Genomic and Transcriptomic Analysis of a Patient with Early-Onset Colorectal Cancer and Therapy-Induced Focal Nodular Hyperplasia: A Case Report.

Early-onset colorectal cancer (EOCRC), defined as colorectal cancer in individuals under 50 years of age, has shown an alarming increase in incidence worldwide. We report a case of a twenty-four-year-old female with a strong family history of colorectal cancer (CRC) but without an identified underlying genetic predisposition syndrome. Two years after primary surgery and adjuvant chemotherapy, the patient developed new liver lesions. Extensive diagnostic imaging was conducted to investigate suspected liver metastases, ultimately leading to a diagnosis of focal nodular hyperplasia. The young age of the patient has prompted comprehensive genomic and transcriptomic profiling in order to identify potential oncogenic drivers and inform further clinical management of the patient. Besides a number of oncogenic mutations identified in the patient's tumour sample, including KRAS G12D, TP53 R248W and TTN L28470V, we have also identified a homozygous deletion of 24.5 MB on chromosome 8. A multivariate Cox regression analysis of this patient's mutation profile conferred a favourable prognosis when compared with the TCGA COADREAD database. Notably, the identified deletion on chromosome 8 includes the WRN gene, which could contribute to the patient's overall positive response to chemotherapy. The complex clinical presentation, including the need for emergency surgery, early age at diagnosis, strong family history, and unexpected findings on surveillance imaging, necessitated a multidisciplinary approach involving medical, radiation, and surgical oncologists, along with psychological support and reproductive medicine specialists. Molecular profiling of the tumour strongly indicates that patients with complex mutational profile and rare genomic rearrangements require a prolonged surveillance and personalised informed interventions.

Pseudomonas aeruginosa Isolates from Water Samples of the Gulf of Mexico Show Similar Virulence Properties but Different Antibiotic Susceptibility Profiles than Clinical Isolates.

Pseudomonas aeruginosa is an opportunistic pathogen found in a wide variety of environments, including soil, water, and habitats associated with animals, humans, and plants. From a One Health perspective, which recognizes the interconnectedness of human, animal, and environmental health, it is important to study the virulence characteristics and antibiotic susceptibility of environmental bacteria. In this study, we compared the virulence properties and the antibiotic resistance profiles of seven isolates collected from the Gulf of Mexico with those of seven clinical strains of P. aeruginosa. Our results indicate that the marine and clinical isolates tested exhibit similar virulence properties; they expressed different virulence factors and were able to kill Galleria mellonella larvae, an animal model commonly used to analyze the pathogenicity of many bacteria, including P. aeruginosa. In contrast, the clinical strains showed higher antibiotic resistance than the marine isolates. Consistently, the clinical strains exhibited a higher prevalence of class 1 integron, an indicator of anthropogenic impact, compared with the marine isolates. Thus, our results indicate that the P. aeruginosa marine strains analyzed in this study, isolated from the Gulf of Mexico, have similar virulence properties, but lower antibiotic resistance, than those from hospitals.

Small Gene Networks Delineate Immune Cell States and Characterize Immunotherapy Response in Melanoma.

Single-cell technologies have elucidated mechanisms responsible for immune checkpoint inhibitor (ICI) response, but are not amenable to a clinical diagnostic setting. In contrast, bulk RNA sequencing (RNA-seq) is now routine for research and clinical applications. Our workflow uses transcription factor (TF)-directed coexpression networks (regulons) inferred from single-cell RNA-seq data to deconvolute immune functional states from bulk RNA-seq data. Regulons preserve the phenotypic variation in CD45+ immune cells from metastatic melanoma samples (n = 19, discovery dataset) treated with ICIs, despite reducing dimensionality by >100-fold. Four cell states, termed exhausted T cells, monocyte lineage cells, memory T cells, and B cells were associated with therapy response, and were characterized by differentially active and cell state-specific regulons. Clustering of bulk RNA-seq melanoma samples from four independent studies (n = 209, validation dataset) according to regulon-inferred scores identified four groups with significantly different response outcomes (P < 0.001). An intercellular link was established between exhausted T cells and monocyte lineage cells, whereby their cell numbers were correlated, and exhausted T cells predicted prognosis as a function of monocyte lineage cell number. The ligand-receptor expression analysis suggested that monocyte lineage cells drive exhausted T cells into terminal exhaustion through programs that regulate antigen presentation, chronic inflammation, and negative costimulation. Together, our results demonstrate how regulon-based characterization of cell states provide robust and functionally informative markers that can deconvolve bulk RNA-seq data to identify ICI responders.

