Unravelling the Role of Long Noncoding RNAs in the Context of Cell-growth and Regeneration

[eng] Long noncoding RNAs (lncRNAs) have proven biological roles in plethora cellular contexts. Nonetheless, only a handful have been clearly characterized, leaving thousands of newly discovered lncRNAs without an associated function, and sometimes considered as transcriptional by-products. To this end, this thesis work had focused on exploring lncRNA functionality in two scenarios. First, in order to discern between lncRNAs affecting cell-growth rate (lncRNA-hits) and lncRNA-not-hits, we built a tree-based classifier based on high-throughput CRISPRi functional screen data in seven human cell lines, as well as, cell-specific ENCODE transcription factor ChIP-seq data; finding that the genomic features used in our study showed small effects and tend to be transcript-specific. Our classifier outperformed previ- ous algorithms, displayed balanced sensitivity and specificity values, and uncovered a lncRNA (LINC00879) involved in cell-growth. Additionally, we unveiled a list of 40 lncRNAs as candidates for experimental validation. Second, we characterized the lncRNA profile during regeneration, using Drosophila wing imaginal disc as a regeneration-model. We selected a candidate lncRNA (CR40469) and evaluated its role in regeneration at the early stage of cell-damage. Subsequently, using RNA- seq data, we observed significant transcriptomic alterations in consequence of the CR40469 genetic deletion, suggesting its role in regeneration. In this study we have generated a list of lncRNAs whose possible biological role in cell-growth and in re- generation can be further studied

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.Peer ReviewedPostprint (published version

Day-night and seasonal variation of human gene expression across tissues.

Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate transcriptomic changes associated with those cycles across multiple tissues. Overall, most variation across tissues during day-night and among seasons was unique to each cycle. Although all tissues remodeled their transcriptomes, brain and gonadal tissues exhibited the highest seasonality, whereas those in the thoracic cavity showed stronger day-night regulation. Core clock genes displayed marked day-night differences across multiple tissues, which were largely conserved in baboon and mouse, but adapted to their nocturnal or diurnal habits. Seasonal variation of expression affected multiple pathways, and it was enriched among genes associated with the immune response, consistent with the seasonality of viral infections. Furthermore, they unveiled cytoarchitectural changes in brain regions. Altogether, our results provide the first combined atlas of how transcriptomes from human tissues adapt to major cycling environmental conditions. This atlas may have multiple applications; for example, drug targets with day-night or seasonal variation in gene expression may benefit from temporally adjusted doses

Day-night and seasonal variation of human gene expression across tissues

Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate transcriptomic changes associated with those cycles across multiple tissues. Overall, most variation across tissues during day-night and among seasons was unique to each cycle. Although all tissues remodeled their transcriptomes, brain and gonadal tissues exhibited the highest seasonality, whereas those in the thoracic cavity showed stronger day-night regulation. Core clock genes displayed marked day-night differences across multiple tissues, which were largely conserved in baboon and mouse, but adapted to their nocturnal or diurnal habits. Seasonal variation of expression affected multiple pathways, and it was enriched among genes associated with the immune response, consistent with the seasonality of viral infections. Furthermore, they unveiled cytoarchitectural changes in brain regions. Altogether, our results provide the first combined atlas of how transcriptomes from human tissues adapt to major cycling environmental conditions. This atlas may have multiple applications; for example, drug targets with day-night or seasonal variation in gene expression may benefit from temporally adjusted doses.The research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health (R01MH101814 and 5U24HG009446 to R.G.), by the Spanish Ministry of Science and Innovation (PGC2018-094017-B-I00 to R.G. and BFU2017-89201-P to M.I.), and by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (ERC-StG-LS2-637591 and ERC-CoG-LS2-101002275 to M.I.). A.R. was a predoctoral fellow of the CONACYT “Becas al Extranjero” Program of Mexico. We acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, Centro de Excelencia Severo Ochoa and CERCA Programme / Generalitat de Catalunya. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Genomic and functional conservation of lncRNAs: lessons from flies

Over the last decade, the increasing interest in long non-coding RNAs (lncRNAs) has led to the discovery of these transcripts in multiple organisms. LncRNAs tend to be specifically, and often lowly, expressed in certain tissues, cell types and biological contexts. Although lncRNAs participate in the regulation of a wide variety of biological processes, including development and disease, most of their functions and mechanisms of action remain unknown. Poor conservation of the DNA sequences encoding for these transcripts makes the identification of lncRNAs orthologues among different species very challenging, especially between evolutionarily distant species such as flies and humans or mice. However, the functions of lncRNAs are unexpectedly preserved among different species supporting the idea that conservation occurs beyond DNA sequences and reinforcing the potential of characterising lncRNAs in animal models. In this review, we describe the features and roles of lncRNAs in the fruit fly Drosophila melanogaster, focusing on genomic and functional comparisons with human and mouse lncRNAs. We also discuss the current state of advances and limitations in the study of lncRNA conservation and future perspectives

