Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance.

Large-scale genomic studies have identified multiple somatic aberrations in breast cancer, including copy number alterations and point mutations. Still, identifying causal variants and emergent vulnerabilities that arise as a consequence of genetic alterations remain major challenges. We performed whole-genome small hairpin RNA (shRNA) "dropout screens" on 77 breast cancer cell lines. Using a hierarchical linear regression algorithm to score our screen results and integrate them with accompanying detailed genetic and proteomic information, we identify vulnerabilities in breast cancer, including candidate "drivers," and reveal general functional genomic properties of cancer cells. Comparisons of gene essentiality with drug sensitivity data suggest potential resistance mechanisms, effects of existing anti-cancer drugs, and opportunities for combination therapy. Finally, we demonstrate the utility of this large dataset by identifying BRD4 as a potential target in luminal breast cancer and PIK3CA mutations as a resistance determinant for BET-inhibitors.

Integration of genomic data enables selective discovery of breast cancer drivers.

Identifying driver genes in cancer remains a crucial bottleneck in therapeutic development and basic understanding of the disease. We developed Helios, an algorithm that integrates genomic data from primary tumors with data from functional RNAi screens to pinpoint driver genes within large recurrently amplified regions of DNA. Applying Helios to breast cancer data identified a set of candidate drivers highly enriched with known drivers (p < 10(-14)). Nine of ten top-scoring Helios genes are known drivers of breast cancer, and in vitro validation of 12 candidates predicted by Helios found ten conferred enhanced anchorage-independent growth, demonstrating Helios's exquisite sensitivity and specificity. We extensively characterized RSF-1, a driver identified by Helios whose amplification correlates with poor prognosis, and found increased tumorigenesis and metastasis in mouse models. We have demonstrated a powerful approach for identifying driver genes and how it can yield important insights into cancer.

An integrated approach to uncover drivers of cancer.

Systematic characterization of cancer genomes has revealed a staggering number of diverse aberrations that differ among individuals, such that the functional importance and physiological impact of most tumor genetic alterations remain poorly defined. We developed a computational framework that integrates chromosomal copy number and gene expression data for detecting aberrations that promote cancer progression. We demonstrate the utility of this framework using a melanoma data set. Our analysis correctly identified known drivers of melanoma and predicted multiple tumor dependencies. Two dependencies, TBC1D16 and RAB27A, confirmed empirically, suggest that abnormal regulation of protein trafficking contributes to proliferation in melanoma. Together, these results demonstrate the ability of integrative Bayesian approaches to identify candidate drivers with biological, and possibly therapeutic, importance in cancer.

miR-424(322)/503 is a breast cancer tumor suppressor whose loss promotes resistance to chemotherapy.

The female mammary gland is a very dynamic organ that undergoes continuous tissue remodeling during adulthood. Although it is well established that the number of menstrual cycles and pregnancy (in this case transiently) increase the risk of breast cancer, the reasons are unclear. Growing clinical and experimental evidence indicates that improper involution plays a role in the development of this malignancy. Recently, we described the miR-424(322)/503 cluster as an important regulator of mammary epithelial involution after pregnancy. Here, through the analysis of ∼3000 primary tumors, we show that miR-424(322)/503 is commonly lost in a subset of aggressive breast cancers and describe the genetic aberrations that inactivate its expression. Furthermore, through the use of a knockout mouse model, we demonstrate for the first time that loss of miR-424(322)/503 promotes breast tumorigenesis in vivo. Remarkably, we found that loss of miR-424(322)/503 promotes chemoresistance due to the up-regulation of two of its targets: BCL-2 and insulin-like growth factor-1 receptor (IGF1R). Importantly, targeted therapies blocking the aberrant activity of these targets restore sensitivity to chemotherapy. Overall, our studies reveal miR-424(322)/503 as a tumor suppressor in breast cancer and provide a link between mammary epithelial involution, tumorigenesis, and the phenomenon of chemoresistance.

What is the ideal timing of cholecystectomy after percutaneous cholecystostomy for acute cholecystitis?

