specimen-collection-and-analysis-of-the-duodenal-microbiome

Specimen Collection and Analysis of the Duodenal Microbiome

Shifts in the microbiome have been correlated with the physiology and pathophysiology of many organ systems both in humans and in mouse models. The gut ...

Veterans Administration Greater Los Angeles Healthcare System

David Geffen School of Medicine at University of California

The first goal of therapy is to assess hemodynamic stability in a patient presenting with evidence of upper gastrointestinal bleeding and, second, to maintain hemodynamic stability using crystalloids or packed red blood cells. The diagnosis of the cause of upper gastrointestinal bleeding should be performed using endoscopic techniques, which should be performed early. Therapy directed at treating the cause of upper gastrointestinal bleeding should be initiated at the time of endoscopy. Pharmacologic management should be based on the prevention of ulcer rebleeding and should be initiated at the time of endoscopic diagnosis. Surgery should be considered only in cases when endoscopic and pharmacologic treatments are deemed a failure.

Pharmacologic Treatment of Upper Gastrointestinal Bleeding.

PAC1 is a recently cloned and characterized heptahelical, G protein-coupled receptor with high affinity to PACAP-27 and PACAP-38 and is differentially coupled to activate intracellular Ca2+ and cAMP. PAC1 is expressed as four major splice variants, each possessing differential coupling to inositol phosphates and intracellular Ca2+. PAC1 has been shown previously to be expressed and regulate the growth and proliferation of nonsquamous cell lung cancer cells, as well as breast cancer cell lines. PAC1 is expressed on the HCT8 human colon cancer cell line and is coupled to the activation of both intracellular cAMP and Ca2+ with consequent stimulation of growth. In the current study, we contrast the effects of pituitary adenylate cyclase-activating polypeptide (PACAP) on the HCT8 colon cancer cell lines to the HCT116 and FET cell lines wherein PAC1 is expressed as the SV1 or HIP splice variant and is coupled to the activation only of cAMP but not of intracellular Ca2+. These data indicate that human colon tumor cells express PAC1 and are differentially coupled to intracellular signal transduction molecules. The ability to activate both cAMP and Ca2+ appears to be a prerequisite for activation of tumor proliferation, indicating a potentially important factor in how PACAP potentiates the growth of certain tumors.

Differential coupling of the PAC1 SV1 splice variant on human colonic tumors to the activation of intracellular cAMP but not intracellular Ca2+ does not activate tumor proliferation.

Rabeprazole controls GERD symptoms in a patient for whom treatment with lansoprazole failed: first report of "cluster GERD.".

To safely manage the hypersecretory state in patients with Zollinger-Ellison syndrome, both upper endoscopy and gastric analysis are required to titrate optimal medical therapy. Conventional gastric analysis requires more than 1 hour to perform and results in significant patient dissatisfaction. In this study, we have validated endoscopic gastric analysis as a novel technique that can effectively replace conventional gastric analysis.

Validation of a new endoscopic technique to assess acid output in Zollinger-Ellison syndrome.

Historically, limited trials evaluating biotherapy in treating metastatic neuroendocrine tumours have yielded mixed results. In this study, the efficacy of a novel combination therapy featuring longacting Sandostatin LAR plus alpha-interferon was evaluated. In a prospective case series, 12 patients with unresectable metastatic neuroendocrine tumours refractory to treatment initiated therapy with Infergen and Sandostatin LAR. Radiological response was followed serially at 3-month intervals. A biochemical response was considered significant if marker levels decreased by > or = 50% compared with baseline. Inhibition of tumour growth lasting for greater than 3 months (mean response 22.6+/-17.7 months) was seen in eight patients. Complete tumour regression was observed in one patient, lasting for 40 months; three patients exhibited partial tumour regression (mean response 29.3+/-24.0 months), and four patients maintained a stable tumour response (mean response 13.3+/-9.2 months). Four patients showed no response to therapy (mean response 5.0+/-6.0 months). All enrolled patients are alive currently. The biochemical response seen in seven patients did not correlate with the radiological response. These results suggest that the novel combination of longacting Sandostatin LAR with an alpha-interferon may be at least as effective as either combination therapy with short-acting octreotide or monotherapy with Sandostatin LAR.

