Longitudinal transcriptional analysis of developing neointimal vascular occlusion and pulmonary hypertension in rats

2004 ◽  
Vol 17 (2) ◽  
pp. 150-156 ◽  
Author(s):  
Laszlo T. Vaszar ◽  
Toshihiko Nishimura ◽  
John D. Storey ◽  
Guohua Zhao ◽  
Daoming Qiu ◽  
...  
Keyword(s):  
Pulmonary Hypertension ◽  
Statistical Significance ◽  
Respir Crit ◽  
Expression Patterns ◽  
Disease Model ◽  
Vascular Occlusion ◽  
Transcriptional Analysis ◽  
Response To Treatment ◽  
Neointimal Formation ◽  
Exploratory Data

Pneumonectomized rats injected with the alkaloid toxin, monocrotaline, develop progressive neointimal pulmonary vascular obliteration and pulmonary hypertension resulting in right ventricular failure and death. The antiproliferative immunosuppressant, triptolide, attenuates neointimal formation and pulmonary hypertension in this disease model (Faul JL, Nishimura T, Berry GJ, Benson GV, Pearl RG, and Kao PN. Am J Respir Crit Care Med 162: 2252–2258, 2000). Pneumonectomized rats, injected with monocrotaline on day 7, were killed at days 14, 21, 28, and 35 for measurements of physiology and gene expression patterns. These data were compared with pneumonectomized, monocrotaline-injected animals that received triptolide from day 5 to day 35. The hypothesis was tested that a group of functionally related genes would be significantly coexpressed during the development of disease and downregulated in response to treatment. Transcriptional analysis using total lung RNA was performed on replicate animals for each experimental time point with exploratory data analysis followed by statistical significance analysis. Marked, statistically significant increases in proteases (particularly derived from mast cells) were noted that parallel the development of vascular obliteration and pulmonary hypertension. Mast-cell-derived proteases may play a role in regulating the development of neointimal pulmonary vascular occlusion and pulmonary hypertension in response to injury.

scholarly journals Immunohistochemical and Transcriptional Analysis of SARS-CoV-2 Entry Factors and Renin-Angiotensin-Aldosterone System Components in Lethal COVID-19

Pathobiology ◽  
2021 ◽  
pp. 1-12
Author(s):  
Jasmin Dionne Haslbauer ◽  
Anna Stalder ◽  
Carl Zinner ◽  
Stefano Bassetti ◽  
Kirsten Diana Mertz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Statistical Significance ◽  
Expression Patterns ◽  
Transcriptional Analysis ◽  
Angiotensin Receptors ◽  
Renin Angiotensin Aldosterone System ◽  
Renin Angiotensin ◽  
P Gene ◽  
Gene Copies ◽  
Heterogeneous Expression

<b><i>Introduction:</i></b> Since angiotensin converting enzyme-2 (ACE2) was discovered as an essential entry factor of SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2), there has been conflicting evidence regarding the role of renin-angiotensin-aldosterone system (RAAS) in COVID-19. This study elucidates pulmonary expression patterns SARS-CoV-2 entry factors (ACE2 and transmembrane protease serine subtype 2, TMPRSS2) and RAAS components in lethal COVID-19. <b><i>Methods:</i></b> Lung tissue from COVID-19 autopsies (<i>n</i> = 27) and controls (<i>n</i> = 23) underwent immunohistochemical staining for RAAS components (angiotensin receptors 1 and 2, ACE2 and Mas-receptor) and bradykinin receptors 1 and 2. Staining of individual cellular populations (alveolar pneumocytes [ALV], desquamated cells [DES] and endothelium [END]) was measured by a binary scale (positive/negative). SARS-CoV-2 was detected using immunohistochemistry against nucleocapsid protein, <i>in-situ</i> hybridization and quantitative reverse transcriptase polymerase chain reaction. Gene expression profiling for <i>ACE2, ACE</i> and <i>TMPRSS2</i> was performed. <b><i>Results:</i></b> Subtle differences were observed when comparing COVID-19 patients and controls not reaching statistical significance, such as a higher incidence of ACE2-positivity in END (52% vs. 39%) but lower positivity in ALVs (63% vs. 70%) and an overall downregulation of <i>ACE2</i> gene expression (0.25 vs. 0.55). However, COVID-19 patients with RAAS inhibitor (RAASi) intake had significantly shorter hospitalization times (5 vs. 12 days), higher viral loads (57,517 vs. 15,980/10<sup>6</sup> RNase P-gene copies) and decreased <i>ACE/ACE2</i>-expression ratios (4.58 vs. 11.07) than patients without. <i>TMPRSS2</i> expression was significantly (1.76-fold) higher in COVID-19 patients than controls. <b><i>Conclusion:</i></b> Our study delineates the heterogeneous expression patterns of RAAS components in the lungs, which vary amongst cellular populations, and implies that COVID-19 patients with RAASi-intake present with a more rapid disease progression, although this requires further investigation.

