A digital PCR-based protocol to detect and quantify RNA editing events at hotspots.
AuthorsOh S,Buisson R
JournalSTAR protocols
PubMed ID35284835
APOBEC3A, CRISPR programmable RNA base editors, or other enzymes can edit RNA transcripts at specific locations or hotspots. Precise quantification of these RNA-editing events is crucial to determine the activity and efficiency of these enzymes in cells. We have developed a quick method to quantify RNA-editing activity using digital PCR, ... More
Evaluation of four human-associated fecal biomarkers in wastewater in Southern Ontario.
The objectives were to investigate a novel combination of gene-knockout with antimicrobial dimethylaminohexadecyl methacrylate (DMAHDM) composite in regulating oral biofilm from a cariogenic state toward a non-cariogenic state. A tri-species biofilm model included cariogenic Streptococcus mutans (S. mutans), and non-cariogenic Streptococcus sanguinis (S. sanguinis) and Streptococcus gordonii (S. gordonii). Biofilm ... More
Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples.
AuthorsLewandowska DW,Zagordi O,Geissberger FD,Kufner V,Schmutz S,Böni J,Metzner KJ,Trkola A,Huber M
JournalMicrobiome
PubMed ID28789678
BACKGROUND: Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in ... More
A combined ANXA2-NDRG1-STAT1 gene signature predicts response to chemoradiotherapy in cervical cancer.
JournalJournal of experimental & clinical cancer research : CR
PubMed ID31242951
BACKGROUND: A better understanding of locally advanced cervical cancer (LACC) is mandatory for further improving the rates of disease control, since a significant proportion of patients still fail to respond or undergo relapse after concurrent chemoradiation treatment (CRT), and survival for these patients has generally remained poor. METHODS: To identify ... More
Novel method to detect microRNAs using chip-based QuantStudio 3D digital PCR.
AuthorsConte D,Verri C,Borzi C,Suatoni P,Pastorino U,Sozzi G,Fortunato O
JournalBMC genomics
PubMed ID26493562
BACKGROUND: Research efforts for the management of cancer, in particular for lung cancer, are directed to identify new strategies for its early detection. MicroRNAs (miRNAs) are a new promising class of circulating biomarkers for cancer detection, but lack of consensus on data normalization methods has affected the diagnostic potential of ... More
Gastrointestinal (GI) complications of diabetes mellitus (DM) significantly impact on patientsâ quality of life. Enteric glial cells (EGC) are the key cell type of enteric nervous system (ENS), which contributes to the destruction of gut homeostasis in DM. Circular RNAs (circRNAs) are a novel type of RNAs abundant in the ... More
Identification of Reduced Host Transcriptomic Signatures for Tuberculosis Disease and Digital PCR-Based Validation and Quantification.
Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantification of the concentrations of signature transcripts in blood have not been reported, but would facilitate diagnostic test development. To identify minimal transcript signatures, we applied a transcript selection procedure to microarray data from ... More
CD44v8-10 mRNA contained in serum exosomes as a diagnostic marker for docetaxel resistance in prostate cancer patients.
AuthorsKato T,Mizutani K,Kawakami K,Fujita Y,Ehara H,Ito M
JournalHeliyon
PubMed ID32642575
BACKGROUND: Docetaxel is first-line chemotherapy for castration-resistant prostate cancer (CRPC), but most patients acquire docetaxel resistance. CD44 has been shown to be involved in drug resistance of cancers including prostate cancer. We hypothesized that CD44 in serum exosomes could be a diagnostic marker for docetaxel resistance in CRPC patients. In ... More
Toxoplasma gondii in edible fishes captured in the Mediterranean basin.
The issue of whether market fish can be involved in the transmission of Toxoplasma gondii in the marine environment is highly debated since toxoplasmosis has been diagnosed frequently in cetaceans stranded along the Mediterranean coastlines in recent times. To support the hypothesis that fishes can harbour and effectively transmit the ... More
A selective splicing variant of hepcidin mRNA in hepatocellular carcinoma cell lines.
