Inherited T-Cell Deficiency Disorders

Cell-mediated immunity is accomplished by T lymphocytes (T cells) and their effector response and interactions with other immune cells. T-cell immunodeficiency diseases include severe combined immunodeficiencies (SCIDs), Wiskott-Aldrich syndrome, ataxia telangiectasia, DiGeorge syndrome (22q11.2 deletion syndrome), immuno-osseous dysplasias, dyskeratosis congenita, and chronic mucocutaneous candidiasis.

Quick Answers for Clinicians

Which testing algorithms are related to this topic?

Immunodeficiency Evaluation for Chronic Infections in Infants and Children Testing Algorithm

Diagnosis

Indications for Testing

Recurrent infections, particularly with opportunistic organisms

Criteria for Diagnosis

Primary Immune Deficiency Treatment Consortium (PIDTC) diagnostic criteria for SCIDs, leaky SCID, Omenn syndrome, and reticular dysgenesis (Shearer, PIDTC, 2014)
Typical SCID	Leaky SCID	Omenn Syndrome	Reticular Dysgenesis
Absence of or very low CD3 T-cell number (<300/µL), and no or very low T-cell function (<10% LLN), based on PHA response, OR	Reduced CD3 T-cell number	Skin rash, generalized	Absence of T cells or very low T-cell number (<300/µL)
Presence of maternal-origin T cells	No maternal engraftment	No maternal engraftment	No or very low T-cell function (<10% LLN), based on PHA response
	<30% of LLN T-cell function, based on PHA response	CD3 cells detectable at level of ≥300/µL	Severe neutropenia (ANC <200/µL)
	<30% of LLN T-cell function, based on PHA response	Absent/low T-cell proliferation (≤30% of normal) to antigens to which patient has been exposed	Sensorineural deafness and/or no granulopoiesis found in bone marrow exam and/or deleterious AK2 mutation
ANC, absolute neutrophil count; LLN, lower level of normal; PHA, phytohemagglutinin Source: Adapted from Shearer, PIDTC, 2014

Laboratory Testing

Initial testing
- HIV testing
  - Infants ≤15 months – quantitative nucleic acid amplification test (NAAT)
  - Adults – screen for antibodies; confirm positive results with Western blot
- CBC with differential – profound thrombocytopenia with small, nonfunctioning platelets suggests Wiskott-Aldrich syndrome
- Immunoglobulin (quantitative) – if low, proceed with B-cell immunodeficiency testing
- Sweat chloride – if positive, proceed with cystic fibrosis genetic testing
- T-cell immunodeficiency profile testing
  - T-cell testing at minimum should include CD4, CD45RA, CD45RO, CD8, CD4:8 ratio, CD3, CD19, and natural killer (NK) cells
  - If abnormal, proceed with lymphocyte antigen- and mitogen-induced lymphocyte proliferation testing
    - Consider anti-CD3/anti-CD28/IL-2-induced lymphocyte proliferation test
Cell-mediated immune screen
- Lymphocyte antigen and mitogen proliferation test
  - Measures tritiated thymidine (³H-TdR) uptake by lymphocytes in response to stimulus (requires 5-7 days)
  - Low with low T cells confirms T-cell disorder
- Lymphocyte antigen and mitogen stimulation with cytokines
Further specific genetic testing based on results of above testing

Differential Diagnosis

Background

Epidemiology

Incidence – rare
Age – most commonly discovered during neonatal period and infancy
- Adult onset rare
Sex – M:F, equal, except for X-linked diseases
- M>F for X-linked severe combined immunodeficiencies (SCIDs) and Wiskott-Aldrich syndrome

Inheritance

For inheritance, refer to Identified Forms of SCID tables

Pathophysiology

Defective lymphocyte responses to stimulants may occur
- Nonspecific mitogens (phytohemagglutinin, concanavalin A, and pokeweed mitogen)
- Specific antigens, such as Candida or tetanus
Characterized by increased susceptibility to infections from opportunistic organisms
- Cytomegalovirus (CMV)
- Candida albicans
- Pneumocystis jirovecii

