Enteropathies Associated with Chronic Diarrhea and Malabsorption in Childhood

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Chapter 9

Enteropathies Associated with Chronic Diarrhea and Malabsorption in Childhood

Pierre Russo


The goal of this chapter is to outline the pathologic features of the major intestinal disorders of infancy and early childhood, with an emphasis on congenital disorders that result in chronic diarrhea and malabsorption, and to illustrate their appearance in small intestinal biopsy and resection specimens (Box 9.1). Other major categories of disorders that cause chronic diarrhea, such as infections, immunodeficiencies (primary and secondary), gluten-sensitive enteropathy and other food allergies, and motility and pancreatic disorders are discussed in other chapters of this book.

Chronic diarrhea occurring in the neonatal period presents particularly difficult diagnostic and therapeutic challenges. Intractable diarrhea of infancy is a term initially coined by Avery and colleagues1 to refer to chronic diarrhea in neonates, most of which remained undiagnosed and was associated with a high mortality rate. Since these initial reports, more precise identification of disorders that cause intractable diarrhea of infancy has led to the use of prolonged parenteral nutrition, immunosuppression, and even bowel transplantation to try to improve survival, emphasizing the need for timely and accurate diagnosis. Investigation of some of these disorders has also led to significant advances in understanding of gastrointestinal (GI) and immunologic functions. For instance, investigation of microvillous inclusion disease has helped identify genes responsible for intracellular vesicular transport. The discovery that mutations in the gene that codes for FOXP3 causes the immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome, as well as its animal homolog in the Scurfy mouse, has led to recognition of the critical role played by that gene in the control of the human immune response, as well as in autoimmunity and immune tolerance.

Biopsy Sampling and Indications In Children

In most pediatric GI practices, intestinal biopsy specimens are most frequently obtained from the duodenum via forceps during endoscopic examination, during which time samples are also obtained from the esophagus and stomach (esophagogastroduodenoscopy, or EGD). Endoscopic forceps biopsies have largely replaced Crosby suction biopsies because of the greater ease of the procedure, greater patient comfort, avoidance of radiation exposure, direct visualization of the GI tract, and the ability to perform multiple biopsies at several sites. In addition to being submitted for routine histology, biopsy samples may be snap-frozen (for disaccharidase analysis) or submitted for electron microscopy (for confirmation of microvillous inclusion disease). Biopsies of both the proximal and distal duodenum are recommended, including endoscopically normal mucosa, because many disorders that affect the duodenum have a focal distribution. For example, pathologic lesions in children with gluten-sensitive enteropathy may be patchy, and villous atrophy may coexist with otherwise normal mucosa.2 Furthermore, villous atrophy may be limited to, or most severe in, the duodenal bulb at the time of clinical presentation.2,3

Since pediatric EGD evolved into a routine outpatient procedure, the indications for its use have changed. For instance, at The Children’s Hospital of Philadelphia, the “first-time” EGD rate increased 12-fold in the 20 years between 1985 and 2005, with isolated abdominal pain replacing GI bleeding as the most frequent indication.4 Much of this increase was driven by the dramatic increase in food allergy–related disorders, such as eosinophilic esophagitis; by the increased prevalence of celiac disease and its clinically atypical forms, for which intestinal biopsy is the gold standard for establishing a diagnosis; and by the routine use of EGD in addition to colonoscopy for evaluation of children with suspected inflammatory bowel disease. In a 2012 study, the most frequent indications for EGD and colonoscopies in children younger than 1 year of age were diarrhea, failure to thrive, reflux, and rectal bleeding.5 Histologic abnormalities were detected in two thirds of cases, and only 2% of the mucosal biopsies were considered insufficient. Sampling of endoscopically normal-appearing mucosa is recommended because it may help assess the “background” features of the mucosa and because histologic examination may reveal clinically relevant findings previously unsuspected by the endoscopist (e.g., granulomas).6,7 One pediatric study found that duodenal biopsy performed routinely for indications such as gastroesophageal reflux, vomiting, abdominal pain, anemia, and evaluation of Crohn’s disease yielded pathologic findings in approximately 17% of cases.7

Some entities, such as congenital transport disorders, are associated with normal intestinal biopsy findings, whereas others, such as autoimmune enteropathy (AIE) or celiac disease, exhibit various degrees of villous atrophy either with or without inflammation. In contrast, a few disorders, such as abetalipoproteinemia or microvillous inclusion disease, usually reveal characteristic findings in intestinal biopsies (Table 9.1).


