FAT atypical cadherin 1 (FAT1), a transmembrane protein, is frequently mutated in various cancer types and has been described as context-dependent tumor suppressor or oncogene. The FAT1 gene is ...mutated in 12-16% of T-cell acute leukemia (T-ALL) and aberrantly expressed in about 54% of T-ALL cases contrasted with absent expression in normal T-cells. Here, we characterized FAT1 expression and profiled the methylation status from T-ALL patients. In our T-ALL cohort, 53% of patient samples were FAT1 positive (FAT1pos) compared to only 16% FAT1 positivity in early T-ALL patient samples. Aberrant expression of FAT1 was strongly associated with FAT1 promotor hypomethylation, yet a subset, mainly consisting of TLX1-driven T-ALL patient samples showed methylation-independent high FAT1 expression. Genes correlating with FAT1 expression revealed enrichment in WNT signaling genes representing the most enriched single pathway. FAT1 knockdown or knockout led to impaired proliferation and downregulation of WNT pathway target genes (CCND1, MYC, LEF1), while FAT1 overexpressing conveyed a proliferative advantage. To conclude, we characterized a subtype pattern of FAT1 gene expression in adult T-ALL patients correlating with promotor methylation status. FAT1 dependent proliferation and WNT signaling discloses an impact on deeper understanding of T-ALL leukemogenesis as a fundament for prospective therapeutic strategies.
Modifying the chromatin structure and interacting with non‐histone proteins, histone deacetylases (HDAC) are involved in vital cellular processes at different levels. We here specifically ...investigated the direct effects of HDAC5 in macrophage activation in response to bacterial or cytokine stimuli. Using murine and human macrophage cell lines, we studied the expression profile and the immunological function of HDAC5 at transcription and protein level in over‐expression as well as RNA interference experiments. Toll‐like receptor‐mediated stimulation of murine RAW264.7 cells significantly reduced HDAC5 mRNA within 7 hrs but presented baseline levels after 24 hrs, a mechanism that was also found for Interferon‐γ treatment. If treated with lipopolysaccharide, RAW264.7 cells transfected for over‐expression only of full‐length but not of mutant HDAC5, significantly elevated secretion of tumour necrosis factor α and of the monocyte chemotactic protein‐1. These effects were accompanied by increased nuclear factor‐κB activity. Accordingly, knock down of HDAC5‐mRNA expression using specific siRNA significantly reduced the production of these cytokines in RAW264.7 or human U937 cells. Taken together, our results suggest a strong regulatory function of HDAC5 in the pro‐inflammatory response of macrophages.
The IL-6-gp130-STAT3 signaling axis is a major regulator of inflammation. Activating mutations in the gene encoding gp130 and germline gain-of-function mutations in STAT3 (STAT3
) are associated with ...multi-organ autoimmunity, severe morbidity, and adverse prognosis. To dissect crucial cellular subsets and disease biology involved in activated gp130 signaling, the gp130-JAK-STAT3 axis was constitutively activated using a transgene,
, specifically targeted to T cells. Activating gp130 signaling in T cells in vivo resulted in fatal, early onset, multi-organ autoimmunity in mice that resembled human STAT3
disease. Female mice had more rapid disease progression than male mice. On a cellular level, gp130 signaling induced the activation and effector cell differentiation of T cells, promoted the expansion of T helper type 17 (T
17) cells, and impaired the activity of regulatory T cells. Transcriptomic profiling of CD4
and CD8
T cells from these mice revealed commonly dysregulated genes and a gene signature that, when applied to human transcriptomic data, improved the segregation of patients with transcriptionally diverse STAT3
mutations from healthy controls. The findings demonstrate that increased gp130-STAT3 signaling leads to T
17-driven autoimmunity that phenotypically resembles human STAT3
disease.
•The SUMO pathway is activated in MM and its magnitude associated with progression and treatment resistance.•SUMO inhibition overcomes proteasome inhibitor resistance by blocking myeloma stress ...resilience, irrespective of p53 state.
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Proteasome inhibition is a highly effective treatment for multiple myeloma (MM). However, virtually all patients develop proteasome inhibitor resistance, which is associated with a poor prognosis. Hyperactive small ubiquitin-like modifier (SUMO) signaling is involved in both cancer pathogenesis and cancer progression. A state of increased SUMOylation has been associated with aggressive cancer biology. We found that relapsed/refractory MM is characterized by a SUMO-high state, and high expression of the SUMO E1-activating enzyme (SAE1/UBA2) is associated with poor overall survival. Consistently, continuous treatment of MM cell lines with carfilzomib (CFZ) enhanced SUMO pathway activity. Treatment of MM cell lines with the SUMO E1-activating enzyme inhibitor subasumstat (TAK-981) showed synergy with CFZ in both CFZ-sensitive and CFZ-resistant MM cell lines, irrespective of the TP53 state. Combination therapy was effective in primary MM cells and in 2 murine MM xenograft models. Mechanistically, combination treatment with subasumstat and CFZ enhanced genotoxic and proteotoxic stress, and induced apoptosis was associated with activity of the prolyl isomerase PIN1. In summary, our findings reveal activated SUMOylation as a therapeutic target in MM and point to combined SUMO/proteasome inhibition as a novel and potent strategy for the treatment of proteasome inhibitor–resistant MM.
