Lymphangioleiomyomatosis and Tuberous Sclerosis Complex

Pulmonary LAM is a rare disease that almost exclusively affects women. It is caused by proliferating smooth muscle–like cells, which can involve small airways, the pulmonary vasculature, and intrathoracic and extrathoracic lymphatic structures. The hallmark feature of the disease is the radiographically apparent numerous, round, thin-walled cysts, generally between 2 and 60 mm in diameter, which are found throughout the lung. Extraparenchymal lung abnormalities include pneumothorax and chylous pleural effusions. Eighty percent of patients develop a pneumothorax at some time during the course of their disease. Pleural effusions are characterized by elevated triglyceride levels and an abundance of chylomicrons. Obstructive and mixed obstructive-restrictive ventilator defects are observed. Renal angiomyolipomas occur in ∼30% of sporadic LAM patients and in >90% of TSC-LAM patients.

LAM can occur either in patients with sporadic (noninherited) disease or in 1–3% of patients with TSC, an autosomal dominant multisystem disorder characterized by hamartomas in multiple organ systems, including the brain, skin, heart, kidneys, and lungs. The ILD manifestation of TSC patients is indistinguishable from sporadic LAM. TSC patients who develop LAM are often women over 30 years of age who have little or no mental retardation. Extrapulmonary features include facial angiofibromas (or adenoma sebaceum), hypomelanotic macules (which are most easily visualized with a Wood light), rough, yellow thickening of skin over the lumbosacral area (shagreen patch), ungual or periungual fibromas, renal angiomyolipomas, renal cysts, subependymal giant cell astrocytomas, brain cysts, hamartomas, cardiac rhabdomyomas, dental pits, epilepsy, learning difficulties, and mental retardation.

TSC is characterized by autosomal dominant inheritance. However, about two-thirds of patients have de novo mutations. There are two genes associated with this syndrome. Mutations in TSC2 occur more frequently, accounting for 75–80% of all cases. Mutations in TSC1 are less common. There are no mutational hot spots within these two genes. In general, TSC2 mutations are associated with more severe disease, more frequent and severe epilepsy, mental retardation, and cortical tubers. Inactivation of both alleles of TSC1 or TSC2 is needed for the development of tumors. Loss of heterozygosity is frequently found in renal angiomyolipomas and supports Knudson’s two-hit model tumor suppressor pathogenesis.

Most sporadic LAM results from two somatic mutations in the TSC2 gene, although rare cases are caused by germline TSC1 mutations. In contrast with TSC patients in whom germline mutations are present in tumor and normal tissue, the mutations in LAM patients are generally not present in normal tissues. This suggests that two mutations arise in a precursor cell of origin and that the mutation-carrying smooth muscle–like cells spread to various organs (lungs, kidneys).

The proteins encoded by these two genes regulate the mammalian target of rapamycin (mTOR) pathway. Inhibition of the mTOR complex corrects the specific molecular defects underlying TSC. mTOR inhibitors cause shrinkage of renal or retroperitoneal angiomyolipomas and subependymal giant cell astrocytomas in TSC patients. In addition, sirolimus stabilizes lung function, reduces respiratory symptoms, and improves the quality of life of LAM patients.

Birt-Hogg-Dubé Syndrome

This disorder, which is also known as Hornstein-Knickenberg syndrome, is characterized by the autosomal dominant inheritance of multiple benign skin tumors, which are usually characterized as fibrofolliculomas. Approximately 90% of affected individuals have evidence of lung cysts, and up to 34% develop kidney tumors. The disease is caused by loss-of-function mutations in the folliculin ( FLCN ) gene. Two different studies, one using whole-genome linkage analysis and the other a candidate gene approach, independently found that kindreds presenting solely with familial spontaneous pneumothorax and/or lung cysts have mutations in FLCN and represent a forme fruste of BHDS. Nearly all mutations, including the common mutation hot spot that introduces a frameshift mutation (c.1285insC and c.1285delC), predict a truncated protein product. The pulmonary cysts are generally bilateral, are usually located in a subpleural distribution in the mid- and lower-lung zones, and are of varying sizes, ranging from round, oval, lentiform, to multiseptated shapes. Because the skin findings typically appear in the fourth decade and the renal malignancy can be a late finding (mean age of 48 years), a spontaneous pneumothorax in the second or third decade of life is often the presenting manifestation. The molecular mechanism of lung cyst formation is incompletely understood.

Genetic testing is indicated for all individuals with suspected BHDS because the presence of a mutation prompts screening for renal cancer for which surgical resection may be curative. As was described in a past case, the phenotype of familial spontaneous pneumothorax may be the presenting feature for the index case that then leads to the identification of an occult renal malignancy in a family member with a FLCN mutation. All first-degree relatives have a 50% chance of having the same germline FLCN mutation.

Dyskeratosis Congenita

Dyskeratosis congenita (DC) is a rare multisystem disorder characterized by the classic triad of a lacy reticular pigmentation on the upper chest and neck, nail dystrophy, and oral leukoplakia. The prevalence is approximately 1 in 1,000,000, with death occurring at a median age of 16 years. Patients are usually healthy at birth and then develop different organ dysfunction, including bone marrow failure, pulmonary fibrosis, and eye, tooth, gastrointestinal, endocrine, skeletal, urologic, and immunologic abnormalities. Significant developmental delay is found for the more severe clinical variants of DC. There is a wide variation in the severity and spectrum of clinical findings, which is only partly explained by locus heterogeneity. The mode of inheritance varies by gene mutation. Most patients in a large international registry are male with X-linked recessive inheritance. Kindreds with autosomal recessive and autosomal dominant patterns of inheritance are less common. For affected male patients, the classic skin and nail findings are present in ∼90%. The abnormal skin findings have been described as poikiloderma vascularis atrophicans or a latticework hypo- and hyperpigmentation defect found especially on the neck, upper chest, and proximal limbs. Bone marrow failure is very common (>85%) and is the leading cause of death.

