moFluMemB - Dataset : Results of data analysis

Title

Viral infection engenders bona fide and bystander subsets of lung-resident memory B cells through a permissive mechanism

Authors
Claude Gregoire,1 Lionel Spinelli,1 Sergio Villazala-Merino,1 Laurine Gil,1 María Pía Holgado,1 Myriam Moussa,1 Chuang Dong,1 Ana Zarubica,2 Mathieu Fallet,1 Jean-Marc Navarro,1 Bernard Malissen,1,2 Pierre Milpied,1,* and Mauro Gaya1,*

Affiliations
1 Centre d'Immunologie de Marseille-Luminy (CIML), Aix Marseille Université, INSERM, CNRS, Marseille, France
2  Centre d'Immunophénomique (CIPHE), Aix Marseille Université, INSERM, CNRS, Marseille, France
* Correspondence: milpied@ciml.univ-mrs.fr (P.M.), gaya@ciml.univ-mrs.fr (M.G.)

Summary
Lung-resident memory B cells (MBCs) provide localized protection against reinfection in the respiratory airways. Currently, the biology of these cells remains largely unexplored. Here, we combined influenza and SARS-CoV-2 infection with fluorescent-reporter mice to identify MBCs regardless of antigen specificity.  We found that two main transcriptionally distinct subsets of MBCs colonized the lung peribronchial niche after infection. These subsets arose from different progenitors and were both class-switched, somatically mutated and intrinsically biased in their differentiation fate towards plasma cells. Combined analysis of antigen-specificity and B cell receptor repertoire segregated these subsets into “bona fide” virus-specific MBCs and “bystander” MBCs with no apparent specificity for eliciting viruses and generated through an alternative permissive mechanism. Thus, diverse transcriptional programs in MBCs are not linked to specific effector fates but rather to divergent strategies of the immune system to simultaneously provide rapid protection from reinfection while diversifying the initial B cell repertoire.

Data:  

• 10x_190712_m_moFluMemB_AnalysisOutput.tar.gz : Complete analysis of the data with HTML analysis reports, flat data files and RDS files with R objects issued from analysis of the data of 10x 5’ scRNA-Seq on memory B cells sorted from single-cell suspensions of spleen, lymph nodes and lungs with enzymatic digestion of lung tissue at 37°C.
• 10x_191105_m_moFluMemB_AnalysisOutput.tar.gz : Complete analysis of the data with HTML analysis reports, flat data files and RDS files with R objects issued from analysis of the data of 10x 5’ scRNA-Seq on memory B cells sorted from single-cell suspensions of spleen, lymph nodes and lungs with mechanical dissociation of lung tissue at 4°C.
• custom_201216_m_moFluMemB_AnalysisOutput.tar.gz : Complete analysis of the data with HTML analysis reports, flat data files and RDS files with R objects issued from analysis of the data of FB5P-seq protocol (Attaf et al., 2020) on memory B cells sorted from single-cell suspensions of lungs with enzymatic digestion of lung tissue at 37°C, with index sorting information for a panel of antibodies identifying subsets of memory B cells. 

See the three other Zenodo deposit for the rest of the data:

https://zenodo.org/records/5564625

https://zenodo.org/record/5565864

https://zenodo.org/record/5566675