects such as its capacity of multiplexing and protocol standardization still require further improvements. Furthermore, the increasing sensitivities and lower costs of next generation sequencing (NGS) methods position dPCR as a confirmatory and complementary technique for NGS results which will likely prove to be very useful for treatment monitoring and assessing minimal residual disease.

10-Plex Digital Polymerase Chain Reaction with Four-Color Melting Curve Analysis for Simultaneous KRAS and BRAF Genotyping.

Digital PCR (dPCR) is a promising method for performing liquid biopsies that quantifies nucleic acids more sensitively than real-time PCR. However, dPCR shows large fluctuations in the fluorescence intensity of droplets or wells due to insufficient PCR amplification in the small partitions, limiting the multiplexing capability of using the fluorescence intensity. In this study, we propose a measurement method that combines dPCR with melting curve analysis for highly multiplexed genotyping. A sample was digitized into a silicon chip with up to 2 × 104 wells in which asymmetric PCR was performed to obtain more single-stranded amplicons that were complementary to molecular beacon probes. Fluorescence images were captured while controlling the temperature of the chip, and the melting curve was measured for each well. Then, genotyping was performed by using the fluorescence intensity, the dye color of the probe, and the melting temperature (Tm). Because the Tm of the PCR products is not highly dependent on the amplification efficiency of PCR, genotyping accuracy is improved by using Tm values, enabling highly multiplexed genotyping. The concept was confirmed by simultaneously identifying wild-type KRAS, BRAF, and eight mutants of these genes (G12D, G12R, G12V, G13D, G12A, G12C, G12S, and V600E) through four-color melting curve analysis. To the best of our knowledge, this is the first demonstration of the genotyping of 10 DNA groups including single mutations of cancer-related genes by combining dPCR with four-color melting curve analysis.

MicroRNAs As Master Regulators of Atherosclerosis: From Pathogenesis to Novel Therapeutic Options.

Significance: Cardiovascular disease (CVD) remains the major cause of morbidity and mortality worldwide. Accumulating evidence indicates that atherosclerosis and its sequelae, coronary artery disease, contribute to the majority of cardiovascular deaths. Atherosclerosis is a chronic inflammatory disease of the arteries in which atherosclerotic plaques form within the vessel wall. Epidemiological studies have identified various risk factors for atherosclerosis, such as diabetes, hyperlipidemia, smoking, genetic predisposition, and sedentary lifestyle. Recent Advances: Through the advancement of genetic manipulation techniques and their use in cardiovascular biology, it was shown that small RNAs, especially microRNAs (miRNAs), are dynamic regulators of disease pathogenesis. They are considered to be central during the regulation of gene expression through numerous mechanisms and provide a means to develop biomarkers and therapeutic tools for the diagnosis and therapy of atherosclerosis. Circulating miRNAs encapsulated within membrane-surrounded vesicles, which originate from diverse subcellular compartments, are now emerging as novel regulators of intercellular communication. The miRNAs, in both freely circulating and vesicle-bound forms, represent a valuable tool for diagnosing and monitoring CVD, recently termed as "liquid biopsy." Critical Issues: However, despite the recent advancements in miRNA-based diagnostics and therapeutics, understanding how miRNAs can regulate atherosclerosis is still crucial to achieving an effective intervention and reducing the disease burden. Future Directions: We provide a landscape of the current developmental progression of RNA therapeutics as a holistic approach for treating CVD in different animal models and clinical trials. Future interrogations are warranted for the development of miRNA-based therapeutics to overcome challenges for the treatment of the disease.

Metabolite therapy guided by liquid biopsy proteomics delays retinal neurodegeneration.

BACKGROUND: Neurodegenerative diseases are incurable disorders caused by progressive neuronal cell death. Retinitis pigmentosa (RP) is a blinding neurodegenerative disease that results in photoreceptor death and progresses to the loss of the entire retinal network. We previously found that proteomic analysis of the adjacent vitreous served as way to indirectly biopsy the retina and identify changes in the retinal proteome. METHODS: We analyzed protein expression in liquid vitreous biopsies from autosomal recessive (ar)RP patients with PDE6A mutations and arRP mice with Pde6ɑ mutations. Proteomic analysis of retina and vitreous samples identified molecular pathways affected at the onset of photoreceptor death. Based on affected molecular pathways, arRP mice were treated with a ketogenic diet or metabolites involved in fatty-acid synthesis, oxidative phosphorylation, and the tricarboxylic acid (TCA) cycle. FINDINGS: Dietary supplementation of a single metabolite, ɑ-ketoglutarate, increased docosahexaeonic acid levels, provided neuroprotection, and enhanced visual function in arRP mice. A ketogenic diet delayed photoreceptor cell loss, while vitamin B supplementation had a limited effect. Finally, desorption electrospray ionization mass spectrometry imaging (DESI-MSI) on ɑ-ketoglutarate-treated mice revealed restoration of metabolites that correlated with our proteomic findings: uridine, dihydrouridine, and thymidine (pyrimidine and purine metabolism), glutamine and glutamate (glutamine/glutamate conversion), and succinic and aconitic acid (TCA cycle). INTERPRETATION: This study demonstrates that replenishing TCA cycle metabolites via oral supplementation prolongs retinal function and provides a neuroprotective effect on the photoreceptor cells and inner retinal network. FUNDING: NIH grants [R01EY026682, R01EY024665, R01EY025225, R01EY024698, R21AG050437, P30EY026877, 5P30EY019007, R01EY018213, F30EYE027986, T32GM007337, 5P30CA013696], NSF grant CHE-1734082.