Interactome dynamics of RAF1-BRAF kinase monomers and dimers.

RAF kinases play major roles in cancer. BRAFV600E mutants drive ~6% of human cancers. Potent kinase inhibitors exist but show variable effects in different cancer types, sometimes even inducing paradoxical RAF kinase activation. Both paradoxical activation and drug resistance are frequently due to enhanced dimerization between RAF1 and BRAF, which maintains or restores the activity of the downstream MEK-ERK pathway. Here, using quantitative proteomics we mapped the interactomes of RAF1 monomers, RAF1-BRAF and RAF1-BRAFV600E dimers identifying and quantifying >1,000 proteins. In addition, we examined the effects of vemurafenib and sorafenib, two different types of clinically used RAF inhibitors. Using regression analysis to compare different conditions we found a large overlapping core interactome but also distinct condition specific differences. Given that RAF proteins have kinase independent functions such dynamic interactome changes could contribute to their functional diversification. Analysing this dataset may provide a deeper understanding of RAF signalling and mechanisms of resistance to RAF inhibitors.

Interpretation of a deep analysis of speech imagery features extracted by a capsule neural network.

Speech imagery has been successfully employed in developing Brain-Computer Interfaces because it is a novel mental strategy that generates brain activity more intuitively than evoked potentials or motor imagery. There are many methods to analyze speech imagery signals, but those based on deep neural networks achieve the best results. However, more research is necessary to understand the properties and features that describe imagined phonemes and words. In this paper, we analyze the statistical properties of speech imagery EEG signals from the KaraOne dataset to design a method that classifies imagined phonemes and words. With this analysis, we propose a Capsule Neural Network that categorizes speech imagery patterns into bilabial, nasal, consonant-vocal, and vowels/iy/ and/uw/. The method is called Capsules for Speech Imagery Analysis (CapsK-SI). The input of CapsK-SI is a set of statistical features of EEG speech imagery signals. The architecture of the Capsule Neural Network is composed of a convolution layer, a primary capsule layer, and a class capsule layer. The average accuracy reached is 90.88%±7 for bilabial, 90.15%±8 for nasal, 94.02%±6 for consonant-vowel, 89.70%±8 for word-phoneme, 94.33%± for/iy/ vowel and, 94.21%±3 for/uw/ vowel detection. Finally, with the activity vectors of the CapsK-SI capsules, we generated brain maps to represent brain activity in the production of bilabial, nasal, and consonant-vocal signals.

B-cell and complement signature in severe hidradenitis suppurativa that does not respond to adalimumab.

BACKGROUND: Hidradenitis suppurativa (HS) is a chronic inflammatory skin disorder with significant morbidity. The pathogenesis remains incompletely understood although immune dysregulation plays an important role. It is challenging to treat and approximately 50% of patients respond clinically to adalimumab, the only licensed treatment. OBJECTIVES: To examine differences between lesional and nonlesional HS skin at baseline using bulk RNA sequencing, and to compare the transcriptome in the skin before and after 12 weeks of treatment with adalimumab. To examine transcriptomic differences between adalimumab responders and nonresponders using Hidradenitis Suppurativa Clinical Response and the International Hidradenitis Suppurativa Severity Score System (IHS4); and to compare transcriptomic differences based on disease severity (Hurley stage and IHS4). METHODS: We completed bulk RNA sequencing on lesional and nonlesional skin samples of patients before and after 12 weeks of treatment with adalimumab. RESULTS: Baseline differentially expressed genes and pathways between lesional and nonlesional skin highlighted chemokines and antimicrobial peptides produced by keratinocytes; B-cell function; T-cell-receptor, interleukin-17 and nuclear factor-κB signalling; and T-helper-cell differentiation. Transcriptomic differences were identified in lesional skin at baseline, between subsequent responders and nonresponders. Patients with severe HS who did not respond to adalimumab had enriched complement and B-cell activation pathways at baseline. In addition, logistic regression identified CCL28 in baseline lesional HS skin as a potential biomarker of treatment response. CONCLUSIONS: This highlights the potential for targeting B-cell and complement pathways in HS treatment and the potential of stratifying patients at baseline to the most suitable treatment based on the skin transcriptome. CCL28 has not previously been identified in HS skin and has potential clinical relevance due to its antimicrobial function and homing of B and T cells at epithelial surfaces. Our results provide data to inform future translational and clinical studies on therapeutics in HS.

