Genomic profiling in GIST: Implications in clinical outcome and future challenges.

Gastrointestinal Stromal Tumors (GIST) are the most frequent mesenchymal neoplasia of the digestive tract. Genomic alterations in KIT, PDFGRA, SDH, and BRAF genes are essential in GIST oncogenesis. Therefore, the mutations in these genes have demonstrated clinical implications. Tumors with deletions in KIT-exon 11 or duplications in exon 9 are associated with a worse prognosis. In contrast, KIT-exon 11 substitutions and duplications are associated with a better clinical outcome. Moreover, mutations in Kit exon 9 and 11 are actionable, due to their response to imatinib, while mutations in PDGFRA respond to sunitinib and/or avapritinib. Although, molecular testing on tissue samples is effective; it is invasive, requires adequate amounts of tissue, and a long experimental process is needed for results. In contrast, liquid biopsy has been proposed as a simple and non-invasive method to test biomarkers in cancer. The most common molecule analyzed by liquid biopsy is circulating tumor DNA (ctDNA). GISTs ctDNA testing has been demonstrated to be effective in identifying known and novel KIT mutations that were not detected using traditional tissue DNA testing and have been useful in determining progression risk and response to TKI therapy. This allows the clinician to have an accurate picture of the genetic changes of the tumor over time. In this work, we aimed to discuss the implications of mutational testing in clinical outcomes, the methods to test ctDNA and the future challenges in the establishment of alternatives of personalized medicine.

Primacy and recency effects in hierarchical renewal in rats.

Previous studies on hierarchical resurgence produced mixed results regarding the order and magnitude of recurrence of responses trained initially (primacy effect) or more recently (recency effect). Although changes in contextual stimuli could explain such differences, in resurgence procedures contextual stimuli are not commonly presented, thus their effects on multiple operants trained sequentially remain unclear. Renewal procedures, in contrast, have been useful to determine the effects of exteroceptive contextual stimuli on response recurrence. Thus, primacy and recency effects were studied using a renewal procedure in which three contexts were presented sequentially. Lever presses by rats were reinforced on a different lever under each training context and were then exposed to extinction in a different context. Presses on a fourth lever were never reinforced. During renewal testing, the three training contexts were presented in the same or inverse order relative to training. A strong primacy effect was found in rats exposed to the original training order. Both primacy and recency effects were found when the rats were exposed to contexts in inverse order. These results suggest that the magnitude of renewal of hierarchically trained responses is affected by training order and order of presentation of contextual stimuli during testing.

A graph-embedded topic model enables characterization of diverse pain phenotypes among UK biobank individuals.

Large biobank repositories of clinical conditions and medications data open opportunities to investigate the phenotypic disease network. We present a graph embedded topic model (GETM). We integrate existing biomedical knowledge graph information in the form of pre-trained graph embedding into the embedded topic model. Via a variational autoencoder framework, we infer patient phenotypic mixture by modeling multi-modal discrete patient medical records. We applied GETM to UK Biobank (UKB) self-reported clinical phenotype data, which contains 443 self-reported medical conditions and 802 medications for 457,461 individuals. Compared to existing methods, GETM demonstrates good imputation performance. With a more focused application on characterizing pain phenotypes, we observe that GETM-inferred phenotypes not only accurately predict the status of chronic musculoskeletal (CMK) pain but also reveal known pain-related topics. Intriguingly, medications and conditions in the cardiovascular category are enriched among the most predictive topics of chronic pain.

3D-printed operant chambers for rats: Design, assembly, and innovations.

