Summary Long-term hematopoietic stem cells (LT-HSCs) maintain hematopoietic output throughout an animal’s lifespan. However, with age the balance is disrupted and LT-HSCs produce a myeloid-biased output, resulting in poor immune responses to infectious challenge and the development of myeloid leukemias. Here, we show that young and aged LT-HSCs respond differently to inflammatory stress, such that aged LT-HSCs produce a cell-intrinsic, myeloid-biased expression program. Using single-cell RNA-seq, we identify a myeloid-biased subset within the LT-HSC population (mLT-HSCs) that is prevalent among aged LT-HSCs. We identify CD61 as a marker of mLT-HSCs, and show that CD61-high LT-HSCs are uniquely primed to respond to acute inflammatory challenge. We predict several transcription factors to regulate mLT-HSCs gene program, and show that Klf5, Ikzf1 and Stat3 play an important role in age-related inflammatory myeloid bias. We have therefore identified and isolated a LT-HSC subset that regulates myeloid versus lymphoid balance under inflammatory challenge and with age.

Single-nucleus RNA-seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate or are frozen, and opens the way to human genetics studies, clinical trials, and precise cell atlases of large organs. However, such applications are currently limited by batch effects, processing, and costs. Here, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter recovered profiles. We develop DemuxEM, a computational tool that detects inter-sample multiplets and assigns singlets to their sample of origin, and validate its accuracy using sex-specific gene expression, species-mixing and natural genetic variation. Our approach will facilitate tissue atlases of isogenic model organisms or from multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.

Single-nucleus RNA-Seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate, including frozen clinical samples. This opens the way, in principle, to large studies, such as those required for human genetics, clinical trials, or precise cell atlases of large organs. However, such applications are currently limited by batch effects, sequential processing, and costs. To address these challenges, we present an approach for multiplexing snRNA-seq, using samplebarcoded antibodies against the nuclear pore complex to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled in multiplex with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter the recovered transcriptome profiles. We further developed demuxEM, a novel computational tool that robustly detects intersample nucleus multiplets and assigns singlets to their samples of origin by antibody barcodes, and validated its accuracy using gender-specific gene expression, speciesmixing and natural genetic variation. Nucleus hashing significantly reduces cost per nucleus, recovering up to about 5 times as many single nuclei per microfluidc channel. Our approach provides a robust technique for diverse studies including tissue atlases of isogenic model organisms or from a single larger human organ, multiple biopsies or longitudinal samples of one donor, and largescale perturbation screens.

There is currently no information available as to whether different renal fibroblast subpopulation can be identified and whether they show differences in functional properties. We therefore compared the growth characteristics of interstitial fibroblasts derived from the rabbit renal cortex and inner medulla (papilla) and sought cell-specific markers for the two populations of cells. Analyses of the population dynamics revealed that the mitotic lifespan of papillary fibroblasts (PF) is approximately 50% longer than that of cortical fibroblasts (CF), with the former going through 20 cumulative population doublings (CPD) before transition into terminally differentiated postmitotic cells compared with 9 CPD in CF. PF and CF populations contained three types of mitotically active cells (MFI, MFII, MFIII) and three types of postmitotic cells (PMFIV, PMFV, PMFVI) differentiating along a terminal cell lineage from MFI through PMFVI. In both PF and CF cultures the percent of MF-type cells decreased and the percent of postmitotic cells increased with successive doublings. Two-dimensional polyacrylamide gel electrophoresis of uniform clonal populations of MFIII-type cells revealed two specific proteins for PF-MFIII-type cells, pf1 and pf2, and three specific proteins for CF-MFIII-type cells, cf1, cf2, and cf3. Additionally, a monoclonal antibody was raised that does not recognize CF in culture, but reacts strongly with PF. These studies demonstrate that rabbit renal PF have a pattern of growth in vitro that is distinct from that of CF and that they can be positively identified by specific immunological and protein markers in vitro.

Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins (effectors) that alter foreign cells' behavior. Immunity proteins preferentially protect neighboring sibling cells, in contrast to canonical toxin-antitoxin systems. A prevailing hypothesis is that when immunity proteins are bound to specific (cognate) protein partners, it is sufficient to disrupt their function; further, there is little-to-no crosstalk with other (non-cognate) effectors. Here, we build on sporadic reports challenging these hypotheses. We show that immunity proteins from a newly defined protein family can bind and protect against non-cognate PD-(D/E)XK-containing effectors from diverse phyla. We describe the domains essential for binding and function and show that binding alone is insufficient for protective activity. Moreover, we found that these effector and immunity genes co-occur in individual human microbiomes. These results expand the growing repertoire of bacterial protection mechanisms and force us to reconsider how non-cognate interactions impact community structure within complex ecosystems.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.