Cyto-reduction of neuroendocrine tumours using Sandostatin LAR in combination with Infergen: results of a case series.

Do COX-2 inhibitors reduce metachronous cancer development?

Nocturnal reflux is a largely undiagnosed and unmanaged condition predisposing to multiple esophageal complications. We evaluated the effects of rabeprazole and pantoprazole on nocturnal intragastric pH and gastric acid output during Day 1 of therapy following the consumption of standard meals.

Comparative efficacy of rabeprazole and pantoprazole in the control of nocturnal Acid output and intragastric acidity.

Pituitary adenylate cyclase-activating polypeptide (PACAP) has been shown to increase the histamine release from gastric enterochromaffin-like (ECL) cells and promote gastric acid secretion in rats. In contrast, in mice, PACAP has been demonstrated to induce a decrease of gastric acid secretion, an effect presumably due to somatostatin release. To more clearly define the role of PACAP in the regulation of gastric acid output, a knockout mouse model for the PACAP-specific receptor PAC1 was applied in this study. Measurements of the basal and stimulated gastric acid secretion and morphological studies on the gastric mucosa were performed in both wild-type and PAC1-deficient mice. Compared with the wild-type mice, the PAC1-deficient mice showed a nearly threefold higher basal gastric acid output, increased gastric mucosa thickness and glands height, and proportional increases in parietal and total cell counts in the gastric mucosa. The PAC1-deficient mice also showed a trend of increased plasma gastrin levels and gastrin gene expression in the gastric mucosa. This study indicates that the expression of PAC1 is clearly important for maintaining the homeostasis of gastric acid secretion. Loss of PACAP receptor during development may lead to a compensatory mechanism regulating gastric acid secretion.

PAC1 deficiency in a murine model induces gastric mucosa hypertrophy and higher basal gastric acid output.

The voltage gated sodium channel SCN4A mutations account for non-dystrophic myotonia and include a heterogeneous group of conditions that include hyperkalemic periodic paralysis, paramyotonica congenita, potassium-aggravated myotonia, and hypokalemic periodic paralysis type 2. This case report proposes that a rare variant p.Pro1629Leu in SCN4A can cause a skeletal muscle deficit with intermittent dysphagia.

A Sodium Channel Myotonia Presenting with Intermittent Dysphagia as a Manifestation of a Rare SCN4A Variant.

Passing the "Acid Test": Do Proton Pump Inhibitors Affect the Composition of the Microbiome?

The global obesity epidemic is driving the concomitant rise in nonalcoholic fatty liver disease (NAFLD). To identify new genes involved in central liver functions, we examined liver RNA-sequence data from 259 patients who underwent morbidly obese bariatric surgery. Of these patients, 84 had normal liver histology, 40 simple steatosis, 43 nonalcoholic steatohepatitis, and the remaining 92 patients had varying degrees of NAFLD based on liver histology. We discovered oligodendrocyte maturation-associated long intergenic noncoding RNA () a long intervening noncoding RNA (lincRNA) in a human liver co-expression network (n = 75 genes) that was strongly associated with statin use and serum triglycerides (TGs).  liver expression was highly correlated with the expression of known cholesterol biosynthesis genes and stearoyl-coenzyme A desaturase ().  is the rate-limiting enzyme in monounsaturated fatty acids and a key TG gene that is known to be up-regulated in liver steatosis and NAFLD and resides adjacent to  on the human chromosome 10q24.31. Next, we functionally demonstrated that  regulates  as an enhancer-RNA (eRNA), thus describing the first lincRNA that functions as an eRNA to regulate lipid metabolism. Specifically, we show that  promotes liver expression of  in  through regional chromosomal DNA-DNA looping interactions.  The primate-specific lincRNA  is a novel epigenetic regulator of the key TG and NAFLD gene .

Novel Lipid Long Intervening Noncoding RNA, Oligodendrocyte Maturation-Associated Long Intergenic Noncoding RNA, Regulates the Liver Steatosis Gene Stearoyl-Coenzyme A Desaturase As an Enhancer RNA.