Clinical Presentation

Clinical presentation is highly variable but can be divided into 2 main types
- Immunodeficiencies with associated or syndromic features (including both immune and nonimmune manifestations, as in Wiskott-Aldrich syndrome and DiGeorge syndrome [22q11.2 deletion syndrome])
  - Ataxia telangiectasia (European Society for Immunodeficiencies [ESID])
    - Progressive cerebellar ataxia
    - Ocular or facial telangiectasia
    - Recurrent respiratory infections
    - Difficulty walking; wheelchair bound by teenage years
    - Increased risk of malignancy – leukemia/lymphoma in 10-15% of patients
  - DiGeorge syndrome (22q11.2 deletion syndrome) (ESID)
    - Cardiac defect – may be conotruncal
    - Persistent infections (fungal or viral)
    - Hypocalcemia, hypocalcemic tetany (due to hypoparathyroidism)
    - Abnormal facies
    - Palatal abnormalities
    - Autoimmune disorders
  - Wiskott-Aldrich syndrome – in males (ESID)
    - Congenital thrombocytopenia with small platelets
    - Bloody diarrhea
    - Otitis, sinusitis
    - Recurrent infections (bacterial or viral)
    - Eczema
    - Commonly, associated autoimmune disease
    - Increased risk for malignancy
- Immunodeficiencies without associated or syndromic features
  - Omenn syndrome (Genetic and Rare Diseases Information Center)
    - Erythroderma and desquamation; alopecia
    - Chronic diarrhea
    - Failure to thrive
    - Lymphadenopathy
    - Eosinophilia
    - Hepatosplenomegaly
    - High susceptibility to infection (viral, fungal, bacterial)
  - SCID – often in first 2-7 months of life (ESID)
    - Failure to thrive
    - Persistent diarrhea
    - Respiratory symptoms and/or thrush
    - Pneumocystis pneumonia
    - Disseminated bacillus Calmette-Guérin infection
    - Refer to Identified Forms of SCID table
  - Leaky SCID (National Organization for Rare Diseases)
    - Severe itchy rashes
    - Enlarged lymph nodes, spleen, and liver
    - Chronic diarrhea

Identified Forms of SCID

Combined Immunodeficiencies (Based on the Classification Update from the International Union of Immunological Societies Primary Immunodeficiency Diseases Committee, Picard, 2018^a)
Gene	T Cells	B Cells	NK Cells	Genetics	Associated Features
T-negative/B-positive SCID
IL2RG	Very low	Normal to high	Low	XL	Impaired cytokine-mediated signaling
JAK3	Very low	Normal to high	Low	AR	Impaired cytokine-mediated signaling
IL7R	Very low	Normal to high	Normal	AR	Impaired cytokine-mediated signaling
PTPRC	Very low	Normal	n/a	AR	—
CD3D	Very low	Normal	Normal	AR	CD3-delta deficiency
CD3E	Very low	Normal	Normal	AR	CD3-epsilon deficiency
CD247	Very low	Normal	Normal	AR	—
CORO1A	Very low	Normal	n/a	AR	Detectable thymus, EBV
LAT	Normal to low number	Normal to low	n/a	AR	Adenopathy, splenomegaly, recurrent infections, autoimmunity
T-negative/B-negative SCID
RAG1^b	Very low	Very low	Normal	AR	Associated with Omenn syndrome
RAG2^b	Very low	Very low	Normal	AR	Associated with Omenn syndrome
DCLRE1C	Very low	Very low	Normal	AR	Radiation sensitivity; Omenn syndrome
PRKDC	Very low	Very low	Normal	AR	Radiation sensitivity; microcephaly
NHEJ1	Very low	Very low	Normal	AR	Radiation sensitivity; microcephaly
LIG4	Very low	Very low	Normal	AR	Radiation sensitivity; microcephaly
AK2	Very low	Normal to low	n/a	AR	Granulocytopenia and deafness; reticular dysgenesis
ADA^b	Very low	Low, decreasing	Low	AR	Bone defects; may have pulmonary alveolar proteinosis; cognitive defects
^aSources in addition to the International Union of Immunological Societies Primary Immunodeficiency Diseases Committee report (Picard, 2018) include Cossu (2010) and van der Burg (2011) ^bGene included on Primary Antibody Deficiency Panel, Sequencing and Deletion/Duplication – ARUP test code 2011156 ADA, adenosine deaminase; AR, autosomal recessive; EBV, Epstein-Barr virus; n/a, not applicable; NK, natural killer; XL, X-linked