Criteria positive and criteria negative anaphylaxis, with a focus on undifferentiated somatoform idiopathic anaphylaxis: A review and case series

2020 ◽  
Vol 41 (6) ◽  
pp. 436-441 ◽  
Author(s):  
Daniel A. Rosloff ◽  
Kunal Patel ◽  
Paul J. Feustel ◽  
Jocelyn Celestin
Keyword(s):  
Diagnostic Criteria ◽  
Statistical Significance ◽  
Case Series ◽  
Poor Response ◽  
Response To Treatment ◽  
Fisher Exact Test ◽  
Subjective Symptoms ◽  
Significant Difference ◽  
Physical Findings ◽  
Idiopathic Anaphylaxis

Background: Undifferentiated somatoform (US) idiopathic anaphylaxis (IA) is considered a psychogenic disorder characterized by a lack of observable physical findings and poor response to treatment. Although failure to diagnose true anaphylaxis can have disastrous consequences, identification of US-IA is crucial to limit unnecessary expenses and use of health care resources. Objective: To better define the presentation and understand the potential relationship between US-IA and underlying psychiatric comorbidities. Methods: We retrospectively reviewed 110 visits by 107 patients to our institution for evaluation and management of anaphylaxis over a 1-year period. The patients were classified as having either criteria positive (CP) or criteria negative (CN) anaphylaxis based on whether they met Second National Institute of Allergy and Infectious Disease/Food Allergy and Anaphylaxis Network Symposium criteria for the clinical diagnosis of anaphylaxis. Patient characteristics, including objective and subjective signs and symptoms, and the presence of psychiatric diagnoses were collected and analyzed. Statistical significance was assessed by using the Fisher exact test. A literature review of US-IA and other psychogenic forms of anaphylaxis was performed. Results: Patients with CP anaphylaxis were more likely to present with hypotension, wheezing, urticaria, and vomiting than were patients with CN anaphylaxis. The patients with CN anaphylaxis were more likely to present with subjective symptoms of sensory throat tightness or swelling compared with patients with CP anaphylaxis. No significant difference was detected in the prevalence of psychiatric conditions between the two groups. Conclusion: Patients who met previously established diagnostic criteria for anaphylaxis were more likely to present with objective physical findings than those who did not meet criteria for true anaphylaxis. CN patients who presented for treatment of anaphylaxis were more likely to present with subjective symptoms. Formal diagnostic criteria should be used by clinicians when evaluating patients with suspected anaphylaxis.

scholarly journals Signalling pathways and mechanistic cues highlighted by transcriptomic analysis of primordial, primary, and secondary ovarian follicles in domestic cat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shauna Kehoe ◽  
Katarina Jewgenow ◽  
Paul R. Johnston ◽  
Susan Mbedi ◽  
Beate C. Braun
Keyword(s):  
Gene Expression ◽  
Transforming Growth Factor ◽  
Ovarian Follicle ◽  
Mammalian Species ◽  
Expression Patterns ◽  
Ovarian Follicles ◽  
Domestic Cat ◽  
Transcriptional Analysis ◽  
Ovarian Folliculogenesis

AbstractIn vitro growth (IVG) of dormant primordial ovarian follicles aims to produce mature competent oocytes for assisted reproduction. Success is dependent on optimal in vitro conditions complemented with an understanding of oocyte and ovarian follicle development in vivo. Complete IVG has not been achieved in any other mammalian species besides mice. Furthermore, ovarian folliculogenesis remains sparsely understood overall. Here, gene expression patterns were characterised by RNA-sequencing in primordial (PrF), primary (PF), and secondary (SF) ovarian follicles from Felis catus (domestic cat) ovaries. Two major transitions were investigated: PrF-PF and PF-SF. Transcriptional analysis revealed a higher proportion in gene expression changes during the PrF-PF transition. Key influencing factors during this transition included the interaction between the extracellular matrix (ECM) and matrix metalloproteinase (MMPs) along with nuclear components such as, histone HIST1H1T (H1.6). Conserved signalling factors and expression patterns previously described during mammalian ovarian folliculogenesis were observed. Species-specific features during domestic cat ovarian folliculogenesis were also found. The signalling pathway terms “PI3K-Akt”, “transforming growth factor-β receptor”, “ErbB”, and “HIF-1” from the functional annotation analysis were studied. Some results highlighted mechanistic cues potentially involved in PrF development in the domestic cat. Overall, this study provides an insight into regulatory factors and pathways during preantral ovarian folliculogenesis in domestic cat.