BACKGROUND: Acute cholecystitis (AC) is one of the most prevalent diseases in clinical practice. Poor surgical candidates may benefit from early percutaneous cholecystostomy (PC) drainage followed by interval cholecystectomy (IC), which is the definitive treatment. The optimal timing between the PC drainage and the IC has not been identified. This study aimed to investigate how the duration between PC and IC affects perioperative outcomes and identify the optimal IC timing to minimize complications. METHODS: This retrospective cohort study included all adult patients diagnosed with AC who underwent PC followed by IC at a single institution center between 2014 and 2022. Patients with a history of hepatobiliary surgery, stones in the common bile duct, cirrhosis, active malignancy, or prolonged immunosuppression were excluded. The analysis did not include cases with major concurrent procedures during cholecystectomy, previously aborted cholecystectomies, or failure of the PC drain to control the inflammation. Linear and logistic regression models were used to analyze the impact of the interval between PC and IC on intra- and perioperative outcomes. RESULTS: One hundred thirty-two patients (62.1% male) with a mean age of 64.4 ± 15 (mean ± SD) years were diagnosed with AC (25% mild, 47.7% moderate, 27.3% severe). All patients underwent PC followed by IC after a median of 64 [48-91] days. Longer ICU stay was associated with longer time intervals between PC and IC (Coef 105.98, p < 0.001). No significant variations were detected in the intraoperative and perioperative outcomes between patients undergoing IC within versus after 8 weeks from PC placement. However, a higher percentage of patients with delayed IC (after 8 weeks) were discharged home (96.4% vs. 83.7%; p = 0.019). CONCLUSIONS: Patients may benefit from undergoing IC after the 8-week cutoff after PC. However, very long periods between PC and IC procedures may increase the risk of longer ICU stay.

Repair of Long Peripheral Nerve Defects in Sheep: A Translational Model for Nerve Regeneration.

Despite advances in microsurgery, full functional recovery of severe peripheral nerve injuries is not commonly attained. The sheep appears as a good preclinical model since it presents nerves with similar characteristics to humans. In this study, we induced 5 or 7 cm resection in the peroneal nerve and repaired with an autograft. Functional evaluation was performed monthly. Electromyographic and ultrasound tests were performed at 6.5 and 9 months postoperation (mpo). No significant differences were found between groups with respect to functional tests, although slow improvements were seen from 5 mpo. Electrophysiological tests showed compound muscle action potentials (CMAP) of small amplitude at 6.5 mpo that increased at 9 mpo, although they were significantly lower than the contralateral side. Ultrasound tests showed significantly reduced size of tibialis anterior (TA) muscle at 6.5 mpo and partially recovered size at 9 mpo. Histological evaluation of the grafts showed good axonal regeneration in all except one sheep from autograft 7 cm (AG7) group, while distal to the graft there was a higher number of axons than in control nerves. The results indicate that sheep nerve repair is a useful model for investigating long-gap peripheral nerve injuries.

The Metagenomic Composition and Effects of Fecal-Microbe-Derived Extracellular Vesicles on Intestinal Permeability Depend on the Patient's Disease.

The composition and impact of fecal-microbe-derived extracellular vesicles (EVs) present in different diseases has not been analyzed. We determined the metagenomic profiling of feces and fecal-microbe-derived EVs from healthy subjects and patients with different diseases (diarrhea, morbid obesity and Crohn's disease (CD)) and the effect of these fecal EVs on the cellular permeability of Caco-2 cells. The control group presented higher proportions of Pseudomonas and Rikenellaceae_RC9_gut_group and lower proportions of Phascolarctobacterium, Veillonella and Veillonellaceae_ge in EVs when compared with the feces from which these EVs were isolated. In contrast, there were significant differences in 20 genera between the feces and EV compositions in the disease groups. Bacteroidales and Pseudomonas were increased, and Faecalibacterium, Ruminococcus, Clostridium and Subdoligranum were decreased in EVs from control patients compared with the other three groups of patients. Tyzzerella, Verrucomicrobiaceae, Candidatus_Paracaedibacter and Akkermansia were increased in EVs from the CD group compared with the morbid obesity and diarrhea groups. Fecal EVs from the morbid obesity, CD and, mainly, diarrhea induced a significant increase in the permeability of Caco-2 cells. In conclusion, the metagenomic composition of fecal-microbe-derived EVs changes depending on the disease of the patients. The modification of the permeability of Caco-2 cells produced by fecal EVs depends on the disease of the patients.

The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.

