Stromal Cell Subsets Research Articles

Immunophenotypical Characterization of Limbal Mesenchymal Stromal Cell Subsets during In Vitro Expansion.

Limbal mesenchymal stromal cells (LMSCs) reside in the limbal niche, supporting corneal integrity and facilitating regeneration. While mesenchymal stem/stromal cells (MSCs) are used in regenerative therapies, there is limited knowledge about LMSC subpopulations and their characteristics. This study characterized human LMSC subpopulations through the flow cytometric assessment of fifteen cell surface markers, including MSC, wound healing, immune regulation, ASC, endothelial, and differentiation markers. Primary LMSCs were established from remnant human corneal transplant specimens and passaged eight times to observe changes during subculture. The results showed the consistent expression of typical MSC markers and distinct subpopulations with the passage-dependent expression of wound healing, immune regulation, and differentiation markers. High CD166 and CD248 expressions indicated a crucial role in ocular surface repair. CD29 expression suggested an immunoregulatory role. Comparable pigment-epithelial-derived factor (PEDF) expression supported anti-inflammatory and anti-angiogenic roles. Sustained CD201 expression indicated maintained differentiation capability, while VEGFR2 expression suggested potential endothelial differentiation. LMSCs showed higher VEGF expression than fibroblasts and endothelial cells, suggesting a potential contribution to ocular surface regeneration through the modulation of angiogenesis and inflammation. These findings highlight the heterogeneity and multipotent potential of LMSC subpopulations during in vitro expansion, informing the development of standardized protocols for regenerative therapies and improving treatments for ocular surface disorders.

Abstract LB114: STING licensing of type I dendritic cells potentiates antitumor immunity

Abstract Stimulator of interferon genes (STING) is an immune adaptor protein that senses cyclic GMP-AMP (cGAMP) in response to self or microbial cytosolic DNA as a danger signal. STING is ubiquitously expressed in diverse cell populations including cancer cells with distinct cellular functions such as activation of type I interferons, autophagy induction, or triggering apoptosis. It is not well understood whether and which subsets of immune cells, stromal cells, or cancer cells are particularly important for STING-mediated antitumor immunity. Here using a polymeric STING-activating nanoparticle (PolySTING) with a “shock-and-lock” dual activation mechanism, we show type 1 conventional dendritic cell (cDC1) is essential for STING-mediated rejection of multiple established and metastatic murine tumors. STING status in the host but not in the cancer cells (Tmem173− / − ) is important for antitumor efficacy. Specific depletion of cDC1 (Batf3− / − ) or STING deficiency in cDC1 (XCR1creSTINGfl/fl ) abolished PolySTING efficacy, whereas depletion of other myeloid cells had little effect. Adoptive transfer of wildtype cDC1 in Batf3− / − mice restored antitumor efficacy while transfer of cDC1 with STING or IRF3 deficiency failed to rescue. PolySTING induced a specific chemokine signature in wildtype but not Batf3− / − mice. Multiplexed immunohistochemistry analysis of STING-activating cDC1s in resected tumors correlates with patient survival while also showing increased expressions after neoadjuvant pembrolizumab therapy in non-small cell lung cancer patients. Therefore, we have defined that a subset of myeloid cells is essential for STING-mediated antitumor immunity with associated biomarkers for prognosis. Citation Format: Jian Wang, Suxin Li, Maggie Wang, Xu Wang, Shuqing Chen, Zhichen Sun, Xiubao Ren, Gang Huang, Baran D. Sumer, Nan Yan, Yang-Xin Fu, Jinming Gao. STING licensing of type I dendritic cells potentiates antitumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB114.

Single-cell profiling of response to neoadjuvant chemo-immunotherapy in surgically resectable esophageal squamous cell carcinoma

BackgroundThe efficacy of neoadjuvant chemo-immunotherapy (NAT) in esophageal squamous cell carcinoma (ESCC) is challenged by the intricate interplay within the tumor microenvironment (TME). Unveiling the immune landscape of ESCC in the context of NAT could shed light on heterogeneity and optimize therapeutic strategies for patients.MethodsWe analyzed single cells from 22 baseline and 24 post-NAT treatment samples of stage II/III ESCC patients to explore the association between the immune landscape and pathological response to neoadjuvant anti-PD-1 combination therapy, including pathological complete response (pCR), major pathological response (MPR), and incomplete pathological response (IPR).ResultsSingle-cell profiling identified 14 major cell subsets of cancer, immune, and stromal cells. Trajectory analysis unveiled an interesting link between cancer cell differentiation and pathological response to NAT. ESCC tumors enriched with less differentiated cancer cells exhibited a potentially favorable pathological response to NAT, while tumors enriched with clusters of more differentiated cancer cells may resist treatment. Deconvolution of transcriptomes in pre-treatment tumors identified gene signatures in response to NAT contributed by specific immune cell populations. Upregulated genes associated with better pathological responses in CD8 + effector T cells primarily involved interferon-gamma (IFNγ) signaling, neutrophil degranulation, and negative regulation of the T cell apoptotic process, whereas downregulated genes were dominated by those in the immune response-activating cell surface receptor signaling pathway. Natural killer cells in pre-treatment tumors from pCR patients showed a similar upregulation of gene expression in response to IFNγ but a downregulation of genes in the neutrophil-mediated immunity pathways. A decreased cellular contexture of regulatory T cells in ESCC TME indicated a potentially favorable pathological response to NAT. Cell–cell communication analysis revealed extensive interactions between CCL5 and its receptor CCR5 in various immune cells of baseline pCR tumors. Immune checkpoint interaction pairs, including CTLA4-CD86, TIGIT-PVR, LGALS9-HAVCR2, and TNFSF4-TNFRSF4, might serve as additional therapeutic targets for ICI therapy in ESCC.ConclusionsThis pioneering study unveiled an intriguing association between cancer cell differentiation and pathological response in esophageal cancer patients, revealing distinct subgroups of tumors for which neoadjuvant chemo-immunotherapy might be effective. We also delineated the immune landscape of ESCC tumors in the context of clinical response to NAT, which provides clinical insights for better understanding how patients respond to the treatment and further identifying novel therapeutic targets for ESCC patients in the future.

MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution

Analyzing immune cell interactions in the bone marrow is vital for understanding hematopoiesis and bone homeostasis. Three-dimensional analysis of the complete, intact bone marrow within the cortex of whole long bones remains a challenge, especially at subcellular resolution. We present a method that stabilizes the marrow and provides subcellular resolution of fluorescent signals throughout the murine femur, enabling identification and spatial characterization of hematopoietic and stromal cell subsets. By combining a pre-processing algorithm for stripe artifact removal with a machine-learning approach, we demonstrate reliable cell segmentation down to the deepest bone marrow regions. This reveals age-related changes in the marrow. It highlights the interaction between CX3CR1+ cells and the vascular system in homeostasis, in contrast to other myeloid cell types, and reveals their spatial characteristics after injury. The broad applicability of this method will contribute to a better understanding of bone marrow biology.

STING licensing of type I dendritic cells potentiates antitumor immunity.

Stimulator of interferon genes (STING) is an immune adaptor protein that senses cyclic GMP-AMP in response to self or microbial cytosolic DNA as a danger signal. STING is ubiquitously expressed in diverse cell populations, including cancer cells, with distinct cellular functions, such as activation of type I interferons, autophagy induction, or triggering apoptosis. It is not well understood whether and which subsets of immune cells, stromal cells, or cancer cells are particularly important for STING-mediated antitumor immunity. Here, using a polymeric STING-activating nanoparticle (PolySTING) with a shock-and-lock dual activation mechanism, we show that conventional type 1 dendritic cells (cDC1s) are essential for STING-mediated rejection of multiple established and metastatic murine tumors. STING status in the host but not in the cancer cells (Tmem173-/-) is important for antitumor efficacy. Specific depletion of cDC1 (Batf3-/-) or STING deficiency in cDC1 (XCR1creSTINGfl/fl) abolished PolySTING efficacy, whereas depletion of other myeloid cells had little effect. Adoptive transfer of wild-type cDC1 in Batf3-/- mice restored antitumor efficacy, whereas transfer of cDC1 with STING or IRF3 deficiency failed to rescue. PolySTING induced a specific chemokine signature in wild-type but not Batf3-/- mice. Multiplexed immunohistochemistry analysis of STING-activating cDC1s in resected tumors correlates with patient survival. Furthermore, STING-cDC1 signature was increased after neoadjuvant pembrolizumab therapy in patients with non-small cell lung cancer. Therefore, we have defined that a subset of myeloid cells is essential for STING-mediated antitumor immunity with associated biomarkers for prognosis.

Investigating the complex interplay between fibroblast activation protein α-positive cancer associated fibroblasts and the tumor microenvironment in the context of cancer immunotherapy.

This study investigates the role of Fibroblast Activation Protein (FAP)-positive cancer-associated fibroblasts (FAP+CAF) in shaping the tumor immune microenvironment, focusing on its association with immune cell functionality and cytokine expression patterns. Utilizing immunohistochemistry, we observed elevated FAP+CAF density in metastatic versus primary renal cell carcinoma (RCC) tumors, with higher FAP+CAF correlating with increased T cell infiltration in RCC, a unique phenomenon illustrating the complex interplay between tumor progression, FAP+CAF density, and immune response. Analysis of immune cell subsets in FAP+CAF-rich stromal areas further revealed significant correlations between FAP+ stroma and various T cell types, particularly in RCC and non-small cell lung cancer (NSCLC). This was complemented by transcriptomic analyses, expanding the range of stromal and immune cell subsets interrogated, as well as to additional tumor types. This enabled evaluating the association of these subsets with tumor infiltration, tumor vascularization and other components of the tumor microenvironment. Our comprehensive study also encompassed cytokine, angiogenesis, and inflammation gene signatures across different cancer types, revealing heterogeneous cellular composition, cytokine expressions and angiogenic profiles. Through cytokine pathway profiling, we explored the relationship between FAP+CAF density and immune cell states, uncovering potential immunosuppressive circuits that limit anti-tumor activity in tumor-resident immune cells. These findings underscore the complexity of tumor biology and the necessity for personalized therapeutic and patient enrichment approaches. The insights gathered from FAP+CAF prevalence, immune infiltration, and gene signatures provide valuable perspectives on tumor microenvironments, aiding in future research and clinical strategy development.

