scholarly journals TAMI-45. PHENOGENOMIC CHARACTERIZATION OF IMMUNOMODULATORY PURINERGIC SIGNALING IN GLIOBLASTOMA

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii222-ii223
Author(s):  
Shannon Coy ◽  
Rumana Rashid ◽  
Sylwia Stopka ◽  
Jia-Ren Lin ◽  
Philipp Euskirchen ◽  
...  
Keyword(s):  
Clinical Outcome ◽  
Single Cell ◽  
Purinergic Signaling ◽  
Progression Free Survival ◽  
Tissue Imaging ◽  
Phenotypic Properties ◽  
Spatially Resolved ◽  
Therapeutic Benefits ◽  
Adenosine Concentration ◽  
Cd73 Expression

Abstract INTRODUCTION Purinergic signaling plays critical roles in the regulation of tumor growth and anti-tumor immunity via autocrine/paracrine binding of metabolites to receptors on neoplastic and non-neoplastic populations. Extracellular purine concentrations are mediated by the ectonucleotidase enzymes CD39 and CD73, which catabolize ATP to adenosine. Within tumors such as glioblastoma, neoplastic, immune, and stromal cells expressing these enzymes may co-localize to generate immunosuppressive adenosine-rich environments. However, the composition, architecture, and phenotypic properties of these tumor ecosystems and their relationship to tumor genotype are poorly characterized. METHODS We quantified CD73 expression by immunohistochemistry in a cohort of CNS tumors [meningiomas(n=222), gliomas(n=244), ependymomas(n=44), medulloblastomas(n=24), and craniopharyngiomas(n=38)]. We used publicly-available single-cell RNA-seq data and 36-marker multiplexed tissue imaging (t-CyCIF) of 139 clinically and genomically annotated glioblastoma resections to characterize CD39 and CD73-expressing populations, define the immune architecture and tumor cell-states at single cell resolution, and identify markers of clinical outcome. We used mass spectrometry imaging (MALDI-MSI) to generate spatially-resolved quantification of purine metabolite levels in glioblastoma resections (n=10). RESULTS CD73 exhibited strong expression in a subset of gliomas and meningiomas but was typically not expressed in ependymomas or medulloblastomas. CD73 expression correlated with poor progression-free-survival in IDH-wildtype glioblastoma (p=0.04). scRNA-seq and t-CyCIF in glioblastoma showed CD73 expression in tumor cells, and CD39 expression in macrophages and endothelial cells. MALDI-MSI showed significantly greater adenosine concentrations (3.5-fold;p=0.04) in glioblastomas with high CD73 expression. scRNA-seq showed direct correlations between stem-like mRNA expression, proliferation, and CD73 expression in DIPG. CD73 expression significantly correlated with EGFR amplification, interferon signaling, and PD-L1 expression in glioblastoma. CONCLUSIONS Phenogenomic analysis of purinergic immunomodulatory signaling revealed significant interplay between CD73 activity and genotype, adenosine concentration, differentiation-state, clinical outcome, and possible interaction between CD39-positive macrophages and CD73-positive neoplastic cells. Anti-CD73 therapy may provide therapeutic benefits in glioblastoma by blunting immunosuppressive and oncogenic adenosine signaling.

scholarly journals Single Cell Spatial Analysis Reveals the Topology of Immunomodulatory Purinergic Signaling in Glioblastoma

2022 ◽  
Author(s):  
Shannon Coy ◽  
Shu Wang ◽  
Sylwia A Stopka ◽  
Jia-Ren Lin ◽  
Rumana Rashid ◽  
...  
Keyword(s):  
Single Cell ◽  
Spatial Organization ◽  
Purinergic Signaling ◽  
Tissue Imaging ◽  
Spatial Proximity ◽  
Spatially Resolved ◽  
Lineage Differentiation ◽  
Regulatory Enzymes ◽  
Immunosuppressive Microenvironment ◽  
Cd73 Expression

Glioblastoma develops an immunosuppressive microenvironment that fosters tumorigenesis and resistance to current therapeutic strategies. Here we use multiplexed tissue imaging and single-cell RNA-sequencing to characterize the composition, spatial organization, and clinical significance of extracellular purinergic signaling in glioblastoma. We show that glioblastoma exhibit strong expression of CD39 and CD73 ectoenzymes, correlating with increased adenosine levels. Microglia are the predominant source of CD39, while CD73 is principally expressed by tumor cells, particularly in tumors with amplification of EGFR and astrocyte-like differentiation. Spatially-resolved single-cell analyses demonstrate strong spatial correlation between tumor CD73 and microglial CD39, and that their spatial proximity is associated with poor clinical outcomes. Together, this data reveals that tumor CD73 expression correlates with tumor genotype, lineage differentiation, and functional states, and that core purine regulatory enzymes expressed by neoplastic and tumor-associated myeloid cells interact to promote a distinctive adenosine-rich signaling niche and immunosuppressive microenvironment potentially amenable to therapeutic targeting.

