Epigenetic mechanisms in colorectal cancer

Mitjançant tècniques d’anàlisi de tot el genoma hem sigut capaços d'identificar regions diferencialment metilades entre teixit de colon normal i tumoral provinents del mateix pacient. Un dels gens més importants és AKR1B1, l'illa CpG associada al promotor d’aquest gen esdevé hipermetilada en un 90% dels càncers colorectals estudiats (més de 200), aquesta troballa ha estat confirmada en dos sets de mostres independents. Sorprenentment, la hipermetilació no està acompanyada per una clara baixada de l’expressió d’AKR1B1, de fet vam observar que aquesta hipermetilació estava associada amb el silenciament dels gens AKR1B10 i AKR1B15 (tots ells membres de la mateixa família d’aldo-keto reductases), localitzats a 60 Kbs de l'illa CpG. Utilitzant tècniques per esbrinar l'estructura de la cromatina dins del nucli vam observar que l'illa CpG es troba en contacte amb el promotor de AKR1B10, el que indica una possible funció d’enhancer per a l'illa CpG. Aquesta funció enhancer va ser corroborada mitjançant assajos de luciferasa i demostrada in situ mitjançant l’alteració de la regió enhancer, utilitzant la tècnica d’edició genòmica CRISPR. A més a més, l’acció enhancer va ser recuperada en models cel·lulars gràcies a l’acció de diverses drogues epigenètiques, que produïen l’activació de l’enhancer (observable per la reaparició de la marca H3K27ac) i la reactivació de l’expressió d’AKR1B10 i AKR1B15. En aquest treball també s’avalua l’impacte de la hipermetilació en la via de l’àcid retinoic, a la qual pertanyen els enzims de la família AKR1B. Observem que la via està fortament hipermetilada i, en conseqüència, silenciada. El fet més remarcable a nivell clínic és que aquestes alteracions poden servir com a marcador de pronòstic de la malaltia i com a marcador de diagnòstic no invasiu.By applying a genome-wide approach to detect differential methylation between colorectal tumors and their paired normal tissue we identified a number of genes that suffer hypermethylation in colorectal cancer. One of the most interesting genes was AKR1B1, which promoter CpG island became hypermethylated in about 90% of all the colorectal cancers samples analyzed. Unexpectedly, this hypermethylation was not accompanied by a clear downregulation of the AKR1B1 transcript. After extending the analysis to the neighboring genes, we realized that this hypermethylation was actually associated with silencing of AKR1B10 and AKR1B15 genes (all of them members of the same aldo-keto reductase gene family), located 60 Kb upstream of the methylated CpG island. Using techniques to elucidate the chromatin structure within the nucleus, we realized that the CpG island was in close contact with the AKR1B10 promoter, what indicates a putative enhancer role for the CpG island. This enhancer function was checked using luciferase assays and was demonstrated in situ through the alteration of the enhancer region, using the genome editing technique CRISPR. Moreover, the enhancer activity was recovered using cellular models through the treatments with different epigenetic drugs, which produced the activation of the enhancer (with the characteristic H3K27ac mark) and the reexpression of AKR1B10 and AKR1B15 genes. In this work we also evaluated the impact of the hypermethylation in the retinoic acid pathway, where AKR1B enzymes belong to. We observed a strong hypermethylation of the retinoic acid pathway and, as a consequence, silencing. The most remarkable finding is that those alterations can be used to predict the outcome of the disease and also as a non-invasive diagnostic marker

