Quantitative metaproteomics and activity-based protein profiling of patient fecal microbiome identifies host and microbial serine-type endopeptidase activity associated with ulcerative colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.

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Identified 176 significantly altered protein groups between healthy and UC patients.

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Serine-type endopeptidase activity is overrepresented in UC patients.

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Fluorophosphonate ABPP shows that endopeptidases are active in fecal samples.

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ABPP enrichment helps identify additional putative serine hydrolases in samples.

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De novo sequencing used to estimate number of MS2 spectra unidentified by ComPIL.

Safety and efficacy of endoscopic spray cryotherapy for esophageal cancer

Although surgery is traditionally the standard of care for esophageal cancer, esophagectomy carries significant morbidity. Alternative endoscopic therapies are needed for patients who are not candidates for conventional treatment. The objective of this study is to assess the safety, efficacy, and tolerability of spray cryotherapy of esophageal adenocarcinoma. This study includes patients with esophageal adenocarcinoma who had failed or were not candidates for conventional therapy enrolled retrospectively and prospectively in an open-label registry and patients in a retrospective cohort from 11 academic and community practices. Endoscopic spray cryotherapy was performed until biopsy proven local tumor eradication or until treatment was halted due to progression of disease, patient withdrawal or comorbidities. Eighty-eight patients with esophageal adenocarcinoma (median age 76, 80.7% male, mean length 5.1 cm) underwent 359 treatments (mean 4.4 per patient). Tumor stages included 39 with T1a, 25 with T1b, 9 with unspecified T1, and 15 with T2. Eighty-six patients completed treatment with complete response of intraluminal disease in 55.8%, including complete response in 76.3% for T1a, 45.8% for T1b, 66.2% for all T1, and 6.7% for T2. Mean follow-up was 18.4 months. There were no deaths or perforations related to spray cryotherapy. Strictures developed in 12 of 88 patients (13.6%) but were present before spray cryotherapy in 3 of 12. This study suggests that endoscopic spray cryotherapy is a safe, well-tolerated, and effective treatment option for early esophageal adenocarcinoma.

A rare case of primary rectal squamous cell carcinoma diagnosed by endoscopic ultrasound

Primary squamous cell carcinoma (SCC) of the rectum is a very rare entity making up to 0.1-0.25/1,000 cases of all colorectal cancers. Here, we present the case of an otherwise healthy 63-year-old female who presented with progressive pelvic discomfort, new onset constipation and a complex mass in presacral region on imaging which was proved to be poorly differentiated SCC of the rectum. The correct diagnosis was achieved by fine needle aspiration (FNA) via endoscopic ultrasound (EUS-guided FNA) as initial conventional colonoscopy failed to establish the diagnosis. Patient completed neoadjuvant chemo-radiation and her tumor was successfully resected. She is following up with oncology clinic for monitoring and further management.

Continuous negative external pressure (cNEP) reduces respiratory impairment during screening colonoscopy: a pilot study

BACKGROUND AND STUDY AIMS

Drugs administered during gastrointestinal procedures cause increased collapsibility of the upper airway, which may lead to respiratory impairment. We evaluated the ability of continuous negative external pressure (cNEP) to lessen respiratory impairment during screening colonoscopy.

PATIENTS AND METHODS

The initial 24 patients served as controls, while the next 30 received cNEP. cNEP was delivered by a soft silicone collar placed over the anterior neck. The primary endpoint was the frequency of respiratory impairment, defined as either: (i) a decline from baseline of > 4 % in oxygen saturation, or (ii) apnea lasting ≥ 20 seconds.

RESULTS

Mean respiratory impairment episodes were 3.50 in the no-cNEP group vs. 1.92 in the cNEP group, a reduction of 45 % (P = 0.022). Apneas ≥ 20 seconds occurred in 74 % of the no-cNEP group and 28 % of the cNEP group (P = 0.002). While 42 % of the no-cNEP group required increased supplemental oxygen, this was true for only 10 % of the cNEP group (P = 0.01). cNEP adverse events were minimal.