JournalBiochemical and biophysical research communications
PubMed ID27264950
Activation of CB2R by synthetic CB2R agonist, PM289, improves brain endothelial barrier properties, decreases inflammatory response and enhances endothelial repair.
AuthorsBullock TA,Galpayage Dona KNU,Hale JF,Morales P,Jagerovic N,Andrews AM,Ramirez SH
JournalNeuroImmune pharmacology and therapeutics
PubMed ID38116176
The Cannabinoid 2 Receptor (CB2R) has been found to provide immunological modulation in different cell types. More recently, detection of CB2R in the cerebral endothelium suggests a possible role in the resolution of inflammation at the level of the bloodâbrainâbarrier (BBB). Here, the notion that CB2R upregulation in brain endothelial ... More
Targeted community wastewater surveillance for SARS-CoV-2 and Mpox virus during a festival mass-gathering event.
AuthorsBrighton K,Fisch S,Wu H,Vigil K,Aw TG
JournalThe Science of the total environment
PubMed ID37793442
Characterization of a novel deep-intronic variant in DYNC2H1 identified by whole-exome sequencing in a patient with a lethal form of a short-rib thoracic dysplasia type III.
Biallelic pathogenic variants in DYNC2H1 are the cause of short-rib thoracic dysplasia type III with or without polydactyly (OMIM #613091), a skeletal ciliopathy characterized by thoracic hypoplasia due to short ribs. In this report, we review the case of a patient who was admitted to the Neonatal Intensive Care Unit ... More
Negative Regulation of the Keap1-Nrf2 Pathway by a p62/Sqstm1 Splicing Variant.
AuthorsKageyama S,Saito T,Obata M,Koide RH,Ichimura Y,Komatsu M
JournalMolecular and cellular biology
PubMed ID29339380
A key antioxidant pathway, the Keap1-Nrf2 system, is regulated by p62/Sqstm1 via multiple mechanisms, including gene expression, posttranslational modifications (such as ubiquitination and phosphorylation), and autophagic degradation of p62/Sqstm1 and Keap1. Here we demonstrate a novel mode of regulation of the Keap1-Nrf2 system, mediated by a splicing variant of p62/Sqstm1 ... More
Unveiling the secrets of adeno-associated virus: novel high-throughput approaches for the quantification of multiple serotypes.
AuthorsMeierrieks F,Kour A,Pätz M,Pflanz K,Wolff MW,Pickl A
JournalMolecular therapy. Methods & clinical development
PubMed ID37822717
Adeno-associated virus (AAV) vectors are among the most prominent viral vectors for in vivo gene therapy, and their investigation and development using high-throughput techniques have gained increasing interest. However, sample throughput remains a bottleneck in most analytical assays. In this study, we compared commonly used analytical methods for AAV genome titer, ... More
Serum HBV DNA plus RNA reflecting cccDNA level before and during NAs treatment in HBeAg positive CHB patients.
Background & Aims: Correlations between serum viral markers and intrahepatic cccDNA in patients undergoing long-term nucleos(t)ide analogues (NAs) treatment haven't been fully explored. In this study, we evaluate the correlation between intrahepatic cccDNA and other serum viral markers and intrahepatic HBV DNA in HBeAg positive chronic hepatitis B (CHB) patients ... More
Comparison of quantitative PCR and digital PCR assays for quantitative detection of infectious bronchitis virus (IBV) genome.
Digital PCR (dPCR) is emerging as an ideal platform for the detection and tracking of genomic variants in cancer due to its high sensitivity and simple workflow. The growing number of clinically actionable cancer biomarkers creates a need for fast, accessible methods that allow for dense information content and high ... More
Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks.
AuthorsNyaruaba R,Mwaliko C,Dobnik D,Neužil P,Amoth P,Mwau M,Yu J,Yang H,Wei H
JournalClinical microbiology reviews
PubMed ID35258315
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject ... More
Digital PCR Discriminates between SARS-CoV-2 Omicron Variants and Immune Escape Mutations.