Epigenetic mechanisms in colorectal cancer

Mitjançant tècniques d'anàlisi de tot el genoma hem sigut capaços d'identificar regions diferencialment metilades entre teixit de colon normal i tumoral provinents del mateix pacient. Un dels gens més importants és AKR1B1, l'illa CpG associada al promotor d'aquest gen esdevé hipermetilada en un 90% dels càncers colorectals estudiats (més de 200), aquesta troballa ha estat confirmada en dos sets de mostres independents. Sorprenentment, la hipermetilació no està acompanyada per una clara baixada de l'expressió d'AKR1B1, de fet vam observar que aquesta hipermetilació estava associada amb el silenciament dels gens AKR1B10 i AKR1B15 (tots ells membres de la mateixa família d'aldo-keto reductases), localitzats a 60 Kbs de l'illa CpG. Utilitzant tècniques per esbrinar l'estructura de la cromatina dins del nucli vam observar que l'illa CpG es troba en contacte amb el promotor de AKR1B10, el que indica una possible funció d'enhancer per a l'illa CpG. Aquesta funció enhancer va ser corroborada mitjançant assajos de luciferasa i demostrada in situ mitjançant l'alteració de la regió enhancer, utilitzant la tècnica d'edició genòmica CRISPR. A més a més, l'acció enhancer va ser recuperada en models cel·lulars gràcies a l'acció de diverses drogues epigenètiques, que produïen l'activació de l'enhancer (observable per la reaparició de la marca H3K27ac) i la reactivació de l'expressió d'AKR1B10 i AKR1B15. En aquest treball també s'avalua l'impacte de la hipermetilació en la via de l'àcid retinoic, a la qual pertanyen els enzims de la família AKR1B. Observem que la via està fortament hipermetilada i, en conseqüència, silenciada. El fet més remarcable a nivell clínic és que aquestes alteracions poden servir com a marcador de pronòstic de la malaltia i com a marcador de diagnòstic no invasiu.By applying a genome-wide approach to detect differential methylation between colorectal tumors and their paired normal tissue we identified a number of genes that suffer hypermethylation in colorectal cancer. One of the most interesting genes was AKR1B1, which promoter CpG island became hypermethylated in about 90% of all the colorectal cancers samples analyzed. Unexpectedly, this hypermethylation was not accompanied by a clear downregulation of the AKR1B1 transcript. After extending the analysis to the neighboring genes, we realized that this hypermethylation was actually associated with silencing of AKR1B10 and AKR1B15 genes (all of them members of the same aldo-keto reductase gene family), located 60 Kb upstream of the methylated CpG island. Using techniques to elucidate the chromatin structure within the nucleus, we realized that the CpG island was in close contact with the AKR1B10 promoter, what indicates a putative enhancer role for the CpG island. This enhancer function was checked using luciferase assays and was demonstrated in situ through the alteration of the enhancer region, using the genome editing technique CRISPR. Moreover, the enhancer activity was recovered using cellular models through the treatments with different epigenetic drugs, which produced the activation of the enhancer (with the characteristic H3K27ac mark) and the reexpression of AKR1B10 and AKR1B15 genes. In this work we also evaluated the impact of the hypermethylation in the retinoic acid pathway, where AKR1B enzymes belong to. We observed a strong hypermethylation of the retinoic acid pathway and, as a consequence, silencing. The most remarkable finding is that those alterations can be used to predict the outcome of the disease and also as a non-invasive diagnostic marker

Epigenetics override pro-inflammatory PTGS transcriptomic signature towards selective hyperactivation of PGE 2 in colorectal cancer

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- et al.[Background]: Misregulation of the PTGS (prostaglandin endoperoxide synthase, also known as cyclooxygenase or COX) pathway may lead to the accumulation of pro-inflammatory signals, which constitutes a hallmark of cancer. To get insight into the role of this signaling pathway in colorectal cancer (CRC), we have characterized the transcriptional and epigenetic landscapes of the PTGS pathway genes in normal and cancer cells. [Results]: Data from four independent series of CRC patients (502 tumors including adenomas and carcinomas and 222 adjacent normal tissues) and two series of colon mucosae from 69 healthy donors have been included in the study. Gene expression was analyzed by real-time PCR and Affymetrix U219 arrays. DNA methylation was analyzed by bisulfite sequencing, dissociation curves, and HumanMethylation450K arrays. Most CRC patients show selective transcriptional deregulation of the enzymes involved in the synthesis of prostanoids and their receptors in both tumor and its adjacent mucosa. DNA methylation alterations exclusively affect the tumor tissue (both adenomas and carcinomas), redirecting the transcriptional deregulation to activation of prostaglandin E 2 (PGE 2 ) function and blockade of other biologically active prostaglandins. In particular, PTGIS, PTGER3, PTGFR, and AKR1B1 were hypermethylated in more than 40 % of all analyzed tumors. [Conclusions]: The transcriptional and epigenetic profiling of the PTGS pathway provides important clues on the biology of the tumor and its microenvironment. This analysis renders candidate markers with potential clinical applicability in risk assessment and early diagnosis and for the design of new therapeutic strategies.IC was funded by Fundação para a Ciência e a Tecnologia (SFRH/BD/28464/2006); JC was funded by a FPI fellowship. ADV was supported in part by a contract from the Ministerio de Economía y Competitividad (MINECO) (PTC2011-1091). This work was supported by the MINECO(SAF2011/23638, SAF2014/52492), the Catalan Institute of Oncology and the Instituto de Salud Carlos III (grant PI11-01439, RD12/0042/0019 and CIBERESP CB06/02/2005), the Generalitat de Catalunya (grant 2014SGR647), and the Asociación Española Contra el Cáncer (AECC).Peer Reviewe