Examples of Combined Immunodeficiencies Typically Less Profound Than SCID^a
Gene	T Cells	B Cells	Genetics	Comment
DOCK2	Low	Normal	AR	Impaired interferon response in hematopoietic and nonhematopoietic cells; normal NK numbers but defective function
CD40LG^b	Normal to low	sIgM+ and sIgD+ B cells present, other surface isotype positive B cells absent	XL	Neutropenia; thrombocytopenia; hemolytic anemia; liver/biliary tract disease; opportunistic infections
CD40^b	Normal	IgM+ and IgD+ cells present, other isotypes absent	AR	Neutropenia; GI and liver/biliary tract disease; opportunistic infections
ICOS^b	Normal	Normal	AR	Recurrent infections; autoimmunity; gastroenteritis; granulomas in some cases
PNP	Progressive decrease	Normal	AR	Autoimmune hemolytic anemia; neurological impairment
CD3G	Normal number; low TCR expression	Normal	AR	—
CD8A	Absent CD8, normal CD4 cells	Normal	AR	Recurrent infections; may be asymptomatic
ZAP70	Low CD8, normal CD4 cells	Normal	AR	In some cases, immune dysregulation, autoimmunity
TAP1, TAP2, or TAPBP	Low CD8, normal CD4 cells	Normal	AR	Vasculitis; pyoderma gangrenosum
B2M	—	Normal	AR	—
CIITA, RFXANK, RFX5, RFXAP	Low CD4 cells	Normal	AR	Respiratory and GI infections; liver/biliary tract disease
ITK	Progressive decrease	Normal	AR	EBV-associated B-cell lymphoproliferation, lymphoma; normal or low IgG
MAGT1	Low CD4 cells	Normal	XL	EBV infection; lymphoma; viral infections; respiratory and GI infections
DOCK8	Low	Low; low CD27+ memory B cells	AR	Eosinophilia; recurrent infections; severe atopy; cutaneous viral, staphylococcal, and fungal infections; cancer susceptibility; low/impaired function NK cells
RHOH	Normal number	Normal	AR	HPV infection; lymphoma; lung granulomas; molluscum contagiosum
SH2D1A^b	Normal or increased activated T cells	Reduced memory B cells	XL	Clinical and immunologic features induced by EBV infection; HLH; lymphoproliferation; aplastic anemia; lymphoma; hypogammaglobulinemia
RMRP	Varies from severely low to normal; impaired lymphocyte proliferation	Normal	AR	Short-limbed dwarfism with metaphyseal dysostosis; sparse hair; bone marrow failure; autoimmunity; cancer/lymphoma susceptibility; impaired spermatogenesis; neuronal dysplasia of the intestine
STK4	Low	Low	AR	Recurrent bacterial, viral/HPV, and candidal infections; intermittent neutropenia; EBV lymphoproliferation; lymphoma; congenital heart disease; autoimmune cytopenias
TRAC	Absent TCR alpha beta cells	Normal	AR	Recurrent viral, bacterial, and fungal infections; immune dysregulation autoimmunity; diarrhea
