Sympathetic and parasympathetic nerve fibers in mouse SCLC

Co-culture with stellate ganglia (SG) promotes the growth of mouse SCLC

High levels of ADRB2 promote the growth of mouse SCLC

ICI treatment reduces the growth of SCLC

ADRB2 regulates the growth of human SCLC cells

Tumor progression is driven by dynamic interactions between cancer cells and their surrounding microenvironment. Here we integrate high-resolution spatial transcriptomics and evolving lineage-tracing technologies to elucidate how tumor expansion, plasticity and metastasis co-evolve with microenvironmental remodeling in a Kras;Trp53-driven mouse model of lung adenocarcinoma. We find that subclonal expansion contributes to a hypoxic, immunosuppressive and fibrotic microenvironment that is associated with the emergence of prometastatic cancer cell states. We use tumor phylogeography to delineate intercellular interactions that are rewired in the expanding tumor niche and use co-culture systems to dissect how intercellular interactions and hypoxia influence cancer cell state. Furthermore, we find that metastases arise from spatially confined primary tumor subclones and remodel the distant metastatic niche into a fibrotic, collagen-rich microenvironment. Together, we present a comprehensive dataset integrating spatial assays and lineage tracing to elucidate how sequential changes in cancer cell state and microenvironmental structures cooperate to promote tumor progression.

The rapid and sensitive detection of specific protein biomarkers is essential for early diagnosis and monitoring of diseases. Magnetic digital microfluidics (MDMF), capable of integrating and miniaturizing chemiluminescence immunoassay (CLIA), offers significant advantages for biomarker detection, including high flexibility, high efficiency, and low sample consumption. Magnetic bead manipulation, as a key component of MDMF, plays a critical role in improving detection sensitivity and accuracy within a short analysis time. In this study, we proposed an automated MDMF-based CLIA system and developed a compact analyzer, enabling faster and more sensitive biomarker detection through optimized magnetic bead manipulation. The system employs a film-sandwiched microfluidic chip, along with a specially designed spliced magnet to generate a stronger and more concentrated magnetic force, significantly enhancing the control over the motion of magnetic beads. By using the magnet to drive magnetic beads through water-in-oil droplets, the system automates the entire CLIA workflow. Through theoretical analysis, simulations, and experiments, we validate the system's advantages in magnetic bead aggregation and transfer, achieving a high magnetic bead collection rate of 97.07% with excellent cleaning effect after three cleaning rounds. The detection of cardiac troponin I (cTnI) can be completed within 10 min, with a limit of detection (LOD) of 2.09 pg mL-1, a detection range of 0.01 to 20 ng mL-1, and a strong linear correlation with conventional CLIA (R2 = 0.9961). This system achieves rapid, sensitive, and automated CLIA, making it a promising platform for clinical diagnostics.

Charting the spatiotemporal dynamics of cell fate determination in development and disease is a long-standing objective in biology. Here we present the design, development, and extensive validation of PEtracer, a prime editing-based, evolving lineage tracing technology compatible with both single-cell sequencing and multimodal imaging methodologies to jointly profile cell state and lineage in dissociated cells or while preserving cellular context in tissues with high spatial resolution. Using PEtracer coupled with MERFISH spatial transcriptomic profiling in a syngeneic mouse model of tumor metastasis, we reconstruct the growth of individually-seeded tumors in vivo and uncover distinct modules of cell-intrinsic and cell-extrinsic factors that coordinate tumor growth. More generally, PEtracer enables systematic characterization of cell state and lineage relationships in intact tissues over biologically-relevant temporal and spatial scales.

SIGNIFICANCE:SCLC is highly aggressive, with limited effective treatment options. We show that ablating sympathetic nerves or inhibiting the ADRB2 receptor slows SCLC progression and prolongs survival in mice. Additionally, ADRB2 inhibition reduces the growth of human SCLC organoids and xenografts by disrupting PKA signaling, identifying a new therapeutic target.

