Mutation in methionyl-tRNA synthetase 1 causing pulmonary alveolar proteinosis

Manoj Madhusudan; Tejaswi Chandra; JT Srikanta

doi:10.4103/ipcares.ipcares_47_23

CASE REPORT

Year : 2023 | Volume : 3 | Issue : 3 | Page : 162-166

Mutation in methionyl-tRNA synthetase 1 causing pulmonary alveolar proteinosis

Manoj Madhusudan, Tejaswi Chandra, JT Srikanta
Department of Pediatric Pulmonology, Interventional Pulmonology and Sleep Medicine, Aster CMI Hospital, Bengaluru, Karnataka, India

Date of Submission	28-Feb-2023
Date of Decision	08-May-2023
Date of Acceptance	31-May-2023
Date of Web Publication	14-Aug-2023

Correspondence Address:
Dr. Manoj Madhusudan
Department of Pediatric Pulmonology, Interventional Pulmonology and Sleep Medicine, Aster CMI Hospital, Bengaluru, Karnataka
India

Source of Support: None, Conflict of Interest: None

DOI: 10.4103/ipcares.ipcares_47_23

Abstract

Background: A chronic history of exertional dyspnea, dry cough, and fatigue, associated with reticulonodular ground-glass opacity indicates an underlying interstitial lung disease (ILD). Pulmonary alveolar proteinosis (PAP) is a rare cause of ILD, in which there is abnormal accumulation of surfactant material in alveoli, thereby impairing gaseous exchange. In children, PAP is usually due to genetic mutations. We report a child with PAP due to mutation in methionyl-transfer RNA synthetase 1 (MARS) gene. Clinical Description: An 8-year-old boy presented with persistent dry cough, and exercise-induced breathlessness for 2 years of age, associated with failure to gain weight. He had multiple exacerbations in the past, requiring common symptomatic treatment, but with minimal improvement. On presentation to us, the child had tachypnea, hypoxia (oxygen saturation [SpO₂]: 85%), and Grade 2 clubbing, with bilateral fine crepitation in bilateral lung fields. Management and Outcome: The child was stabilized by providing oxygen via high-flow nasal cannula. Blood investigations were largely normal. His chest X-ray and computerized tomography (CT) of the chest were suggestive of childhood ILD. A lung biopsy revealed periodic acid–Schiff-positive eosinophilic granular material in the alveolar spaces without any fibrosis, suggesting a diagnosis of PAP. Next-generation sequencing revealed a compound heterozygous mutation of the MARS1 gene resulting in PAP. Parental segregation analysis showed each one to be a carrier of one of the genes. Therapeutic whole-lung lavage (WLL) was carried out, following which symptoms improved markedly. SpO₂ increased and the child was able to be weaned off oxygen and discharged. Three years, postdischarge, the child is asymptomatic and thriving well. Conclusions: PAP may be a cause of ILD in a child. Although the etiology can be ascertained by high-resolution CT of the chest and bronchoalveolar lavage, further genetic analysis should also be undertaken in children to identify the exact defect. WLL can provide a good outcome in children with PAP due to MARS mutation.

Keywords: Genetic, interstitial lung disease, pediatric, whole-lung lavage

How to cite this article:
Madhusudan M, Chandra T, Srikanta J T. Mutation in methionyl-tRNA synthetase 1 causing pulmonary alveolar proteinosis. Indian Pediatr Case Rep 2023;3:162-6

How to cite this URL:
Madhusudan M, Chandra T, Srikanta J T. Mutation in methionyl-tRNA synthetase 1 causing pulmonary alveolar proteinosis. Indian Pediatr Case Rep [serial online] 2023 [cited 2023 Sep 30];3:162-6. Available from: http://www.ipcares.org/text.asp?2023/3/3/162/383628

Pulmonary alveolar proteinosis (PAP) is a type of interstitial lung disease (ILD), in which there is abnormal accumulation of surfactant material in the alveoli, due to its defective clearance by alveolar macrophages. The deposited phospho-lipo-proteinaceous, eosinophilic, periodic acid–Schiff (PAS)-positive material in the alveoli affects gaseous exchange. Affected individuals present with dry cough, respiratory distress, and hypoxemia. The condition may be primary (autoimmune due to circulating autoantibodies against Granulocyte Macrophage Colony stimulating factor [GM-CSF] or hereditary due to defects in genes encoding GM-CSF receptors) or secondary due to various causes such as infections, immunodeficiency, metabolic, hematological disorders, rheumatological diseases, or inhalation of chemicals or minerals or congenital heart disease.^[1],[2] While autoimmune causes are the most common in adults, genetic causes predominate in children.^[2] We report a child with PAP due to a novel mutation in methionyl-transfer RNA synthetase 1 (MARS-1) gene.

