Abstract SAR11 bacteria, the most abundant organisms in the global ocean, are an extensively studied example of streamlining, an adaptation to extremely low nutrient levels. To understand the regulation of gene function in streamlined cells, we developed a proteome map for the SAR11 type strain HTCC1062 under 13 growth conditions. We detected 95% (1284 out of 1354) of the previously predicted proteins from the HTCC1062 genome, corrected 24 predicted coding regions, and discovered 80 previously unannotated proteins, many of which had frame-shifted or overlapping reading frames. HTCC1062 cells expressed almost their entire genome (> 87.7% of predicted proteins) under all growth conditions, demonstrating that they allocate relatively little coding capacity to auxiliary functions that are deployed infrequently in response to environmental challenges. Most proteins involved in fundamental cellular processes were stable. A highly compact genome and relatively stable proteome are critical for the organization of these simple, free-living planktonic cells, providing a unique model for interpreting the cell biology of a larger number of uncultured cell types.
Single-cell technologies have transformed our view of normal and malignant hematopoiesis, yet a framework linking lifelong homeostatic hematopoiesis to hematological diseases in blood ecosystem remains incomplete. Here, we constructed a high-resolution landscape of the entire hematopoietic system by integrating transcriptomes of ∼1 million cells from 207 healthy samples spanning five developmental stages (fetal, neonatal, childhood, adult, elderly), and identified 96 blood cell clusters, including a VNN2-marked monocyte subset in the fetus and TSHZ2-marked T cell subsets exhibiting distinct age-dependent dynamics. We uncovered a reversal in hematopoietic stem cell/multipotent progenitor (HSC/MPP) stemness around childhood and a postnatal lymphoid bias shift from reduced early B/T lineage potential to enhanced natural killer (NK) cytotoxicity, coordinately orchestrated by intracellular transcription factor activity and intercellular interactions. Projecting 116 pan-malignancy samples (9 hematological malignancies) to our refined blood cell reference, we identified the upregulation of MYC and MHC II signaling as relatively conserved features correlating with poor prognosis, while hematopoiesis-related modules exhibited subtype-specific distributions with divergent clinical implications. Importantly, we developed a prognostic framework incorporating two core signatures shared across hematological malignancies and subtype-specific features. We further revealed an antagonism between inflammatory and cytotoxic programs across malignancies. Together, we established a panoramic landscape of the human hematopoietic system and elaborated its lifelong behaviors, in which a steady-state reference enabled the delineation of pathological hallmarks across hematological malignancies.
Sepsis is systemic inflammation with high mortality, accompanied by multi-organ failure including acute respiratory distress syndrome. Extracellular vesicles (EVs) encapsulating bioactive cargoes, mediate cell-cell communication to exert systemic regulation. However, whether and how host lung tissue responds quickly to plasma bacterial infection through EVs in sepsis is poorly understood. Here, we identify that peripheral blood macrophages secrete more exosomal G6PD protein to induce lung injury by rewiring purine metabolism during sepsis. Guanine accumulation reduces H3K27 trimethylation and subsequently induces Nos2, Ccl6 and Il6 expression by suppressing de novo EZH2 synthesis. Macrophage-specific Rab27a or G6pd knockout mice had low exosomal G6PD protein in serum, and failed to exert lung injury upon bacterial infection. Beyond, targeting macrophage-derived G6PD by G6PD inhibitors or engineered EVs delivering si-G6pd relieves lung injury in septic mice. In summary, our findings reveal that circulating G6PD promotes lung injury by rewiring purine metabolism and remodeling the epigenetic profile in sepsis, shedding light on the critical role of EVs as a pro-inflammatory signal and targeting G6PD for future sepsis diagnosis and treatment.
Tryptophan catabolism by the gut microbiota is increasingly recognized as a hub connecting environmental challenges to cardiovascular health. By systematically profiling tryptophan metabolites in humans who had moved from low altitude to an altitude of 4300 m and in mice exposed to hypobaric hypoxia, we found that circulating and fecal levels of indole-3-propionic acid (IPA), a gut microbiota-derived tryptophan metabolite, are reduced in both settings, and these reductions correlate with the severity of cardiac injury. IPA supplementation in mice ameliorated hypobaric hypoxia-induced cardiac dysfunction. Mechanistically, IPA directly bound to hypoxia-inducible factor-1α (HIF-1α) at residue P564, competitively inhibiting its interaction with von Hippel-Lindau protein and preventing proteasomal degradation, thereby stabilizing HIF-1α. HIF-1α activation shifted cardiac metabolic substrate utilization from fatty acids to glucose and reduced oxygen consumption. Cardiomyocyte-specific HIF-1α knockout completely abolished IPA's cardioprotective effects. Moreover, gut microbiota depletion abrogated the protective effect of tryptophan against hypobaric hypoxia exposure. Finally, IPA protected against myocardial infarction in a HIF-1α-dependent manner. These results suggest that IPA is an endogenous HIF-1α agonist to protect the heart against hypoxia/ischemia, representing a promising therapeutic candidate for hypoxic/ischemic diseases.
Hypervirulent Acinetobacter baumannii (hvAB) is a leading cause of refractory bacterial pneumonia. However, cellular and molecular mechanisms underlying hvAB-induced host protection and pulmonary immunopathology remain poorly understood. Here, we performed longitudinal single-cell RNA sequencing on lung tissues in a mouse model of hvAB pneumonia and delineated a time-dependent innate immune landscape of the infected lung. Functional experiments demonstrated that neutrophil (Neu) was dispensable for hvAB clearance but exacerbated acute lung injury through Neu extracellular traps formation (NETosis). Lung-resident CD11b- alveolar macrophage (AM) was indispensable for host defense and for restraining early Neu infiltration. Upon hvAB infection, CD11b- AM underwent phenotypic switching to a hyper-activated CD11b+ pro-inflammatory state, characterized by markedly decreased phagocytic activity and robustly enhanced IL-1β secretion. Mechanistically, IL-17A acted as a key pathogenic mediator by driving excessive Neu recruitment, aberrant NETosis, and progressive AM loss. IL-17A was predominantly produced by group 3 innate lymphoid cell (ILC3) in an IL-1β-dependent manner. Collectively, our study defined a critical pathogenic AM-ILC3-Neu axis and highlighted a paradoxical dual role of AM in driving host defense and pulmonary immunopathology through dynamic phenotypic switching. We suggested that targeting AM phenotypic plasticity represented a promising therapeutic strategy to alleviate excessive immunopathology while preserving protective host defense during hvAB pneumonia.