The mammary gland is a very dynamic organ that undergoes continuous remodeling. The critical regulators of this process are not fully understood. Here we identify the microRNA cluster miR-424(322)/503 as an important regulator of epithelial involution after pregnancy. Through the generation of a knockout mouse model, we found that regression of the secretory acini of the mammary gland was compromised in the absence of miR-424(322)/503. Mechanistically, we show that miR-424(322)/503 orchestrates cell life and death decisions by targeting BCL-2 and IGF1R (insulin growth factor-1 receptor). Furthermore, we demonstrate that the expression of this microRNA cluster is regulated by TGF-ß, a well-characterized regulator of mammary involution. Overall, our data suggest a model in which activation of the TGF-ß pathway after weaning induces the transcription of miR-424(322)/503, which in turn down-regulates the expression of key genes. Here, we unveil a previously unknown, multilayered regulation of epithelial tissue remodeling coordinated by the microRNA cluster miR-424(322)/503.

Endoscopic septotomy of Zenker's diverticulum with Stag-Beetle Knife™: A descriptive observational study and literature review. / Septotomía endoscópica del divertículo de Zenker mediante Stag-Beetle-KnifeTM: estudio observacional descriptivo y revisión de la literatura.

INTRODUCTION: Zenker's diverticulum (ZD) is a protrusion of the hypopharyngeal mucosa with a prevalence of 2/100,000 inhabitants. The symptoms of the patients determine the need for treatment, which can be surgical or endoscopic. The latter, known as endoscopic septotomy or diverticulotomy (ED), this involves dissecting the diverticular septum, which can be performed with different dissection devices. AIM: The aim of our study was to evaluate the efficacy and safety of ED with Stag-Beetle-Knife™ device, as well as to conduct a literature review to assess the position of the technique in the current scientific panorama. MATERIAL AND METHODS: Descriptive retrospective study that includes patients who underwent ED with SB-Knife™ between June 2017 and February 2020. Literature review of the available evidence between January 2013 and April 2020 of ED with SB-Knife™ technique and its variants. RESULTS: Twelve patients (66% male) with a median age of 70.5 years were collected. The median size of diverticular was 32.5mm and complete remission was observed in 75% of the cases. Fourteen interventions were performed with a technical success of 92.8. There were no serious complications. A literature review was carried out, finding 13 papers, of which 8 were finally included (6 retrospective studies, a series of cases and a clinical case). CONCLUSION: Based on our experience and the reviewed literature, we consider ED with SB-Knife™ is a safe, effective and reproducible technique, and may be a better alternative to surgery in patients with ZD.

Corrigendum to "Energy efficiency in software: A case study on sustainability in personal health records" [J. Clean. Prod. 282 (2021) 124262].

[This corrects the article DOI: 10.1016/j.jclepro.2020.124262.].

Energy efficiency in software: A case study on sustainability in personal health records.

A personal health record is an eHealth technology in which users can observe their progress over time for a given condition. A research gap was identified in the literature concerning the study of the amount of energy that these systems need for their operation, and the energy efficiency that may be attained depending on their design. After the selection of five representative personal health records, a total of 20 tasks commonly done, and based on previous work, were performed with regard to two proposed scenarios, namely patient use and health personnel usage. The power consumption of the main components of a host machine was measured during the performance of the proposed duties. To that end, a hardware tool called the Energy Efficiency Tester was employed. The data collected were analyzed statistically, and significant differences were found in the respective consumption of the display (χ2 (4) = 23.782, p = 0.000), the processor (χ2 (4) = 29.018, p = 0.000) and the whole PC (χ2 (4) = 28.582, p = 0.000). For all of these components, NoMoreClipBoard was the personal health record that required the least energy (57.699 W for the display, 3.162 W for the processor and 181.113 W for the whole PC). A total of two strong correlations were found in the energy consumption between the hard disk and the graphics card (r = 0.791, p < 0.001), and the processor and the PC (r = 0.950, p < 0.001). Some features generated special amounts of power consumption, such as the news wall found on PatientsLikeMe, or the use of load icons that had an impact on most PC components. In addition, an in-depth analysis of the user interfaces was performed. A discussion was carried out on the design of the user interfaces, also taking into account recommendations drawn from the literature, checking for their implementation in the personal health records selected. With the aim of promoting sustainability among software developers, a best practice guideline on sustainable software design was proposed. Basic sustainability recommendations were collected for professionals to consider when developing a software system in general, and a personal health record in particular.

