Tumor Biomarker In-Solution Quantification, Standard Production, and Multiplex Detection

The diagnosis and monitoring of cancer have been facilitated by discovering tumor “biomarkers” and methods to detect their presence. Yet, for certain cancers, we still lack sensitive and specific biomarkers or the means to quantify subtle concentration changes successfully. The identification of new biomarkers of disease and improving the sensitivity of detection will remain key to changing clinical outcomes. Patient liquid biopsies (serum and plasma) are the most easily obtained sources for noninvasive analysis of proteins that tumor cells release directly and via extracellular microvesicles and tumor shedding. Therefore, an emphasis on creating reliable assays using serum/plasma and “direct, in-solution” ELISA approaches has built an industry centered on patient protein biomarker analysis. A need for improved dynamic range and automation has resulted in the application of ELISA principles to paramagnetic beads with chemiluminescent or fluorescent detection. In the clinical testing lab, chemiluminescent paramagnetic assays are run on automated machines that test a single analyte, minimize technical variation, and are not limited by serum sample volumes. This differs slightly from the R&D setting, where serum samples are often limiting; therefore, multiplexing antibodies to test multiple biomarkers in low serum volumes may be preferred. This review summarizes the development of historical biomarker “standards”, paramagnetic particle assay principles, chemiluminescent or fluorescent biomarker detection advancements, and multiplexing for sensitive detection of novel serum biomarkers.

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Analyzing the dynamic range of fluorescent detection in microarray scanner

2006 International Symposium on Biophotonics, Nanophotonics and Metamaterials ◽

10.1109/metamat.2006.335017 ◽

2006 ◽

Author(s):

Wang Liqiang ◽

Lu Zukang

Keyword(s):

Dynamic Range ◽

Fluorescent Detection ◽

Microarray Scanner

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Metal ion-modulated graphene-DNAzyme interactions: design of a nanoprobe for fluorescent detection of lead(ii) ions with high sensitivity, selectivity and tunable dynamic range

Chemical Communications ◽

10.1039/c1cc11486g ◽

2011 ◽

Vol 47 (22) ◽

pp. 6278 ◽

Cited By ~ 138

Author(s):

Yanqin Wen ◽

Cheng Peng ◽

Di Li ◽

Lin Zhuo ◽

Shijiang He ◽

...

Keyword(s):

Metal Ion ◽

Dynamic Range ◽

High Sensitivity ◽

Fluorescent Detection

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Gemcitabine (Gem) and nab-paclitaxel (NP) ± nivolumab (nivo) ± CD40 agonistic monoclonal antibody APX005M (sotigalimab), in patients (Pts) with untreated metastatic pancreatic adenocarcinoma (mPDAC): Phase (Ph) 2 final results.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.4019 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 4019-4019

Author(s):

Mark H. O'Hara ◽

Eileen Mary O'Reilly ◽

Robert A. Wolff ◽

Zev A. Wainberg ◽

Andrew H. Ko ◽

...

Keyword(s):

Monoclonal Antibody ◽

Type I Error ◽

Acute Hepatic Failure ◽

Tumor Burden ◽

Clinical Activity ◽

Tumor Biomarker ◽

Type I ◽

Open Label ◽

Comparison Results ◽

Biomarker Analysis

4019 Background: Results from a ph1b trial evaluating gem/NP with CD40 agonistic monoclonal antibody APX005M ± nivo demonstrated promising clinical activity in pts with untreated mPDAC (O’Hara 2021). Herein, we report results from the follow-on, randomized (rand) ph2 trial evaluating gem/NP ± nivo ± APX005M. Methods: Pts with untreated mPDAC were rand to 1 of 3 open-label arms: gem/NP/nivo (A), gem/NP/APX005M (B), gem/NP/nivo/APX005M (C). All pts were treated with 1000 mg/m2 gem and 125 mg/m2 NP. Patients received 240 mg nivo in arms A and C and 0.3 mg/kg APX005M (RP2D) IV in arms B and C. Ph1b pts were included in ph2 analyses. 1° endpoint: 1-year OS rate of each arm, compared to a 35% historical OS rate for gem/NP (Von Hoff 2013). Key 2° endpoints: ORR, DCR, DOR, PFS and safety. Tumor and blood were collected for biomarker analysis. Planned enrollment of 35 pts/arm provided 81% power for testing the alternative of 58% OS rate vs 35%, using a 1-sided, 1-sample Z test with 5% type I error. Trial was not powered for cross-arm comparison. Results: 93 pts were rand in ph2 (N = 34, 30, 29 to A, B, C); when ph1b pts included, a total of 105 pts (34, 36, 35) were analyzed for efficacy and 108 pts (36, 37, 35) for safety. Min follow-up was 14 months (mos). Baseline characteristics were balanced across arms, inclusive of tumor burden, presence of liver metastases and stage at initial diagnosis (stage 1-3 vs 4). 1-year OS rate was 57% (1-sided p = 0.007 vs 35% historical rate, 95% lower CI bound = 41%) for A, 51% (p = 0.029, 95% bound = 36%) for B and 41% (p = 0.236, 95% bound = 27%) for C. Median OS and secondary endpoints are listed in Table. TRAE rates were similar across arms and to ph1b. 8 (7%) pts experienced an AE leading to tx discontinuation (6, 1, 1 in A, B, C), 40 (37%) pts experienced a serious TRAE (14, 15, 11 in A, B, C) and 2 pts died due to TRAEs; 1 each in B (acute hepatic failure) and C (intracranial hemorrhage). Conclusions: In this ongoing, seamless ph1b/2 trial of gem/NP ± nivo ± APX005M in pts with mPDAC, antitumor activity was observed in all arms. 1° endpoint of 1-year OS > 35% was met when combining gem/NP with either nivo or APX005M; however, not the combination. Safety was manageable; consistent with ph1b. Detailed multiomic immune and tumor biomarker analyses are underway to elucidate mechanisms of action and inform pt subsets that benefit most from these combinations. Clinical trial information: NCT03214250. [Table: see text]

