The n e w e ng l a n d j o u r na l of
Case Records of the Massachusetts General Hospital
From the Departments of Medicine
(F.P.C., Y.-B.C., S.B.), Pathology (S.G.S.),
and Pediatrics (F.A.H.), Massachusetts
General Hospital, and the Departments
of Medicine (F.P.C., Y.-B.C., S.B.), Pathol-
ogy (S.G.S.), and Pediatrics (F.A.H.),
Harvard Medical School — both in Boston.
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DOI: 10.1056/NEJMcpc2201236
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m e dic i n e
Founded by Richard C. Cabot
Eric S. Rosenberg, M.D., Editor
David M. Dudzinski, M.D., Meridale V. Baggett, M.D., Kathy M. Tran, M.D.,
Dennis C. Sgroi, M.D., Jo‑Anne O. Shepard, M.D., Associate Editors
Emily K. McDonald, Tara Corpuz, Production Editors
Case 29-2022: A 33-Year-Old Man with Chronic
Diarrhea and Autoimmune Enteropathy
Francis P. Colizzo, M.D., Stuti G. Shroff, M.B., B.S., Ph.D.,
Frances A. High, M.D., Ph.D., Yi‑Bin Chen, M.D., and Sara Barmettler, M.D.​​
Pr e sen tat ion of C a se
Dr. Dilara Hatipoglu (Medicine): A 33-year-old man was evaluated in the gastroenter-
ology clinic of this hospital because of relapsing chronic diarrhea and a diagnosis
of autoimmune enteropathy.
Diarrhea had initially developed in the patient during infancy. When the patient
was 2 months of age, he had poor growth and frequent bowel movements with
loose stools. When he began to eat solid foods, diarrhea continued, and a hydro-
lyzed-protein diet was started. His parents were instructed to remove dairy, soy,
and gluten from his diet, but diarrhea did not abate. Allergy skin-prick testing
with cow’s milk and soy antigens was negative.
When the patient was 10 months of age, failure to thrive and diarrhea per-
sisted, and generalized edema and nephrotic syndrome developed. Esophagogas-
troduodenoscopy (EGD) was performed, and histopathological examination of a
small-intestinal biopsy specimen reportedly revealed villous atrophy, crypt hyper-
plasia, and diffuse inflammation. Transmission electron microscopy reportedly
showed mild degenerative changes of the surface epithelium and mild focal micro-
villous atrophy; there were no immune deposits, and the basement membrane was
normal.
Renal biopsy was also performed, and histopathological examination of a renal
biopsy specimen revealed glomeruli with diffuse thickening of the basement mem-
brane; there was no proliferation of cells or mesangial matrix. Transmission elec-
tron microscopy showed total effacement of the epithelial cell foot processes and
an irregularly thickened glomerular basement membrane with numerous subepi-
thelial and intramembranous electron-dense deposits. The patient received a work-
ing diagnosis of nephrotic syndrome due to membranous glomerulonephritis, and
treatment with prednisone was started.
Diarrhea abated, proteinuria and generalized edema resolved, and growth re-
sumed. However, during the next 2 years, intermittent relapses of diarrhea and
nephrotic syndrome occurred when the dose of prednisone was decreased. When
the patient was 3 years of age, treatment with chlorambucil was started for recur-
rent membranous glomerulonephritis, and there were no relapses for 1 year.
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 Case Records of the Massachuset ts Gener al Hospital

A B
* *

C D
*
* *

Figure 1. Small-Intestinal Biopsy Specimens.

On hematoxylin and eosin staining, a specimen of duodenal mucosa obtained 6 years before this presentation
(Panel A) shows marked villous blunting (arrows) and lymphoplasmacytic expansion of the lamina propria. A specimen
of duodenal mucosa obtained at presentation (Panels B and C) shows marked villous blunting (Panel B, arrows),
lymphoplasmacytic expansion of the lamina propria, and an increase in intraepithelial lymphocytes (Panels B and C,
asterisks). A specimen of ileal mucosa obtained at presentation (Panel D) shows findings similar to those observed
in the duodenum, with mild villous blunting (arrows), lymphoplasmacytic expansion of the lamina propria, and an
increase in intraepithelial lymphocytes (asterisks).

