I am the director of the Celiac Disease Program at Stanford and I am highly experienced in diagnosis and management of celiac disease and gluten associated disorders.
My objective is to provide excellent and compassionate clinical care for my patients while seeking a better understanding of diseases I treat, particularly Celiac disease (CeD), eosinophilic esophagitis (EoE). My top priorities are patient care and translational research to make new discoveries and improve the care my patients.

Clinical Focus

  • Gastroenterology
  • Celiac Disease
  • Gluten Sensitivity
  • Esophageal Motility Disorders
  • Eosinophilic esophagitis
  • Eosinophilic Gastrointestinal Disorders
  • Gastroesophageal reflux disease
  • Scleroderma
  • Enterology

Professional Education

  • Board Certification: American Board of Internal Medicine, Gastroenterology (2023)
  • Fellowship: Beth Israel Deaconess Medical Center Dept of Gastroenterology (2009) MA
  • Residency: Massachusetts General Hospital Internal Medicine Residency (2005) MA
  • Medical Education: Albert Einstein College of Medicine (2002) NY
  • Board Certification: American Board of Internal Medicine, Gastroenterology (2009)

Clinical Trials

  • Functional Luminal Imaging Probe (FLIP) Topography Use in Patients With Scleroderma and Trouble Swallowing Not Recruiting

    FLIP topography has been FDA cleared to evaluate a variety of esophageal conditions, but has never been evaluated in patients with scleroderma. The investigators hope to evaluate this technology in patients who have scleroderma and various esophageal symptoms, and compare to non-scleroderma patients.

    Stanford is currently not accepting patients for this trial. For more information, please contact John O Clarke, MD, 650-736-5555.

    View full details

  • PTG-100 for Patients With Celiac Disease Not Recruiting

    The goal of this study is to learn whether or not the drug PTG-100 can reduce or prevent inflammatory injury to the small intestine that occurs when people with celiac disease eat food products containing gluten. This is a clinical research study to determine the safety and efficacy of PTG-100 in preventing gluten-induced inflammatory injury to the small intestine in patients with celiac disease. 30 patients will receive either placebo (fake drug) or PTG-100 (real drug) in capsule form twice daily for 42 days. They will also receive a gluten challenge twice daily in the form of a cookie or equivalent. An upper gastrointestinal endoscopy and exam including small bowel mucosa biopsy will be performed at the start of the treatment period and again at the end. Blood samples will be routinely taken to evaluate safety and the drug's mechanism of action throughout the study, and symptoms will be recorded using the celiac symptoms index (CSI) survey.

    Stanford is currently not accepting patients for this trial. For more information, please contact Aubrey. Adiao, 650-721-3177.

    View full details

All Publications

  • Baclofen and gastroesophageal reflux disease: seeing the forest through the trees. Clinical and translational gastroenterology Clarke, J. O., Fernandez-Becker, N. Q., Regalia, K. A., Triadafilopoulos, G. 2018; 9 (3): 137


    Baclofen has been shown to decrease reflux events and increase lower esophageal sphincter pressure, yet has never established a clear role in the treatment of gastroesophageal reflux disease (GERD). Lei and colleagues have shown in a recent elegant study that baclofen reduces the frequency and initiation of secondary peristalsis and heightens esophageal sensitivity to capsaicin-mediated stimulation. These findings may help explain both the benefit of baclofen in conditions such as rumination and supragastric belching, as well as the apparent lack of benefit of baclofen and other GABAB agonists in long-term treatment of GERD.

    View details for PubMedID 29599487

  • Clinical examinations: a medical student's perspective reply ADVANCES IN MEDICAL EDUCATION AND PRACTICE Shields, H. M., Fernandez-Becker, N. Q., Flier, S. N., Vaughn, B. P., Tukey, M. H., Pelletier, S. R., Horst, D. A. 2018; 9: 3–4
  • Efficacy of Video Capsule Endoscopy in the Management of Suspected Small Bowel Bleeding in Patients With Continuous Flow Left Ventricular Assist Devices. Gastroenterology research Zikos, T. A., Pan, J. n., Limketkai, B. n., Banerjee, D. n., Fernandez-Becker, N. n. 2017; 10 (5): 280–87


    Continuous flow left ventricular assist device (CF-LVAD) patients have a high prevalence of gastrointestinal bleeding from the small bowel. Video capsule endoscopy (VCE) is often used for diagnosis in these patients, but efficacy has yet to be determined. In this study, we evaluated the efficacy of VCE in the management of CF-LVAD patients with suspected small bowel bleeding by comparing to a non-VCE CF-LVAD control group.We retrospectively reviewed the charts of all patients with CF-LVADs implanted at Stanford Hospital from January 2010 to October 2015. Patients were included in the study if there was a clinical suspicion of small bowel bleeding and either a negative upper endoscopy or colonoscopy.A total of 26 patients met inclusion criteria for a total of 15 encounters where VCE was done, and 25 where VCE was not done. There were no statistical differences when comparing these groups in terms of medical therapy use (thalidomide or octreotide), enteroscopy use (double-balloon or push), intervention on lesions, or any 30-day outcomes. There was no advantage to VCE with regard to the composite endpoint time to re-bleed or death related to re-bleeding (median 114 vs. 161 days, P = 0.15) after removing patients who did not get a VCE due to death or critical illness.We did not find VCE changed management or outcomes in CF-LVAD patients with suspected small bowel bleeding at our institution when compared to a non-VCE control group. Our experience is small and single center, and larger, multi-center studies could further elucidate the utility of VCE in this patient population.

    View details for PubMedID 29118868

    View details for PubMedCentralID PMC5667693

  • Use of a footstool improves rectal balloon expulsion in some patients with defecatory disorders. Neurogastroenterology and motility Ulsh, L., Halawi, H., Triadafilopoulos, G., Gurland, B., Nguyen, L., Garcia, P., Sonu, I., Fernandez-Becker, N., Becker, L., Sheth, V., Neshatian, L. 2024: e14781


    Whether patients with defecatory disorders (DDs) with favorable response to a footstool have distinctive anorectal pressure characteristics is unknown. We aimed to identify the clinical phenotype and anorectal pressure profile of patients with DDs who benefit from a footstool.This is a retrospective review of patients with high resolution anorectal manometry (HR-ARM) and balloon expulsion test (BET) from a tertiary referral center. BET was repeated with a 7-inch-high footstool in those who failed it after 120 s. Data were compared among groups with respect to BET results.Of the 667 patients with DDs, a total of 251 (38%) had failed BET. A footstool corrected BET in 41 (16%) of those with failed BET. Gender-specific differences were noted in anorectal pressures, among patients with and without normal BET, revealing gender-based nuances in pathophysiology of DDs. Comparing patients who passed BET with footstool with those who did not, the presence of optimal stool consistency, with reduced instances of loose stools and decreased reliance on laxatives were significant. Additionally, in women who benefited from a footstool, lower anal pressures at rest and simulated defecation were observed. Independent factors associated with a successful BET with a footstool in women included age <50, Bristol 3 or 4 stool consistency, lower anal resting pressure and higher rectoanal pressure gradient.Identification of distinctive clinical and anorectal phenotype of patients who benefited from a footstool could provide insight into the factors influencing the efficacy of footstool utilization and allow for an individualized treatment approach in patients with DDs.

