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Microvillus inclusion disease is a congenital disorder characterized by secretory diarrhea. Patients demonstrate villus atrophy, loss of microvilli, and internalized inclusions of microvilli within the cytoplasm of small intestinal enterocytes. The exact molecular defect in these patients is not known. Two infants are described in this report with microvillus inclusion disease. Case 1 was a 3-month-old boy who developed secretory diarrhea shortly after birth. Case 2 was a 9-month-old boy who had abrupt onset diarrhea at 2 weeks of age resulting in weight loss and dehydration. Light microscopy revealed total villus atrophy with minimal crypt hyperplasia, and electron microscopic examination revealed variably shortened microvilli and cytoplasmic microvillus inclusions in both patients.Poly (A)+ RNA was purified from duodenal biopsies and RT-PCR reactions were performed. Normal human intestinal RNA was used as a positive control. Primers specific for human NHE-1, NHE-2, NHE-3 (2 sets), sodium-glucose transporter (SGLT1), and β-actin were used.Results showed that NHE-1 and β-actin cDNAs amplified to similar levels in both patient and control samples. However, the expression of NHE-2 and SGLT1 was much higher in the control sample than in the patient samples. Additionally, NHE-3 mRNA was not detected in the patient samples using two sets of NHE-3 specific primers.The patients with microvillus inclusion disease have defects in apical but not basolateral membrane transport systems, and these defects are related to the pathogenesis of the disease.