Granulocyte Adhesion Research Articles

Dysregulated gene subnetworks in breast invasive carcinoma reveal novel tumor suppressor genes

Breast invasive carcinoma (BRCA) is the most malignant and leading cause of death in women. Global efforts are ongoing for improvement in early detection, prevention, and treatment. In this milieu, a comprehensive analysis of RNA-sequencing data of 1097 BRCA samples and 114 normal adjacent tissues is done to identify dysregulated genes in major molecular classes of BRCA in various clinical stages. Significantly enriched pathways in distinct molecular classes of BRCA have been identified. Pathways such as interferon signaling, tryptophan degradation, granulocyte adhesion & diapedesis, and catecholamine biosynthesis were found to be significantly enriched in Estrogen/Progesterone Receptor positive/Human Epidermal Growth Factor Receptor 2 negative, pathways such as RAR activation, adipogenesis, the role of JAK1/2 in interferon signaling, TGF-β and STAT3 signaling intricated in Estrogen/Progesterone Receptor negative/Human Epidermal Growth Factor Receptor 2 positive and pathways as IL-1/IL-8, TNFR1/TNFR2, TWEAK, and relaxin signaling were found in triple-negative breast cancer. The dysregulated genes were clustered based on their mutation frequency which revealed nine mutated clusters, some of which were well characterized in cancer while others were less characterized. Each cluster was analyzed in detail which led to the identification of NLGN3, MAML2, TTN, SYNE1, ANK2 as candidate genes in BRCA. They are central hubs in the protein–protein-interaction network, indicating their important regulatory roles. Experimentally, the Real-Time Quantitative Reverse Transcription PCR and western blot confirmed our computational predictions in cell lines. Further, immunohistochemistry corroborated the results in ~ 100 tissue samples. We could experimentally show that the NLGN3 & ANK2 have tumor-suppressor roles in BRCA as shown by cell viability assay, transwell migration, colony forming and wound healing assay. The cell viability and migration was found to be significantly reduced in MCF7 and MDA-MB-231 cell lines in which the selected genes were over-expressed as compared to control cell lines. The wound healing assay also demonstrated a significant decrease in wound closure at 12 h and 24 h time intervals in MCF7 & MDA-MB-231 cells. These findings established the tumor suppressor roles of NLGN3 & ANK2 in BRCA. This will have important ramifications for the therapeutics discovery against BRCA.

Blood- and Urine-Based Liquid Biopsy for Early-Stage Cancer Investigation: Taken Clear Renal Cell Carcinoma as a Model

Liquid biopsy is a noninvasive technique that can provide valuable information for disease characterization by using biofluids as a source of biomarkers. Proteins found in biofluids can offer a wealth of information for understanding pathological processes. In this study, we used early-stage clear cell renal cell carcinoma (ccRCC) as a model to explore the proteomic relationships among tissue, plasma, and urine. We analyzed samples of tumor tissue, plasma, and urine from a cohort of 27 ccRCC patients with T1-2 stage and 27 matched healthy controls, using liquid chromatography-mass spectrometry (LC-MS) for proteomic analysis. We integrated the differential proteins found in the three types of samples to explore ccRCC-associated molecular changes. Our results showed that both plasma and urine proteomes could reflect functional changes in tumor tissue. In plasma, cytoskeletal proteins and metabolic enzymes were differentially expressed, while in urine, adhesion molecules and defense proteins showed differential levels. The differential proteins found in plasma and urine both reflect the binding and catalytic activity of tumor tissue. Additionally, proteins only changed in biofluids could reflect body immune response changes, with plasma proteins involved in actin cytoskeleton and oxidative stress, and urine proteins involved in granulocyte adhesion and leukocyte extravasation signaling. Plasma and urine proteins could effectively distinguish RCC from control, with good performances (plasma/urine: 92.6%/92.6% specificity, 96.3%/92.6% sensitivity, and an area under the curve of 0.981/0.97). In conclusion, biofluids could not only reflect functional changes in tumor tissue but also reflect changes in the body's immune response. These findings will benefit the understanding of body biomarkers in tumors and the discovery of potential disease biomarkers.

Glomerular endothelial glycocalyx-derived heparan sulfate inhibits glomerular leukocyte influx and attenuates experimental glomerulonephritis.

Proliferative forms of glomerulonephritis are characterized by the influx of leukocytes, albuminuria, and loss of kidney function. The glomerular endothelial glycocalyx is a thick carbohydrate layer that covers the endothelium and is comprised of heparan sulfate (HS), which plays a pivotal role in glomerular inflammation by facilitating endothelial-leukocyte trafficking. We hypothesize that the exogenous glomerular glycocalyx may reduce the glomerular influx of inflammatory cells during glomerulonephritis. Indeed, administration of mouse glomerular endothelial cell (mGEnC)-derived glycocalyx constituents, or the low-molecular-weight heparin enoxaparin, reduced proteinuria in mice with experimental glomerulonephritis. Glomerular influx of granulocytes and macrophages, as well as glomerular fibrin deposition, was reduced by the administration of mGEnC-derived glycocalyx constituents, thereby explaining the improved clinical outcome. HSglx also inhibited granulocyte adhesion to human glomerular endothelial cells in vitro. Notably, a specific HSglx fraction inhibited both CD11b and L-selectin binding to activated mGEnCs. Mass spectrometry analysis of this specific fraction revealed six HS oligosaccharides, ranging from tetra- to hexasaccharides with 2-7 sulfates. In summary, we demonstrate that exogenous HSglx reduces albuminuria during glomerulonephritis, which is possibly mediated via multiple mechanisms. Our results justify the further development of structurally defined HS-based therapeutics for patients with (acute) inflammatory glomerular diseases, which may be applicable to non-renal inflammatory diseases as well.

