A mechanism based integrated multi-omics approach for biomarker discovery
Sweden (IFMSA-Sweden) - Karolinska Institutet, Stockholm
Department of Laboratory Medicine, ANA Futura
Matti Sällberg
Ujjwal Neogi
4 weeks
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
No No No No No No No Yes No No No No
Type of Research Project
- Clinical Project with Laboratory work
What is the background of the project?
The Neogi lab work towards unraveling the mechanism of aging in people living with HIV (PLHIV) on successful therapy to identify biomarkers for potential future clinical intervention. In a few years, improvement and development of new omics technologies have notably improved personalized medicine, in prevention or treatment settings, by providing a broad range of information ranging from genetics to metabolites. The rapidly increasing accessibility of genetic and biomolecular expression data from new high throughput technologies are the foundation to shift the traditional phenotype-first approach to genetic or molecular data-first approaches. Systems biology approaches are increasingly implemented in biomedical research and scientific disciplines are getting more and more diversified. It is, thus, important to get a complete understanding of which genetic and environmental factors affect the complexities of human-aging, which will be valuable for society as a whole. Until today, most of the studies aiming at identifying premature aging of the immune system have focused either on clinical features, on the outcome of specified age-related disorders or selected immunological aspects.
What is the aim of the project?
The aim of the study is to understand to what extent people living with HIV/AIDS have accelerated aging of the immune system due to the systemic inflammation compared to demographically and lifestyle-matched healthy individuals.
What techniques and methods are used?
The intended learning objective will be to understand how the omics techniques can be taken to the lab and how that translates to clinical practice. The methods that will then be used are R-programming, transcriptomics, proteomics and metabolomics data will be generated from RNAseq and mass-spectrometry data respectively, western blot flow cytometry, and quantitive polymerase chain reaction (qPCR) analysis. Results will be generated from omics –data and translated to the lab for basic scientific analysis.
What is the role of the student?
- The student will mainly observe
- The student will observe the practical experiments but will be highly involved in the analysis of the results
- The tasks will be done under supervision
What are the tasks expected to be accomplished by the student?
The student will mainly work on the project on the computer if the knowledge in R-programming is available. The students will also observe how the results generated from the omics –data has translated to the lab for basic scientific analysis. The student will spend time with bioinformatician to understand the transcriptomics, proteomics and metabolomics data generated from RNAseq and mass-spectrometry data respectively. The student will observe western blot, flow cytometry, and qPCR analysis. If a student has the experience to pipette, he/she can do some hands-on training also.
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
Yes. The student will accompany Ph.D. students and PostDocs in the lab who are highly experienced in the specific tasks. The student will be given few review articles for basic understanding. A Skype meeting with the student before hand as well.
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- The student will prepare a poster
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
Basic knowledge in R programming (not necessary) and ability to work with a pipette is sufficient.
Are there any legal limitations in the student’s involvement
Type of students accepted
This project accepts:
- Medical students
- Graduated students (less than 6 months)
- Pre-Medical students from the American-British system
- Students in biomedical fields
- Lorenzon R; Mariotti-Ferrandiz E; Aheng C; et al Clinical and multi-omics cross-phenotyping of patients with autoimmune and autoinflammatory diseases: the observational TRANSIMMUNOM protocol BMJ Open 2018;8:e021037