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Motivations: Gene regulatory networks (GRNs) are traditionally inferred from gene expression profiles monitoring a specific condition or treatment. In the last decade, integrative strategies have successfully emerged to guide GRN inference from gene expression with complementary prior data. However, datasets used as prior information and validation gold standards are often related and limited to a subset of genes. This lack of complete and independent evaluation calls for new criteria to robustly estimate the optimal intensity of prior data integration in the inference process., Results: We address this issue for two regression-based GRN inference models, a weighted random forest (weigthedRF) and a generalized linear model estimated under a weighted LASSO penalty with stability selection (weightedLASSO). These approaches are applied to data from the root response to nitrate induction in Arabidopsis thaliana. For each gene, we measure how the integration of transcription factor binding motifs influences model prediction. We propose a new approach, DIOgene, that uses model prediction error and a simulated null hypothesis in order to optimize data integration strength in a hypothesis-driven, gene-specific manner. This integration scheme reveals a strong diversity of optimal integration intensities between genes, and offers good performance in minimizing prediction error as well as retrieving experimental interactions. Experimental results show that DIOgene compares favorably against state-of-the-art approaches and allows to recover master regulators of nitrate induction., Availability and Implementation: The R code and notebooks demonstrating the use of the proposed approaches are available in the repository https://github.com/OceaneCsn/integrative_GRN_N_induction., (© The Author(s) 2024. Published by Oxford University Press.)

The action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Objectives: Intraoperative conversion from video-assisted thoracic surgery (VATS) to thoracotomy may occur during anatomical lung resection. The objectives of the present study were to identify risk factors for intraoperative conversion and to develop a predictive score., Methods: We performed a multicentre retrospective analysis of French thoracic surgery departments that contributed data on anatomical lung resections to the Epithor database over a 10-year period (from January-2010 to December-2019). Using univariate and multivariate logistic regression analyses, we determined risk factors for intraoperative conversion and elaborated the Epithor conversion score (ECS). The ECS was then validated in a cohort of patients operated on between January- and June-2020., Results: From January-2010 to December-2019, 210,037 patients had been registered in the Epithor database. Of these, 55,030 had undergone anatomical lung resection. We excluded patients who had upfront a thoracotomy or robotic-assisted thoracoscopic surgery (n = 40,293) and those with missing data (6,794). Hence, 7943 patients with intent-to-treat VATS were assessed: 7100 with a full VATS procedure and 843 patients with intraoperative conversion to thoracotomy (conversion rate: 10.6%). Thirteen potential risk factors were identified among patients' preoperative characteristics and planned surgical procedures and were weighted accordingly to give the ECS. The score showed acceptable discriminatory power (area under the curve: 0.62 in the development cohort and 0.64 in the validation cohort) and good calibration (P = 0.23 in the development cohort and 0.30 in the validation cohort)., Conclusions: Thirteen potential preoperative risk factors were identified, enabling us to develop and validate the ECS-an easy-to-use, reproducible tool for estimating the risk of intraoperative conversion during VATS., (© The Author(s) 2022. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.)