Intestinal Development in Children

Villi appear in the duodenum during the eighth week after fertilization, and crypts of Lieberkühn are seen during the ninth week. They spread caudally in the gut, affecting the distal ileum by the 14th week of gestation. The definitive histologic features of the duodenum are established by the 14th week after fertilization, and the histology closely resembles that of a newborn by 20 weeks’ gestation. The transition from pyloric to duodenal mucosa is gradual in some individuals. Duodenal-like villi may be found in the distal pylorus, and pyloric-like epithelium may be found in the duodenum. Enteroendocrine and goblet cells appear differentiate before 14 weeks’ gestation under the control of transcription factors such as Math1.8,9 The ratio of villus height to crypt depth in the duodenum of a newborn is similar to that in an adult. Newborns usually lack plasma cells in the first week of life and gradually acquire them during the first month. At that time, immunoglobulin M (IgM)-containing plasma cells predominate, but by 3 months of life, immunoglobulin A (IgA) plasma cells predominate. Normal numbers of plasma cells and normal ratios of IgA, IgM, and IgG antibodies are attained by the first year of life.10

Congenital Disorders of Intestinal Digestion, Absorption, and Transport

Specific gene defects associated with various disorders of substrate transport have been characterized (Table 9.2). Genetic studies are instrumental in providing a picture of enterocyte function at the molecular level. Except for disorders associated with fat processing, small intestinal biopsies in these cases are typically normal or only very slightly abnormal. Normal-appearing small bowel mucosa from a patient with prolonged diarrhea, especially a young infant, should alert the clinician to these entities. Only those disorders with significant histologic findings or with confounding clinical features are discussed here.

Table 9.2

Molecular Basis of Disorders of Digestion, Absorption, and Transport

Disease Gene Location Function
Disaccharidase Deficiency
Congenital lactase deficiency LCT 2q21 Lactase-phlorizin hydrolase activity
Sucrase-isomaltase deficiency SI (EC 3q25-q26 Isomaltase-sucrase activity
Maltase-glucoamylase deficiency MGAM 7q34 Maltase-glucoamylase activity
Ion and Nutrient Transport Defects
Glucose-galactose malabsorption SLC5A1 (SGLT1) 22q13.1 Na+/glucose contransporter
Fructose malabsorption SLC2A5 (GLUT5) 1p36 Fructose transporter
Fanconi-Bickel syndrome SLC2A2 (GLUT2) 3q26 Basolateral glucose transporter
Cystic fibrosis CFTR 7q31.2 cAMP-dependent Cl channel
Acrodermatitis enteropathica SLC39A4 (ZIP4) 8q24.3 Zn2+ transporter
Congenital chloride diarrhea SLC26A3 (DRA) 7q22-q31.1 Cl/base exchanger
Congenital sodium diarrhea SPINT2 19q13.1 Serine-protease inhibitor
Congenital bile acid diarrhea SLC10A2 (ASBT) 13q3 Ileal Na+/bile salt cotransporter
Lysinuric protein intolerance SLC7A7 14q11 Hydrolyzes endo-/exopeptidases amino acid basolateral transport
Pancreatic Insufficiency
Enterokinase deficiency TMPRSS15 (PRSS7) 21q21 Proenterokinase
Trypsinogen deficiency PRSS1 7q35 Trypsinogen synthesis
Pancreatic lipase deficiency PNLIP 10q26.1 Hydrolyzes triglycerides to fatty acids
Lipid Trafficking
Abetalipoproteinemia MTTP 4q22 Transfer lipids to apolipoprotein
Hypobetalipoproteinema APOB 2p24 Apolipoprotein that forms chylomicrons
Chylomicron retention disease SAR1B 5q31.1 Intracellular chylomicron trafficking


cAMP, Cyclic adenosine monophosphate.