Ten years ago, we started a project at the National Autonomous University of Mexico with the purpose of building custom-made operant conditioning chambers that could be used in research and laboratory courses. The focus was to reduce the cost and improve the flexibility of operant chambers by integrating advances in electronics and manufacturing processes such as 3D printing and laser-cutting technologies. With these technologies we designed and built customizable and reliable operant chambers for rats in which responses can be recorded using levers or photocells. Reinforcement is delivered precisely using a pellet or a water dispenser and auditory and visual stimuli are presented with buzzers and LEDs. An Arduino microcontroller board connected to a PC running programs written in Visual Basic controls and records experimental events. The origins and latest improvements of the project are described and instructions to build one operant chamber are provided. Additionally, we describe a few examples of modifications of the design with the purpose of researching a wider range of behavioral phenomena. The designs and programs are open-source and open-distribution so they can be downloaded for free and can be modified freely by users to adapt to numerous experimental settings.

Psychological Distress, Fatigue and Quality of Life in Patients with Gastrointestinal Stromal Tumors.

Background: Gastrointestinal stromal tumors (GIST) represent 1% of all gastrointestinal tumors and are included in the list of rare diseases. Objective: 1) To evaluate levels of psychological distress, fatigue, and quality of life. 2) To identify the variables that most influence distress among Mexican patients with GIST. Design: A cross-sectional study was conducted with a consecutive sample of 100 patients with GIST, who completed the following questionnaires online: Hospital Anxiety and Depression Scale (HADS) as a measure of distress, Multidimensional Fatigue Inventory (MFI), and Quality of Life Questionnaire (QLQ C30). Results: Distress was present in 31% of patients. No association was found between distress and sociodemographic/clinical variables. The patients with distress demonstrated higher scores in all fatigue dimensions and, regarding quality of life, had more symptoms and were lower functioning. Distress was positively associated with all fatigue dimensions and with QLQ C30 symptoms. Negative associations were found between distress and QLQ C30 functioning dimensions. The predictors of psychological distress were general fatigue, reduced motivation, and emotional functioning. Conclusion: The percentage of patients with distress was akin to the levels found in patients with the most common types of cancer. Fatigue in patients with GIST should be evaluated and managed to improve distress levels.

High-flow nasal cannula therapy for hypoxemic respiratory failure in patients with COVID-19.

INTRODUCTION: High-flow nasal cannula (HFNC) therapy in patients with hypoxemic respiratory failure due to COVID-19 is poorly understood and remains controversial. METHODS: We evaluated a large cohort of patients with COVID-19-related hypoxemic respiratory failure at the temporary COVID-19 hospital in Mexico City. The primary outcome was the success rate of HFNC to prevent the progression to invasive mechanical ventilation (IMV). We also evaluated the risk factors associated with HFNC success or failure. RESULTS: HFNC use effectively prevented IMV in 71.4% of patients [270 of 378 patients; 95% confidence interval (CI) 66.6-75.8%]. Factors that were significantly different at admission included age, the presence of hypertension, and the Charlson comorbidity index. Predictors of therapy failure (adjusted hazard ratio, 95% CI) included the comorbidity-age-lymphocyte count-lactate dehydrogenase (CALL) score at admission (1.27, 1.09-1.47; p < 0.01), Rox index at 1 hour (0.82, 0.7-0.96; p = 0.02), and no prior steroid treatment (0.34, 95% CI 0.19-0.62; p < 0.0001). Patients with HFNC success rarely required admission to the intensive care unit and had shorter lengths of hospital stay [19/270 (7.0%) and 15.0 (interquartile range, 11-20) days, respectively] than those who required IMV [104/108 (96.3%) and 26.5 (20-36) days, respectively]. CONCLUSION: Treating patients with HFNC at admission led to improvement in respiratory parameters in many patients with COVID-19.

Impact of preemptive hospitalization on health outcomes at the temporary COVID-19 hospital in Mexico City: a prospective observational study.