When the patient was 4 years of age, there
was a recurrence of diarrhea associated with
fever and hemolytic anemia. Stool culture, stool
testing for Clostridioides difficile toxin, and exami-
nation of the stool for ova and parasites were all
negative. EGD was performed, and histopatho-
logical examination of a small-intestinal biopsy
specimen reportedly revealed villous atrophy,
crypt hyperplasia, and active enteritis. The blood
IgE level was 501 IU per milliliter (reference
range, 0 to 100). The blood level of endomysial
antibodies was not elevated, but anti–epithelial
cell antibodies were detected. The patient re-
ceived a diagnosis of autoimmune enteropathy,
and treatment with intravenous glucocorticoids
and cyclosporine was begun.
After several months, treatment with gluco-
corticoids and cyclosporine was stopped, and
tacrolimus was begun. Tacrolimus was stopped
after several years, when the patient’s symptoms
resolved. From 5 to 13 years of age, he had no
enteropathy, anemia, or nephropathy.
Beginning at 13 years of age, the patient was
hospitalized for recurrences of diarrhea and ne-
phropathy every 2 to 4 years during the 20 years
before this evaluation. Six years before this
evaluation, EGD and colonoscopy were per-
formed, and the duodenal and colonic mucosa
appeared diffusely edematous. Biopsy specimens
were obtained.
Dr. Stuti G. Shroff: Examination of a duodenal
biopsy specimen (Fig. 1) revealed marked villous
blunting, an increase in lymphoplasmacytic in-
flammatory cells in the lamina propria (known
as lymphoplasmacytic expansion of the lamina
propria), and a patchy increase in intraepithelial
lymphocytes. Examination of a colonic biopsy
specimen revealed mild focal active colitis that
spared the rectum.
Dr. Hatipoglu: Treatment with intravenous

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 The n e w e ng l a n d j o u r na l
methylprednisolone was begun, and diarrhea
abated. For the next 2 years, relapses of diarrhea
and nephrotic syndrome were treated with intra-
venous methylprednisolone or oral prednisone
in combination with cyclosporine, tacrolimus,
and mycophenolate mofetil.
Four years before this evaluation, antibodies
against the M-type phospholipase A2 receptor
were not detected. Renal biopsy was performed,
and histopathological examination of a renal bi-
opsy specimen again revealed evidence of mem-
branous glomerulonephritis. Treatment was
changed to prednisone, budesonide, and abata-
cept, and symptoms abated. After 2 years, the
patient stopped taking abatacept. After another
2 years, diarrhea recurred, and the patient was
referred to the gastroenterology clinic of this
hospital.
In the gastroenterology clinic, additional his-
tory was obtained. There was a history of hyper-
tension, gallstones, and rosacea. Eczema had
developed when the patient was 10 months of
age and had occurred intermittently into adult-
hood; it had abated with the administration of
immunosuppressive agents. Anaphylactic shock
had occurred when the patient was 2 years of
age after he had been exposed to uncooked egg.
At that time, allergy testing was performed, and
the patient’s parents were instructed to remove
eggs, tree nuts, peanuts, fish, and shellfish from
his diet, in addition to removing dairy, soy, and
gluten.
Current medications included prednisone,
budesonide, and losartan. There were no known
drug allergies. The patient lived in a Mid-Atlantic
state and worked as a salesperson. He did not
smoke tobacco and drank beer rarely. His family
history included ovarian cancer in his mother
and skin cancer in his father; his brother was
healthy.
On examination, the temperature was 37.0°C,
the blood pressure 131/94 mm Hg, the heart rate
106 beats per minute, and the oxygen saturation
97% while the patient was breathing ambient
air. The body-mass index (the weight in kilo-
grams divided by the square of the height in
meters) was 24.1. The patient had short stature
and diffuse erythema of the face and neck.
There was mild tenderness in the left lower ab-
domen. The results of a lactulose breath test
were normal, as was the fecal calprotectin level.
Testing for antibodies to tissue transglutamin-
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of m e dic i n e
ase was negative. Other laboratory test results
are shown in Table 1. EGD and colonoscopy
were performed, and the findings were consis-
tent with duodenitis, gastritis, and atrophy of
the colon. Biopsy specimens were obtained.
Dr. Shroff: Histopathological examination of
ileal and duodenal biopsy specimens (Fig. 1) re-
vealed villous blunting, lymphoplasmacytic ex-
pansion of the lamina propria, and intraepithe-
lial lymphocytosis.
Dr. Hatipoglu: A diagnostic test was performed.
Differ en t i a l Di agnosis
Dr. Francis P. Colizzo: I participated in the care of
this patient and am aware of the final diagnosis.
This 33-year-old man had a long-standing diag-
nosis of autoimmune enteropathy, which had
been complicated by hemolytic anemia, membra-
nous nephropathy with proteinuria, and eczema.
Symptoms were intermittently controlled with
the administration of glucocorticoids and other
immunosuppressive agents, but full and durable
remission was never established. Could the pa-
tient’s current presentation with relapsing diar-
rhea be caused by persistence or exacerbation of
his primary condition, autoimmune enteropathy?
Or could it be caused by another condition that
he acquired because of chronic immunosuppres-
sion? Alternatively, could his diagnosis of auto-
immune enteropathy, which he had carried for
most of his life, be incorrect? The first step in
caring for this patient is to reconsider the dif-
ferential diagnosis of chronic diarrhea and mal-
absorption that can occur in association with
villous atrophy and enteropathy.
Autoimmune Enteropathy
Autoimmune enteropathy is a rare condition that
is more common among infants and children
than among adults. It can occur as a primary
process or be due to another immune-mediated
process. Symptoms include chronic diarrhea,
malabsorption, and weight loss. Extraintestinal
manifestations can include hemolytic anemia,
nephritis, and dermatitis, all of which had oc-
curred in this patient. Thyroiditis and hepatitis
have also been reported as extraintestinal mani-
festations of autoimmune enteropathy.
The proposed diagnostic criteria for autoim-
mune enteropathy include the detection of vil-
lous atrophy on biopsy of the small intestine,
 Case Records of the Massachuset ts Gener al Hospital