Abstract 3764: Expression patterns of microRNAs and associated target genes in ulcerated primary cutaneous melanoma

Abstract Tumor ulceration in cutaneous melanoma represents one of the top prognostic indicators for clinical outcome, associated with reduced progression free and overall survival. Despite this influence, the underlying biology driving tumor ulceration remains largely unexplored. One of the potential mediators of ulceration are microRNAs (miRNAs). These short, non-coding RNAs are frequently dysregulated in cancer and can impact tumor biology via mediation of gene expression. Distinct miRNA expression patterns have been identified in melanoma that can function as predictive biomarkers of disease progression and metastasis. However, the presence of a unique miRNA profile in ulcerated melanoma has not yet been assessed. miRNA and mRNA expression was assessed in 35 ulcerated and non-ulcerated cutaneous melanomas using the NanoString Human miRNA and Tumor Signaling 360 mRNA assays and validated in an independent cohort. Linear models and moderated t-tests were used to detect differential expression between ulcerated and non-ulcerated tumors. Pathway enrichment and functional annotations were determined using public databases. Pearson correlations were employed to predict miRNA-mRNA binding pairs. Differentially expressed mRNAs were identified as miRNA targets using Ingenuity Pathway Analysis. Comparison between groups revealed significant upregulation of 13 miRNAs in ulcerated relative to non-ulcerated tumors (p <0.03). 4 of these miRNAs were also significantly upregulated in the validation cohort (miR-363-3p, miR-196b-5p, miR-135b-5p and miR-223-3p, p <0.02). Conversely, 11 miRNAs were significantly downregulated in ulcerated relative to non-ulcerated tumors (p <0.05), of which, miR-376c-5p was also significantly downregulated in the validation cohort (p=0.009). 21 mRNAs were differentially expressed in ulcerated relative to non-ulcerated tumors, with 3 being significant in the validation cohort as well (FPR, IL-11, and ADM, p <0.05). 9 of these 21 mRNAs were then identified as predicted targets of multiple differentially expressed miRNAs in ulcerated tumors. 2 of the differentially expressed mRNAs had an inverse correlation in expression with regulatory miRNAs in our tumor samples (SOCS3 and miR-218-5p, and IL7R and miR-376c-5p). Each of the mRNAs significantly upregulated in both the original and validation cohorts have been previously associated with angiogenesis, migration or pro-metastatic cell survival in the context of cancer and pathway analysis identified significant enrichment for “granulocyte adhesion and diapedesis” (p=0.02) in ulcerated tumors. This study demonstrates that a unique subset of miRNAs and mRNAs are differentially expressed in ulcerated melanoma when compared to non-ulcerated. These findings also provide novel insight regarding how increased angiogenesis and metastasis may contribute to melanoma tumor ulceration. Citation Format: Emily Schwarz, Mallory J. DiVincenzo, Casey Ren, Zoe Barricklow, Maribelle Moufawad, Lianbo Yu, Paolo Fadda, Colin Angell, Sara Zelinskas, Steven Sun, John H. Howard, Catherine Chung, Craig Slingluff, Alejandro A. Gru, Kari Kendra, William E. Carson. Expression patterns of microRNAs and associated target genes in ulcerated primary cutaneous melanoma. [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 3764.

Mechanism of action deconvolution of the small-molecule pathological tau aggregation inhibitor Anle138b

BackgroundA key histopathological hallmark of Alzheimer’s disease (AD) is the presence of neurofibrillary tangles of aggregated microtubule-associated protein tau in neurons. Anle138b is a small molecule which has previously shown efficacy in mice in reducing tau aggregates and rescuing AD disease phenotypes.MethodsIn this work, we employed bioinformatics analysis—including pathway enrichment and causal reasoning—of an in vitro tauopathy model. The model consisted of cultured rat cortical neurons either unseeded or seeded with tau aggregates derived from human AD patients, both of which were treated with Anle138b to generate hypotheses for its mode of action. In parallel, we used a collection of human target prediction models to predict direct targets of Anle138b based on its chemical structure.ResultsCombining the different approaches, we found evidence supporting the hypothesis that the action of Anle138b involves several processes which are key to AD progression, including cholesterol homeostasis and neuroinflammation. On the pathway level, we found significantly enriched pathways related to these two processes including those entitled “Superpathway of cholesterol biosynthesis” and “Granulocyte adhesion and diapedesis”. With causal reasoning, we inferred differential activity of SREBF1/2 (involved in cholesterol regulation) and mediators of the inflammatory response such as NFKB1 and RELA. Notably, our findings were also observed in Anle138b-treated unseeded neurons, meaning that the inferred processes are independent of tau pathology and thus represent the direct action of the compound in the cellular system. Through structure-based ligand-target prediction, we predicted the intracellular cholesterol carrier NPC1 as well as NF-κB subunits as potential targets of Anle138b, with structurally similar compounds in the model training set known to target the same proteins.ConclusionsThis study has generated feasible hypotheses for the potential mechanism of action of Anle138b, which will enable the development of future molecular interventions aiming to reduce tau pathology in AD patients.