CONCLUSIONS

During screening colonoscopy, sedation-related respiratory impairment is significantly reduced by cNEP.ClinicalTrials.gov NCT01895062.

Safety and efficacy of endoscopic spray cryotherapy for Barrett's dysplasia: results of the National Cryospray Registry

Retrospective series have shown the efficacy of endoscopic spray cryotherapy in eradicating high-grade dysplasia (HGD) in Barrett's esophagus (BE); however, prospective data are lacking, and efficacy for low-grade dysplasia (LGD) is unclear. The aim of this study was to assess the efficacy and safety of spray cryotherapy in patients with LGD or HGD. A multicenter, prospective open-label registry enrolled patients with dysplastic BE. Spray cryotherapy was performed every 2-3 months until there was no endoscopic evidence of BE and no histological evidence of dysplasia, followed by surveillance endoscopies up to 2 years. Primary outcome measures were complete eradication of dysplasia (CE-D) and complete eradication of all intestinal metaplasia (CE-IM). Ninety-six subjects with Barrett's dysplasia (67% HGD; 65% long-segment BE; mean length 4.5 cm) underwent 321 treatments (mean 3.3 per subject). Mean age was 67 years, 83% were male. Eighty patients (83%) completed treatment with follow-up endoscopy (mean duration 21 months). In patients with LGD, rate of CE-D was 91% (21/23) and rate of CE-IM was 61% (14/23). In HGD, CE-D rate was 81% (46/57) and CE-IM was 65% (37/57). In patients with short-segment BE (SSBE) with any dysplasia, CE-D was achieved in 97% (30/31) and CE-IM in 77% (24/31). There were no esophageal perforations or related deaths. One subject developed a stricture, which did not require dilation. One patient was hospitalized for bleeding in the setting of non-steroidal anti-inflammatory drug use. In the largest prospective cohort to date, data suggest endoscopic spray cryotherapy is a safe and effective modality for eradication of BE with LGD or HGD, particularly with SSBE.

Malignant cell contamination may lead to false-positive findings at endosonographic fine needle aspiration for tumor staging

BACKGROUND AND STUDY AIMS

Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) of lymph nodes is used for staging of gastrointestinal malignancies. False-positive rates of 5 % - 7 % are not well understood. Elements of EUS examinations that contribute to false-positive cytological findings were investigated.

PATIENTS AND METHODS

13 patients undergoing EUS staging of gastrointestinal luminal malignancy were consecutively enrolled together with 3 patients with extraluminal tumors (pancreas, lung) defined as controls. After EUS, cellular debris and fluid were collected from the FNA needle catheter, instrument channel, and endoscope tip for cytologic and histologic investigation.

RESULTS

6 of 13 patients (46 %) had malignant cells contaminating the FNA needle catheter, instrument channel, or endoscope tip. Malignant cells were present in the instrument channel in 5 cases (38 %), exterior tip of echoendoscope in 4 (31 %) and needle catheter in 2 (15 %).

CONCLUSIONS

Echoendoscopes used for FNA in patients with luminal tumors are at risk for malignant cell contamination of the instrument channel, FNA needle catheter, and echoendoscope tip. FNA needle contamination can contribute to false-positive findings.

Small-bowel endoscopy core curriculum

This is one of a series of documents prepared by the ASGE Training Committee. This curriculum document contains recommendations for training, intended for use by endoscopy training directors, endoscopists involved in teaching endoscopy, and trainees in endoscopy. It was developed as an overview of techniques currently favored for the performance and training of small-bowel endoscopy and to serve as a guide to published references, videotapes, and other resources available to the trainer. By providing information to endoscopy trainers about the common practices used by experts in performing the technical aspects of the procedure, the ASGE hopes to improve the teaching and performance of small-bowel endoscopy.

The noncolonic microbiome: does it really matter?