Epigenetics override pro-inflammatory PTGS transcriptomic signature towards selective hyperactivation of PGE2 in colorectal cancer

Background: Misregulation of the PTGS (prostaglandin endoperoxide synthase, also known as cyclooxygenase or COX) pathway may lead to the accumulation of pro-inflammatory signals, which constitutes a hallmark of cancer. To get insight into the role of this signaling pathway in colorectal cancer (CRC), we have characterized the transcriptional and epigenetic landscapes of the PTGS pathway genes in normal and cancer cells. Results: Data from four independent series of CRC patients (502 tumors including adenomas and carcinomas and 222 adjacent normal tissues) and two series of colon mucosae from 69 healthy donors have been included in the study. Gene expression was analyzed by real-time PCR and Affymetrix U219 arrays. DNA methylation was analyzed by bisulfite sequencing, dissociation curves, and HumanMethylation450K arrays. Most CRC patients show selective transcriptional deregulation of the enzymes involved in the synthesis of prostanoids and their receptors in both tumor and its adjacent mucosa. DNA methylation alterations exclusively affect the tumor tissue (both adenomas and carcinomas), redirecting the transcriptional deregulation to activation of prostaglandin E2 (PGE2) function and blockade of other biologically active prostaglandins. In particular, PTGIS, PTGER3, PTGFR, and AKR1B1 were hypermethylated in more than 40 % of all analyzed tumors. Conclusions: The transcriptional and epigenetic profiling of the PTGS pathway provides important clues on the biology of the tumor and its microenvironment. This analysis renders candidate markers with potential clinical applicability in risk assessment and early diagnosis and for the design of new therapeutic strategies

Programa d’avaluació de la conducta violenta en el CP Quatre Camins

Aquesta investigació avalua exhaustivament el “Programa d’Avaluació de la Conducta Violenta” que el Centre Penitenciari Quatre Camins (CPQC) implementa des de l’any 2016 per a la millora del treball amb les persones internes que han comés delictes violents. Aquest Programa implica passar d’un model d’intervenció centrat en el delicte a un model centrat en els riscos i necessitats criminògenes dels interns amb conductes violentes, tal com aconsellen el model RNR (Risc –Necessitat- Responsivitat) d’Andrews i Bonta i el model transteòric de canvi de Prochaska i Diclemente. La recerca compara 2 grups d’interns de perfils similars (grup control i grup programa) però que han seguit un model d’intervenció diferent (el grup control segueix la intervenció anterior al canvi, i el grup programa la intervenció nova). Si el canvi de model d’intervenció resulta eficient, els indicadors han de donar millors resultats en el grup que ha fet el nou programa respecte al grup control que ha seguit el model anterior. La recerca aporta detalls de les característiques i perfils dels diferents grups de condemnats per delictes violents del CPQC. Es donen resultats del procés seguit pels interns d’ambdós grups en relació amb el seu procés rehabilitador. I, finalment, també mostra les opinions dels professionals i dels interns implicats en la nova metodologia, com a part de l’avaluació dels processos de treball que ha comportat per al CPQC aquest nou Programa. Aquesta investigació és fruit de la col·laboració entre els professionals del CPQC i de l’equip de recerca del CEJFE i és un exemple paradigmàtic de l’ús de la metodologia d’investigació-acció

Programa de evaluación de la conducta violenta en el Centro Penitenciario Quatre Camins

Esta investigación evalúa exhaustivamente el “Programa de Evaluación de la Conducta Violenta” que el Centro Penitenciario Cuatro Caminos (CPQC) implementa desde el año 2016 para la mejora del trabajo con las personas internas que han cometido delitos violentos. Este Programa implica pasar de un modelo de intervención centrado en el delito a un modelo centrado en los riesgos y necesidades criminógenas de los internos con conductos violentas, tal como aconsejan al modelo RNR (Riesgo –Necesidad- Responsivitat) de Andrews i Bonta y el modelo transteórico de cambio de Prochaska y Diclemente. La investigación compara 2 grupos de internos de perfiles similares (grupo control y grupo programa) pero que han seguido a un modelo de intervención diferente (el grupo control sigue la intervención anterior al cambio, y el grupo programa la intervención nueva). Si el cambio de modelo de intervención resulta eficiente, los indicadores tienen que dar mejores resultados en el grupo que ha hecho el nuevo programa con respecto al grupo control que ha seguido el modelo anterior. La investigación aporta detalles de las características y perfiles de los diferentes grupos de condenados por delitos violentos del CPQC. Se dan resultados del proceso seguido por los internos de ambos grupos en relación con su proceso rehabilitador. Y, finalmente, también muestra las opiniones de los profesionales y de los internos implicados en la nueva metodología, como aparte de la evaluación de los procesos de trabajo que ha comportado para el CPQC este nuevo Programa. Esta investigación es fruto de la colaboración entre los profesionales del CPQC y del equipo de investigación del CEJFE y es un ejemplo paradigmático del uso de la metodología de investigación-acción