After bone marrow failure, pulmonary fibrosis is the most serious and life-threatening complication of DC. In most cases it presents either after hematopoietic cell transplantation or as a later manifestation of disease in those over the age of 30 years. Patients with pulmonary disease have rales, digital clubbing, a restrictive pulmonary defect, a reduced diffusion capacity, and diffuse interstitial markings on high-resolution computed tomography (HRCT) imaging of the chest. Lung histopathology generally features a mixture of cellular inflammatory infiltrates and interstitial fibrosis. Clinical survival of DC patients after the development of ILD is poor as pulmonary disease is generally rapidly progressive. Death is usually 12–40 months after the onset of clinical symptoms.

Mutations in 11 different genes have been described in DC patients. Regardless of the pattern of genetic inheritance or the individual genetic mutation, all DC patients exhibit short telomere lengths for their age. Telomeres are specialized structures essential for maintenance of integrity of chromosomal ends composed of nucleotide repeats (TTAGGG) _n and telomere-specific accessory proteins. Positional cloning first led to the identification of mutations in the DKC1 gene in those with the X-linked recessive form of the disease. Dyskerin is a nucleolar protein that copurifies with the catalytically active RNA and protein component of telomerase. Mutations in both genes encoding telomerase (hTR, encoded by TERC gene and TERT ) have been found in patients with autosomal dominant DC ; biallelic mutations in TERT have been found in patients with autosomal recessive DC. Germline mutations in TINF2 , a component of the shelterin complex that protects the telomeric ends of chromosomes, mostly occur de novo and are found in patients with autosomal dominant DC. Mutations in the gene ACD , encoding another member of the shelterin complex, TPP1, have been found in two kindreds with DC. Compound heterozygous mutations in CTC1 were first described in patients with Coats plus and in the phenotypically similar disorder cranioretinal microangiopathy with calcifications and cysts and then were later described in patients with autosomal recessive DC. CTC1 is part of the trimeric telomere capping complex that cooperates with the shelterin complex to protect telomeres. Homozygous mutations in NOLA2 and NOLA3 account for less than 1% of DC mutations; these genes encode NHP2 and NOP10, respectively, which maintain the stability and proper trafficking of a complex of H/ACA small nucleolar RNAs, including the telomerase RNA, hTR. Mutations in WRAP53 have been described linked to DC; this gene encodes TCAB1 that binds telomerase and directs its localization to nuclear Cajal bodies, an important step in telomere maintenance. Whole exome sequencing has led to the identification of heterozygous or compound heterozygous mutations in RTEL1 . This gene encodes a DNA helicase that is crucial for telomere maintenance and DNA repair. Homozygous or compound heterozygous mutations in PARN have most recently been linked to autosomal recessive DC. The PARN protein belongs to a family of conserved exoribonucleases that shorten the poly(A) tail of messenger RNA through deadenylation. One of the RNA species that is modified by PARN is hTR or the RNA component of telomerase. Thus, mutations in PARN lead to defective hTR and telomerase biogenesis and telomere disease.

Genetic anticipation has been seen in DC kindreds with TERC and TERT mutations. Inheritance of progressively shorter telomere lengths in each subsequent generation of mutation carriers provides a molecular explanation for the observation of an earlier age of onset in more severely affected individuals with each successive generation. Siblings who do not inherit the mutated gene can inherit short telomere lengths from the affected parent. Thus, DC patients have to inherit both short telomere lengths and a deleterious telomerase mutation to demonstrate anticipation.

RIDDLE Syndrome

Patients with this very rare autosomal recessive disorder have a syndrome of increased sensitivity to radiation, immunodeficiency, learning difficulties, dysmorphic features, short stature, and pulmonary fibrosis in later years. The syndrome is caused by homozygous or compound heterozygous mutations in the RNF168 gene, an E3 ubiquitin ligase critical for double-stranded DNA break (DSB) repair. It promotes ubiquitination of H2A and H2AX, which, in turn, mediates accumulation of 53BP1 and BRACA1 at DSBs to promote DNA repair. It also has a role in TRF2-mediated protection of telomeres.

Hermansky-Pudlak Syndrome

Hermansky-Pudlak syndrome (HPS) is an autosomal recessive disease first described in 1959. It is characterized by oculocutaneous albinism, a bleeding diathesis resulting from platelet storage pool deficiency, and in some cases, pulmonary fibrosis. It is now known that HPS is caused by defects of multiple cytoplasmic organelles, including melanosomes, platelet-dense granules, and lysosomes leading to diverse clinical features. Other clinical features of the disease include granulomatous colitis, neutropenia, immunodeficiency, cutaneous malignancies, cardiomyopathy, and renal failure. Currently the diagnosis is confirmed by the absence of dense bodies on whole-mount electron microscopy of platelets. Mutations in nine different genes cause this disease. Each of these genes functions in trafficking of vesicular cargo proteins to cytoplasmic organelles or in organelle biogenesis and maturation. HPS is the most common single gene disorder in Puerto Rico with an estimated frequency of about 1 in 1800 and a carrier frequency of 1 in 21. Mutations in HPS1 and HPS3 are found in 75% and 25% of Puerto Rican patients, respectively.