Endosteal stem cells at the bone-blood interface: A double-edged sword for rapid bone formation: Bone marrow endosteal stem cells provide a robust source of bone-making osteoblasts both in normal and abnormal bone formation.

Endosteal stem cells are a subclass of bone marrow skeletal stem cell populations that are particularly important for rapid bone formation occurring in growth and regeneration. These stem cells are strategically located near the bone surface in a specialized microenvironment of the endosteal niche. These stem cells are abundant in young stages but eventually depleted and replaced by other stem cell types residing in a non-endosteal perisinusoidal niche. Single-cell molecular profiling and in vivo cell lineage analyses play key roles in discovering endosteal stem cells. Importantly, endosteal stem cells can transform into bone tumor-making cells when deleterious mutations occur in tumor suppressor genes. The emerging hypothesis is that osteoblast-chondrocyte transitional identities confer a special subset of endosteal stromal cells with stem cell-like properties, which may make them susceptible for tumorigenic transformation. Endosteal stem cells are likely to represent an important therapeutic target of bone diseases caused by aberrant bone formation.

An Organotypic Human Lymph Node Model Reveals the Importance of Fibroblastic Reticular Cells for Dendritic Cell Function.

Human lymph node (HuLN) models have emerged with invaluable potential for immunological research and therapeutic application given their fundamental role in human health and disease. While fibroblastic reticular cells (FRCs) are instrumental to HuLN functioning, their inclusion and recognition of importance for organotypic in vitro lymphoid models remain limited. Here, we established an in vitro three-dimensional (3D) model in a collagen-fibrin hydrogel with primary FRCs and a dendritic cell (DC) cell line(MUTZ-3 DC). To study and characterise the cellular interactions seen in this 3D FRC-DC organotypic model compared to the native HuLN; flow cytometry, immunohistochemistry, immunofluorescence and cytokine/chemokine analysis were performed. FRCs were pivotal for survival, proliferation and localisation of MUTZ-3 DCs. Additionally, we found that CD1a expression was absent on MUTZ-3 DCs that developed in the presence of FRCs during cytokine-induced MUTZ-3 DC differentiation, which was also seen with primary monocyte-derived DCs (moDCs). This phenotype resembled HuLN-resident DCs, which we detected in primary HuLNs, and these CD1a- MUTZ-3 DCs induced T cell proliferation within a mixed leukocyte reaction (MLR), indicating a functional DC status. FRCs expressed podoplanin (PDPN), CD90 (Thy-1), CD146 (MCAM) and Gremlin-1, thereby resembling the DC supporting stromal cell subset identified in HuLNs. This 3D FRC-DC organotypic model highlights the influence and importance of FRCs for DC functioning in a more realistic HuLN microenvironment. As such, this work provides a starting point for the development of an in vitro HuLN.

Identification of FOXO1 as a geroprotector in human synovium through single-nucleus transcriptomic profiling.

The synovium, a thin layer of tissue that is adjacent to the joints and secretes synovial fluid, undergoes changes in aging that contribute to intense shoulder pain and other joint diseases. However, the mechanism underlying human synovial aging remains poorly characterized. Here, we generated a comprehensive transcriptomic profile of synovial cells present in the subacromial synovium from young and aged individuals. By delineating aging-related transcriptomic changes across different cell types and their associated regulatory networks, we identified two subsets of mesenchymal stromal cells (MSCs) in human synovium, which are lining and sublining MSCs, and found that angiogenesis and fibrosis-associated genes were upregulated whereas genes associated with cell adhesion and cartilage development were downregulated in aged MSCs. Moreover, the specific cell-cell communications in aged synovium mirrors that of aging-related inflammation and tissue remodeling, including vascular hyperplasia and tissue fibrosis. In particular, we identified forkhead box O1 (FOXO1) as one of the major regulons for aging differentially expressed genes (DEGs) in synovial MSCs, and validated its downregulation in both lining and sublining MSC populations of the aged synovium. In human FOXO1-depleted MSCs derived from human embryonic stem cells, we recapitulated the senescent phenotype observed in the subacromial synovium of aged donors. These data indicate an important role of FOXO1 in the regulation of human synovial aging. Overall, our study improves our understanding of synovial aging during joint degeneration, thereby informing the development of novel intervention strategies aimed at rejuvenating the aged joint.

