Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single-cell transcriptome analysis.

Molecular and cellular characterization of tumors is essential due to the complex and heterogeneous nature of cancer. In recent decades, many bioinformatic tools and experimental techniques have been developed to achieve personalized characterization of tumors. However, sample handling continues to be a major challenge as limitations such as prior treatments before sample acquisition, the amount of tissue obtained, transportation, or the inability to process fresh samples pose a hurdle for experimental strategies that require viable cell suspensions. Here, we present an optimized protocol that allows the recovery of highly viable cell suspensions from breast cancer primary tumor biopsies. Using these cell suspensions we have successfully characterized genome architecture through Hi-C. Also, we have evaluated single-cell gene expression and the tumor cellular microenvironment through single-cell RNAseq. Both technologies are key in the detailed and personalized molecular characterization of tumor samples. The protocol described here is a cost-effective alternative to obtain viable cell suspensions from biopsies simply and efficiently.

Gene expression profiling of inflammatory cytokines in esophageal biopsies of different phenotypes of gastroesophageal reflux disease: a cross-sectional study.

BACKGROUND: The clinical endoscopic phenotypes of gastroesophageal reflux disease (GERD) are classified as Barrett's esophagus (BE), erosive esophagitis (EE) and non-erosive gastroesophageal reflux disease (NERD). NERD is subclassified as abnormal acid exposure (AAE) and normal acid exposure (NAE) based on pH monitoring study results. The aim of this study was to characterize genes involved in the pathophysiology and immune response of GERD. METHODS: This is an observational and cross-sectional study. All patients with BE, EE, AAE, and NAE and a control group were subjected to superior endoscopy (with biopsies of esophageal mucosa). Relative mRNA quantification of cytokine and target genes was conducted by quantitative Polymerase Chain Reaction (RT-qPCR). Changes in the expression of genes associated with inflammation were assessed for each disease phenotype. Statistical analysis of differential gene expression was performed using the Mann-Whitney U non-parametric test. A p value < 0.05 was considered significant. RESULTS: A total of 82 patients were included and were divided into the following groups: Group BE, 16 (19.51%); Group EE, 23 (28.04%); Group AAE, 13 (15.86%); NAE 13 (15.86%); and Control Group, 17 (20.73%). Compared with the control group, patients with BE exhibited increased IL-8 expression (p < 0.05) and increased levels of IL-10, MMP-3, and MMP-9. Patients with EE exhibited increased levels of IL-1B, IL-6 and IL-10 (p < 0.05), and patients with AAE exhibited increased expression of IL-1B, IL-6, IFN-γ and TNF-α (p < 0.05). AAE exhibited increased IL-1B and TNF-α expression compared with NAE (p < 0.05). CONCLUSION: This study demonstrates the differential expression of mediators of inflammation in the esophageal mucosa of patients with different GERD endoscopic phenotypes. IL-1B and TNF-α could be useful to differentially diagnose AAE and NAE in the non-erosive phenotype using endoscopic biopsies.

Can topical epinephrine application to the papilla prevent pancreatitis after endoscopic retrograde cholangiopancreatography? Results from a double blind, multicentre, placebo controlled, randomised clinical trial.

BACKGROUND AND STUDY AIMS: Post-endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis (PEP) is a complication associated with important morbidity, occasional mortality and high costs. Preventive strategies are suboptimal as PEP continues to affect 4% to 9% of patients. Spraying epinephrine on the papilla may decrease oedema and prevent PEP. This study aimed to compare rectal indomethacin plus epinephrine (EI) versus rectal indomethacin plus sterile water (WI) for the prevention of PEP. PATIENTS AND METHODS: This multicentre randomised controlled trial included patients aged >18 years with an indication for ERCP and naive major papilla. All patients received 100 mg of rectal indomethacin and 10 mL of sterile water or a 1:10 000 epinephrine dilution. Patients were asked about PEP symptoms via telephone 24 hours and 7 days after the procedure. The trial was stopped half way through after a new publication reported an increased incidence of PEP among patients receiving epinephrine. RESULTS: Of the 3602 patients deemed eligible, 3054 were excluded after screening. The remaining 548 patients were randomised to EI group (n=275) or WI group (n=273). The EI and WI groups had similar baseline characteristics. Patients in the EI group had a similar incidence of PEP to those in the WI group (3.6% (10/275) vs 5.12% (14/273), p=0.41). Pancreatic duct guidewire insertion was identified as a risk factor for PEP (OR 4.38, 95% CI (1.44 to 13.29), p=0.009). CONCLUSION: Spraying epinephrine on the papilla was no more effective than rectal indomethacin alone for the prevention of PEP. TRIAL REGISTRATION NUMBER: This study was registered with ClinicalTrials.gov (NCT02959112).

Prevalence of burnout syndrome in gastroenterologists and endoscopists: results of a national survey in Mexico.