ILD generally causes symptoms in the 30s and, when it occurs, is generally fatal within a decade. Patients have progressive restrictive disease with a highly variable course. Pulmonary fibrosis has been described most frequently in patients with HPS1 mutations, and more rarely in patients with HPS2 or HPS4 mutations. In this regard, molecular subtyping is important to assess the risk of developing pulmonary fibrosis. In one of the largest studies, the mean age of onset was 35 years with a range of 15–53 years. The variability of pulmonary findings was generally not attributable to prior environmental exposures. Over 80% of patients had abnormalities on CT scans, which were generally predictive of the degree of physiologic impairment and mortality. Most patients demonstrate a peripheral distribution of HRCT reticulations with a trend toward increasing involvement of the central portions of the lungs with progressive severity as a result of peribronchovascular thickening and bronchiectasis. Surgical lung biopsies demonstrate lung remodeling, numerous chronic inflammatory cells, and distinctive clusters of clear vacuolated type II pneumocytes with florid foamy swelling and degeneration (“giant lamellar body degeneration”). Despite an early positive study, a follow-up clinical trial showed no benefit of pirfenidone for the treatment of Hermansky-Pudlak pulmonary fibrosis.

Pathogenesis of pulmonary fibrosis is incompletely understood. Studies of a mouse model of disease that is homozygous for both HPS1 and HPS2 mutations demonstrate additive effects of the genetic defects toward the development of spontaneous pulmonary fibrosis. Subpleural reticulations begin at 3 months and extensive fibrosis is seen by 9 months. The histology of the mouse lung replicates the human phenotype with “giant lamellar body degeneration” of the type II cells and demonstrates decreased phospholipid and surfactant protein (SP)-B and C secretion. The underlying molecular mechanism of murine HPS-associated pulmonary fibrosis seems related to endoplasmic reticulum (ER) stress and chronic alveolar epithelial type II cell injury.

NKX2-1 –Related Disorders

These disorders include benign hereditary chorea, neonatal respiratory distress, and congenital hypothyroidism; it is also known as brain-lung-thyroid syndrome. Childhood-onset chorea is the hallmark clinical feature of this disorder. Pulmonary disease is the second most common presentation, with nearly half of the patients having some type of pulmonary manifestation. These include neonatal respiratory distress with or without pulmonary hypertension, neuroendocrine cell hyperplasia, ILD in children between the ages of 4 months to 7 years, and pulmonary fibrosis in older individuals. Defective surfactant homeostasis and recurrent respiratory infections have been found to be a prominent feature in some subjects. Mutations include missense, nonsense, and deletions of the NKX2-1 gene.

Neurofibromatosis

Neurofibromatosis (NF1) is an autosomal dominant disorder that affects all ethnic groups. Type I, von Recklinghausen disease or classic NF1, is characterized by multiple (>6) café au lait spots, axillary and inguinal freckling, multiple cutaneous neurofibromas, and iris Lisch nodules. Pulmonary manifestations are less common. The incidence of ILD in NF1 has been estimated at 6–12%. It is characterized by lower lobe–predominant diffuse interstitial fibrosis and honeycombing. Thin-walled bullae are present in almost all patients with ILD or may be seen in isolation; they are large, asymmetric, and typically involve the upper lobes. Histologic evidence of an alveolitis and interstitial fibrosis has been found in patients with normal chest X-rays or those with only apical bullae. Although there is near complete penetrance of the disease after childhood, the ILD is not observed until adulthood, typically in patients older than 40 years of age. The disease is often progressive and may lead to pulmonary hypertension and right-sided heart failure. The pathogenesis of NF-associated ILD is unknown.

Poikiloderma, With Tendon Contractures, Myopathy, and Pulmonary Fibrosis

This rare disorder usually affects individuals from early childhood; presenting features include thin hair, telangiectasias and pigmentary abnormalities on sun-exposed areas, and tendon contractures frequently involving the ankles and feet. There is incomplete penetrance of pulmonary fibrosis; >50% of cases have lung involvement. When it is present, the pulmonary fibrosis generally develops during the second decade of life, is progressive, and can lead to death. The histopathology for at least one case was consistent with usual interstitial pneumonia. Different missense mutations in the FAM111B gene have been found in unrelated cases of different ancestry. The function of this gene is unclear.

Interstitial Lung Disease, Nephrotic Syndrome, and Epidermolysis Bullosa

Infants with this congenital autosomal recessive disorder present with disease in multiple organs. The pulmonary and renal features cause significant morbidity and mortality, although dermatologic features are common (epidermolysis bullosa, thin hair, dystrophic nails, onycholysis). The lung involvement is characterized radiographically by diffuse ground-glass opacity and interlobular septal thickening. Histology demonstrates abnormal alveolarization with poorly septated (“simplified”) alveolar spaces. All mutations are homozygous deletion/frameshift or missense mutations in ITGA3 , which encode an integrin alpha chain belonging to a family of cell surface adhesion proteins. One of the missense mutations prevents proper posttranslational modification of the integrin alpha chain with defective cell surface expression.

Stimulator of Interferon Genes–Associated Vasculopathy, Infantile-Onset

Patients with this autosomal dominant disorder have an autoimmune vasculopathy that causes severe skin lesions affecting the face, ears, nose, and digits, resulting in ulceration and necrosis beginning in infancy. Over 85% have an ILD apparent on HRCT chest imaging. Lung biopsy samples demonstrate a scattered mix of lymphocytic inflammatory infiltrate, follicular hyperplasia and B-cell germinal centers, interstitial fibrosis, and emphysematous changes. Patients can have livedo reticularis, Raynaud phenomenon, myositis, joint involvement, immune complex deposition, hypergammaglobulinemia, leukopenia, and autoantibodies (antinuclear, antiphospholipid, anticardiolipin). All cases are caused by heterozygous, missense, gain-of-function mutations in the TMEM173 gene, which encodes the STING (stimulator of interferon genes). Mutations lead to activation of STAT1.