Reduction in Lymphoid-Supporting Factors By Mesenchymal Stromal Cells Drives Myeloid-Biased Hematopoiesis at Middle Age

The bone marrow “niche” for hematopoietic stem cells (HSCs) encompasses various cell types, extracellular matrices and secreted factors that maintain the specialized functions of HSCs such as quiescence, self-renewal, and production of multipotent progenitor cells. In old age, changes in this niche contribute to dysfunction of HSCs and the hematopoietic system including increased inflammation and myeloid-biased molecular programs. We have observed that HSC and hematopoietic aging phenotypes become apparent by mid-age (Young et al. Cell Stem Cell 2021, Young et al. J Exp Med 2016), leading to the hypothesis that evaluating alterations in the niche at this stage would reveal the earliest changes initiating HSC aging. To test this hypothesis, we examined both the hematopoietic and non-hematopoietic compartments in individual middle-aged (12-14 months of age, n = 9) and compared them to young C57BL/6 mice (2-4 months of age, n = 5). Immunostaining of femurs showed an increase in sinusoid volume, vessel dysmorphia, and an increase in megakaryocyte abundance in the bone marrow of middle-aged mice. No alterations were observed in arterioles nor adipocyte volume. This data provides supporting evidence that a subset of HSC niche remodeling phenotypes observed in old age are present by mid-age. We then performed single-cell RNA-seq to comprehensively assess changes in abundance and transcriptomes of hematopoietic and non-hematopoietic cells at mid-age. Analysis of this data revealed significant expansion of HSCs in middle-aged mice. In the expanded HSC population, a reduction in B lymphoid differentiation signatures was observed without alterations in inflammation or myeloid differentiation signatures. Computational predictions suggested that the reduced B lymphopoiesis program in middle-aged HSCs resulted from decreased interaction with soluble factors produced by subsets of mesenchymal stromal cells (MSCs), rather than endothelial cells or other hematopoietic cell compartments. Specifically, reduced MSC-to-HSC interactions were linked to a decline in signaling mediated by adiponectin (ADIPOQ; Adipoq), stem cell factor (SCF; Kitl), midkine (MDK; Mdk), and insulin-like growth factor 1 (IGF1; Igf1). Among these, reductions in Kitl and Igf1 in MSCs were correlated with the loss of B lymphopoiesis programs in HSCs comparing individual middle-aged mice. To test the functional impact of the decline in Igf1 in MSCs on lymphopoiesis, we created three MSC-selective Igf1 conditional knockout mouse models using distinct Cre recombinases (Lepr-Cre, nestin-CreER and Prx1-CreER). In all three of these models, MSC-selective knockout of Igf1 reduced B lymphopoiesis resulting in myeloid-biased hematopoiesis, replicating hematopoietic aging phenotypes observed at middle age. These findings indicate that the decline in B lymphopoiesis from HSCs during aging is initiated by a reduction in lymphoid-supporting factors produced by MSCs in the bone marrow microenvironment, and this occurs independently of inflammation or activation of myeloid-promoting transcriptional programs in HSCs.

Genome-Scale High-Resolution Spatial Mapping of the Pro-Tumorigenic Cellular Niche in Classic Hodgkin Lymphoma

Introduction: A fundamental hallmark of cancer is that tumor cells repurpose the tissue microenvironment to promote their own survival. An increased understanding of these mechanisms may lead to improved microenvironment-directed therapies, particularly in lymphoid malignancies. In classic Hodgkin lymphoma (cHL), the rare malignant Hodgkin Reed Sternberg (HRS) cells are surrounded by a CD4+ T-cell and macrophage-rich inflammatory infiltrate. Recent multiplexed immunofluorescence studies suggest that the micron-scale niche around HRS cells is composed of distinct populations of PD-L1+ macrophages and CD4+ T cells, including regulatory CTLA4+ and LAG3+ subsets (Carey et al. Blood 2017, Patel et al. Blood 2019 and Aoki et al. Cancer Discov 2020). However, the topography of the intact tumor microenvironment of cHL requires further definition. Recent single-cell RNA sequencing studies have led to important insights into the biology of cHL; however, they do not adequately capture myeloid cells, fibroblasts, and HRS cells, likely due to the relative fragility of these cells in conventional tissue dissociation protocols. In this study, we use tandem single nucleus and spatially resolved RNA sequencing to systematically dissect the pro-tumorigenic cellular niche of cHL to define potentially targetable microenvironmental dependencies. Methods: Using single nucleus (10X Chromium V3.1 gene expression) and spatially resolved RNA sequencing (Slide-seqV2 and 10X Visium), we generated a dataset of 12 newly diagnosed cHL and 7 reactive lymphoid tissues comprising over 324,855 nuclei and 2.5 million spatially resolved gene expression profiles to construct a genome-scale single cell and spatially resolved atlas of cHL. To validate the expression of ligands/receptors on proximal cell types within the HRS cell niche at single-cell resolution, we also generated an orthogonal 1000-plex image-based spatial transcriptomic dataset (CosMx Spatial Molecular Imager). Additionally, we developed a novel Bayesian consensus tensor factorization approach (C-ZIPTF) to infer shared cancer-associated immune signatures and ligand-receptor interactions. Results: Single nucleus RNA sequencing captures a diversity of cell types and cell states in cHL, including distinct myeloid and stromal cell subsets and HRS cells. Copy number inference analysis identifies the HRS cells, and unsupervised consensus tensor factorization reveals recurrent HRS cell transcriptional states, including aberrant myeloid, stromal, neuronal, and secretory/cytokine programs. Of all clinical and histological parameters, EBV infection status showed the strongest association with HRS cell transcriptional state. Regulatory T cells, macrophages, and fibroblasts are quantitatively increased in cHL compared to reactive lymphoid tissues and additionally exhibit qualitatively altered expression programs. Using C-ZIPTF, we identify disease-defining and prognostically relevant immunosuppressive regulatory T cell and myeloid cell programs and an activated pro-fibrotic myofibroblast-like fibroblast signature. Spatial analysis provides strong evidence for a “niche” model, i.e., the spatial organization of cell types and states around HRS cells. Specifically, CD4+ T cells and myeloid cells are spatially enriched in the immediate proximity of HRS cells and, plasma cells are depleted. Moreover, the CD4+ T cells and myeloid cells exhibit a specialized pro-tumorigenic gene expression program with increased expression of multiple immunosuppressive cytokines, checkpoint molecules, and putative growth factors for HRS cells. Spatially-aware ligand-receptor interaction analysis enables systematic identification and prioritization of novel growth factors for HRS cells. Functional testing of these putative growth factors using an ex vivo 3D cell culture system confirms their growth-promoting effect on primary HRS cells. Conclusions: The HRS cells in cHL are surrounded by a distinctive pro-tumorigenic cellular niche that not only mediates immune evasion but may also directly promote tumor cell growth. These observations provide a rich set of hypotheses for preclinical model development and microenvironment-directed therapies. More broadly, our study demonstrates the power of spatial genomic approaches to deconvolute the molecular architecture of pro-tumorigenic cellular niches in tumor ecosystems.