    View details for DOI 10.1111/nmo.14781

    View details for PubMedID 38488172

  • The association between vitamin-D deficiency and fecal incontinence. Neurogastroenterology and motility Neshatian, L., Grant, G., Fernandez-Becker, N., Yuan, Y., Garcia, P., Becker, L., Gurland, B., Triadafilopoulos, G. 2024: e14753


    BACKGROUND: Vitamin-D is essential for musculoskeletal health. We aimed to determine whether patients with fecal incontinence (FI): (1) are more likely to have vitamin-D deficiency and, (2) have higher rates of comorbid medical conditions.METHODS: We examined 18- to 90-year-old subjects who had 25-hydroxy vitamin-D levels, and no vitamin-D supplementation within 3months of testing, in a large, single-institutional electronic health records dataset, between 2017 and 2022. Cox proportional hazards survival analysis was used to assess association of vitamin-D deficiency on FI.KEY RESULTS: Of 100,111 unique individuals tested for serum 25-hydroxy vitamin-D, 1205 (1.2%) had an established diagnosis of FI. Most patients with FI were female (75.9% vs. 68.7%, p=0.0255), Caucasian (66.3% vs. 52%, p=0.0001), and older (64.2 vs. 53.8, p<0.0001). Smoking (6.56% vs. 2.64%, p=0.0001) and GI comorbidities, including constipation (44.9% vs. 9.17%, p=0.0001), irritable bowel syndrome (20.91% vs. 3.72%, p=0.0001), and diarrhea (28.55% vs. 5.2%, p=0.0001) were more common among FI patients. Charlson Comorbidity Index score was significantly higher in patients with FI (5.5 vs. 2.7, p<0.0001). Significantly higher proportions of patients with FI had vitamin-D deficiency (7.14% vs. 4.45%, p<0.0001). Moreover, after propensity-score matching, rate of new FI diagnosis was higher in patients with vitamin-D deficiency; HR 1.9 (95% CI [1.14-3.15]), p=0.0131.CONCLUSION & INFERENCES: Patients with FI had higher rates of vitamin-D deficiency along with increased overall morbidity. Future research is needed to determine whether increased rate of FI in patients with vitamin-D deficiency is related to frailty associated with increased medical morbidities.

    View details for DOI 10.1111/nmo.14753

    View details for PubMedID 38316640

  • A Case of mRNA Vaccine-Induced Autoimmunity Hu, K., Fernandez-Becker, N. LIPPINCOTT WILLIAMS & WILKINS. 2023: S2132
  • Cromolyn Reduces Symptoms in Patients With Irritable Bowel Syndrome, Functional Dyspepsia, or Gastroparesis Karhu, E., Linda Anh Nguyen, Sonu, I., Neshatian, L., Gottfried-Blackmore, A., Fernandez-Becker, N., Spencer, S. LIPPINCOTT WILLIAMS & WILKINS. 2023: S492
  • Esophageal Expert Development of a Disease-Specific Question Prompt List for Adults With Eosinophilic Esophagitis: A Modified Delphi Study Achalu, S., Berry, R., Bhargava, M., Bredenoord, A. J., Chang, J. W., Dellon, E. S., Falk, G., Fernandez-Becker, N., Hirano, I., Horsley-Silva, J. L., Leiman, D., Lynch, K., Peterson, K., Kamal, A. N. LIPPINCOTT WILLIAMS & WILKINS. 2023: S370
  • Development and Validation of a Machine Learning System to Identify Reflux Events in Esophageal 24-hour pH/Impedance Studies. Clinical and translational gastroenterology Zhou, M. J., Zikos, T., Goel, K., Goel, K., Gu, A., Re, C., Rodriguez, D., Clarke, J. O., Garcia, P., Fernandez-Becker, N., Sonu, I., Kamal, A., Sinha, S. R. 2023


    INTRODUCTION: Esophageal 24-hour pH/impedance testing is routinely performed to diagnose gastroesophageal reflux disease (GERD). Interpretation of these studies is time-intensive for expert physicians and has high inter-reader variability. There are no commercially available machine learning tools to assist with automated identification of reflux events in these studies.METHODS: A machine learning system to identify reflux events in 24-hour pH/impedance studies was developed, which included an initial signal processing step and a machine learning model. Gold standard reflux events were defined by a group of expert physicians. Performance metrics were computed to compare the machine learning system, current automated detection software (Reflux Reader v6.1), and an expert physician reader.RESULTS: The study cohort included 45 patients (20/5/20 patients in the training/validation/test sets, respectively). Mean age was 51 (standard deviation [SD] 14.5) years, 47% of patients were male, and 78% of studies were performed off proton pump inhibitor (PPI). Comparing the machine learning system vs. current automated software vs. expert physician reader, AUC was 0.87 (95% CI 0.85-0.89) vs. 0.40 (95% CI 0.37-0.42) vs. 0.83 (95% CI 0.81-0.86), respectively; sensitivity was 68.7% vs. 61.1% vs. 79.4%, respectively; and specificity was 80.8% vs. 18.6% vs. 87.3%, respectively.DISCUSSION: We trained and validated a novel machine learning system to successfully identify reflux events in 24-hour pH/impedance studies. Our model performance was superior to that of existing software and comparable to that of a human reader. Machine learning tools could significantly improve automated interpretation of pH/impedance studies.

    View details for DOI 10.14309/ctg.0000000000000634

    View details for PubMedID 37578060

  • The integrated relaxation pressure may not be an appropriate gold standard for deglutitive relaxation due to reliance on a single intragastric reference sensor. Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society Fass, O. Z., Regalia, K. A., Sweatt, A. J., Nandwani, M. C., Zikos, T. A., Fernandez-Becker, N. Q., Nguyen, L. A., Sonu, I. S., Triadafilopoulos, G., Clarke, J. O. 2023: e14635


    BACKGROUND: Integrated relaxation pressure (IRP) calculation depends on the selection of a single gastric reference sensor. Variable gastric pressure readings due to sensor selection can lead to diagnostic uncertainty. This study aimed to examine the effect of gastric reference sensor selection on IRP measurement and diagnosis.METHODS: We identified high-resolution manometry (HRM) conducted between January and November 2017 with at least six intragastric reference sensors. IRP measurements and Chicago Classification 3.0 (CCv3) diagnoses were obtained for each of six gastric reference sensors. Studies were categorized as "stable" (no change in diagnosis) or "variable" (change in diagnosis with gastric reference selection). Variable diagnoses were further divided into "variable normal/dysmotility" (≥1 normal IRP measurement and≥1 CCv3 diagnosis), or "variable dysmotility" (≥1 CCv3 diagnosis, only elevated IRP measurements). Bland-Altman plots were used to compare IRP measurements within HRM studies.KEY RESULTS: The analysis included 100 HRM studies, among which 18% had variable normal/dysmotility, and 10% had variable dysmotility. The average IRP difference between reference sensors was 6.7mmHg for variable normal/dysmotility and 5.9mmHg for variable dysmotility. The average difference between the proximal-most and distal-most sensors was -1.52mmHg (lower limit of agreement -10.03mmHg, upper limit of agreement 7.00mmHg).CONCLUSIONS & INFERENCES: IRP values can vary greatly depending on the reference sensor used, leading to inconsistent diagnoses in 28% of HRM studies. Choosing the correct gastric reference sensor is crucial for accurate test results and avoiding misdiagnosis. Standardization of reference sensor selection or supportive testing for uncertain results should be considered.

    View details for DOI 10.1111/nmo.14635

    View details for PubMedID 37357376

  • Multiplexed Tissue Imaging for Immune Cells Profiling During Peanut Allergy Immunotherapy Kaushik, A., Angoshtari, R., Kwow, S., Kambham, N., Fernandez-Becker, N., Manohar, M., Angelo, M., Galli, S., Nadeau, K., Dekruyff, R., Chinthrajah, S. MOSBY-ELSEVIER. 2023: AB34
  • Quality Indicators for the Diagnosis and Management of Eosinophilic Esophagitis. The American journal of gastroenterology Leiman, D. A., Kamal, A. N., Otaki, F., Bredenoord, A. J., Dellon, E. S., Falk, G. W., Fernandez-Becker, N. Q., Gonsalves, N., Hirano, I., Katzka, D. A., Peterson, K., Yadlapati, R., Kathpalia, P. 2023


    Despite best practice recommendations for managing eosinophilic esophagitis (EoE), variation in care exists.We used established methodology for quality indicator development to identify metrics to define quality for the treatment of EoE.Among 29 proposed quality indicator statements, 9 (31%) were adopted as highly valid across all categories. Two (22%) of these statements were identified as having existing or suspected quality gaps.We identified highly valid EoE quality indicators for adult gastroenterologists, which can be used for quality improvement with resulting benefits for patient outcomes.

