Search

Gene fusions are vital biomarkers for tumor diagnosis and drug development, with precise detection becoming increasingly important. This review explores the links between gene fusions and common tumors, systematically evaluating detection technologies like fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), immunohistochemistry (IHC), electrochemiluminescence (ECL), and next-generation sequencing (NGS). FISH is the gold standard for DNA-level rearrangements, while PCR and NGS are widely used, with PCR confirming known fusions and NGS offering comprehensive genome-wide detection. Bioinformatic tools like STAR-Fusion, FusionCatcher, and Arriba are assessed for diagnostic accuracy. The review highlights how artificial intelligence (AI), particularly deep learning (DL) technologies like convolutional neural networks (CNNs) and recurrent neural networks (RNNs), is transforming gene fusion research by accurately detecting and annotating genes from genomic data, eliminating biases. Finally, we present an overview of advanced technologies for gene fusion analysis, emphasizing their potential to uncover unknown gene fusions. Highlights: • This review explores the intricate relationship between gene fusions and prevalent tumors, comprehensively reviewing techniques for gene fusion testing. • It evaluates the strengths and limitations of key assays like fluorescence in situ hybridization, polymerase chain reaction, and next-generation sequencing, and explores the emerging use of electrochemiluminescence for high-sensitivity gene fusion detection. • It emphasizes the diagnostic accuracy of bioinformatics tools such as STAR-Fusion, FusionCatcher, Arriba, and underscores the transformative role of artificial intelligence, particularly deep learning technologies, in revolutionizing gene fusion research. [ABSTRACT FROM AUTHOR]

Detecting low‐frequency DNA mutations hotspots cluster is critical for cancer diagnosis but remains challenging. Quantitative PCR (qPCR) is constrained by sensitivity, and allele‐specific PCR is restricted by throughput. Here we develop a long blocker displacement amplification (LBDA) coupled with qPCR for ultrasensitive and multiplexed variants detection. By designing long blocker oligos to perfectly match wildtype sequences while mispairing with mutants, long blockers enable 14–44 nt enrichment regions which is 2‐fold longer than normal BDA in the experiments. For wild template with a specific nucleotide, LBDA can detect different mutation types down to 0.5 % variant allele frequency (VAF) in one reaction, with median enrichment fold of 1,000 on 21 mutant DNA templates compared to the wild type. We applied LBDA‐qPCR to detect KRAS and NRAS mutation hotspots, utilizing a single plex assay capable of covering 81 mutations and tested in synthetic templates and colorectal cancer tissue samples. Moreover, the mutation types were verified through Sanger sequencing, demonstrating concordance with results obtained from next generation sequencing. Overall, LBDA‐qPCR provides a simple yet ultrasensitive approach for multiplexed detection of low VAF mutations hotspots, presenting a powerful tool for cancer diagnosis and monitoring. [ABSTRACT FROM AUTHOR]

Detecting low‐frequency DNA mutations hotspots cluster is critical for cancer diagnosis but remains challenging. Quantitative PCR (qPCR) is constrained by sensitivity, and allele‐specific PCR is restricted by throughput. Here we develop a long blocker displacement amplification (LBDA) coupled with qPCR for ultrasensitive and multiplexed variants detection. By designing long blocker oligos to perfectly match wildtype sequences while mispairing with mutants, long blockers enable 14–44 nt enrichment regions which is 2‐fold longer than normal BDA in the experiments. For wild template with a specific nucleotide, LBDA can detect different mutation types down to 0.5 % variant allele frequency (VAF) in one reaction, with median enrichment fold of 1,000 on 21 mutant DNA templates compared to the wild type. We applied LBDA‐qPCR to detect KRAS and NRAS mutation hotspots, utilizing a single plex assay capable of covering 81 mutations and tested in synthetic templates and colorectal cancer tissue samples. Moreover, the mutation types were verified through Sanger sequencing, demonstrating concordance with results obtained from next generation sequencing. Overall, LBDA‐qPCR provides a simple yet ultrasensitive approach for multiplexed detection of low VAF mutations hotspots, presenting a powerful tool for cancer diagnosis and monitoring. [ABSTRACT FROM AUTHOR]

Ultraviolet blood irradiation has been used as a physical therapy to treat many nonspecific diseases in clinics; however, the underlying mechanisms remain largely unclear. Neutrophils, the first line of host defense, play a crucial role in a variety of inflammatory responses. In the present work, we investigated the effects of ultraviolet light A (UVA) on the immune functions of human neutrophils at the single-cell level by using an inverted fluorescence microscope. N-Formyl-methionyl-leucyl-phenylalanine (FMLP), a classic physiological chemotactic peptide, was used to induce a series of immune responses in neutrophils in vitro. FMLP-induced calcium mobilization, migration, and phagocytosis in human neutrophils was significantly blocked after treatment with 365nm UVA irradiation, demonstrating the immunosuppressive effects of UVA irradiation on neutrophils. Similar responses were also observed when the cells were pretreated with H2O2, a type of reactive oxygen species (ROS). Furthermore, UVA irradiation resulted in an increase in NAD(P)H, a member of host oxidative stress in cells. Taken together, our data indicate that UVA irradiation results in immunosuppression associated with the production of ROS in human neutrophils. [ABSTRACT FROM AUTHOR]