Table 1. Laboratory Data.*

Variable Reference Range, Adults† On Presentation

Hemoglobin (g/dl) 13.5–17.5 17.9
Hematocrit (%) 41.0–53.0 53.9
Platelet count (per μl) 150,000–400,000 244,000
White-cell count (per μl) 4500–11,000 13,680
Differential count (per μl)
Neutrophils 1800–7700 10,670
Lymphocytes 1000–4800 1560
Monocytes 200–1200 1130
Eosinophils 0–900 80
Basophils 0–300 70
Sodium (mmol/liter) 135–145 142
Potassium (mmol/liter) 3.4–5.0 3.8
Chloride (mmol/liter) 98–108 107
Carbon dioxide (mmol/liter) 23–32 21
Anion gap (mmol/liter) 3–17 14
Urea nitrogen (mg/dl) 8–25 14
Creatinine (mg/dl) 0.60–1.50 0.78
Alanine aminotransferase (U/liter) 10–55 32
Aspartate aminotransferase (U/liter) 10–40 23
Alkaline phosphatase (U/liter) 45–115 167
Albumin (g/dl) 3.3–5.0 3.9
Total protein (g/dl) 6.0–8.3 6.4
IgA (mg/dl) 69–309 356
IgG (mg/dl) 614–1295 900
IgM (mg/dl) 53–334 108
IgE (IU/ml) 0–100 664
Vitamin A (μg/dl) 32.5–78.0 28.8
Vitamin E (mg/liter) 5.5–17.0 7.1
Vitamin B12 (pg/ml) >231 155
Vitamin D (ng/ml) 20–80 6
Zinc (μg/ml) 0.66–1.10 0.57
Erythrocyte sedimentation rate (mm/hr) 0–13 2

* To convert the values for urea nitrogen to millimoles per liter, multiply by 0.357. To convert the values for creatinine to
micromoles per liter, multiply by 88.4. To convert the values for vitamin A to micromoles per liter, multiply by 0.03491.
To convert the values for vitamin B12 to picomoles per liter, multiply by 0.7378. To convert the values for vitamin D to
nanomoles per liter, multiply by 2.599.
† Reference values are affected by many variables, including the patient population and the laboratory methods used. The
ranges used at Massachusetts General Hospital are for adults who are not pregnant and do not have medical conditions
that could affect the results. They may therefore not be appropriate for all patients.

along with a decrease in goblet cells in the tis-
sue; the presence of antienterocyte antibodies;
and chronic diarrhea with malabsorption.1 Anti–
epithelial cell antibodies had been detected in
this patient when he was 4 years of age. At that
time, antienterocyte antibody testing was not yet
available, and the patient met criteria for the
diagnosis of autoimmune enteropathy. When I
initially evaluated this patient, serum testing for
antienterocyte antibodies was positive at a titer