About 100 trillion microorganisms compose the microbiome of the gastrointestinal tract and are predominantly found within the colon. Until recently, few bacteria were thought to inhabit the normal healthy esophagus and stomach. However, contemporary studies using molecular techniques have contradicted these assumptions. In this review, we summarize the pertinent findings of these studies that demonstrate established, complex mixed-microbial communities within the foregut in both health and disease. These studies contribute to improved understanding of interactions between the host immunity and the microbiome that may ultimately allow for novel therapeutic targets.

The microbiome and obesity: is obesity linked to our gut flora?

The human gut is a lush microbial ecosystem containing about 100 trillion microorganisms, whose collective genome, the microbiome, contains 100-fold more genes than the entire human genome. The symbiosis of our extended genome plays a role in host homeostasis and energy extraction from diet. In this article, we summarize some of the studies that have advanced the understanding of the microbiome and its effects on metabolism, obesity, and health. Metagenomic studies demonstrated that certain mixes of gut microbiota may protect or predispose the host to obesity. Furthermore, microbiota transplantation studies in germ-free murine models showed that the efficient energy extraction traits of obese-type gut flora are transmissible. The proposed methods by which the microbiome may contribute to obesity include increasing dietary energy harvest, promoting fat deposition, and triggering systemic inflammation. Future treatments for obesity may involve modulation of gut microbiota using probiotics or prebiotics.

The Effect of Metformin and Standard Therapy versus Standard Therapy alone in Nondiabetic Patients with Insulin Resistance and Nonalcoholic Steatohepatitis (NASH): A Pilot Trial

Nonalcoholic steatohepatitis (NASH) is increasing in prevalence and is related to underlying insulin resistance. The aim of this study was to assess the efficacy of metformin on the characteristic histopathologic lesions of NASH. This was a 12-month prospective, randomized, placebo-controlled trial comparing diet and exercise alone to diet, exercise and metformin in nondiabetic patients with insulin resistance and NASH. Patients were randomized to either group A or B. Group A received placebo, dietary counseling, recommendations for weight loss and exercise four times per week. Group B received long-acting metformin 500 mg daily (titrated to 1000 mg daily) plus dietary counseling, recommendations for weight loss and exercise four times per week. Histopathology was assessed at 12 months and biopsies were scored by two pathologists who were blinded to all data. Twenty-three subjects were screened and 19 were randomized to either group A (n ¼10) or group B (n¼ 9). Seven of the 10 subjects in group A completed the study including repeat liver biopsy while all patients in group B completed the study. Body mass index improved in both groups decreasing by 1.7 kg/m(2) in group A and 0.9 kg/m(2) in group B (not significant, control versus treatment). Homeostasis model assessment of insulin resistance scores improved in both groups decreasing by 1.14 in group A and 1.58 in group B (not significant, control versus treatment). No significant difference in histopathology was seen between groups on follow-up liver biopsy. Metformin appeared to have little effect in improvement in liver function tests or liver histology in nondiabetic patients with insulin resistance and NASH. Decrease in BMI through diet and exercise significantly improved HOMA-IR scores, serum aminotransferases and liver histology.

Herpes simplex virus and the alimentary tract

Herpes simplex virus (HSV) infection is well known as a sexually transmitted disease. However, relatively little has been published concerning the presentations and treatment of HSV infection within the gastrointestinal tract, where HSV most commonly affects the esophagus in both immunocompromised and immunocompetent patients. HSV proctitis is not uncommon and occurs primarily in males having sex with males. In patients with normal immune systems, gastrointestinal HSV infections are generally self-limited and rarely require antiviral therapy. Treatment of infection is suggested for immunocompromised patients, though no large randomized controlled trials have been performed. This article reviews the manifestations of HSV infection within the luminal gastrointestinal tract and options for diagnosis and treatment.