Embryogenesis requires substantial coordination to translate genetic programs to the collective behavior of differentiating cells, but understanding how cellular decisions control tissue morphology remains conceptually and technically challenging. Here, we combine continuous Cas9-based molecular recording with a mouse embryonic stem cell-based model of the embryonic trunk to build single-cell phylogenies that describe the behavior of transient, multipotent neuro-mesodermal progenitors (NMPs) as they commit into neural and somitic cell types. We find that NMPs show subtle transcriptional signatures related to their recent differentiation and contribute to downstream lineages through a surprisingly broad distribution of individual fate outcomes. Although decision-making can be heavily influenced by environmental cues to induce morphological phenotypes, axial progenitors intrinsically mature over developmental time to favor the neural lineage. Using these data, we present an experimental and analytical framework for exploring the non-homeostatic dynamics of transient progenitor populations as they shape complex tissues during critical developmental windows.

Macrophages hold tremendous promise as effectors of cancer immunotherapy, but the best strategies to provoke these cells to attack tumors remain unknown. Here, we evaluated the therapeutic potential of targeting two distinct macrophage immune checkpoints: CD47 and CD24. We found that antibodies targeting these antigens could elicit maximal levels of phagocytosis when combined together in vitro. However, to our surprise, via unbiased genome-wide CRISPR screens, we found that CD24 primarily acts as a target of opsonization rather than an immune checkpoint. In a series of in vitro and in vivo genetic validation studies, we found that CD24 was neither necessary nor sufficient to protect cancer cells from macrophage phagocytosis in most mouse and human tumor models. Instead, anti-CD24 antibodies exhibit robust Fc-dependent activity, and as a consequence, they cause significant on-target hematologic toxicity in mice. To overcome these challenges and leverage our findings for therapeutic purposes, we engineered a collection of 77 novel bispecific antibodies that bind to a tumor antigen with one arm and engage macrophages with the second arm. We discovered multiple novel bispecifics that maximally activate macrophage-mediated cytotoxicity and reduce binding to healthy blood cells, including bispecifics targeting macrophage immune checkpoint molecules in combination with EGFR, TROP2, and CD71. Overall, our findings indicate that CD47 predominates over CD24 as a macrophage immune checkpoint in cancer, and that the novel bispecifics we created may be optimal immunotherapies to direct myeloid cells to eradicate solid tumors.

The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems2-5, simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.

Macrophage immune checkpoint inhibitors, such as anti-CD47 antibodies, show promise in clinical trials for solid and hematologic malignancies. However, the best strategies to use these therapies remain unknown, and ongoing studies suggest they may be most effective when used in combination with other anticancer agents. Here, we developed an unbiased, high-throughput screening platform to identify drugs that render lung cancer cells more vulnerable to macrophage attack, and we found that therapeutic synergy exists between genotype-directed therapies and anti-CD47 antibodies. In validation studies, we found that the combination of genotype-directed therapies and CD47 blockade elicited robust phagocytosis and eliminated persister cells in vitro and maximized antitumor responses in vivo. Importantly, these findings broadly applied to lung cancers with various RTK/MAPK pathway alterations - including EGFR mutations, ALK fusions, or KRASG12C mutations. We observed downregulation of β2-microglobulin and CD73 as molecular mechanisms contributing to enhanced sensitivity to macrophage attack. Our findings demonstrate that dual inhibition of the RTK/MAPK pathway and the CD47/SIRPa axis is a promising immunotherapeutic strategy. Our study provides strong rationale for testing this therapeutic combination in patients with lung cancers bearing driver mutations.

Tumor progression is driven by dynamic interactions between cancer cells and their surrounding microenvironment. Investigating the spatiotemporal evolution of tumors can provide crucial insights into how intrinsic changes within cancer cells and extrinsic alterations in the microenvironment cooperate to drive different stages of tumor progression. Here, we integrate high-resolution spatial transcriptomics and evolving lineage tracing technologies to elucidate how tumor expansion, plasticity, and metastasis co-evolve with microenvironmental remodeling in a Kras;p53-driven mouse model of lung adenocarcinoma. We find that rapid tumor expansion contributes to a hypoxic, immunosuppressive, and fibrotic microenvironment that is associated with the emergence of pro-metastatic cancer cell states. Furthermore, metastases arise from spatially-confined subclones of primary tumors and remodel the distant metastatic niche into a fibrotic, collagen-rich microenvironment. Together, we present a comprehensive dataset integrating spatial assays and lineage tracing to elucidate how sequential changes in cancer cell state and microenvironmental structures cooperate to promote tumor progression.