Paediatric COVID-19 mortality: a database analysis of the impact of health resource disparity

Background The impact of the COVID-19 pandemic on paediatric populations varied between high-income countries (HICs) versus low-income to middle-income countries (LMICs). We sought to investigate differences in paediatric clinical outcomes and identify factors contributing to disparity between countries.Methods The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) COVID-19 database was queried to include children under 19 years of age admitted to hospital from January 2020 to April 2021 with suspected or confirmed COVID-19 diagnosis. Univariate and multivariable analysis of contributing factors for mortality were assessed by country group (HICs vs LMICs) as defined by the World Bank criteria.Results A total of 12 860 children (3819 from 21 HICs and 9041 from 15 LMICs) participated in this study. Of these, 8961 were laboratory-confirmed and 3899 suspected COVID-19 cases. About 52% of LMICs children were black, and more than 40% were infants and adolescent. Overall in-hospital mortality rate (95% CI) was 3.3% [=(3.0% to 3.6%), higher in LMICs than HICs (4.0% (3.6% to 4.4%) and 1.7% (1.3% to 2.1%), respectively). There were significant differences between country income groups in intervention profile, with higher use of antibiotics, antivirals, corticosteroids, prone positioning, high flow nasal cannula, non-invasive and invasive mechanical ventilation in HICs. Out of the 439 mechanically ventilated children, mortality occurred in 106 (24.1%) subjects, which was higher in LMICs than HICs (89 (43.6%) vs 17 (7.2%) respectively). Pre-existing infectious comorbidities (tuberculosis and HIV) and some complications (bacterial pneumonia, acute respiratory distress syndrome and myocarditis) were significantly higher in LMICs compared with HICs. On multivariable analysis, LMIC as country income group was associated with increased risk of mortality (adjusted HR 4.73 (3.16 to 7.10)).Conclusion Mortality and morbidities were higher in LMICs than HICs, and it may be attributable to differences in patient demographics, complications and access to supportive and treatment modalities

Respiratory support in patients with severe COVID-19 in the International Severe Acute Respiratory and Emerging Infection (ISARIC) COVID-19 study: a prospective, multinational, observational study

Background: Up to 30% of hospitalised patients with COVID-19 require advanced respiratory support, including high-flow nasal cannulas (HFNC), non-invasive mechanical ventilation (NIV), or invasive mechanical ventilation (IMV). We aimed to describe the clinical characteristics, outcomes and risk factors for failing non-invasive respiratory support in patients treated with severe COVID-19 during the first two years of the pandemic in high-income countries (HICs) and low middle-income countries (LMICs). Methods: This is a multinational, multicentre, prospective cohort study embedded in the ISARIC-WHO COVID-19 Clinical Characterisation Protocol. Patients with laboratory-confirmed SARS-CoV-2 infection who required hospital admission were recruited prospectively. Patients treated with HFNC, NIV, or IMV within the first 24 h of hospital admission were included in this study. Descriptive statistics, random forest, and logistic regression analyses were used to describe clinical characteristics and compare clinical outcomes among patients treated with the different types of advanced respiratory support. Results: A total of 66,565 patients were included in this study. Overall, 82.6% of patients were treated in HIC, and 40.6% were admitted to the hospital during the first pandemic wave. During the first 24 h after hospital admission, patients in HICs were more frequently treated with HFNC (48.0%), followed by NIV (38.6%) and IMV (13.4%). In contrast, patients admitted in lower- and middle-income countries (LMICs) were less frequently treated with HFNC (16.1%) and the majority received IMV (59.1%). The failure rate of non-invasive respiratory support (i.e. HFNC or NIV) was 15.5%, of which 71.2% were from HIC and 28.8% from LMIC. The variables most strongly associated with non-invasive ventilation failure, defined as progression to IMV, were high leukocyte counts at hospital admission (OR [95%CI]; 5.86 [4.83-7.10]), treatment in an LMIC (OR [95%CI]; 2.04 [1.97-2.11]), and tachypnoea at hospital admission (OR [95%CI]; 1.16 [1.14-1.18]). Patients who failed HFNC/NIV had a higher 28-day fatality ratio (OR [95%CI]; 1.27 [1.25-1.30]). Conclusions: In the present international cohort, the most frequently used advanced respiratory support was the HFNC. However, IMV was used more often in LMIC. Higher leucocyte count, tachypnoea, and treatment in LMIC were risk factors for HFNC/NIV failure. HFNC/NIV failure was related to worse clinical outcomes, such as 28-day mortality. Trial registration This is a prospective observational study; therefore, no health care interventions were applied to participants, and trial registration is not applicable