Objectives: The carotid approach for transcatheter aortic valve replacement (TAVR) has been shown to be feasible and safe. The goal of this study was to compare the 30-day outcomes of trans-carotid (TC) and transfemoral (TF) TAVR., Methods: This retrospective study enrolled 500 consecutive patients treated by TC-TAVR (n = 100) or TF-TAVR (n = 400) with percutaneous closure between January 2018 and January 2020 at the Nantes University Hospital. The primary end-point was the occurrence of cardiovascular death and cerebrovascular events at 30 days., Results: The mean age was 79.9 ± 8.1 in the TC group and 81.3 ± 6.9 (P = 0.069) in the TF group. The TC group had more men (69% vs 50.5%; P = 0.001) and more patients with peripheral vascular disease (86% vs 14.8%; P < 0.0001). Cardiac characteristics were similar between the groups, and the EuroSCORE II was 3.8 ± 2.6% vs 4.6 ± 6.0%, respectively (P = 0.443). The 30-day mortality was 2% in the TC group versus 1% in the TF group (P = 0.345). TC-TAVR was not associated with an increased risk of stroke (2% vs 2.5%; P = 0.999) or major vascular complications (2% vs 4%; P = 0.548). More permanent pacemakers were implanted in the TF group (14.9% vs 5.6%; P = 0.015), and no moderate or severe aortic regurgitation was observed in the TC group (0 vs 3.3%; P = 0.08). TC-TAVR was not associated with an increased risk of mortality or stroke at 30 days (odds ratio 1.32; 95% confidence interval 0.42-4.21; P = 0.63) in the multivariable analysis., Conclusions: No statistically significant differences between TC-TAVR and TF-TAVR were observed; therefore, TC-TAVR should be the first alternative in patients with anatomical contraindications to the femoral route., (© The Author(s) 2021. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.)

The ubiquitous family of dimeric transcription factors AP-1 is made up of Fos and Jun family proteins. It has long been thought to operate principally at gene promoters and how it controls transcription is still ill-understood. The Fos family protein Fra-1 is overexpressed in triple negative breast cancers (TNBCs) where it contributes to tumor aggressiveness. To address its transcriptional actions in TNBCs, we combined transcriptomics, ChIP-seqs, machine learning and NG Capture-C. Additionally, we studied its Fos family kin Fra-2 also expressed in TNBCs, albeit much less. Consistently with their pleiotropic effects, Fra-1 and Fra-2 up- and downregulate individually, together or redundantly many genes associated with a wide range of biological processes. Target gene regulation is principally due to binding of Fra-1 and Fra-2 at regulatory elements located distantly from cognate promoters where Fra-1 modulates the recruitment of the transcriptional co-regulator p300/CBP and where differences in AP-1 variant motif recognition can underlie preferential Fra-1- or Fra-2 bindings. Our work also shows no major role for Fra-1 in chromatin architecture control at target gene loci, but suggests collaboration between Fra-1-bound and -unbound enhancers within chromatin hubs sometimes including promoters for other Fra-1-regulated genes. Our work impacts our view of AP-1., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Context: Hypoglycemia is a major barrier to optimal glycemic control in insulin-treated diabetes. Recent guidelines from the American Diabetes Association have subcategorized "non-severe" hypoglycemia into level 1 (<3.9 mmol/L) and 2 (<3 mmol/L) hypoglycemia. Gastric emptying of carbohydrate is a major determinant of postprandial glycemia but its role in hypoglycemia counter-regulation remains underappreciated. "Marked" hypoglycemia (~2.6 mmol/L) accelerates gastric emptying and increases carbohydrate absorption in health and type 1 diabetes, but the impact of "mild" hypoglycemia (3.0-3.9 mmol/L) is unknown., Objective: To determine the effects of 2 levels of hypoglycemia, 2.6 mmol/L ("marked") and 3.6 mmol/L ("mild"), on gastric emptying in health., Design, Setting, and Subjects: Fourteen healthy male participants (mean age: 32.9 ± 8.3 years; body mass index: 24.5 ± 3.4 kg/m2) from the general community underwent measurement of gastric emptying of a radiolabeled solid meal (100 g beef) by scintigraphy over 120 minutes on 3 separate occasions, while blood glucose was maintained at either ~2.6 mmol/L, ~3.6 mmol/L, or ~6 mmol/L in random order from 15 minutes before until 60 minutes after meal ingestion using glucose-insulin clamp. Blood glucose was then maintained at 6 mmol/L from 60 to 120 minutes on all days., Results: Gastric emptying was accelerated during both mild (P = 0.011) and marked (P = 0.001) hypoglycemia when compared to euglycemia, and was more rapid during marked compared with mild hypoglycemia (P = 0.008). Hypoglycemia-induced gastric emptying acceleration during mild (r = 0.57, P = 0.030) and marked (r = 0.76, P = 0.0014) hypoglycemia was related to gastric emptying during euglycemia., Conclusion: In health, acceleration of gastric emptying by insulin-induced hypoglycemia is dependent on the degree of hypoglycemia and baseline rate of emptying., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Endocrine Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Objectives: At our centre, the SynCardia temporary Total Artificial Heart (TAH-t) (SynCardia Systems, LLC, Tucson, AZ, USA) is used to provide long-term support for patients with biventricular failure as a bridge to a transplant. However, a heart transplant (HT) after such support remains challenging. The aim of this retrospective study was to assess the immediate and long-term results following an HT in the cohort of patients who had a TAH-t implant., Methods: A total of 73 patients were implanted with the TAH-t between 1988 and 2019 in our centre. Of these 73 consecutive patients, 50 (68%) received an HT and are included in this retrospective analysis of prospectively collected data., Results: In the selected cohort, in-hospital mortality after an HT was 10% (n = 5). The median intensive care unit stay was 33 days (range 5-278). The median hospital stay was 41 days (range 28-650). A partial or total pericardiectomy was performed during the HT procedure in 21 patients (42%) due to a severe pericardial reaction. Long-term survival rates after an HT at 5, 10 and 12 years were 79.1 ± 5.9% (n = 32), 76.5 ± 6.3% (n = 22) and 72.4 ± 7.1% (n = 12), respectively, which was similar to the long-term survival for a primary HT without TAH-t during the same period (n = 686). An HT performed within 3-6 months post-TAH-t implantation appeared to provide the best survival (P = 0.007). Eight (16%) patients required chronic dialysis during the subsequent follow-up period, with 3 patients requiring a kidney transplant., Conclusions: The long-term outcomes with the SynCardia TAH-t as a bridge to transplant in patients with severe biventricular failure are very encouraging. Our review noted that an HT following TAH-t can be technically challenging, especially in the case of a severe pericardial reaction, with potential pitfalls that should be recognized preoperatively., (© The Author(s) 2020. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.)