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Imfirst: A phase IIIb, safety, single arm study of carboplatin (CB) or cisplatin (CP) plus etoposide (ET) with atezolizumab (ATZ) in patients with untreated extensive-stage small cell lung cancer (ES-SCLC) in Spain—Primary safety results of the induction phase.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.8567 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 8567-8567

Author(s):

Maria Rosario García Campelo ◽

Manuel Domine ◽

Javier De Castro ◽

Alberto Moreno ◽

Santiago Ponce Aix ◽

...

Keyword(s):

Adverse Events ◽

Safety Profile ◽

Performance Status ◽

Maintenance Phase ◽

Tumor Biomarker ◽

Induction Phase ◽

Ecog Performance Status ◽

Serious Adverse Events ◽

Biomarker Analysis ◽

Significant Clinical Improvement

8567 Background: Clinical trial (CT) IMpower133 met both primary endpoints and is the first CT to show significant clinical improvement over standard chemotherapy (C) with a good safety profile in first line (1L) ES-SCLC. The addition of ATZ to CB + ET resulted in an OS landmark of 34% and 22% compared to 21% and 16.8% of patients alive at 18 and 24 months respectively versus C. IMfirst evaluates ATZ + CB or CP + ET in a broader patient population than the pivotal study. ECOG Performance status (PS) 2, asymptomatic untreated brain metastases, underlying stable autoimmune diseases and HIV+ pts are eligible. IMfirst also includes the possibility of 6 C induction cycles according to investigator´s choice and consolidation radiotherapy. Methods: To evaluate the safety and efficacy of ATZ added to CB or CP + ET as 1L treatment in an interventional real world setting of ES-SCLC. Exploratory endpoints include tumor biomarker analysis related to ATZ. Results: As of Oct 2020, 117 pts had been enrolled, 105 treated with ATZ + CB + ET and 12 with ATZ + CP + ET. The median age was 65 years (Y) (range 35-89); 84 males; 14 pts (12%) had CNS metastases and 66 pts were current smokers and 50 former smokers, one had never smoked. The PS was 0 in 28 pts (24%), 1 in 75 (64%) and 2 in 14 (12%). The median of cycles of ATZ received was 4 for all the pts (range 1-12) and 2 for the pts (40) in maintenance phase (range 1-8). Number of pts with adverse events (AEs) was 109, 36 with Serious Adverse Events (SAEs) and 63 with AEs. 8 pts had SAEs related to treatment, 4 had adverse events of special interest and 13 pts discontinued the treatment due to AEs: 6 to ATZ, 12 to CB or CP and 10 to ET, 1 patient discontinued ATZ due to a related AE. Table shows the treatment related AEs (TRAEs). No grade 5 TRAEs were reported. Conclusions: IMfirst induction phase analysis confirms the safety profile of ATZ plus C in a broader population of patients. Efficacy, biomarker and further safety analyses will be presented in the future with longer follow up.[Table: see text]

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Clinical Relevance of Serum Galactose Deficient IgA1 in Patients with IgA Nephropathy

Journal of Clinical Medicine ◽

10.3390/jcm9113549 ◽

2020 ◽

Vol 9 (11) ◽

pp. 3549

Author(s):

Jin Sug Kim ◽

Hyeon Seok Hwang ◽

Sang Ho Lee ◽

Yang Gyun Kim ◽

Ju-Young Moon ◽

...

