Topics overview: REAP-seq, miRNA expression and promoters in primary mammalian cells, Control of stereochemistry substantially increases the efficacy of antisense oligonucleotides, atlas of B-cell clonal lineages, MISAG and MIMAG of bacteria and archaea.
1. Multiplexed quantification of proteins and transcripts in single cells
Vanessa M Peterson at Merck & Co., Inc. in Massachusetts, USA and his colleagues present a tool to measure gene and protein expression levels in single cells with DNA-labeled antibodies and droplet microfluidics. Using the RNA expression and protein sequencing assay (REAP-seq), they quantified proteins with 82 barcoded antibodies and >20,000 genes in a single workflow. They used REAP-seq to assess the costimulatory effects of a CD27 agonist on human CD8+ lymphocytes and to identify and characterize an unknown cell type.
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2. An integrated expression atlas of miRNAs and their promoters in human and mouse
MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, Derek de Rie at RIKEN Center for Life Science Technologies in Yokohama, Japan and his colleagues created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. They also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. They thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.
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3. Control of phosphorothioate stereochemistry substantially increases the efficacy of antisense oligonucleotides
Whereas stereochemical purity in drugs has become the standard for small molecules, stereoisomeric mixtures containing as many as a half million components persist in antisense oligonucleotide (ASO) therapeutics because it has been feasible neither to separate the individual stereoisomers, nor to synthesize stereochemically pure ASOs. Here Naoki Iwamoto at Wave Life Sciences in Massachusetts, USA and his colleagues report the development of a scalable synthetic process that yields therapeutic ASOs having high stereochemical and chemical purity. Using this method, they synthesized rationally designed stereopure components of mipomersen, a drug comprising 524,288 stereoisomers. They demonstrate that phosphorothioate (PS) stereochemistry substantially affects the pharmacologic properties of ASOs. They report that Sp-configured PS linkages are stabilized relative to Rp, providing stereochemical protection from pharmacologic inactivation of the drug. Further, they elucidated a triplet stereochemical code in the stereopure ASOs, 3′-SpSpRp, that promotes target RNA cleavage by RNase H1 in vitro and provides a more durable response in mice than stereorandom ASOs.
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4. An atlas of B-cell clonal distribution in the human body
B-cell responses result in clonal expansion, and can occur in a variety of tissues. To define how B-cell clones are distributed in the body, Wenzhao Meng at Perelman School of Medicine, University of Pennsylvania in Pennsylvania, USA and his colleagues sequenced 933,427 B-cell clonal lineages and mapped them to eight different anatomic compartments in six human organ donors. They show that large B-cell clones partition into two broad networks—one spans the blood, bone marrow, spleen and lung, while the other is restricted to tissues within the gastrointestinal (GI) tract (jejunum, ileum and colon). Notably, GI tract clones display extensive sharing of sequence variants among different portions of the tract and have higher frequencies of somatic hypermutation, suggesting extensive and serial rounds of clonal expansion and selection. Their findings provide an anatomic atlas of B-cell clonal lineages, their properties and tissue connections. This resource serves as a foundation for studies of tissue-based immunity, including vaccine responses, infections, autoimmunity and cancer.
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5. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Robert M Bowers at Department of Energy Joint Genome Institute in California, USA and his colleagues present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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