Unraveling the regulation of pyocyanin synthesis by RsmA through MvaU and RpoS in Pseudomonas aeruginosa ID4365.

Pyocyanin is a phenazine with redox activity produced by Pseudomonas aeruginosa that is harmful to other bacteria and eukaryotic organisms by generating reactive oxygen species. Gene regulation of pyocyanin synthesis has been addressed in the PAO1 and PA14 strains and involves the three-quorum sensing systems Las, Rhl, and Pqs; the regulators RsaL, MvaU, and RpoS, and the posttranscriptional Rsm system, among others. Here, we determined how RsmA regulates pyocyanin synthesis in P. aeruginosa ID4365, an overproducer strain. We found that, in the protease peptone glucose ammonium salts medium, rsmA inactivation increases pyocyanin production compared with the wild-type strains ID4365, PAO, and PA14. We showed that RsmA regulates inversely the expression of both phz operons involved in pyocyanin synthesis; particularly the phz2 operon is positively regulated at the transcriptional level indirectly through MvaU. In addition, we found that the phz1 operon contributes mainly to pyocyanin synthesis and that RsmA negatively regulates phzM and phzS expression. Finally, we showed that translation of the sigma factor RpoS is positively regulated by RsmA, and the expression of rpoS under an independent promoter decreases pyocyanin production in the IDrsmA strain. These results indicate that RsmA regulates not only the genes for pyocyanin production but also their regulators.

KBoost: a new method to infer gene regulatory networks from gene expression data.

Reconstructing gene regulatory networks is crucial to understand biological processes and holds potential for developing personalized treatment. Yet, it is still an open problem as state-of-the-art algorithms are often not able to process large amounts of data within reasonable time. Furthermore, many of the existing methods predict numerous false positives and have limited capabilities to integrate other sources of information, such as previously known interactions. Here we introduce KBoost, an algorithm that uses kernel PCA regression, boosting and Bayesian model averaging for fast and accurate reconstruction of gene regulatory networks. We have benchmarked KBoost against other high performing algorithms using three different datasets. The results show that our method compares favorably to other methods across datasets. We have also applied KBoost to a large cohort of close to 2000 breast cancer patients and 24,000 genes in less than 2 h on standard hardware. Our results show that molecularly defined breast cancer subtypes also feature differences in their GRNs. An implementation of KBoost in the form of an R package is available at: https://github.com/Luisiglm/KBoost and as a Bioconductor software package.

Infections after spine instrumentation: effectiveness of short antibiotic treatment in a large multicentre cohort.

BACKGROUND AND OBJECTIVES: Available information about infection after spine instrumentation (IASI) and its management are scarce. We aimed to analyse DAIR (debridement, antibiotics and implant retention) prognosis and evaluate effectiveness of short antibiotic courses on early forms. METHODS: Multicentre retrospective study of patients with IASI managed surgically (January 2010-December 2016). Risk factors for failure were analysed by multivariate Cox regression and differences between short and long antibiotic treatment were evaluated with a propensity score-matched analysis. RESULTS: Of the 411 IASI cases, 300 (73%) presented in the first month after surgery, 48 in the second month, 22 in the third and 41 thereafter. Infections within the first 2 months (early cases) occurred mainly to older patients, with local inflammatory signs and predominance of Enterobacteriaceae, unlike those in the later periods. When managed with DAIR, prognosis of early cases was better than later ones (failure rate 10.4% versus 26.1%, respectively; P = 0.02). Risk factors for DAIR failure in early cases were female sex, Charlson Score, large fusions (>6 levels) and polymicrobial infections (adjusted HRs of 2.4, 1.3, 2.6 and 2.26, respectively). Propensity score matching proved shorter courses of antibiotics (4-6 weeks) as effective as longer courses (failure rates 11.4% and 10.5%, respectively; P = 0.870). CONCLUSIONS: IASIs within the first 2 months could be managed effectively with DAIR and shorter antibiotic courses. Clinicians should be cautious when faced with patients with comorbidities, large fusions and/or polymicrobial infections.

