Sp3 is essential for normal lung morphogenesis and cell cycle progression during mouse embryonic development

Members of the Sp family of transcription factors regulate gene expression via binding GC boxes within promoter regions. Unlike Sp1, which stimulates transcription, the closely related Sp3 can either repress or activate gene expression and is required for perinatal survival in mice. Here, we use RNA-seq and cellular phenotyping to show how Sp3 regulates murine fetal cell differentiation and proliferation. Homozygous Sp3-/- mice were smaller than wild-type and Sp+/- littermates, died soon after birth and had abnormal lung morphogenesis. RNA-seq of Sp3-/- fetal lung mesenchymal cells identified alterations in extracellular matrix production, developmental signaling pathways and myofibroblast/lipofibroblast differentiation. The lungs of Sp3-/- mice contained multiple structural defects, with abnormal endothelial cell morphology, lack of elastic fiber formation, and accumulation of lipid droplets within mesenchymal lipofibroblasts. Sp3-/- cells and mice also displayed cell cycle arrest, with accumulation in G0/G1 and reduced expression of numerous cell cycle regulators including Ccne1. These data detail the global impact of Sp3 on in vivo mouse gene expression and development.

Abstract A16: Liquid biopsy for the detection and characterization of canine lymphoma

Lymphoma is the most common hematologic malignancy in dogs, with some subtypes being highly similar to their human counterparts in terms of molecular, pathologic, and biologic features. Despite the rapid growth in our understanding of canine lymphoma, tools for early detection, personalized therapy, and treatment monitoring are still lacking. Blood-based liquid biopsy using next-generation sequencing (NGS) of cell-free DNA is gaining adoption in human medicine and is now available for canine patients. This non-invasive tool affords new opportunities to profile the genomic landscape of naturally occurring canine lymphomas across large cohorts of patients, and given the high homology (>90%) between human and canine cancer genomes, findings in canine lymphomas may afford unique opportunities for comparative oncology studies for the benefit of both species. One hundred sixteen dogs diagnosed with lymphoma (63 intermediate to large B-cell, 21 intermediate to large T-cell, 6 T-zone, and 26 unphenotyped) were included in this analysis, enrolled as part of a larger liquid biopsy clinical validation study. Lymphomas with inconclusive immunophenotype or other types of indolent lymphomas were excluded. A blood sample was collected from each dog following diagnosis and prior to undergoing therapy to evaluate the ability of liquid biopsy to non-invasively detect the presence and characterize the genomic signature of the cancer. In a subset of patients, longitudinal blood samples and clinical outcomes were also collected. Of all lymphoma-diagnosed dogs, 56% were purebred (representing 32 distinct breeds); 57% were male; median age was 8 years; and median weight was 28.4kg. The overall detection rate for lymphoma by liquid biopsy was 92.2% (107/116); with detection rates of 57% for localized/regional disease (Stages I and II) and 95% for disseminated/metastatic disease (Stages III, IV, and V). By immunophenotype, the detection rate for B-cell lymphoma was 97%, T-cell 91%, T-zone 50%, and unphenotyped 92%. A variety of genomic alterations were identified in patients with positive liquid biopsy results, including single nucleotide variants in common oncogenes and tumor suppressor genes, and copy number variants across the genome (including CNVs previously described in tumor tissue of canine lymphoma patients). In patients with longitudinal samples, the presence or absence of cancer signal appeared to be closely related to remission status at corresponding time points. A novel NGS-based liquid biopsy tool has demonstrated the ability to identify genomic alterations in blood samples of dogs with lymphoma, including alterations previously described in human and canine lymphoma tissue. This technology may also provide a non-invasive method for longitudinal monitoring of treatment response in dogs with lymphoma. These findings, and the high degree of homology between the human and canine disease, support the utility of liquid biopsy for the study of canine lymphoma as a comparative oncology model for accelerated biomarker discovery and therapeutic development.