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.This work was supported by the following grants and contracts: 1) From the US NIH: Contract HHSN261200800001E (Leidos Prime contract with NCI); Contracts 10XS170 (NDRI), 10XS171 (Roswell Park Cancer Institute), 10 × 172 (Science Care Inc.), and 12ST1039 (IDOX); Contract 10ST1035 (Van Andel Institute); Contract HHSN268201000029C (Broad Institute); R01 DA006227-17 (U Miami Brain Bank) 2) Ipatimup and i3s are partially funded by the Portuguese Foundation for Science and Technology (FCT); FEDER funds through the COMPETE 2020—Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT/MCTES in the framework POCI-01-0145-FEDER-007274; 3) NORTE-01-0145-FEDER-000029, supported by NORTE 2020, under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF); 4) FCT Fellowships SFRH/BPD/89764/2012 to PO, PD/BD/128007/2016 to AS; Salary support to PGF by POPH—QREN Type 4.2, European Social Fund and MCTES, program Investigador FCT, IF/01127/2014. 5) BIO2014-57291-R from the Spanish Ministry of Economy and Competitiveness and “Plataforma de Recursos Biomoleculares y Bioinformáticos” PT13/0001/0007 from the ISCIII, and EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 6,676559) Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ and CERCA Programme/Generalitat de Catalunya, 7) Ministerio de Educación, Cultura y Deporte, under the FPU programme (Formación de Profesorado Universitario) with pre-doctoral fellowship FPU15/03635 to MMA. 8) Award Number 1R01MH101814 and 3R01MH101814-03S1 from the National Human Genome Research Institute. European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement RNA-MAPS_294653, Ministerio de Economía, Industria y Competitividad, referencia MEIC BIO2015-70777-P y los Fondos Estructurales de la Unión Europea (FEDER) and ISCIII del Ministerio de Economía y Competitividad, referencia PT13/0001/0021 cofinaciada por el Fondo Europeo de Desarrollo Regional (FEDER). 9) MS received funding from CNPq (grant 310132/2015-0 and 427541/2016-6), and from FAPERJ (grant E_06/2015)

30-Day Morbidity and Mortality of Bariatric Surgery During the COVID-19 Pandemic: a Multinational Cohort Study of 7704 Patients from 42 Countries.

BACKGROUND There are data on the safety of cancer surgery and the efficacy of preventive strategies on the prevention of postoperative symptomatic COVID-19 in these patients. But there is little such data for any elective surgery. The main objectives of this study were to examine the safety of bariatric surgery (BS) during the coronavirus disease 2019 (COVID-19) pandemic and to determine the efficacy of perioperative COVID-19 protective strategies on postoperative symptomatic COVID-19 rates. METHODS We conducted an international cohort study to determine all-cause and COVID-19-specific 30-day morbidity and mortality of BS performed between 01/05/2020 and 31/10/2020. RESULTS Four hundred ninety-nine surgeons from 185 centres in 42 countries provided data on 7704 patients. Elective primary BS (n = 7084) was associated with a 30-day morbidity of 6.76% (n = 479) and a 30-day mortality of 0.14% (n = 10). Emergency BS, revisional BS, insulin-treated type 2 diabetes, and untreated obstructive sleep apnoea were associated with increased complications on multivariable analysis. Forty-three patients developed symptomatic COVID-19 postoperatively, with a higher risk in non-whites. Preoperative self-isolation, preoperative testing for SARS-CoV-2, and surgery in institutions not concurrently treating COVID-19 patients did not reduce the incidence of postoperative COVID-19. Postoperative symptomatic COVID-19 was more likely if the surgery was performed during a COVID-19 peak in that country. CONCLUSIONS BS can be performed safely during the COVID-19 pandemic with appropriate perioperative protocols. There was no relationship between preoperative testing for COVID-19 and self-isolation with symptomatic postoperative COVID-19. The risk of postoperative COVID-19 risk was greater in non-whites or if BS was performed during a local peak

Effect of BMI on safety of bariatric surgery during the COVID-19 pandemic, procedure choice, and safety protocols - An analysis from the GENEVA Study