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 The n e w e ng l a n d j o u r na l of m e dic i n e

of 1:10. However, potential causes other than colonization with colonic microbes and is treat-
autoimmune enteropathy were considered, given ed with oral antibiotic agents. This patient had
the refractory nature of the diarrhea and the no confirmed underlying conditions that are
other substantial clinical symptoms. known to confer a predisposition to small-intes-
tinal bacterial overgrowth, such as inflamma-
Celiac Disease tory bowel disease, diverticula in the small in-
Patients with celiac disease also have diarrhea, testine, intestinal resections, motility disorders,
malabsorption, and weight loss. Extraintestinal diabetes, scleroderma, or IgA deficiency. In ad-
manifestations can include IgA nephropathy and dition, his extraintestinal manifestations would
dermatitis herpetiformis, neither of which had not be explained by small-intestinal bacterial
occurred in this patient. In addition, celiac dis- overgrowth. A lactulose breath test was negative,
ease is not typically associated with hemolytic which argues against this diagnosis, but because
anemia,2 which had been a prominent feature of carbohydrate breath tests have variable sensitiv-
this patient’s disease course. ity and specificity, this finding does not rule out
In patients with celiac disease, serologic small-intestinal bacterial overgrowth.
evaluation confirms the presence of tissue trans-
glutaminase IgA; if the patient has selective IgA Intolerance of Cow’s Milk
deficiency, tissue transglutaminase IgG can be Cow’s milk intolerance is common among in-
measured. In this patient, serologic testing for fants and young children. It causes diarrhea and
tissue transglutaminase IgA was negative in the can be associated with eczema. Cow’s milk in-
absence of IgA deficiency. Furthermore, celiac tolerance usually resolves with age, whereas this
disease is treated with elimination of gluten patient’s symptoms persisted into adulthood. In
from the diet, and this patient’s symptoms did addition, skin-prick testing with cow’s milk anti-
not abate with dietary gluten elimination. Col- gen was negative, and symptoms persisted de-
lagenous sprue is a rare subtype of celiac disease spite elimination of cow’s milk from the diet.
that is often refractory to conventional treat-
ment, but it is characterized by the presence of Eosinophilic Gastroenteritis
a subepithelial collagen band on histopathologi- Eosinophilic gastroenteritis is most prevalent
cal examination of a biopsy specimen from the among children younger than 5 years of age and
small intestine, a finding that was not seen in is often associated with a coexisting atopic con-
this patient. dition. Because there is usually an underlying
allergic component, eosinophilia and an elevated
Inflammatory Bowel Disease blood IgE level can be present. The blood IgE
Inflammatory bowel disease can cause diarrhea level was sometimes elevated in this patient, and
and malabsorption, but it rarely develops in in- the absence of eosinophilia could be explained
fancy. However, an entity described as very-early- by ongoing treatment with glucocorticoids. How-
onset inflammatory bowel disease has been re- ever, there was no evidence of tissue involvement
ported; it has been associated with certain with eosinophilic infiltration in the mucosa or
genetic variants.3 Although inflammatory bowel muscularis layers on multiple biopsies of the
disease is not typically associated with renal small intestine.
manifestations, granulomatous interstitial ne-
phritis and IgA nephropathy have been reported Enteropathy Associated with Angiotensin-
in some patients with inflammatory bowel dis- Receptor Blockers
ease.4,5 This patient had no evidence of inflam-Sprue-like enteropathy has been reported in pa-
matory bowel disease on endoscopy, and his fe- tients taking the angiotensin II–receptor blocker
cal calprotectin level was normal. olmesartan. There have been very few case re-
ports of this condition occurring with the use of
Small-Intestinal Bacterial Overgrowth losartan,6 which was the angiotensin II–recep-
Small-intestinal bacterial overgrowth is a con- tor blocker that this patient was taking. This
dition characterized by bloating, diarrhea, and patient’s symptoms predated his use of losartan,
cramping. It is caused by excessive small-bowel so this medication is unlikely to be the cause of

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 Case Records of the Massachuset ts Gener al Hospital