Autoimmune Disease With Facial Dysmorphism

This autosomal recessive disease has been described only in children with features of failure to thrive, developmental delay, dysmorphic features, autoantibodies, and inflammatory cell infiltration of the lungs, liver, and gut. Chronic lung disease was found in 9 of 10 children. Three had a chronic oxygen requirement and died of respiratory failure. Surgical lung biopsy from one case showed a cellular, nonspecific interstitial pneumonitis (NSIP). All affected children in one large Amish kindred were homozygous for a frameshift mutation in the ITCH gene that is predicted to cause a truncation of an E3 ubiquitin ligase. Of note, mice with a small genomic inversion that disrupts the Itch and agouti genes develop a similar spectrum of immunologic disease of the spleen, lymph nodes, stomach, and skin, as well as chronic pulmonary interstitial inflammation and alveolar proteinosis.

Autoimmune Interstitial Lung, Joint, and Kidney Disease

This rare syndrome was recently elucidating by whole exome sequencing of patients from five unrelated families with autoimmune interstitial lung, joint, and kidney disease. All patients had high-titer autoantibodies, ILD, and inflammatory arthritis. The average age at presentation was 3.5 years, with a range of 6 months to 22 years. Some patients presented with pulmonary hemorrhage that required immunosuppression. Lung biopsies showed lymphocytic interstitial infiltration with lung-infiltrating CD4 ⁺ T cells and CD20 ⁺ B cells within germinal centers. All mutations affect the same functional domain of the COPA protein, impair intracellular ER-Golgi transport, and lead to ER stress and upregulation of cytokines.

GATA2 Deficiency

Haploinsufficiency of the hematopoietic transcription factor GATA2 leads to a wide spectrum of diseases including primary immunodeficiency syndromes such as dendritic cell, monocyte, B lymphocyte, and NK lymphocyte deficiency (DCML) and monocytopenia and mycobacterial infection syndrome (MONOMAC); primary lymphedema with myelodysplasia (Emberger syndrome); and susceptibility to myelodysplastic syndrome and acute myeloid leukemia. Besides immunodeficiency (with predisposition especially to severe viral, disseminated nontuberculous mycobacterial, and invasive fungal infections), pulmonary disease, vascular/lymphatic dysfunction, and hearing loss are common. Most individuals have some manifestation of pulmonary disease; 79% have a diffusion defect, 63% with abnormal pulmonary function tests, 18% with biopsy-proved pulmonary alveolar proteinosis (PAP), and 9% with pulmonary arterial hypertension. All lack anti–GM-CSF antibodies and are resistant to subcutaneous or inhaled granulocyte-macrophage colony–stimulating factor (GM-CSF) therapy. Chest CT findings include reticulonodular opacities, “crazy paving,” and paraseptal emphysema. Median age at first presentation is 20 years, but is highly variable (5 months to 78 years). Most mutations are predicted to cause a loss of function of the mutated allele, leading to haploinsufficiency and autosomal dominant inheritance. Hematopoietic stem cell transplantation is indicated for severe disease.

Immunodeficiency Syndromes

Common variable immunodeficiency (CVID) syndromes are all associated with an increased susceptibility to recurrent infections, especially sinopulmonary infections. There is a high variability of clinical features. Respiratory complications are frequently responsible for patient morbidity and mortality and include acute infections, sequelae of infections (bronchiectasis), noninfectious immune-mediated infiltrates such as granulomatous lymphocytic interstitial lung disease (GLILD) and lymphoma, and progressive respiratory failure. When severe, bronchiectasis is generally associated with obstructive lung disease; GLILD is typically associated with restrictive physiology and decreased diffusion capacity. Lung disease is frequently found in patients with CVID, as >90% have radiographic abnormalities apparent on chest CT. This genetically heterogeneous group of diseases includes those with variable antibody and B-cell, T-cell, and NK-cell deficiencies, as well as defective responses to vaccination. Mutations in multiple genes, including ICOS , TNFRSF13B (encoding the transmembrane activator and CAML interactor TACI), TNFRSF13C (encoding the B-cell activating factor), CD19 , CD20 , CD81 , CD21 , LRBA , IL21 , NFKB1 , NFKB2 , and IKZF1 (encoding the hematopoietic zinc finger transcription factor), lead to sporadic, autosomal recessive, and autosomal dominant patterns of disease.

X-linked agammaglobulinemia (XLA) is an immunodeficiency disorder that occurs almost exclusively in males from a failure of B-cell maturation. Although there is a high prevalence of pneumonia in XLA, there is a lower prevalence of chronic lung disease with 47% and 25% demonstrating abnormal pulmonary function studies and bronchiectasis, respectively. Although the degree of immune dysregulation may be lower, the rate of progression of lung function decline is greater for those with XLA. Between 85% and 90% of cases are caused by mutations in BTK , the gene encoding Bruton tyrosine kinase and a key regulator in B-cell development. The remaining cases include a genetically heterogeneous group of patients with mutations in IGHM (encoding the mu heavy-chain), IGLL1 (encoding immunoglobulin lambda-like-1), CD79A , BLNK , CD79B , and TCF3 .

Autosomal dominant hyper-IgE syndrome is an immune deficiency disorder characterized by the triad of recurrent staphylococcal skin abscesses, pneumonias, and elevations of IgE (usually >2000 IU/mL). Survival is typically into adulthood, but death is usually secondary to infections. Diagnosis requires a high level of suspicion due to variability of phenotypic features. A clinical scoring system has been developed that combines immunologic (elevated IgE, eosinophilia >700/μL, decreased T-helper [Th]17 cells, recurrent infections) and nonimmune features (retained primary teeth, scoliosis, joint hyperextensibility, bone fractures following minimal trauma, a typical facial appearance, and vascular abnormalities). Pneumatoceles and bronchiectasis, which result from aberrant healing of the pneumonias, are seen in ∼70% of patients and lead to significant mortality. Patients have heterozygous missense, splice site, or small deletions in the STAT3 gene. Most mutations cluster in the DNA-binding domain of this transcription factor, which regulates responses to many different cytokines. Patients’ purified native T cells are unable to differentiate in vitro into IL-17–producing Th17 cells, which play a critical role in the clearance of fungal and extracellular bacterial infections of the lung and skin. Most patients represent sporadic cases, but autosomal dominant transmission has been seen in some kindreds.