Sickness Presenteeism in the Aftermath of COVID-19: Is Presenteeism Remote-Work Behavior the New (Ab)normal?

Due to the confinement imposed by the COVID-19 pandemic situation, companies adopted remote work more than ever. The rapid rise of remote work also affected local life and many employers introduced or extended their telework activities because of the associated advantages. However, despite the evident positive benefits, some employees were pressured to work remotely while ill. This evidence brought new challenges to the presenteeism literature. This article investigates how individual, economic/societal, and organizational/sectorial/supervisory-related variables can moderate the role of a contagious disease, such as the COVID-19, in explaining presenteeism behavior. Moreover, the current research presents a multi-level conceptual model (i.e., organizational, individual, supervisory factors) to describe how a new construct of remote-work presenteeism behavior mediates the relationship between different post pandemic health conditions (e.g., allergies, back pain, depression, anxiety) and future cumulative negative consequences. The authors suggested that the widespread pervasive adoption of remote work because of COVID-19 has important implications for the presenteeism literature and opens avenues for further research.

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D.

Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.

An Integrated Global Analysis of Compartmentalized HRAS Signaling.

Modern omics technologies allow us to obtain global information on different types of biological networks. However, integrating these different types of analyses into a coherent framework for a comprehensive biological interpretation remains challenging. Here, we present a conceptual framework that integrates protein interaction, phosphoproteomics, and transcriptomics data. Applying this method to analyze HRAS signaling from different subcellular compartments shows that spatially defined networks contribute specific functions to HRAS signaling. Changes in HRAS protein interactions at different sites lead to different kinase activation patterns that differentially regulate gene transcription. HRAS-mediated signaling is the strongest from the cell membrane, but it regulates the largest number of genes from the endoplasmic reticulum. The integrated networks provide a topologically and functionally resolved view of HRAS signaling. They reveal distinct HRAS functions including the control of cell migration from the endoplasmic reticulum and TP53-dependent cell survival when signaling from the Golgi apparatus.

Working conditions in hospitals revisited: A moderated-mediated model of job context and presenteeism.

This study examines whether the relationship between the employees' perceived job autonomy may be prone to the contextual influence of supervisor support and presenteeism climate in explaining the attendance behaviors of presenteeism-the employees' decision to attend work despite being ill or not feeling well. Does work context play a role on presenteeism climate and the specific act of presenteeism? This study includes 213 health care employees (e.g., nurses, doctors) working in one private hospital in Lebanon. We used the ordinary least squared (OLS) regressions path analytical framework and bootstrapping methods to estimate the hypothesized moderated-mediation models. Our findings indicate that healthcare job resources (job autonomy) is correlated with the presenteeism climate and the occurrence of presenteeism attendance behaviors. We also found that this relationship is mediated by presenteeism climate and that supervisor support moderates the observed indirect relationship. This study extends the organizational attendance research domain to presenteeism climate by explaining for both doctors and nurses how contextual variables explains the relationship between jobs resources and presenteeism attendance behaviors. Supervisor support plays an important role in encouraging task autonomy and thus allowing employees increase their perception of empowerment to manage their actions at work. Overall, healthcare managers should ensure that employees understand their roles and duties and have an up-to-date, clearly defined role (e.g., job description) so that they can meet their organizations' goals.

Factors associated to apical overfilling after a thermoplastic obturation technique - Calamus® or Guttacore®: a randomized clinical experiment.