From Canani RB, Terrin G, Cardillo G, et al. Congenital diarrheal disorders: improved understanding of gene defects is leading to advances in intestinal physiology and clinical management. J Pediatr Gastroenterol Nutr. 2010;50:362.

Carbohydrate Malabsorption and Disaccharidase Deficiencies

Clinically, congenital disaccharidase deficiency and carbohydrate malabsorption is an osmotic type of diarrhea caused by unabsorbed solute in the ileum. The normal rapid transit of the GI tract in children results in a more severe form of diarrhea than in adults. Histologically, the appearance of the small intestine in these cases is usually unremarkable. Therefore, the diagnosis is usually confined by determination of disacchariadase activity in homogenates of small bowel biopsy specimens or by breath testing.

Congenital disaccharidase and transporter deficiencies are rare; these disorders are much more likely to be secondary, resulting from diffuse mucosal damage due to infectious gastroenteritis, gluten-sensitive enteropathy, or other food allergies. Accelerated crypt shedding, which occurs in mucosal injury, may outpace expression of brush border enzymes and transporter proteins, leading to worsening of the diarrhea and malabsorption. This may be one reason why tacrolimus, which reduces the rate of T cell–driven crypt cell proliferation and shedding, has been found to be effective in conditions such as “tufting” enteropathy and AIE.11,12


Carbohydrate absorption begins with the breakdown of complex carbohydrates by salivary and gastric enzymes into oligosaccharides, which are then hydrolyzed to monosaccharides by specific disaccharidases located at the enterocyte brush border. There are also facilitative hexose transporters located at the basolateral membrane. The latter have been cloned and functionally characterized in several different tissues: GLUT1, erythrocyte; GLUT2, hepatocyte; GLUT3, brain; GLUT4, muscle and fat; and GLUT5, small intestine.

There are four major disaccharidase enzymes: lactase-phlorizin hydrolase (or lactase-glycosyl ceramidase), sucrase-isomaltase, maltase-glucoamylase, and trehalase.11 Lactase-phlorizin hydrolase degrades lactose, the main carbohydrate in milk. Sucrase-isomaltase is responsible for the degradation of dietary sucrose. Maltase-glucoamylase hydrolyses starch into small polymers. Trehalose occurs mainly in mushrooms. Trehalase deficiency is extremely rare. It has been described only in older children and adults. The expression of these enzymes on the intestinal brush border appears to follow a time-dependent sequence. Lactase-phlorizin hydrolase, which is highly expressed at birth, typically declines in early life in most individuals (although it persists through adult life in whites). Sucrase-isomaltase, which is undetectable at birth, reaches adult levels within the first few months of life. These changes coincide with a switch from milk to a more solid diet.

Lactose malabsorption in children can be caused by primary, genetically determined deficiency of lactase-phlorizin hydrolase, which follows a variable clinical course, or by a secondary lactase deficiency resulting from mucosal injury, as in infectious diarrhea, celiac disease, or Crohn’s disease.12 Congenital sucrose-isomaltase deficiency typically becomes clinically apparent when the child begins to consume fruits and juices.13 Glucose-galactose malabsorption is a rare autosomal recessive disorder that is caused by a mutation in the gene on chromosome 22 that encodes the sodium/glucose cotransporter, solute carrier family 5, member 1 (SLC5A1, also known as SGLT1), which can result in severe chronic diarrhea.14 Congenital fructose malabsorption is caused by a mutation in the gene for the hexose transporter isoform, GLUT5, which is located on chromosome 1 and designated SLC2A5.15,16

Lipid Trafficking Disorders

Fat absorption by enterocytes begins with emulsification and solubilization of cholesterol in the intestinal lumen by biliary lipids and salts. Most clinical disorders of fat malabsorption result from severe liver disease, pancreatic disease (e.g., cystic fibrosis), or extensive ileal resection (as in Crohn’s disease), with loss of the enterohepatic circulation of bile acids. Intestinal biopsies play a limited role in the diagnosis of these disorders. However, primary disorders involving abnormalities of fat transport within enterocytes, although uncommon, may result in a characteristic vacuolization of enterocytes in intestinal biopsy specimens.

