Protocol for analysis of single-cell sequencing data by Seqtometry.

Seqtometry (sequencing-to-measurement) is an analytical platform for single-cell analysis based on direct profiling of gene expression and accessibility achieved by advanced scoring with gene signatures. Here, we present a protocol for single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) analysis using Seqtometry. We describe steps for preprocessing, imputation, scoring, and plotting, with extensions to large datasets and integration of multiple datasets. This protocol yields results in the form of biologically interpretable dimensions for direct identification and comprehensive characterization of specific cells. For complete details on the use and execution of this protocol, please refer to Kousnetsov et al.1.

Single-cell sequencing analysis within biologically relevant dimensions.

The currently predominant approach to transcriptomic and epigenomic single-cell analysis depends on a rigid perspective constrained by reduced dimensions and algorithmically derived and annotated clusters. Here, we developed Seqtometry (sequencing-to-measurement), a single-cell analytical strategy based on biologically relevant dimensions enabled by advanced scoring with multiple gene sets (signatures) for examination of gene expression and accessibility across various organ systems. By utilizing information only in the form of specific signatures, Seqtometry bypasses unsupervised clustering and individual annotations of clusters. Instead, Seqtometry combines qualitative and quantitative cell-type identification with specific characterization of diverse biological processes under experimental or disease conditions. Comprehensive analysis by Seqtometry of various immune cells as well as other cells from different organs and disease-induced states, including multiple myeloma and Alzheimer's disease, surpasses corresponding cluster-based analytical output. We propose Seqtometry as a single-cell sequencing analysis approach applicable for both basic and clinical research.

Roles of Hopx in the differentiation and functions of immune cells.

Homeodomain only protein (Hopx, HOPX) is a highly evolutionarily conserved, homeodomain-containing, small protein expressed in multiple tissues and cell types, including those of hematopoietic origin. The quasi-ubiquitous presence of Hopx contrasts with its specialized and context-dependent roles in various cell lineages. Recently, versatile functions of Hopx have been revealed in immune cells, including T lymphocytes with effector and regulatory roles. The induction of Hopx expression can indicate early developmental and differentiation pathways, and early Hopx expression characterizes the recently identified pre-effector T cells that become destined for subsequent effector differentiation. Further, specific molecular mechanisms of Hopx are indispensable for the functional homeostasis of peripherally induced regulatory T cells (pTreg cells). Here we offer a perspective on these diverse roles of Hopx in immune cells and discuss the recent advances that helped to clarify the relevant functions and mechanisms of Hopx.