Urine Cell Transcriptomes Implicate Specific Renal Inflammatory Pathways Associated With Difficult-to-Control Hypertension.

Background The renal mechanisms involved in the maintenance of human hypertension and resistance to treatment are not well understood. Animal studies suggest that chronic renal inflammation contributes to hypertension. We studied cells shed in first-morning urine samples from individuals who were hypertensive who exhibited difficult-to-control blood pressure (BP). We performed bulk RNA sequencing of these shed cells to develop transcriptome-wide associations with BP. We also analyzed nephron-specific genes and used an unbiased bioinformatic approach to find signaling pathways activated in difficult-to-control hypertension. Methods and Results Participants who completed the SPRINT (Systolic Blood Pressure Intervention Trial) at a single trial site were recruited, and cells shed in first-morning urine samples collected. A total of 47 participants were divided into 2 groups based on hypertension control. The BP-difficult group (n=29) had systolic BP>140 mm Hg, >120 mm Hg after intensive treatment for hypertension, or required more than the median number of antihypertensive drugs used in SPRINT. The easy-to-control BP group (n=18) comprised the remainder of the participants. A total of 60 differentially expressed genes were identified with a >2-fold change in the BP-difficult group. In BP-difficult participants, 2 of the most upregulated genes were associated with inflammation: Tumor Necrosis Factor Alpha Induced Protien 6 (fold change, 7.76; P=0.006) and Serpin Family B Member 9 (fold change, 5.10; P=0.007). Biological pathway analysis revealed an overrepresentation of inflammatory networks, including interferon signaling, granulocyte adhesion and diapedesis, and Janus Kinase family kinases in the BP-difficult group (P<0.001). Conclusions We conclude that transcriptomes from cells shed in first-morning urine identify a gene expression profile in difficult-to-control hypertension that associates with renal inflammation.

OP01 Sequencing-based gene network analysis reveals a profound role for ferroptosis key gene GPX4 in post-operative endoscopic recurrence in Crohn’s disease

Abstract Background An ileocolonic resection with ileocolonic anastomosis is often required in patients with Crohn’s disease (CD). Postoperative recurrence (POR) is common, with host-luminal interactions being implicated. However, these interactions are poorly understood. We aimed to obtain insights in the early mechanisms of POR CD focusing on sequencing-based gene networks in the mucosa. Methods We included 36 CD patients who underwent ileocolonic resection with ileocolonic anastomosis, and collected mucosal biopsies from the neoterminal ileum 6 months after surgery (Table 1). We defined POR by a Rutgeerts score ≥i2b at month 6, and compared this to complete absence of endoscopic activity (i0). All biopsies underwent single-end RNA sequencing (Illumina TruSeq Stranded mRNA). Gene co-expression network clusters were identified using weighted gene co-expression network analysis (R\WGCNA), were tested for correlation with the primary outcome POR and clinical factors, and multiple testing correction was applied (FDR&amp;lt;0.05). Cellular deconvolution was performed using xCell; and top enriched pathways and upstream regulators were analysed using IPA (p&amp;lt;0.05). Results WGCNA analysis identified 25 co-expression clusters, of which five correlated with the postoperative outcome (clusters V, VI, IX, XV, XXV) (Fig.1). All but cluster XXV were upregulated in POR, with a profound immune-related enrichment in cluster V and VI (eg. (a)granulocyte adhesion and diapedesis, and IL17 signalling); microRNA biogenesis (cluster IX) and wound healing and fibrosis signalling (cluster XV). Interestingly, one cluster (XXV) was inversely correlated with POR, and genes within this cluster were mainly involved in autophagy, ferroptosis and oxidative stress response. The main hub gene (r=0.95, FDR=8.17E-19) within this cluster XXV was GPX4 (Glutathione peroxidase 4), a negative regulator of ferroptosis. Moreover, after cellular deconvolution, we found a positive correlation between the epithelial gene enrichment signature and the expression of GPX4 (r=0.52, p=0.0011). Finally, the main upstream regulator of the genes within this cluster XXV was HNF4A, a transcription factor known to regulate ferroptotic response. Conclusion We identified a mucosal transcriptomic signature associated with postoperative CD recurrence. Both autophagy and ferroptosis were found to be key protective pathways for recurrence with GPX4 as central hub. Our results complement recent findings of impaired epithelial GPX4 activity in ileal CD lesions evoking an inflammatory response to dietary lipids (Mayr et al Nat Comm 2020).

Aptamer proteomics for biomarker discovery in heart failure with reduced ejection fraction