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

Introduction Rare non-hematopoietic cells in the bone marrow make essential contributions to hematopoiesis. Despite tremendous progress in understanding the mouse bone marrow microenvironment, the precise identity of human non-hematopoietic bone marrow cells and their spatial organization remain largely uncharacterized. Here, we performed single cell transcriptomics and spatial proteomics, assembling the first comprehensive atlas of human bone marrow cellular composition and organization. Methods Using fresh femoral head samples obtained from orthopedic hip replacement surgeries, we first performed single-cell RNA sequencing (scRNA-Seq) to create a comprehensive human bone marrow atlas profiling 29,325 enriched non-hematopoietic cells as well as 53,417 hematopoietic cells from enzymatically digested femoral heads from 12 individuals. We next employed Co-Detection by Indexing (CODEX) multiplexed imaging of 18 bone marrow samples, including both healthy and acute myeloid leukemia (AML) samples, to spatially profile over one million single cells with a novel 53-antibody panel. Results Our transcriptional analysis revealed nine distinct non-hematopoietic bone marrow cell types including mesenchymal stromal cell (MSC) subsets, osteolineage cells, vascular smooth muscle cells, and both sinusoidal and arterial endothelial cells (Figure 1A). We found that MSCs were heterogeneous and hierarchically organized. One specific cell cluster, which we termed Fibro-MSCs, corresponded to previous descriptions of mesenchymal stem cells and was both computationally and functionally shown to be the most stem/progenitor-like. Next, we performed computational cellular communication analysis which revealed that two MSC subsets, Adipo and THY1+ MSCs, provided the majority of canonical hematopoietic supportive factors such as CXCL12, KITLG, IL7, and PTN. Next, we used CODEX to systematically study spatial relationships between these cells. Consistent with the scRNA-Seq cellular communication analysis, we found that Adipo and THY1+ MSCs were in the bone marrow interacting with hematopoietic cells, while osteolineage cells and Fibro-MSCs were found within the trabecular bone region. We then performed unsupervised neighborhood analysis to analyze the distinct niches of the bone marrow. We discovered a relatively hyperoxygenated arterio-endosteal niche for early myelopoiesis, where early myeloid progenitors were characterized by very low levels of HIF1α, in contrast to HIF1α hi neutrophils which were found largely residing near sinusoids. We also employed point pattern statistics and permutation tests to analyze the proximity of cell types to manually identified structures in the bone marrow. This analysis revealed that CD34+ hematopoietic stem and progenitor cells (HSPCs) were frequently contacting adipocytes (Figure 1B), but not sinusoids or bone. Collectively, these results led us to propose a data-driven working model for how human myelopoiesis is spatially organized, with the earliest myeloid progenitors being specified from HSPCs near adipocytes, then migrating to the peri-arteriolar/peri-endosteal early myeloid progenitor niche, and then finally localizing near sinusoids which facilitates bone marrow egress as they mature to neutrophils. To evaluate if our CODEX atlas could be used to study disease states, we mapped new bone marrow images from acute myeloid leukemia (AML) patients and controls to our reference. We used machine learning to identify true mutant cells based on NPM1c expression patterns. We discovered Adipo and THY1+ MSC expansion in AML patients compared to controls, with expanded MSCs spatially associated with leukemic blasts. Our results highlight the potential of our CODEX atlas to contextualize new datasets and study bone marrow organization in disease states, and provide further rationale to study MSC-AML blast interactions. Conclusions Taken together, our scRNA-Seq and CODEX data act in concert, demonstrating the diversity of non-hematopoietic stromal elements, establishing the source of hematopoietic cytokines, and defining the spatial organization in healthy human bone marrow. We envision our multiomic, spatially resolved atlas of human bone marrow will serve as a critical resource for future study of the bone marrow microenvironment in both healthy and disease states.