    View details for DOI 10.14309/ajg.0000000000002138

    View details for PubMedID 36599135

  • The Impact of Intermittent Fasting on Patients With Suspected Gastroesophageal Reflux Disease. Journal of clinical gastroenterology Jiang, Y., Sonu, I., Garcia, P., Fernandez-Becker, N. Q., Kamal, A. N., Zikos, T. A., Singh, S., Neshatian, L., Triadafilopoulos, G., Goodman, S. N., Clarke, J. O. 2022


    GOAL: The aim was to investigate the short-term impact of time restricted feeding on patients with suspected gastroesophageal reflux disease (GERD).BACKGROUND: Lifestyle modifications are often suggested, but the role of diet in GERD is unclear. Intermittent fasting is popular in the media and has demonstrated potential benefits with weight loss and inflammatory conditions as well as alterations in gastrointestinal hormones.STUDY: Patients who were referred for 96-hour ambulatory wireless pH monitoring off proton pump inhibitor to investigate GERD symptoms were screened for eligibility. Patients were instructed to maintain their baseline diet for the first 2 days of pH monitoring and switch to an intermittent fasting regimen (16 consecutive hour fast and 8h eating window) for the second 2 days. Objective measures of reflux and GERD symptom severity were collected and analyzed.RESULTS: A total of 25 participants were analyzed. 9/25 (36%) fully adhered to the intermittent fasting regimen, with 21/25 (84%) demonstrating at least partial compliance. Mean acid exposure time on fasting days was 3.5% versus 4.3% on nonfasting days. Intermittent fasting was associated with a 0.64 reduction in acid exposure time (95% CI: -2.32, 1.05). There was a reduction in GERD symptom scores of heartburn and regurgitation during periods of intermittent fasting (14.3 vs. 9.9; difference of -4.46, 95% CI: -7.6,-1.32).CONCLUSIONS: Initial adherence to time restricted eating may be difficult for patients. There is weak statistical evidence to suggest that intermittent fasting mildly reduces acid exposure. Our data show that short-term intermittent fasting improves symptoms of both regurgitation and heartburn.

    View details for DOI 10.1097/MCG.0000000000001788

    View details for PubMedID 36730832

  • Hiding in Planus Sight: Localized Ulcerative Jejunitis in a Patient with Celiac Disease. Digestive diseases and sciences Zhou, W., Triadafilopoulos, G., Fernandez-Becker, N. 2022

    View details for DOI 10.1007/s10620-022-07693-4

    View details for PubMedID 36125592

  • KIR+CD8+ T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19. Science (New York, N.Y.) Li, J., Zaslavsky, M., Su, Y., Guo, J., Sikora, M. J., van Unen, V., Christophersen, A., Chiou, S., Chen, L., Li, J., Ji, X., Wilhelmy, J., McSween, A. M., Palanski, B. A., Mallajosyula, V. V., Bracey, N. A., Dhondalay, G. K., Bhamidipati, K., Pai, J., Kipp, L. B., Dunn, J. E., Hauser, S. L., Oksenberg, J. R., Satpathy, A. T., Robinson, W. H., Dekker, C. L., Steinmetz, L. M., Khosla, C., Utz, P. J., Sollid, L. M., Chien, Y., Heath, J. R., Fernandez-Becker, N. Q., Nadeau, K. C., Saligrama, N., Davis, M. M. 2022: eabi9591


    Here we find that CD8+ T cells expressing inhibitory killer cell immunoglobulin-like receptors (KIRs) are the human equivalent of Ly49+CD8+ regulatory T cells in mice and are increased in the blood and inflamed tissues of patients with a variety of autoimmune diseases. Moreover, these CD8+ T cells efficiently eliminated pathogenic gliadin-specific CD4+ T cells from celiac disease patients' leukocytes in vitro. We also find elevated levels of KIR+CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 patients, which correlated with disease severity and vasculitis. Selective ablation of Ly49+CD8+ T cells in virus-infected mice led to autoimmunity post infection. Our results indicate that in both species, these regulatory CD8+ T cells act uniquely to suppress pathogenic T cells in autoimmune and infectious diseases.

    View details for DOI 10.1126/science.abi9591

    View details for PubMedID 35258337

  • An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease. Nature communications Palanski, B. A., Weng, N., Zhang, L., Hilmer, A. J., Fall, L. A., Swaminathan, K., Jabri, B., Sousa, C., Fernandez-Becker, N. Q., Khosla, C., Elias, J. E. 2022; 13 (1): 888


    Celiac disease (CeD) is an autoimmune disorder induced by consuming gluten proteins from wheat, barley, and rye. Glutens resist gastrointestinal proteolysis, resulting in peptides that elicit inflammation in patients with CeD. Despite well-established connections between glutens and CeD, chemically defined, bioavailable peptides produced from dietary proteins have never been identified from humans in an unbiased manner. This is largely attributable to technical challenges, impeding our knowledge of potentially diverse peptide species that encounter the immune system. Here, we develop a liquid chromatographic-mass spectrometric workflow for untargeted sequence analysis of the urinary peptidome. We detect over 600 distinct dietary peptides, of which ~35% have a CeD-relevant T cell epitope and ~5% are known to stimulate innate immune responses. Remarkably, gluten peptides from patients with CeD qualitatively and quantitatively differ from controls. Our results provide a new foundation for understanding gluten immunogenicity, improving CeD management, and characterizing the dietary and urinary peptidomes.

    View details for DOI 10.1038/s41467-022-28353-1

    View details for PubMedID 35173144

  • Gastrointestinal γδ T cells reveal differentially expressed transcripts and enriched pathways during peanut oral immunotherapy. Allergy Zhang, W., Krishna Dhondalay, G., Liu, T. A., Kaushik, A., Hoh, R., Kwok, S., Kambham, N., Fernandez-Becker, N. Q., Andorf, S., Desai, M., Galli, S. J., Boyd, S. D., Nadeau, K. C., Manohar, M., DeKruyff, R. H., Chinthrajah, R. S. 2022

    View details for DOI 10.1111/all.15250

    View details for PubMedID 35143054

  • The Effects of Intermittent Fasting on Gastroesophageal Reflux Disease Jiang, Y., Goodman, S., Sonu, I., Garcia, P., Fernandez-Becker, N., Kamal, A., Zikos, T., Singh, S., Neshatian, L., Triadafilopoulos, G., Clarke, J. LIPPINCOTT WILLIAMS & WILKINS. 2021: S214
  • Gastric Mucosal Immune Profiling and Dysregulation in Idiopathic Gastroparesis. Clinical and translational gastroenterology Gottfried-Blackmore, A. n., Namkoong, H. n., Adler, E. n., Martin, B. n., Gubatan, J. n., Fernandez-Becker, N. n., Clarke, J. O., Idoyaga, J. n., Nguyen, L. n., Habtezion, A. n. 2021; 12 (5): e00349


    It is unclear how immune perturbations may influence the pathogenesis of idiopathic gastroparesis, a prevalent functional disorder of the stomach which lacks animal models. Several studies have noted altered immune characteristics in the deep gastric muscle layer associated with gastroparesis, but data are lacking for the mucosal layer, which is endoscopically accessible. We hypothesized that immune dysregulation is present in the gastroduodenal mucosa in idiopathic gastroparesis and that specific immune profiles are associated with gastroparesis clinical parameters.In this cross-sectional prospective case-control study, routine endoscopic biopsies were used for comprehensive immune profiling by flow cytometry, multicytokine array, and gene expression in 3 segments of the stomach and the duodenal bulb. Associations of immune endpoints with clinical parameters of gastroparesis were also explored.The gastric mucosa displayed large regional variation of distinct immune profiles. Furthermore, several-fold increases in innate and adaptive immune cells were found in gastroparesis. Various immune cell types showed positive correlations with duration of disease, proton pump inhibitor dosing, and delayed gastric emptying.This initial observational study showed immune compartmentalization of the human stomach mucosa and significant immune dysregulation at the level of leukocyte infiltration in idiopathic gastroparesis patients that extends to the duodenum. Select immune cells, such as macrophages, may correlate with clinicopathological traits of gastroparesis. This work supports further mucosal studies to advance our understanding of gastroparesis pathophysiology.