Abetalipoproteinemia, hypolipoproteinemia, and chylomicron retention disease (Anderson disease) share many characteristics, including fat malabsorption, low levels of serum lipids, failure to thrive in childhood, neurologic and visual problems resulting from malabsorption of fat-soluble vitamins, and accumulation of lipid droplets in the enterocytes. These conditions are associated with disorders of apolipoproteins, which reside on the surface of chylomicrons. Apoliproproteins native to the intestine are apolipoprotein A-I (apo A-I), apo A-IV, and apo B, which has two forms, apo B-100 and apo B-48, both encoded by the same gene located on chromosome 2.17 Localization of apolipoproteins in the Golgi apparatus and along the microvilli of enterocytes has been demonstrated by immuno-electron microscopy.18


Abetalipoproteinemia is an autosomal recessive disorder characterized by absence of apo B-containing lipoproteins. The molecular basis is a mutation of MTTP, the gene that codes for microsomal triglyceride transfer protein, which is located on chromosome 4q22 (see Table 9.2).19 MTTP is responsible for the assembly of lipoprotein particles and for the proper folding of apo B, which prevents its premature degradation.20 Because of the mutation, fatty acids within intestinal cells cannot be exported as chylomicrons. Patients develop diarrhea and fat malabsorption usually within the first few months of life, with acanthocytosis; deficiencies in fat-soluble vitamins then result in retinitis pigmentosa and neurologic symptoms. However, there is clinical heterogeneity because signs and symptoms may occasionally manifest in older individuals. Serum levels of cholesterol and triglycerides are typically low and, most importantly, do not rise after a fatty meal. Small bowel biopsies typically reveal preserved villi (Fig. 9.1, A), but characteristic multivacuolated, fat-filled enterocytes may be seen in specimens from fasting patients, which on electron microscopy are irregular in size and generally not membrane bound (see Fig. 9.1, B). In addition, lipid does not accumulate in the extracellular space. Hepatic biopsies typically reveal steatosis, with numerous non-membrane-bound lipid droplets within hepatocyte cytoplasm.21 Fibrosis evolving to cirrhosis has been reported in some patients.22


Hypobetalipoproteinemia is an autosomal dominant disorder caused by a mutation in the APOB gene located on chromosome 2, which leads to the development of a truncated apo B protein.23 Homozygous patients have a clinical and histologic phenotype that is essentially indistinguishable from abetalipoproteinemia, whereas heterozygous patients have only a mild disease.

Chylomicron Retention Disease

Anderson disease is similar to abetalipoproteinemia in its GI manifestations and impact on growth, although acanthocytosis is usually absent and neurologic and ocular abnormalities are much less severe. However, in contrast to abetalipoproteinemia, serum fasting triglyceride levels are typically normal, and hypocholesterolemia is less marked. The causative gene, SAR1B, codes for a guanosine triphosphatase (GTPase) that is associated with coat protein carriers involved in transport from the endoplasmic reticulum to the Golgi apparatus, particularly transport of chylomicrons and low-density lipoproteins.24 The pathologic features in small bowel biopsy specimens are essentially indistinguishable from those of abetalipoproteinemia (see Fig. 9.1, C).

Minor degrees of enterocyte vacuolization (e.g., resulting from a recent feed) are common in intestinal biopsy specimens in infants. In these cases, vacuolization is not as marked or as diffused as in abetalipoproteinemia or chylomicron storage disease. In addition, lipid droplets are present in the intercellular spaces and lacteals after feeding but are absent from these spaces in disorders that cause impaired lipid transport. By contrast, lipid-containing macrophages are present in the lamina propria in several storage disorders in which digestive symptoms can occasionally be significant and in which an intestinal biopsy is obtained in the course of a workup for failure to thrive (see Metabolic Diseases).