his symptoms; however, a brief trial involving tis, which were seen in this patient, have been
discontinuation of this medication would be described in patients with IPEX syndrome. Intes-
appropriate. tinal biopsy typically reveals features consistent
with autoimmune enteropathy: villous atrophy,
Inborn Errors of Immunity intraepithelial lymphocytes, and plasma cells.
Inborn errors of immunity, also known as pri- Immunosuppressive therapy is the mainstay of
mary immunodeficiencies, are disorders that treatment. However, immunosuppression typi-
stem from defects in immune regulation or tol- cally controls symptoms only transiently, with-
erance and can mimic inflammatory bowel dis- out long-term remission, which is consistent
ease. Many of these conditions can be fatal with this patient’s disease course.
early in life. The most common primary immu- Given this patient’s history, clinical presenta-
nodeficiency — common variable immune defi- tion, and constellation of symptoms, I suspected
ciency — can be ruled out in this patient, given that IPEX syndrome was the most likely diagno-
the absence of immunoglobulin deficiencies. sis. To establish this diagnosis, I referred the
Two additional primary immunodeficiencies mer- patient to the allergy and clinical immunology
it consideration in this patient: autoimmune poly- unit for further evaluation and consideration for
endocrinopathy, candidiasis, and ectodermal genetic testing.
dystrophy (APECED) and immune dysregulation,
polyendocrinopathy, enteropathy, X-linked (IPEX) Cl inic a l Impr e ssion
syndrome.
Dr. Sara Barmettler: When the patient was evalu-
APECED ated in the allergy and clinical immunology
APECED, also known as autoimmune polyendo- unit, further history was obtained. In addition to
crine syndrome type 1 (APS-1), results from a the history of refractory autoimmune enteropa-
defect in the autoimmune regulator gene (AIRE) thy, there was a history of infection, which was
that leads to a loss of central immune tolerance.7 notable for pneumonia as well as other sinopul-
Patients with APECED present with mucocutane- monary infections. These features, in combina-
ous candidiasis, ectodermal dystrophy, and mul- tion with the history of eczematous dermatitis,
tiple endocrine diseases. Hypoparathyroidism food allergy, hemolytic anemia, and proteinuria,
and adrenal insufficiency are the most common were suggestive of a systemic syndrome of im-
endocrine diseases; diabetes mellitus or hypo- mune dysregulation.
thyroidism (or both) can also occur. APECED is Additional testing was performed. A com-
often associated with underlying autoimmune plete blood count with differential count ob-
enteropathy, and gastrointestinal manifestations tained after the discontinuation of oral predni-
can vary widely. However, this patient did not sone showed eosinophilia. Results of serum
have any of the typical endocrine diseases asso- protein electrophoresis and serum levels of free
ciated with APECED or have mucocutaneous light chains were normal. IgG and IgM levels
candidiasis. were normal; IgE and IgA levels were elevated.
On functional antibody testing, there were pro-
IPEX Syndrome tective levels of tetanus IgG, Streptococcus pneu-
IPEX syndrome is an immune dysregulatory dis- moniae IgG, and Haemophilus influenzae type b IgG.
order that typically develops in infancy. It is due Flow cytometry showed normal absolute CD3+,
to a defect in the gene encoding forkhead box CD4+, and CD8+ T-cell counts, along with a
protein 3 (FOXP3) that leads to dysfunctional slightly low CD19+ B-cell count. The CD4+
regulatory T cells.8 Patients with IPEX syndrome T‑cell compartment was skewed toward a mem-
present with a classic triad of manifestations: ory phenotype, and the CD8+ compartment had
autoimmune endocrinopathies (typically neonatal increased expression of HLA class II antigens
type 1 diabetes mellitus and thyroiditis), auto- that was consistent with an activated phenotype.
immune enteropathy (associated with failure to Testing for antienterocyte antibodies performed
thrive and severe chronic diarrhea), and eczema- at a reference laboratory was positive, with lin-
tous dermatitis. Hemolytic anemia and nephri- ear IgG and IgA staining of the apical enterocyte

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 The n e w e ng l a n d j o u r na l of m e dic i n e

Table 2. Results of Genetic Testing.*

Gene Variant Zygosity Classification Disease Associations

FOXP3 c.754A→G Hemizygous Uncertain IPEX syndrome (MIM number
(p.Lys252Glu) significance 304790, X-linked recessive)
RMRP n.−24_−10dup Heterozygous Likely pathogenic Cartilage–hair hypoplasia (MIM
(promoter) number 250250, autosomal
­recessive)
SH3BP2 c.428+1G→C Heterozygous Uncertain Cherubism (MIM number 118400,
(splice donor) significance autosomal dominant)

* IPEX denotes immune dysregulation, polyendocrinopathy, enteropathy, X-linked, and MIM Mendelian Inheritance in Man.