Citation Format: Angela L McCleary-Wheeler, Kristina M Kruglyak, Gilberto E Hernandez, Prachi Nakashe, Lisa M McLennan, Thuy Jennings, Jill M Rafalko, Lauren E Holtvoigt, Daniel S Grosu, Jason Chibuk, Susan C Hicks, John A Tynan, Ilya Chorny, Dana WY Tsui, Andi Flory. Liquid biopsy for the detection and characterization of canine lymphoma [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A16.

Abstract 1612: Comparative oncology analysis of canine cancer by tumor and liquid biopsy testing for biomarker and therapeutic discovery in humans and dogs

Human and canine cancers share a high level of homology. Characterizing their respective genomic landscapes can expand the knowledge base of comparative oncology and support biomarker discovery and therapeutic development for the benefit of both species. Genomic profiling via tumor biopsy infers risk to the patient in both human and veterinary medicine and is often complicated by tumor heterogeneity. Blood-based liquid biopsy has been shown to open new opportunities to profile the cancer genome noninvasively in both species. The goal of this study was to benchmark the occurrence of homologous genomic variants in a variety of canine cancers that have a counterpart in humans, including lymphoma (B-cell and T-cell), soft-tissue sarcoma, osteosarcoma, and melanoma, among others, utilizing tumor and liquid biopsy profiling. The study was performed in a prospective cohort of over 300 client-owned dogs that received a confirmed cancer diagnosis either at the time of enrollment or after sample collection. A blood sample was collected prior to biopsy or surgical resection of the tumor to evaluate the use of liquid biopsy to noninvasively profile the cancer genome. Tumor tissue samples were collected at the time of surgical resection. In a subset of the subjects, blood samples were collected 3 to 30 days following surgical removal of the tumor, and longitudinally during cancer therapy and monitoring. The Cancer Gene Census (CGC) and COSMIC databases were interrogated, and a high degree of homology (>90%) between human and canine oncogenes and tumor suppressor genes was observed. A custom panel was designed encompassing 95 of the top 100 human DNA single nucleotide variants from COSMIC that had a canine orthologue, and targeted sequencing was performed on all tissue and blood samples. A large number of these variants—many of which are actionable in human cancer— were detected in the tumor samples and pre-surgical plasma samples. In some patients, tumor-derived variants were detected in the post-surgical plasma that confirmed the presence of residual disease after surgery. As disease progressed, an increase in the variant allele fraction (VAF) of the tumor-derived mutations was observed and tracked with the patient’s clinical course. Additionally, the presence of variants that may be targetable by human cancer drugs were identified in a subset of patients. These findings demonstrate the potential of liquid biopsy to characterize the genomic landscape of canine cancers at diagnosis and throughout treatment, similar to observations reported in human cancers. This builds the foundation for comparative oncology to translate the knowledge of precision medicine between humans and dogs, to facilitate biomarker discovery, and to track emergence of potential actionable biomarkers in various therapeutic contexts to the benefit of both species.

Citation Format: Ilya Chorny, Kristina M. Kruglyak, John A. Tynan, Gilberto E. Hernandez, Prachi Nakashe, Susan Hicks, Rita Motalli-Pepio, Lisa McLennan, Lauren E. Holtvoigt, Jill M. Rafalko, Jason Chibuk, Angela L. McCleary-Wheeler, Andi Flory, Daniel S. Grosu, Dana W. Tsui. Comparative oncology analysis of canine cancer by tumor and liquid biopsy testing for biomarker and therapeutic discovery in humans and dogs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1612.

