Periodic Reporting for period 1 - droplet-small-seq (High-throughput droplet-based single-cell small RNA sequencing technology)
Período documentado: 2021-10-01 hasta 2023-09-30
Given the biological importance of non-coding RNAs, the main objective of this project was to develop a high-throughput droplet-based scRNA-seq technology and apply it to investigate the regulatory roles of miRNAs. The small RNA sequencing technology established during the course of this project was successfully applied on leukemia cell model, demonstrating its proof-of-principle. While ongoing efforts are dedicated to its application in primary cells, we have already gained broad insights by employing single-cell long RNA-seq with inDrops-2, followed by trajectory analysis and in silico miRNA-target prediction. We identified potential miRNAs targeting hematopoietic lineage-specific genes and valuable insights in possible regulation of hemopoiesis.
To reach our targeted audience, comprising scientists in the field, we presented the droplet-small-seq results at the “EMBO | EMBL Symposium: The non-coding genome” (Heidelberg, Germany). Results of the project will be shared via reputable, open-access, peer-reviewed journals. Presently, we have deposited a preprint to the bioRxiv for a manuscript detailing an improved scRNA-seq method (inDrops-2), which we also use as a basis for small RNA-seq. To gain experience in analyzing scRNA-seq data, the fellow contributed to a study deciphering microenvironment of clear cell renal cell carcinoma, which is also deposited on the bioRxiv. Although outside the scope of the project, the acknowledgment of the MSCA fellowship appears in a letter, which was written in response to authors who misinterpreted the fellow and his former colleagues' previous research and misapplied Mendelian Randomization analysis. Besides the previously mentioned manuscripts, we collected sufficient results that will be reported in at least one more publication. This publication will provide a detailed description of the single-cell small RNA-seq method and currently ongoing efforts for its application in primary cells such as peripheral PBMC and CD34+ cells.
Our project has attracted attention from international media outlets, such as GenomeWeb. To share his experiences about writing a successful MSCA application and to encourage others to apply for the fellowship, the fellow gave a talk at the “Baltic MSCA Postdoctoral Fellowships Inspiration Day” event, jointly organized by the Estonian, Latvian and Lithuanian Research Councils. Moreover, the project was also selected as one of the Widening Countries Inspirational Stories by the MSCA-NET.