LCK	Low CD4+ and T regulatory cells	Normal	AR	Recurrent infections; immune dysregulation; autoimmunity
MALT1^b	Normal number	Normal	AR	Bacterial, fungal, and viral infections
CARD11^b	Normal number	Normal predominance of transitional B cells	AD, AR	Pneumocystis jirovecii pneumonia, bacterial and viral infections
BCL10	Normal number	Normal number	AR	Recurrent bacterial and viral infections; candidiasis; gastroenteritis
BCL11B	Low	Normal	AD	Congenital abnormalities, neonatal teeth, facies abnormalities, absent corpus callosum, neurocognitive defects
IL21^b	Normal number	Low	AR	Severe onset early colitis; sinopulmonary infections
IL21R^b	Normal number	Normal number	AD, AR	Recurrent infections; susceptibility to cryptosporidium and pneumocystis infections and liver disease
TNFRSF4	Normal number	Normal number	AR	Kaposi sarcoma; impaired immunity to HHV8
IKBKB	Normal number	Normal number	AR	Recurrent bacterial, viral, and fungal infections; opportunistic infections
PIK3CD^b	—	Low or absent pro-B cells	AD	Severe bacterial infections; EBV
LRBA^b	Normal/decreased CD4 number	Low or normal number	AR	Recurrent infections; IBD; autoimmunity; EBV infection
CD27^b	Normal	No memory B cells	AR	Clinical and immunologic features triggered by EBV infection; HLH; aplastic anemia; lymphoma; hypogammaglobulinemia; low iNKT cells
RELB	Normal number	—	AR	Recurrent infections
MSN	Normal number	Low number	XL	Recurrent infections with bacteria, varicella, neutropenia
TFRC	Normal number	Normal number, low memory B cells	AR	Recurrent infections, neutropenia, thrombocytopenia
MAP3K14^b	Normal number	Low	AR	Recurrent bacterial, viral, and Cryptosporidium infections; low NK cell number
CTPS1	Normal or decreased	Normal or decreased	AR	Recurrent/chronic viral infections (particularly EBV, VZV), lymphoproliferation; B-cell NHL
^aBased on the International Union of Immunological Societies Primary Immunodeficiency Diseases Committee report (Picard, 2018); see original source for additional detail about T-cell and B-cell status and function ^bGene included on Primary Antibody Deficiency Panel, Sequencing and Deletion/Duplication – ARUP test code 2011156 AD, autosomal dominant; AR, autosomal recessive; CMV, cytomegalovirus; EBV, Epstein-Barr virus; GI, gastrointestinal; HHV8, human herpesvirus 8; HLH, hemophagocytic lymphohistiocytoses; HPV, human papillomavirus; IBD, irritable bowel disease; iNK, invariant natural killer; NHL, non-Hodgkin lymphoma; NK, natural killer; TEMRA, terminal differentiated effector memory cells; Treg, regulatory T cells; VZV, varicella-zoster virus; XL, X-linked