The aims of this study were to analyze whether age, tooth type and sex are related to radiographically visible extrusion of filling material as an unintended outcome in teeth undergoing endodontic treatment with a thermoplastic obturation technique (Calamus® or GuttaCore®) and to determine whether the presence of such overfilling is associated to postoperative pain. We selected 120 teeth with diagnoses involving vital pulp and indication for endodontic treatment. Biomechanical preparation was performed using the Protaper Next® system with X2 or X3 master apical file. Teeth were randomly divided into 2 groups (n=60). Teeth in Group 1 were filled with the Guttacore® system and teeth in Group 2 were filled with single cone technique and Calamus® obturation system. Thermoplastic obturation techniques were found to cause overfilling in 53. 33% of the total cases (64 teeth) (56. 66% in Guttacore® group and 50% in the Calamus® group). Anterior teeth were found to be associated to presence of overfilling (p= 0. 024) (OR = 4. 35). Of the 120 teeth treated, 10 (8. 33%) presented postoperative pain and radiographically visible overfilling. The association between presence of extruded filling material and mild/moderate pain was statistically significant withp = 0. 002. To conclude, endodontic thermoplastic obturation with Guttacore® and Calamus® systems are significantly associated with the probability of filling material extrusion, and overfilling is associated to postoperative pain. Anterior teeth are 4 times more likely to be overfilled with the obturation techniques tested.

Los objetivos de esta investigación fueron: Analizar si factores como la edad, el tipo de diente y el género están asociados con la extrusión de material obturador radiográficamente visible como desenlace imprevisto en dientes sometidos a tratamiento endodóntico con una técnica de obturación termoplástica (Calamus® o GuttaCore®) y determinar si la presencia de esta sobreobturación está asociada con dolor posoperatorio. Se seleccionaron 120 dientes con diagnósticos que implicaban pulpa vital y con indicación de tratamiento de endodoncia. La preparación biomecánica se llevó a cabo con el sistema ProtaperNext® con lima apical principal X2 o X3. Los dientes se dividieron aleatoriamente de la siguiente forma (n=60): El grupo 1 se obturó con el sistema Guttacore® y el grupo 2 se obturó con una técnica de obturación de cono único y el sistema de obturación Calamus®. Se observó quelas técnicas de obturación termoplástica generaron sobreobturación en 53. 33% del total (64 dientes), 56. 66% se presentaron en el grupo de obturación con Guttacore® y 50% en el grupo de la técnica con el sistema Calamus®. Se encontró que los dientes anteriores presentaron asociación con la presencia de sobreobturación (p= 0. 024) (OR=4. 35). De los 120 dientes tratados, 10 (8. 33 %) presentaron dolor posoperatorio y sobreobturación radiográficamente visible. La asociación entre la presencia de extrusión de material de obturación y dolor leve-moderado fue estadísticamente significativa con un valorp= 0. 002. Como conclusión las técnicas de obturación termoplástica en endodoncia Guttacore® y el sistema Calamus® están asociadas significativamente con la probabilidad de extrusión de material obturador y dicha sobreobturación está asociada con dolor posoperatorio, los dientes anteriores presentan 4 veces más riesgo de sobreobturación con las técnicas de obturación utilizadas.

Factors associated to apical overfilling after a thermoplastic obturation technique - Calamus(R) or Guttacore(R): a randomized clinical experiment / Factores asociados con la presencia de sobreobturación apical posterior a una técnica de obturación termoplástica Calamus® o Guttacore®: experimento clínico aleatorizado