INTRODUCTION: In response to the evolution of the coronavirus disease 2019 (COVID-19) pandemic, the admission protocol for the temporary COVID-19 hospital in Mexico City has been updated to hospitalize patients preemptively with an oxygen saturation (SpO2) of >90%. METHODS: This prospective, observational, single-center study compared the progression and outcomes of patients who were preemptively hospitalized versus those who were hospitalized based on an SpO2 ⩽90%. We recorded patient demographics, clinical characteristics, COVID-19 symptoms, and oxygen requirement at admission. We calculated the risk of disease progression and the benefit of preemptive hospitalization, stratified by CALL Score: age, lymphocyte count, and lactate dehydrogenase (<8 and ⩾8) at admission. RESULTS: Preemptive hospitalization significantly reduced the requirement for oxygen therapy (odds ratio 0.45, 95% confidence interval 0.31-0.66), admission to the intensive care unit (ICU) (0.37, 0.23-0.60), requirement for invasive mechanical ventilation (IMV) (0.40, 0.25-0.64), and mortality (0.22, 0.10-0.50). Stratification by CALL score at admission showed that the benefit of preemptive hospitalization remained significant for patients requiring oxygen therapy (0.51, 0.31-0.83), admission to the ICU (0.48, 0.27-0.86), and IMV (0.51, 0.28-0.92). Mortality risk remained significantly reduced (0.19, 0.07-0.48). CONCLUSION: Preemptive hospitalization reduced the rate of disease progression and may be beneficial for improving COVID-19 patient outcomes.

A functional polymorphism in the ATP-Binding Cassette B1 transporter predicts pharmacologic response to combination of nortriptyline and morphine in neuropathic pain patients.

Many genetic markers have been associated with variations in treatment response to analgesics, but none have been assessed in the context of combination therapies. In this study, the treatment effects of nortriptyline and morphine were tested for an association with genetic markers relevant to pain pathways. Treatment effects were determined for single and combination therapies. A total of 24 functional single nucleotide polymorphisms were tested within the gene loci of mu-opioid receptor (OPRM1) gene locus, ATP-Binding Cassette B1 Transporter (ABCB1), Cytochrome P450 gene family (CYP2C19 and CYP2D6), catecholamine inactivator Catechol-O-Methyl Transferase (COMT), and serotonin receptor 2A (HTR2A). Genotyping was performed in a population of neuropathic pain patients who previously participated in a clinical trial. For monotherapy, neither nortriptyline nor morphine responses were associated with single nucleotide polymorphisms. However, for nortriptyline + morphine combination therapy, the single nucleotide polymorphism rs1045642 within the drug efflux pump ABCB1 transporter significantly predicted analgesic response. The presence of the C allele accounted for 51% of pain variance in this subgroup in response to combination treatment. The T-allele homozygotes demonstrated only 20% improvement in pain scores, whereas the C-allele homozygotes 88%. There was no significant contribution of rs1045642 to the medication side effects under all treatment conditions. The UK Biobank data set was then used to validate this genetic association. Here, patients receiving similar combination therapy (opioid + tricyclic antidepressant) carrying the C allele of rs1045642 displayed 33% fewer body pain sites than patients without that allele, suggesting better pain control. In all, our results show a robust effect of the rs1045642 polymorphism in response to chronic pain treatment with a nortriptyline + morphine combination.

Human pain genetics database: a resource dedicated to human pain genetics research.

The Human Pain Genetics Database (HPGDB) is a comprehensive variant-focused inventory of genetic contributors to human pain. After curation, the HPGDB currently includes 294 studies reporting associations between 434 distinct genetic variants and various pain phenotypes. Variants were then submitted to a comprehensive analysis. First, they were validated in an independent high-powered replication cohort by testing the association of each variant with 10 different pain phenotypes (n = 1320-26,973). One hundred fifty-five variants replicated successfully (false discovery rate 20%) in at least one pain phenotype, and the association P values of the HPGDB variants were significantly lower compared with those of random controls. Among the 155 replicated variants, 21 had been included in the HPGDB because of their association with analgesia-related and 13 with nociception-related phenotypes, confirming analgesia and nociception as pathways of vulnerability for pain phenotypes. Furthermore, many genetic variants were associated with multiple pain phenotypes, and the strength of their association correlated between many pairs of phenotypes. These genetic variants explained a considerable amount of the variance between different pairs of pain phenotypes, indicating a shared genetic basis among pain phenotypes. In addition, we found that HPGDB variants show many pleiotropic associations, indicating that genetic pathophysiological mechanisms are also shared among painful and nonpainful conditions. Finally, we demonstrated that the HPGDB data set is significantly enriched for functional variants that modify gene expression, are deleterious, and colocalize with open chromatin regions. As such, the HPGDB provides a validated data set that represents a valuable resource for researchers in the human pain field.

