We are developing novel technologies for high throughput analysis of genomes, transcriptomes and proteins. The most recent method developed by the group is called Droplet Barcode Sequencing (DBS). In two pioneering studies, we demonstrated use of DBS for DNA barcoding (Borgström et al. 2015 and Redin et al., 2017). We then further developed DBS allowing for haplotyping of the entire human genome (Redin et al., 2019). The DBS technology is now being applied to haplotype-resolve cancer genomes to link somatic mutations to each other and also to structural variants in a haplotype context. This will ultimately result in better understanding of the cumulative effects of interactions between genetic variations across long distances that may lead to carcinogenesis. In addition to the molecular method, we are developing bioinformatics pipelines capable to handle DBS linked-read data.
The DBS technology is also applied for analysis of proteins (Stiller et al., 2019). This method, denoted DBS for protein analysis (DBS-Pro) was recently further developed for characterizing surface proteins on individual exosomes (Banijamali et al. 2022). In this proof-of-concept study we demonstrated that DBS-Pro allows for analysis of single exosomes. A total of over 120,000 individual exosomes obtained from a NSCLC cell line and from three malignant pleural effusion fluid of NSCLC patients were analyzed based on their surface proteins. We also showed that the method enables single vesicle surface protein profiling and by extension characterization of exosome-subtypes, which is essential to identify the cellular origin of vesicles in cancer samples. In addition, for high resolution exosome characterization, we are today trying to utilize DBS for simultaneous analysis of transcripts and proteins of single vesicles.
DIVISION OF GENE TECHNOLOGY
Telephone +46 8 790 98 21
Address: Tomtebodavägen 23A, Solna
E-mail: afshin.ahmadian@scilifelab.se