ARUP Laboratory Tests

Detect HIV-1 RNA

3003760

Human Immunodeficiency Virus 1 (HIV-1) by Qualitative NAAT 3003760

Method

Qualitative Transcription-Mediated Amplification

Detect and quantify HIV-1

"Not Detected" result does not rule out the presence of inhibitors or HIV-1 virus RNA concentrations below the assay detection level

3000867

Human Immunodeficiency Virus 1 (HIV-1) by Quantitative NAAT, Plasma 3000867

Method

Quantitative Transcription-Mediated Amplification

Screen for HIV-1,2 antibodies and antigens

2006526

Human Immunodeficiency Virus (HIV) Combo Antigen/Antibody (HIV-1/O/2) by CIA, with Reflex to HIV-1 Antibody Confirmation by Western Blot (Temporary Delay as of 05/12/2021 no referral available) 2006526

Method

Qualitative Chemiluminescent Immunoassay /Qualitative Western Blot

Reflex pattern: if HIV-1,2 combo antigen/antibodies screen is repeatedly reactive, then HIV-1 antibody confirmation by Western Blot will be added

Assess for thrombocytopenia

0040003

CBC with Platelet Count and Automated Differential 0040003

Method

Automated Cell Count/Differential

Initial test in the workup of immunoglobulin disorders

In adults and older children with suspected hypogammaglobulinemia, order in conjunction with serum protein electrophoresis and immunofixation

0050630

Immunoglobulins (IgA, IgG, IgM), Quantitative 0050630

Method

Quantitative Immunoturbidimetry

Assess thymic function in suspected severe combined immunodeficiency (SCID), DiGeorge syndrome (22q11.2 deletion syndrome), and other T-cell immune deficiency disorders

Evaluate immune reconstitution during highly active antiviral therapy (HAART) in HIV patients and post chemotherapy and hematopoietic cell transplant

2010179

CD4+ T-Cell Recent Thymic Emigrants (RTEs) 2010179

Method

Quantitative Flow Cytometry

Useful for assessing primary T-cell immunodeficiency disorders

Test enumerates the percent and absolute cell count of lymphocyte subsets in whole blood for CD3 (total T cells), CD4 (helper T cells), CD45RA (naive helper T cells), CD45RO (memory helper T cells), CD8 (cytotoxic T cells), CD4:CD8 ratio, CD19 (B cells), natural killer (NK) cells

0095862

Lymphocyte Subset Panel 6 - Total Lymphocyte Enumeration with CD45RA and CD45RO 0095862

Method

Quantitative Flow Cytometry

Acceptable lymphocyte subset panel for the investigation of primary immunodeficiency disorders

Test enumerates the percent and absolute cell count of lymphocyte subsets in whole blood for CD2, CD3 (total T cells), human leukocyte antigen-antigen D related (HLA-DR), CD4 (helper T cells), CD45RA (naive helper T cells), CD45RO (memory helper T cells), CD8 (cytotoxic T cells), CD4:CD8 ratio, CD19 (B cells), NK cells

0095899

Lymphocyte Subset Panel 7 - Congenital Immunodeficiencies 0095899

Method

Quantitative Flow Cytometry

Evaluate NK- and NKT-cell subsets

2013805

Natural Killer Cell and Natural Killer T-Cell Panel 2013805

Method

Semi-Quantitative Flow Cytometry

Panel includes:

Pct CD3-CD16-/+CD56br/dim (total NK cells)
Abs CD3-CD16-/+CD56br/dim (total NK cells)
Pct CD3-CD16+CD56dim (cytotoxic NK cells)
Abs CD3-CD16+CD56dim (cytotoxic NK cells)
Pct CD3-CD16-CD56br (cyto secreting NK)
Abs CD3-CD16-CD56br (cyto secreting NK)
Pct CD3-CD57+ (CD57 NK cells)
Abs CD3-CD57+ (CD57 NK cells)
Pct CD3+CD56+ (CD56 NKT cells)
Abs CD3+CD56+ (CD56 NKT cells)
Pct CD3+CD57+ (CD57 NKT cells)
Abs CD3+CD57+ (CD57 NKT cells)
Pct CD45+CD3+ (T cells)
Abs CD45+CD3+ (T cells)
Pct CD45+CD3- (non T cells)
Abs CD45+CD3- (non T cells)
Natural killer T-cell panel interpretation

Evaluate NK cells in patients with suspected immune deficiency

0092404

Natural Killer Cells Enumeration 0092404

Method

Quantitative Flow Cytometry

Primarily for evaluating lymphocyte function in patients with suspected cellular immune dysfunction, such as primary and secondary immunodeficiencies

Other uses include monitoring lymphocyte recovery and competence after hematopoietic stem cell transplantation and monitoring lymphocyte function during immunosuppressive therapy

3001319

Lymphocyte Proliferation, Antigen-Mitogen Panel by Flow Cytometry (24-Hr Critical Room Temp) 3001319

Method

Cell Culture/Flow Cytometry

Primarily for research and to support attempts to understand the pathogenesis of immune, infectious, allergic, or inflammatory disorders

Test for lymphocyte proliferation in response to:

Phytohemagglutinin
Concanavalin A
Pokeweed mitogen
Candida antigen
Tetanus antigen

0096056

Lymphocyte Antigen and Mitogen Proliferation Panel 0096056

Method

Cell Culture

Primarily for evaluating T-cell function in patients with suspected cellular immune dysfunction, such as primary and secondary immunodeficiencies

Other uses include monitoring lymphocyte recovery and competence after hematopoietic stem cell transplantation and monitoring lymphocyte function during immunosuppressive therapy

Not a first-level test; order after lymphocyte proliferation, mitogen induced, by flow cytometry has been performed

3001337

Lymphocyte Proliferation, Anti-CD3, Anti-CD28 and IL-2 Induced, by Flow Cytometry (24-Hr Critical Room Temp) 3001337

Method

Cell Culture/Flow Cytometry

Related Tests

Primarily for evaluating recall antigen responses in patients with suspected cellular immune dysfunction, such as primary and secondary immunodeficiencies

Other uses include monitoring lymphocyte recovery and competence after hematopoietic stem cell transplantation and monitoring lymphocyte function during immunosuppressive therapy

Do not order for patients younger than 3 months unless clinical history of candidiasis is present

3001320

Lymphocyte Proliferation, Antigen Induced, by Flow Cytometry (24-Hr Critical Room Temp) 3001320

Method

Cell Culture/Flow Cytometry

Primarily for evaluating lymphocyte function in patients with suspected cellular immune dysfunction, such as primary and secondary immunodeficiencies

Other uses include monitoring lymphocyte recovery and competence after hematopoietic stem cell transplantation and monitoring lymphocyte function during immunosuppressive therapy

3001321

Lymphocyte Proliferation, Mitogen Induced, by Flow Cytometry (48-Hr Critical Room Temp) 3001321

Method

Cell Culture/Flow Cytometry

Rapid test for Candida and tetanus antigens

Use to evaluate chronic infections

0096055

Lymphocyte Antigen Proliferation 0096055

Method

Cell Culture

Medical Experts

Contributor

Delgado

Julio Delgado, MD, MS

Executive Vice President, ARUP Laboratories

Division Chief of Clinical Pathology, University of Utah and ARUP Laboratories

Professor of Pathology (Clinical), University of Utah

Medical Director, Protein Immunology and Immunologic Flow Laboratories, ARUP Laboratories

Contributor

Hillyard

David R. Hillyard, MD

Professor of Pathology, University of Utah

Medical Director, Molecular Infectious Diseases, ARUP Laboratories

Contributor

Lamb

Allen N. Lamb, PhD, FACMG

Retired Former Professor of Pathology (Clinical), University of Utah

Retired Former Laboratory Section Chief, Cytogenetics and Genomic Microarray, ARUP Laboratories

Contributor

Slev

Patricia R. Slev, PhD, D(ABCC)

Associate Professor of Pathology (Clinical), Codirector, Clinical Chemistry Fellowship program, University of Utah

Section Chief, Immunology; Medical Director, Immunology Core Laboratory; Medical Director, Serologic Hepatitis and Retrovirus and Immunology Core Laboratory; Medical Director, Microbial Immunology, ARUP Laboratories

Contributor

Wittwer

Carl T. Wittwer, MD, PhD

Professor of Pathology, University of Utah

Medical Director, Immunologic Flow Cytometry, ARUP Laboratories

References

Additional Resources

Shearer WT, Dunn E, Notarangelo LD, et al. Establishing diagnostic criteria for severe combined immunodeficiency disease (SCID), leaky SCID, and Omenn syndrome: the Primary Immune Deficiency Treatment Consortium experience. J Allergy Clin Immunol. 2014; 133 (4): 1092-8.

21479529

van der Burg M, Gennery AR. Educational paper. The expanding clinical and immunological spectrum of severe combined immunodeficiency. Eur J Pediatr. 2011; 170 (5): 561-71.

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Inherited T-Cell Deficiency Disorders

Quick Answers for Clinicians