The generation of long-lasting high affinity antibodies is one of the core pillars of our immune system ensuring life-long protection against infection. Dysregulation of this process can cause severe pathological conditions, such as alloimmunization during blood transfusions or self-reactivity in auto-immune disease.  High affinity antibodies are formed as product of a germinal center (GC) reaction, in which activated B cells proliferate and differentiated into antibodies-secreting cells (ASC). Understanding the exact mechanisms controlling this process within the GC is fundamental to devise strategies to modulate antibodies formation in both health and disease

During the past Sars-CoV2 pandemic we had the unique opportunity to investigate B cell differentiation dynamics in human settings by specifically analyzing Sars-CoV2 spike-specific B cells isolated from infected individuals or individuals undergoing mRNA vaccination. In particular, we generated a multi-omics single-cell dataset containing more than 40’000 spike-specific B cells from 24 individuals at three timepoints after vaccination of which we analyzed transcriptome, surface protein expression and B-cell receptor (BCR) sequence.

The aim of this project is to use this multi-omics single cell dataset to delineate B cell differentiation pathways by coupling transcriptome-based trajectory inference (also-called pseudotime) with BCR-based clonal lineages. The first, which is a general single-cell analysis approach, tries order cells along a continuous progression path leveraging on minor transcriptomic differences among cells. The latter, which is applicable only to B cells, leverages the sequence of the B cell receptor (BCR), which is unique to each B cell and inherited by its progeny, to reconstruct lineage trees of single B cell responses. These trees are inferred from the accumulation of mutations in the BCR sequence (somatic hypermutations, SHM) that arise during the germinal center reaction, where B cells iteratively mutate and are selected for improved antigen binding.

Your task within this project will be to evaluate which is the best computational approach to reconstruct BCR-based clonal lineages starting from single-cell data. You will be testing selected recently published methodologies on our spike-specific B cells datasets and perform comparative analysis on the obtained reconstructed lineages. Knowledge of R/Phyton is required.