scholarly journals Abnormal Long Non-Coding RNAs Expression Patterns Have the Potential Ability for Predicting Survival and Treatment Response in Breast Cancer

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 996
Author(s):  
Ana Carolina Pavanelli ◽  
Flavia Rotea Mangone ◽  
Luciana R. C. Barros ◽  
Juliana Machado-Rugolo ◽  
Vera L. Capelozzi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
Predictive Value ◽  
Expression Patterns ◽  
Survival Rates ◽  
In Silico Analysis ◽  
Cancer Prognosis ◽  
Response To Treatment ◽  
Breast Cancer Patients ◽  
Non Coding Rnas

Abnormal long non-coding RNAs (lncRNAs) expression has been documented to have oncogene or tumor suppressor functions in the development and progression of cancer, emerging as promising independent biomarkers for molecular cancer stratification and patients’ prognosis. Examining the relationship between lncRNAs and the survival rates in malignancies creates new scenarios for precision medicine and targeted therapy. Breast cancer (BRCA) is a heterogeneous malignancy. Despite advances in its molecular classification, there are still gaps to explain in its multifaceted presentations and a substantial lack of biomarkers that can better predict patients’ prognosis in response to different therapeutic strategies. Here, we performed a re-analysis of gene expression data generated using cDNA microarrays in a previous study of our group, aiming to identify differentially expressed lncRNAs (DELncRNAs) with a potential predictive value for response to treatment with taxanes in breast cancer patients. Results revealed 157 DELncRNAs (90 up- and 67 down-regulated). We validated these new biomarkers as having prognostic and predictive value for breast cancer using in silico analysis in public databases. Data from TCGA showed that compared to normal tissue, MIAT was up-regulated, while KCNQ1OT1, LOC100270804, and FLJ10038 were down-regulated in breast tumor tissues. KCNQ1OT1, LOC100270804, and FLJ10038 median levels were found to be significantly higher in the luminal subtype. The ROC plotter platform results showed that reduced expression of these three DElncRNAs was associated with breast cancer patients who did not respond to taxane treatment. Kaplan–Meier survival analysis revealed that a lower expression of the selected lncRNAs was significantly associated with worse relapse-free survival (RFS) in breast cancer patients. Further validation of the expression of these DELncRNAs might be helpful to better tailor breast cancer prognosis and treatment.

scholarly journals Molecular Characterization and Functional Analysis of PR-1-Like Proteins Identified from the Wheat Head Blight Fungus Fusarium graminearum

2018 ◽  
Vol 108 (4) ◽  
pp. 510-520 ◽  
Author(s):  
Shunwen Lu ◽  
Michael C. Edwards
Keyword(s):  
Functional Analysis ◽  
Fusarium Graminearum ◽  
Expression Patterns ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Transcriptional Analysis ◽  
Fungal Genome ◽  
Dimensional Structure ◽  
Head Blight ◽  
Fungal Virulence