Clinical Description

An 8-year-old school-going boy, belonging to a place in the Southern part of India, was brought with symptoms of dry cough, shortness of breath with exercise, and poor weight gain, occurring intermittently since the age of 2 years. He was the first born out of a nonconsanguineous marriage with an uneventful antenatal and perinatal history. There was no family history of any chronic respiratory disorder. The child was developmentally normal and had an average Indian diet.

The child was apparently well till 2 years of age, when he presented with an episode of dry cough, associated with fast and distressed breathing, without fever, requiring hospitalization for nebulization. Subsequently, the child developed multiple such episodes, each lasting for 10–14 days at a stretch, initially occurring at a frequency of 2–3 episodes/year, later occurring more frequently. In between episodes, the child did not recover fully with persistence of some degree of fast breathing and respiratory distress. There was no history of rash, joint pain, or any significant environmental exposures to dust, allergens, pollen, or pets. There was no history suggestive of cardiac disease such as pedal edema or gastroesophageal reflux disease such as vomiting, retching, or heart burns. The child had been treated with multiple courses of antibiotics, inhaled corticosteroids, and even empirically with a course of anti-tubercular therapy, with minimal benefit. He was referred to us for further evaluation.

On examination, the child was conscious, afebrile, and tachypneic with a respiratory rate of 50/min having intercostal and subcostal retractions, with oxygen saturation (SpO₂) of 85% on room air. He was hemodynamically stable with a heart rate of 120/min and a blood pressure of 110/70 mmHg. He did not have pallor, icterus, lymphadenopathy, or any appreciable cyanosis but had a Grade 2 clubbing. His height was 112 cm (−2.08 Z score) and weight 17 kg (−1.88 Z score) and body mass index (BMI) of 13.55, implying that the child was stunted with a low normal weight and BMI. There was no apparent dysmorphism. Chest auscultation revealed fine crepitation in the bilateral inter- and infrascapular regions. Another systemic examination was normal.

Management and Outcome

The child was treated with oxygen support via high-flow nasal cannula (3 L/min flow, 40% FiO₂) empirical antibiotics (ceftriaxone), and other supportive measures. Meanwhile, his investigations were sent which revealed hemoglobin 10.2 g/dL and total white cell count 7500/mm³ (neutrophils 50% and lymphocytes 42%). Arterial blood gas was suggestive of hypoxemia (PO₂ 58 mmHg) with normal pH (7.37) and PCO₂ (42 mmHg). His C-reactive protein was negative, and Liver function tests revealed a serum bilirubin of 0.9 mg/dL (total) with 0.4 mg/dL conjugated bilirubin, aspartate transaminase 32 IU/L, alanine transaminase 29 IU/L, blood urea was 28 mg/dL, serum creatinine 0.6 mg/dL, serum sodium 138 mEq/L, potassium 4.2 mEq/L, and serum chloride 98 mEq/L.

The history and clinical examination favored a diagnosis of childhood ILD (ChILD). The chest X-ray showed bilateral symmetrical ground-glass opacities with relative sparing of the apices [Figure 1]a, and computerized tomography (CT) of the chest showed widespread symmetrical ground-glass opacities with interlobular septal thickening, both consistent with ChILD. A pulmonary function test was attempted, but the child was unable to comply. Intravenous steroid, in the form of methyl-prednisolone (2 mg/kg/day), was administered. The child was afebrile and blood culture was sterile and antibiotics were stopped after 5 days. There was marginal clinical improvement with the above management. The child remained hemodynamically stable but persisted to have respiratory distress (45/min), subcostal and intercostal retractions, and hypoxia (SpO₂ 87% in room air). As there were no features toward an infective etiology and as the yield of a lung biopsy was better than a lavage, bronchoalveolar lavage was deferred. He underwent a video-assisted thoracoscopic lung biopsy on day 5 of hospitalization. There were no postprocedural complications. The child was discharged on home oxygen on day 8, and reports were followed up on an outpatient basis.

