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During infection, Legionella pneumophila translocates over 300 effector proteins into the host cytosol, allowing the pathogen to establish an endoplasmic reticulum (ER)-like Legionella -containing vacuole (LCV) that supports bacterial replication. Here, we perform a genome-wide CRISPR-Cas9 screen and secondary targeted screens in U937 human monocyte/macrophage-like cells to systematically identify host factors that regulate killing by L. pneumophila. The screens reveal known host factors hijacked by L. pneumophila , as well as genes spanning diverse trafficking and signaling pathways previously not linked to L. pneumophila pathogenesis. We further characterize C1orf43 and KIAA1109 as regulators of phagocytosis and show that RAB10 and its chaperone RABIF are required for optimal L. pneumophila replication and ER recruitment to the LCV. Finally, we show that Rab10 protein is recruited to the LCV and ubiquitinated by the effectors SidC/SdcA. Collectively, our results provide a wealth of previously undescribed insights into L. pneumophila pathogenesis and mammalian cell function. • CRISPR screen reveals host genes regulating distinct steps of L. pneumophila infection • Previously uncharacterized genes C1ORF43 and KIAA1109 regulate phagocytosis • Host Rab10 is hijacked by SidC/SdcA to promote ER recruitment and bacterial replication Jeng et al. perform a genome-wide CRISPR knockout screen to systematically identify host factors that regulate killing by Legionella pneumophila. The screen identifies hundreds of known and unknown factors. Among these, the authors further characterize regulators of phagocytosis, intracellular bacterial replication, and formation of the Legionella -containing vacuole (LCV). [ABSTRACT FROM AUTHOR]

Determining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes that control protein levels. We quantified the relative protein levels from over 12,000 genes across 32 normal human tissues. Tissue-specific or tissue-enriched proteins were identified and compared to transcriptome data. Many ubiquitous transcripts are found to encode tissue-specific proteins. Discordance of RNA and protein enrichment revealed potential sites of synthesis and action of secreted proteins. The tissue-specific distribution of proteins also provides an in-depth view of complex biological events that require the interplay of multiple tissues. Most importantly, our study demonstrated that protein tissue-enrichment information can explain phenotypes of genetic diseases, which cannot be obtained by transcript information alone. Overall, our results demonstrate how understanding protein levels can provide insights into regulation, secretome, metabolism, and human diseases. • Quantified proteins from more than 12,000 genes across 32 normal human tissues • Discordance of RNA and protein enrichment provides evidence of protein secretion • Tissue-specific distribution of enzymes indicates a coordinated control of metabolism • Tissue-enriched proteins provide insights into phenotypes of genetic diseases Proteomics analysis across human tissues from the GTeX resource reveals insight into tissue-specific pathways and phenotypes arising from genetic diseases. [ABSTRACT FROM AUTHOR]

To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease., Competing Interests: Declaration of interests M.P.S. is a co-founder and the scientific advisory board member of Personalis, Qbio, January, SensOmics, Filtricine, Akna, Protos, Mirvie, NiMo, Onza, Oralome, Marble Therapeutics, and Iollo. He is also on the scientific advisory board of Danaher, Genapsys, and Jupiter. A.H. is a founder and shareholder of Arxeon. Y.Z. and G.M.W. are co-founders of General Biomics., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

As our closest living relatives, non-human primates uniquely enable explorations of human health, disease, development, and evolution. Considerable effort has thus been devoted to generating induced pluripotent stem cells (iPSCs) from multiple non-human primate species. Here, we establish improved culture methods for chimpanzee (Pan troglodytes) and pig-tailed macaque (Macaca nemestrina) iPSCs. Such iPSCs spontaneously differentiate in conventional culture conditions, but can be readily propagated by inhibiting endogenous WNT signaling. As a unique functional test of these iPSCs, we injected them into the pre-implantation embryos of another non-human species, rhesus macaques (Macaca mulatta). Ectopic expression of gene BCL2 enhances the survival and proliferation of chimpanzee and pig-tailed macaque iPSCs within the pre-implantation embryo, although the identity and long-term contribution of the transplanted cells warrants further investigation. In summary, we disclose transcriptomic and proteomic data, cell lines, and cell culture resources that may be broadly enabling for non-human primate iPSCs research., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)