    View details for DOI 10.14309/ctg.0000000000000349

    View details for PubMedID 33979305

  • Eosinophilic Esophagitis: Incidence, Diagnosis, Management, and Future Directions. Gastroenterology clinics of North America Fernandez-Becker, N. Q. 2021; 50 (4): 825-841


    Eosinophilic esophagitis (EoE) is an antigen-mediated esophageal disease defined by the presence of esophageal eosinophilia and symptoms of esophageal dysfunction. The pathophysiology involves an allergen-driven Th2 T cell response that triggers infiltration of eosinophils into the esophagus leading to inflammation, remodeling, and fibrosis. This results in disruption of esophageal function and accompanying symptoms - most notably dysphagia. Effective therapies target inflammation or fibrostenotic complications and include proton pump inhibitors, swallowed topical steroids, dietary exclusion, and dilation. Clinical trials testing promising biologic therapies are ongoing.

    View details for DOI 10.1016/j.gtc.2021.08.001

    View details for PubMedID 34717873

  • Achalasia: physiology and diagnosis. Annals of the New York Academy of Sciences Rieder, E., Fernandez-Becker, N. Q., Sarosiek, J., Guillaume, A., Azagury, D. E., Clarke, J. O. 2020


    Achalasia is a rare motility disorder with incomplete relaxation of the lower esophageal sphincter and ineffective contractions of the esophageal body. It has been hypothesized that achalasia does not result from only one pathway but rather involves a combination of infectious, autoimmune, and familial etiological components. On the basis of other observations, a novel hypothesis suggests that a muscular form of eosinophilic esophagitis is involved in the pathophysiology of achalasia in some patients. This appears to progressively diminish the myenteric plexus at stage III, gradually destroy it at stage II, and finally eliminate it at stage I, the most advanced and final stage of achalasia. Although high-resolution manometry has identified these three different types of achalasia, another subset of patients with a normal-appearing sphincter relaxation has been proposed. Provocative maneuvers, such as the rapid drinking challenge, have recently been demonstrated to improve diagnosis in certain borderline patients, but have to be studied in more detail. However, whether the different types of achalasia will have a long-term impact on tailored therapies is still a matter of debate. Additionally, novel aspects of the standard timed barium swallow appear to be an important adjunct of diagnosis, as it has been shown to have a diagnostic as well as a predictive value.

    View details for DOI 10.1111/nyas.14510

    View details for PubMedID 33140485

  • Not in the Same Vein: Inflammatory Bowel Disease, Malignancy, and Enterocolic Lymphocytic Phlebitis. Digestive diseases and sciences Farber, O. N., Weingarden, A., Lee, C., Braxton, D. R., Bingham, D., Scott, G., Fernandez-Becker, N., Goff, D., Shelton, A., Kin, C. 2020

    View details for DOI 10.1007/s10620-020-06425-w

    View details for PubMedID 32594463

  • Marijuana, Ondansetron, and Promethazine Are Perceived as Most Effective Treatments for Gastrointestinal Nausea. Digestive diseases and sciences Zikos, T. A., Nguyen, L., Kamal, A., Fernandez-Becker, N., Regalia, K., Nandwani, M., Sonu, I., Garcia, M., Okafor, P., Neshatian, L., Grewal, D., Garcia, P., Triadafilopoulos, G., Clarke, J. O. 2020


    BACKGROUND: Many anti-nausea treatments are available for chronic gastrointestinal syndromes, but data on efficacy and comparative effectiveness are sparse.AIMS: To conduct a sectional survey study of patients with chronic nausea to assess comparative effectiveness of commonly used anti-nausea treatments.METHODS: Outpatients at a single center presenting for gastroenterology evaluation were asked to rate anti-nausea efficacy on a scale of 0 (no efficacy) to 5 (very effective) of 29 commonly used anti-nausea treatments and provide other information about their symptoms. Additional information was collected from the patients' chart. The primary outcome was to determine which treatments were better or worse than average using a t test. The secondary outcome was to assess differential response by individual patient characteristics using multiple linear regression.RESULTS: One hundred and fifty-three patients completed the survey. The mean efficacy score of all anti-nausea treatments evaluated was 1.73. After adjustment, three treatments had scores statically higher than the mean, including marijuana (2.75, p<0.0001), ondansetron (2.64, p<0.0001), and promethazine (2.46, p<0.0001). Several treatments, including many neuromodulators, complementary and alternative treatments, erythromycin, and diphenhydramine had scores statistically below average. Patients with more severe nausea responded better to marijuana (p=0.036) and diphenhydramine (p<0.001) and less so to metoclopramide (p=0.020). There was otherwise no significant differential response by age, gender, nausea localization, underlying gastrointestinal cause of nausea, and GCSI.CONCLUSIONS: When treating nausea in patients with chronic gastrointestinal syndromes, clinicians may consider trying higher performing treatments first, and forgoing lower performing treatments. Further prospective research is needed, particularly with respect to highly effective treatments.

    View details for DOI 10.1007/s10620-020-06195-5

    View details for PubMedID 32185665

  • Clinical and immunomodulatory effects of transcutaneous vagal nerve stimulation for idiopathic gastroparesis Gottfried-Blackmore, A., Namkoong, H., Adler, E. P., Fernandez-Becker, N., Clarke, J., Habtezion, A., Nguyen, L. WILEY. 2020
  • RNA-Seq of Gastrointestinal Biopsies During Oral Immunotherapy Reveals Changes in IgA Pathway Zhang, W., Dhondalay, G., Hoh, R., Tupa, D., Bunning, B., Fernandez-Becker, N., Kambham, N., Boyd, S., Galli, S., Andorf, S., Manohar, M., Chinthrajah, S., Nadeau, K. MOSBY-ELSEVIER. 2020: AB132
  • Peanut oral immunotherapy induces gastrointestinal eosinophilia in a longitudinal randomized controlled trial Wright, B., Fernandez-Becker, N., Kambham, N., Purington, N., Cao, S., Tupa, D., Zhang, W., Rank, M., Kita, H., Katzka, D., Shim, K., Bunning, B., Doyle, A., Jacobsen, E., Boyd, S., Manohar, M., Galli, S., Nadeau, K., Chinthrajah, S. MOSBY-ELSEVIER. 2020: AB84
  • Gastric antral vascular ectasia in systemic sclerosis: Association with anti-RNA polymerase III and negative anti-nuclear antibodies. Seminars in arthritis and rheumatism Serling-Boyd, N. n., Chung, M. P., Li, S. n., Becker, L. n., Fernandez-Becker, N. n., Clarke, J. n., Fiorentino, D. n., Chung, L. n. 2020; 50 (5): 938–42


    Gastric antral vascular ectasia (GAVE) is a vascular manifestation of systemic sclerosis (SSc) that can lead to iron deficiency anemia or acute gastrointestinal (GI) bleeding. We aimed to identify clinical features associated with GAVE.We performed a cohort study of SSc patients who were seen at Stanford between 2004 and 2018 and had undergone esophagogastroduodenoscopy (EGD). We compared the clinical features of those with and without GAVE, and multivariable logistic regression was performed to identify clinical correlates with GAVE.A total of 225 patients with SSc who underwent EGD were included in this study and 19 (8.4%) had GAVE. Those with GAVE were more likely to have scleroderma renal crisis (SRC) (21% vs 3%; p < 0.01), positive anti-RNA polymerase III antibody (71% vs 19%; p < 0.01), nucleolar pattern of anti-nuclear antibody (ANA) (33% vs 11%; p=0.04), and negative ANA (<1:80 by immunofluorescence) (33% vs 11%; p=0.02). On multivariate analysis with multiple imputation, anti-RNA polymerase III positivity (OR 4.57; 95% CI (1.57 - 13.23), p < 0.01) and ANA negativity (OR 3.75; 95% CI (1.21 - 11.62), p=0.02) remained significantly associated with GAVE.Positive anti-RNA polymerase III antibody and ANA negativity were significantly associated with GAVE. Further studies are necessary to determine whether patients with these autoantibody profiles should undergo screening endoscopies for GAVE.