membranes. An inborn error of immunity was The FOXP3 variant was classified by the diag-
suspected, and genetic testing was performed. nostic laboratory as a variant of uncertain sig-
nificance. All variants detected by means of
clinical diagnostic genetic testing are classified
Cl inic a l Di agnosis
according to guidelines published by the Ameri-
Inborn error of immunity. can College of Medical Genetics and Genomics
and the Association for Molecular Pathology.9
On the basis of an evidence-based framework,
Dr . Fr a ncis P. C ol i z z o’s
Di agnosis each variant is given one of five classifications
— pathogenic, likely pathogenic, uncertain sig-
Inborn error of immunity, most likely immune nificance, likely benign, or benign — to help
dysregulation, polyendocrinopathy, enteropathy, determine the likelihood that the variant will
X-linked (IPEX) syndrome. cause disease. Variants of uncertain significance
are common findings on genetic testing that
can be challenging to interpret. They cannot be
Gene t ic Te s t ing
a nd In ter pr e tat ion used alone to establish a clinical diagnosis or to
direct clinical management. Familial segrega-
Variant and Classification tion studies and functional studies on the gene
Dr. Frances A. High: The patient underwent panel- product can aid in determining the clinical rel-
based genetic testing, including sequencing as evance of a variant of uncertain significance.
well as deletion and duplication analysis of 207 Familial segregation studies for the FOXP3
genes associated with primary immunodeficien- variant were performed and showed that the
cies and monogenic inflammatory bowel dis- variant was inherited from the patient’s mother,
ease. This testing revealed three rare variants in who was a heterozygous carrier. The variant was
three different genes: a hemizygous missense absent in his father and unaffected brother.
variant in FOXP3, a heterozygous promoter vari- These findings are consistent with the X-linked
ant in the gene encoding the RNA component of recessive inheritance pattern of IPEX syndrome.
mitochondrial RNA–processing endoribonuclease
(RMRP), and a heterozygous splice-donor variant IPEX Syndrome Manifestations and Effects
in the gene encoding SH3 domain–binding pro- on Regulatory T Cells
tein 2 (SH3BP2) (Table 2). The RMRP and SH3BP2 Dr. Barmettler: IPEX syndrome is caused by loss-
variants were not thought to be relevant because of-function variants in FOXP3,10-12 which is a
of the mismatch between the clinical phenotype master transcriptional regulator that is funda-
of the patient and the reported disease associa- mental to the function of CD4+ CD25+ regula-
tions and inheritance patterns of the genes. tory T cells.13 Regulatory T cells suppress the
However, FOXP3 is associated with the X-linked activation and effector functions of self-reactive
recessive disease IPEX syndrome, so the FOXP3 and potentially pathogenic lymphocytes.14 Loss-
variant found in this patient warranted addi- of-function variants in FOXP3 cause quantitative
tional investigation. or functional deficiencies in regulatory T cells,

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 Case Records of the Massachuset ts Gener al Hospital

Classic triad Other manifestations

Neurologic abnormalities
• Developmental delay
• Seizures

Damaged
Hematologic disorders
beta cells • Immune thrombocytopenic
purpura
Autoimmune endocrinopathies • Autoimmune hemolytic
anemia
• Autoimmune neutropenia

Healthy villi
Pulmonary disease
Villous atrophy • Acute respiratory distress
syndrome
• Infections
• Interstitial lung disease

Gastrointestinal disease
Small intestine
Autoimmune hepatitis
Autoimmune enteropathy
Renal disease
• Interstitial nephritis
• Hematuria
• Proteinuria
• Rapidly progressive
glomerulonephritis

Infectious disease
• Sepsis
• Meningitis
• Pneumonia
• Osteomyelitis
Eczematous dermatitis

Figure 2. Clinical Manifestations of IPEX Syndrome.

The classic triad of manifestations associated with immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome
comprises autoimmune endocrinopathies, autoimmune enteropathy, and eczematous dermatitis. Other manifestations include neuro-
logic abnormalities, hematologic disorders, and pulmonary, gastrointestinal, renal, and infectious diseases. Red shading indicates mani-
festations that occurred in this patient.

which lead to immune dysregulation. This dys-
regulation can manifest as autoimmune disease
and allergic inflammation.10,12,15,16
In addition to the classic triad of manifesta-
tions associated with IPEX syndrome (autoim-
mune endocrinopathies, autoimmune enteropa-
thy, and eczematous dermatitis), numerous other
manifestations have been described, including
neurologic abnormalities, hematologic disorders
(e.g., immune-mediated cytopenias), pulmonary
disease, hepatitis, renal disease, and infections
(Fig. 2).17-20 Allergic inflammation can include
eczema, food allergies, eosinophilia, and an ele-
vated total IgE level.20

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 The n e w e ng l a n d j o u r na l of m e dic i n e

CNS1 CNS2 CNS3

Gene
E-1 E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11

Promoter

N-terminal proline-rich domain ZF domain LZ domain FKH DNA-binding domain

Protein
N C

c.754A→G (p.Lys252Glu)
• No frequency in gnomAD
• SIFT: “deleterious”
• PolyPhen-2: “probably damaging”

Figure 3. FOXP3 Functional Domains and Variant in This Patient.