Amino Acid Transport Disorders

Disorders of amino acid transport rarely cause prominent GI manifestations, except for lysinuric protein intolerance (LPI), which results from mutations in the SLCA7 gene. This gene codes for the light chain subunit of the heterodimer amino acid transporter at the basolateral membrane of intestinal and renal epithelial cells.25 Clinically, LPI manifests with failure to thrive, vomiting, and diarrhea. Hepatosplenomegaly, hematologic anomalies, and neurologic involvement including hyperammonemic coma are recurrent clinical features. The urea cycle intermediates ornithine and arginine fail to exit from intestinal epithelium in LPI, resulting in a urea cycle dysfunction with hyperammonemia and alterations of mental status. Two major complications, pulmonary alveolar proteinosis and renal disease, are increasingly observed in patients with LPI.26,27 The condition is recognized by the presence of markedly elevated urinary levels of lysine and other dibasic amino acids; DNA testing may be required for confirmation of the diagnosis. One 5-year-old boy who was reported to have chronic diarrhea and a “flat gut” on small intestinal biopsy was unsuccessfully treated with a gluten-free diet.28 Other complications associated with this disorder include systemic lupus erythematosus, hemophagocytic lymphohistiocytosis,29 and sudden infant death.30

Electrolytes and Trace Elements

The biology of intestinal ion transport is a complex field. Disorders range from rare selective deficiencies to multisystem diseases such as cystic fibrosis. Defects that manifest primarily with severe diarrhea in infancy include congenital chloride diarrhea and congenital sodium diarrhea. Intestinal biopsy findings in these cases have been reported to be normal or to show only mild partial villus atrophy.31 Congenital chloride diarrhea is caused by mutations in the gene for solute-linked carrier family 26, member 3 (SLC26A3). It manifests as a life-threatening congenital diarrhea. Long-term manifestations include renal disease, spermatoceles, and male subfertility.32 Congenital sodium diarrhea results in hyponatremia and metabolic acidosis. The syndromic form of this disorder has been linked to mutations in SPINT2 and is also characterized by cloanal and anal atresia, hypertelorism, double kidney, cleft palate, and digital anomalies.13

Acrodermatitis enteropathica is an autosomal recessive disorder that is caused by a defect in intestinal absorption of zinc. Mutations in a candidate gene, ZIP4 (SLC39A4), result in defective epithelial transport in the intestine and kidney.13 There is a characteristic clinical syndrome of diarrhea combined with acral and orificial skin lesions. Rodin and Goldman found pancreatic islet hyperplasia, absence of the thymus and germinal centers, and plasmacytosis of the spleen and lymph nodes in autopsy studies.33 Inclusion bodies in Paneth cells have been reported in patients with this disorder.34,35 A decrease in villus height is observed in animal models of zinc deficiency and is corrected by zinc supplementation.36 Interference with chylomicron development and function has been noted.37 Severe zinc deficiency is also seen in other disorders, such as the Cronkhite-Canada syndrome.38

Menkes disease is an X-linked disorder that results from a defect in intestinal absorption of copper. Affected patients present with characteristic hair shaft anomalies (pili torti), cerebral degeneration, hypopigmentation, abnormal bones, vomiting and diarrhea, and, occasionally, protein-losing enteropathy (PLE). The disorder maps to Xq12-q13 and is caused by mutations in the ATP7A gene, which encodes a copper-transporting P1B-type adenosine triphosphatase that is part of a family of membrane proteins responsible for cation transport across membranes.39,40


Congenital vitamin B12 transport disorders include congenital intrinsic factor deficiency, selective absence of intrinsic factor without any gastric anomaly, congenital pancreatic insufficiency of various causes, and congenital selective vitamin B12 malabsorption—the latter an autosomal recessive disorder characterized by megaloblastic anemia, hepatosplenomegaly, vomiting, diarrhea and proteinuria. These disorders are caused by mutations in the gene CUBN, which encodes an ileal cell surface receptor protein known as cubilin.41 None of these disorders results in any characteristic histologic changes on intestinal biopsies.

