Bioinformatics Analysis and Visualisation of Medical Genomics Data

av Blaz Oder, 11 - 27 mars 2023

I am writing this travel report in relation to the Radiumhemmets Research Fund travel grant that I received for participation in the Bioinformatics Analysis and Visualisation of Medical Genomics Data course at the University of Tokyo, Japan, from March 15-22, 2023.

The course was jointly organized by Karolinska Institutet and the University of Tokyo (KI course: 5633) and took place at each institution for one week. It provided advanced training in bioinformatics analysis and visualization techniques for omics data, with an emphasis on single-cell omics data, and comprised lectures, a journal club session, workshops, and presentations of our projects and bioinformatics analyses. The course was highly in line with my doctoral project “Single-cell multi-omics analyses in chronic lymphocytic leukemia” as well as my Individual Study Plan and degree objectives.

The lectures were delivered by renowned bioinformatics experts including Lea Mikkola from the Turku Bioscience Center, University of Turku who gave a fascinating lecture on single-cell and spatial omics, highlighted crucial factors to consider when designing omics studies, and discussed potential pitfalls in single-cell and spatial omics studies; Ryuichiro Natako and Luis Augusto Eijy Nagai from the Laboratory of Computational Genomics, Institute for Quantitative Biosciences, University of Tokyo who discussed bioinformatics software development and public database utilization for large-scale epigenomics and single-cell omics data analysis; Kenta Nakai from the Laboratory of Functional Analysis in silico, Institute of Medical Science, University of Tokyo who presented bioinformatics approaches for inferring enhancer-promoter interactions; Sung-Joon Park from the Human Genome Center, Institute of Medical Science, University of Tokyo who delved into the crosstalk landscape of transcriptional regulators and the impact of chromatin re-organization in gene regulation and covered computational approaches (iterative regression modeling and graph embedding) for gene regulation inference; Juha Kere from the Department of Biosciences and Nutrition, Karolinska Institutet who discussed the prediction of complex disorders; and Yutaka Suzuki from the Laboratory of Systems Genomics at the University of Tokyo who discussed the role of bioinformatics in cancer research and drug discovery. Overall, the lectures were diverse and informative, and the speakers were knowledgeable and engaging, making the experience both educational and enjoyable.

I actively participated in the journal club session, wherein we analyzed and discussed various scientific publications pertaining to bioinformatics and omics data analysis, including “Unbiased integration of single cell transcriptome replicates” by Loza et al. (NAR Genomics and Bioinformatics, 2022), “Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data” by Nakajima et al. (Nucleic Acids Research, 2021), “Altered cervicovaginal microbiota in premenopausal ovarian cancer patients” by Morikawa et al. (Gene, 2022), “Bioinformatical dissection of fission yeast DNA replication origins” by Masuda et al. (Open Biology, 2020), “Generation of 3D lacrimal gland organoids from human pluripotent stem cells” by Hayashi et al. (Nature, 2022), and “Human white adipose tissue displays selective insulin resistance in the obese state” by Mileti et al. (Diabetes, 2021). During the session, I presented an article entitled ”A single-cell and spatially resolved atlas of human breast cancers” authored by Wu et al. and published in Nature Genetics in 2021.

During the workshops and under the mentorship of Lea Mikkola, I leveraged the single-cell RNA sequencing data from the aforementioned publication to reproduce selected figures and perform other bioinformatics analyses to test my formulated hypotheses. Thanks to the comprehensive R training that I received during the first week of the course, I was able to effectively use the R programming language to analyze the data. The gained knowledge proved instrumental in my ability to produce high-quality figures. Through my analyses, I identified promising novel biomarkers that could potentially enhance the classification of breast cancer patients. I presented my findings through an oral presentation, which was well-received by the course instructors and other participants. The presentation helped me to refine my communication skills and provided an opportunity to showcase my ability to utilize the knowledge I had gained in the course.

Throughout the course, I acquired theoretical knowledge and practical skills in bioinformatics data analysis while also having the chance to learn from and network with fellow attendees and esteemed professionals with diverse areas of expertise. In addition, I had the privilege of engaging with several PhD students from the University of Tokyo who are working on projects similar to mine. During our discussions, we exchanged concepts and ideas for some of the challenges we face in our respective projects, and we agreed to stay in touch and explore potential future collaboration opportunities.

In conclusion, I would like to express my gratitude to the Radiumhemmets Research Fund for the travel grant that supported my participation in this course. I am confident that the knowledge and skills I acquired during the course will have a positive impact on my current and future research projects, and I look forward to exploring potential collaborations with some of the participants and lecturers. The experience of traveling to Japan and immersing myself in a different culture was also invaluable, and I believe it has broadened my horizons and offered me novel perspectives in general.

Thank you for your support.