AuthorsHolland SC,Holland LA,Smith MF,Lee MB,Hu JC,Lim ES
JournalMicrobiology spectrum
PubMed ID37306573
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, mutations arise that will allow the virus to evade immune defenses and therapeutics. Assays that can identify these mutations can be used to guide personalized patient treatment plans. Digital PCR (dPCR) is a fast and reliable complement to whole-genome ... More
EGFR mutation testing from pleural effusions of non-small cell lung cancer patients at the institute for oncology and radiology of Serbia.
AuthorsVukovic M,Tanic M,Damjanovic A,Pavlovic M,Stanojevic A,Zivic K,Karadzic V,Jankovic R,Cavic M
JournalTranslational oncology
PubMed ID37659221
BACKGROUND: The use tumor-derived cell-free DNA extracted from body fluids is being evaluated for genetic testing in lung cancer. The aim of this study was to explore the feasibility and utility of implementation of EGFR molecular testing from pleural effusions in non-small cell lung cancer in the clinical diagnostics workflow. ... More
Replication-Deficient Zika Vector-Based Vaccine Provides Maternal and Fetal Protection in Mouse Model.
AuthorsGarcia G Jr,Chakravarty N,Abu AE,Jeyachandran AV,Takano KA,Brown R,Morizono K,Arumugaswami V
JournalMicrobiology spectrum
PubMed ID36169338
Zika virus (ZIKV), a mosquito-borne human pathogen, causes dire congenital brain developmental abnormalities in children of infected mothers. The global health crisis precipitated by this virus has led to a concerted effort to develop effective therapies and prophylactic measures although, unfortunately, not very successfully. The error-prone nature of RNA viral ... More
Comparative study of droplet-digital PCR and absolute Q digital PCR for ctDNA detection in early-stage breast cancer patients.
JournalClinica chimica acta; international journal of clinical chemistry
PubMed ID38007055
Detection of newly produced T and B lymphocytes by digital PCR in blood stored dry on nylon flocked swabs.
AuthorsTessitore MV,Sottini A,Roccaro AM,Ghidini C,Bernardi S,Martellosio G,Serana F,Imberti L
JournalJournal of translational medicine
PubMed ID28381232
BACKGROUND: A normal number of T-cell receptor excision circles (TRECs) and K-deleting recombination excision circles (KRECs) is considered a biomarker for adequate new T- and B-cell production. In newborns, detection of TRECs and KRECs by real time PCR from dried blood spotted on filter paper is used for the screening ... More
An atypical LIR motif within UBA5 (ubiquitin like modifier activating enzyme 5) interacts with GABARAP proteins and mediates membrane localization of UBA5.
Short linear motifs, known as LC3-interacting regions (LIRs), interact with mactoautophagy/autophagy modifiers (Atg8/LC3/GABARAP proteins) via a conserved universal mechanism. Typically, this includes the occupancy of 2 hydrophobic pockets on the surface of Atg8-family proteins by 2 specific aromatic and hydrophobic residues within the LIR motifs. Here, we describe an alternative ... More
Therapy-induced APOBEC3A drives evolution of persistent cancer cells.
Acquired drug resistance to anti-cancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified (1â4), the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood. Genomic profiling of patient tumors has implicated APOBEC cytidine deaminases in tumor evolution; however, their ... More
Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA.
The adaptive evolution of SARS-CoV-2 variants is driven by selection for increased viral fitness in transmissibility and immune evasion. Understanding the dynamics of how an emergent variant sweeps across populations can better inform public health response preparedness for future variants. Here, we investigated the state-level genomic epidemiology of SARS-CoV-2 through ... More
Serum HBsAg and HBcrAg is associated with inflammation in HBeAg-positive chronic hepatitis B patients.
JournalFrontiers in cellular and infection microbiology
PubMed ID37065191
BACKGROUNDS & AIMS: Liver inflammation is the main risk factor for developing liver fibrosis, cirrhosis, and even hepatocellular carcinoma in chronic hepatitis B (CHB) patients. To replace biopsy, additional non-invasive biomarkers to diagnose and grade liver necroinflammation are urgently required in clinical practice. METHOD: Ninety-four CHB patients, including 74 HBeAg-positive ... More
No extraction? No problem. Direct to PCR processing of tongue swabs for diagnosis of tuberculosis disease as an alternative to sputum collection.
