T Cells Specific for a Mycobacterial Glycolipid Expand after Intravenous Bacillus Calmette-Guérin Vaccination

Intradermal vaccination with Mycobacterium bovis bacillus Calmette-Guérin (BCG) protects infants from disseminated tuberculosis, and i.v. BCG protects nonhuman primates (NHP) against pulmonary and extrapulmonary tuberculosis. In humans and NHP, protection is thought to be mediated by T cells, which typically recognize bacterial peptide Ags bound to MHC proteins. However, during vertebrate evolution, T cells acquired the capacity to recognize lipid Ags bound to CD1a, CD1b, and CD1c proteins expressed on APCs. It is unknown whether BCG induces T cell immunity to mycobacterial lipids and whether CD1-restricted T cells are resident in the lung. In this study, we developed and validated Macaca mulatta (Mamu) CD1b and CD1c tetramers to probe ex vivo phenotypes and functions of T cells specific for glucose monomycolate (GMM), an immunodominant mycobacterial lipid Ag. We discovered that CD1b and CD1c present GMM to T cells in both humans and NHP. We show that GMM-specific T cells are expanded in rhesus macaque blood 4 wk after i.v. BCG, which has been shown to protect NHP with near-sterilizing efficacy upon M. tuberculosis challenge. After vaccination, these T cells are detected at high frequency within bronchoalveolar fluid and express CD69 and CD103, markers associated with resident memory T cells. Thus, our data expand the repertoire of T cells known to be induced by whole cell mycobacterial vaccines, such as BCG, and show that lipid Ag-specific T cells are resident in the lungs, where they may contribute to protective immunity

CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation.

Library searching is a powerful technique for detecting peptides using either data independent or data dependent acquisition. While both large-scale spectrum library curators and deep learning prediction approaches have focused on beam-type CID fragmentation (HCD), resonance CID fragmentation remains a popular technique. Here we demonstrate an approach to model the differences between HCD and CID spectra, and present a software tool, CIDer, for converting libraries between the two fragmentation methods. We demonstrate that just using a combination of simple linear models and basic principles of peptide fragmentation, we can explain up to 43% of the variation between ions fragmented by HCD and CID across an array of collision energy settings. We further show that in some circumstances, searching converted CID libraries can detect more peptides than searching existing CID libraries or libraries of machine learning predictions from FASTA databases. These results suggest that leveraging information in existing libraries by converting between HCD and CID libraries may be an effective interim solution while large-scale CID libraries are being developed

Evolution of microRNA in primates

<div><p>MicroRNA play an important role in post-transcriptional regulation of most transcripts in the human genome, but their evolution across the primate lineage is largely uncharacterized. A particular miRNA can have one to thousands of messenger RNA targets, establishing the potential for a small change in sequence or overall miRNA structure to have profound phenotypic effects. However, the majority of non-human primate miRNA is predicted solely by homology to the human genome and lacks experimental validation. In the present study, we sequenced thirteen species representing a wide range of the primate phylogeny. Hundreds of miRNA were validated, and the number of species with experimentally validated miRNA was tripled. These species include a sister taxon to humans (bonobo) and basal primates (aye-aye, mouse lemur, galago). Consistent with previous studies, we found the seed region and mature miRNA to be highly conserved across primates, with overall structural conservation of the pre-miRNA hairpin. However, there were a number of interesting exceptions, including a seed shift due to structural changes in miR-501. We also identified an increase in the number of miR-320 paralogs throughout primate evolution. Many of these non-conserved miRNA appear to regulate neuronal processes, illustrating the importance of investigating miRNA to learn more about human evolution.</p></div

Mean pairwise sequence identity compared to the Structure Conservation Index (SCI).

<p>In general, an SCI near or above the mean pairwise identity indicates structural conservation (dotted gray line). The black line is the linear regression for our data (R² = 0.1719).</p

Alignment of miR-2355 homologous sequences.

<p>The black line indicates species that have experimental support for the transcription of miR-2355, either in miRBase (human, cow) or from this study (chimpanzee, bonobo, gorilla, and orangutan). The red boxes outline the mature and star sequences within the miRNA. Variants only found among the great apes are highlighted in yellow, while all other variants are marked in grey. Humans have experienced a reversion at position 15 of the mature miRNA, restoring that nucleotide to its ancestral state.</p

Distribution of the number of non-human primate species from our dataset sequenced for a particular miRNA that was previously computational predicted by homology alone.

<p>140/163 (86%) have experimental support from at least two primates. Because of the difficulty distinguishing between paralogs with identical mature sequences, only the paralog with the most coverage from a family of miRNA is shown in this chart.</p

miRNA biogenesis.

<p>miRNA genes are transcribed from the genome, resulting in a primary miRNA transcript. Regions of the primary miRNA form a hairpin structure that is recognized by the endonuclease drosha, which cleaves the double-stranded stem region of the hairpin to create a pre-miRNA of ~83 nt in length. The pre-miRNA is exported to the cytoplasm where it is further processed by dicer, which cleaves off the loop region of the hairpin. This results in an approximately 22 to 23 nt double-stranded RNA called the miRNA-miRNA* duplex. The mature miRNA strand is loaded into the RNA-induced silencing complex (RISC), where its 8 nt seed region complementarily base pairs with messenger RNA targets, leading to their downregulation.</p

Summary of all variants found within the mature region of a miRNA ortholog group.

<p>Summary of all variants found within the mature region of a miRNA ortholog group.</p