Activated PI3K-delta syndrome is a monogenic autosomal dominant disease that leads to overactivation of the PI3K signaling pathway and lymphoproliferation. This autosomal dominant disease is characterized by recurrent sinopulmonary infections, reduced IgG2, increased serum IgM, and impaired vaccine responses. In one series, 75% of patients had CT evidence of bronchiectasis or mosaic attenuation. The lymphoid aggregates within the lung and can lead to the compression of nearby bronchi. Heterozygous missense mutations in PIK3CD result in increased phosphorylation of AKT, consistent with a gain of function.

CTLA4 deficiency syndrome is an autosomal dominant immunodeficiency characterized by T-cell immune dysregulation. Pulmonary manifestations mirror CVID with recurrent respiratory infections and GLILD. Lymphocytic infiltration is found for other organs, including the bone marrow, kidney, brain, liver, spleen, and lymph nodes. Heterozygous loss-of-function mutations in CTLA4 have been recently described.

X-linked reticulate pigmentary disorder is a rare immunodeficiency disorder with features of recurrent infections and systemic sterile inflammation. Affected patients typically develop recurrent pneumonias in the first few months of life. By childhood, affected males develop diffuse skin hyperpigmentation with a distinctive reticulate pattern, bronchiectasis, hypohidrosis, corneal scarring, enterocolitis, and recurrent urethral strictures. A recurrent intronic mutation has been found that disrupts the expression of the catalytic subunit of DNA polymerase-alpha ( POLA1 ) and leads to increased production of type I interferons.

Inborn Errors of Metabolism

Gaucher disease is an autosomal recessive lysosomal storage disease characterized by the accumulation of the glycolipid glucosylceramide due to the deficiency of the enzyme acid-beta glucosidase. Diagnosis relies on the demonstration of deficient enzyme activity in cells or the identification of two disease-causing mutations in the GBA gene. Patients can display a large variety of symptoms, ranging from patients who are completely asymptomatic to those who present with perinatal lethality. The usual clinical findings include hepatosplenomegaly, anemia, thrombocytopenia, and bone manifestations including osteopenia, lytic lesions, bone crisis, and skeletal deformities. Infiltration of Gaucher cells into the alveoli, interstitium, and pulmonary capillaries can lead to lung involvement. Over 65% of patients with type I disease have pulmonary function abnormalities, but only a fraction (<5%) have diffuse lower lobe linear infiltrates, restrictive physiologic impairment, and a reduced diffusion capacity consistent with ILD. Enzyme replacement therapy can reduce organ volumes and improve the hematologic parameters and bone pain but is usually poorly effective in treating the lung manifestations of this disease. Other therapeutic treatments, such as substrate reduction therapy as well as others, are in development.

Niemann–Pick disease types A and B are caused by an inherited deficiency of acid sphingomyelinase activity. Type C is caused by defective movement of lipids, including cholesterol, from endosomes and lysosomes. Patients demonstrate a range of ages and can have diverse symptoms affecting the lung, liver, spleen, bone marrow, skeleton, brain, muscle, mental ability, and movement. The pulmonary manifestations include ILD and recurrent lung infections. In some patients the ILD is predominantly in the bases with thickened interlobular septa, interlobular lines, and ground-glass opacities.

Lysinuric protein intolerance is an autosomal recessive disease caused by an inherited defect of cationic amino acid transport. There is excess urinary clearance of these amino acids and deficient intestinal absorption, which leads to depleted body pools. Most patients present in infancy with failure to thrive, growth retardation, protein aversion, muscular hypotonia, hepatosplenomegaly, and osteoporosis. In one study, all patients who developed a fatal respiratory insufficiency, usually PAP, were children less than 15 years of age. Most adult patients have evidence of an ILD on CT scans with interlobular and intralobular septal thickening and subpleural cysts, but only a few are symptomatic.

Surfactant Metabolism Dysfunction, Type 1: SFTPB Mutations

SP-B deficiency is inherited in an autosomal recessive manner, and the majority of affected patients develop respiratory failure in the neonatal period with rapid progression of disease and death at 3–6 months. A few mutations that seem to confer a milder phenotype have been found. Children with these mutations have partial expression of the SP-B protein, survive longer, and go on to develop a chronic ILD.

Surfactant Metabolism Dysfunction, Type 2: SFTPC Mutations

Autosomal dominant lung disease due to mutations in the gene encoding SP-C, SFTPC , was first described in 2001 by Nogee and colleagues. The index case was a full-term infant who developed respiratory symptoms at 6 weeks of age. An open lung biopsy revealed histologic features of NSIP. The child’s mother had been diagnosed with desquamative interstitial pneumonitis at 1 year of age, and the child’s maternal grandfather had died from lifelong respiratory illness of unknown cause. Both the mother and her infant had a heterozygous mutation at the splice donor site in intron 4 (c.460+1G > A), which resulted in skipping of exon 4 and deletion of 37 amino acids. In the next year, a large five-generation kindred was described with 14 affected family members. The age at diagnosis for the affected individuals ranged from 4 months to 57 years and included four adults with surgical lung biopsy evidence of usual interstitial pneumonitis and three children with NSIP. Genomic sequencing revealed a rare heterozygous missense SP-C mutation (L188Q) in all analyzed individuals. Human type II alveolar epithelial cells from one of the patients and mouse lung epithelial cells producing the mutant SP-C protein showed abnormal lamellar bodies. Since these two studies, over 30 different mutations in SFTPC have been identified in children and adults. A missense mutation (c.218T > C) that changes a conserved isoleucine at position 73 to a threonine is one of the more common and accounts for 25–35% of abnormal alleles. There is incomplete penetrance of the ILD phenotype and phenotypic heterogeneity. The disease ranges from severe respiratory distress in infants to IPF in older adults. Mutations of SFTPC are rare in individuals without a family history of pulmonary fibrosis. At present, the disease phenotype is thought to be caused by aberrant protein-folding, which elicits the unfolded protein response, ER stress, and apoptosis of alveolar epithelial cells.