Pain with traumatic brain injury and psychological disorders.

Traumatic brain injury (TBI) is the cause for long-term disability in more than 3 million patients in the US alone, with chronic pain being the most frequently reported complain. To date, predisposing mechanisms for chronic pain in TBI patients are largely unknown. Psychological disorders, including post-traumatic stress disorder, depression and anxiety following TBI are commonly reported comorbidities to post-traumatic pain. Long term consequences can be debilitating and affect quality of life even when the injury is mild. In this review, we present the most commonly reported chronic pain conditions across the spectrum of severity of TBI, mainly focusing on mild TBI. We discuss chronic post- traumatic headaches, widespread pain as well as post-traumatic central pain. We discuss pain in the context of injury severity and military versus civilian populations. We are only starting to understand the biological mechanisms behind post-traumatic pain and associated psychological distress following TBI, with genetic, biochemical and imaging studies pointing to the dopaminergic, neurotrophic factors and the role of Apolipoprotein. Physiological and neurological mechanisms are proposed to partially explain this interaction between post-traumatic pain and psychological distress. Nevertheless, the evidence for the role of structural brain damage remains incomplete and to a large extent debatable, as it is still difficult to establish clear causality between brain trauma and chronic pain. Finally, general aspects of management of chronic pain post-TBI are addressed.

Resurgence of response duration in human participants.

Previously reinforced responses can reappear when reinforcement is withdrawn from current responding. This is known as resurgence. Although resurgence of response topography, spacing, and patterns over time has been demonstrated, there is no evidence of resurgence of response duration. This experiment explored resurgence of response duration in humans. In Phase 1 a multiple schedule of reinforcement with two components was used. In each component a chained variable-interval 30s, variable-ratio 3 schedule was implemented. In the terminal link of the chained schedule, response durations between 0.1 and 0.5s were reinforced during one component, and between 2 and 8s in the other component. In Phase 2, response requirement during the terminal link of the chained schedule was inverted between components relative to Phase 1. In Phase 3 the chained schedule was changed to a variable-interval 30-s, extinction 30s. Resurgence of the durations trained during Phase 1 was observed. It was concluded that duration is a response dimension that reappears during extinction.

Post-concussion symptoms and chronic pain after mild traumatic brain injury are modulated by multiple locus effect in the BDNF gene through the expression of antisense: A pilot prospective control study.

Background: Mild traumatic brain injury (mTBI) often results in post-concussion symptoms, chronic pain, and sleepiness. Genetic factors are thought to play an important role in poor prognosis. Aims: The aims of this study are to (1) document the prevalence of pain and post-concussion symptoms in mTBI patients in acute and chronic phases (2) determine whether candidate genes predispose to post-concussive symptoms and pain. Methods: Posttraumatic symptoms, evaluated using the Rivermead Post-Concussion Symptoms Questionnaire, and pain were assessed in 94 mTBI patients in the acute phase as well as in 22 healthy controls. Assessment was repeated in 36 patients after one year who agreed to participate in the follow-up visit. Gene polymorphisms and expression were assessed in mTBI patients and healthy controls. Results: In the acute phase, mTBI patients with pain (69%) presented more psychological symptoms and sleepiness and were less able to return to work than those without pain. At one year, 19% of mTBI patients had persistent pain and psychological distress. Two haplotypes (H2 and H3) in the brain-derived neurotrophic factor (BDNF) gene were shown to be respectively deleterious and protective against post-concussion symptoms and pain in both acute and chronic phases. Protective haplotype H3 was associated with a decreased expression of the anti-sense of BDNF (BDNF-AS). Deleterious haplotype H2 predicted the development of chronic pain at one year, whereas H3 was protective. Conclusions: This pilot study suggests a protective mechanism of a multilocus effect in BDNF, through BDNF-AS, against post-concussion symptoms and pain in the acute phase and possibly chronic pain at one year post-mTBI. The role of antisense RNA should be validated in larger cohorts.