Prevalence of irritable bowel syndrome and depression in fibromyalgia

The purpose of this study was to determine the point prevalence of depressive symptoms, using the PRIME-MD questionnaire, and irritable bowel syndrome (IBS), while comparing the Rome II to the Rome I criteria, in patients with fibromyalgia (FM) and rheumatologic controls in an outpatient setting. The prevalence of IBS in FM patients (n = 105) was 63% by Rome I and 81% by Rome II criteria. The prevalence of IBS in controls (n = 62) was 15% by Rome I and 24% by Rome II criteria (FM vs. control; P < 0.001). Depressive symptoms were met in 40% of FM patients and 8% of controls (P < 0.001). The coexistence of IBS and depressive symptoms in the FM patients was 31% (Rome I) and 34% (Rome II). The prevalence of IBS and depressive symptoms was higher in FM patients compared to the control population. Identification of IBS and depressive symptoms in FM patients might enable clinicians to better meet the needs of this patient population.

Hepatocellular Carcinoma in a Patient with Human Immunodeficiency Virus and Hepatitis B Virus Coinfection: An Emerging Problem?

Infections with hepatitis B virus (HBV) and human immunodeficiency virus (HIV) have similar risk factors and routes of transmission. It is estimated that 64 to 84% of HIV-infected individuals have positive markers for anti-HBc antibodies, with the chronic HBV infection rate approaching 16%. There is, however, a paucity of information on HBV/HIV coinfection, and its clinical implications remain unclear. We review the literature and report our recent experience with a 44-year-old man with HBV/HIV coinfection who developed metastatic hepatocellular carcinoma despite quiescent HBV and HIV disease courses. Highly active antiretroviral therapy has revolutionized HIV disease. As a result, morbidity and mortality from other underlying chronic, non-HIV-related diseases, such as the HBV infection and hepatocellular carcinoma reported here, will likely continue to increase in the HIV-infected patient population.

Gastrointestinal tuberculosis

Gastrointestinal tuberculosis is defined as infection of the peritoneum, hollow or solid abdominal organs, and abdominal lymphatics with Mycobacterium tuberculosis organisms. Gastrointestinal tuberculosis is relatively rare in the United States and is the sixth most common extrapulmonary location. Populations at risk include immigrants to the United States, the homeless, prisoners, residents of long-term care facilities, and the immunocompromised. The peritoneum and the ileocecal region are the most likely sites of infection and are involved in the majority of cases by hematogenous spread or through swallowing of infected sputum from primary pulmonary tuberculosis. Pulmonary tuberculosis is apparent in less than half of patients. Patients usually present with abdominal pain, weight loss, fever, anorexia, change in bowel habits, nausea, and vomiting. The diagnosis is often delayed and is usually made through a combination of radiologic, endoscopic, microbiologic, histologic, and molecular techniques. Antimicrobial treatment is the same as for pulmonary tuberculosis. Surgery is occasionally required.

Evaluation of unexplained acute and acute recurrent pancreatitis using endoscopic retrograde cholangiopancreatography, sphincter of Oddi manometry and endoscopic ultrasound

BACKGROUND AND STUDY AIMS

Unexplained pancreatitis represents a diagnostic challenge. The aim of this study was to determine the diagnostic utility of endoscopic retrograde cholangiopancreatography (ERCP) with sphincter of Oddi manometry (SOM), bile analysis, and endoscopic ultrasound (EUS) in evaluating such patients.

PATIENTS AND METHODS

Of 162 patients referred for evaluation of pancreatitis, 72 with a known cause were excluded. The remainder ( n=90) was classified as having prior acute ( n=24) or recurrent acute pancreatitis ( n=66). Bile sampling and SOM were performed at the time of ERCP. EUS was used to assess for tumors and for chronic pancreatitis. Clinical outcomes were evaluated by questionnaire.

RESULTS

ERCP was successful in 88/89 patients (99 %). Manometry was successful in 63/67 patients (94 %), and 56 patients underwent EUS. Findings were categorized into five distinct etiologies: sphincter of Oddi dysfunction (SOD) ( n=28; 31 %), pancreas divisum ( n=18; 20 %), biliary ( n=18; 20 %), idiopathic ( n=18; 20 %) and tumor-related ( n=8; 9 %). Features of moderate or severe chronic pancreatitis by EUS and ERCP criteria were found in 18 patients (21 %); an additional nine patients had chronic pancreatitis by EUS criteria alone. EUS identified all the tumors. The condition was improved in 96 % of all patients undergoing endoscopic therapy.