Surfactant Metabolism Dysfunction, Type 3: ABCA3 Mutations

There is a significant amount of phenotypic overlap between patients with SFTPB mutations and those with defects in ABCA3 . Like SP-B deficiency, the disease is inherited in an autosomal recessive manner. Since the first mutation was discovered in 2004, more than 200 different mutations have been found. Mutations in ABCA3 are the most common inherited defects in surfactant metabolism presenting either with severe neonatal disease or as diffuse lung disease in infancy or childhood. ABCA3 is an ATP-binding cassette transporter that localizes to the limiting membrane of lamellar bodies where it functions in translocating phospholipids, primarily phosphatidylcholine, into these organelles for assembly and storage of surfactant in type II AECs. The functional consequences of the ABCA3 mutations include decreased expression of the protein, abnormal localization of the protein to the lamellar membrane, production of surfactant that is deficient in phosphatidylcholine, and increased alveolar surface tension.

Surfactant Metabolism Dysfunction, Types 4 and 5: CSF2RA and CSF3RB Mutations

Protein alveolar proteinosis (PAP) is a rare form of lung disease characterized by intraalveolar accumulation of surfactant, which results in respiratory insufficiency. Histopathology specimens from affected patients demonstrate distal airspaces filled with foamy alveolar macrophages and a granular, eosinophilic material that stains positively with PAS reagent. In general, the underlying lung architecture is normal unless infection is present. When the accumulated surfactant is removed, as is done with whole-lung lavage, the gas exchange properties of the lung improve. Approximately 90% of PAP cases are acquired and are referred to as primary PAP. Circulating autoantibodies to GM-CSF can be found in over 92% of patients with primary PAP. These antibodies block GM-CSF signaling in vivo, reduce alveolar macrophage surfactant catabolism, and impair surfactant clearance. Secondary PAP occurs in several different clinical settings, such as in association with hematologic malignancies, immunosuppression, inhalation of inorganic dusts, and certain infections.

The GM-CSF receptor is composed of an α- and a β-chain, encoded by the CSF2RA and CSF2RB genes, respectively. Mutations in both CSF2RA and CSF2RB have been identified in children with PAP. In 2011, a case of adult-onset hereditary PAP was reported in Japan. Here, a 36-year-old woman with PAP had elevated circulating levels of GM-CSF, no measurable anti-GM-CSF antibodies, and reduced expression of the GM-CSF receptor β-chain. Genetic sequencing revealed a homozygous, single-base deletion at nucleotide 631 in exon 6 of CSF2RB . Both of the patient’s parents were heterozygous for the mutation. Hereditary PAP follows an autosomal recessive pattern. Mice with deletion of the gene encoding GM-CSF or its receptor demonstrate a phenotype very similar to adults with primary PAP.

Interstitial Lung and Liver Disease

A specific and severe type of PAP has been described affecting infants and children on Réunion Island. Since 1970, 34 children have been diagnosed and treated, giving rise to an incidence of disease of 1 in at least 10,000 newborns. The lung disease progresses to lung fibrosis despite regular whole-lung lavage. It has recently been found that patients have biallelic mutations in MARS , the gene encoding methionine tRNA ligase. Compound heterozygous mutations in the same gene have been found in one patient with multiorgan disease, predominated by liver failure. The increased prevalence of disease on Réunion Island and in nearby Tunisia and France is due to founder mutations. A potential benefit of high-dose methionine supplementation has not yet been studied in these patients.

Pulmonary Fibrosis, Telomere Related, Type 1

Heterozygous mutations in the gene encoding the protein component ( TERT ) of telomerase have been found in ∼15% of patients with autosomal dominant familial pulmonary fibrosis. The frequency of TERT mutations in patients with sporadic adult-onset ILD is less common. Telomerase is a multimeric ribonucleoprotein enzyme that catalyzes the addition of a repetitive DNA sequence to the ends of chromosomes known as telomeres. Each of the mutations is rare and associated with decreased in vitro activity of telomerase and short leukocyte telomere lengths. TERT mutations are the most common genetic mutations found in adult patients with ILD. In addition, adult-onset pulmonary fibrosis is the most common manifestation of TERT mutations. Other clinical manifestations of TERT mutations include DC (see earlier discussion), aplastic anemia and other forms of bone marrow failure, liver disease including liver cirrhosis, early graying of hair, and an increased risk for myelodysplastic syndrome and acute myeloid leukemia. Altogether, disparate clinical presentations and diseases linked together by defects in telomere-related genes and characterized by short telomere lengths are known as monogenic short telomere syndromes or telomeropathies.

The penetrance of pulmonary fibrosis in TERT mutation carriers is age and gender dependent. The penetrance of pulmonary fibrosis for men aged 40–49, 50–59, and >60 years is 14%, 38%, and 60%, respectively. Women show the same age-dependent increase in penetrance. Microscopic honeycombing and fibroblastic foci are commonly found in surgical lung biopsies. While approximately half of patients carry a diagnosis of idiopathic pulmonary fibrosis (IPF), others have diagnoses of another idiopathic interstitial pneumonia, unclassifiable lung fibrosis, chronic hypersensitivity pneumonitis, pleuroparenchymal fibroelastosis, idiopathic fibrosis with autoimmune features, or, rarely, a connective tissue disease–associated ILD. Many TERT mutation carriers with pulmonary fibrosis report past cigarette smoking or an exposure to a fibrogenic environmental insult, suggesting that injurious environmental exposures in conjunction with the underlying inherited genetic predisposition lead to the lung disease. Disease progression is inexorable, with a mean transplant-free survival of <3 years after diagnosis. TERT mutation patients undergoing lung transplant generally have a higher risk of cytopenias and other extrapulmonary complications.