Objectives: Our goal was to study the immediate outcome after an emergency frozen elephant trunk procedure with a Thoraflex™ Hybrid prosthesis (THP) in patients included in the EPI-Flex national registry and operated on in 21 French centres., Methods: All patients operated on in France between April 2016 and April 2019 for acute aortic syndromes and who had an frozen elephant trunk procedure with a THP were included in the study. The main end point was in-hospital mortality. The secondary end point was neuromorbidity, including paraplegia. The evolution of the main end point was monitored using a variable life-adjusted display graph with cumulative sum derivatives in order to stop inclusions in case the observed mortality became out of range compared to an expected mortality between 15% and 20%., Results: Enrolment ended on the scheduled date and included 109 patients. Most cases (54%) were performed at 3 centres, where more than 10 THP each were implanted (10-26). The observed mortality in the large-volume centres (22%) was comparable to that observed in the low-volume centres (20%). The individually risk-adjusted cumulative sum revealed that observed in-hospital mortality was statistically in line with that predicted by the log EuroSCORE. Analysis of the secondary end point revealed 8% cases of paraplegia, all of which appeared after treatment of the thoracic type A aortic dissection., Conclusions: In France, THP for emergency frozen elephant trunk surgery outside high-volume centres did not result in excessive in-hospital deaths. However, a word of caution must be expressed regarding the prevention of medullar ischaemia even in emergency aortic surgery., (© The Author(s) 2020. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.)