BACKGROUND: Burnout syndrome (BOS) is characterized by emotional exhaustion, depersonalization and reduced personal accomplishment. It affects doctors, patients and their inter-relationship. There is a lack of data on BOS in Mexico. The main objective of the present study is to evaluate the prevalence of BOS in physician members of the Mexican gastroenterological association (MGA) and Mexican association for gastrointestinal endoscopy (MAGE). MATERIALS AND METHODS: Cross sectional, prospective study through anonymous electronic survey via e-mail, sent to members of the MGA (n = 1192) and MAGE (n = 600). The survey included questions about basic sociodemographic information, Maslach Burnout Inventory, and factors potentially associated with BOS. Continuous variables were summarized as means and ANOVA or Kruskal-Wallis test were used to compare groups. Nominal variables were summarized as proportions and Fisher's exact test or Χ2 test were used, as appropriate. RESULTS: A total of 1792 e-mail invitations were delivered and 411 answers were received with a response rate of 22.9%. The prevalence of BOS according to the Maslach Burnout Inventory was 26.3% (108/411). The prevalence of BOS according to the single-item self-defined burnout question (SISDBOQ) was 32.6% (134/411). The Kappa coefficient for emotional exhaustion between the SISDBOQ and Maslach inventory was 0.48 (p = 0.0001). Factors associated with BOS included performing endoscopic procedures (OR 2.9 (1.2-6.6); p = 0.008), lack of support from colleagues upon complications (OR 0.2 (0.1-0.4); p = 0.0001), receiving frequent reprimands from superiors (OR 2.4 (1.5-3.8); p = 0.0001), work unrelated to medicine (OR 2.4 (1.4-3.9); p = 0.0001), work violence/harassment (OR 3.0 (1.9-4.9); p = 0.0001) and living in a big city (OR 1.9 (1.2-3); p = 0.005). CONCLUSION: BOS is a frequent entity in Mexican gastroenterologists and endoscopists. There are potentially modifiable factors associated with BOS.

A low-residue diet before colonoscopy tends to improve tolerability by patients with no differences in preparation quality: a randomized trial.

BACKGROUND: The pre-colonoscopy diet traditionally involves 24 h of a clear liquid diet (CLD) in combination with a lavage solution; however, this preparation is poorly tolerated. AIM: To compare the impact on the quality of bowel cleansing and tolerability of a CLD versus a low-residue diet (LRD). METHODS: We performed a randomized trial. Subjects were randomized to CLD or LRD the day before of elective colonoscopy. All subjects received a 4-L preparation of single-dose PEG beginning 16 h prior to colonoscopy. The Boston bowel preparation scale was used to evaluate bowel cleansing; an adequate-quality preparation was defined as a score ≥ 2 per segment. RESULTS: A total of 205 subjects were included with a mean age (SD) of 55.6 (12.6) years; 133 (64.9%) of them were female. A total of 105 subjects were randomized to receive CLD and 100 to LRD. No significant differences in bowel preparation quality were observed between groups according to the section of colon: right colon (70% vs. 73%, p = 0.08), transverse colon (82% vs. 79%, p = 0.062), or left colon (80% vs. 78.7%, p = 0.28). There was a tendency toward less-frequent nausea (p = 0.08) and vomiting (p = 0.07) in patients with LRD. No differences between groups regarding ADR (12% vs. 10%) were noted. CONCLUSIONS: An LRD before colonoscopy resulted in a tendency toward improved tolerability by patients, with no differences in the quality of bowel preparation.

Increased Mortality from Extrapancreatic Infections in Hospitalized Patients with Acute Pancreatitis.

Nosocomial extrapancreatic infections in patients with acute pancreatitis (AP) are associated with a higher mortality even after adjusting the risk for the severity of the pancreatitis. The aim of this study was to describe the clinical features of hospitalized patients with AP who died during their hospitalization and to evaluate risk factors associated with mortality. We performed a descriptive study of the clinical features of adult patients who died from AP during their hospitalization and a case control study with a paired group of patients that survived AP during a 10-year period. Data of interest were collected from the medical records and are presented with appropriate measures of central tendency and dispersion. For the case control study, the primary outcome evaluated was death, and to evaluate associated clinical features and determine differences between groups, we performed the χ 2 or Fisher's exact tests for categorical variables and the Student t-test or Mann-Whitney U test for continuous variables as appropriate. We found 48 patients with acute pancreatitis who died within the period of the study during hospitalization; from these, 50% were men, mean age was 53.2 years, and the most common etiology was biliary obstruction by gallstones in 45.8%. The global mortality rate was of 2.5%. A total of 43.7% patients had infected pancreatic necrosis, and in 58.3%, some extrapancreatic infection was documented, being the most common urinary tract infection in 50%, bacteremia in 50% and pneumonia in 33.3%. Clinical features associated with mortality were the presence of organ failure (p < 0.001), nosocomial complications (p < 0.001), infected necrosis (p < 0.001), and extrapancreatic infections (p = 0.002). From the different extrapancreatic infections, only bacteremia (p = 0.001) and pneumonia (p = 0.011) were associated with higher mortality. In conclusion, extrapancreatic infections are associated with increased mortality among hospitalized patients with acute pancreatitis, in particular, bacteremia and pneumonia with an isolated pathogen.

Higher adenoma detection rate with the endocuff: a randomized trial.

Background and study aim Different techniques have been introduced to improve the endoscopist's view and enhance the detection of polyps. The endocuff is a polymer sleeve cap that is connected to the tip of the colonoscope in order to improve visualization of the mucosa during colonoscopy. The aim of the study was to compare adenoma detection rates (ADR) of endocuff-assisted colonoscopy and conventional colonoscopy. Patients and methods Patients 50 years or older were randomized into two groups: an endocuff-assisted colonoscopy group and a conventional colonoscopy group without the endocuff. Results A total of 337 patients were included: 174 in the endocuff group and 163 in the conventional group. The median age was 61 years (interquartile range 55 - 70 years), and 74 % were women. The ADR was higher in the endocuff group than in the conventional group (22.4 % vs. 13.5 %; P = 0.02). The mean number of adenomas was 0.30 (SD 0.25) in the endocuff group and 0.21 (SD 0.26) in the conventional group (P â€Š= 0.02). The rate of ileal intubation was lower in the endocuff group (73 % vs. 87 %; P < 0.001). No serious adverse events occurred with the use of the endocuff. Conclusions Endocuff colonoscopy achieved a greater ADR than conventional colonoscopy.Trial registered at ClinicalTrials.gov (NTC02387593).