Genetic anticipation is seen for TERT mutation patients, with an earlier age of diagnosis of lung fibrosis in subsequent generations. Similar to DC, progressively shorter telomere lengths are found in subsequent generations of TERT mutation carriers, and these shorter telomere lengths explain genetic anticipation seen in kindreds.

Pulmonary Fibrosis, Telomere Related, Type 2

Heterozygous mutations in the gene encoding the RNA component ( TERC ) of telomerase have been found in ∼3% of patients with autosomal dominant familial pulmonary fibrosis. Each of the mutations is rare and associated with decreased in vitro activity of telomerase and short leukocyte telomere lengths. A wide range of progressive adult-onset pulmonary fibrosis subtypes are seen in patients with TERC mutations. Patients with TERC mutations are generally diagnosed with ILD at an earlier age (51 years) than TERT mutation carriers (58 years). In addition, they have a higher incidence of hematologic comorbidities, especially leukopenia, thrombocytopenia, aplastic anemia, or myelodysplastic syndrome.

Pulmonary Fibrosis, Telomere Related, Type 3

Autosomal dominant pulmonary fibrosis with incomplete penetrance has been linked to rare mutations in RTEL1 . RTEL1 surpassed the threshold for genomewide significance when comparing the number of observed versus expected novel damaging or conserved missense mutations in familial pulmonary fibrosis cases and controls. Across independent studies, RTEL1 mutations are rare and associated with short leukocyte telomere lengths. This gene encodes the regulator of telomere elongation helicase 1 and has a known role in telomere maintenance. Mutations in RTEL1 were previously shown to cause Hoyeraal-Hreidarsson syndrome, a severe variant of DC (see earlier discussion), in which affected children generally have very short telomere lengths and biallelic mutations. In contrast, those affected with adult-onset pulmonary fibrosis are heterozygous for rare missense or loss-of-function RTEL1 mutations. Similar to patients with TERT mutations, ∼50% of heterozygous RTEL1 mutation carriers have hematologic manifestations such as anemia or macrocytosis. A wide range of progressive adult-onset pulmonary fibrosis subtypes are seen in patients with RTEL1 mutations. Genetic anticipation is also seen in RTEL1 kindreds.

Pulmonary Fibrosis, Telomere Related, Type 4

Exome sequencing has linked autosomal dominant pulmonary fibrosis with incomplete penetrance to mutations in PARN , the gene encoding a polyadenylate-specific ribonuclease. PARN surpassed the threshold for genomewide significance when comparing the number of observed versus expected novel damaging mutations in cases and controls. Most mutations are predicted to cause protein loss of function (splice site, nonsense, and frameshift). One large kindred was identified by linking together two smaller and previously unknowingly related kindreds with familial pulmonary fibrosis and an identical splice-site PARN mutation. The kinship of the two families was confirmed by demonstrating that the two probands share ∼6% of their overall genome, including the genomic segment on which the PARN mutation is located. As a further test for the relevance of the PARN mutations, the cosegregation of the mutations with pulmonary fibrosis was compared across extended kindreds. The overall backward LOD score across all informative PARN kindreds was 3.6, reflecting an odds ratio of 1:4096 in favor of linkage.

Other clinical manifestations of PARN mutations include DC (see earlier discussion), in which biallelic mutations in the gene are frequently found. Patient cells show deficiencies in trimming of small nucleolar RNAs, including abnormally adenylated hTR. In general, leukocyte telomere lengths of PARN mutation patients are shorter than in controls, but longer than in subjects with TERT , TERC , or RTEL1 mutations. Patients with PARN mutations are generally diagnosed with ILD at an older age (64 years) than TERT mutation carriers (58 years). However, once pulmonary fibrosis is diagnosed, the respiratory disease progresses and patients have a mean transplant-free survival of 5.7 years from diagnosis.

Pulmonary Fibrosis, Other Telomere Related

Genes found to be mutated in DC patients are candidate genes for patients with adult-onset pulmonary fibrosis and short telomere lengths. Similar to the other short telomere syndromes mentioned earlier, many individuals have clinical features that overlap with DC, including bone marrow abnormalities and skin changes. A missense mutation in the DKC1 , encoding dyskerin, has been reported in a kindred with two affected older males with interstitial fibrosis, hyperpigmented skin changes, dyskeratotic nails, and macrocytic anemia. Blood leukocyte telomere lengths were short. The expression of hTR in a lymphoblastoid cell line derived from the proband was lower than that of controls, even though expression of DKC1 was not reduced. Female mutation carriers were unaffected.

TINF2 encodes one of the shelterin complex proteins that functions to protect the telomeric ends of chromosomes. Exome sequencing revealed a complex spice acceptor site and missense mutation on the same TINF2 allele, with predominant expression of the missense mutation in lung-derived DNA from a female patient with pulmonary fibrosis and infertility. Heterozygous loss of function mutations in NAF1 have most recently been linked to pulmonary fibrosis-emphysema, short telomere lengths, bone marrow failure, and liver disease. NAF1 has been shown to be essential for the biogenesis of telomerase RNA.

