Characterization of CD41+ cells in the lymph node

Lymph nodes (LNs) are the critical sites of immunity, and the stromal cells of LNs are crucial to their function. Our understanding of the stromal compartment of the LN has deepened recently with the characterization of nontraditional stromal cells. CD41 (integrin αIIb) is known to be expressed by platelets and hematolymphoid cells. We identified two distinct populations of CD41⁺Lyve1⁺ and CD41⁺Lyve1^- cells in the LNs. CD41⁺Lyve1^- cells appear in the LN mostly at the later stages of the lives of mice. We identified CD41⁺ cells in human LNs as well. We demonstrated that murine CD41⁺ cells express mesodermal markers, such as Sca-1, CD105 and CD29, but lack platelet markers. We did not observe the presence of platelets around the HEVs or within proximity to fibroblastic reticular cells of the LN. Examination of thoracic duct lymph fluid showed the presence of CD41⁺Lyve1^- cells, suggesting that these cells recirculate throughout the body. FTY720 reduced their trafficking to lymph fluid, suggesting that their egress is controlled by the S1P1 pathway. CD41⁺Lyve1^- cells of the LNs were sensitive to radiation, suggestive of their replicative nature. Single cell RNA sequencing data showed that the CD41⁺ cell population in naïve mouse LNs expressed largely stromal cell markers. Further studies are required to examine more deeply the role of CD41⁺ cells in the function of LNs.

Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets

Background

Multiple sclerosis (MS) is an autoimmune condition of the central nervous system with a well-characterized genetic background. Prior analyses of MS genetics have identified broad enrichments across peripheral immune cells, yet the driver immune subsets are unclear.

Results

We utilize chromatin accessibility data across hematopoietic cells to identify cell type-specific enrichments of MS genetic signals. We find that CD4 T and B cells are independently enriched for MS genetics and further refine the driver subsets to T_h17 and memory B cells, respectively. We replicate our findings in data from untreated and treated MS patients and find that immunomodulatory treatments suppress chromatin accessibility at driver cell types. Integration of statistical fine-mapping and chromatin interactions nominate numerous putative causal genes, illustrating complex interplay between shared and cell-specific genes.

Conclusions

Overall, our study finds that open chromatin regions in CD4 T cells and B cells independently drive MS genetic signals. Our study highlights how careful integration of genetics and epigenetics can provide fine-scale insights into causal cell types and nominate new genes and pathways for disease.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02694-y.

DNA methylation profiles unique to Kalahari KhoeSan individuals

Genomes of KhoeSan individuals of the Kalahari Desert provide the greatest understanding of single nucleotide diversity in the human genome. Compared with individuals in industrialized environments, the KhoeSan have a unique foraging and hunting lifestyle. Given these dramatic environmental differences, and the responsiveness of the methylome to environmental exposures of many types, we hypothesized that DNA methylation patterns would differ between KhoeSan and neighbouring agropastoral and/or industrial Bantu. We analysed Illumina HumanMethylation 450 k array data generated from blood samples from 38 KhoeSan and 42 Bantu, and 6 Europeans. After removing CpG positions associated with annotated and novel polymorphisms and controlling for white blood cell composition, sex, age and technical variation we identified 816 differentially methylated CpG loci, out of which 133 had an absolute beta-value difference of at least 0.05. Notably SLC39A4/ZIP4, which plays a role in zinc transport, was one of the most differentially methylated loci. Although the chronological ages of the KhoeSan are not formally recorded, we compared historically estimated ages to methylation-based calculations. This study demonstrates that the epigenetic profile of KhoeSan individuals reveals differences from other populations, and along with extensive genetic diversity, this community brings increased accessibility and understanding to the diversity of the human genome.

MethylToSNP: identifying SNPs in Illumina DNA methylation array data

Background

Current array-based methods for the measurement of DNA methylation rely on the process of sodium bisulfite conversion to differentiate between methylated and unmethylated cytosine bases in DNA. In the absence of genotype data this process can lead to ambiguity in data interpretation when a sample has polymorphisms at a methylation probe site. A common way to minimize this problem is to exclude such potentially problematic sites, with some methods removing as much as 60% of array probes from consideration before data analysis.

Results

Here, we present an algorithm implemented in an R Bioconductor package, MethylToSNP, which detects a characteristic data pattern to infer sites likely to be confounded by polymorphisms. Additionally, the tool provides a stringent reliability score to allow thresholding on SNP predictions. We calibrated parameters and thresholds used by the algorithm on simulated and real methylation data sets. We illustrate findings using methylation data from YRI (Yoruba in Ibadan, Nigeria), CEPH (European descent) and KhoeSan (southern African) populations. Our polymorphism predictions made using MethylToSNP have been validated through SNP databases and bisulfite and genomic sequencing.

Conclusions

The benefits of this method are threefold. First, it prevents extensive data loss by considering only SNPs specific to the individuals in the study. Second, it offers the possibility to identify new polymorphisms in samples for which there is little known about the genetic landscape. Third, it identifies variants as they exist in functional regions of a genome, such as in CTCF (transcriptional repressor) sites and enhancers, that may be common alleles or personal mutations with potential to deleteriously affect genomic regulatory activities. We demonstrate that MethylToSNP is applicable to the Illumina 450K and Illumina 850K EPIC array data and is also backwards compatible to the 27K methylation arrays. Going forward, this kind of nuanced approach can increase the amount of information derived from precious data sets by considering samples of the project individually to enable more informed decisions about data cleaning.

Characterization of Trichodesmium-associated viral communities in the eastern Gulf of Mexico

Trichodesmium surface aggregations shape the co-occurring microbial community by providing organic carbon and nitrogen and surfaces on which microorganisms can aggregate. Rapid collapse of Trichodesmium aggregations leads to drastic changes in the chemical and physical properties of surrounding waters, eliciting a response from the microbial community and their associated viruses. Three viral metagenomes were constructed from experimentally lysed Trichodesmium collected from two locations in the eastern Gulf of Mexico. Trichodesmium were either treated with mitomycin C to induce potential lysogens or incubated in the absence of mitomycin C. Comparative analyses of viral contiguous sequences indicated that viral composition was responsive to treatment type. Cyanophages were more represented within incubations treated with mitomycin C, while gammaproteobacterial phages were more represented within the untreated incubation. The detection of latent bacteriophage integrases in both the chemically treated and untreated incubations suggests that Trichodesmium death may lead to prophage induction within associated microorganisms. While no single cyanophage-like genotype associated with Trichodesmium lysis could be identified that might point to an infectious Trichodesmium phage, reads resembling Trichodesmium were recovered. These data reveal a diverse consortium of lytic and temperate phages associated with Trichodesmium whose patterns of representation within treated and untreated libraries offer insights into the activities of host and viral communities during Trichodesmium aggregation collapse.