SATB2 Cytoplasmic Expression is Characteristic of a Subset of Ovarian Stromal Cells and Sex Cord Stromal Tumors.

Special AT-rich sequence-binding protein 2 (SATB2) is a nuclear transcription factor that shows consistent nuclear staining in colorectal adenocarcinoma and osteosarcoma. Following the observation of cytoplasmic staining with this marker in luteinized ovarian stromal cells, we studied the expression of SATB2 in ovarian stromal cells, various types of follicular cysts, and sex cord-stromal tumors. Eighty-five cases were stained for SATB2. Ovarian hilar Leydig cells (n = 12), luteinized stromal cells (n = 10), corpora lutea (n = 4), luteinized follicular cysts (n = 4), and stromal hyperthecosis (n = 6) exhibited consistent, usually diffuse, granular cytoplasmic staining. In addition, Leydig cell tumors (n = 1) and steroid cell tumors (n = 4) showed diffuse cytoplasmic staining. SATB2 also exhibited cytoplasmic staining in most Sertoli-Leydig cell tumors (n = 16) and gynandroblastomas (n = 3) confined to the Leydig cell component. Adult granulosa cell tumors (n = 14), juvenile granulosa cell tumors (n = 3), sex cord tumors with annular tubules (n = 3), cellular fibromas (n = 3), sclerosing stromal tumors (n = 1), and thecomas (n = 1) were negative apart from cytoplasmic staining in associated luteinized stromal cells. SATB2 cytoplasmic staining has not been previously described in these lesions but is characteristic of a variety of ovarian stromal cells and sex cord-stromal tumors, in particular, those exhibiting luteinization or a Leydig or steroid cell component. SATB2 staining may be of value in identifying luteinized or Leydig cells when these are morphologically inconspicuous.

Transinteractome analysis reveals distinct niche requirements for isotype-based plasma cell subsets in the bone marrow.

Bone marrow (BM) long-lived plasma cells (PCs) are essential for long-term protection against infection, and their persistence within this organ relies on interactions with Cxcl12-expressing stromal cells that are still not clearly identified. Here, using single cell RNAseq and in silico transinteractome analyses, we identified Leptin receptor positive (LepR+ ) mesenchymal cells as the stromal cell subset most likely to interact with PCs within the BM. Moreover, we demonstrated that depending on the isotype they express, PCs may use different sets of integrins and adhesion molecules to interact with these stromal cells. Altogether, our results constitute an unprecedented characterization of PC subset stromal niches and open new avenues for the specific targeting of BM PCs based on their isotype.

Abstract A27: Cellular barcoding of the leukemic niche reveals an apelin-mediated clonal expansion of niche endothelial and mesenchymal stromal cell clones

Abstract Hematopoietic stem and progenitor cells (HSPCs) reside in niches that provide regulatory signals for their function. Perturbations such as acute leukemia induce cellular and molecular insults to the niche to support disease progression. Mutation of the MYC oncogene family is a frequent event leading to leukemogenesis. We developed a new zebrafish model of acute erythroid leukemia (AEL) by overexpression of human CMYC under the blood specific promotor draculin (drl). Analyses of drl:CMYC marrows demonstrated a significant expansion of progenitors and a decrease of erythroid, lymphoid and myeloid mature cells (fc=4.8, -4.5, -3.3, -6.5; p<0.000001). RNA-Sequencing of drl:CMYC marrows revealed an upregulation of the erythroid master regulator gata1a (fc=1.4, p=0.01) and fetal hemoglobins hbbe1.1/2 (fc=4.7, 2.9; p=0.0004). Primary and secondary transplantation of drl:CMYC marrows resulted in engraftment and disease propagation (7/7; 17/18). We used the cellular barcoding GESTALT technique to uniquely barcode single cells using CRISPR-CAS9 during embryonic development. We induced a round of barcoding at the one-cell stage and another one at 28 hours post-fertilization, the time of HSC birth. We injected these GESTALT embryos with drl:CMYC to induce AEL, barcode HSPCs and their niche to perform clone tracing. The number of HSPC clones was decreased by half compared to controls (p=0.008) indicative of a clonal expansion of the disease. We performed barcode and single-cell transcriptome profiling of flk1:GFP+ niche endothelial cells and found a significant decrease in the number of endothelial cells clones (fc= -3.5, p<0.05) paired with the identification of a novel AEL venous endothelial population upregulating 99 genes (fc>1; p<0.05) suggestive of angiogenesis likely supporting leukemogenesis. We sorted cxcl12a:dsRed+ niche stromal cells and found that AEL marrows have significantly less stromal clones (fc= -2.1, p<0.01) that are selectively amplified (>20% of the stromal compartment). We hypothesized that AEL expands a subset of stromal cells to promote disease progression and scRNA-Seq of 3,263 cxcl12a:dsRed+ stromal cells revealed an increased fraction of lepr+ mesenchymal stromal cells (MSCs, 66 vs 24% in controls). We hypothesized that AEL progenitors secrete a signal that can specifically remodel the marrow niche and we mined our scRNA-Sequencing data for a candidate ligand significantly upregulated in AEL cells compared to control HSPCs (fc>1; p<0.05) and paired receptors expressed on more than 20% of AEL associated endothelial and/or stromal cells. We identified the peptide hormone apelin expressed by the leukemia and tested if apelin alone could remodel the normal marrow niche endothelial and stromal cells by overexpressing apelin under the drl promotor. Adult marrow analyses revealed a decrease in the absolute number of stromal cells per marrow (fc= -2.2, p<0.001). Together our data support a model in which leukemia induces a clonal expansion of HSPC niche clones via apelin signaling to promote disease progression. Citation Format: Chloé S Baron, Serine Avagyan, Song Yang, Aaron McKenna, Leonard Zon. Cellular barcoding of the leukemic niche reveals an apelin-mediated clonal expansion of niche endothelial and mesenchymal stromal cell clones [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A27.