To investigate the immune response and mechanisms associated with severe coronavirus disease 2019 (COVID-19), we performed single-cell RNA sequencing on nasopharyngeal and bronchial samples from 19 ...clinically well-characterized patients with moderate or critical disease and from five healthy controls. We identified airway epithelial cell types and states vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In patients with COVID-19, epithelial cells showed an average three-fold increase in expression of the SARS-CoV-2 entry receptor ACE2, which correlated with interferon signals by immune cells. Compared to moderate cases, critical cases exhibited stronger interactions between epithelial and immune cells, as indicated by ligand-receptor expression profiles, and activated immune cells, including inflammatory macrophages expressing CCL2, CCL3, CCL20, CXCL1, CXCL3, CXCL10, IL8, IL1B and TNF. The transcriptional differences in critical cases compared to moderate cases likely contribute to clinical observations of heightened inflammatory tissue damage, lung injury and respiratory failure. Our data suggest that pharmacologic inhibition of the CCR1 and/or CCR5 pathways might suppress immune hyperactivation in critical COVID-19.
Programming experience is an important confounding parameter in controlled experiments regarding program comprehension. In literature, ways to measure or control programming experience vary. Often, ...researchers neglect it or do not specify how they controlled for it. We set out to find a well-defined understanding of programming experience and a way to measure it. From published comprehension experiments, we extracted questions that assess programming experience. In a controlled experiment, we compare the answers of computer-science students to these questions with their performance in solving program-comprehension tasks. We found that self estimation seems to be a reliable way to measure programming experience. Furthermore, we applied exploratory and confirmatory factor analyses to extract and evaluate a model of programming experience. With our analysis, we initiate a path toward validly and reliably measuring and describing programming experience to better understand and control its influence in program-comprehension experiments.
In coronavirus disease 2019 (COVID-19), hypertension and cardiovascular diseases are major risk factors for critical disease progression. However, the underlying causes and the effects of the main ...anti-hypertensive therapies-angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs)-remain unclear. Combining clinical data (n = 144) and single-cell sequencing data of airway samples (n = 48) with in vitro experiments, we observed a distinct inflammatory predisposition of immune cells in patients with hypertension that correlated with critical COVID-19 progression. ACEI treatment was associated with dampened COVID-19-related hyperinflammation and with increased cell intrinsic antiviral responses, whereas ARB treatment related to enhanced epithelial-immune cell interactions. Macrophages and neutrophils of patients with hypertension, in particular under ARB treatment, exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1. Although the limited size of our cohort does not allow us to establish clinical efficacy, our data suggest that the clinical benefits of ACEI treatment in patients with COVID-19 who have hypertension warrant further investigation.
Variability-Aware Static Analysis at Scale Rhein, Alexander Von; Liebig, JöRG; Janker, Andreas ...
ACM transactions on software engineering and methodology,
11/2018, Letnik:
27, Številka:
4
Journal Article
Recenzirano
The advent of variability management and generator technology enables users to derive individual system variants from a configurable code base by selecting desired configuration options. This ...approach gives rise to the generation of possibly billions of variants, which, however, cannot be efficiently analyzed for bugs and other properties with classic analysis techniques. To address this issue, researchers and practitioners have developed sampling heuristics and, recently, variability-aware analysis techniques. While sampling reduces the analysis effort significantly, the information obtained is necessarily incomplete, and it is unknown whether state-of-the-art sampling techniques scale to billions of variants. Variability-aware analysis techniques process the configurable code base directly, exploiting similarities among individual variants with the goal of reducing analysis effort. However, while being promising, so far, variability-aware analysis techniques have been applied mostly only to small academic examples. To learn about the mutual strengths and weaknesses of variability-aware and sample-based static-analysis techniques, we compared the two by means of seven concrete control-flow and data-flow analyses, applied to five real-world subject systems: B
usybox
, O
pen
SSL, SQL
ite
, the x86 L
inux
kernel, and
u
C
libc
. In particular, we compare the efficiency (analysis execution time) of the static analyses and their effectiveness (potential bugs found). Overall, we found that variability-aware analysis outperforms most sample-based static-analysis techniques with respect to efficiency and effectiveness. For example, checking all variants of O
pen
SSL with a variability-aware static analysis is faster than checking even only two variants with an analysis that does not exploit similarities among variants.
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