scholarly journals Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Mayar Allam ◽  
Thomas Hu ◽  
Shuangyi Cai ◽  
Krishnan Laxminarayanan ◽  
Robert B. Hughley ◽  
...  
Keyword(s):  
Single Cell ◽  
Biological Tissues ◽  
Chronic Tonsillitis ◽  
Tissue Imaging ◽  
Imaging Data ◽  
Mass Cytometry ◽  
Tissue Sections ◽  
Spatially Resolved ◽  
Cell Granularity ◽  
Health And Disease

AbstractDeep molecular profiling of biological tissues is an indicator of health and disease. We used imaging mass cytometry (IMC) to acquire spatially resolved 20-plex protein data in tissue sections from normal and chronic tonsillitis cases. We present SpatialViz, a suite of algorithms to explore spatial relationships in multiplexed tissue images by visualizing and quantifying single-cell granularity and anatomical complexity in diverse multiplexed tissue imaging data. Single-cell and spatial maps confirmed that CD68+ cells were correlated with the enhanced Granzyme B expression and CD3+ cells exhibited enrichment of CD4+ phenotype in chronic tonsillitis. SpatialViz revealed morphological distributions of cellular organizations in distinct anatomical areas, spatially resolved single-cell associations across anatomical categories, and distance maps between the markers. Spatial topographic maps showed the unique organization of different tissue layers. The spatial reference framework generated network-based comparisons of multiplex data from healthy and diseased tonsils. SpatialViz is broadly applicable to multiplexed tissue biology.

scholarly journals Treating the patient and not just the cancer: therapeutic burden in prostate cancer

2021 ◽  
Author(s):  
Daniel E. Spratt ◽  
Neal Shore ◽  
Oliver Sartor ◽  
Dana Rathkopf ◽  
Kara Olivier
Keyword(s):  
Prostate Cancer ◽  
Second Generation ◽  
Locally Advanced ◽  
Progression Free Survival ◽  
Patient Treatment ◽  
Free Survival ◽  
Androgen Ablation ◽  
Therapeutic Benefits ◽  
Age Related ◽  
Concomitant Medications

Abstract Background Prostate cancer (PC) is a leading cause of death in older men. Androgen deprivation therapy (ADT) is considered the standard-of-care for men with locally advanced disease. However, continuous androgen ablation is associated with acute and long-term adverse effects and most patients will eventually develop castration-resistant PC (CRPC). The recent approval of three, second-generation androgen receptor inhibitors (ARIs), apalutamide, enzalutamide, and darolutamide, has transformed the treatment landscape of PC. Treatment with these second-generation ARIs have produced positive trends in metastasis-free survival, progression-free survival, and overall survival. For patients with non-metastatic CRPC, who are mainly asymptomatic from their disease, maintaining quality of life is a major objective when prescribing therapy. Polypharmacy for age-related comorbidities also is common in this population and may increase the potential for drug–drug interactions (DDIs). Method This review summarizes the multiple factors that may contribute to the therapeutic burden of patients with CRPC, including the interplay between age, comorbidities, concomitant medications, the use of ARIs, and financial distress. Conclusions As the treatment landscape in PC continues to rapidly evolve, consideration must be given to the balance between therapeutic benefits and potential treatment-emergent adverse events that may be further complicated by DDIs with concomitant medications. Patient-centered communication is a crucial aspect of alleviating this burden, and healthcare professionals (HCPs) may benefit from training in effective patient communication. HCPs should closely and frequently monitor patient treatment responses, in order to better understand symptom onset and exacerbation. Patients also should be encouraged to participate in exercise programs, and health information and support groups, which may assist them in preventing or mitigating certain determinants of the therapeutic burden associated with PC and its management.

scholarly journals Comprehensive single-cell sequencing reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of nasopharyngeal carcinoma

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lanqi Gong ◽  
Dora Lai-Wan Kwong ◽  
Wei Dai ◽  
Pingan Wu ◽  
Shanshan Li ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Single Cell ◽  
Rna Sequencing ◽  
Progression Free Survival ◽  
Developmental Trajectory ◽  
Free Survival ◽  
Genetic Profiling ◽  
Single Cell Rna Sequencing ◽  
Infiltrating Cells ◽  
Patient Prognosis