Abstract Background Though current heart failure (HF) biomarkers are highly prognostic, systematically characterizing associations between circulating proteins and risk of subsequent events may improve clinical risk prediction and illuminate new biological pathways. Large-scale assays measuring thousands of proteins now enable unbiased proteomic investigation in clinical trials. Purpose To identify and replicate serum proteins associated with HF events in patients with chronic HF with reduced ejection fraction (HFrEF), and to develop and validate a proteomic risk score. Methods Serum levels of 4076 proteins were measured at baseline in the ATMOSPHERE (n=1261, 487 events over 6 years) and PARADIGM-HF (n=1257, 287 events over 4 years) trials of chronic HFrEF using a modified aptamer-based proteomics assay. Proteins associated with the primary endpoint, HF hospitalization or cardiovascular death, were identified in the ATMOSPHERE discovery cohort (false discovery rate&amp;lt;0.05) by Cox regression adjusted for age, sex, treatment arm, and anticoagulant use, and replicated in PARADIGM-HF (Bonferroni-corrected p&amp;lt;0.05). A proteomic risk score was derived in ATMOSPHERE using Cox LASSO penalized regression and evaluated in PARADIGM-HF compared to the MAGGIC clinical risk score and N-terminal pro-B-type natriuretic peptide (NT-proBNP). For proteins associated with the primary endpoint, pathway analysis was conducted using Ingenuity Pathway analysis and an exploratory two-sample Mendelian randomization was performed using genetic and outcome data from both trials and protein quantitative trait loci from deCODE to infer which identified proteins contribute to HF prognosis. Results We identified 377 serum proteins associated with the primary endpoint in ATMOSPHERE and replicated 167 in PARADIGM-HF. Prognostic proteins included known HF biomarkers Growth Differentiation Factor 15, NT-proBNP, and Angiopoietin-2, and also a previously unrecognized HF biomarker: Sushi, Von Willebrand Factor Type A, EGF And Pentraxin Domain Containing 1 (SVEP1) (HR 1.60 [95% CI 1.44–1.79] per standard deviation [SD], p=2x10–17) (Table 1). Proteins related to hepatic fibrosis, granulocyte adhesion, and inhibition of matrix metalloproteinases were over-represented. A 64-protein risk score derived in ATMOSPHERE predicted clinical events in PARADIGM-HF with greater discrimination (c-statistic 0.70) than the MAGGIC clinical score (c-statistic 0.61), NT-proBNP (c-statistic 0.65), or both (c-statistic 0.66) (Figure 1). Genetically predicted levels of NT-proBNP, WISP2, FSTL1, and CTSS were associated with the primary endpoint by Mendelian randomization. Conclusions We identify SVEP1, an extracellular matrix protein known to cause inflammation in vascular smooth muscle cells, as a previously unrecognized HF biomarker. A 64-protein score improved risk discrimination compared with NT-proBNP and may assist in identifying high-risk patients for clinical trials or disease management programs. Funding Acknowledgement Type of funding sources: Private company. Main funding source(s): The ATMOSPHERE and PARADIGM-HF trials were sponsored by Novartis

Inflammatory and Proliferative Pathway Activation in Human Esophageal Myofibroblasts Treated with Acidic Bile Salts.

Subepithelial human esophageal myofibroblasts (HEMFs) in gastroesophageal reflux disease (GERD) are exposed to luminal contents via impaired squamous epithelium barrier integrity. The supernatant of HEMFs treated with acidic bile salts reflective of in vivo reflux increases squamous epithelial thickness. We aimed to identify the involved mechanisms using an unbiased approach. Acidic-bile-salt-treated primary HEMF cultures (n = 4) were submitted for RNA-Seq and analyzed with Partek Flow followed by Ingenuity Pathway Analysis (IPA). A total of 1165 molecules (579 downregulated, 586 upregulated) were differentially expressed, with most top regulated molecules either extracellular or in the plasma membrane. Increases in HEMF CXCL-8, IL-6, AREG, and EREG mRNA, and protein secretion were confirmed. Top identified canonical pathways were agranulocyte and granulocyte adhesion and diapedesis, PI3K/AKT signaling, CCR5 signaling in macrophages, and the STAT3 pathway. Top diseases and biological functions were cellular growth and development, hematopoiesis, immune cell trafficking, and cell-mediated response. The targets of the top upstream regulator ErbB2 included CXCL-8, IL-6, and AREG and the inhibition of CXCL-8 in the HEMF supernatant decreased squamous epithelial proliferation. Our work shows an inflammatory/immune cell and proliferative pathways activation in HEMFs in the GERD environment and identifies CXCL-8 as a HEMF-derived chemokine with paracrine proliferative effects on squamous epithelium.

Pulmonary toxicity and gene expression changes in response to whole-body inhalation exposure to multi-walled carbon nanotubes in rats

Purpose: To investigate the molecular mechanisms underlying the pulmonary toxicity induced by exposure to one form of multi-walled carbon nanotubes (MWCNT-7). Materials and methods: Rats were exposed, by whole-body inhalation, to air or an aerosol containing MWCNT-7 particles at target cumulative doses (concentration x time) ranging from 22.5 to 180 (mg/m3)h over a three-day (6 hours/day) period and toxicity and global gene expression profiles were determined in the lungs. Results: MWCNT-7 particles, associated with alveolar macrophages (AMs), were detected in rat lungs following the exposure. Mild to moderate lung pathological changes consisting of increased cellularity, thickening of the alveolar wall, alveolitis, fibrosis, and granuloma formation were detected. Bronchoalveolar lavage (BAL) toxicity parameters such as lactate dehydrogenase activity, number of AMs and polymorphonuclear leukocytes (PMNs), intracellular oxidant generation by phagocytes, and levels of cytokines were significantly (p < 0.05) increased in response to exposure to MWCNT-7. Global gene expression profiling identified several significantly differentially expressed genes (fold change >1.5 and FDR p value <0.05) in all the MWCNT-7 exposed rats. Bioinformatic analysis of the gene expression data identified significant enrichment of several diseases/biological function categories (for example, cancer, leukocyte migration, inflammatory response, mitosis, and movement of phagocytes) and canonical pathways (for example, kinetochore metaphase signaling pathway, granulocyte and agranulocyte adhesion and diapedesis, acute phase response, and LXR/RXR activation). The alterations in the lung toxicity parameters and gene expression changes exhibited a dose-response to the MWCNT exposure. Conclusions: Taken together, the data provided insights into the molecular mechanisms underlying the pulmonary toxicity induced by inhalation exposure of rats to MWCNT-7.