Sputum collection and testing for tuberculosis (TB) have been problematic due to the potential for aerosolization, difficulty in generating a quality sample, and complex DNA extraction methods. Tongue swabs are inexpensive, minimally invasive, and a promising alternative to sputum collection. We investigated the diagnostic accuracy of tongue swabs for TB ... More
Serum HBV RNA predicts HBeAg clearance and seroconversion in patients with chronic hepatitis B treated with nucleos(t)ide analogues.
This study evaluated the predictive value of serum HBV DNA, HBV RNA, HBcrAg, HBsAg, intrahepatic HBV DNA and cccDNA for HBeAg clearance and seroconversion during longâterm treatment with nucleos(t)ide analogues (NAs) in patients with chronic hepatitis B (CHB). A single centre, prospective cohort of CHB patients was used for this ... More
Multidrug-resistant mutations to antiviral and antibody therapy in an immunocompromised patient infected with SARS-CoV-2.
AuthorsHirotsu Y, Kobayashi H, Kakizaki Y, Saito A, Tsutsui T, Kawaguchi M, Shimamura S, Hata K, Hanawa S, Toyama J, Miyashita Y, and Omata M
JournalMed (New York, N.Y.)
PubMed ID37683636
The circular RNA Ataxia Telangiectasia Mutated regulates oxidative stress in smooth muscle cells in expanding abdominal aortic aneurysms
AuthorsFrancesca Fasolo, Greg Winski, Zhaolong Li, Zhiyan Wu, Hanna Winter, Julia Ritzer, Nadiya Glukha, Joy Roy, Rebecka Hultgren, Jessica Pauli, Albert Busch, Nadja Sachs, Christoph Knappich, Hans-Henning Eckstein, Reinier A. Boon, Valentina Paloschi, and Lars Maegdefessel
JournalMolecular Therapy Nucleic Acids
PubMed ID
Monitoring of kinetics and exhaustion markers of circulating CAR-T cells as early predictive factors in patients with B-cell malignancies.
AuthorsGarcía-Calderón C, Sierro-Martínez B, García-Guerrero E, Sanoja-Flores L, Muñoz-García R, Ruiz-Maldonado V, Jimenez-Leon, Delgado-Serrano J, Molinos-Quintana A, Guijarro-Albaladejo B, Carrasco-Brocal I, Lucena J, García-Lozano J, Blázquez-Goñi C, Reguera-Ortega J, González-Escribano M, Reinoso-Segura M, Briones J, Pérez-Simón J, and Caballero-Velázque T
JournalFrontiers in immunology
PubMed ID37122702
Precision cancer monitoring using a novel, fully integrated, microfluidic array partitioning digital PCR platform.
AuthorsDueck M, Lin R, Zayac A, Gallagher S, Chao A, Jiang L, Datwani, S, Hung P, and Stieglitz E
JournalScientific reports
PubMed ID31862911
The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020.
AuthorsHuggett JF
JournalClinical chemistry
PubMed ID32746458
New methods for the quantification of mixed chimerism in transplantation.
AuthorsPicard C, Frassati C, Cherouat N, Maioli S, Maskovtchenko P, Cherel M, Chiaroni J, Pedini P
JournalFrontiers in immunology
PubMed ID36742303
Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA.
AuthorsSmith MF, Holland SC, Lee MB, Hu JC, Pham NC, Sullins RA, Holland LA, Mu T, Thomas AW, Fitch R, Driver EM, Halden RU, Villegas-Gold M, Sanders S, Krauss JL, Nordstrom L, Mulrow M, White M, Murugan V, and Lim ES
JournalmBio
PubMed ID36622143
SARS-CoV-2 RNAemia Predicts Clinical Deterioration and Extrapulmonary Complications from COVID-19.
