Long non-coding RNAs (IncRNAs) are a class of transcripts with lengths exceeding 200 nucleotides that do not encode proteins. Despite their crucial roles in cellular functions and biological processes, only a minority of the over 20,000 annotated IncRNAs have been functionally characterized. Here, we established a high-throughput, CRISPR-Interference (CRISPRi) arrayed screening platform with serial cellular and molecular phenotyping to systematically characterize IncRNA functions. We reasoned that the integration of a comprehensive cellular and molecular phenotype can increase the probability of uncovering cellular functions and pathways controlled by IncRNA transcripts.
Detecting low-frequency mutations within a high-abundance wild-type (WT) background is essential for precision cancer diagnostics. Standard methods like qPCR and NGS, while effective, are hindered by high costs, complexity, and lengthy workflows. Electrochemical biosensors using mutation-specific capture probes offer a simpler, cost-effective alternative but lack the selectivity needed for detecting low-abundance mutations. To address this, we developed a high-throughput platform for systematically evaluating the hybridization affinity between biorecognition elements (capture probes) and target DNA under varied conditions.
BACKGROUND: High-risk neuroblastoma tumors respond differently to therapy due to their unique molecular makeup and tumor microenvironment. Therefore, molecularly profiling of these tumors helps tailoring treatment. Spatial transcriptomics enables detailed transcriptional profiling while preserving spatial context. We are working on a customized version of this technology using a DNA microarray printer and an in-house developed library preparation protocol.
AIMS: We aim to develop a novel, cost-effective spatial transcriptomics platform, providing an unbiased transcriptome view at single-cell resolution.
Traditional blood collection for whole blood gene expression profiling and biomarker analysis often requires a visit to a healthcare professional, posing challenges for special populations (sick, fragile health, immobile), or for large-scale studies requiring repeated sampling. Blood microsampling, the process of obtaining small volumes of capillary blood, holds great promise to overcome these challenges. We have developed a cost-effective, high-throughput platform for processing self-collected blood microsamples using Mitra Volumetric Adsorptive Microsampling (VAMS) devices for downstream RNA sequencing.
Long non-coding RNAs (lncRNAs) are a class of transcripts with lengths exceeding 200 nucleotides that do not encode proteins. Despite their crucial roles in cellular functions and biological processes, only a minority of the over 20,000 annotated lncRNAs have been functionally characterized. Here, we established a high-throughput, CRISPR-Interference (CRISPRi) arrayed screening plaKorm with serial cellular and molecular phenotyping to systematically characterize lncRNA functions. We reasoned that the integration of a comprehensive cellular and molecular phenotype can increase the probability of uncovering cellular functions and pathways controlled by lncRNA transcripts.
Neuroblastoma is a childhood cancer of the sympathetic nervous system. Recent studies have shown that neuroblastoma tumors are composed of two cell identities, i.e. the adrenergic and mesenchymal identity. Both identities are driven by a core regulatory transcriptional circuitry, which acts as an autoregulatory positive feedforward loop, to delineate the cell identity through regulation of its target genes. We identified the long non-coding RNA NESPR to be specifically expressed in neuroblastoma cells of the adrenergic cell identity.
PhD student Annelien Morlion presents her recent work on plasma cell-free RNA profiles in cancer type and patient-specific changes.
Background: Circulating nucleic acids in blood plasma form an attractive resource to study human health and disease. While the presence of extracellular RNAs in plasma has been firmly established, their origin and clinical utility for management of cancer patients is less understood.
Methods: In this study, we applied messenger RNA capture sequencing of blood plasma cell-free RNA from 266 cancer patients and cancer-free controls (discovery n=208, 25 cancer types; validation n=58, 3 types).
Post-doctoral fellow Anneleen Decock presents her recent work on reporting pre-analytical variables in RNA-focused blood plasma studies.
Background: Blood-derived liquid biopsies are appealing biomaterials for various purposes in many medical disciplines as they offer a wide spectrum of analytes to be studied, including extracellular RNA (cell-free RNA; exRNA). The outcome of exRNA measurements is greatly influenced by pre-analytical variables, stressing the importance of disclosing pre-analytic variables in publications to enable adequate interpretation and comparison of research results.
Doctoral researcher Annelien Morlion presented her work on changes in blood plasma cell-free RNA profiles of cancer patients and how heterogeneity can be exploited for cancer classification