Transcriptomic Profiles Reveal Downregulation of Low-Density Lipoprotein Particle Receptor Pathway Activity in Patients Surviving Severe COVID-19

To assess the biology of the lethal endpoint in patients with SARS-CoV-2 infection, we compared the transcriptional response to the virus in patients who survived or died during severe COVID-19. We applied gene expression profiling to generate transcriptional signatures for peripheral blood mononuclear cells (PBMCs) from patients with SARS-CoV-2 infection at the time when they were placed in the Intensive Care Unit of the Pavlov First State Medical University of St. Petersburg (Russia). Three different bioinformatics approaches to RNA-seq analysis identified a downregulation of three common pathways in survivors compared with nonsurvivors among patients with severe COVID-19, namely, low-density lipoprotein (LDL) particle receptor activity (GO:0005041), important for maintaining cholesterol homeostasis, leukocyte differentiation (GO:0002521), and cargo receptor activity (GO:0038024). Specifically, PBMCs from surviving patients were characterized by reduced expression of PPARG, CD36, STAB1, ITGAV, and ANXA2. Taken together, our findings suggest that LDL particle receptor pathway activity in patients with COVID-19 infection is associated with poor disease prognosis.

Curcumin Affects Parkinson Protein 7 (PARK7; DJ-1) Expression and Regulates Proliferation and Apoptosis of Breast Cancer Cells by Up-Regulating miR-203

PTEN can inhibit PI3 K/AKT signaling pathway and DJ-1 negatively regualtes PTEN. Curcumin (Cur) regulates PTEN-PI3 K/AKT pathway. Bioinformatics analysis showed a targeting relationship between miR-203 and DJ-1, but it is unclear whether Cur regulates DJ-1-PTEN/PI3 K/AKT pathway through miR-203. We assessed Cur’s role in breast cancer cells. MCF-10A and MDA-MB-231 cells were cultured and expression of miR-203, DJ-1 and PTEN mRNA was measured by qRT-PCR. MDA-MB-231 cells were treated with 0, 10 μM Cur followed by analysis cell proliferation by CCK-8 assay, cell apoptosis by flow cytometry, miR-203, DJ-1 and PTEN mRNA level by qRT-PCR. MDA-MB-231 cells were divided into 3 groups: 0 μM, 10 μM Cur+miR-NC treatment group, 10 μM+miR-203 inhibitor group to measure cell apoptosis and proliferation. Compared with MCF-10A cells, miR-203 and DJ-1 mRNA in MDA-MB-231 cells was significantly upregulated and PTEN mRNA expression was decreased. Cur treatment significantly decreased cell proliferation, promoted caspase-3 activity and cell apoptosis, as well as elevated miR-203 and PTEN mRNA level and decreased DJ-1 mRNA level. miR-203 inhibitor transfection can antagonize Cur’s effect on upregulation of miR-203, increase DJ-1 expression, decrease PTEN expression, enhance PI3 K/AKT pathway activity, and antagonize Cur’s anti-tumor effect. Curcumin increases miR-203 expression, down-regulates DJ-1 expression, affects PTEN-PI3 K/AKT pathway activity, and play an anti-tumor effect through inhibiting breast cancer cell proliferation and promoting apoptosis.

Protein proximity networks and functional evaluation of the Casein Kinase 1 γ family reveals unique roles for CK1γ3 in WNT signaling

The WNT/β-catenin signaling pathway is evolutionarily conserved and controls normal embryonic development, adult tissue homeostasis and regeneration. Aberrant activation or suppression of WNT signaling contributes to cancer initiation and progression, developmental disorders, neurodegeneration, and bone disease. Despite great need and more than 40 years of research, targeted therapies for the WNT pathway have yet to be fully realized. Kinases are exceptionally druggable and occupy key nodes within the WNT signaling network, but several pathway-relevant kinases remain understudied and ′dark′. Here we studied the function of the CSNK1γ subfamily of human kinases. miniTurbo-based proximity biotinylation and mass spectrometry analysis of CSNK1γ1, CSNK1γ2, and CSNK1γ3 revealed numerous established components of the β-catenin-dependent and independent WNT signaling pathway, as well as novel interactors. In gain-of-function experiments leveraging a panel of transcriptional reporters, CSNK1γ3 but not CSNK1γ1 or CSNK1γ2 activated β-catenin-dependent WNT signaling and the Notch pathway. Within the family, CSNK1γ3 expression uniquely induced LRP6 phosphorylation. Conversely, siRNA-mediated silencing of CSNK1γ3 alone had no impact on WNT signaling, though co-silencing of all three family members decreased WNT pathway activity. We characterized two moderately selective and potent small molecule inhibitors of the CSNK1γ family. These inhibitors and a CSNK1γ3 kinase dead mutant suppressed but did not eliminate WNT-driven LRP6 phosphorylation and β-catenin stabilization. Our data suggest that while CSNK1γ3 expression uniquely drives pathway activity, potential functional redundancy within the family necessitates loss of all three family members to suppress the WNT signaling pathway.