 The gut microbiome is a key factor in chronic liver disease progression. In prior research, we found that the duodenal microbiome was associated with sex, ethnicity, and cirrhosis complications. Here, we examined the association between diet and the duodenal microbiome in patients with liver cirrhosis. This study included 51 participants who completed a detailed food frequency questionnaire and donated duodenal biopsies for microbiome characterization by 16S ribosomal RNA gene sequencing. Data were analyzed for alpha diversity, beta diversity, and association of taxa abundance with diet quality and components using QIIME 2 pipelines. Diet quality was assessed through calculation of the Healthy Eating Index 2010. Participants with higher adherence to protein recommendations exhibited increased microbial richness and evenness ( = 0.03) and a different microbial profile compared to those with lower adherence ( = 0.03).  and  were increased in association with increased protein adherence. Fiber consumption was also associated with the duodenal microbial profile ( = 0.01), with several taxa exhibiting significantly decreased or increased abundance in association with fiber intake. Coffee drinking was associated with microbial richness and evenness ( = 0.001), and there was a dose-response association between coffee drinking and relative abundance of  ( = 0.01). We conclude that protein, fiber, and coffee are associated with diversity and composition of the duodenal microbiome in liver cirrhosis.

Dietary Protein, Fiber and Coffee Are Associated with Small Intestine Microbiome Composition and Diversity in Patients with Liver Cirrhosis.

High protein calorie restriction diets have shown clinical efficacy for obesity, but the mechanisms are not fully known. The intestinal microbiome is a mediator of obesity and preclinical data support an effect of high protein diet (HPD) on the gut microbiome of obesity, but there are few studies in humans.

Article	Year
Pharmacologic Treatment of Upper Gastrointestinal Bleeding. Current treatment options in gastroenterology\| PubMed ID: 12628074	2003
Differential coupling of the PAC1 SV1 splice variant on human colonic tumors to the activation of intracellular cAMP but not intracellular Ca2+ does not activate tumor proliferation. Journal of molecular neuroscience : MN\| PubMed ID: 14742913	2004
Rabeprazole controls GERD symptoms in a patient for whom treatment with lansoprazole failed: first report of "cluster GERD.". Digestive diseases and sciences\| PubMed ID: 15912621	2005
Validation of a new endoscopic technique to assess acid output in Zollinger-Ellison syndrome. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association\| PubMed ID: 17101299	2006
Cyto-reduction of neuroendocrine tumours using Sandostatin LAR in combination with Infergen: results of a case series. The Journal of pharmacy and pharmacology\| PubMed ID: 17331326	2006
Do COX-2 inhibitors reduce metachronous cancer development? Current gastroenterology reports\| PubMed ID: 19903417	2009
Comparative efficacy of rabeprazole and pantoprazole in the control of nocturnal Acid output and intragastric acidity. Gut and liver\| PubMed ID: 20485608	2008
PAC1 deficiency in a murine model induces gastric mucosa hypertrophy and higher basal gastric acid output. Journal of molecular neuroscience : MN\| PubMed ID: 20821075	2011
A Sodium Channel Myotonia Presenting with Intermittent Dysphagia as a Manifestation of a Rare SCN4A Variant. Journal of molecular neuroscience : MN\| PubMed ID: 28012096	2017
Passing the "Acid Test": Do Proton Pump Inhibitors Affect the Composition of the Microbiome? Digestive diseases and sciences\| PubMed ID: 30218426	2018
Novel Lipid Long Intervening Noncoding RNA, Oligodendrocyte Maturation-Associated Long Intergenic Noncoding RNA, Regulates the Liver Steatosis Gene Stearoyl-Coenzyme A Desaturase As an Enhan... Hepatology communications\| PubMed ID: 31592021	2019
Dietary Protein, Fiber and Coffee Are Associated with Small Intestine Microbiome Composition and Diversity in Patients with Liver Cirrhosis. Nutrients\| PubMed ID: 32414035	2020
A High Protein Calorie Restriction Diet Alters the Gut Microbiome in Obesity. Nutrients\| PubMed ID: 33096810	2020

Joseph R. Pisegna

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