    View details for DOI 10.1016/j.semarthrit.2020.06.016

    View details for PubMedID 32906028

  • Eosinophilic esophagitis: updates on key unanswered questions. Annals of the New York Academy of Sciences Fernandez-Becker, N. Q., Raja, S. n., Scarpignato, C. n., Lynch, K. L., Ahuja, N. K., Horsley-Silva, J. L. 2020


    Eosinophilic esophagitis (EoE) is a clinicopathologic disease characterized by symptoms of esophageal dysfunction and esophageal eosinophilia. In the last decade, there has been a dramatic increase in its prevalence for reasons that are not completely understood. The underlying pathophysiology involves an antigen-mediated TH 2 immune response that draws eosinophils to the esophagus, causing mucosal inflammation, esophageal remodeling, and fibrosis. This ultimately leads to esophageal dysfunction that most commonly manifests as dysphagia. In this review, we will discuss updates on key questions regarding the diagnosis and treatment of EoE.

    View details for DOI 10.1111/nyas.14421

    View details for PubMedID 32762154

  • The functional lumen imaging probe in gastrointestinal disorders: the past, present, and future. Annals of the New York Academy of Sciences Clarke, J. O., Ahuja, N. K., Fernandez-Becker, N. Q., Gregersen, H. n., Kamal, A. N., Khan, A. n., Lynch, K. L., Vela, M. F. 2020


    The functional lumen imaging probe (FLIP) is a diagnostic tool that utilizes impedance planimetry to allow the assessment of luminal diameter and distensibility. It has been used primarily in esophageal diseases, in particular, in the assessment of achalasia, esophagogastric junction outflow obstruction, and eosinophilic esophagitis (EoE). The usage and publications have increased over the past decade and it is now an essential tool in the armamentarium of the esophagologist. Indications are emerging outside of the esophagus, in particular with regard to gastroparesis. Our paper will review the history of FLIP, optimal current usage, data for key esophageal disorders (including achalasia, reflux, and EoE), data for nonesophageal disorders, and our sense as to whether FLIP is ready for prime time, as well as gaps in evidence and suggestions for future research.

    View details for DOI 10.1111/nyas.14463

    View details for PubMedID 32814368

  • Baseline impedance via manometry and ambulatory reflux testing are not equivalent when utilized in the evaluation of potential extra-esophageal gastroesophageal reflux disease. Journal of thoracic disease Zikos, T. A., Triadafilopoulos, G. n., Kamal, A. n., Podboy, A. n., Sonu, I. S., Regalia, K. A., Nandwani, M. C., Nguyen, L. A., Fernandez-Becker, N. Q., Clarke, J. O. 2020; 12 (10): 5628–38


    Esophageal baseline impedance (BI) shows promise for the diagnosis of gastroesophageal reflux disease (GERD), but means of acquisition and relevance to extra-esophageal manifestations of GERD (EE-GERD) remain unclear. In this study we aim to (I) evaluate concordance between BI as measured by 24-hour pH-impedance (pH-MII) and high-resolution impedance manometry (HRIM), and (II) assess relationship to potential EE-GERD symptoms.In this prospective open cohort study, patients presenting for outpatient HRIM and pH-MII studies were prospectively enrolled. All patients completed the GERD-HRQL, NOSE, and respiratory symptom index questionnaire (RSI), plus questions regarding wheezing and dental procedures. HRIM and pH-MII were evaluated with calculation of BI. Correlations were assessed using either Pearson's correlation or Spearman's rank coefficients.70 HRIM patients were enrolled, 35 of whom underwent pH-MII. There was no correlation between BI measurements as assessed by HRIM and pH-MII proximally, but there was moderate-weak correlation distally (r=0.34 to 0.5). Distal acid exposure time correlated with distal BI only for measurements by pH-MII (rho= -0.5 to -0.65), and not by HRIM. There was no relationship between proximal acid exposure time and proximal BI. There were no correlations when comparing proximal or distal BI measurements, acid exposure times, and impedance events to symptoms.Concordance between BI as measured by HRIM and pH-MII is poor, especially proximally, suggesting that these two methods are not interchangeable. There is no correlation between BI both distally/proximally and symptoms of either GERD/EE-GERD, suggesting that many symptoms are unrelated to acid or that BI is not an adequate marker to assess EE-GERD symptoms.

    View details for DOI 10.21037/jtd-20-1623

    View details for PubMedID 33209395

    View details for PubMedCentralID PMC7656325

  • Origins and clonal convergence of gastrointestinal IgE+ B cells in human peanut allergy. Science immunology Hoh, R. A., Joshi, S. A., Lee, J. Y., Martin, B. A., Varma, S. n., Kwok, S. n., Nielsen, S. C., Nejad, P. n., Haraguchi, E. n., Dixit, P. S., Shutthanandan, S. V., Roskin, K. M., Zhang, W. n., Tupa, D. n., Bunning, B. J., Manohar, M. n., Tibshirani, R. n., Fernandez-Becker, N. Q., Kambham, N. n., West, R. B., Hamilton, R. G., Tsai, M. n., Galli, S. J., Chinthrajah, R. S., Nadeau, K. C., Boyd, S. D. 2020; 5 (45)


    B cells in human food allergy have been studied predominantly in the blood. Little is known about IgE+ B cells or plasma cells in tissues exposed to dietary antigens. We characterized IgE+ clones in blood, stomach, duodenum, and esophagus of 19 peanut-allergic patients, using high-throughput DNA sequencing. IgE+ cells in allergic patients are enriched in stomach and duodenum, and have a plasma cell phenotype. Clonally related IgE+ and non-IgE-expressing cell frequencies in tissues suggest local isotype switching, including transitions between IgA and IgE isotypes. Highly similar antibody sequences specific for peanut allergen Ara h 2 are shared between patients, indicating that common immunoglobulin genetic rearrangements may contribute to pathogenesis. These data define the gastrointestinal tract as a reservoir of IgE+ B lineage cells in food allergy.

    View details for DOI 10.1126/sciimmunol.aay4209

    View details for PubMedID 32139586

  • Gastrointestinal Eosinophil Responses in a Longitudinal, Randomized Trial of Peanut Oral Immunotherapy. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association Wright, B. L., Fernandez-Becker, N. Q., Kambham, N. n., Purington, N. n., Cao, S. n., Tupa, D. n., Zhang, W. n., Sindher, S. B., Rank, M. A., Kita, H. n., Katzka, D. A., Shim, K. P., Bunning, B. J., Doyle, A. D., Jacobsen, E. A., Tsai, M. n., Boyd, S. D., Manohar, M. n., Chinthrajah, R. S. 2020


    Gastrointestinal side effects are common during oral immunotherapy (OIT) and eosinophilic esophagitis (EoE) is a potential complication. We aimed to characterize eosinophilic gastrointestinal responses to peanut OIT, in which peanut protein is given orally, with incremental increases in dose over time.Twenty adults with IgE-mediated peanut allergy were randomly assigned to groups given peanut OIT (n=15) or placebo (n=5); 1 additional subject withdrew before randomization. Serial gastrointestinal biopsies were collected at baseline (n=21, 0 weeks), following dose escalation (n=10, 52 weeks), and during the maintenance phase (n=11, 104 weeks). Endoscopic findings were characterized using the EoE endoscopic reference score. Biopsies were assessed for eosinophils per high-power field (eos/hpf) and other pathology features using EoE histologic scoring system scores. We performed immunohistochemical analyses of eosinophil peroxidase deposition, quantified using automated image analysis.At baseline, no subjects reported current gastrointestinal symptoms. However, 3 of the 21 subjects (14%) had esophageal peak eosinophil counts ≥15 eos/hpf and all subjects had dilated intercellular spaces (DIS). OIT induced or exacerbated esophageal eosinophilia (EE) at 52 weeks in most subjects (peak eosinophil counts >5 eos/hpf in 6 of 7 patients [86%]; peak eosinophil counts ≥15 eos/hpf in 4 of 7 patients [57%]). One subject met clinicopathologic criteria for EoE and withdrew; no significant changes in esophageal peak eosinophil counts were observed in the placebo group. EE in the OIT group corresponded with significant increases in EoE histologic scoring system scores and deposition of eosinophil peroxidase. In 4 of 6 participants (67%), OIT-induced EE and gastrointestinal eosinophilia resolved by the end of the maintenance phase. Gastrointestinal symptoms were not clearly associated with EE or gastrointestinal eosinophilia.In this pilot study, we found that peanut OIT-induced EE and gastrointestinal eosinophilia are usually transient and are not always associated with gastrointestinal symptoms. no: NCT02103270.