AbstractThe tumor microenvironment (TME) of nasopharyngeal carcinoma (NPC) harbors a heterogeneous and dynamic stromal population. A comprehensive understanding of this tumor-specific ecosystem is necessary to enhance cancer diagnosis, therapeutics, and prognosis. However, recent advances based on bulk RNA sequencing remain insufficient to construct an in-depth landscape of infiltrating stromal cells in NPC. Here we apply single-cell RNA sequencing to 66,627 cells from 14 patients, integrated with clonotype identification on T and B cells. We identify and characterize five major stromal clusters and 36 distinct subpopulations based on genetic profiling. By comparing with the infiltrating cells in the non-malignant microenvironment, we report highly representative features in the TME, including phenotypic abundance, genetic alternations, immune dynamics, clonal expansion, developmental trajectory, and molecular interactions that profoundly influence patient prognosis and therapeutic outcome. The key findings are further independently validated in two single-cell RNA sequencing cohorts and two bulk RNA-sequencing cohorts. In the present study, we reveal the correlation between NPC-specific characteristics and progression-free survival. Together, these data facilitate the understanding of the stromal landscape and immune dynamics in NPC patients and provides deeper insights into the development of prognostic biomarkers and therapeutic targets in the TME.

scholarly journals Single-cell transcriptomic analysis of mIHC images via antigen mapping

2021 ◽  
Vol 7 (10) ◽  
pp. eabc5464
Author(s):  
Kiya W. Govek ◽  
Emma C. Troisi ◽  
Zhen Miao ◽  
Rachael G. Aubin ◽  
Steven Woodhouse ◽  
...  
Keyword(s):  
Single Cell ◽  
Spatial Patterns ◽  
Cell Types ◽  
Level Of Detail ◽  
Cell Populations ◽  
Sequencing Data ◽  
Spatially Resolved ◽  
Murine Spleen ◽  
Single Cell Rna Sequencing ◽  
Antibody Panel

Highly multiplexed immunohistochemistry (mIHC) enables the staining and quantification of dozens of antigens in a tissue section with single-cell resolution. However, annotating cell populations that differ little in the profiled antigens or for which the antibody panel does not include specific markers is challenging. To overcome this obstacle, we have developed an approach for enriching mIHC images with single-cell RNA sequencing data, building upon recent experimental procedures for augmenting single-cell transcriptomes with concurrent antigen measurements. Spatially-resolved Transcriptomics via Epitope Anchoring (STvEA) performs transcriptome-guided annotation of highly multiplexed cytometry datasets. It increases the level of detail in histological analyses by enabling the systematic annotation of nuanced cell populations, spatial patterns of transcription, and interactions between cell types. We demonstrate the utility of STvEA by uncovering the architecture of poorly characterized cell types in the murine spleen using published cytometry and mIHC data of this organ.

scholarly journals Spatial and single-cell transcriptional landscape of human cerebellar development

2020 ◽  
Author(s):  
Kimberly A. Aldinger ◽  
Zach Thomson ◽  
Parthiv Haldipur ◽  
Mei Deng ◽  
Andrew E. Timms ◽  
...  
Keyword(s):  
Single Cell ◽  
Emotional Regulation ◽  
Cell Types ◽  
Molecular Organization ◽  
Cerebellar Development ◽  
Disease Genes ◽  
Spatially Resolved ◽  
Human Cerebellum ◽  
Spatial Composition ◽  
And Function

ABSTRACTCerebellar development and function require precise regulation of molecular and cellular programs to coordinate motor functions and integrate network signals required for cognition and emotional regulation. However, molecular understanding of human cerebellar development is limited. Here, we combined spatially resolved and single-cell transcriptomics to systematically map the molecular, cellular, and spatial composition of early and mid-gestational human cerebellum. This enabled us to transcriptionally profile major cell types and examine the dynamics of gene expression within cell types and lineages across development. The resulting ‘Developmental Cell Atlas of the Human Cerebellum’ demonstrates that the molecular organization of the cerebellar anlage reflects cytoarchitecturally distinct regions and developmentally transient cell types that are insufficiently captured in bulk transcriptional profiles. By mapping disease genes onto cell types, we implicate the dysregulation of specific cerebellar cell types, especially Purkinje cells, in pediatric and adult neurological disorders. These data provide a critical resource for understanding human cerebellar development with implications for the cellular basis of cerebellar diseases.

scholarly journals Cell Atlas technologies and insights into tissue architecture

2020 ◽  
Vol 477 (8) ◽  
pp. 1427-1442 ◽  
Author(s):  
Anna Wilbrey-Clark ◽  
Kenny Roberts ◽  
Sarah A. Teichmann
Keyword(s):  
Single Cell ◽  
Molecular Level ◽  
Cell Types ◽  
Tissue Architecture ◽  
Robert Hooke ◽  
Spatially Resolved ◽  
Gene And Protein Expression ◽  
Basic Biology ◽  
And Function ◽  
Fundamental Units

