Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging.

Non-hematopoietic cells are essential contributors to hematopoiesis. However, heterogeneity and spatial organization of these cells in human bone marrow remain largely uncharacterized. We used single-cell RNA sequencing (scRNA-seq) to profile 29,325 non-hematopoietic cells and discovered nine transcriptionally distinct subtypes. We simultaneously profiled 53,417 hematopoietic cells and predicted their interactions with non-hematopoietic subsets. We employed co-detection by indexing (CODEX) to spatially profile over 1.2 million cells. We integrated scRNA-seq and CODEX data to link predicted cellular signaling with spatial proximity. Our analysis revealed a hyperoxygenated arterio-endosteal neighborhood for early myelopoiesis, and an adipocytic localization for early hematopoietic stem and progenitor cells (HSPCs). We used our CODEX atlas to annotate new images and uncovered mesenchymal stromal cell (MSC) expansion and spatial neighborhoods co-enriched for leukemic blasts and MSCs in acute myeloid leukemia (AML) patient samples. This spatially resolved, multiomic atlas of human bone marrow provides a reference for investigation of cellular interactions that drive hematopoiesis.

Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging.

The bone marrow is the organ responsible for blood production. Diverse non-hematopoietic cells contribute essentially to hematopoiesis. However, these cells and their spatial organization remain largely uncharacterized as they have been technically challenging to study in humans. Here, we used fresh femoral head samples and performed single-cell RNA sequencing (scRNA-Seq) to profile 29,325 enriched non-hematopoietic bone marrow cells and discover nine transcriptionally distinct subtypes. We next employed CO-detection by inDEXing (CODEX) multiplexed imaging of 18 individuals, including both healthy and acute myeloid leukemia (AML) samples, to spatially profile over one million single cells with a novel 53-antibody panel. We discovered a relatively hyperoxygenated arterio-endosteal niche for early myelopoiesis, and an adipocytic, but not endosteal or perivascular, niche for early hematopoietic stem and progenitor cells. We used our atlas to predict cell type labels in new bone marrow images and used these predictions to uncover mesenchymal stromal cell (MSC) expansion and leukemic blast/MSC-enriched spatial neighborhoods in AML patient samples. Our work represents the first comprehensive, spatially-resolved multiomic atlas of human bone marrow and will serve as a reference for future investigation of cellular interactions that drive hematopoiesis.

Collagen and soy peptides attenuate contractile loss from UVA damage and enhance the antioxidant capacity of dermal fibroblasts.

BACKGROUND: Wrinkles and extracellular matrix (ECM) loss are common signs of skin aging and are thought to be the result of damage caused by reactive oxygen species (ROS); ROS induces an imbalance between ECM degradation and production. OBJECTIVES: In this study, we evaluate soy peptides (SP) and collagen peptides (CP), alone and in combination, for their ability to inhibit ROS formation and increase ECM gene expression in order to ameliorate the signs of skin aging. METHODS: Using tert-Butyl hydroperoxide (t-BuOOH)-treated dermal fibroblasts, we explored the potential of CP and SP to inhibit ROS formation by flow cytometry, as well as their effect on ECM component genes by real-time quantitative PCR. In addition, we examined the effect of CP and SP on UVA irradiated fibroblasts in a 3D collagen lattice model that measured contractility. RESULTS: The results showed that the combination of CP and SP synergistically reduces ROS formation. This combination also increased expression of collagen I, collagen II, elastin, and fibronectin in t-BuOOH-treated or untreated dermal fibroblasts. In the UVA-treated 3D collagen lattice model, the results show that CP and SP significantly improved fibroblast contractility when compared to UVA control (P < 0.05). CONCLUSIONS: In conclusion, CP and SP attenuate the loss of contractility due to UVA damage, inhibit t-BuOOH-induced ROS formation, and improve expression of ECM component genes.

Deep-learning-assisted biophysical imaging cytometry at massive throughput delineates cell population heterogeneity.

The association of the intrinsic optical and biophysical properties of cells to homeostasis and pathogenesis has long been acknowledged. Defining these label-free cellular features obviates the need for costly and time-consuming labelling protocols that perturb the living cells. However, wide-ranging applicability of such label-free cell-based assays requires sufficient throughput, statistical power and sensitivity that are unattainable with current technologies. To close this gap, we present a large-scale, integrative imaging flow cytometry platform and strategy that allows hierarchical analysis of intrinsic morphological descriptors of single-cell optical and mass density within a population of millions of cells. The optofluidic cytometry system also enables the synchronous single-cell acquisition of and correlation with fluorescently labeled biochemical markers. Combined with deep neural network and transfer learning, this massive single-cell profiling strategy demonstrates the label-free power to delineate the biophysical signatures of the cancer subtypes, to detect rare populations of cells in the heterogeneous samples (10-5), and to assess the efficacy of targeted therapeutics. This technique could spearhead the development of optofluidic imaging cell-based assays that stratify the underlying physiological and pathological processes based on the information-rich biophysical cellular phenotypes.

Photophysics of halogenated fluoresceins: involvement of both intramolecular electron transfer and heavy atom effect in the deactivation of excited states.

The fluorescence quantum yield (Phi(f)), fluorescence lifetime (tau(f)), intersystem crossing quantum yield (Phi(isc)) and redox potentials of seven halogenated fluoresceins in their dianion forms were measured and compared in methanol to get a deep insight into the effect of halogeno atoms on their photophysics. It is found that the heavy atom effect alone cannot explain the experimental results, as (1) Phi(f) for chlorinated dyes exceeds that of fluorescein and close to unity, (2) the sum of Phi(f) and Phi(isc) for brominated and iodinated xanthene dyes is remarkably less than unity. The observations can be rationalized by the involvement of intramolecular photoinduced electron transfer, in which the benzoate acts as the electron donor while the xanthene moiety is the acceptor. The more negative reduction potential of excited singlet state for chlorinated fluoresceins results in their much smaller k(et), and hence higher Phi(f).