Evolution of polypharmacy in a spanish population (2005-2015): A database study.

PURPOSE: To analyze the evolution of the prevalence of polypharmacy and excessive polypharmacy in a Spanish population, and to improve the identification of patients with polypharmacy. METHODS: A descriptive, annual cross-sectional observational study was carried out. PATIENTS: individuals over 14 years of age included in a multiregional primary care database of the Spanish population (BIFAP). ANALYSIS: prescription data. Period 2005-2015. VARIABLES: proportion of patients with polypharmacy (simultaneous prescription of ≥5 drugs) and excessive polypharmacy (≥10 drugs) for at least 6 months, according to sex and age groups. A trend analysis of the studied period was performed (overall, and by sex and age groups). RESULTS: The data are reported on a comparative basis (2005 vs 2015). Number of patients analyzed: 2664743 vs 4 002 877. The prevalence of polypharmacy increased significantly (2.5% vs 8.9%, P-value for trend <0.001), being greater in females throughout the study period and in the group aged ≥80 years (P-value for trends <0.001). The prevalence of excessive polypharmacy also increased significantly (0.1% vs 1%, P-value for trend <0.001), being higher in the group aged ≥80 years (P-value for trend <0.001). The proportion of patients with no chronic treatment decreased (80.2% vs 63.1%). CONCLUSIONS: The prevalence of polypharmacy in this Spanish population has tripled in the period 2005-2015, while excessive polypharmacy has increased 10-fold. These increments are seen in both sexes and in all age groups, particularly in individuals over 80 years of age. The proportion of patients without chronic treatments has decreased.

Development of a catheter-based technique for endoluminal radiofrequency sealing of pancreatic duct.

Introduction: Endoluminal sealing of the pancreatic duct by glue or sutures facilitates the management of the pancreatic stump. Our objective was to develop a catheter-based alternative for endoluminal radiofrequency (RF) sealing of the pancreatic duct. Materials and methods: We devised a novel RF ablation technique based on impedance-guided catheter pullback. First, bench tests were performed on ex vivo models to tune up the technique before the in vivo study, after which endoluminal RF sealing of a ∼10 cm non-transected pancreatic duct was conducted on porcine models using a 3 Fr catheter. After 30 days, sealing effectiveness was assessed by a permeability test and a histological analysis. Results: The RF technique was feasible in all cases and delivered ∼5 W of power on an initial impedance of 308 ± 60 Ω. Electrical impedance evolution was similar in all cases and provided guidance for modulating the pullback speed to avoid tissue sticking and achieve a continuous lesion. During the follow-up the animals rate of weight gain was significantly reduced (p < 0.05). Apart from signs of exocrine atrophy, no other postoperative complications were found. At necropsy, the permeability test failed and the catheter could not be reintroduced endoluminally, confirming that sealing had been successful. The histological analysis revealed a homogeneous exocrine atrophy along the ablated segment in all the animals. Conclusions: Catheter-based RF ablation could be used effectively and safely for endoluminal sealing of the pancreatic duct. The findings suggest that a fully continuous lesion may not be required to obtain complete exocrine atrophy.

Neuromuscular block monitoring after the administration of 1 mg/kg intravenous cis-atracurium in the anaesthetized pig.

Neuromuscular blocking agents should be included as part of a balanced anaesthetic protocol to improve anaesthetic management, although doses are not always established for each species. Cis-atracurium is a benzylisoquinolinium neuromuscular blocking agent with an intermediate duration of action devoid of significant adverse effects previously used in pigs with a wide dosage range. Cis-atracurium was administered at 1 mg/kg bolus to sixteen pigs to establish its time profile and effects. The pigs were premedicated intramuscularly with 4 mg/kg azaperone, 8 mg/kg ketamine and 0.2 mg/kg morphine IM and maintained with isoflurane in oxygen. After cis-atracurium administration, neuromuscular monitoring via acceleromyography was started until the recovery of the 90% of the train of four ratio. Complete decrease in the train of four ratio was accomplished in eleven pigs. Onset of action was 70 s, with a recovery of the fourth twitch at 26 min and a recovery of a train of four ratio greater than 90% in 60 min. In conclusion, 1 mg/kg intravenous cis-atracurium in the pig allowed for a rapid onset of action and a complete recovery after 60 min although high variability in the time profile is seen.