Figure 1: (a) Chest X-ray at presentation showing bilateral symmetric ground-glass opacity with relative sparing of the apices. (b) Chest X-ray 48 h after whole-lung lavage showing significant clearing of the opacities

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The report of the histopathological examination revealed accumulation of PAS-positive eosinophilic granular material in the alveolar spaces without any fibrosis, suggesting a diagnosis of PAP [Figure 2]. Evaluation for the underlying etiology was done. Immunoglobulin profile was normal: IgG 520 mg/dL, IgA 35 mg/dL, IgM 80 mg/dL, and IgE 34 mg/dL), and so were T/B/NK cell markers (T-cells 1750/mm³, B-cells 1225/mm³, and NK cells 895/mm³). Screening for HIV was negative. The complete blood count and peripheral smear were normal. The child did not have any manifestations such as arthritis rash or uveitis suggestive of a systemic autoimmune disease. As PAP secondary to autoantibodies to granulocyte-monocyte colony-stimulating factor (GM-CSF) occurs primarily in adults, and in view of resource constraints, this investigation was deferred.

Figure 2: Histopathology showing granular proteinaceous accumulates inside the alveoli (red arrows), suggesting pulmonary alveolar proteinosis

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With such an early presentation of PAP, and having ruled out secondary causes, an underlying genetic cause was suspected. The DNA extracted from the child's blood was used to perform targeted gene capture using a custom capture kit and the libraries were sequenced to mean >80–100X coverage on the Illumina sequencing platform. The sequences obtained were aligned to the human reference genome (GRCh38.p13) using a Sentieon aligner. This revealed a compound heterozygous variant in the MARS1 gene. The first was a novel variant, present in exon 8 (c.841C>G chr12:G.57892010C>G;) that results in the amino acid substitution of Valine for Leucine at codon 281 (p.Leu281Val; ENST00000262027.5). The second was a variant in exon 15 (c.1793G>A chr12:G.57906573G>A;) that results in the amino acid substitution of Histidine for Arginine at codon 598 (p.Arg598His; ENST00000262027.5), having a minor allele frequency of 0.004% in the gnomAD database. Sanger sequencing of both the variants in asymptomatic parents was done. The p.Leu281Val variant was detected in heterozygous condition in the asymptomatic mother and was not detected in the father. The p.Arg598His variant was detected in heterozygous condition in the asymptomatic father and was not detected in the mother of the index patient. Due to a lack of literature evidence and as per the American College of Medical Genetics guidelines, both the MARS1 variants were classified as variants of uncertain significance (VUS).

The child was readmitted 1 week after biopsy confirmation, for whole-lung lavage (WLL), which is considered the standard of care for PAP. He was intubated with a 26 French size double-lumen endotracheal tube. First, his left lung was ventilated with the one lumen of the ETT, using a flexible video bronchoscope, the subsegments of his right lung were irrigated sequentially with aliquots of 100–150 mL of saline. The aspirate was turbid initially. The cycle was repeated until the effluent from the lungs became clear. The same process was repeated in the left lung, in the same sitting, after ventilating the right lung. In total, he underwent 6 L of saline lavage on the right and 5 L on the left side during the procedure [Figure 3]. The entire procedure lasted 4 h. In 48 h postprocedure, his chest X-ray showed clearing of the infiltrates [Figure 1]b, and his saturations improved to 97% in room air. The child was then weaned off oxygen and finally discharged.

Figure 3: Thick milky proteinaceous aspirate from the lung during whole-lung lavage

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Currently, he is under follow-up for the last 3 years during which time he underwent two cycles of WLL. The last cycle was done a year prior and presently the child is comfortable, with stable vitals, maintaining normal saturations in room air.

Discussion

Pulmonary alveolar proteinosis is a rare condition in children with an estimated incidence of <1 in 1,000,000.^[2] It is a result of an imbalance between surfactant production and clearance characterized by the accumulation of proteinaceous surfactant-rich fluid in the alveoli as a result of a defective clearance. This results in impaired oxygen exchange and varying degrees of hypoxemia.

The condition may be primary or secondary. Primary PAP may be autoimmune or hereditary. Autoimmune PAP is characterized by circulating autoantibodies against GM-CSF in the serum and/or bronchoalveolar lavage fluid and is the most common cause of PAP in adults.^[3] Hereditary PAP is caused by defects in genes encoding GM-CSF receptors. Mutations in the α (CD116) or β (CD131) chain of the GM-CSF receptor result in interruption of GM-CSF signaling, mostly manifesting in childhood, but may also be diagnosed in adults.^[4]