The Antiseptic and Antineoplastic Agent Taurolidine Modulates Key Leukocyte Functions

Although taurolidine is known to exert a wide spectrum of biological actions, its effects on immune cells have not been characterized in detail. In this study, we investigated the ex vivo effects of taurolidine on relevant innate and adaptive immune cell functions. Leukocyte functions in whole blood were assessed following treatment with various taurolidine concentrations. Viability of peripheral blood mononuclear cells (PBMCs) and granulocytes was measured using the WST-1 assay. PBMC function was assessed by measuring TNFα and IFNγ production after stimulation with lipopolysaccharide (LPS) or Candida, respectively. Reactive oxygen species (ROS) production by granulocytes was measured in whole blood using luminol-enhanced chemiluminescence. Granulocyte degranulation and activation were evaluated by membrane expression of degranulation (CD63, CD66B) and adhesion markers (CD62L, CD11b) using immunofluorescent staining followed by flow-cytometric analysis. Taurolidine decreased viability of PBMCs and granulocytes: after 2 h, IC50 concentrations were 500 and 520 μg/ml, respectively. Following prolonged exposure (≥24 h) of PBMCs, the IC50 concentrations declined to 40 μg/ml. PBMC cytokine production significantly decreased at taurolidine concentrations below the cytotoxic threshold, whereas no changes in ROS production were observed. The expression of all granulocyte adhesion and degranulation markers increased at concentrations higher than 500 μg/ml (the cytotoxic level of taurolidine). Taurolidine exhibits a dose- and time-dependent cytotoxicity toward PBMCs and granulocytes. The effects on PBMCs, as exemplified by a decrease in cytokine production, occurred below the toxic threshold, whereas granulocyte function (ROS production) remained unchanged at these taurolidine concentrations. Granulocyte activation and degranulation markers only increased at cytotoxic taurolidine concentrations.

Deficiency of Leukocyte Surface Glycoproteins Mol, LFA-1, and Leu M5 in a Dog With Recurrent Bacterial Infections: An Animal Model

A dog with severe recurrent bacterial infections, impaired pus formation, delayed wound healing, and severe persistent leukocytosis was the result of a mother-son mating. Assessment of leukocyte function revealed profound abnormalities in adherence-dependent activities including impaired granulocyte adhesion to glass/plastic surfaces or nylon wool, decreased granulocyte aggregation and chemotaxis, and diminished lymphocyte blastogenesis, but normal neutrophil oxidative activity, serum immunoglobulin, and complement levels. By immunofluorescence analysis, CD11b and CD18 monoclonal antibodies specific for the 155-kd alpha polypeptide of Mo1 (gp 155, 94) and the 94 kd beta peptide common to Mo1, LFA-1 (gp 170, 94), and Leu M5 (p 150, 94) (surface molecules that promote leukocyte adhesion) failed to bind to unstimulated and A23187 calcium ionophore-stimulated granulocytes or mononuclear cells of the affected dog as compared with strong specific binding to canine control cells. The Mo1 glycoproteins were only barely detectable by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of immunoprecipitates from lysates of 125I surface-labeled neutrophils from the affected dog as compared with intense bands seen with canine control cell precipitates. We conclude that this dog has a severe leukocyte surface glycoprotein deficiency syndrome that is similar, if not identical, to that recently recognized in humans. Dogs with deficiency of leukocyte Mo1, LFA-1, and Leu M5 expression may represent a useful animal model to characterize further the molecular basis for an inherited disorder in leukocyte effector function.

High-dimensional profiling reveals phenotypic heterogeneity and disease-specific alterations of granulocytes in COVID-19

Since the outset of the COVID-19 pandemic, increasing evidence suggests that the innate immune responses play an important role in the disease development. A dysregulated inflammatory state has been proposed as a key driver of clinical complications in COVID-19, with a potential detrimental role of granulocytes. However, a comprehensive phenotypic description of circulating granulocytes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients is lacking. In this study, we used high-dimensional flow cytometry for granulocyte immunophenotyping in peripheral blood collected from COVID-19 patients during acute and convalescent phases. Severe COVID-19 was associated with increased levels of both mature and immature neutrophils, and decreased counts of eosinophils and basophils. Distinct immunotypes were evident in COVID-19 patients, with altered expression of several receptors involved in activation, adhesion, and migration of granulocytes (e.g., CD62L, CD11a/b, CD69, CD63, CXCR4). Paired sampling revealed recovery and phenotypic restoration of the granulocytic signature in the convalescent phase. The identified granulocyte immunotypes correlated with distinct sets of soluble inflammatory markers, supporting pathophysiologic relevance. Furthermore, clinical features, including multiorgan dysfunction and respiratory function, could be predicted using combined laboratory measurements and immunophenotyping. This study provides a comprehensive granulocyte characterization in COVID-19 and reveals specific immunotypes with potential predictive value for key clinical features associated with COVID-19.