The group 1 pathogenesis-related (PR-1) proteins originally identified from plants and their homologs are also found in other eukaryotic kingdoms. Studies on nonplant PR-1-like (PR-1L) proteins have been pursued widely in humans and animals but rarely in filamentous ascomycetes. Here, we report the characterization of four PR-1L proteins identified from the ascomycete fungus Fusarium graminearum, the primary cause of Fusarium head blight of wheat and barley (designated FgPR-1L). Molecular cloning revealed that the four FgPR-1L proteins are all encoded by small open reading frames (612 to 909 bp) that are often interrupted by introns, in contrast to plant PR-1 genes that lack introns. Sequence analysis indicated that all FgPR-1L proteins contain the PR-1-specific three-dimensional structure, and one of them features a C-terminal transmembrane (TM) domain that has not been reported for any stand-alone PR-1 proteins. Transcriptional analysis revealed that the four FgPR-1L genes are expressed in axenic cultures and in planta with different spatial or temporal expression patterns. Phylogenetic analysis indicated that fungal PR-1L proteins fall into three major groups, one of which harbors FgPR-1L-2-related TM-containing proteins from both phytopathogenic and human-pathogenic ascomycetes. Low-temperature sodium dodecyl sulfate polyacrylamide gel electrophoresis and proteolytic assays indicated that the recombinant FgPR-1L-4 protein exists as a monomer and is resistant to subtilisin of the serine protease family. Functional analysis confirmed that deletion of the FgPR-1L-4 gene from the fungal genome results in significantly reduced virulence on susceptible wheat. This study provides the first example that the F. graminearum–wheat interaction involves a pathogen-derived PR-1L protein that affects fungal virulence on the host.

Nonhypoalbuminemic Inflammatory Bowel Disease in Dogs as Disease Model

2021 ◽  
Author(s):  
Juan Hernandez ◽  
Elodie Rouillé ◽  
Florian Chocteau ◽  
Marie Allard ◽  
Karine Haurogné ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Immune Responses ◽  
Bowel Disease ◽  
Interindividual Variability ◽  
Expression Patterns ◽  
Disease Model ◽  
Protein Loss ◽  
Tissue Concentrations ◽  
Inflammatory Bowel ◽  
Antibody Levels

Abstract Background The incidence of inflammatory bowel disease (IBD) is increasing worldwide, emphasizing the need of relevant models, as dogs spontaneously affected by IBD may be, for better knowledge of the disease’s physiopathology. Methods We studied 22 client-owned dogs suffering from IBD without protein loss and 14 control dogs. Biopsies were obtained from the duodenum, ileum, and colon. Inflammatory grade was assessed by histopathology, immunohistochemistry, and chemokine analysis. The expression of Toll-like receptors (TLR) in mucosa was immunohistochemically evaluated. Antibody levels against bacterial ligands (lipopolysaccharide [LPS] and flagellin) were measured in sera using enzyme-linked immunoassay. Results Dogs with IBD showed low to severe clinical disease. Histopathologically, the gut of dogs with IBD did not exhibit significant alterations compared with controls except in the colon. The number of CD3+ T lymphocytes was decreased in the ileum and colon of dogs with IBD compared with controls, whereas the numbers of Foxp3+, CD20+, and CD204+ cells were similar in the 2 groups. Three chemokines, but no cytokines, were detected at the protein level in the mucosa, and the disease poorly affected their tissue concentrations. Dogs with IBD exhibited higher serum reactivity against LPS and flagellin than controls but similar immunoreactivity against the receptors TLR4 and TLR5. In addition, TLR2 and TLR9 showed similar expression patterns in both groups of dogs. Conclusions Our data described dysregulated immune responses in dogs affected by IBD without protein loss. Despite fairly homogeneous dog cohorts, we were still faced with interindividual variability, and new studies with larger cohorts are needed to validate the dog as a model.

scholarly journals Systems Approaches to Treatment Response to Imatinib in Severe Asthma: A Pilot Study

2021 ◽  
Vol 11 (4) ◽  
pp. 240
Author(s):  
Seung Han Baek ◽  
Dinah Foer ◽  
Katherine N. Cahill ◽  
Elliot Israel ◽  
Enrico Maiorino ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Trial ◽  
Systems Biology ◽  
Pilot Study ◽  
Severe Asthma ◽  
Treated Patient ◽  
Expression Patterns ◽  
Airflow Limitation ◽  
Response To Treatment ◽  
Imatinib Treatment

There is an acute need for advances in pharmacologic therapies and a better understanding of novel drug targets for severe asthma. Imatinib, a tyrosine kinase inhibitor, has been shown to improve forced expiratory volume in 1 s (FEV1) in a clinical trial of patients with severe asthma. In a pilot study, we applied systems biology approaches to epithelium gene expression from these clinical trial patients treated with imatinib to better understand lung function response with imatinib treatment. Bronchial brushings from ten imatinib-treated patient samples and 14 placebo-treated patient samples were analyzed. We used personalized perturbation profiles (PEEPs) to characterize gene expression patterns at the individual patient level. We found that strong responders—patients with greater than 20% increase in FEV1—uniquely shared multiple downregulated mitochondrial-related pathways. In comparison, weak responders (5–10% FEV1 increase), and non-responders to imatinib shared none of these pathways. The use of PEEP highlights its potential for application as a systems biology tool to develop individual-level approaches to predicting disease phenotypes and response to treatment in populations needing innovative therapies. These results support a role for mitochondrial pathways in airflow limitation in severe asthma and as potential therapeutic targets in larger clinical trials.

