Ulcerative colitis unsupervised classification using single cell colonic data

Ulcerative colitis is a relapsing inflammatory bowel disease affecting the gut's mucosa. The disease is characterized by rectal bleeding, abdominal pain, and diarrhea, among others, due to the damaged caused in the epithelial barrier. Its etiology remains unknown, but there are several factors that might trigger it, like the environment, genetics, and the immune system. Moreover, treatment response among patients is highly variable; even in those classified with the same severity of the disease. For this reason, a new way of classifying patientsthat understands patient's variability at the molecular level is needed. In this way, single-cell RNA-seq arise as a technique that can provide insights on the transcriptome of cells and help understand the way the different cell types found in the gut mucosa act in the disease

Redox-dependent and redox-independent functions of Caenorhabditis elegans thioredoxin 1

Thioredoxins (TRX) are traditionally considered as enzymes catalyzing redox reactions. However, redox-independent functions of thioredoxins have been described in different organisms, although the underlying molecular mechanisms are yet unknown. We report here the characterization of the first generated endogenous redox-inactive thioredoxin in an animal model, the TRX-1 in the nematode Caenorhabditis elegans. We find that TRX-1 dually regulates the formation of an endurance larval stage (dauer) by interacting with the insulin pathway in a redox-independent manner and the cGMP pathway in a redox-dependent manner. Moreover, the requirement of TRX-1 for the extended longevity of worms with compromised insulin signalling or under calorie restriction relies on TRX-1 redox activity. In contrast, the nuclear translocation of the SKN-1 transcription factor and increased LIPS-6 protein levels in the intestine upon trx-1 deficiency are strictly redox-independent. Finally, we identify a novel function of C. elegans TRX-1 in male food-leaving behaviour that is redox-dependent. Taken together, our results position C. elegans as an ideal model to gain mechanistic insight into the redox-independent functions of metazoan thioredoxins, overcoming the limitations imposed by the embryonic lethal phenotypes of thioredoxin mutants in higher organisms.NIH Office of Research Infrastructure P40 OD010440Spanish Ministry of Economy and Competitiveness BFU2015- 64408-PFondo Social Europeo BFU2015- 64408-PNational Institute of Allergy and Infectious Diseases of the National Institutes of Health R01AI07640

Genetic Study of SARS-CoV-2 Non Structural Protein 12 in COVID-19 Patients Non Responders to Remdesivir

Remdesivir (RDV) was the first antiviral drug approved by the FDA to treat severe coronavirus disease-2019 (COVID-19) patients. RDV inhibits SARS-CoV-2 replication by stalling the non structural protein 12 (nsp12) subunit of the RNA-dependent RNA polymerase (RdRp). No evidence of global widespread RDV-resistance mutations has been reported, however, defining genetic pathways to RDV resistance and determining emergent mutations prior and subsequent antiviral therapy in clinical settings is necessary. This study identified 57/149 (38.3%) patients who did not respond to one course (5-days) (n = 36/111, 32.4%) or prolonged (5 to 20 days) (n = 21/38, 55.3%) RDV therapy by subgenomic RNA detection. Genetic variants in the nsp12 gene were detected in 29/49 (59.2%) non responder patients by Illumina sequencing, including the de novo E83D mutation that emerged in an immunosuppressed patient after receiving 10 + 8 days of RDV, and the L838I detected at baseline and/or after prolonged RDV treatment in 9/49 (18.4%) non responder subjects. Although 3D protein modeling predicted no interference with RDV, the amino acid substitutions detected in the nsp12 involved changes on the electrostatic outer surface and in secondary structures that may alter antiviral response. It is important for health surveillance to study potential mutations associated with drug resistance as well as the benefit of RDV retreatment, especially in immunosuppressed patients and in those with persistent replication. IMPORTANCE This study provides clinical and microbiologic data of an extended population of hospitalized patients for COVID-19 pneumonia who experienced treatment failure, detected by the presence of subgenomic RNA (sgRNA). The genetic variants found in the nsp12 pharmacological target of RDV bring into focus the importance of monitoring emergent mutations, one of the objectives of the World Health Organization (WHO) for health surveillance. These mutations become even more crucial as RDV keeps being prescribed and new molecules are being repurposed for the treatment of COVID-19. The present article offers new perspectives for the clinical management of non responder patients treated and retreated with RDV and emphasizes the need of further research of the benefit of combinatorial therapies and RDV retreatment, especially in immunosuppressed patients with persistent replication after therapy.This work was financed by a Gilead Sciences grant (IN-ES-540-6089) and CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, España (CB21/13/00081). This work was financed by ad hoc patronage funds for research on COVID-19 from donations from citizens and organizations to the Hospital Clínic de Barcelona-Fundació Clínic per a la Recerca Biomèdica.S

