Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data.

Lipidomics is of growing importance for clinical and biomedical research due to many associations between lipid metabolism and diseases. The discovery of these associations is facilitated by improved lipid identification and quantification. Sophisticated computational methods are advantageous for interpreting such large-scale data for understanding metabolic processes and their underlying (patho)mechanisms. To generate hypothesis about these mechanisms, the combination of metabolic networks and graph algorithms is a powerful option to pinpoint molecular disease drivers and their interactions. Here we present lipid network explorer (LINEX$^2$), a lipid network analysis framework that fuels biological interpretation of alterations in lipid compositions. By integrating lipid-metabolic reactions from public databases, we generate dataset-specific lipid interaction networks. To aid interpretation of these networks, we present an enrichment graph algorithm that infers changes in enzymatic activity in the context of their multispecificity from lipidomics data. Our inference method successfully recovered the MBOAT7 enzyme from knock-out data. Furthermore, we mechanistically interpret lipidomic alterations of adipocytes in obesity by leveraging network enrichment and lipid moieties. We address the general lack of lipidomics data mining options to elucidate potential disease mechanisms and make lipidomics more clinically relevant.

Cytosolic glutaredoxin 1 is upregulated in AMD and controls retinal pigment epithelial cells proliferation via ß-catenin.

Thioredoxin (Trx) family proteins are key players in redox signaling. Here, we have analyzed glutaredoxin (Grx) 1 and Grx2 in age-related macular degeneration (AMD) and in retinal pigment epithelial (ARPE-19) cells. We hypothesized that these redoxins regulate cellular functions and signaling circuits such as cell proliferation, Wnt signaling and VEGF release that have been correlated to the pathophysiology of AMD. ARPE-19 cells were transfected with specific siRNAs to silence the expression of Grx1 and Grx2 and were analyzed for proliferation/viability, migration capacity, ß-catenin activation, and VEGF release. An active site-mutated C-X-X-S Grx1 was utilized to trap interacting proteins present in ARPE-19 cell extracts. In both, AMD retinas and in ARPE-19 cells incubated under hypoxia/reoxygenation conditions, Grx1 showed an increased nuclear localization. Grx1-silenced ARPE-19 cells showed a significantly reduced proliferation and migration rate. Our trapping approach showed that Grx1 interacts with ß-catenin in a dithiol-disulfide exchange reaction. Knock-down of Grx1 led to a reduction in both total and active ß-catenin levels. These findings add redox control to the regulatory mechanisms of ß-catenin signaling in the retinal pigment epithelium and open the door to novel therapeutic approaches in AMD that is currently treated with VEGF-inhibitors.

Exposure based cognitive behavioral group therapy for IBS at a gastroenterological clinic - a clinical effectiveness study.

BACKGROUND: Patients with irritable bowel syndrome (IBS) may benefit from psychological treatment when diet changes and medications do not sufficiently reduce symptoms. Our research team has developed an exposure based cognitive behavioral therapy protocol (ECBT), which has been shown to be effective in several randomized controlled trials. AIM: To investigate the effectiveness of ECBT in clinical routine care at a gastroenterological clinic in Stockholm and to find predictors for treatment outcome. METHOD: A ten session ECBT based on our protocol was given face to face by licensed psychologists in groups of 4-6 patients. A total of 129 patients provided information regarding IBS symptoms, quality of life, gastrointestinal symptom-specific anxiety (GSA), and depression pre and post-treatment. We used linear regression analyses to identify patient characteristics that predicted treatment outcome. RESULTS: The primary outcome was symptom severity measured with The Gastrointestinal Symptom Rating Scale for IBS (GSRS-IBS). Average pre-and post-treatment GSRS-IBS scores were 49.24 (SD = 11.54) and 37.03 (SD = 10.03), corresponding to a 34.0% reduction in symptom severity (p < .001). Reductions were also found in GSA, 43.9% (p < .001) and depression, 38.6% (p < .001). IBS-related quality of life was on average increased by 68.2% (p < .001). The effect sizes were large and varied between (Cohen's d) 0.95 and 1.84. None of the patients' pre-treatment characteristics predicted outcome. CONCLUSION: We conclude that ECBT for IBS delivered face-to-face in a group-format is very effective, also in a routine care setting. We did not find any reliable predictors for treatment outcome. The trial was registered at Clinicaltrials.gov with ID: NCT04756414.

LFA1 and ICAM1 are critical for fusion and spread of murine leukemia virus in vivo.