Comparative oncology analysis using genomic profiling of canine cancers by tissue and liquid biopsy testing reveals actionable somatic alterations with orthologs in human cancers

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Background: Targeted therapies offer great potential for cancer treatment in humans; however, enrollment in clinical trials may be slow, particularly for rare cancer types. The high homology between human and canine cancer genomes provides an opportunity for comparative oncology analyses that can inform the development of therapeutics for the benefit of both species. Currently, there is no well-established canine cancer genomic database. This study presents preliminary findings from an ongoing initiative aimed at building a foundational database of canine cancer genomic variants and their human orthologs via tissue and liquid biopsy profiling of multiple cancer types. Methods: Matched blood and tissue samples were collected from an all-comers cohort of over 150 cancer-diagnosed, client-owned dogs undergoing surgical resection or tissue sampling by biopsy. Cancer types included those found in both humans and dogs, such as lymphoma, osteosarcoma, mammary gland tumors and melanoma. Blood samples were processed to obtain plasma and white blood cells, and all samples were subjected to DNA extraction, library preparation, and next-generation sequencing. Somatic variants detected by liquid biopsy and tissue testing were mapped to human orthologs targeted by therapeutic agents approved by the FDA or listed in NCCN guidelines, and to orthologs with therapeutic or prognostic levels of evidence annotated in human oncology databases. Results: Somatic alterations were identified in over half of the tissue and/or liquid biopsy samples tested. Results from tissue and liquid biopsy showed high concordance, and liquid biopsy revealed additional alterations that may have been missed in single-site tissue biopsies due to tumor heterogeneity. Of the mutations identified in plasma and/or tissue but absent in matched white blood cells, 10% mapped to a human ortholog listed as a biomarker targeted by either an approved therapeutic agent or a therapeutic currently undergoing clinical trials; examples include NRAS, HRAS and AKT1 mutations. Over 10% of canine cancer patients also harbored orthologs of somatic TP53 mutations reported to be prognostic in multiple human cancers. In particular, TP53 mutations were found in > 20% of canine osteosarcoma patients, which aligns with prior findings in human osteosarcoma and highlights the potential of comparative oncology for cancer types that are rare in humans but common in dogs. Conclusions: The results confirm the homology between canine and human cancers and emphasize the potential to translate genomic knowledge for biomarker discovery and therapeutic development between species. The high concordance between tumor and liquid biopsy findings support the prospect of using a noninvasive blood test to expand the genomic characterization effort to much larger cohorts of cancer-diagnosed dogs.

Blood-Based Liquid Biopsy for Comprehensive Cancer Genomic Profiling Using Next-Generation Sequencing: An Emerging Paradigm for Non-invasive Cancer Detection and Management in Dogs

This proof-of-concept study demonstrates that blood-based liquid biopsy using next generation sequencing of cell-free DNA can non-invasively detect multiple classes of genomic alterations in dogs with cancer, including alterations that originate from spatially separated tumor sites. Eleven dogs with a variety of confirmed cancer diagnoses (including localized and disseminated disease) who were scheduled for surgical resection, and five presumably cancer-free dogs, were enrolled. Blood was collected from each subject, and multiple spatially separated tumor tissue samples were collected during surgery from 9 of the cancer subjects. All samples were analyzed using an advanced prototype of a novel liquid biopsy test designed to non-invasively interrogate multiple classes of genomic alterations for the detection, characterization, and management of cancer in dogs. In five of the nine cancer patients with matched tumor and plasma samples, pre-surgical liquid biopsy testing identified genomic alterations, including single nucleotide variants and copy number variants, that matched alterations independently detected in corresponding tumor tissue samples. Importantly, the pre-surgical liquid biopsy test detected alterations observed in spatially separated tissue samples from the same subject, demonstrating the potential of blood-based testing for comprehensive genomic profiling of heterogeneous tumors. Among the three patients with post-surgical blood samples, genomic alterations remained detectable in one patient with incomplete tumor resection, suggesting utility for non-invasive detection of minimal residual disease following curative-intent treatment. Liquid biopsy allows for non-invasive profiling of cancer-associated genomic alterations with a simple blood draw and has potential to overcome the limitations of tissue-based testing posed by tissue-level genomic heterogeneity.