Objectives: Postcardiotomy cardiogenic shock (PCCS) is associated with high mortality rates of 50-80%. Although veno-arterial extracorporeal membrane oxygenation has been used as mechanical circulatory support in patients with PCCS, it is associated with a high rate of complications and poor quality of life. The Impella 5.0 and Impella Left Direct (LD) (Impella 5.0/LD) are minimally invasive left ventricular assist devices that provide effective haemodynamic support resulting in left ventricular unloading and systemic perfusion. Our goal was to describe the outcome of patients with PCCS supported with the Impella 5.0/LD at La Pitié-Salpêtrière Hospital., Methods: We retrospectively reviewed consecutive patients supported with the Impella 5.0/LD for PCCS between December 2010 and June 2015. Survival outcome and in-hospital complications were assessed., Results: A total of 29 patients (63 ± 14 years, 17% women) with PCCS were supported with the Impella 5.0/LD. At baseline, 69% experienced chronic heart failure, 66% had dilated cardiomyopathy and 57% had valvular disease. The mean EuroSCORE II was 22 ± 17 and the ejection fraction was 28 ± 11%. Most of the patients underwent isolated valve surgery (45%) or isolated coronary artery bypass grafting (38%). The mean duration of Impella support was 9 ± 7 days. Weaning from the Impella was successful in 72.4%, and 58.6% survived to discharge. Recovery of native heart function was observed in 100% of discharged patients. Survival to 30 days and to 1 year from Impella implant was 58.6% and 51.7%, respectively., Conclusions: The Impella 5.0 and the Impella LD represent an excellent treatment option for critically ill patients with PCCS and are associated with favourable survival outcome and native heart recovery., (© The Author(s) 2019. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.)

The FANTOM5 consortium recently characterized 65,423 human enhancers from 1829 cell and tissue samples using the Cap Analysis of Gene Expression technology. We showed that the guanine and cytosine content at enhancer regions distinguishes two classes of enhancers harboring distinct DNA structural properties at flanking regions. A functional analysis of their predicted gene targets highlighted one class of enhancers as significantly enriched for associations with immune response genes. Moreover, these enhancers were specifically enriched for regulatory motifs recognized by transcription factors involved in immune response. We observed that enhancers enriched for links to immune response genes were more cell-type specific, preferentially activated upon bacterial infection, and with specific response activity. Looking at chromatin capture data, we found that the two classes of enhancers were lying in distinct topologically associating domains and chromatin loops. Our results suggest that specific nucleotide compositions encode for classes of enhancers that are functionally distinct and specifically organized in the human genome., (Copyright © 2018 by the Genetics Society of America.)

Objectives: To describe the management of thoracic reconstructions in the presence of primary chest-wall infection (PCWI) or secondary deep chest-wall infection (SCWI), focussing on local tolerance of a titanium rib osteosynthesis system., Methods: PCWI included infected chest wall tumours (CWT), infected T3 non-small-cell lung carcinoma (NSCLC) and open flail chest. SCWI was defined by deep infection of previous thoracic-wall reconstructions. Infection was identified by preoperative bacterial analysis of the tumour or surgical site. In PCWI, a one-step procedure combined extensive resection of infected tissues and rigid reconstruction of the defect; skeletal rigidity was achieved using titanium implants. In SCWI, we removed all synthetic material except titanium implants. In both groups, the surgical field was thoroughly cleaned and implants were wrapped or covered by flaps., Results: From January 2005 to December 2011, 11 patients (54 ± 10.2 years) with either PCWI (3 CWT, 3 T3 NSCLC, 1 open flail chest) or SCWI (3 CWT, 1 funnel chest) were treated. Infection was polymicrobial in all but 1 case. Bacteria observed in PCWI patients were multidrug resistant. In PCWI, we resected 4.2 ± 0.6 ribs en bloc with the lung (n = 5), the skin and the pectoralis major and then used mesh and 2.1 ± 1.2 titanium implants for reconstruction (n = 6). The mean defect was 1154.4 ± 318 cm(3). Surgical SCWI management removed polytetrafluoroethylene-mesh and preserved the titanium implants. A Vicryl mesh (n = 3) and greater omentum flap (n = 3) were added. One of the 2 postoperative deaths in the PCWI group was related to infection recurrence. No other patient had infection at the 6-month follow-up with leucocyte-labelled scintigraphy., Conclusion: Titanium rib osteosynthesis is reliable in two complex and life-threatening situations: PCWIs and SCWIs. In combination with a flap, this allows rapid, reliable, rigid reconstruction of infected full-thickness chest-wall defects in a single-step procedure.

