Li Ding

The bone marrow immune microenvironment (BMME) is a critical factor in multiple myeloma (MM) pathogenesis. Despite higher incidence of MM among self-identified African Americans, the relationship between African genetic similarity and the BMME remains unclear. We present the largest analysis to date assessing the impact of Ancestry on the BMME in myeloma (N=320, including 64 with ≥50% African genetic similarity, AFR-High) leveraging our recently generated Immune Atlas. AFR-High was associated with enrichment of late T-effector cells, driven by rare cytotoxic CD4⁺ T cells, suggesting a distinct adaptive BMME. AFR-High exhibited expansion of late-differentiated adaptive NK cells with high cytotoxic GNLY and GZMH expression. AFR-High depicted reduced CD14⁺ monocytes, increased CD16⁺ non-classical monocytes, and expansion of macrophage-like monocyte populations with enrichment of metabolic adaptation, efferocytosis and phagocytic clearance programs, and immunoregulatory pathways. These findings reveal a shift from an innate inflammatory immune landscape toward adaptive cytotoxic and immunoregulatory remodeling associated with African genetic similarity in MM.

Metastasis is the leading cause of cancer-related deaths. However, the core determinants and mechanistic principles underlying the metastatic cascade remain elusive. Small cell lung cancer (SCLC) is a highly aggressive malignancy with exceptional metastatic potential and limited therapeutic options. Here, we present Metastasis Originated Barcode Sequencing (MOBA-seq), a high-throughput in vivo platform that systematically maps genetic regulators across the metastatic cascade at single-colony resolution. MOBA-seq integrates scalable barcode-based lineage tracing with a computational pipeline that quantitatively deconvolutes genotype-specific effects on metastatic seeding, dormancy, and clonal expansion across hundreds of thousands of metastatic events. Applying this approach to more than 400 candidate regulators of SCLC, we uncovered tissue-specific metastatic suppressors and universal metastatic essential genes. We identified metastatic seeding as the predominant determinant of metastasis. Comparative analysis across recipient mice of distinct genetic backgrounds further revealed that innate immune surveillance constrains metastatic progression by reducing metastatic seeding and enforcing dormancy, with additional modulation by sex and tissue context. We validated the frequently mutated gene CREBBP as a key metastasis suppressor whose loss enhances SCLC metastasis through both tumor-intrinsic and immune-modulatory mechanisms. This work establishes a scalable and quantitative platform for mapping the metastatic fitness landscape at single-colony resolution across hundreds of thousands of in vivo data points. Our approach offers a broadly applicable framework for dissecting the interactions between cancer-intrinsic and microenvironmental factors governing tumor initiation, progression, and therapeutic response.

Supplementary Fig. 1. Lightsheet. Supplementary Fig. 2. 3D serial section workflow and motivation. Supplementary Figure 3. Serial section ROIs for HT206B1 (breast). Supplementary Fig. 4. Genes associated with 3D transition ROIs in breast and prostate. Supplementary Fig. 5. Serial section ROIs for HT913Z1 (prostate). Supplementary Fig. 6. 3D proximity of TAMs to non-invasive and invasive epithelial regions in HT704B1. Supplementary Fig. 7. Expression of cohort-level transition genes. Supplementary Fig. 8. Quantification and validation of transition markers. Supplementary Fig. 9. Wound healing assays for MGP and PLAT knockdowns in breast cancer cell lines. Supplementary Fig. 10. Wound healing assays for GDF15, FASN, ALDH1A3, and ANPEP knockdowns in PC-3 prostate cancer cell line. Supplementary Fig. 11. Expression for GDF15, ANPEP, ALDH3A1, and FASN in four prostate cancer cell lines, including PC-3.

Breast and prostate cancers are both hormone-driven adenocarcinomas that undergo analogous invasion programs. Using lightsheet microscopy on intact tumors, we identified transitional junctions between precancerous and invasive regions. We then developed a multimodal serial-section workflow integrating volumetric reconstruction with spatial transcriptomics. Analysis of 319 spatial assays from 51 cases revealed gene expression features and novel structural insights defining the shift from precancer to invasive disease. In breast cancer, loss of MGP and PLAT was associated with invasive transition and promoted tumorigenesis in functional assays. In prostate cancer, GDF15, ALDH1A3, ANPEP, and FASN were upregulated along invasive progression, and their knockdown in PC-3 cells suppressed proliferation and migration. Enrichment of tumor-associated macrophages (SPP1+ and MS4A6A+) along non–triple-negative breast cancer breast cancer transitions highlights immune involvement as a potential driver of invasiveness. Significance:Our method of defining precise spatial locations of invasive transition allows for the direct interrogation of transition drivers, presenting new therapeutic targets for the two most prevalent cancers and providing a framework for studying spatially defined mechanisms of tumor progression.See related commentary by Jing and Li, p. 1720

HT944B1_S2H3 whole 3D rotation.

HT704B1 CODEX PanCKred CD68cyan KRT5white.

Supplementary Mov. 11 from Spatial Mapping of the Precancer-to-Cancer Transition in Breast and Prostate

Supplementary Mov. 12 from Spatial Mapping of the Precancer-to-Cancer Transition in Breast and Prostate

Supplementary Mov. 14 from Spatial Mapping of the Precancer-to-Cancer Transition in Breast and Prostate