Developmental Immaturity of Siglec Receptor Expression on Neonatal Alveolar Macrophages Predisposes to Severe Group B Streptococcal Infection

Streptococcus agalactiae (Group B Streptococcus, GBS) is the most common neonatal pathogen. However, the cellular and molecular mechanisms for neonatal susceptibility to GBS pneumonia and sepsis are incompletely understood. Here we optimized a mouse model of GBS pneumonia to test the role of alveolar macrophage (ΑΜΦ) maturation in host vulnerability to disease. Compared with juvenile and adult mice, neonatal mice infected with GBS had increased mortality and persistence of lung injury. In addition, neonatal mice were defective in GBS phagocytosis and killing. ΑΜΦ depletion and disruption of ΑΜΦ differentiation in Csf2^−/− mice both impaired GBS clearance. AMΦ engage the heavily sialylated GBS capsule via the cell surface Siglec receptors Sn and Siglec-E. Although both newborn and adult ΑΜΦ expressed Siglec-E, newborn ΑΜΦ expressed significantly lower levels of Sn. We propose that a developmental delay in Sn expression on ΑΜΦ may prevent effective killing and clearing of GBS from the newborn lung.

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Newborn mice fail to kill GBS, developing persistent lung injury

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Mature AMΦ detect the Sialic acid capsule on GBS to mediate bacterial clearance

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Immature newborn AMΦ lack mature Siglec expression required for killing GBS

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GBS engages the inhibitory Siglec-E on newborn AMΦ to suppress innate immunity

Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants

Lung macrophages mature after birth, placing newborn infants, particularly those born preterm, within a unique window of susceptibility to disease. We hypothesized that in preterm infants, lung macrophage immaturity contributes to the development of bronchopulmonary dysplasia (BPD), the most common serious complication of prematurity. By measuring changes in lung macrophage gene expression in preterm patients at risk of BPD, we show here that patients eventually developing BPD had higher inflammatory mediator expression even on the first day of life. Surprisingly, the ex vivo response to LPS was similar across all samples. Our analysis did however uncover macrophage signature genes whose expression increased in the first week of life specifically in patients resilient to disease. We propose that these changes describe the dynamics of human lung macrophage differentiation. Our study therefore provides new mechanistic insight into both neonatal lung disease and human developmental immunology.

Developmental immaturity of sialic acid recognition mediates neonatal susceptibility to GBS pneumonia

Group B Streptococcus (GBS) is a major neonatal pathogen but rarely causes disease in adults. We previously showed in mice that GBS escapes killing in the neonatal lung via its heavily sialylated capsule. Immune cells detect sialic acid moieties via expression of a repertoire of Siglec receptors. Combinatory expression of proinflammatory and anti-inflammatory Siglec receptors allows differentiation between host and pathogenic microbial sialic acid modifications. We test here the hypothesis that neonatal alveolar macrophages (AMs) fail to detect and kill GBS due to developmental immaturity of Siglec receptor expression. Adult AMs express the proinflammatory sialic acid receptor Sialoadhesin (Sn, Siglec-1) and the anti-inflammatory receptors Siglec-E and Siglec-F. However, real time PCR, immunofluorescence, and FACS detected only Siglec-E in neonatal lung macrophage populations. Sn expression increased soon after birth and was restricted to AMs. The timing of increased Sn expression in newborn mice correlated with susceptibility to GBS. Mice infected with GBS on day 1 suffered early onset mortality, while mice infected on day 2 displayed late onset disease. Mice infected on day 3 survived GBS infection. Further implicating AM immaturity, Csf2−/− mice, which have defects in AM differentiation, lacked Sn expression and had reduced GBS clearance following infection. The presence of Siglec-E but absence of Sn in newborn AMs appeared to promote tolerance to GBS. Newborn SigE−/− mice had increased GBS phagocytosis and killing compared to WT controls. We therefore conclude that GBS exploits developmental immaturity of Siglec expression in AMs via its sialic acid capsule in causing neonatal disease.