A rare congenital disorder of intracellular vitamin B12 metabolism belonging to the cobalamin C (CblC) family has also been described. Patients present with diarrhea, renal failure, and systemic thromboemboli in association with a striking gastric atrophy.42 PLE responsive to hydroxycobalamin treatment has been reported in one patient with this disorder,43 presumably on the basis of the gastric anomaly.

Bile Acids

Heubi and colleagues44 described a severe type of refractory diarrhea caused by a primary disorder of bile acid absorption; intestinal biopsy findings were normal. A defect in the gene coding for an ileal Na+-dependent bile acid transporter, SLC10A2, has been found in this disorder.45 Bile acid–related diarrheal illnesses are much more commonly secondary to chronic pancreatic insufficiency46 or to loss of ileal surface, as occurs with short gut syndrome resulting from necrotizing enterocolitis47 or with extensive ileal resection in Crohn’s disease.48,49

Congenital Defects of Intestinal Epithelial Differentiation

Microvillus Inclusion Disease

Clinical Features

Initially described by Davidson et al in 197850 and subsequently recognized worldwide, microvillus inclusion disease (MVID) is an autosomal recessive disease characterized by refractory secretory diarrhea usually within the first week of life, although late-onset symptoms may manifest in the first few months of life.51 Investigation of clusters of cases within the Navajo population identified mutations in the gene MYO5B.52 Homozygosity mapping of an extended Turkish kindred allowed Muller and colleagues to locate the gene locus to chromosome 18q21.53 MYO5B codes for myosin Vb, part of a family of proteins responsible for actin-dependent organelle transport and regulation of endosome recycling. Mutations in the MYO5A gene cause Griscelli syndrome, an immunodeficiency disorder also characterized by abnormal transfer of melanin granules to keratinocytes.53


Small bowel biopsy specimens in MVID are usually characterized by severe villus atrophy, mild or moderate crypt hyperplasia, and a variable degree of inflammation in the lamina propria, but without crypt destruction (Fig. 9.2, A). The diagnosis may be strongly suspected on paraffin-embedded sections by the absence of a distinct brush border using the periodic acid–Schiff (PAS) stain, and by the presence of PAS-positive diastase-resistant densities in the apex of enterocytes (see Fig. 9.2, B and C). Similar observations are seen on immunohistochemical staining for alkaline phosphatase and anti-CD10. More recently, similar results using antibodies directed against anti-Rab11a, a small GTPase protein on the surface of recycling endosomes, has provided further evidence that MVID is a disorder of apical plasma membrane recycling.54 The pathognomonic ultrastructural features include absent or small stubby microvilli, vesicular structures located toward the apex of enterocytes containing microvilli, and granules containing dense amorphous material (Fig. 9.3). Microvillus inclusions have also been reported in the colon, gallbladder, and renal tubular epithelium in these patients.55 A variety of ultrastructural features have also been noted in patients with this disorder, and finding the “typical” inclusions may require a prolonged search.56

Atypical inclusions include the presence of numerous small electron-lucent vesicles and accumulation of osmiophilic vermiform structures.57 Cases with these features have been previously reported as “MVID with atypical features” or as “microvillous dystrophy.”58,59 Genetic analysis helps in defining whether the ultrastructural (and sometimes clinical) variability represent different entities or variations in the spectrum of manifestations of a single disorder, especially given the enormous prognostic and therapeutic implications.


Patients with MVID are dependent on total parenteral nutrition (TPN). Medical therapy in these patients is generally ineffective, and improved survival may require small bowel transplantation.60 An intriguing instance of apparent resolution of the disease with improvement of the mucosal features in a patient on long-term TPN has been reported.61

Congenital Tufting Enteropathy (Epithelial Dysplasia)

Clinical Features

Congenital tufting enteropathy (CTE) was first described by Reifen and colleagues62 in patients presenting in the neonatal period with watery diarrhea. The prenatal history is usually uneventful. The disease appears to be inherited in an autosomal recessive fashion, as suggested by the finding of other affected siblings and frequent parental consanguinity. The incidence is estimated at 1 : 50,000 to 1 : 100,000 live births in Europe, and it is more frequent in patients of Arabic origin.63

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