scholarly journals Mixed Transcriptome Analysis Revealed the Possible Interaction Mechanisms between Zizania latifolia and Ustilago esculenta Inducing Jiaobai Stem-Gall Formation

2021 ◽  
Vol 22 (22) ◽  
pp. 12258
Author(s):  
Zhi-Ping Zhang ◽  
Si-Xiao Song ◽  
Yan-Cheng Liu ◽  
Xin-Rui Zhu ◽  
Yi-Feng Jiang ◽  
...  
Keyword(s):  
Host Plant ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Hormonal Control ◽  
Transcriptional Analysis ◽  
Gall Formation ◽  
Specific Expression ◽  
Zizania Latifolia ◽  
Stem Gall ◽  
Ustilago Esculenta

The smut fungus Ustilago esculenta infects Zizania latifolia and induces stem expansion to form a unique vegetable named Jiaobai. Although previous studies have demonstrated that hormonal control is essential for triggering stem swelling, the role of hormones synthesized by Z. latifolia and U. esculenta and the underlying molecular mechanism are not yet clear. To study the mechanism that triggers swollen stem formation, we analyzed the gene expression pattern of both interacting organisms during the initial trigger of culm gall formation, at which time the infective hyphae also propagated extensively and penetrated host stem cells. Transcriptional analysis indicated that abundant genes involving fungal pathogenicity and plant resistance were reprogrammed to maintain the subtle balance between the parasite and host. In addition, the expression of genes involved in auxin biosynthesis of U. esculenta obviously decreased during stem swelling, while a large number of genes related to the synthesis, metabolism and signal transduction of hormones of the host plant were stimulated and showed specific expression patterns, particularly, the expression of ZlYUCCA9 (a flavin monooxygenase, the key enzyme in indole-3-acetic acid (IAA) biosynthesis pathway) increased significantly. Simultaneously, the content of IAA increased significantly, while the contents of cytokinin and gibberellin showed the opposite trend. We speculated that auxin produced by the host plant, rather than the fungus, triggers stem swelling. Furthermore, from the differently expressed genes, two candidate Cys2-His2 (C2H2) zinc finger proteins, GME3058_g and GME5963_g, were identified from U. esculenta, which may conduct fungus growth and infection at the initial stage of stem-gall formation.

scholarly journals Clinicopathological Variables and Outcome in Chronic Myeloid Leukemia Associated With BCR-ABL1 Transcript Type and Body Weight: An Outcome of European LeukemiaNet Project

2021 ◽  
Vol 28 ◽  
pp. 107327482110384
Author(s):  
Mohammad A. J. Abdulla ◽  
Prem Chandra ◽  
Susanna El Akiki ◽  
Mahmood B. Aldapt ◽  
Sundus Sardar ◽  
...  
Keyword(s):  
Body Weight ◽  
Survival Curve ◽  
Statistical Significance ◽  
Response Assessment ◽  
Test Methods ◽  
Response To Treatment ◽  
Molecular Response ◽  
Kaplan Meier ◽  
Significant Difference ◽  
Transcript Type

Objective It is debatable whether BCR-ABL1 transcript type has an impact on outcome of treatment of patients with CML, and it is not widely studied whether body weight influences response to treatment. In this study, we tried to find out if any of these factors has an impact on response to treatment and outcome. Methodology We conducted a retrospective analysis of the files of 79 patients being treated in our center for CML with known BCR-ABL1 breakpoints, and patients’ management and response assessment was done based on ELN 2013 guidelines. The analysis was performed based on two main groups, obese vs. normal BMI, and then based on BCR-ABL1 transcripts: e13a2 vs. e14a2. Cumulative incidence of MMR, CCyR, and DMR were estimated using the Kaplan–Meier survival curve method, and comparisons between groups were performed by the Log-rank/Gray test methods. Results/conclusion In the patient-cohort studied, there was no statistically significant difference in molecular response between patients with CML based on body weight or transcript type although patients in the obesity group achieved higher and faster MMR with no statistical significance.

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