Pulmonary Fibrosis and Adenocarcinoma, Related to Surfactant A Mutations

Novel missense mutations in the gene encoding SP-A2 ( SFTPA2 ) were discovered by genomewide linkage followed by sequencing candidate genes within the linked region. Affected individuals have evidence of pulmonary fibrosis and/or lung adenocarcinoma with features of bronchoalveolar cell carcinoma. A second study reported three additional rare SFTPA2 mutations in patients with adult-onset pulmonary fibrosis and a personal or family history of adenocarcinoma. A third study has recently described the cosegregation of ILD and lung adenocarcinoma in an extended kindred with a germline mutation in SFTPA1 that is predicted to change a conserved tryptophan at position 211 (Trp211Arg). While most of the affected individuals in the SFTPA1 kindred were affected with an ILD after age 30 (range 31–69 years at diagnosis), one was diagnosed at 7 months of age and died of respiratory failure 2 months later. Thus, a wide range of age at the time of diagnosis is observed, from respiratory insufficiency in infancy to lung fibrosis and adenocarcinoma in adulthood. All known mutations in the surfactant A genes affect highly conserved residues in the carbohydrate recognition domain of the proteins. Two of the mutations are predicted to alter the same glycine at amino acid position 231 (Gly231Val, Gly231Arg).

Cells expressing mutant proteins fail to secrete mature protein into the culture media. In addition, expression of these mutant proteins led to fewer intracellular oligomers, greater protein instability, and increased markers of ER stress. Family members with these heterozygous mutations secrete comparable amounts of total SP-A into the alveolar space, as compared with control family members, suggesting that the pathogenic mechanism may be related to ER stress of the resident epithelial alveolar cells.

Susceptibility to Pulmonary Fibrosis, Common Variants

Using a genomewide screen, a common variant located 3 kb upstream of the MUC5B transcription start site (rs35705950) was found to be present at a higher frequency in IPF patients. This variant is found in ∼9% of controls (an overall allele frequency of 0.10) and 38% of patients with IPF. The odds ratio for IPF disease among subjects who are heterozygous or homozygous for the minor allele of this single nucleotide polymorphism (SNP) was 9.0 (CI 6.2–13.1) and 21.8 (5.1–93.5), respectively. The variant allele was associated with upregulation of MUC5B expression (up to 37.4 times as high when compared with those homozygous for the wild-type allele) in lung tissue of unaffected subjects.

A genomewide association study (GWAS) was performed comparing the frequency of common SNPs in patients with fibrotic idiopathic interstitial pneumonia (n = 1616) with controls (n = 4683). A replication analysis included 876 cases and 1890 controls. A MUC5B promoter variant (rs868903) was again found to be significantly associated with fibrotic lung disease, with a metaanalysis P value of 9.2 × 10 ⁻²⁶ . A broad region on 11p15, including the MUC5B , MUC2 , and TOLLIP genes, was found to demonstrate genomewide significance. After adjusting for the MUC5B promoter SNP found in the earlier study (rs35705950), most of the variants in this broad region were no longer significantly associated, suggesting that the associations seen for the other SNPs may be due to linkage disequilibrium. The MUC5B promoter (rs35705950) has been found in the Framingham Heart Study to be associated with interstitial lung abnormalities, thus linking it to an early manifestation of IPF. Mucins undergo a complex maturation process in airway cells, with glycosylation and disulfide multimerization, before secretion. As genetic perturbations leading to increased mucin production cause elevated ER stress signaling, it is interesting to speculate that the MUC5B promoter variant may lead to increased susceptibility to lung fibrosis through its effects on increased mucin expression and ER stress.

The GWAS study confirmed the association of IPF with variants in the TERT and TERC genes, with metaanalysis p values of 1.7 × 10 ⁻¹⁹ and 4.5 × 10 ⁻⁸ , respectively. Overall, common variants in three telomere length–related genes ( TERT, TERC, and OBFC1 ) were found to be associated with lung fibrosis in this study. The GWAS study also found seven new loci that reached genomewide statistical significance. These loci are located near genes involved with host defense, cell-cell adhesion, and DNA repair.

Pulmonary Alveolar Microlithiasis

Pulmonary alveolar microlithiasis (PAM) is a rare disorder characterized by laminated calcium phosphate concretions within the alveoli. PAM is inherited in an autosomal recessive manner and is particularly prevalent in Turkey, Italy, the United States, and Japan. The chest radiographs of patients with PAM show diffuse, bilateral, micronodular opacities, which obscure the heart border, mediastinum, and diaphragmatic surfaces. Despite the “sandstormlike” appearance, the clinical presentation of PAM is variable. Early in the disease course, patients are often asymptomatic, but over time develop cough, dyspnea, and a restrictive defect with reduced diffusion. In 2006, Corut et al. reported the discovery of several mutations in the gene encoding the type IIb sodium-phosphate cotransporter protein ( SCL34A2 ) in individuals with PAM. The group used linkage analysis of a large consanguineous family in which six members were affected by PAM, and ultimately identified six homozygous mutations in SCL34A2 that predict loss of protein function. A separate group in Japan used genomewide SNP mapping to identify candidate genes in six patients with PAM, and they independently identified SCL34A2 as a gene of interest. Two patients had homozygous frameshift mutations and four had splice-site mutations of the gene. None of the mutations was identified in normal controls. Since these initial discoveries, additional missense and frameshift mutations, as well as intragenetic deletions, have been identified. The gene is expressed in high levels in the lung, predominantly in type II epithelial cells. Epithelial deletion of the mouse Npt2b gene in the lung leads to a progressive pulmonary process characterized by diffuse alveolar microliths, restrictive physiology, and alveolar phospholipidosis. Microliths are readily dissolved by whole-lung EDTA lavage. A low-phosphate diet prevents microlith formation in young mice and decreases the burden of pulmonary calcium deposits in older mice. The effectiveness of such a diet has not yet been studied in human patients.