Keyword(s):

Iga Nephropathy ◽

Clinical Relevance ◽

Interstitial Fibrosis ◽

Healthy Controls ◽

Ckd Progression ◽

Serum Samples ◽

Tubular Atrophy ◽

Appropriate Treatment ◽

Cox Proportional Hazard Models ◽

New Biomarkers

New biomarkers of IgA nephropathy (IgAN) are needed for non-invasive diagnosis and appropriate treatment. There is emerging evidence that galactose deficient IgA1 (Gd-IgA1) is a pivotal molecule in the pathogenesis of IgAN. However, few studies have investigated the role of Gd-IgA1 as a biomarker in IgAN. In this study, we investigated the clinical relevance of serum Gd-IgA1 levels in patients with IgAN. Two hundred and thirty biopsy-proven IgAN patients, 74 disease controls (patients with non-IgAN nephropathy), and 15 healthy controls were enrolled in this study. Levels of serum Gd-IgA1 were measured using an ELISA kit in serum samples obtained the day of renal biopsy. We compared levels of serum Gd-IgA1 according to the type of glomerular disease and analyzed the association between Gd-IgA1 levels and clinical and pathological parameters in patients with IgAN. We then divided IgAN patients into two groups according to Gd-IgA1 level and investigated the predictive value of Gd-IgA1 for progression of chronic kidney disease (CKD). Serum Gd-IgA1 levels were significantly higher in IgAN patients than disease controls and healthy controls. In patients with IgAN, serum Gd-IA1 levels were significantly correlated with estimated glomerular filtration rate, serum IgA level, and tubular atrophy/interstitial fibrosis. CKD progression was more frequent in IgAN patients with higher serum Gd-IgA1 levels than in those with lower serum Gd-IgA1 levels. Cox proportional hazard models showed that high GdIgA1 level was an independent risk factor for CKD progression after adjusting for several confounders. Our results suggest that serum Gd-IgA1 level is a useful diagnostic and prognostic marker in IgAN patients. Further studies with a larger sample size and longer follow-up duration are needed.

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Identification of miRNAs Enriched in Extracellular Vesicles Derived from Serum Samples of Breast Cancer Patients

Biomolecules ◽

10.3390/biom10010150 ◽

2020 ◽

Vol 10 (1) ◽

pp. 150 ◽

Cited By ~ 7

Author(s):

Patricia M. M. Ozawa ◽

Evelyn Vieira ◽

Débora S. Lemos ◽

Ingrid L. Melo Souza ◽

Silvio M. Zanata ◽

...

Keyword(s):

Breast Cancer ◽

Extracellular Vesicles ◽

Area Under The Curve ◽

Precipitation Method ◽

Sequencing Analysis ◽

Breast Cancer Patients ◽

Serum Samples ◽

Luminal A ◽

Liquid Biopsies ◽

Advanced Tumor

MicroRNAs derived from extracellular vesicles (EV-miRNAs) are circulating miRNAs considered as potential new diagnostic markers for cancer that can be easily detected in liquid biopsies. In this study, we performed RNA sequencing analysis as a screening strategy to identify EV-miRNAs derived from serum of clinically well-annotated breast cancer (BC) patients from the south of Brazil. EVs from three groups of samples (healthy controls (CT), luminal A (LA), and triple-negative (TNBC)) were isolated from serum using a precipitation method and analyzed by RNA-seq (screening phase). Subsequently, four EV-miRNAs (miR-142-5p, miR-150-5p, miR-320a, and miR-4433b-5p) were selected to be quantified by quantitative real-time PCR (RT-qPCR) in individual samples (test phase). A panel composed of miR-142-5p, miR-320a, and miR-4433b-5p distinguished BC patients from CT with an area under the curve (AUC) of 0.8387 (93.33% sensitivity, 68.75% specificity). The combination of miR-142-5p and miR-320a distinguished LA patients from CT with an AUC of 0.9410 (100% sensitivity, 93.80% specificity). Interestingly, decreased expression of miR-142-5p and miR-150-5p were significantly associated with more advanced tumor grades (grade III), while the decreased expression of miR-142-5p and miR-320a was associated with a larger tumor size. These results provide insights into the potential application of EVs-miRNAs from serum as novel specific markers for early diagnosis of BC.

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High-Accuracy Determination of Microsatellite Instability Compatible with Liquid Biopsies

Clinical Chemistry ◽

10.1093/clinchem/hvaa013 ◽

2020 ◽

Vol 66 (4) ◽

pp. 606-613 ◽

Cited By ~ 3

Author(s):

Amanda Bortolini Silveira ◽

François-Clément Bidard ◽

Amélie Kasperek ◽

Samia Melaabi ◽

Marie-Laure Tanguy ◽

...