Plasma Fms-Related Tyrosine Kinase 3 Ligand (Flt3L) Levels at Diagnosis Correlate with Treatment Response in Chronic Myeloid Leukemia

Background: Proteins such as cytokines and growth factors are important in cellular communication. They are also known to mediate messages between cancer cells and the immune system. CML is known to be an immunogenic cancer and function of the immune system has been linked to good treatment responses and successful treatment discontinuation. To understand the crosstalk between leukemic cells and the microenvironment we analyzed the plasma cytokine profile of CML patients with multiplex proteomic array at diagnosis and during treatment.Methods: Peripheral blood (PB) samples were collected from 33 CML patients at diagnosis and during treatment (3 and 12 months after treatment initiation). Patients received either bosutinib, imatinib or dasatinib as first-line therapy. The dasatinib treated patients received low-dose IFN-a after 3 months of dasatinib monotherapy. In addition, PB of 17 healthy volunteers was collected. The plasma cytokine profile was studied with multiplexed cytokine and growth factor panel that consists of 92 proteins (Proseek Multiplex Inflammation I96×96, Olink). Wilcox test was used to determine significant differences between patient and healthy volunteers, and p<0.05 was used as a cut-off value. Ingenuity pathway analysis (IPA) was performed to characterize aberrant disease associated pathways in CML.Results: The analysis of the cytokine panel showed that 43 proteins were upregulated in CML patients at diagnosis compared to the healthy. The IPA demonstrated that these cytokines and growth factors were related to the granulocyte adhesion and diapedesis and Th1 pathway. Top upstream regulators of these cytokines were NFKB1, RELA, STAT3, NFKBIA and RELB. The most pronounced differences were observed in the following proteins: Interleukin 10 receptor, beta subunit (IL-10RB), tumor necrosis factor receptor superfamily member 9 (TNFRSF9), CD5, Chemokine (C-C motif) ligand 23 (CCL23), Caspase-8 (CASP-8), CD244, adenosine deaminase (ADA), tumor growth factor a (TGFA), hepatocyte growth factor (HGF), tumor necrosis factor superfamily member 14 (TNFSF14), S100 calcium-binding protein A12 (EN-RAGE), urokinase-type plasminogen activator (uPA), vascular endothelial growth factor A (VEGFA) and oncostatin M (OSM). The levels of most proteins normalized to the levels of the healthy controls already after 3 months of treatment initiation regardless of the tyrosine kinase inhibitor (TKI) used suggesting that these proteins were related to the leukemic growth. Only the levels of IL-10RB and TNFRSF9 remained high compared to the healthy even during treatment.Interestingly, some of the protein levels at diagnosis correlated with BCR-ABL1 values (IS) at 3 months. Proteins such as Flt3L (r=-0.45, p=0.01), MCP-4 (r=-0.42, p=0.02), AXIN1 (r=-0.39, p=0.03), CXCL10 (r=-0.38, p=0.04) and CCL19 (r=-0.44, p=0.01) had a negative correlation and IL-4 (r=0.40, p=0.03) had a positive correlation, but only the Flt3L (r=-0.44, p=0.01) correlated also with the BCR-ABL1 values at 12 months. Patients who were treated with dasatinib therapy had increased levels of Flt3L at 3 months (p=0.008) and the level further increased at 12 months after the addition of IFN-a compared to the patients who received only imatinib or bosutinib (p=0.01).Conclusions: Multiplex plasma proteomic analysis provides tools for biomarker discovery and treatment monitoring. During first 3 months of TKI therapy most of the plasma cytokines and growth factors which were upregulated at the time of diagnosis returned to the levels of healthy controls. Flt3L levels at the diagnosis correlated negatively with the treatment response during the TKI therapy. As Flt3L is known to increase stem cell proliferation, low levels of Flt3L may lead to more quiescent stem cells and possible therapy resistance. During dasatinib and IFN-a treatment Flt3L levels increased above the levels noted in healthy controls. DisclosuresMustjoki:Ariad: Research Funding; Pfizer: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; BMS: Honoraria, Research Funding; Celgene: Honoraria.

Glucocorticoid Mediated Transcriptional Activity in Human Corneal Epithelial Cells Lacking the Glucocorticoid Receptor