Maternal starvation primes progeny response to nutritional stress

Organisms adapt to environmental changes in order to survive. Mothers exposed to nutritional stresses can induce an adaptive response in their offspring. However, the molecular mechanisms behind such inheritable links are not clear. Here we report that in Drosophila, starvation of mothers primes the progeny against subsequent nutritional stress. We found that RpL10Ab represses TOR pathway activity by genetically interacting with TOR pathway components TSC2 and Rheb. In addition, starved mothers produce offspring with lower levels of RpL10Ab in the germline, which results in higher TOR pathway activity, conferring greater resistance to starvation-induced oocyte loss. The RpL10Ab locus encodes for the RpL10Ab mRNA and a stable intronic sequence RNA (sisR-8), which collectively repress RpL10Ab pre-mRNA splicing in a negative feedback mechanism. During starvation, an increase in maternally deposited RpL10Ab and sisR-8 transcripts leads to the reduction of RpL10Ab expression in the offspring. Our study suggests that the maternally deposited RpL10Ab and sisR-8 transcripts trigger a negative feedback loop that mediates intergenerational adaptation to nutritional stress as a starvation response.

Androgen Receptor Pathway Activity Assay for Sepsis Diagnosis and Prediction of Favorable Prognosis

Introduction: Sepsis is a life-threatening complication of a bacterial infection. It is hard to predict which patients with a bacterial infection will develop sepsis, and accurate and timely diagnosis as well as assessment of prognosis is difficult. Aside from antibiotics-based treatment of the causative infection and supportive measures, treatment options have remained limited. Better understanding of the immuno-pathophysiology of sepsis is expected to lead to improved diagnostic and therapeutic solutions.Functional activity of the innate (inflammatory) and adaptive immune response is controlled by a dedicated set of cellular signal transduction pathways, that are active in the various immune cell types. To develop an immune response-based diagnostic assay for sepsis and provide novel therapeutic targets, signal transduction pathway activities have been analyzed in whole blood samples from patients with sepsis.Methods: A validated and previously published set of signal transduction pathway (STP) assays, enabling determination of immune cell function, was used to analyze public Affymetrix expression microarray data from clinical studies containing data from pediatric and adult patients with sepsis. STP assays enable quantitative measurement of STP activity on individual patient sample data, and were used to calculate activity of androgen receptor (AR), estrogen receptor (ER), JAK-STAT1/2, JAK-STAT3, Notch, Hedgehog, TGFβ, FOXO-PI3K, MAPK-AP1, and NFκB signal transduction pathways.Results: Activity of AR and TGFβ pathways was increased in children and adults with sepsis. Using the mean plus two standard deviations of normal pathway activity (in healthy individuals) as threshold for abnormal STP activity, diagnostic assay parameters were determined. For diagnosis of pediatric sepsis, the AR pathway assay showed high sensitivity (77%) and specificity (97%), with a positive prediction value (PPV) of 99% and negative prediction value (NPV) of 50%. For prediction of favorable prognosis (survival), PPV was 95%, NPV was 21%. The TGFβ pathway activity assay performed slightly less for diagnosing sepsis, with a sensitivity of 64% and specificity of 98% (PPV 99%, NPV 39%).Conclusion: The AR and TGFβ pathways have an immunosuppressive role, suggesting a causal relation between increased pathway activity and sepsis immunopathology. STP assays have been converted to qPCR assays for further evaluation of clinical utility for sepsis diagnosis and prediction of prognosis, as well as for prediction of risk at developing sepsis in patients with a bacterial infection. STPs may present novel therapeutic targets in sepsis.

