Fumio Arai

Recurrence and metastasis remain major causes of cancer mortality, sustained by therapy–resistant micrometastatic cells. Bone is a frequent site of breast–cancer relapse, yet the cues that reawaken disseminated cells remain poorly defined. We identify a previously unrecognized, highly plastic CXCL16⁺ macrophage population that integrates tumor–associated macrophage programs found in distant metastatic sites such as lung and brain with non–tumor disease–associated traits in bone marrow. These CXCL16⁺ macrophages establish a transient niche that restrains disseminated cancer–cell proliferation. Single–cell transcriptomics delineate functional remodeling of myeloid niches within the bone metastatic microenvironment: a CXCL16⁺ macrophage niche that transiently constrains metastatic growth, and G–CSF⁺ macrophage and neutrophil niches that reignite tumor outgrowth. In primary tumors, cancer–associated fibroblasts (CAFs) aberrantly secrete G–CSF in response to cancer–cell signals, expanding G–CSF–receptor–positive subset of cancer cells with high metastatic potential. In advanced human bone metastases, CXCL16⁺ macrophages localize to CAF–rich stroma but are excluded from cancer–cell clusters, indicating immune evasion. Together, these findings uncover CAF–bone–marrow cross–talk as a therapeutic target linking stromal inflammation, immune remodeling, and metastatic progression.

The stem cell niche is a specialised microenvironment essential for maintaining haematopoietic stem cells (HSCs). Here we identify a distinct subset of mesenchymal stem cells (MSCs) expressing integrin α8 (Itga8⁺ MSCs) within the bone marrow (BM) endosteum. These cells exhibit distinct MSC properties and higher haematopoietic supportive activity than other MSC subsets. Depletion of Itga8⁺ MSCs decreased HSC numbers, reduced quiescence of endosteal HSCs and diminished BM repopulating capacity. Itga8⁺ MSCs support haematopoiesis through cell adhesion-related mechanisms. Single-cell RNA sequencing further identified Itga8⁺ MSCs as a distinct subpopulation within bone-lining cells. Moreover, we identified Mfap4 as a candidate factor expressed in Itga8⁺ MSCs, and Mfap4 supported the BM reconstitution capacity of HSCs. These results suggest that Itga8⁺ MSCs represent a distinct niche cell population for HSC maintenance. This work provides new insights into HSC regulation and strategies to optimise in vitro HSC maintenance and enhance in vivo engraftment.

Protection of telomeres 1a (POT1a) is a telomere binding protein. A decrease of POT1a is related to myeloid-skewed haematopoiesis with ageing, suggesting that protection of telomeres is essential to sustain multi-potency. Since mesenchymal stem cells (MSCs) are a constituent of the hematopoietic niche in bone marrow, their dysfunction is associated with haematopoietic failure. However, the importance of telomere protection in MSCs has yet to be elucidated. Here, we show that genetic deletion of POT1a in MSCs leads to intracellular accumulation of fatty acids and excessive ROS and DNA damage, resulting in impaired osteogenic-differentiation. Furthermore, MSC-specific POT1a deficient mice exhibited skeletal retardation due to reduction of IL-7 producing bone lining osteoblasts. Single-cell gene expression profiling of bone marrow from POT1a deficient mice revealed that B-lymphopoiesis was selectively impaired. These results demonstrate that bone marrow microenvironments composed of POT1a deficient MSCs fail to support B-lymphopoiesis, which may underpin age-related myeloid-bias in haematopoiesis.

Mbtd1 (mbt domain containing 1 ) encodes a nuclear protein containing a zinc finger domain and four malignant brain tumor (MBT) repeats. We previously generated Mbtd1 -deficient mice and found that MBTD1 is highly expressed in fetal hematopoietic stem cells (HSCs) and sustains the number and function of fetal HSCs. However, since Mbtd1 -deficient mice die soon after birth possibly due to skeletal abnormalities, its role in adult hematopoiesis remains unclear. To address this issue, we generated Mbtd1 conditional knockout mice and analyzed adult hematopoietic tissues deficient in Mbtd1 . We observed that the numbers of HSCs and progenitors increased and Mbtd1 -deficient HSCs exhibited hyperactive cell cycle, resulting in a defective response to exogenous stresses. Mechanistically, we found that MBTD1 directly binds to the promoter region of FoxO3a , encoding a forkhead protein essential for HSC quiescence, and interacts with components of TIP60 chromatin remodeling complex and other proteins involved in HSC and other stem cell functions. Restoration of FOXO3a activity in Mbtd1- deficient HSCs in vivo rescued cell cycle and pool size abnormalities. These findings indicate that MBTD1 is a critical regulator for HSC pool size and function, mainly through the maintenance of cell cycle quiescence by FOXO3a.

Biomedical research often involves conducting experiments on model organisms in the anticipation that the biology learnt will transfer to humans. Previous comparative studies of mouse and human tissues were limited by the use of bulk-cell material. Here we show that transfer learning—the branch of machine learning that concerns passing information from one domain to another—can be used to efficiently map bone marrow biology between species, using data obtained from single-cell RNA sequencing. We first trained a multiclass logistic regression model to recognize different cell types in mouse bone marrow achieving equivalent performance to more complex artificial neural networks. Furthermore, it was able to identify individual human bone marrow cells with 83% overall accuracy. However, some human cell types were not easily identified, indicating important differences in biology. When re-training the mouse classifier using data from human, less than 10 human cells of a given type were needed to accurately learn its representation. In some cases, human cell identities could be inferred directly from the mouse classifier via zero-shot learning. These results show how simple machine learning models can be used to reconstruct complex biology from limited data, with broad implications for biomedical research.

Modern single cell experiments have revealed unexpected heterogeneity in apparently functionally ‘pure’ cell populations. However, we are still lacking a conceptual framework to understand this heterogeneity. Here, we propose that cellular memories—changes in the molecular status of a cell in response to a stimulus, that modify the ability of the cell to respond to future stimuli—are an essential ingredient in any such theory. We illustrate this idea by considering a simple age-structured model of stem cell proliferation that takes account of mitotic memories. Using this model we argue that asynchronous mitosis generates heterogeneity that is central to stem cell population function. This model naturally explains why stem cell numbers increase through life, yet regenerative potency simultaneously declines.

Modern single cell experiments have revealed unexpected heterogeneity in apparently functionally ‘pure’ cell populations. However, we are still lacking a conceptual framework to understand this heterogeneity. Here, we propose that cellular memories – the ability of individual cells to record their developmental past and adapt their response to their environment accordingly – are an essential ingredient in any such theory. We illustrate this idea by considering a simple age-structured model of stem cell proliferation. Using this model we argue that heterogeneity is central to stem cell population function, and memories naturally explain why stem cell numbers increase through life, yet regenerative potency simultaneously declines.