Contexte: Le traumatisme cranio-cérébral léger (TCCL) donne souvent lieu à des symptômes post-commotionnels, de la douleur chronique et de la somnolence. On croit que des facteurs génétiques jouent un rôle important dans le pronostic défavorable.Buts: Les buts de cette étude sont : 1) documenter la prévalence de la douleur et des symptômes post-commotionnels chez les patients ayant subi un TCCL, au cours des phases aigue et chronique; ii) déterminer si des gènes du candidat le prédisposent à la douleur et aux symptômes post-commotionnels.Méthodes: La douleur et les symptômes post-traumatiques, évalués à l'aide du questionnaire Rivermead sur les symptômes post-commotionnels, ont été évalués chez 94 patients ayant subi un TCCL au cours de la phase aigue, ainsi que chez 22 sujets témoins. Après un an, 36 patients qui avaient accepté de participer à une visite de suivi ont à nouveau été évalués. Les polymorphismes et l'expression des gènes ont été évalués chez les patients ayant subi un TCCL et chez les sujets témoins.Résultats: Au cours de la phase aigue, les patients ayant subi un TCCL avec douleur (69 %) présentaient davantage de symptômes psychologiques et de somnolence et étaient moins aptes à retourner au travail que les patients sans douleur. Après un an, 19 % des patients ayant subi un TCCL souffraient d'une douleur persistante et de détresse psychologique. Deux haplotypes (H2 et H3) dans le gène BDNF se sont montrés respectivement délétère et protecteur contre les symptômes post-commotionnels et contre la douleur, tant au cours de la phase aigue que de la phase chronique. Le haplotype protecteur H3 a été associé à une diminution de l'expression de l'anti-sens de BDNF (BDNF-AS). Le haplotype délétère H2 a prédit le développement de la douleur chronique un an plus tard, tandis que H3 a été protecteur.Conclusions: Cette étude pilote suggère l'existence d'un mécanisme protecteur d'un effet multilocus dans BDNF à travers BDNF-AS, contre les symptômes post-commotionnels et la douleur au cours de la phase aigue et possiblement au cours de la phase chronique, un an après le TCCL. Le rôle de la RNA anti-sens devrait être validé avec de plus grandes cohortes.

α4-Containing GABA(A) Receptors are Required for Antagonism of Ethanol-Induced Motor Incoordination and Hypnosis by the Imidazobenzodiazepine Ro15-4513.