Effect of age on cis-atracurium besylate pharmacokinetics following a single 1 mg kg-1 intravenous bolus in young pigs.

OBJECTIVE: To determine the cis-atracurium pharmacokinetic data and laudanosine production of a single 1 mg kg-1 cis-atracurium dose in the pig and to compare the pharmacokinetics between two groups of different ages. STUDY DESIGN: Prospective experimental study. ANIMALS: Sixteen female pigs in two groups. Group A included eight animals aged 2.0-2.5 months and weighed 26.6 ± 3.6 kg. Group B included eight animals aged 4.0-5.0 months and weighed 57.4 ± 8.3 kg. METHODS: The pigs were anaesthetized and monitored throughout the procedure. Arterial blood samples collected at 0, 0.5, 1, 2, 5, 10, 20, 30, 45, 60, 90, 120 and 180 minutes after cis-atracurium injection were cooled and centrifuged. Plasma was acidified and stored at -20 °C for subsequent cis-atracurium and laudanosine analyses. RESULTS: Anaesthetic parameters were within normal ranges throughout the procedure. Plasma cis-atracurium and laudanosine concentrations were measured for the 16 pigs. Elimination rate constant, elimination half-life, area under the curve, mean residence time, distribution volume and total clearance were calculated for each pig. Statistical differences (p < 0.05) in the elimination rate constant, elimination half-life, mean residence time and distribution volume values were observed between the two groups. Elimination half-life, mean residence time and distribution volume values were higher and elimination rate constant lower in younger pigs than in older pigs. No plasma laudanosine concentrations were detected in any pig. CONCLUSION AND CLINICAL RELEVANCE: Longer duration of plasma cis-atracurium concentrations were observed in younger pigs. Distribution volume was also higher in younger pigs. Conversely, total clearance and area under the curve were similar between the two age groups. No laudanosine production was detected, suggesting a different cis-atracurium metabolism in the pig compared with other species.

Clinical markers to predict progression from acute to chronic kidney disease in Mesoamerican nephropathy.

An epidemic of chronic kidney disease (CKD) of unknown etiology, known as Mesoamerican Nephropathy (MeN), has been ongoing in Latin America for at least two decades. MeN primarily affects young adults without traditional CKD risk factors, and agricultural workers are disproportionately afflicted. We previously identified an acute phase of MeN that involves acute kidney injury (AKI) with tubulointerstitial nephritis and systemic inflammation. Because clinical disease progression in MeN is not yet understood, we sought to determine clinical predictors for progression from acute MeN to CKD. Through ongoing surveillance in Nicaragua, local physicians reported cases of acute MeN and CKD among agricultural workers. We analyzed clinical data collected during the acute MeN encounter to identify factors associated with progression to CKD. From February 2015 to May 2017, 586 agricultural workers (median age 27.8 years, 90% male) presented with acute MeN. The majority had a normal baseline creatinine, and leukocyturia (98.8%) and peripheral leukocytosis (80.7%) were common. Ultimately, 49 (8.4%) progressed to CKD, the majority of those within 6 months. CKD was attributed to MeN in all cases, and none had diabetes or hypertension. The strongest predictors of CKD progression were anemia and paresthesias at presentation, while leukocytosis was associated with renal recovery. Clinical markers of acute MeN may help clinicians identify patients at high risk for rapid progression to CKD, which in turn can inform early clinical management. Future studies should seek to determine the underlying etiology of disease and identify optimal interventions to interrupt the pathophysiologic process of MeN.

Early detection of acute tubulointerstitial nephritis in the genesis of Mesoamerican nephropathy.