Background: It has been suggested that patients with a Body Mass Index (BMI) of > 60 kg/m2 should be offered expedited Bariatric Surgery (BS) during the Coronavirus Disease-2019 (COVID-19) pandemic. The main objective of this study was to assess the safety of this approach. Methods: We conducted a global study of patients who underwent BS between 1/05/2020 and 31/10/2020. Patients were divided into three groups according to their preoperative BMI -Group I (BMI < 50 kg/m2), Group II (BMI 50-60 kg/m2), and Group III (BMI > 60 kg/m2). The effect of preoperative BMI on 30-day morbidity and mortality, procedure choice, COVID-19 specific safety protocols, and comorbidities was assessed. Results: This study included 7084 patients (5197;73.4 % females). The mean preoperative weight and BMI were 119.49 & PLUSMN; 24.4 Kgs and 43.03 & PLUSMN; 6.9 Kg/m2, respectively. Group I included 6024 (85 %) patients, whereas Groups II and III included 905 (13 %) and 155 (2 %) patients, respectively.The 30-day mortality rate was higher in Group III (p = 0.001). The complication rate and COVID-19 infection were not different. Comorbidities were significantly more likely in Group III (p = < 0.001). A significantly higher proportion of patients in group III received Sleeve Gastrectomy or One Anastomosis Gastric Bypass compared to other groups. Patients with a BMI of > 70 kg/m2 had a 30-day mortality of 7.7 % (2/26). None of these patients underwent a Roux-en-Y Gastric Bypass. Conclusion: The 30-day mortality rate was significantly higher in patients with BMI > 60 kg/m2. There was, however, no significant difference in complications rates in different BMI groups, probably due to differences in procedure selection

Safety of Bariatric Surgery in ≥ 65-Year-Old Patients During the COVID-19 Pandemic

Background Age >= 65 years is regarded as a relative contraindication for bariatric surgery. Advanced age is also a recognised risk factor for adverse outcomes with Coronavirus Disease-2019 (COVID-19) which continues to wreak havoc on global populations. This study aimed to assess the safety of bariatric surgery (BS) in this particular age group during the COVID-19 pandemic in comparison with the younger cohort.Methods We conducted a prospective international study of patients who underwent BS between 1/05/2020 and 31/10/2020. Patients were divided into two groups - patients >= 65-years-old (Group I) and patients < 65-years-old (Group II). The two groups were compared for 30-day morbidity and mortality.Results There were 149 patients in Group 1 and 6923 patients in Group II. The mean age, preoperative weight, and BMI were 67.6 +/- 2.5 years, 119.5 +/- 24.5 kg, and 43 +/- 7 in Group I and 39.8 +/- 11.3 years, 117.7 +/- 20.4 kg, and 43.7 +/- 7 in Group II, respectively. Approximately, 95% of patients in Group 1 had at least one co-morbidity compared to 68% of patients in Group 2 (p = < 0.001). The 30-day morbidity was significantly higher in Group I ( 11.4%) compared to Group II (6.6%) (p = 0.022). However, the 30-day mortality and COVID-19 infection rates were not significantly different between the two groups.Conclusions Bariatric surgery during the COVID-19 pandemic is associated with a higher complication rate in those >= 65 years of age compared to those < 65 years old. However, the mortality and postoperative COVID-19 infection rates are not significantly different between the two groups

30-Day morbidity and mortality of bariatric metabolic surgery in adolescence during the COVID-19 pandemic – The GENEVA study

Background: Metabolic and bariatric surgery (MBS) is an effective treatment for adolescents with severe obesity. Objectives: This study examined the safety of MBS in adolescents during the coronavirus disease 2019 (COVID-19) pandemic. Methods: This was a global, multicentre and observational cohort study of MBS performed between May 01, 2020, and October 10,2020, in 68 centres from 24 countries. Data collection included in-hospital and 30-day COVID-19 and surgery-specific morbidity/mortality. Results: One hundred and seventy adolescent patients (mean age: 17.75 ± 1.30 years), mostly females (n = 122, 71.8%), underwent MBS during the study period. The mean pre-operative weight and body mass index were 122.16 ± 15.92 kg and 43.7 ± 7.11 kg/m2, respectively. Although majority of patients had pre-operative testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (n = 146; 85.9%), only 42.4% (n = 72) of the patients were asked to self-isolate pre-operatively. Two patients developed symptomatic SARS-CoV-2 infection post-operatively (1.2%). The overall complication rate was 5.3% (n = 9). There was no mortality in this cohort. Conclusions: MBS in adolescents with obesity is safe during the COVID-19 pandemic when performed within the context of local precautionary procedures (such as pre-operative testing). The 30-day morbidity rates were similar to those reported pre-pandemic. These data will help facilitate the safe re-introduction of MBS services for this group of patients