The age-related changes in lymph node stromal cells underlie defects in peripheral T cell maintenance and immune function decline in old mice.

Abstract Older adults are more vulnerable to infection and cancer, and poorly respond to vaccination. The structural stromal cells in the lymph nodes (LN) are essential regulators of T cell homeostasis and immune response. However, how does aging of LN stromal cells contribute to T cell maintenance defects and functional immunity is incompletely understood. Here we used single cell RNA-Seq of purified stromal cells from adult (3mo) and old (21mo) peripheral LN of C57BL/6 mice to characterize the age-related transcriptional differences in major stromal cell subsets. Our data revealed the enrichment of CCL19 hiand CCL19 lowwhile diminution of Nr4a1 +and Inmt +FRC in old LN. The enriched FRC in old LN exhibited a gene signature of cellular and oxidative stress response, mitochondrial defects, and negative regulation of immunity. The ex vivo functional characterization revealed that old LN stromal cells exhibit elevated mitochondrial reactive oxygen species coupled with increased mitochondrial mass and reduced membrane potential, indicative of mitochondrial defects during the senescence. Interestingly, these defects are observed in older but not mid-age LN. Furthermore, in vitro co-culture of LN stromal cells and purified naive T (T N) cells showed that old LN stromal cells poorly support CD8 T Ncell survival. Finally, boosting the function of old LN stromal cells using agonistic anti-LTbR or mitigating oxidative stress using N-Acetyl Cysteine reversed this effect, via stabilization of BCL2 in T Ncells. Thus, these results suggest that age-related adverse changes in LN stromal cells contribute to defects in maintenance of T Ncells, and highlight that these defects could be reversed to restore T Ncell homeostasis and functional immunity. This work is supported by grants from NIH (P01 AG052359 and R37 AG020719) to Dr. Janko Nikolich-Zugich.

Abstract 4353: Utilizing scRNA sequencing to understand biomarkers of response and resistance to Sacitizumab Govetican in localized TNBC

Abstract Triple-Negative Breast Cancer (TNBC) is an aggressive breast cancer subset, which lacks expression of estrogen receptors, progesterone receptors, and human epidermal growth factor receptor-2. This subset of breast cancer disproportionately affects Black and African American women and improving TNBC treatment options is vital to reducing breast cancer mortality. The novel antibody-drug conjugate, Sacitizumab Govetican (SG), which targets TROP2 at the cell surface, has shown promising clinical results from the NeoSTAR trial (NCT04230109), a phase II study evaluating neoadjuvant SG therapy in a localized TNBC setting. As part of the NeoSTAR clinical trial, we have collected and processed pre- and post- SG treatment patient samples, with the aim of understanding response to this monotherapy. Herein, we identify biomarkers of response and resistance to SG monotherapy through the use of single cell RNA sequencing of matched pre- and post-treatment patient biopsies combined with exome sequencing these patient samples. Pre-treatment core needle biopsy samples, and if applicable, post-treatment residual disease biopsies were dissociated into single cell suspensions and subjected to single cell RNA sequencing. Additionally, fixed patient tissue samples were processed accordingly for exome sequencing analyses. Overall, we analyzed over 144,000 cells from 37 total scRNA seq libraries with an average of 3800 cells per biopsy sample, demonstrating the feasibility of this method. From these analyses, we observed several cell-type differences between patients who achieved a pathological complete response (pCR) and patients who had residual disease (RD). Specifically, our data shows that tumor infiltrating lymphocytes are a potential prognostic biomarker of response to SG. Furthermore, we detected alterations in among stromal and immune cell subsets, among non-responders, indicating that these cell types maybe indicative of SG resistance. Taken together, we outline biomarkers of response to SG treatment for an improved understanding of resistance mechanisms in the neoadjuvant setting to improve TNBC outcomes among patients. Citation Format: Nicole Peiris, Simona Cristea, Mengran Zhang, Siang Koh, James Coates, Ilze Smidt, Veerle Bossuyt, Laura Spring, Aditya Bardia, Leif Ellisen. Utilizing scRNA sequencing to understand biomarkers of response and resistance to Sacitizumab Govetican in localized TNBC. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4353.