Respiratory support in patients with severe COVID-19 in the International Severe Acute Respiratory and Emerging Infection (ISARIC) COVID-19 study: a prospective, multinational, observational study

Background: Up to 30% of hospitalised patients with COVID-19 require advanced respiratory support, including high-flow nasal cannulas (HFNC), non-invasive mechanical ventilation (NIV), or invasive mechanical ventilation (IMV). We aimed to describe the clinical characteristics, outcomes and risk factors for failing non-invasive respiratory support in patients treated with severe COVID-19 during the first two years of the pandemic in high-income countries (HICs) and low middle-income countries (LMICs). Methods: This is a multinational, multicentre, prospective cohort study embedded in the ISARIC-WHO COVID-19 Clinical Characterisation Protocol. Patients with laboratory-confirmed SARS-CoV-2 infection who required hospital admission were recruited prospectively. Patients treated with HFNC, NIV, or IMV within the first 24 h of hospital admission were included in this study. Descriptive statistics, random forest, and logistic regression analyses were used to describe clinical characteristics and compare clinical outcomes among patients treated with the different types of advanced respiratory support. Results: A total of 66,565 patients were included in this study. Overall, 82.6% of patients were treated in HIC, and 40.6% were admitted to the hospital during the first pandemic wave. During the first 24 h after hospital admission, patients in HICs were more frequently treated with HFNC (48.0%), followed by NIV (38.6%) and IMV (13.4%). In contrast, patients admitted in lower- and middle-income countries (LMICs) were less frequently treated with HFNC (16.1%) and the majority received IMV (59.1%). The failure rate of non-invasive respiratory support (i.e. HFNC or NIV) was 15.5%, of which 71.2% were from HIC and 28.8% from LMIC. The variables most strongly associated with non-invasive ventilation failure, defined as progression to IMV, were high leukocyte counts at hospital admission (OR [95%CI]; 5.86 [4.83–7.10]), treatment in an LMIC (OR [95%CI]; 2.04 [1.97–2.11]), and tachypnoea at hospital admission (OR [95%CI]; 1.16 [1.14–1.18]). Patients who failed HFNC/NIV had a higher 28-day fatality ratio (OR [95%CI]; 1.27 [1.25–1.30]). Conclusions: In the present international cohort, the most frequently used advanced respiratory support was the HFNC. However, IMV was used more often in LMIC. Higher leucocyte count, tachypnoea, and treatment in LMIC were risk factors for HFNC/NIV failure. HFNC/NIV failure was related to worse clinical outcomes, such as 28-day mortality. Trial registration This is a prospective observational study; therefore, no health care interventions were applied to participants, and trial registration is not applicable

Association of Country Income Level With the Characteristics and Outcomes of Critically Ill Patients Hospitalized With Acute Kidney Injury and COVID-19

Introduction: Acute kidney injury (AKI) has been identified as one of the most common and significant problems in hospitalized patients with COVID-19. However, studies examining the relationship between COVID-19 and AKI in low- and low-middle income countries (LLMIC) are lacking. Given that AKI is known to carry a higher mortality rate in these countries, it is important to understand differences in this population. Methods: This prospective, observational study examines the AKI incidence and characteristics of 32,210 patients with COVID-19 from 49 countries across all income levels who were admitted to an intensive care unit during their hospital stay. Results: Among patients with COVID-19 admitted to the intensive care unit, AKI incidence was highest in patients in LLMIC, followed by patients in upper-middle income countries (UMIC) and high-income countries (HIC) (53%, 38%, and 30%, respectively), whereas dialysis rates were lowest among patients with AKI from LLMIC and highest among those from HIC (27% vs. 45%). Patients with AKI in LLMIC had the largest proportion of community-acquired AKI (CA-AKI) and highest rate of in-hospital death (79% vs. 54% in HIC and 66% in UMIC). The association between AKI, being from LLMIC and in-hospital death persisted even after adjusting for disease severity. Conclusions: AKI is a particularly devastating complication of COVID-19 among patients from poorer nations where the gaps in accessibility and quality of healthcare delivery have a major impact on patient outcomes