IPEX syndrome is caused by loss-of-function variants in the gene encoding forkhead box protein 3 (FOXP3). These
variants cause quantitative or functional deficiencies in regulatory T cells, which lead to immune dysregulation. This
dysregulation can manifest as autoimmune disease and allergic inflammation. There are several functional domains
of the gene product. The N-terminal proline-rich domain regulates transcription. The zinc-finger (ZF) domain is in-
volved in protein–DNA interactions. The leucine-zipper (LZ) domain mediates homodimerization and heterodimeriza-
tion with FOXP3 and other FOXP transcription factors. The forkhead (FKH) DNA-binding domain interacts with the
interleukin-2 promoter and other target genes. This patient had a variant in the LZ domain: c.754A→G (p.Lys252Glu).
This variant is not present in population databases (no frequency in the Genome Aggregation Database [gnomAD]).
The Sorting Intolerant from Tolerant (SIFT) prediction for this variant was “deleterious,” and the Polymorphism
Phenotyping v2 (PolyPhen-2) prediction was “probably damaging.” Conserved noncoding enhancer sequences
(CNSs) are target sites of epigenetic modifications.23 E1 through E11 are the exons of the canonical FOXP3 tran-
script (Ensembl transcript ID, ENST00000376207.4).

Disease-causing variants have been described phism Phenotyping v2 (PolyPhen-2) prediction26

in the coding regions and in the noncoding re-
gions of FOXP3; no clear genotype–phenotype
correlations have been identified.16,19-22 Of note,
FOXP3 variants have variable penetrance, with
the same variant causing different clinical pre-
sentations across carriers, including family
members.20
This patient’s clinical presentation was con-
sistent with IPEX syndrome, and genetic testing
showed a variant of uncertain significance in
FOXP3: FOXP3, exon 8, c.754A→G (p.Lys252Glu).
This sequence change replaced lysine with glu-
tamic acid at codon 252 of the protein FOXP3.
The lysine residue is moderately conserved, and
there is a small physicochemical difference be-
tween lysine and glutamic acid. This mutation is
in the leucine-zipper domain (Fig. 3), which
mediates homodimerization and heterodimer-
ization.24 This variant is not present in popula-
tion databases (no frequency in the Genome
Aggregation Database [gnomAD]). The Sorting
Intolerant from Tolerant (SIFT) prediction25 for
this variant was “deleterious,” and the Polymor-
was “probably damaging.”
The next step was to perform functional
studies on regulatory T cells from the patient.
Results of phenotyping of regulatory T cells,
performed at the Medical College of Wisconsin
by means of surface-marker flow cytometric
analysis, were abnormal. There was an elevated
total percentage of FOXP3+ CD4+ T cells in cir-
culation, and these cells had atypical expression
of CD25 and CTLA4. In healthy persons, regula-
tory T cells constitutively express high levels of
CD25 and CTLA4, because FOXP3 drives their
expression. In this patient, many FOXP3+ regu-
latory T cells had reduced expression of CTLA4
and CD25. Within the clinical spectrum of IPEX
syndrome, a decrease in circulating FOXP3+
regulatory T cells is seen in persons with FOXP3
variants that result in loss of protein expres-
sion.17 In contrast, persons with FOXP3 missense
mutations may have regulatory T cells in which
FOXP3 is present but partially functioning or
nonfunctioning.16,18 This patient had a missense
variant in which FOXP3 was present, but he ap-