AuthorsRam-Mohan N, Kim D, Zudock EJ, Hashemi MM, Tjandra KC, Rogers AJ, Blish CA, Nadeau KC, Newberry JA, Quinn JV, O'Hara R, Ashley E, Nguyen H, Jiang L, Hung P, Blomkalns AL, Yang S, Stanford COVID-19 Biobank Study Group
JournalClinical infectious diseases : an official publication of the Infectious Diseases Society of America
PubMed ID33949665
Detection of bacterial co-infections and prediction of fatal outcomes in COVID-19 patients presenting to the emergency department using a 29 mRNA host response classifier.
AuthorsRam-Mohan N, Rogers AJ, Blish CA, Nadeau KC, Zudock EJ, Kim D, Quinn JV, Sun L, Liesenfeld, Standford COVID-19 Biobank Study Group, Yang S
JournalmedRxiv : the preprint server for health sciences
PubMed ID35313598
Using a 29-mRNA Host Response Classifier To Detect Bacterial Coinfections and Predict Outcomes in COVID-19 Patients Presenting to the Emergency Department.
AuthorsRam-Mohan N, Rogers AJ, Blish CA, Nadeau, Zudock EJ, Kim D, Quinn JV, Sun L, Liesenfeld O, Stanford COVID-19 Biobank Study Group, Yang S
JournalMicrobiology spectrum
PubMed ID36250865
Disruption of the circadian clock drives Apc loss of heterozygosity to accelerate colorectal cancer.
AuthorsChun SK, Fortin BM, Fellows RC, Habowski, AN, Verlande A, Song WA, Mahieu AL, Lefebvre AEYT, Sterrenberg JN, Velez, LM, Digman MA, Edwards RA, Pannunzio NR, Seldin MM, Waterman ML, Masri S
JournalScience advances
PubMed ID35947664
Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks.
AuthorsNyaruaba R, Mwaliko C, Dobnik D, Neuzil P, Amoth P, Mwau M, Yu J, Yang H, Wei H
JournalClinical microbiology reviews
PubMed ID35258315
Characterization of a novel deep-intronic variant in DYNC2H1 identified by whole-exome sequencing in a patient with a lethal form of a short-rib thoracic dysplasia type III.
AuthorsBuchh M, Gillespie PJ, Treat K, Abreu MA, Schwantes-An THL, Helm BM, Fang F, Xuei X, Mantcheva L, Suhrie KR, Graham BH, Conboy E, Vetrini F
JournalCold Spring Harbor Molecular Case Studies
PubMed ID36442996
Replication-Deficient Zika Vector-Based Vaccine Provides Maternal and Fetal Protection in Mouse Model.
AuthorsGarcia G, Chakravarty N, Abu AE, Jeyachandran AV, Takano KA, Brown R, Morizono K, Arumugaswami V
JournalMicrobiology spectrum
PubMed ID36169338
Digital PCR Discriminates between SARS-CoV-2 Omicron Variants and Immune Escape Mutations.
AuthorsHolland SC, Holland LA, Smith MF, Lee MB, Hu JC, Lim ES
JournalMicrobiology spectrum
PubMed ID37306573
LAMP for in-field quantitative assessments of airborne grapevine downy mildew inoculum.
AuthorsDouillet A, Laurent B, Beslay J, Massot M, Raynal M, Delmotte F
JournalJournal of applied microbiology
PubMed ID35977551
Application of digital PCR for public health-related water quality monitoring.
AuthorsTiwari A, Ahmed Q, Oikarinen S, Sherchan S, Heikinheimo A, Jiang G, Simpson SL, Greaves J, Bivins A
JournalThe Science of the total environment
PubMed ID35523326
A digital PCR-based protocol to detect and quantify RNA editing events at hotspots.
AuthorsOh S, Buisson R
JournalSTAR protocols
PubMed ID35284835
Current commercial dPCR platforms: technology and market review.
AuthorsTan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S
JournalCritical reviews in biotechnology
PubMed ID35291902
Development and validation of a 4-color multiplexing spinal muscular atrophy (SMA) genotyping assay on a novel integrated digital PCR instrument.
AuthorsJiang L, Lin R, Gallagher S, Zayac A, Butchbach ME, Hung P