The aims of this study were to analyze whether age, tooth type and sex are related to radiographically visible extrusion of filling material as an unintended outcome in teeth undergoing endodontic treatment with a thermoplastic obturation technique (Calamus® or GuttaCore®) and to determine whether the presence of such overfilling is associated to postoperative pain. We selected 120 teeth with diagnoses involving vital pulp and indication for endodontic treatment. Biomechanical preparation was performed using the Protaper Next® system with X2 or X3 master apical file. Teeth were randomly divided into 2 groups (n=60). Teeth in Group 1 were filled with the Guttacore® system and teeth in Group 2 were filled with single cone technique and Calamus® obturation system. Thermoplastic obturation techniques were found to cause overfilling in 53.33% of the total cases (64 teeth) (56.66% in Guttacore® group and 50% in the Calamus® group). Anterior teeth were found to be associated to presence of overfilling (p= 0.024) (OR = 4.35). Of the 120 teeth treated, 10 (8.33%) presented postoperative pain and radiographically visible overfilling. The association between presence of extruded filling material and mild/moderate pain was statistically significant with p = 0.002. To conclude, endodontic thermoplastic obturation with Guttacore® and Calamus® systems are significantly associated with the probability of filling material extrusion, and overfilling is associated to postoperative pain. Anterior teeth are 4 times more likely to be overfilled with the obturation techniques tested (AU)

Los objetivos de esta investigación fueron: Analizar si factores como la edad, el tipo de diente y el género están asociados con la extrusión de material obturador radiográficamente visible como desenlace imprevisto en dientes sometidos a tratamiento endodóntico con una técnica de obturación termoplástica (Calamus® o GuttaCore®) y determinar si la presencia de esta sobreobturación está asociada con dolor posoperatorio. Se seleccionaron 120 dientes con diagnósticos que implicaban pulpa vital y con indicación de tratamiento de endodoncia. La preparación biomecánica se llevó a cabo con el sistema ProtaperNext® con lima apical principal X2 o X3. Los dientes se dividieron aleatoriamente de la siguiente forma (n=60): El grupo 1 se obturó con el sistema Guttacore® y el grupo 2 se obturó con una técnica de obturación de cono único y el sistema de obturación Calamus®. Se observó quelas técnicas de obturación termoplástica generaron sobreobturación en 53.33% del total (64 dientes), 56.66% se presentaron en el grupo de obturación con Guttacore® y 50% en el grupo de la técnica con el sistema Calamus®. Se encontró que los dientes anteriores presentaron asociación con la presencia de sobreobturación (p= 0.024) (OR=4.35). De los 120 dientes tratados, 10 (8.33 %) presentaron dolor posoperatorio y sobreobturación radiográficamente visible. La asociación entre la presencia de extrusión de material de obturación y dolor levemoderado fue estadísticamente significativa con un valor p= 0.002. Como conclusión las técnicas de obturación termoplástica en endodoncia Guttacore® y el sistema Calamus® están asociadas significativamente con la probabilidad de extrusión de material obturador y dicha sobreobturación está asociada con dolor posoperatorio, los dientes anteriores presentan 4 veces más riesgo de sobreobturación con las técnicas de obturación utilizadas (AU)

Workplace Bullying and Presenteeism: The Path Through Emotional Exhaustion and Psychological Wellbeing.

OBJECTIVE: Workplace bullying is an increasing phenomenon that concerns managers and employees. However, few studies have investigated how workplace bullying relates with work-related exhaustion and indicators of productivity loss due to presenteeism. Thus, the aim of the present study was to examine the intervening variables of emotional exhaustion and psychological wellbeing in the direct and indirect relationships between workplace bullying and indicators of productivity loss due to presenteeism. METHOD: In a cross-sectional study, we tested a structural equation model using web survey data of 353 workers from a service company, with the variables: workplace bullying (Quine, 1999), emotional exhaustion (Maslach Burnout Inventory; MBI), psychological wellbeing (GHQ-28), and indicators of productivity loss due to presenteeism (SPS-6). All variables presented acceptable psychometric evidence. RESULTS: The final model revealed a reasonable fit. Workplace bullying was significantly and positively related to emotional exhaustion, which in turn, was significantly related to the loss of psychological wellbeing. Workplace bullying, emotional exhaustion, and the loss of psychological wellbeing were negatively related to concentration (avoiding distraction). Emotional exhaustion and psychological wellbeing mediated the studied structural relationships. CONCLUSIONS: Our study contributes to theory and practice, since occupational health professionals should be aware that burnout and the loss of wellbeing may be related to workplace bullying and that productivity loss due to presenteeism may be a warning sign. Leaders can understand the underlying mechanism that explains employees' productivity loss due to presenteeism by addressing workplace bullying and its negative relation with emotional exhaustion and wellbeing.