CONCLUSION

An etiology was identified in the majority of patients with unexplained pancreatitis. SOD represented the most common finding. Moderate to severe chronic pancreatitis was found in over one-fifth of these patients. Bile analysis, SOM, and EUS are useful tools in the evaluation of unexplained acute pancreatitis.

EUS and fine-needle aspiration in the evaluation of mediastinal masses superior to the aortic arch

BACKGROUND

Mediastinal lesions require a tissue diagnosis. This cannot be obtained with CT-guided biopsy or bronchoscopy in many patients. Co-morbid diseases increase the risk of mediastinoscopy in some of these patients. EUS with fine-needle aspiration (FNA) is frequently used to obtain tissue from the mediastinum, but there have been no case series published of FNA of lesions superior to the aortic arch.

METHODS

This is the report of a case series of 4 patients with mediastinal masses superior to the aortic arch. EUS with a linear array echoendoscope and FNA were performed to evaluate each lesion.

OBSERVATIONS

All 4 patients underwent the procedure without complication, and cytologic material obtained in 3 was diagnostic. One patient had a nondiagnostic aspirate and underwent mediastinoscopy.

CONCLUSIONS

EUS with FNA is a safe and effective method for tissue diagnosis of mediastinal lesions. Heretofore, mediastinoscopy or transtracheal biopsy was required for diagnosis in patients with lesions superior to the aortic arch. However, for such lesions EUS with FNA appears to be an excellent alternative for establishing a diagnosis.

Eradication of Helicobacter pylori normalizes elevated mucosal levels of epidermal growth factor and its receptor

OBJECTIVE

Helicobacter pylori (H. pylori) infection has been linked to gastric cancer. The factors that promote carcinogenesis remain unknown. Epidermal growth factor (EGF) has been shown to be a potent epithelial mitogen and oncoprotein when sustained over expression occurs. Our aim was to compare gastric mucosal levels of EGF and its receptor (EGFR) among controls, H. pylori infected subjects, and subjects following H. pylori eradication using quantitative flow cytometric analysis.

METHODS

Patients referred for evaluation of dyspepsia underwent EGD and six antral biopsies were performed (two each for rapid urease testing (RUT), histopathology, and flow cytometry). Controls were those found to be H. pylori negative while subjects had confirmed infection. The study patients were treated, then had repeat EGD with biopsies.

RESULTS

There were 17 controls and 28 cases. Mean EGF and EGFR values were 2.69 and 2.46 for controls and 4.67 and 4.64 for subjects. Subjects' mean EGF was 73% higher (p = .035) and EGFR was 88% higher (p = 0.029) than controls. After treatment, the subjects' mean values declined 55% (p = 0.0001) for EGF and 40% (p = 0.002) for EGFR. Three subjects had persistent infection and showed no change in their EGF/EGFR levels. No difference was found among factor levels with respect to endoscopic findings.

CONCLUSIONS

Both EGF and EGFR from gastric antral biopsies are increased nearly 2-fold in infection with H. pylori. Infection eradication reduces levels of both factors to those of controls. One major pathogenic mechanism for gastric mucosal hyperproliferation and possibly carcinogenesis related to H. pylori may be the over expression of EGF and increased receptor density of EGFR on gastric mucosal cells.

Upper gastrointestinal tract bleeding

Upper GI bleeding is a serious and common emergency. Most upper GI bleeding will stop spontaneously but determining which patients will continue to bleed or rebleed is very difficult in the ED. Resuscitation and stabilization are the primary goals of the emergency physician. Hemorrhage control with pharmacotherapy or balloon tamponade may be necessary until urgent or emergent consultation with a gastroenterologist or surgeon is obtained. Early detection and treatment of H. pylori and the development of safer NSAIDs should alter the future of upper GI bleeding dramatically.