    View details for DOI 10.1016/j.cgh.2020.05.019

    View details for PubMedID 32434067

  • Open-label pilot study: Non-invasive vagal nerve stimulation improves symptoms and gastric emptying in patients with idiopathic gastroparesis. Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society Gottfried-Blackmore, A., Adler, E. P., Fernandez-Becker, N., Clarke, J., Habtezion, A., Nguyen, L. 2019: e13769


    BACKGROUND: Gastroparesis, a chronic motility disorder characterized by delayed gastric emptying, abdominal pain, nausea, and vomiting, remains largely unexplained. Medical therapy is limited, reflecting the complex physiology of gastric sensorimotor function. Vagus nerve stimulation is an attractive therapeutic modality for gastroparesis, but prior methods required invasive surgery. In this open-label pilot study, we aimed to assess the benefit of non-invasive vagal nerve stimulation in patients with mild to moderate idiopathic gastroparesis.METHODS: Patients self-administered the gammaCore vagal nerve stimulator for 4weeks. The gastroparesis cardinal symptom index daily diary (GCSI-dd) was assessed during a two-week run-in period, ≥4weeks of therapy, and 4weeks after therapy was completed. Gastric emptying and autonomic function testing were also performed. The primary endpoint was an absolute reduction in CGSI-dd of 0.75 after nVNS.RESULTS: There was a total improvement in symptom scores (2.56±0.76 to 1.87±1.05; P=.01), with 6/15 (40%) participants meeting our primary endpoint. Therapy was associated with a reduction in gastric emptying (T1/2 155 vs 129minutes; P=.053, CI -0.4 to 45). Therapy did not correct autonomic function abnormalities, but was associated with modulation of reflex parasympathetic activity.CONCLUSIONS: Short-term non-invasive vagal nerve stimulation led to improved cardinal symptoms and accelerated gastric emptying in a subset of patients with idiopathic gastroparesis. Responders had more severe gastric delay at baseline and clinical improvement correlated with duration of therapy, but not with improvements in gastric emptying. Larger randomized sham-controlled trials of greater duration are needed to confirm the results of this pilot study.

    View details for DOI 10.1111/nmo.13769

    View details for PubMedID 31802596

  • Ninety-Six Hour Wireless Esophageal pH Study in Patients with GERD Shows that Restrictive Diet Reduces Esophageal Acid Exposure. Digestive diseases and sciences Triadafilopoulos, G., Korzilius, J. W., Zikos, T., Sonu, I., Fernandez-Becker, N. Q., Nguyen, L., Clarke, J. O. 2019


    BACKGROUND: Prolonged (96h) pH monitoring may explore the effect of diet on pH and symptoms in patients with GERD.AIMS: To assess the usefulness of a 96h esophageal pH study in patients with GER symptoms under different diets (pro- and anti-GER).METHODS: Prospective study of 66 patients with GERD undergoing wireless 96h pH monitoring. Two-day periods, one on liberal (pro-reflux) and another on restricted (anti-reflux) diet assessed esophageal acid exposure and symptoms. The primary end point was normalization of acid exposure time while on restricted diet. Secondary end point was a>50% reduction in symptoms with restricted diet.RESULTS: Normal (pH time<4 of<6%) was found in 34 patients (51.5%) while on the initial 48h (liberal) diet [median % time<4: 3.2 (95% CI, 1.9, 4.0)] and remained normal while on restricted diet [median % time<4: 2.6 (95% CI, 0.8, 3.4)]. Abnormal acid exposure (% pH time<4:>6%) was found in 32 patients (48.5%) while on initial 48h liberal diet [median % time<4: 10.5, (95% CI 8.9, 12.6)], and decreased significantly with restricted diet [median % time<4: 4.5 (95% CI 3.1, 7.3)] (p=0.001), and normalized with anti-GERD diet in 21 patients (65.6%). Only 11/66 patients were candidates for proton pump inhibitor (PPI) use; 34 had either normal pH studies or normalized them with restricted diet (n=21). Symptoms did not improve with restricted diet.CONCLUSIONS: The 96-h esophageal pH study tests for GERD under pro- and anti-GER diets and allows minimization of PPI therapy to only 16.6% of patients.

    View details for DOI 10.1007/s10620-019-05940-9

    View details for PubMedID 31734874

  • Human Intestinal Enteroids Model MHC-II in the Gut Epithelium FRONTIERS IN IMMUNOLOGY Wosen, J. E., Ilstad-Minnihan, A., Co, J. Y., Jiang, W., Mukhopadhyay, D., Fernandez-Becker, N. Q., Kuo, C. J., Amieva, M. R., Mellins, E. D. 2019; 10
  • Human Intestinal Enteroids Model MHC-II in the Gut Epithelium. Frontiers in immunology Wosen, J. E., Ilstad-Minnihan, A., Co, J. Y., Jiang, W., Mukhopadhyay, D., Fernandez-Becker, N. Q., Kuo, C. J., Amieva, M. R., Mellins, E. D. 2019; 10: 1970


    The role of intestinal epithelial cells (IECs) in mucosal tolerance and immunity remains poorly understood. We present a method for inducing MHC class II (MHC-II) in human enteroids, "mini-guts" derived from small intestinal crypt stem cells, and show that the intracellular MHC-II peptide-pathway is intact and functional in IECs. Our approach enables human enteroids to be used for novel in vitro studies into IEC MHC-II regulation and function during health and disease.

    View details for DOI 10.3389/fimmu.2019.01970

    View details for PubMedID 31481960

    View details for PubMedCentralID PMC6710476

  • RPC4046, a Monoclonal Antibody Against IL13, Reduces Histologic and Endoscopic Activity in Patients With Eosinophilic Esophagitis GASTROENTEROLOGY Hirano, I., Collins, M. H., Assouline-Dayan, Y., Evans, L., Gupta, S., Schoepfer, A. M., Straumann, A., Safroneeva, E., Grimm, M., Smith, H., Tompkins, C., Woo, A., Peach, R., Frohna, P., Gujrathi, S., Penenberg, D. N., Li, C., Opiteck, G. J., Olson, A., Aranda, R., Rothenberg, M. E., Dellon, E. S., Donnellan, F., Iacucci, M., Paterson, W., Schoepfer, A., Abonia, P., Ayub, K., Coates, A., Cohen, S., Dellon, E., Desta, T., Falk, G., Fein, S., Fernandez-Becker, N., Fleischer, D., Friedenberg, K., Ghishan, F., Glover, S., Goldstein, G., Gopal, V., Gross, C., Nardi, R., Kugathasan, S., Lacy, B., Lewis, J., Menard-Katcher, P., Mitlyng, B., Moawad, F., Perez, R., Peterson, K., Ramirez, F., Reeves-Darby, V., Schey, R., Shad, J., Vaezi, M., Wo, J., Zakko, S., HEROES Study Grp 2019; 156 (3): 592-+


    Eosinophilic esophagitis (EoE) is a chronic, esophageal, type 2 inflammatory response associated with increased serum levels of interleukin 13 (IL13), which might contribute to its pathogenesis. RPC4046, a recombinant humanized monoclonal antibody against IL13, prevents its binding to the receptor subunits IL13RA1 and IL13RA2. We performed a phase 2 trial to evaluate the efficacy and safety of RPC4046 in patients with EoE.We performed a multicenter, double-blind trial of 99 adults with active EoE randomly assigned (1:1:1) to groups given RPC4046 (180 or 360 mg) or placebo once weekly for 16 weeks, from September 2014 through December 2015. Patients were seen at day 1 (baseline) and weeks 2, 4, 8, 12, and 16. They underwent esophagogastroduodenoscopy and biopsies were collected at baseline and week 16. Patients completed a daily dysphagia symptom diary through week 16 and patient-reported outcome data were collected. The primary outcome was change in mean esophageal eosinophil count in the 5 high-power fields (hpfs) with the highest level of inflammation.At week 16, mean changes in esophageal eosinophil count per hpf were a reduction of 94.8 ± 67.3 in patients who received 180 mg RPC4046 (P < .0001) and a reduction of 99.9 ± 79.5 in patients who received 360 mg RPC4046 (P < .0001) compared with a reduction of 4.4 ± 59.9 in patients who received placebo. The 360-mg RPC4046 group, compared with the placebo group, showed significant reductions in validated endoscopic severity score at all esophageal locations (P < .0001), validated histologic grade and stage scores (both P < .0001), and clinician's global assessment of disease severity (P = .0352); they had a numerical reduction in scores from the dysphagia symptom diary (P = .0733). Significant reductions in esophageal eosinophil counts and histologic and endoscopic features were observed in patients with steroid-refractory EoE who received RPC4046. The most common adverse events were headache and upper respiratory tract infection.In a phase 2 trial of patients with EoE, we found RPC4046 (a monoclonal antibody against IL13) to reduce histologic and endoscopic features compared with placebo. RPC4046 was well tolerated. no: NCT02098473.