Objectives: Evaluation of the feasibility, safety and oncological validity of video-assisted thoracic lobectomy (VATS). The VATS study exclusion criteria included T3 or T4 tumours, central hilar tumours, tumours visible on bronchoscopy requiring sleeve resection, hilar lymphadenopathy, N2 disease, history of neoadjuvant chemotherapy or radiation, previous thoracic surgery or pleurodesis., Methods: A retrospective study of 410 patients (143 women, mean age 61.5 ± 13.1 years (84-15) treated by VATS lobectomy between 1996 and 2011 was performed at our institution. VATS lobectomy was performed for lung cancer (n = 364, 88.9%), pulmonary metastasis (n = 25, 5.8%) and non-neoplastic diseases (n = 21, 5.1%). In lung cancer, a systematic radical lymph node dissection was performed., Results: There was no intraoperative death. The conversion rate was 6.1% (n = 25): bleeding (n = 4), extended pleural adhesion (n = 6, 1.4%), technical difficulty (n = 6, 1.4%), tumour extension to the fissure or mediastinum or adenopathy (n = 7, 1.7%) and intolerance to one-lung ventilation (n = 2, 0.4%). The postoperative mortality rate was 1.2% (n = 5). Major complications occurred in 21 patients (5.1%). The mean number of mediastinal nodes removed was 14.6 (5-44) and 42 patients (10.2%) presented N2 disease at the definitive staging. The mean operating time was 152 (85-315) min. The mean drainage duration was 3.2 days (1-15). Mean postoperative length of hospital stay before return at home was 6.8 days (3-75) and 5.5 days in patients without major complications. There was no port site recurrence. Kaplan-Meier 3-year survival rates were 76.5% for Stage I and 87.3% for Stage IA, 58% for Stage II and 61% for Stage III., Conclusions: VATS lobectomy is an acceptable alternative and seems equivalent to open lobectomy in terms of complications and oncological value. Our experience prompts us to consider VATS lobectomy for early stage NSCLC as the first surgical approach in view of the improvement in outcome, provided that the procedure is performed by a surgeon with adequate experience with this approach.

Objectives: The reconstruction of large full thickness chest wall defect after resection of T3/T4 non-small cell lung cancer (NSCLC) or primary chest wall tumours presents a technical challenge for thoracic surgeons and is a critical factor in determining post-operative outcome. When the defect is large, complications are common with a 27% mean rate of respiratory morbidity., Methods: Since 2006, 31 patients underwent reconstruction for wide chest wall defects using titanium implants and strong mesh. The reconstruction was achieved using a layer of polytetrafluoroethylene or a XCM biologic tissue mesh shaped to match the defect and sutured under maximum tension to re-establish the skeletal continuity. The mesh was placed close to the lung and was fixed onto the bony framework and onto the titanium plate. In one case, we used XCM biologic tissue because of a large infected T3 NSCLC. A horizontal titanium rib osteosynthesis system was used to reestablish the rigidity of the thoracic wall by bridging the defect except for one case in which we use a vertical rib osteosynthesis system., Results: Twenty-six patients underwent a complete R0 resection with the removal of a mean of 4.67 ± 1.5 [3-9] ribs, including the sternum in 14 cases. The mean defect area was 198 ± 91.2 [95-400] cm&sup2;. Reconstruction required a mean of 2.06 ± 1.1 [1-4] titanium plates. There were two cases of deep wound infection that required surgical removal of the osteosynthesis system in one patient. Only one patient developed a major complication in the form of respiratory failure. There were two postoperative deaths neither of which was directly related to the surgical procedure., Conclusions: Our experience and initial results show that titanium rib osteosynthesis in combination with strong biologic or synthetic mesh can easily and safely be used in a one-stage procedure for the reconstruction of major chest wall defects.