Differential Immune Activation in Fetal Macrophage Populations

Distinct macrophage subsets populate the developing embryo and fetus in distinct waves. However little is known about the functional differences between in utero macrophage populations or how they might contribute to fetal and neonatal immunity. Here we tested the innate immune response of mouse macrophages derived from the embryonic yolk sac and from fetal liver. When isolated from liver or lung, CD11bHI fetal liver derived macrophages responded to the TLR4 agonist LPS by expressing and releasing inflammatory cytokines. However F4/80HI macrophages from the yolk sac did not respond to LPS treatment. While differences in TLR4 expression did not appear to explain these data, F4/80HI macrophages had much lower NLRP3 inflammasome expression compared to CD11bHI macrophages. Gene expression profiling also demonstrated LPS-induced expression of inflammatory genes in CD11bHI macrophages, but not in F4/80HI cells. Genes expressed in LPS-treated CD11bHI macrophages were more likely to contain predicted NF-κB binding sites in their promoter regions. Our data show that CD11bHI macrophages derived from fetal liver are the major pro-inflammatory cells in the developing fetus. These findings could have important implications in better understanding the fetal inflammatory response and the unique features of neonatal immunity.

VHL-dependent regulation of a β-dystroglycan glycoform and glycogene expression in renal cancer

Identification of novel biomarkers and targets in renal cell carcinoma (RCC) remains a priority and one cellular compartment that is a rich potential source of such molecules is the plasma membrane. A shotgun proteomic analysis of cell surface proteins enriched by cell surface biotinylation and avidin affinity chromatography was explored using the UMRC2- renal cancer cell line, which lacks von Hippel-Lindau (VHL) tumour suppressor gene function, to determine whether proteins of interest could be detected. Of the 814 proteins identified ~22% were plasma membrane or membrane-associated, including several with known associations with cancer. This included β-dystroglycan, the transmembrane subunit of the DAG1 gene product. VHL-dependent changes in the form of β-dystroglycan were detected in UMRC2-/+VHL transfectants. Deglycosylation experiments showed that this was due to differential sialylation. Analysis of normal kidney cortex and conventional RCC tissues showed that a similar change also occurred in vivo. Investigation of the expression of genes involved in glycosylation in UMRC2-/+VHL cells using a focussed microarray highlighted a number of enzymes involved in sialylation; upregulation of bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) was validated in UMRC2- cells compared with their +VHL counterparts and also found in conventional RCC tissue. These results implicate VHL in the regulation of glycosylation and raise interesting questions regarding the extent and importance of such changes in RCC.

Glycophenotypic alterations induced by Pteridium aquilinum in mice gastric mucosa: synergistic effect with Helicobacter pylori infection

The bracken fern Pteridium aquilinum is a plant known to be carcinogenic to animals. Epidemiological studies have shown an association between bracken fern exposure and gastric cancer development in humans. The biological effects of exposure to this plant within the gastric carcinogenesis process are not fully understood. In the present work, effects in the gastric mucosa of mice treated with Pteridium aquilinum were evaluated, as well as molecular mechanisms underlying the synergistic role with Helicobacter pylori infection. Our results showed that exposure to Pteridium aquilinum induces histomorphological modifications including increased expression of acidic glycoconjugates in the gastric mucosa. The transcriptome analysis of gastric mucosa showed that upon exposure to Pteridium aquilinum several glycosyltransferase genes were differently expressed, including Galntl4, C1galt1 and St3gal2, that are mainly involved in the biosynthesis of simple mucin-type carbohydrate antigens. Concomitant treatment with Pteridium aquilinum and infection with Helicobacter pylori also resulted in differently expressed glycosyltransferase genes underlying the biosynthesis of terminal sialylated Lewis antigens, including Sialyl-Lewis^x. These results disclose the molecular basis for the altered pattern of glycan structures observed in the mice gastric mucosa. The gene transcription alterations and the induced glycophenotypic changes observed in the gastric mucosa contribute for the understanding of the molecular mechanisms underlying the role of Pteridium aquilinum in the gastric carcinogenesis process.

Dynamics of populations with age-difference and diffusion: localization

"In this paper we study the behavior of the solutions of the Gurtin-MacCamy model for the dynamics of populations with [spatial] diffusion and age-dependence. We give sufficient conditions on the birth and death modules for the population to remain localized in a fixed interval or to ultimately cover all the domain."