Multi-omics blood atlas reveals unique features of immune and platelet responses to SARS-CoV-2 Omicron breakthrough infection.

Although host responses to the ancestral SARS-CoV-2 strain are well described, those to the new Omicron variants are less resolved. We profiled the clinical phenomes, transcriptomes, proteomes, metabolomes, and immune repertoires of >1,000 blood cell or plasma specimens from SARS-CoV-2 Omicron patients. Using in-depth integrated multi-omics, we dissected the host response dynamics during multiple disease phases to reveal the molecular and cellular landscapes in the blood. Specifically, we detected enhanced interferon-mediated antiviral signatures of platelets in Omicron-infected patients, and platelets preferentially formed widespread aggregates with leukocytes to modulate immune cell functions. In addition, patients who were re-tested positive for viral RNA showed marked reductions in B cell receptor clones, antibody generation, and neutralizing capacity against Omicron. Finally, we developed a machine learning model that accurately predicted the probability of re-positivity in Omicron patients. Our study may inspire a paradigm shift in studying systemic diseases and emerging public health concerns.

The heterogeneity of megakaryocytes and platelets and implications for ex vivo platelet generation.

Platelets, the chief effector of hemostasis, are small anucleate blood cells generated from megakaryocytes (MKs), and the defects in platelet production or function lead to a variety of bleeding complications. Emerging evidence indicates that MKs and platelets are much more diverse than previously appreciated and involved in many physiological and pathological processes besides hemostasis, such as innate and adaptive immune responses, angiogenesis, and tumor metastasis, while the ontogenic variations in MK and platelet function have also become a focus in the field. However, whether MKs and platelets fulfill these distinct functions by utilizing distinct subpopulations remains poorly understood. New studies aimed at deciphering the MK transcriptome at the single-cell level have provided some key insights into the functional heterogeneity of MKs. In this review, we will discuss some of the recent discoveries of functional and developmental heterogeneity of MKs and its potential link to the heterogeneity of platelets. We will also discuss the implications of these findings while focusing on the ex vivo generation of platelets from human pluripotent stem cells. The improved understanding of the heterogeneity underlying human MK development and platelet production should open new avenues for future platelet regeneration and clinical treatment of related diseases.

Decoding Human Megakaryocyte Development.

Despite our growing understanding of embryonic immune development, rare early megakaryocytes (MKs) remain relatively understudied. Here we used single-cell RNA sequencing of human MKs from embryonic yolk sac (YS) and fetal liver (FL) to characterize the transcriptome, cellular heterogeneity, and developmental trajectories of early megakaryopoiesis. In the YS and FL, we found heterogeneous MK subpopulations with distinct developmental routes and patterns of gene expression that could reflect early functional specialization. Intriguingly, we identified a subpopulation of CD42b+CD14+ MKs in vivo that exhibit high expression of genes associated with immune responses and can also be derived from human embryonic stem cells (hESCs) in vitro. Furthermore, we identified THBS1 as an early marker for MK-biased embryonic endothelial cells. Overall, we provide important insights and invaluable resources for dissection of the molecular and cellular programs underlying early human megakaryopoiesis.