The cornea is the dome-shaped transparent outermost layer of the eye, forming a physical barrier to protect the internal structures of the eye. Glucocorticoids are a mainstay in the treatment of ophthalmic diseases for their anti-inflammatory and anti-angiogenic properties. However, high doses or chronic use of glucocorticoid therapy can lead to vision-impairing effects such as increase in intraocular pressure and the formation of cataracts. The exact signaling pathways responsible for these undesirable effects of glucocorticoid use is poorly understood. One of the major molecular actions of glucocorticoids is to regulate transcription through its cognate nuclear receptor, the glucocorticoid receptor. We have previously reported the effect of glucocorticoids on global gene expression and their role in wound healing and barrier function in immortalized human corneal epithelial cells (HCE-T). In the current study, we knocked down glucocorticoid receptor using siRNA (GRKD) to determine the function of the glucocorticoid receptor in HCE-T cells. Successful knockdown of glucocorticoid receptor was confirmed by RT-PCR and immunoblot experiments. Genome-wide microarray analysis was performed and an FDR adjusted p value less than 0.01 was considered the cut off to create the list of differentially expressed genes (DEGs). Comparison of GRKD cells to HCE-T cells expressing endogenous glucocorticoid receptor (referred as NTC for No Target Control siRNA) revealed that expression of 2150 genes was altered in HCE-T cells when glucocorticoid receptor was knocked down, indicating that glucocorticoid receptor in corneal epithelial cells regulates a large cohort of genes. Inhibition of matrix metalloproteases, granulocyte adhesion and diapedesis, cyclins and cell cycle regulation were the top canonical pathways predicted by Ingenuity Pathway Analysis (IPA) to be altered in GRKD cells. In a 6-hour treatment with dexamethasone (Dex), a synthetic glucocorticoid, or with vehicle as a control, NTC cells had 2039 Dex-regulated genes, while Dex was still able to regulate 1087 genes in GRKD cells. Of these 1087 genes, 895 genes were uniquely regulated by Dex in GRKD cells suggesting that glucocorticoids might be signaling through another receptor in corneal epithelial cells. The top canonical pathways predicted to be altered by Dex in GRKD cells included PI3K/ATK Signaling, ERK5 Signaling, Prostrate Cancer Signaling, Aldosterone Signaling in Epithelial Cells, and PPAR signaling. These findings suggest that Dex could regulate large cohorts of genes through other nuclear receptors in corneal epithelial cells. Given the wide use of ophthalmic Dex in forms including eyedrops, ointments, gels, and implants, it is of clinical significance to understand the molecular actions of synthetic glucocorticoids since they appear to be ligands for multiple nuclear receptors in ocular cells and tissues.

Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus.

Bovine respiratory disease (BRD) causes substantial morbidity and mortality, affecting cattle of all ages. One of the main causes of BRD is an initial inflammatory response to bovine respiratory syncytial virus (BRSV). MicroRNAs are novel and emerging non-coding small RNAs that regulate many biological processes and are implicated in various inflammatory diseases. The objective of the present study was to elucidate the changes in the bovine bronchial lymph node miRNA transcriptome in response to BRSV following an experimental viral challenge. Holstein-Friesian calves were either administered a challenge dose of BRSV (103.5 TCID50/ml × 15 ml) (n = 12) or were mock inoculated with sterile phosphate buffered saline (n = 6). Daily scoring of clinical signs was performed and calves were euthanized at day 7 post-challenge. Bronchial lymph nodes were collected for subsequent RNA extraction and sequencing (75 bp). Read counts for known miRNAs were generated using the miRDeep2 package using the UMD3.1 reference genome and the bovine mature miRNA sequences from the miRBase database (release 22). EdgeR was used for differential expression analysis and Targetscan was used to identify target genes for the differentially expressed (DE) miRNAs. Target genes were examined for enriched pathways and gene ontologies using Ingenuity Pathway Analysis (Qiagen). Multi-dimensional scaling (MDS) based on miRNA gene expression changes, revealed a clearly defined separation between the BRSV challenged and control calves, although the clinical manifestation of disease was only mild. One hundred and nineteen DE miRNAs (P < 0.05, FDR < 0.1, fold change > 1.5) were detected between the BRSV challenged and control calves. The DE miRNAs were predicted to target 465 genes which were previously found to be DE in bronchial lymph node tissue, between these BRSV challenged and control calves. Of the DE predicted target genes, 455 had fold changes that were inverse to the corresponding DE miRNAs. There were eight enriched pathways among the DE predicted target genes with inverse fold changes to their corresponding DE miRNA including: granulocyte and agranulocyte adhesion and diapedesis, interferon signalling and role of pathogen recognition receptors in recognition of bacteria and viruses. Functions predicted to be increased included: T cell response, apoptosis of leukocytes, immune response of cells and stimulation of cells. Pathogen recognition and proliferation of cytotoxic T cells are vital for the recognition of the virus and its subsequent elimination.

Therapeutic wavelengths of ultraviolet B radiation activate apoptotic, circadian rhythm, redox signalling and key canonical pathways in psoriatic epidermis

Ultraviolet B radiation (UVB) exerts pleiotropic effects on human skin. DNA damage response and repair pathways are activated by UVB; if damage cannot be repaired, apoptosis ensues. Although cumulative UVB exposure predisposes to skin cancer, UVB phototherapy is widely used as an effective treatment for psoriasis. Previous studies defined the therapeutic action spectrum of UVB and showed that psoriasis is resistant to apoptosis. This study aimed to investigate early molecular responses within psoriasis plaques following irradiation with single equi-erythemogenic doses of clinically-effective (311 nm, narrow-band) compared to clinically-ineffective (290 nm) UVB. Forty-eight micro-dissected epidermal samples from 20 psoriatic patients were analyzed using microarrays. Our bioinformatic analysis compared gene expression between 311 nm irradiated, 290 nm irradiated and control psoriasis epidermis to specifically identify 311 nm UVB differentially expressed genes (DEGs) and their upstream regulatory pathways. Key DEGs and pathways were validated by immunohistochemical analysis.There was a dynamic induction and repression of 311 nm UVB DEGs between 6 h and 18 h, only a limited number of DEGs maintained their designated expression status between time-points. Key disease and function pathways included apoptosis, cell death, cell migration and leucocyte chemotaxis. DNA damage response pathways, NRF2-mediated oxidative stress response and P53 signalling were key nodes, interconnecting apoptosis and cell cycle arrest. Interferon signalling, dendritic cell maturation, granulocyte adhesion and atherosclerotic pathways were also differentially regulated. Consistent with these findings, top transcriptional regulators of 311 nm UVB DEGs related to: a) apoptosis, DNA damage response and cell cycle control; b) innate/acquired immune regulation and inflammation; c) hypoxia/redox response and angiogenesis; d) circadian rhythmicity; f) EGR/AP1 signalling and keratinocyte differentiation; and g) mitochondrial biogenesis.This research provides important insights into the molecular targets of 311 nm UVB, underscoring key roles for apoptosis and cell death. These and the other key pathways delineated may be central to the therapeutic effects of 311 nm in psoriasis.