Therapeutic management of neuro-oncologic patients - potential relevance of CSF liquid biopsy.

Background: In the era of precision medicine, cancer treatment is increasingly tailored according to tumor-specific genomic alterations. The analysis of tumor-derived circulating nucleic acids in cerebrospinal fluid (CSF) by next generation sequencing (NGS) may facilitate precision medicine in the field of CNS cancer. We therefore evaluated whether NGS from CSF of neuro-oncologic patients reliably detects tumor-specific genomic alterations and whether this may help to guide the management of patients with CNS cancer in clinical practice. Patient and methods: CSF samples from 27 patients with various primary and secondary CNS malignancies were collected and evaluated by NGS using a targeted, amplicon-based NGS-panel (Oncomine Focus Assay). All cases were discussed within the framework of a molecular tumor board at the Comprehensive Cancer Center Munich. Results: NGS was technically successful in 23/27 patients (85%). Genomic alterations were detectable in 20/27 patients (74%), 11/27 (40%) of which were potentially actionable. After discussion in the MTB, a change of therapeutic management was recommended in 7/27 (26%) of the cases. However, due to rapid clinical progression, only 4/27 (15%) of the patients were treated according to the recommendation. In a subset of patients (6/27, 22%), a high number of mutations of unknown significance suggestive of a high tumor mutational burden (TMB) were detected. Conclusions: NGS from cerebrospinal fluid is feasible in routine clinical practice and yields therapeutically relevant alterations in a large subset of patients. Integration of this approach into a precision cancer medicine program might help to improve therapeutic options for patients with CNS cancer.

Predicting treatment Response based on Dual assessment of magnetic resonance Imaging kinetics and Circulating Tumor cells in patients with Head and Neck cancer (PREDICT-HN): matching 'liquid biopsy' and quantitative tumor modeling.

BACKGROUND: Magnetic resonance imaging (MRI) has improved capacity to visualize tumor and soft tissue involvement in head and neck cancers. Using advanced MRI, we can interrogate cell density using diffusion weighted imaging, a quantitative imaging that can be used during radiotherapy, when diffuse inflammatory reaction precludes PET imaging, and can assist with target delineation as well. Correlation of circulating tumor cells (CTCs) measurements with 3D quantitative tumor characterization could potentially allow selective, patient-specific response-adapted escalation or de-escalation of local therapy, and improve the therapeutic ratio, curing the greatest number of patients with the least toxicity. METHODS: The proposed study is designed as a prospective observational study and will collect pretreatment CT, MRI and PET/CT images, weekly serial MR imaging during RT and post treatment CT, MRI and PET/CT images. In addition, blood sample will be collected for biomarker analysis at those time intervals. CTC assessments will be performed on the CellSave tube using the FDA-approved CellSearch® Circulating Tumor Cell Kit (Janssen Diagnostics), and plasma from the EDTA blood samples will be collected, labeled with a de-identifying number, and stored at - 80 °C for future analyses. DISCUSSION: The primary objective of the study is to evaluate the prognostic value and correlation of weekly tumor response kinetics (gross tumor volume and MR signal changes) and circulating tumor cells of mucosal head and neck cancers during radiation therapy using MRI in predicting treatment response and clinical outcomes. This study will provide landmark information as to the utility of CTCs ('liquid biopsy) and tumor-specific functional quantitative imaging changes during treatment to guide personalization of treatment for future patients. Combining the biological information from CTCs and the structural information from MRI may provide more information than either modality alone. In addition, this study could potentially allow us to determine the optimal time to obtain MR imaging and/ or CTCs during radiotherapy to assess tumor response and provide guidance for patient selection and stratification for future dose escalation or de-escalation strategies. TRIAL REGISTRATION: Clinicaltrials.gov ( NCT03491176 ). Date of registration: 9th April 2018. (retrospectively registered). Date of enrolment of the first participant: 30th May 2017.

Concordance between Comprehensive Cancer Genome Profiling in Plasma and Tumor Specimens.

INTRODUCTION: Detection of somatic genomic alterations in the plasma of patients with cancer ("liquid biopsy") are increasingly being used in the clinic. However, the concordance of alterations identified in liquid biopsies with those detected in cancer specimens is not routinely being determined. METHODS: We sought to systematically compare alterations found by a massively parallel sequencing liquid biopsy assay covering 39 genes (NEOliquid [NEO New Oncology GmbH, Köln, Germany]) with those identified through routine diagnostic testing in a certified central pathology laboratory in a cohort of patients with nonsquamous NSCLC. NEOliquid is based on enrichment of the genomic territory of interest by hybrid capture and is thus capable of detecting point mutations, small insertions and deletions, copy number alterations, and gene rearrangements/fusions in a single assay. RESULTS: In a cohort of 82 patients with matched blood/tissue samples, the concordance between NEOliquid and tissue-based routine testing was 98%, the sensitivity of NEOliquid was higher than 70%, and the specificity was 100%. Discordant cases included those with insufficient amounts of circulaating tumor DNA in plasma and cases in which known driver mutations (e.g., isocitrate dehydrogenase (NADP(+)), 1 systolic gene [IDH1] R132H, kinesin family member 5B gene [KIF5b-ret proto-oncogene [RET], or MNNG HOS Transforming gene [MET] exon 14) were found in the plasma but were not interrogated by routine tissue analyses. CONCLUSIONS: In summary, NEOliquid offers accurate and reliable detection of clinically relevant driver alterations in plasma of patients with cancer.