Murine leukemia virus (MLV)-presenting cells form stable intercellular contacts with target cells during infection of lymphoid tissue, indicating a role of cell-cell contacts in retrovirus dissemination. Whether host cell adhesion proteins are required for retrovirus spread in vivo remains unknown. Here, we demonstrate that the lymphocyte-function-associated-antigen-1 (LFA1) and its ligand intercellular-adhesion-molecule-1 (ICAM1) are important for cell-contact-dependent transmission of MLV between leukocytes. Infection experiments in LFA1- and ICAM1-deficient mice demonstrate a defect in MLV spread within lymph nodes. Co-culture of primary leukocytes reveals a specific requirement for ICAM1 on donor cells and LFA1 on target cells for cell-contact-dependent spread through trans- and cis-infection. Importantly, adoptive transfer experiments combined with a newly established MLV-fusion assay confirm that the directed LFA1-ICAM1 interaction is important for retrovirus fusion and transmission in vivo. Taken together, our data provide insights on how retroviruses exploit host proteins and the biology of cell-cell interactions for dissemination.

Investigating Global Lipidome Alterations with the Lipid Network Explorer.

Lipids play an important role in biological systems and have the potential to serve as biomarkers in medical applications. Advances in lipidomics allow identification of hundreds of lipid species from biological samples. However, a systems biological analysis of the lipidome, by incorporating pathway information remains challenging, leaving lipidomics behind compared to other omics disciplines. An especially uncharted territory is the integration of statistical and network-based approaches for studying global lipidome changes. Here we developed the Lipid Network Explorer (LINEX), a web-tool addressing this gap by providing a way to visualize and analyze functional lipid metabolic networks. It utilizes metabolic rules to match biochemically connected lipids on a species level and combine it with a statistical correlation and testing analysis. Researchers can customize the biochemical rules considered, to their tissue or organism specific analysis and easily share them. We demonstrate the benefits of combining network-based analyses with statistics using publicly available lipidomics data sets. LINEX facilitates a biochemical knowledge-based data analysis for lipidomics. It is availableas a web-application and as a publicly available docker container.

Provoking symptoms to relieve symptoms: a randomized controlled dismantling study of exposure therapy in irritable bowel syndrome.

An internet-delivered cognitive behavioral treatment (ICBT) based on systematic exposure exercises has previously shown beneficial effects for patients with irritable bowel syndrome (IBS). Exposure exercises may be perceived as difficult for patients to perform because of the elicited short-term distress and clinicians may be reluctant to use these interventions. The aim of this study was to compare ICBT with the same protocol without systematic exposure (ICBT-WE) to assess if exposure had any incremental value. This randomized controlled dismantling study included 309 participants diagnosed with IBS. The treatment interventions lasted for 10 weeks and included online therapist contact. ICBT-WE comprised mindfulness, work with life values, acceptance, and encouraged reduced avoidance behaviors, while ICBT also included systematic exposure to IBS symptoms and related situations. Severity of IBS symptoms was measured with the Gastrointestinal Symptom Rating Scale - IBS version (GSRS-IBS). The between-group Cohen's d on GSRS-IBS was 0.47 (95% CI: 0.23-0.70) at post-treatment and 0.48 (95% CI: 0.20-0.76) at 6-month follow-up, favoring ICBT. We conclude that the systematic exposure included in the ICBT protocol has incremental effects over the other components in the protocol. This study provides evidence for the utility of exposure exercises in psychological treatments for IBS.

Internet-delivered exposure and mindfulness based therapy for irritable bowel syndrome--a randomized controlled trial.

The aim of this study was to investigate if cognitive behavior therapy (CBT) based on exposure and mindfulness exercises delivered via the Internet would be effective in treating participants with irritable bowel syndrome (IBS). Participants were recruited through self-referral. Eighty-six participants were included in the study and randomized to treatment or control condition (an online discussion forum). One participant was excluded after randomization. The main outcome measure was IBS-symptom severity and secondary measures included IBS-related quality of life, GI-specific anxiety, depression and general functioning. Participants were assessed at pre-treatment, post-treatment and 3 month follow-up (treatment condition only). Four participants (5% of total sample) in the treatment condition did not participate in post-treatment assessment. Participants in the treatment condition reported a 42% decrease and participants in the control group reported a 12% increase in primary IBS-symptoms. Compared to the control condition, participants in the treatment group improved on all secondary outcome measures with a large between group effect size on quality of life (Cohen's d = 1.21). We conclude that CBT-based on exposure and mindfulness delivered via the Internet can be effective in treating IBS-patients, alleviating the total burden of symptoms and increasing quality of life.