Alcohol (ethanol) is widely consumed for its desirable effects but unfortunately has strong addiction potential. Some imidazobenzodiazepines such as Ro15-4513 are able to antagonize many ethanol-induced behaviors. Controversial biochemical and pharmacological evidence suggest that the effects of these ethanol antagonists and ethanol are mediated specifically via overlapping binding sites on α4/δ-containing GABA(A)-Rs. To investigate the requirement of α4-containing GABA(A)-Rs in the mechanism of action of Ro15-4513 on behavior, wildtype (WT) and α4 knockout (KO) mice were compared for antagonism of ethanol-induced motor incoordination and hypnosis. Motor effects of ethanol were tested in two different fixed speed rotarod assays. In the first experiment, mice were injected with 2.0 g/kg ethanol followed 5 min later by 10 mg/kg Ro15-4513 (or vehicle) and tested on a rotarod at 8 rpm. In the second experiment, mice received a single injection of 1.5 g/kg ethanol ± 3 mg/kg Ro15-4513 and were tested on a rotarod at 12 rpm. In both experiments, the robust Ro15-4513 antagonism of ethanol-induced motor ataxia that was observed in WT mice was absent in KO mice. A loss of righting reflex (LORR) assay was used to test Ro15-4513 (20 mg/kg) antagonism of ethanol (3.5 g/kg)-induced hypnosis. An effect of sex was observed on the LORR assay, so males and females were analyzed separately. In male mice, Ro15-4513 markedly reduced ethanol-induced LORR in WT controls, but α4 KO mice were insensitive to this effect of Ro15-4513. In contrast, female KO mice did not differ from WT controls in the antagonistic effects of Ro15-4513 on ethanol-induced LORR. We conclude that Ro15-4513 requires α4-containing receptors for antagonism of ethanol-induced LORR (in males) and motor ataxia.

Identification of anesthetic binding sites on human serum albumin using a novel etomidate photolabel.

We have synthesized a novel analog of the general anesthetic etomidate in which the ethoxy group has been replaced by an azide group, and which can be used as a photolabel to identify etomidate binding sites. This acyl azide analog is a potent general anesthetic in both rats and tadpoles and, as with etomidate, is stereoselective in its actions, with the R(+) enantiomer being significantly more potent than the S(-) enantiomer. Its effects on alpha1beta2gamma2s GABA(A) receptors expressed in HEK-293 cells are virtually indistinguishable from the parent compound etomidate, showing stereoselective potentiation of GABA-induced currents, as well as direct mimetic effects at higher concentrations. In addition, a point mutation (beta2 N265M), which is known to attenuate the potentiating actions of etomidate, also blocks the effects of the acyl azide analog. We have investigated the utility of the analog to identify etomidate binding sites by using it to photolabel human serum albumin, a protein that binds approximately 75% of etomidate in human plasma and which is thought to play a major role in its pharmacokinetics. Using HPLC/mass spectrometry we have identified two anesthetic binding sites on HSA. One site is the well-characterized drug binding site I, located in HSA subdomain IIA, and the second site is also an established drug binding site located in subdomain IIIB, which also binds propofol. The acyl azide etomidate may prove to be a useful new photolabel to identify anesthetic binding sites on the GABA(A) receptor or other putative targets.

Expansion of gas bubbles by nitrous oxide and xenon.

BACKGROUND: Nitrous oxide is well known to expand gas bubbles trapped in enclosed spaces and is contraindicated in situations where this may occur. Xenon, an anesthetic gas with similar physical properties to nitrous oxide, is also likely to expand gas bubbles, and it has been predicted that microbubbles in the circulation may expand dramatically when exposed to xenon. Because of the possibility that xenon will be used during cardiopulmonary bypass surgery, a procedure that is likely to introduce microbubbles into the circulation, the authors reinvestigated the extent to which xenon expands gas bubbles in aqueous solution. METHODS: Gas bubbles of either air or oxygen were formed in an aqueous solution, and their size was monitored using optical microscopy when they were exposed to a rapidly flowing solution of xenon, nitrous oxide, or a xenon-oxygen mixture. RESULTS: Both nitrous oxide and xenon rapidly expanded air bubbles, although nitrous oxide caused a much larger expansion. The observed expansion was not greatly dependent on the initial size of the bubble but was significantly greater at lower temperatures. Under conditions relevant to cardiopulmonary bypass surgery (50% xenon-50% oxygen, 30 degrees C), the increase in diameter was modest (9.7 +/- 0.8%). CONCLUSIONS: Although xenon does expand small air and oxygen bubbles, the extent to which this occurs under clinically relevant conditions of concentration and temperature is modest.