Cellular micro(mi)RNAs are able to recognize viral RNAs through imperfect micro-homologies. Similar to the miRNA-mediated repression of cellular translation, this recognition is thought to tether the RNAi machinery, in particular Argonaute 2 (AGO2) on viral messengers and eventually to modulate virus replication. Here, we unveil another pathway by which AGO2 can interact with retroviral mRNAs. We show that AGO2 interacts with the retroviral Group Specific Antigen (GAG) core proteins and preferentially binds unspliced RNAs through the RNA packaging sequences without affecting RNA stability or eliciting translation repression. Using RNAi experiments, we provide evidences that these interactions, observed with both the human immunodeficiency virus 1 (HIV-1) and the primate foamy virus 1 (PFV-1), are required for retroviral replication. Taken together, our results place AGO2 at the core of the retroviral life cycle and reveal original AGO2 functions that are not related to miRNAs and translation repression.

We report a case of reconstruction of a large full-thickness posterolateral defect of the chest wall after resection of a stage III non-small cell lung carcinoma (NSCLC) using the combination of a vertical expandable prosthetic titanium device and a polytetrafluoroethylene (PTFE) mesh. A 40-year-old female presented with a NSCLC classified as type IIIA and required both neoadjuvant radiotherapy and chemotherapy. An en bloc resection including the left upper lobe, posterolateral segments of five ribs (K3-K7) and vertebral bodies (T3-T6) was performed through a posterior J-shaped approach. A vertical rib osteosynthesis system was used to ensure thoracic wall stability and mechanical organ protection, prevent ventilatory impairment, avoid incarceration of the tip of the scapula, and maintain an acceptable cosmetic aspect. The device was locked onto the middle arch of the second and eighth ribs. We hung the PTFE mesh from the titanium bars with multiple non-absorbable sutures under maximal tension. Final pathological classification was T4N0M0 with an R0 final resection status. After an uneventful course, the patient was discharged on postoperative day 10. This first experience indicates that vertical rib osteosynthesis combined with a PTFE mesh can be used safely and easily in a one-stage procedure for major posterior chest wall defects.

In plants, small interfering RNAs (siRNAs) and microRNAs (miRNAs) are effectors of RNA silencing, a process involved in defense through RNA interference (RNAi) and in development. Plant viruses are natural targets of RNA silencing, and as a counterdefensive strategy, they have evolved highly diverse silencing suppressor proteins. Although viral suppressors are usually thought to act at distinct steps of the silencing machinery, there had been no consensus system so far that allowed a strict side-by-side analysis of those factors. We have set up such a system in Arabidopsis thaliana and used it to compare the effects of five unrelated viral silencing suppressors on the siRNA and miRNA pathways. Although all the suppressors inhibited RNAi, only three of them induced developmental defects, indicating that the two pathways are only partially overlapping. These developmental defects were remarkably similar, and their penetrance correlated with inhibition of miRNA-guided cleavage of endogenous transcripts and not with altered miRNA accumulation per se. Among the suppressors investigated, the tombusviral P19 protein coimmunoprecipitated with siRNA duplexes and miRNA duplexes corresponding to the primary cleavage products of miRNA precursors. Thus, it is likely that P19 prevents RNA silencing by sequestering both classes of small RNAs. Moreover, the finding here that P19 binds siRNAs and suppresses RNAi in Hela cells also suggests that this factor may be useful to dissect the RNA silencing pathways in animals. Finally, the differential effects of the silencing suppressors tested here upon other types of Arabidopsis silencing-related small RNAs revealed a surprising variety of biosynthetic and, presumably, functional pathways for those molecules. Therefore, silencing suppressors are valuable probes of the complexity of RNA silencing.