Mass Spectrometry-Based Tissue Imaging of the Tumor Microenvironment.

Multiplex ion beam imaging (MIBI) and imaging mass cytometry (IMC) enable highly multiplexed antibody (40+) staining of frozen or formalin fixed, paraffin-embedded (FFPE) human or murine tissues through detection of metal ions liberated from primary antibodies by time-of-flight mass spectrometry (TOF). These methods make detection of more than 50 targets theoretically possible while maintaining spatial orientation. As such, they are ideal tools to identify the multiple immune, epithelial, and stromal cell subsets in the tumor microenvironment and to characterize spatial relationships and tumor-immune status in either murine models or human samples. This chapter summarizes methods for antibody conjugation and validation, staining, and preliminary data collection using IMC or MIBI in both human and mouse pancreatic adenocarcinoma samples. These protocols are intended to facilitate use of these complex platforms in not only tissue-based tumor immunology studies but also tissue-based oncology or immunology studies more broadly.

Single-cell profiling of the microenvironment in decidual tissue from women with missed abortions

To define the decidual microenvironment in euploid and aneuploid missed abortions and elective termination of pregnancies. Prospective, multicenter, observational study. Tertiary hospital and descriptive analysis of transcriptomic data. A total of 34 patients experienced abortions, including 6 women who underwent elective terminations of pregnancy of unplanned pregnancies and 28 cases with missed abortions. All patients underwent their operations from Sep, 2021 to Sep,2022. All women underwent villous copy number variation sequencing. Meanwhile, single-cell RNA sequencing were performed in the decidual tissues of 16 women, and reverse transcription quantitative polymerase chain reaction were performed in the decidual tissues of 18 women. Single-cell RNA sequencing was used to explore the changes in the microenvironment of decidual tissues in abortions. Single-cell RNA sequencing indicated that the microenvironment of the decidual tissue of the missed-abortion group was altered, and that the stromal cells (SCs), natural killer cells, macrophages, and epithelial cells all reflected functional imbalances compared with the elective terminations of pregnancy group. We also noted a correlation between the proportion of senescent SCs and chromosomal abnormalities in missed-abortion embryos. The proportion of senescent decidual SCs in the decidual tissue of missed-abortion patients with common chromosomal abnormalities of the fetus was higher, and this was not conducive to fetal growth and was closely related to missed abortion. In addition, we ascertained that the strength of the HLA-KIR interaction between NK1 and NK2 subsets and non-senescent stromal cell subsets in the missed abortion decidual tissues was weakened, potentially playing a role in the occurrence of missed abortion. The decidualization of SCs in the missed-abortion decidual tissues was impaired, the clearance of senescent SCs by NK cells was weakened, the killing toxicity of non-senescent SCs was enhanced, macrophages were insufficiently resident at the maternal-fetal interface, and epithelial cell differentiation was unbalanced-all creating a maternal microenvironment that was not conducive to fetal growth. We posit that interfering with the expression of dysregulated genes in the missed-abortion decidual tissues and reversing the maternal microenvironment might constitute an effective means toward improving the clinical outcome of missed abortions. Intriguingly, we observed a correlation between stromal cell senescence and embryonic chromosomal abnormalities. Thus, we hypothesize that the DIO2 marker of senescent SCs can be used as a risk indicator for the occurrence of missed miscarriages with chromosomal abnormalities of the embryos, and that it can be applied to guide the clinical diagnosis and treatment of recurrent abortion. NCT04425317.

ScAB detects multiresolution cell states with clinical significance by integrating single-cell genomics and bulk sequencing data.

Although single-cell sequencing has provided a powerful tool to deconvolute cellular heterogeneity of diseases like cancer, extrapolating clinical significance or identifying clinically-relevant cells remains challenging. Here, we propose a novel computational method scAB, which integrates single-cell genomics data with clinically annotated bulk sequencing data via a knowledge- and graph-guided matrix factorization model. Once combined, scAB provides a coarse- and fine-grain multiresolution perspective of phenotype-associated cell states and prognostic signatures previously not visible by single-cell genomics. We use scAB to enhance live cancer single-cell RNA-seq data, identifying clinically-relevant previously unrecognized cancer and stromal cell subsets whose signatures show a stronger poor-survival association. The identified fine-grain cell subsets are associated with distinct cancer hallmarks and prognosis power. Furthermore, scAB demonstrates its utility as a biomarker identification tool, with the ability to predict immunotherapy, drug responses and survival when applied to melanoma single-cell RNA-seq datasets and glioma single-cell ATAC-seq datasets. Across multiple single-cell and bulk datasets from different cancer types, we also demonstrate the superior performance of scAB in generating prognosis signatures and survival predictions over existing models. Overall, scAB provides an efficient tool for prioritizing clinically-relevant cell subsets and predictive signatures, utilizing large publicly available databases to improve prognosis and treatments.