    View details for DOI 10.1053/j.gastro.2018.10.051

    View details for Web of Science ID 000457714300022

    View details for PubMedID 30395812

  • Esophageal Eosinophilia is Present in Some Peanut Allergic Patients Fernandez-Becker, N., Wright, B. L., Kambham, N., Shim, K. P., Purington, N., Long, A. J., Tsai, M., Boyd, S., Galli, S. J., Nadeau, K. C., Chinthrajah, R. MOSBY-ELSEVIER. 2019: AB310
  • An Unexpected Colonic Mass AMERICAN JOURNAL OF GASTROENTEROLOGY Li, A. A., Cholankeril, G., Berry, G. J., Fernandez-Becker, N. 2019; 114 (1): 180–81
  • Double Threat: Interplay of Celiac Disease with Inflammatory Bowel Disease. Digestive diseases and sciences Gubatan, J. n., Triadafilopoulos, G. n., Fernandez-Becker, N. Q. 2019

    View details for DOI 10.1007/s10620-019-05994-9

    View details for PubMedID 31828460

  • A Positive Correlation Between Gastric and Esophageal Dysmotility Suggests Common Causality DIGESTIVE DISEASES AND SCIENCES Zikos, T. A., Clarke, J. O., Triadafilopoulos, G., Regalia, K. A., Sonu, I. S., Fernandez-Becker, N. Q., Nandwani, M. C., Nguyen, L. A. 2018; 63 (12): 3417–24
  • Baseline Gastrointestinal Eosinophilia Is Common in Oral Immunotherapy Subjects With IgE-Mediated Peanut Allergy FRONTIERS IN IMMUNOLOGY Wright, B. L., Fernandez-Becker, N. Q., Kambham, N., Purington, N., Tupa, D., Zhang, W., Rank, M. A., Kita, H., Shim, K. P., Bunning, B. J., Doyle, A. D., Jacobsen, E. A., Boyd, S. D., Tsai, M., Maecker, H., Manohar, M., Galli, S. J., Nadeau, K. C., Chinthrajah, R. 2018; 9
  • An Unexpected Colonic Mass. The American journal of gastroenterology Li, A. A., Cholankeril, G., Berry, G. J., Fernandez-Becker, N. 2018

    View details for PubMedID 30333533

  • Use of Esophageal pH Monitoring to Minimize Proton-Pump Inhibitor Utilization in Patients with Gastroesophageal Reflux Symptoms DIGESTIVE DISEASES AND SCIENCES Triadafilopoulos, G., Zikos, T., Regalia, K., Sonu, I., Fernandez-Becker, N. Q., Nguyen, L., Nandwani, M. R., Clarke, J. O. 2018; 63 (10): 2673–80
  • Multi-Organ RNA-Sequencing of Patients with Systemic Sclerosis (SSc) Finds That Intrinsic Subsets Are Conserved across Organ Systems Mehta, B. K., Franks, J., Wang, Y., Cai, G., Toledo, D. M., Wood, T. A., Archambault, K. A., Kosarek, N., Kolstad, K. D., Stark, M., Valenzuela, A., Fiorentino, D., Fernandez-Becker, N., Becker, L., Nguyen, L., Clarke, J., Boin, F., Wolters, P., Chung, L., Whitfield, M. L. WILEY. 2018
  • Identification of Risk Factors for Gastric Antral Vascular Ectasia (GAVE) Among Systemic Sclerosis Patients Serling-Boyd, N., Li, S., Fiorentino, D., Becker, L., Fernandez-Becker, N., Clarke, J., Chung, L. WILEY. 2018
  • Use of Esophageal pH Monitoring to Minimize Proton-Pump Inhibitor Utilization in Patients with Gastroesophageal Reflux Symptoms. Digestive diseases and sciences Triadafilopoulos, G., Zikos, T., Regalia, K., Sonu, I., Fernandez-Becker, N. Q., Nguyen, L., Nandwani, M. C., Clarke, J. O. 2018


    BACKGROUND: Due to concerns about long-term PPI use in patients with acid reflux, we aimed at minimizing PPI use, either by avoiding initiating therapy, downscaling to other therapies, or introducing endoscopic or surgical options.AIMS: To examine the role of esophageal ambulatory pHmetry in minimizing PPI use in patients with heartburn and acid regurgitation.METHODS: Retrospective cohort analysis of patients with reflux symptoms, who underwent endoscopy, manometry, and ambulatory pHmetry to define the need for PPI. Patients were classified as: (1) never users; (2) partial responders to PPI; (3) users with complete response to PPI. Patients were then managed as: (1) PPI non-users; (2) PPI-initiated, and (3) PPI-continued.RESULTS: Of 286 patients with heartburn and regurgitation, 103 (36%) were found to have normal and 183 (64%) abnormal esophageal acid exposure (AET). In the normal AET group, 44/103 had not been treated and were not initiated on PPI. Of the 59 who had previously received PPI, 52 stopped and 7 continued PPI. Hence, PPI were avoided in 96/103 patients (93%). In the abnormal AET group, 61/183 had not been treated and 38 were initiated on PPI and 23 on other therapies. In the 122 patients previously treated with PPI, 24 were not treated with PPI, but with H2RAs, prokinetics, endoscopic, or surgical therapy. Hence, PPI therapy was avoided in 47/183 patients (26%).CONCLUSIONS: In patients with GER symptoms, esophageal pHmetry may avert PPI use in 50%. In the era of caution regarding PPIs, early testing may provide assurance and justification.

    View details for PubMedID 29959725

  • A Positive Correlation Between Gastric and Esophageal Dysmotility Suggests Common Causality. Digestive diseases and sciences Zikos, T. A., Clarke, J. O., Triadafilopoulos, G., Regalia, K. A., Sonu, I. S., Fernandez-Becker, N. Q., Nandwani, M. C., Nguyen, L. A. 2018


    BACKGROUND: Gastric and esophageal dysmotility syndromes are some of the most common motility diagnoses, but little is known about their interrelationship.AIMS: The aim of our study was to determine if a correlation exists between gastric and esophageal dysmotility syndromes.METHODS: We reviewed the records of all patients who underwent both solid gastric emptying scintigraphy (GES) and high-resolution esophageal manometry (HRM) withina 2 year period, with both done between August 2012 and August 2017. All GESs were classified as either rapid, normal, or delayed. All HRMs were classified according to the Chicago Classification 3.0. Correlations were assessed using Fisher's exact test and multiple logistic regression.RESULTS: In total, 482 patients met inclusion criteria. Of patients with a normal, delayed, and rapid GES, 53.1, 64.5, and 77.3% had an abnormal HRM, respectively (p<0.05 vs. normal GES). Likewise, patients with an abnormal HRM were more likely to have an abnormal GES (54.9 vs. 41.8%, p=0.005). Multiple logistic regression showed abnormal GES [odds ratio (OR) 2.14], age (OR 1.013), scleroderma (OR 6.29), and dysphagia (OR 2.63) were independent predictors of an abnormal HRM. Likewise, an abnormal HRM (OR 2.11), diabetes (OR 1.85), heart or lung transplantation (OR 2.61), and autonomic dysfunction (OR 2.37) were independent predictors of an abnormal GES.CONCLUSIONS: The correlation between an abnormal GES and HRM argues for common pathogenic mechanisms of these motility disorders, and possibly common future treatment options. Clinicians should have a high index of suspicion for another motility disorder if one is present.