Keyword(s):

Microsatellite Instability ◽

Large Scale ◽

Digital Pcr ◽

Circulating Tumor Dna ◽

Diagnostic Tools ◽

Tumor Biomarker ◽

Analytical Sensitivity ◽

Liquid Biopsies ◽

Tumor Dna ◽

Large Scale Screening

Abstract Background Microsatellite instability (MSI) has recently emerged as a predictive pan-tumor biomarker of immunotherapy efficacy, stimulating the development of diagnostic tools compatible with large-scale screening of patients. In this context, noninvasive detection of MSI from circulating tumor DNA stands as a promising diagnostic and posttreatment monitoring tool. Methods We developed drop-off droplet-digital PCR (ddPCR) assays targeting BAT-26, activin A receptor type 2A (ACVR2A), and defensin beta 105A/B (DEFB105A/B) microsatellite markers. Performances of the assays were measured on reconstitution experiments of various mutant allelic fractions, on 185 tumor samples with known MSI status, and on 72 blood samples collected from 42 patients with advanced colorectal or endometrial cancers before and/or during therapy. Results The 3 ddPCR assays reached analytical sensitivity <0.1% variant allelic frequency and could reliably detect and quantify MSI in both tumor and body fluid samples. High concordance between MSI status determination by the three-marker ddPCR test and the reference pentaplex method were observed (100% for colorectal tumors and 93% for other tumor types). Moreover, the 3 assays showed correlations with r ≥ 0.99 with other circulating tumor DNA markers and their dynamic during treatment correlated well with clinical response. Conclusions This innovative approach for MSI detection provides a noninvasive, cost-effective, and fast diagnostic tool, well suited for large-scale screening of patients that may benefit from immunotherapy agents, as well as for monitoring treatment responses.

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Green synthesis of a deep-ultraviolet carbonized nanoprobe for ratiometric fluorescent detection of feroxacin and enrofloxacin in food and serum samples

The Analyst ◽

10.1039/d0an02114h ◽

2021 ◽

Author(s):

Zhong-Xia Wang ◽

Xing Jin ◽

Wen-Juan Wang ◽

Fen-Ying Kong ◽

Jing Zhu ◽

...

Keyword(s):

Green Synthesis ◽

Fluorescent Probe ◽

Bovine Serum ◽

Fluorescent Detection ◽

Serum Samples ◽

Deep Ultraviolet ◽

Filtration Effect ◽

Ratiometric Fluorescent Probe

A sensitive ratiometric fluorescent probe for EFC and FXC detection in milk and bovine serum samples based on the internal filtration effect.

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The Caris registry: Building a biomarker-focused database to advance patient care.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.e21152 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. e21152-e21152

Author(s):

Sheri Sanders ◽

Wendy Schroeder ◽

Alan Wright ◽

Jeff Field

Keyword(s):

Clinical Outcomes ◽

Clinical Decision Making ◽

Information Access ◽

Data Entry ◽

Clinical Decision ◽

Outcome Data ◽

Medical Community ◽

Tumor Biomarker ◽

Biomarker Analysis ◽

Biomarker Research

e21152 Background: The medical community is continually searching for the best way to treat cancer. The value and utility of biomarkers in guiding treatment decisions is widely accepted but remains a challenge for the bedside clinician and requires ongoing validation and correlation to clinical outcomes. Caris Life Sciences has a dedicated team of scientists who study volumes of scientific literature, synthesize biomarker research and by way of an evidence-based electronic rules engine, translates the application of the literature to biomarker analysis of tumor tissue (The Target Now Report) in support of biomarker-drug association evidence useful in clinical decision-making. Subsequently, Caris initiated the Caris Registry to capture clinical disease, treatment and outcome data from patients who have a Target Now Report. Methods: The Caris Registry is a web-based data entry platform based on an IRB approved protocol. The eligible subject for the Registry will have a qualified Target Now Report. All clinical data elements are defined and supported by the NCI caBIG standardized data dictionary. Disease history/status, treatments and outcomes are captured at enrollment with Day 1 defined as the date of the Target Now Report and every 9 months for 5 years or death whichever is first. Results: As of January 19, 2012, there are 68 participating centers across the country and 43 centers pending IRB submission. There are 852 Target Now cases enrolled with the following cancer lineage distribution: Breast 209, Ovary 169, Lung 117, Colon 79, Endometrium 33, and other 245. There are 323 completed follow up reports and 175 completed end of study reports capturing vital status and cancer related deaths. Conclusions: Caris has successfully launched a scientifically valid and regulatory compliant Registry and database intended to become a robust library of tumor biomarker results linked to clinical outcomes data. As the library grows, data mining could provide vital information access to researchers, pharmaceutical firms, government, academia and insurers for use in drug development, molecular and biomarker research, economic impact assessments, healthcare policy discussion and most importantly directing personalized cancer treatment.

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