Etsuo A. Susaki

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.

Hydra is a freshwater cnidarian genus that provides a unique comparative model for aging research, contrasting the immortal Hydra vulgaris with the aging-inducible Hydra oligactis. Here, we report a high-quality, chromosome-level genome assembly of H. vulgaris strain AEP.JNIG. Our assembly is comparable in quality to existing resources, facilitating the analysis of genomic diversity across laboratory strains. Epigenomic profiling revealed that gene-body hypermethylation correlates with transcriptional stability and the suppression of spurious transcription in evolutionary conserved genes, suggesting an epigenetic mechanism for genomic integrity. Furthermore, comparative genomics demonstrated that while Hydra conserves fundamental pathways associated with major biological processes implicated in aging, the immortal H. vulgaris paradoxically lacks canonical anti-aging genes (eg Klotho, nicotinamide phosphoribosyltransferase) found in the aging-inducible H. oligactis. Instead, H. vulgaris exhibits a distinct metabolic signature related to mitochondrial energy production and nucleoside triphosphate biosynthesis. Collectively, our comparative genomics results suggest multiple potential mechanisms associated with the H. vulgaris immortality and the aging traits of H. oligactis, providing novel targets for future functional studies.

Tissue clearing–based three-dimensional (3D) imaging has opened up organ- and body-wide 3D spatial biology, yet its broader adoption remains limited by the cost, complexity, and modality-specific fragmentation of high-end light-sheet fluorescence microscopy (LSFM). Existing systems force trade-offs among multicolor capability, resolution, field of view, and cost, splintering advanced imaging into separate, specialized instruments. Here we present an off-the-shelf LSFM ecosystem, descSPIM-Advanced, that unifies these capabilities as individually optimized yet interoperable variants within one accessible framework. Galaxy resolves 11 colors in phantoms and 7 in 3D samples without multi-round staining; Deepsky reaches ~1.09 μm lateral resolution for 3D histology of lung and kidney; Fullmoon provides a 23.8 mm × 28.1 mm field of view, capturing a tenfold-expanded whole mouse brain in a single field; and SLIM enables low-cost deployment (~US$15,000; assembled in 2–5 h). A shared Mission Control Center standardizes acquisition across configurations, democratizing versatile cleared-tissue imaging across scales and applications.

Hydra is a freshwater cnidarian genus that provides a unique comparative model for aging research, contrasting the immortal H. vulgaris with the aging-inducible H. oligactis. Here, we report a high-quality, chromosome-level genome assembly of H. vulgaris strain AEP.JNIG. Our assembly is comparable in quality to existing resources, facilitating the analysis of genomic diversity across laboratory strains. Epigenomic profiling revealed that gene-body hypermethylation correlates with transcriptional stability and the suppression of spurious transcription in evolutionary conserved genes, suggesting an epigenetic mechanism for genomic integrity. Furthermore, comparative genomics demonstrated that while Hydra conserves fundamental Hallmarks of Aging pathways, the immortal H. vulgaris paradoxically lacks canonical anti-aging genes (e.g., Klotho, NAMPT) found in the aging-inducible H. oligactis . Instead, H. vulgaris exhibits a distinct metabolic signature related to mitochondrial energy production and NTP synthesis. Collectively, our comparative genomics results suggest multiple potential mechanisms associated with the H. vulgaris immortality and the aging traits of H. oligactis , providing novel targets for future functional studies. Significance statement: Why do some organisms age while others appear not to? The freshwater animal Hydra provides a unique opportunity to investigate this question, as closely related species display contrasting aging phenotypes. We generated a high-quality genome assembly for a new strain of a non-aging species and conducted comparative analyses with related strains and an aging species. Even closely related strains can accumulate substantial genetic divergence over time, and stable DNA modification patterns were associated with consistent gene activity, suggesting a mechanism that may help maintain cellular balance. Surprisingly, several well-known longevity genes are present in the aging species but absent in the non-aging one. This suggests that extended lifespan may not simply depend on possessing more “anti-aging” genes, but instead may reflect differences in how core biological processes are organized. Our study provides new insights into the genetic basis of aging and highlights Hydra as a powerful model for understanding longevity.

Objectives A combination of tissue clearing technology and light-sheet fluorescence microscopy enables volumetric analysis of intact biological specimens. To analyze complex spatial organizations of molecules and cells, the number of imaging channels available for simultaneous visualization from a single sample is a key parameter. This study aimed to expand the previously reported DIY compact light-sheet microscope, descSPIM, for four-color volumetric imaging of whole biological samples.Materials A four-color-labeled optical phantom and an entire E12.5 mouse embryo labeled with a nuclear stain and three distinct antibodies were used.Methods We modified the previously reported DIY compact light-sheet microscope, descSPIM, for four-color volumetric imaging. Chromatic aberration was evaluated across the visible wavelength range (400-700 nm) using the four-color-labeled optical phantom. Four-color three-dimensional imaging was then performed on the entire E12.5 mouse embryo.Results The chromatic aberration of the extended descSPIM was mostly negligible across the visible wavelength range (400-700 nm). The extended system also enabled four-color three-dimensional imaging covering the entire E12.5 mouse embryo.Conclusions Together, these results validate the reliability and expandability of the extended system, supporting its broader use for multicolor imaging of cleared tissue samples.

The three-dimensional (3D) anatomical structure of living organisms is intrinsically linked to their functions, yet modern life sciences have not fully explored this aspect. Recently, the combination of efficient tissue clearing techniques and light-sheet fluorescence microscopy for rapid 3D imaging has improved access to 3D spatial information in biological systems. This technology has found applications in various fields, including neuroscience, cancer research and clinical histopathology, leading to significant insights. It allows imaging of entire organs or even whole bodies of animals and humans at multiple scales. Moreover, it enables a form of spatial omics by capturing and analyzing cellome information, which represents the complete spatial organization of cells. While current 3D imaging of cleared tissues has limitations in obtaining sufficient molecular information, emerging technologies such as multi-round tissue staining and super-multicolor imaging are expected to address these constraints. 3D imaging using tissue clearing and light-sheet microscopy thus offers a valuable research tool in the current and future life sciences for acquiring and analyzing large-scale biological spatial information.

The homeostatic regulation of sleep is characterized by rebound sleep after prolonged wakefulness, but the molecular and cellular mechanisms underlying this regulation are still unknown. In this study, we show that Ca²⁺/calmodulin-dependent protein kinase II (CaMKII)-dependent activity control of parvalbumin (PV)-expressing cortical neurons is involved in homeostatic regulation of sleep in male mice. Prolonged wakefulness enhances cortical PV-neuron activity. Chemogenetic suppression or activation of cortical PV neurons inhibits or induces rebound sleep, implying that rebound sleep is dependent on increased activity of cortical PV neurons. Furthermore, we discovered that CaMKII kinase activity boosts the activity of cortical PV neurons, and that kinase activity is important for homeostatic sleep rebound. Here, we propose that CaMKII-dependent PV-neuron activity represents negative feedback inhibition of cortical neural excitability, which serves as the distributive cortical circuits for sleep homeostatic regulation.

Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000–50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced (https://github.com/dbsb-juntendo/descSPIM), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies.

Here, we summarize the literature relevant to recent advances in three‐dimensional (3D) histopathology in relation to clinical oncology, highlighting serial sectioning, tissue clearing, light‐sheet microscopy, and digital image analysis with artificial intelligence. We look forward to a future where 3D histopathology expands our understanding of human pathophysiology and improves patient care through cross‐disciplinary collaboration and innovation.