Home NATURALEZA Amplifying mutational profiling of extracellular vesicle mRNA with SCOPE

Amplifying mutational profiling of extracellular vesicle mRNA with SCOPE

21
0


  • Ignatiadis, M., Sledge, G. W. & Jeffrey, S. S. Liquid biopsy enters the clinic—implementation issues and future challenges. Nat. Rev. Clin. Oncol. 18, 297–312 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Heitzer, E., Haque, I. S., Roberts, C. E. S. & Speicher, M. R. Current and future perspectives of liquid biopsies in genomics-driven oncology. Nat. Rev. Genet. 20, 71–88 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Killingsworth, B., Welsh, J. A. & Jones, J. C. EV translational horizons as viewed across the complex landscape of liquid biopsies. Front. Cell Dev. Biol. 9, 556837 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Parikh, A. R. et al. Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers. Nat. Med. 25, 1415–1421 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pantel, K. & Alix-Panabières, C. Liquid biopsy and minimal residual disease—latest advances and implications for cure. Nat. Rev. Clin. Oncol. 16, 409–424 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Siravegna, G., Marsoni, S., Siena, S. & Bardelli, A. Integrating liquid biopsies into the management of cancer. Nat. Rev. Clin. Oncol. 14, 531–548 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shao, H. et al. New technologies for analysis of extracellular vesicles. Chem. Rev. 118, 1917–1950 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Im, H. et al. Label-free detection and molecular profiling of exosomes with a nano-plasmonic sensor. Nat. Biotechnol. 32, 490–495 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jo, A. et al. Inaugurating high-throughput profiling of extracellular vesicles for earlier ovarian cancer detection. Adv. Sci. 10, e2301930 (2023).

    Article 

    Google Scholar
     

  • Dixson, A. C., Dawson, T. R., Di Vizio, D. & Weaver, A. M. Context-specific regulation of extracellular vesicle biogenesis and cargo selection. Nat. Rev. Mol. Cell Biol. 24, 454–476 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Skog, J. et al. Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers. Nat. Cell Biol. 10, 1470–1476 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Vitale, S. R. et al. Detection of tumor-derived extracellular vesicles in plasma from patients with solid cancer. BMC Cancer 21, 315 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • van de Haar, J. et al. Codon-specific KRAS mutations predict survival benefit of trifluridine/tipiracil in metastatic colorectal cancer. Nat. Med. 29, 605–614 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Shao, H. et al. Chip-based analysis of exosomal mRNA mediating drug resistance in glioblastoma. Nat. Commun. 6, 6999 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Park, J. et al. An integrated magneto-electrochemical device for the rapid profiling of tumour extracellular vesicles from blood plasma. Nat. Biomed. Eng. 5, 678–689 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Noerholm, M. et al. RNA expression patterns in serum microvesicles from patients with glioblastoma multiforme and controls. BMC Cancer 12, 22 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wei, Z. et al. Coding and noncoding landscape of extracellular RNA released by human glioma stem cells. Nat. Commun. 8, 1145 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Hong, J. S., Son, T., Castro, C. M. & Im, H. CRISPR/Cas13a-based microRNA detection in tumor-derived extracellular vesicles. Adv. Sci. 10, e2301766 (2023).

    Article 

    Google Scholar
     

  • Yan, H. et al. A one-pot isothermal Cas12-based assay for the sensitive detection of microRNAs. Nat. Biomed. Eng. 7, 1583–1601 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ramshani, Z. et al. Extracellular vesicle microRNA quantification from plasma using an integrated microfluidic device. Commun. Biol. 2, 189 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Li, Y. et al. EV-origin: enumerating the tissue-cellular origin of circulating extracellular vesicles using exLR profile. Comput. Struct. Biotechnol. J. 18, 2851–2859 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pickar-Oliver, A. & Gersbach, C. A. The next generation of CRISPR–Cas technologies and applications. Nat. Rev. Mol. Cell Biol. 20, 490–507 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kaminski, M. M., Abudayyeh, O. O., Gootenberg, J. S., Zhang, F. & Collins, J. J. CRISPR-based diagnostics. Nat. Biomed. Eng. 5, 643–656 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Abudayyeh, O. O. & Gootenberg, J. S. CRISPR diagnostics. Science 372, 914–915 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Potapov, V. & Ong, J. L. Examining sources of error in PCR by single-molecule sequencing. PLoS ONE 12, e0169774 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Kebschull, J. M. & Zador, A. M. Sources of PCR-induced distortions in high-throughput sequencing data sets. Nucleic Acids Res. 43, e143 (2015).