Estudio del papel de la actividad redox en la función de la tiorredoxina TRX-1 de Caenorhabditis elegans

Tipología: Investigación.-- Trabajo Fin de Grado. Facultad de Medicina, Departamento de Fisiología Médica y Biofísica. Grado en Biomedicina Básica y Experimental. Lugar de realización: Instituto de Biomedicina de Sevilla (IBiS) / Hospital Universitario Virgen del Rocío (HUVR) / CSIC/Universidad de Sevilla / Departamento de Fisiología Médica y Biofísica.Thioredoxins are widely known as proteins that regulate redox homeostasis by reducing proteins and reactive oxygen species (ROS) thanks to the pair of cysteine residues that constitute their active site. A balance of ROS is essential for the organism as low levels of ROS are needed for intracellular signaling while at high doses ROS can be damaging agents for cellular components. Caenorhabditis elegans, an excellent model organism used for biomedical research, has a thioredoxin system similar to that of higher organisms. C. elegansTRX-1is the worm orthologue of human TRX1, displaying a 40% sequence homology. C. elegansTRX-1 is expressed in ASJ neurons, a pair of sensorial neurons found on the amphid of the nematode. These sensorial neurons participate in diverse worm functions like thermoregulation, light sensibility, dauer(an alternative larva stage) entrance and exit, lipid metabolism or ageing. While most functional activities of thioredoxins are dependent on their redox capabilities, there are some reports of these proteins acting in intracellular signaling in a non-redox manner. In this work, we have addressed whether some functions of C. elegansTRX-1 are dependent on its redox enzymatic activity. Our results show that induction of the dauerstage is regulated by both redox and redox-independent mechanisms while the induction of lips-6, an intestinal lipase, is independent of TRX-1 redox function

Redox-dependent and redox-independent functions of Caenorhabditis elegans thioredoxin 1

Thioredoxins (TRX) are traditionally considered as enzymes catalyzing redox reactions. However, redox-independent functions of thioredoxins have been described in different organisms, although the underlying molecular mechanisms are yet unknown. We report here the characterization of the first generated endogenous redox-inactive thioredoxin in an animal model, the TRX-1 in the nematode Caenorhabditis elegans. We find that TRX-1 dually regulates the formation of an endurance larval stage (dauer) by interacting with the insulin pathway in a redox-independent manner and the cGMP pathway in a redox-dependent manner. Moreover, the requirement of TRX-1 for the extended longevity of worms with compromised insulin signalling or under calorie restriction relies on TRX-1 redox activity. In contrast, the nuclear translocation of the SKN-1 transcription factor and increased LIPS-6 protein levels in the intestine upon trx-1 deficiency are strictly redox-independent. Finally, we identify a novel function of C. elegans TRX-1 in male food-leaving behaviour that is redox-dependent. Taken together, our results position C. elegans as an ideal model to gain mechanistic insight into the redox-independent functions of metazoan thioredoxins, overcoming the limitations imposed by the embryonic lethal phenotypes of thioredoxin mutants in higher organisms.We thank the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440), for providing worm strains and SunyBiotech Corporation for the generation of the trx-1(sgps) strain. We thank Prof. Stefan Taubert for providing the lips-6::gfp reporter strain. AMV was supported by a grant from the Spanish Ministry of Economy and Competitiveness (BFU2015-64408-P), cofinanced by the Fondo Social Europeo (FEDER). DAG was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award number R01AI076406. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. AMV is a member of the GENIE and EU-ROS Cost Actions of the European Union

Redox-dependent and redox-independent functions of Caenorhabditis elegans thioredoxin 1.

Thioredoxins (TRX) are traditionally considered as enzymes catalyzing redox reactions. However, redox-independent functions of thioredoxins have been described in different organisms, although the underlying molecular mechanisms are yet unknown. We report here the characterization of the first generated endogenous redox-inactive thioredoxin in an animal model, the TRX-1 in the nematode Caenorhabditis elegans. We find that TRX-1 dually regulates the formation of an endurance larval stage (dauer) by interacting with the insulin pathway in a redox-independent manner and the cGMP pathway in a redox-dependent manner. Moreover, the requirement of TRX-1 for the extended longevity of worms with compromised insulin signalling or under calorie restriction relies on TRX-1 redox activity. In contrast, the nuclear translocation of the SKN-1 transcription factor and increased LIPS-6 protein levels in the intestine upon trx-1 deficiency are strictly redox-independent. Finally, we identify a novel function of C. elegans TRX-1 in male food-leaving behaviour that is redox-dependent. Taken together, our results position C. elegans as an ideal model to gain mechanistic insight into the redox-independent functions of metazoan thioredoxins, overcoming the limitations imposed by the embryonic lethal phenotypes of thioredoxin mutants in higher organisms