Abstract Macrophages hold tremendous promise as effectors of cancer immunotherapy, but the best strategies to provoke these cells to attack tumors remain unknown. Here, we evaluated the therapeutic potential of targeting two distinct macrophage immune checkpoints: CD47 and CD24. We found that antibodies targeting these antigens could elicit maximal levels of phagocytosis when combined together in vitro. However, to our surprise, via unbiased genome-wide CRISPR screens, we found that CD24 primarily acts as a target of opsonization rather than an immune checkpoint. In a series of in vitro and in vivo genetic validation studies, we found that CD24 was neither necessary nor sufficient to protect cancer cells from macrophage phagocytosis in most mouse and human tumor models. Instead, anti-CD24 antibodies exhibit robust Fc-dependent activity, and as a consequence, they cause significant on-target hematologic toxicity that was life-threatening in syngeneic mice. To overcome these challenges and leverage our findings for therapeutic purposes, we engineered a collection of 77 novel bispecific antibodies that bind to a tumor antigen with one arm and engage macrophages with the second arm. We discovered multiple novel bispecifics that maximally activate macrophage-mediated cytotoxicity and reduce binding to healthy blood cells, including bispecifics targeting macrophage immune checkpoint molecules in combination with EGFR, TROP2, and CD71. Overall, our findings indicate that CD47 predominates over CD24 as a macrophage immune checkpoint in cancer, and that the novel bispecifics we created may be optimal immunotherapies to direct myeloid cells to eradicate solid tumors. Citation Format: Anna Meglan, Juliet Allen, Kyle Vaccaro, José Velarde, Victor Chen, Juliano Ribeiro, Jasmine Blandin, Ranjan Mishra, Raymond Ho, Jennifer Love, Ferenc Reinhardt, George W Bell, Jin Chen, Robert Weinberg, Dian Yang, Jonathan Weissman, Kipp Weiskopf. CD47 predominates over CD24 as a macrophage immune checkpoint in cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2024 Oct 18-21; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2024;12(10 Suppl):Abstract nr A055.

PDF file 91K, KPT-Late mice with lung tumor initiated with adenoviral or lentiviral Cre vectors have similar progression and metastasis

Supplementary Table S1, Gene sets that are enriched in Hmga2/GFP-positive and -negative PDAC cells; Supplementary Table S2, A stringent list of Blimp1-dependent genes that are either induced or repressed under hypoxia; Supplementary Table S3, GO terms enriched in hypoxia-induced, Blimp1-dependent genes by FuncAssociate 3.0.

- PDF file 2159K, Inhibitory effects of imipramine, promethazine, and bepridil on SCLC cells in culture

Supplementary Figure S1. Isolation of the Hmga2-GFPpos PDAC sub-population from the KPCcolors mice and GFPpos PDAC cells are a highly metastatic state;Supplementary Figure S2. Highly metastatic PDAC cells have a gene signature that is not enriched for CSC markers and distal PDAC metastases reveal minor gene expression changes related to glucose metabolism;Supplementary Figure S3. Identification of top candidate pro-metastatic genes and interrogation of Blimp1 function in PDAC metastasis;Supplementary Figure S4. Hmga2positive PDAC areas overlap with hypoxic areas and Hmga2 protein is slightly induced by hypoxia but not critical to the expression of hypoxia-induced target genes;Supplementary Figure S5. Hypoxia-induced Blimp1 expression is linked to functional HRE motifs 240 kb upstream of its transcription start site;Supplementary Figure S6. Blimp1 may contribute to migratory and clonal growth ability and is critical for a subset of hypoxia-induced gene expression changes that are independent of changes in chromatin accessibility;Supplementary Figure S7. Blimp1 regulates a subset of hypoxia-induced genes; Supplementary Figure S8. Blimp1 is required for hypoxia-induced cell cycle arrest and the expression of metastasis modulators.

PDF file 1080K, Molecular characterization of disseminated cancer cells is required to understand the stage of metastatic progression at which Nkx2-1 and genes associated with the Nkx2-1neg state function