1132 n engl j med 387;12 nejm.org September 22, 2022

The New England Journal of Medicine

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Copyright © 2022 Massachusetts Medical Society. All rights reserved.
 Case Records of the Massachuset ts Gener al Hospital
pears to have had a hypomorphic variant that
affected the function of FOXP3. Overall, the re-
sults of flow cytometry in this patient were
consistent with regulatory T-cell dysfunction
and T-cell hyperactivation, findings that suggest
a hypomorphic FOXP3 variant.
In this patient, the clinical history, the detec-
tion of a FOXP3 variant that was also present in
his mother (a finding consistent with X-linked
inheritance), the abnormal results on phenotyp-
ing of regulatory T cells by means of surface-
marker flow cytometric analysis, and the demon-
stration of an increase in effector and activated
CD4+ and CD8+ T cells in circulation led to a
diagnosis of IPEX syndrome.
Gene t ic Di agnosis
Immune dysregulation, polyendocrinopathy, en-
teropathy, X-linked (IPEX) syndrome caused by a
hemizygous variant in FOXP3.
Discussion of M a nagemen t
Dr. Colizzo: While the results of further diagnostic
testing were pending, the approach to treatment
was focused on symptom control. Initially, pred-
nisone and budesonide were continued. A trial
involving discontinuation of losartan did not
improve the patient’s condition, so losartan
therapy was restarted for the treatment of hyper-
tension. Symptoms did not abate, and treatment
with intravenous vedolizumab was initiated. Vedo­
lizumab is an α4β7 integrin blocker that works
by binding the receptor and preventing interac-
tion with the mucosal addressin cell adhesion
molecule 1.
After 3 months of treatment, the frequency of
bowel movements decreased to once every other
day, and the prednisone dose was successfully
reduced. However, after 6 months of treatment,
symptoms recurred, with only transient improve-
ment after the vedolizumab dose was intensi-
fied. Treatment with intravenous abatacept was
initiated again, with initial improvement; subse-
quently, frequent diarrhea with dehydration con-
tinued and proteinuria worsened. An alternative
option for more definitive therapy was discussed
with the patient, and he opted for a referral to
be evaluated for allogeneic hematopoietic-cell
transplantation (HCT).
Dr. Yi-Bin Chen: HCT is increasingly being used
n engl j med 387;12  nejm.org  September 22, 2022
The New England Journal of Medicine
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Copyright © 2022 Massachusetts Medical Society. All rights reserved.
for the treatment of nonmalignant diseases, in-
cluding bone marrow failure syndromes, hemo-
globinopathies, inborn errors of immunity, and
inherited metabolic disorders. The rationale for
the use of HCT in treating patients with IPEX
syndrome is straightforward: restoration of
functional regulatory T cells should restore the
normal immunologic balance, providing relief
from autoimmune manifestations as well as
obviating the need for continued immunosup-
pressive therapy. Multiple case reports and small
series have shown success with the use of HCT
in patients with IPEX syndrome. A large interna-
tional series involving 96 patients with IPEX
syndrome who were treated at 38 institutions
has also been reported.20 Patients treated with
medical therapy alone had lifelong manifesta-
tions and needed continued immunosuppressive
therapy. Among the 58 patients who underwent
HCT, overall survival was 73.2% with a median
follow-up of 2.7 years. The extent and severity of
organ involvement before HCT were predictive
of outcomes after HCT.
Given the absence of coexisting conditions
and the well-controlled disease in this patient,
HCT was recommended. A thorough donor
search revealed his brother to be haploidentical
(and negative for the familial FOXP3 variant) and
also identified several fully matched unrelated
donors. At the time that HCT was being planned,
the coronavirus disease 2019 (Covid-19) pan-
demic made obtaining fresh bone marrow from
unrelated donors quite difficult, so the decision
was made to proceed with haploidentical bone
marrow transplantation with his brother as the
donor. We followed our standard reduced-inten-
sity HCT platform that we use for nonmalignant
disease, which involves the use of anti–T-cell
globulin, a bone marrow graft source, and high-
dose cyclophosphamide for the prevention graft-
versus-host disease, as well as delayed tapering
of immunosuppressive therapy.27,28
The patient had the expected early complica-
tions associated with haploidentical HCT but
recovered with brisk donor-derived engraftment.
Two months after HCT, he received a diagnosis
of BK virus–associated hemorrhagic cystitis.
Three months after HCT, diarrhea recurred, and
chimerism studies showed secondary graft rejec-
tion with autologous hematopoietic recovery.
Prednisone was added to control diarrhea, and
the patient was subsequently admitted for a
1133
 Case Records of the Massachuset ts Gener al Hospital

second, allogeneic HCT, this time with higher-
intensity conditioning, without the use of anti–
T-cell globulin, and with the use of fresh bone
marrow from a fully matched unrelated donor.
There were no clinically significant complica-
tions after the second HCT, and donor neutro-
phil engraftment was established on day 16
after transplantation. Eight months after the
second HCT, the patient has not had graft-ver-
sus-host disease and has normal gastrointesti-
nal functioning. The dose of systemic immuno-
suppression is being tapered, and he has
recently returned to work with a full perfor-
mance status.
Fina l Di agnosis
Immune dysregulation, polyendocrinopathy, en-
teropathy, X-linked (IPEX) syndrome.
This case was presented at the Medicine Case Conference.
Disclosure forms provided by the authors are available with
the full text of this article at NEJM.org.

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