    View details for PubMedID 29946871

  • Baclofen and gastroesophageal reflux disease: seeing the forest through the trees CLINICAL AND TRANSLATIONAL GASTROENTEROLOGY Clarke, J. O., Fernandez-Becker, N. Q., Regalia, K. A., Triadafilopoulos, G. 2018; 9
  • Outcomes of Endoscopic Procedures on Patients With Left-Ventricular Assist Devices: Experiences From a Single-Center Retrospective Case Series Pan, J. Y., Zikos, T., Chang, M. S., Limketkai, B., Banerjee, D., Fernandez-Becker, N. MOSBY-ELSEVIER. 2017: AB207–AB208
  • Multi-Organ RNA-Sequencing of Systemic Sclerosis (SSc) Patients Shows Reproducible Gene Expression Profiles Across Organ Systems Mehta, B. K., Johnson, M. E., Archambault, K. A., Wood, T. A., Valenzuela, A., Crawford, A., Fiorentino, D., Fernandez-Becker, N., Becker, L., Nguyen, L., Boin, F., Wolters, P., Chung, L., Whitfield, M. WILEY. 2016
  • Intestinal pseudo-obstruction in patients with systemic sclerosis: an analysis of the Nationwide Inpatient Sample. Rheumatology Valenzuela, A., Li, S., Becker, L., Fernandez-Becker, N., Khanna, D., Nguyen, L., Chung, L. 2016; 55 (4): 654-658


    Intestinal pseudo-obstruction is a rare gastrointestinal complication in patients with SSc without large studies examining its prevalence or outcomes. We aimed to compare outcomes in SSc patients with intestinal pseudo-obstruction to patients with intestinal pseudo-obstruction secondary to other causes, and SSc patients without intestinal pseudo-obstruction.This is a case-control study using the Healthcare Cost and Utilization Project Nationwide Inpatient Sample for the period 2002-2011. We included patients with the previously validated International Classification of Diseases-Clinical Modification-9 code 710.1 for SSc in combination with codes for intestinal pseudo-obstruction, and determined length of hospitalization and the risks for surgical procedures, use of total parenteral nutrition (TPN) and in-hospital mortality.A total of 193 610 SSc hospitalizations occurred in the USA between 2002 and 2011, of which 5.4% (n = 10 386) were associated with a concurrent intestinal pseudo-obstruction diagnosis (cases). In-hospital mortality was 7.3%. In multivariate analyses, cases were more likely to die during the inpatient stay and to receive TPN than patients with idiopathic intestinal pseudo-obstruction (control group 1), patients with intestinal pseudo-obstruction and diabetes (control group 2), and SSc patients without intestinal pseudo-obstruction (control group 3). Cases had longer in-hospital stay than control groups 2 and 3, and were less likely to undergo surgical procedures than control groups 1 and 2.Intestinal pseudo-obstruction is a rare cause of hospitalization in patients with SSc, but is associated with high in-hospital mortality in comparison with other SSc patients and those with intestinal pseudo-obstruction secondary to other causes.

    View details for DOI 10.1093/rheumatology/kev393

    View details for PubMedID 26615031

  • Colonic plasmacytomas: a rare complication of plasma cell leukemia. Endoscopy Hang, C. T., Perumpail, R. B., Huang, R. J., Fernandez-Pol, S., Fernandez-Becker, N. Q. 2015; 47: E77-8

    View details for DOI 10.1055/s-0034-1390722

    View details for PubMedID 25926223

  • Intestinal Pseudo-Obstruction in Patients with Systemic Sclerosis: An Analysis of the Nationwide Inpatient Sample. Valenzuela, A., Li, S., Becker, L., Fernandez-Becker, N., Khanna, D., Linda Nguyen, Chung, L. WILEY-BLACKWELL. 2014: S1310
  • Dietary gluten triggers concomitant activation of CD4(+) and CD8(+) alpha beta T cells and gamma delta T cells in celiac disease PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Han, A., Newell, E. W., Glanville, J., Fernandez-Becker, N., Khosla, C., Chien, Y., Davis, M. M. 2013; 110 (32): 13073-13078
  • In silico analysis of T-bet activity in peripheral blood mononuclear cells in patients with inflammatory bowel disease (IBD). In silico biology Fernandez-Becker, N. Q., Moss, A. C. 2009; 9 (5-6): 355-363


    T-bet (TBX21) is a transcription factor that regulates T-cell differentiation, and has recently been implicated in the pathogenesis of Crohn's disease (CD). The regulatory networks through which T-bet affects immune function are unknown. An NCBI gene expression profile from patients with CD and controls was analyzed. T-bet transcription factor binding sites and promoter modules were identified using promoter analysis software. Functional correlations between T-bet-containing promoters were determined using data mining and ontological analysis. T-bet expression in CD peripheral blood mononuclear cells (PBMCs) (n=59) was significantly reduced compared to control (n=42) (p<0.0001) and ulcerative colitis PBMCs (n=26), (p=0.005). The promoter regions of all genes differentially-expressed in CD were probed for T-bet Transcription Factor Binding Sites (TFBSs). Twenty-three genes contained transcription-factor binding sites for T-bet; 8 were down-regulated, and 15 were up-regulated in CD-PBMCs. Three genes (S100A16, ABHD3 and EZH1) that were down-regulated in CD-PBMCs contained a complex promoter module consisting of T-bet and EGRF transcription-factor binding sites. Ontological analysis revealed that a significant number of differentially-expressed genes that contain T-bet binding sites are involved in innate immunity (8 genes, Z-score 4.11) and signal transduction (5 genes, Z-score 2.65). This combination of gene expression datasets and promoter analysis has identified a network of genes that contain simple T-bet binding sites, and complex T-bet promoter modules, in their promoter regions. These results implicate a mechanism through which T-bet may influence innate immunity in CD.

    View details for DOI 10.3233/ISB-2009-0410

    View details for PubMedID 22430437

  • Separable and redundant regulatory determinants in Cactus mediate its dorsal group dependent degradation DEVELOPMENT Fernandez, N. Q., Grosshans, J., Goltz, J. S., Stein, D. 2001; 128 (15): 2963-2974


    Dorsal-ventral polarity within the Drosophila syncytial blastoderm embryo is determined by the maternally encoded dorsal group signal transduction pathway that regulates nuclear localization of the transcription factor Dorsal. Nuclear uptake of Dorsal, a Rel/NFkappaB homolog, is controlled by the interaction with its cognate IkappaB inhibitor protein Cactus, which is degraded on the ventral side of the embryo in response to dorsal group signaling. Previous studies have suggested that an N-terminally located kinase target motif similar to that found in IkappaB proteins is involved in the spatially controlled degradation of Cactus. We report studies of the in vivo function and distribution of fusion proteins comprising segments of Cactus attached to Escherichia coli beta-galactosidase (lacZ). Full-length Cactus-lacZ expressed in vivo normalizes the ventralized phenotype of embryos that lack Cactus and faithfully reconstitutes dorsal group-regulated degradation, while fusion protein constructs that lack the first 125 amino acids of Cactus escape dorsal group-dependent degradation. Furthermore, Cactus-lacZ constructs that lack only the putative IkappaB-dependent kinase target-like motif can nevertheless undergo spatially regulated dorsal group-dependent degradation and we have identified the regulatory determinant responsible for dorsal group-dependent degradation of Cactus in the absence of this motif. Taken together, our studies indicate the presence of two distinct redundantly acting determinants in the N terminus of Cactus that direct dorsal group-dependent degradation. Strikingly, the regulatory domain of human IkappaBalpha can also direct polarized degradation of Cactus-lacZ fusion protein.

    View details for Web of Science ID 000170604900011

    View details for PubMedID 11532919