-40.1. Clonal expansion: diversity and abundance
+39.1. Clonal expansion: diversity and abundance
In general, lymphocytes are in a dormant state until receiving an external signal (epitope recognition of foreign agent) or stimulation from autocrine agents (signaling from the same organism as a response from the innate immune system). As a consequence, the specific cells proliferate dramatically to fulfill the defense response they are programmed to perform in a process known as clonal expansion [Polonsky et al., 2016]. This refers to the recognition of the proliferation of specific cells given the high number of the same IR through many, different cells (expanded clones). This expansion provides hints of differentiation from naive lymphocytes to mature effector and memory lymphocytes, helping in the interpretation and expected results regarding previous cell annotation [Polonsky et al., 2016]. On the other hand, the analysis of expanded clones should consider derivative processes such as clonal competitions (two or more clones in expansion competing for the same space), clonal dominance (one single clonal expanded cell outnumbering the rest of the clonal cells), and bystander activation (activation of T-cells by cytokines but not for T-cell receptor coupling) [Naxerova, 2020][Ashcroft et al., 2017][Kim and Shin, 2019].
The dynamical changes in terms of the number of cells per clonotype in a given space allow applying concepts from population biology such as diversity and abundance. Diversity is defined as number of species and their amount in an area or community, whereas abundance is the number, or frequency of individuals of the same species [Travlos et al., 2018]. Here, we can replace the term species with clones to make clear their relevance in single-cell IRs analysis. If a high clonal expansion has been detected in a specific cell type, e.g., effector CD8+ T-cells, the number of clones is expected to reduce because the expanded clones are taken space from the total available sacrificing receptor alternatives in the process. Therefore, we could expect a reduction in the diversity for this cell-type. On the other hand, we could expect an increase in abundance regarding the expanded clones given they have increased the number of individuals (cells) belonging to this specific clone (observed by the number of cells per clone ID).
-40.2. Gene segment usage and spectratype
+39.2. Gene segment usage and spectratype
The process shaping a T-cell or B-cell receptor by rearrangement of the V(D)J segments is thinking to generate random sequences and, in consequence, the distribution of V(D)J sequences should follow a uniform distribution. Nevertheless, it has been observed that V(D)J gene usage frequency is largely consistent across different individuals, which suggests a preference selection in terms of the V(D)J gene segments used [Elhanati et al., 2014]. That allows the analysis of gene segment usage in terms of abundance of most used gene segments per cell type and frequency of most abundant segment per cell type per individual [Chernyshev et al., 2021]. Likewise, considering we know the amino aicd composition of the immune receptors for each cell, it is possible to identify the exact combinations of V(D)J segments of interest.
On the other hand, the recombination of V(D)J gene segments and the imprecise junction of V and J segments produce CDR3 regions with variable lengths. Spectratype analysis is seen as the measurement of the heterogeneity of CDR3 regions by their length diversity across the different cell types [Ciupe et al., 2013]. This measurement, in combination with clonal expansion and gene segment usage provides pieces of evidence to define well-described immunodominant clonotypes.