Since Robert Hooke first described the existence of ‘cells’ in 1665, scientists have sought to identify and further characterise these fundamental units of life. While our understanding of cell location, morphology and function has expanded greatly; our understanding of cell types and states at the molecular level, and how these function within tissue architecture, is still limited. A greater understanding of our cells could revolutionise basic biology and medicine. Atlasing initiatives like the Human Cell Atlas aim to identify all cell types at the molecular level, including their physical locations, and to make this reference data openly available to the scientific community. This is made possible by a recent technology revolution: both in single-cell molecular profiling, particularly single-cell RNA sequencing, and in spatially resolved methods for assessing gene and protein expression. Here, we review available and upcoming atlasing technologies, the biological insights gained to date and the promise of this field for the future.

A single-cell and spatially resolved atlas of human breast cancers

2021 ◽  
Vol 53 (9) ◽  
pp. 1334-1347
Author(s):  
Sunny Z. Wu ◽  
Ghamdan Al-Eryani ◽  
Daniel Lee Roden ◽  
Simon Junankar ◽  
Kate Harvey ◽  
...  
Keyword(s):  
Single Cell ◽  
Breast Cancers ◽  
Human Breast ◽  
Spatially Resolved

Combined aCGH and Mutational Analysis of CLL Patients with 17p Deletion.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2091-2091
Author(s):  
Hannah C. Rudenko ◽  
Vasantha Brito-Babapulle ◽  
David Gonzalez ◽  
Pilar Martinez ◽  
Paola E. Leone ◽  
...  
Keyword(s):  
Clinical Outcome ◽  
Mutational Analysis ◽  
Survival Curve ◽  
Progression Free Survival ◽  
Tp53 Gene ◽  
Chromosome 9 ◽  
Research Centre ◽  
Genomic Changes ◽  
Mutational Status ◽  
Trisomy 12

Abstract We have utilised aCGH (Breakthrough Breast Cancer Research Centre 5.8K array) and mutational analysis of the TP53 gene (exons 4–10) on 74 cases of CLL to define the extent of deletion at 17p, TP53 mutational status, additional genomic changes, and how this affects clinical outcome. 17p- cases were selected by FISH (n=37, Vysis LSI P53 probe) and 37 cases were selected as being representative of the survival curve of CLL patients without 17p-. FISH identified 22 cases with TP53- in ≥ 50% of cells, 4 cases with TP53- 20–50% and 11 cases with TP53- ≤ 20%. aCGH can detect abnormalities present in >50% of cells and all of the TP53- cases greater than 50% by FISH were detected with deletion ranging between 6-20Mb in length, the majority encompassing the entire p-arm. In addition aCGH detected deletion of 17p in 5/15 cases with TP53- <50%, and 2/37 with no detectable TP53- by FISH, these deletions clustered at 17p13.3 and 17p11.2, and did not involve the TP53 gene. Cases with 17p- >20% have a poor clinical outcome (median survival 11 months, median progression free survival 3 months), the majority of these (85%) also have a mutation of TP53 whereas in cases with ≤ 20% 17p- only 10% were mutated. The 17p- group was characterised by additional recurrent deletions involving 18p, 20p and 22q, which tended to occur as single additional events. Understanding the order in which these events occur is important, 18p- was found in 6 cases, 2 of which had <50% 17p- by FISH, suggesting that 18p- is present in a higher percentage of cells and by implication occurs prior to the 17p deletion, a similar finding was also present for the 20p- cases. 18p deletion varied in length between 5.9Mb and 12Mb, with the minimally deleted region (MDR) involving a 2.5Mb region spanning 18p11.23-p11.22. 20p- was found in 8 cases of which 3 covered almost the entire p-arm, and 5 formed 2 clusters at each end of the p-arm. 22q- was found in 8 cases, with only 1 outside of the 17p- group. Out of these 8 cases with deletion, 6 covered almost the complete q-arm but a MDR was difficult to define, however if the non-17p- case is excluded the MDR covers 1.4Mb at 22q12.3. Recurrent abnormalities were also found on other chromosomes, but did not differ between the two groups. These included regions with previously identified abnormalities; trisomy 12 (n=11), loss of 6q14.1–24.3 (n=11), loss of 11q12.1–25 (n=17) and loss of 13q12.1–21.1 (n=6) as well as detection of novel abnormalities; gain of 4p16.3–16.1 (n=23), gain of 11p15.5–15.3 (n=22), gain of 22q11.21–13.33 (n=22) and deletions on chromosome 9 (n=9). These results show that deletion of TP53 and mutation of the other allele are critical adverse prognostic factors. We have also defined a genetic background (18p-, 20p- and 22q-) on which these changes arise.

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