    PubMed 

    Google Scholar
     

  • Gootenberg, J. S. et al. Nucleic acid detection with CRISPR–Cas13a/C2c2. Science 356, 438–442 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Truong, N. P., Jia, Z., Burges, M., McMillan, N. A. & Monteiro, M. J. Self-catalyzed degradation of linear cationic poly(2-dimethylaminoethyl acrylate) in water. Biomacromolecules 12, 1876–1882 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Maslak, M. & Martin, C. T. Kinetic analysis of T7 RNA polymerase transcription initiation from promoters containing single-stranded regions. Biochemistry 32, 4281–4285 (1993).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Avaro, A. S. & Santiago, J. G. Uncertainty quantification of Michaelis-Menten kinetic rates and its application to the analysis of CRISPR-based diagnostics. Angew. Chem. Int. Ed. Engl. 61, e202209527 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Newman, A. M. et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat. Med. 20, 548–554 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Diehl, F. et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc. Natl Acad. Sci. USA 102, 16368–16373 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, R. et al. Therapeutically reprogrammed nutrient signalling enhances nanoparticulate albumin bound drug uptake and efficacy in KRAS-mutant cancer. Nat. Nanotechnol. 16, 830–839 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pfirschke, C. et al. Immunogenic chemotherapy sensitizes tumors to checkpoint blockade therapy. Immunity 44, 343–354 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • DuPage, M., Dooley, A. L. & Jacks, T. Conditional mouse lung cancer models using adenoviral or lentiviral delivery of Cre recombinase. Nat. Protoc. 4, 1064–1072 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mendiratta, G. et al. Cancer gene mutation frequencies for the U.S. population. Nat. Commun. 12, 5961 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Welsh, J. A. et al. Minimal information for studies of extracellular vesicles (MISEV2023): from basic to advanced approaches. J. Extracell. Vesicles 13, e12404 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Weller, M. et al. EANO guidelines on the diagnosis and treatment of diffuse gliomas of adulthood. Nat. Rev. Clin. Oncol. 18, 170–186 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Guo, G. et al. Ligand-independent EGFR signaling. Cancer Res. 75, 3436–3441 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, W. W. et al. BEAMing and droplet digital PCR analysis of mutant IDH1 mRNA in glioma patient serum and cerebrospinal fluid extracellular vesicles. Mol. Ther. Nucleic Acids 2, e109 (2013).

    Article 
    PubMed 

    Google Scholar
     

  • SongTao, Q. et al. IDH mutations predict longer survival and response to temozolomide in secondary glioblastoma. Cancer Sci. 103, 269–273 (2012).

    Article 
    PubMed 

    Google Scholar
     

  • Batool, S. M. et al. Highly sensitive EGFRvIII detection in circulating extracellular vesicle RNA of glioma patients. Clin. Cancer Res. 28, 4070–4082 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Krug, A. K. et al. Improved EGFR mutation detection using combined exosomal RNA and circulating tumor DNA in NSCLC patient plasma. Ann. Oncol. 29, 700–706 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Srivastava, P. & Prasad, D. Isothermal nucleic acid amplification and its uses in modern diagnostic technologies. 3 Biotech 13, 200 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Ueda, T., Tohda, H., Chikazumi, N., Eckstein, F. & Watanabe, K. Phosphorothioate-containing RNAs show mRNA activity in the prokaryotic translation systems in vitro. Nucleic Acids Res. 19, 547–552 (1991).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lane, R. E., Korbie, D., Trau, M. & Hill, M. M. Optimizing size exclusion chromatography for extracellular vesicle enrichment and proteomic analysis from clinically relevant samples. Proteomics 19, e1800156 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Lee, K. et al. Multiplexed profiling of single extracellular vesicles. ACS Nano 12, 494–503 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang, J. et al. Engineering a tunable micropattern-array assay to sort single extracellular vesicles and particles to detect RNA and protein in situ. J. Extracell. Vesicles 12, e12369 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Schraa, S. J. et al. Circulating tumor DNA guided adjuvant chemotherapy in stage II colon cancer (MEDOCC-CrEATE): study protocol for a trial within a cohort study. BMC Cancer 20, 790 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Koga, T. et al. Mapping of genomic EGFRvIII deletions in glioblastoma: insight into rearrangement mechanisms and biomarker development. Neuro Oncol. 20, 1310–1320 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Muralidharan, K. et al. TERT promoter mutation analysis for blood-based diagnosis and monitoring of gliomas. Clin. Cancer Res. 27, 169–178 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shen, S. Y. et al. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature 563, 579–583 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chang, M. T. et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Nat. Biotechnol. 34, 155–163 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Miller, M. L. et al. Pan-cancer analysis of mutation hotspots in protein domains. Cell Syst. 1, 197–209 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sequist, L. V. et al. Genotypic and histological evolution of lung cancers acquiring resistance to EGFR inhibitors. Sci. Transl. Med. 3, 75ra26 (2011).

    Article 
    PubMed 

    Google Scholar
     

  • Krook, M. A. et al. Fibroblast growth factor receptors in cancer: genetic alterations, diagnostics, therapeutic targets and mechanisms of resistance. Br. J. Cancer 124, 880–892 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cohen, J. D. et al. Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science 359, 926–930 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gootenberg, J. S. et al. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360, 439–444 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     



  • Source link

    LEAVE A REPLY

    Please enter your comment!
    Please enter your name here