Gene expression based inference of drug resistance in cancer

Inter and intra-tumoral heterogeneity are major stumbling blocks in the treatment of cancer and are responsible for imparting differential drug responses in cancer patients. Recently, the availability of large-scale drug screening datasets has provided an opportunity for predicting appropriate patient-tailored therapies by employing machine learning approaches. In this study, we report a predictive modeling approach to infer treatment response in cancers using gene expression data. In particular, we demonstrate the benefits of considering integrated chemogenomics approach, utilizing the molecular drug descriptors and pathway activity information as opposed to gene expression levels. We performed extensive validation of our approach on tissue-derived single-cell and bulk expression data. Further, we constructed several prostate cancer cell lines and xenografts, exposed to differential treatment conditions to assess the predictability of the outcomes. Our approach was further assessed on pan-cancer RNA-sequencing data from The Cancer Genome Atlas (TCGA) archives, as well as an independent clinical trial study describing the treatment journey of three melanoma patients. To summarise, we benchmarked the proposed approach on cancer RNA-seq data, obtained from cell lines, xenografts, as well as humans. We concluded that pathway-activity patterns in cancer cells are reasonably indicative of drug resistance, and therefore can be leveraged in personalized treatment recommendations.

Impact of Environmental Stressors on the Metabolic Functioning of a Temperate Cnidarian-Dinoflagellate Symbiosis

<p>Cnidarian-dinoflagellate symbioses occur across a wide latitudinal range, from temperate to tropical locations in both hemispheres. In the tropics, this association provides the foundation for the development of highly diverse coral reef ecosystems. Tropical associations are particularly sensitive to thermal variability, however, leading to dysfunction of the relationship and eventual expulsion of the symbiont, known as ‘coral bleaching’. In contrast, temperate associations maintain stable symbiotic relationships in highly fluctuating thermal environments. The reason behind the relative thermal tolerance of temperate associations is still unclear, though the ability to maintain cellular homeostasis through adjustments to metabolic processes is likely a core feature of their resilience. Both a field study and laboratory experiment were conducted to determine the metabolic responses to thermal change of the symbiosis between the temperate anemone Anthopleura aureoradiata and the dinoflagellate Symbiodinium. For the field component, A. aureoradiata were collected from Point Halswell in Wellington Harbour in both summer and winter. For the laboratory experiment, specimens collected at Pautahanui inlet were thermally acclimated in the laboratory, after which temperatures were altered over the course of one week to either 8°C (cold) or 28°C (hot) and maintained at these temperatures for six weeks. Gas chromatography coupled to mass spectrometry was then employed to determine the identity and relative quantity of a wide range of metabolites involved in primary metabolism including organic acids, fatty acids, amino acids and sugars. Based on these data, pathway activity profiling was used to determine the activity of different metabolic pathways both between seasons and in response to cold and heat treatment. A wide range of changes to metabolic processes were observed in both host and symbiont. Photosynthetic capacity was reduced in the symbionts at low temperatures and increased at high temperatures. The only organic acid to be significantly impacted was propanedioic acid, which increased in the host in response to cold treatment, potentially related to increased translocation from the symbiont. Altered fatty acid content in both host and symbiont was related to the role of fatty acids as energy sources and storage compounds and in cell signalling processes. Changes in fatty acid-associated metabolic pathways were exemplified by arachidonic acid and linoleic acid metabolism. Alterations to free amino acids and amino acid related pathways in both host and symbiont were associated with their role as antioxidants and osmoprotectants and the catabolism of amino acids for the production of energy. In symbionts only, altered amino acid content was associated with the role of amino acids in the production of alkaloids. Changes in a number of sugar derivatives in both host and symbiont were associated with their role as antioxidants and osmoprotectants. Altered sugar metabolism in the symbiont clearly indicated an increase in the production of energy rich sugar molecules and production of cellular energy in summer/hot conditions and a decrease in winter/cold conditions. Notably impacted pathways included the Calvin cycle, glycolysis, the pentose phosphate pathway and oxidative phosphorylation. Patterns of sugar related pathway activity in the host were generally opposite to that observed in the symbiont. Overall, prominent but opposing changes in the host and symbiont were detected in the central carbohydrate and energy metabolic pathways. In general, the activity of these pathways increased in the host in winter/cold conditions and decreased in summer/hot conditions, while in the symbiont the pattern was the opposite. These findings highlight the role of metabolic processes in enabling the persistence of a temperate cnidarian-dinoflagellate symbiosis in the face of large temperature fluctuations. This work provides a foundation upon which a deeper understanding of metabolic functioning in the cnidarian-dinoflagellate symbiosis can be built and provides a comparative platform for studies of the more thermally sensitive tropical associations.</p>