Lung toxicity and gene expression changes in response to whole-body inhalation exposure to cellulose nanocrystal in rats

Objective Human exposure to cellulose nanocrystal (CNC) is possible during the production and/or use of products containing CNC. The objectives of the current study were to determine the lung toxicity of CNC and the underlying molecular mechanisms of the toxicity. Methods Rats were exposed to air or CNC (20 mg/m3, six hours/day, 14 d) by whole-body inhalation and lung toxicity and global gene expression profile were determined. Results Significant increases in lactate dehydrogenase activity, pro-inflammatory cytokine levels, phagocyte oxidant production, and macrophage and neutrophil counts were detected in the bronchoalveolar lavage cells or fluid from the CNC exposed rats. Mild lung histological changes, such as the accumulation of macrophages and neutrophils, were detected in the CNC exposed rats. Gene expression profiling by next generation sequencing identified 531 genes whose expressions were significantly different in the lungs of the CNC exposed rats, compared with the controls. Bioinformatic analysis of the lung gene expression data identified significant enrichment in several biological functions and canonical pathways including those related to inflammation (cellular movement, immune cell trafficking, inflammatory diseases and response, respiratory disease, complement system, acute phase response, leukocyte extravasation signaling, granulocyte and agranulocyte adhesion and diapedesis, IL-10 signaling, and phagosome formation and maturation) and oxidative stress (NRF2-mediated oxidative stress response, production of nitric oxide and reactive oxygen species in macrophages, and free radical scavenging). Conclusion Our data demonstrated that inhalation exposure of rats to CNC resulted in lung toxicity mediated mainly through the induction of inflammation and oxidative stress.

Transcriptomics‐Based and AOP‐Informed Structure–Activity Relationships to Predict Pulmonary Pathology Induced by Multiwalled Carbon Nanotubes

This study presents a novel strategy that employs quantitative structure-activity relationship models for nanomaterials (Nano-QSAR) for predicting transcriptomic pathway level response using lung tissue inflammation, an essential key event (KEs) in the existing adverse outcome pathway (AOP) for lung fibrosis, as a model response. Transcriptomic profiles of mouse lungs exposed to ten different multiwalled carbon nanotubes (MWCNTs) are analyzed using statistical and bioinformatics tools. Three pathways "agranulocyte adhesion and diapedesis," "granulocyte adhesion and diapedesis," and "acute phase signaling," that (1) are commonly perturbed across the MWCNTs panel, (2) show dose response (Benchmark dose, BMDs), and (3) are anchored to the KEs identified in the lung fibrosis AOP, are considered in modelling. The three pathways are associated with tissue inflammation. The results show that the aspect ratio (κ) of MWCNTs is directly correlated with the pathway BMDs. The study establishes a methodology for QSAR construction based on canonical pathways and proposes a MWCNTs grouping strategy based on the κ-values of the specific pathway associated genes. Finally, the study shows how the AOP framework can help guide QSAR modelling efforts; conversely, the outcome of the QSAR modelling can aid in refining certain aspects of the AOP in question (here, lung fibrosis).

БИОФИЗИЧЕСКИЕ СВОЙСТВА КЛЕТОЧНОЙ ПОВЕРХНОСТИ И ФУНКЦИОНАЛЬНАЯ АКТИВНОСТЬ ГРАНУЛОЦИТОВ БОЛЬНЫХ ОСТРЫМ ЛИМФОБЛАСТНЫМ ЛЕЙКОЗОМ ПРИ МОДЕЛИРОВАНИИ НАГРУЗКИ С АТФ IN VITRO

The current study is devoted to the investigation of the biophysical properties of the cell surface and the functional activity of granulocytes in patients with acute lymphoblastic leukemia when simulating the ATP load in vitro. The experiment was performed on the peripheral blood of patients with acute lymphoblastic leukemia (ALL) who underwent a standard course of chemotherapy. In experimental tests, exogenous loading with ATP was simulated in vitro by adding 100.0 μM adenosine-5-triphosphate disodium salt trihydrate to the granulocyte suspension. Incubation with the drug was carried out for 15 min at 370 C. As a control, a suspension of granulocytes in RPMI 1640 medium from the same patient, but without the addition of the drug, was used, this was incubated for 15 min at a temperature of 370 C. After the incubation time, the biophysical properties (rigidity, charge of the cell surface, the strength of intercellular adhesion) of granulocytes in experimental and control samples were studied using atomic force microscopy, and the migration activity of cells was also assessed in a direct capillary test under agarose. A model with exogenous ATP in ALL patients showed a decrease in the rigidity and potential of the plasma membrane surface, an increase in the adhesive properties and migration activity of granulocytes. The revealed effects point to the key role of the ATP molecule in the mechanisms of intercellular signaling in the microvasculature.