Mesoamerican nephropathy is a devastating disease of unknown etiology that affects mostly young agricultural workers in Central America. An understanding of the mechanism of injury and the early disease process is urgently needed and will aid in identification of the underlying cause and direct treatment and prevention efforts. We sought to describe the renal pathology in Mesoamerican nephropathy at its earliest clinical appearance in prospectively identified acute case patients in Nicaragua. We considered those with elevated (or increased at least 0.3 mg/dL or 1.5-fold from baseline) serum creatinine, leukocyturia, and either leukocytosis or neutrophilia for inclusion in this biopsy study. Renal tissue was obtained by ultrasound-guided biopsy for examination by light, immunofluorescence, and electron microscopy. All 11 individuals who underwent renal biopsy showed tubulointerstitial nephritis, with varying degrees of inflammation and chronicity. Interstitial cellular infiltrates (predominantly T lymphocytes and monocytes), mostly in the corticomedullary junction; neutrophilic accumulation in the tubular lumens; largely preserved glomeruli; few mild ischemic changes; and no immune deposits were noted. The acute components of tubulointerstitial nephritis were acute tubular cell injury, interstitial edema, and early fibrosis. Chronic tubulointerstitial nephritis included severe tubular atrophy, thickened tubular basement membrane, and interstitial fibrosis. Thus, renal histopathology in Mesoamerican nephropathy reveals primary interstitial disease with intact glomeruli.

Sensory Polymeric Foams as a Tool for Improving Sensing Performance of Sensory Polymers.

Microcellular sensory polymers prepared from solid sensory polymeric films were tested in an aqueous Hg(II) detection process to analyze their sensory behavior. First, solid acrylic-based polymeric films of 100 µm thickness were obtained via radical copolymerization process. Secondly, dithizone sensoring motifs were anchored in a simple five-step route, obtaining handleable colorimetric sensory films. To create the microporous structure, films were foamed in a ScCO2 batch process, carried out at 350 bar and 60 °C, resulting in homogeneous morphologies with cell sizes around 5 µm. The comparative behavior of the solid and foamed sensory films was tested in the detection of mercury in pure water media at 2.2 pH, resulting in a reduction of the response time (RT) around 25% and limits of detection and quantification (LOD and LOQ) four times lower when using foamed films, due to the increase of the specific surface associated to the microcellular structure.

Validity and reliability of Doppler ultrasonography and direct arterial blood pressure measurements in anaesthetized dogs weighing less than 5 kg.

OBJECTIVE: To assess the validity and reliability of Doppler ultrasonography (DOP) as compared with invasive arterial blood pressure measurements in anaesthetized dogs weighing less than 5 kg. STUDY DESIGN: Controlled, prospective, clinical study. ANIMALS: A total of 41 privately owned dogs weighing less than 5 kg. METHODS: The dogs were anaesthetized, and an intra-arterial catheter was placed aseptically in the dorsal pedal artery of the pelvic limb to perform invasive blood pressure (IBP) measurement. The contralateral metatarsal surface of the foot was clipped in order to perform DOP. Both techniques were used to record blood pressure measurements every 5 minutes during surgical procedures. The blood pressure measurements were categorized into two groups: hypotensive [mean arterial pressure (MAP) < 60 mmHg] and normotensive (MAP between 60 and 120 mmHg). A linear mixed model was used to compare the DOP and IBP values. The results were evaluated according to the requirements of the American College of Veterinary Internal Medicine (ACVIM) guidelines for the validation of devices. RESULTS: DOP provided higher values compared to the systolic arterial blood pressure (SAP) and MAP of IBP measurements. The closest agreement between the two techniques was found for SAP; the bias was 8.8, and limits of agreement (LOA) were -32.9 and 50.4. Similar results were observed when the IBP technique was categorized. The closest agreement was for SAP in animals categorized as normotensive; the bias was 8.2, and LOAs were -32.8 and 49.2. The level of agreement between DOP and IBP did not meet the ACVIM recommendations. CONCLUSIONS AND CLINICAL RELEVANCE: Our results suggest there is poor agreement between DOP and IBP measurements in anaesthetized dogs weighing less than 5 kg. Hence, the use of DOP in these animals could be misleading.

Solvent-Free Off-On Detection of the Improvised Explosive Triacetone Triperoxide (TATP) with Fluorogenic Materials.

A fluorogenic perylenediimide-functionalized polyacrylate capable of generating color and fluorescence changes in the presence of triacetone triperoxide TATP), an improvised explosive used in terrorist attacks, under solvent-free, solid-state conditions has been developed. The material works by accumulating volatile TATP until it reaches a threshold; therefore, triggering colorimetric and fluorescent responses.