There is another group of genetic defects causing PAP which is known as surfactant dysfunction syndromes. Genetic mutations that are included in this group include SFTPB, SFTPC, ABCA3, and transcription termination factor 1 and mostly present during the neonatal period.^[5] A wide variety of secondary causes can lead to PAP. Secondary causes of PAP result in reduction in number and function of alveolar macrophages. Opportunistic infections such as Nocardia, mycobacterial infection (mostly Mycobacterium tuberculosis), and fungal infections have been reported to cause PAP.^[6] Many hematologic disorders may cause PAP, both in children and in adults. The condition is seen in patients with GATA2 haploinsufficiency, in association with familial myelodysplastic syndrome, acute myeloid leukemia, human papillomavirus, or Epstein–Barr virus-associated tumors.^[7] Other etiologies causing secondary PAP include immunodeficiency, metabolic, rheumatological diseases, or inhalation of chemicals or minerals or congenital heart disease.^[1],[2],[4] Other genetic defects which cause PAP in children include mutations in the methionyl-transfer RNA synthetase (MARS) gene, stimulator of interferon response cGAMP interactor, and COPA genes.^[2] The comprehensive list of diseases causing PAP is shown in [Box 1].

In our case, we identified a compound heterozygous mutation in the MARS1 gene which was reported as VUS, in view of the absence of functional evidence for pathogenicity of the genes. With the early onset of the disease and the absence of features favoring any secondary causes, a genetic cause of PAP seemed most likely in our child. As most causes of a genetic etiology have been ruled by the analysis, and the parental segregation analysis showed each one to be a carrier of 1 of the genes, the compound heterozygous variant in the MARS1 gene looked the most plausible cause for the phenotype in our child.

The MARS gene encodes for methionyl-transfer RNA synthetase (MetRS), which catalyzes the ligation of methionine to t-RNA, a critical step in protein synthesis.^[1],[8] The deficiency results in PAP, as a result of reduced aminoacylation and deficient translation, affecting surfactant composition or homeostasis.^[4] MARS mutation leading to PAP was first described by van Meel et al.,^[9] in an infant on Reunion Island near Africa, having ChILD, liver disease, hypothyroidism, and failure to thrive. Since then, only a handful of cases have been identified, mostly from the same demographic location.^[10] In the described cases till date, PAP with MARS mutation usually displays an early onset and a severe prognosis with frequent progression to pulmonary fibrosis (70%), associated liver involvement (90%), systemic inflammation (90%), and failure to thrive (90%). Other extrapulmonary manifestations include intermittent lactic acidosis, aminoaciduria, hypothyroidism, and transfusion-dependent anemia.^[5] In our case, the child had early-onset ILD, although liver involvement, hypothyroidism, aminoaciduria, and transfusion-dependent anemia were not yet present.

Clinically, individuals affected with PAP typically have an insidious and progressive course.^[3] Children with PAP present with progressive dyspnea, dry cough, exercise intolerance, poor growth, and less commonly with fever, chest pain, or hemoptysis, more so in the presence of secondary infections. Physical examination may range from normal to presence of tachypnea, hypoxia, inspiratory crackles, cyanosis, and digital clubbing. In this condition, there is characteristically discordance between auscultatory findings which are minimal and radiographic findings which include extensive infiltrates.^[3],[11] Chest X-ray usually reveals a bilateral ill-defined nodular or confluent pattern, often more prominent in the perihilar region giving the appearance of “bat wing” as seen in pulmonary edema, however, without cardiomegaly. In younger infants and children, the infiltrates are more diffuse as in ILD.^[3] High-resolution CT (HRCT) shows patchy, ground-glass opacification with superimposed interlobular septal and intralobular thickening in typical polygonal shapes, a pattern commonly referred to as “crazy paving.” Crazy-paving pattern, which combines ground-glass opacity and a superimposed reticular pattern though characteristic of PAP, is not specific to it. Other conditions where such imaging pattern may be seen include hemorrhage, acute respiratory distress syndrome, acute interstitial pneumonia, eosinophilic pneumonia, diffuse alveolar damage, and some pneumonia due to certain organisms.^[4] Routine investigations are usually normal. When pulmonary function test can be done, it may reveal a normal but most commonly shows a restrictive pattern.^[11]

Characteristic clinical and radiographic findings often give a clue to diagnosis of PAP. Confirmation is done with bronchoalveolar lavage wherever possible, which shows opaque, milky appearance and contains large and foamy alveolar macrophages and increased numbers of lymphocytes. Multiple, large, acellular, eosinophilic bodies may be seen in a diffuse background of granular material that stains with PAS.^[11] Lung biopsy may be informative if diagnosis remains uncertain and shows abundant accumulation of surfactant protein with relative preservation of lung parenchyma unless there is infection.^[11] In a report, lung biopsies were performed in around 80% of the children to make the diagnosis of PAP.^[12]

Genetic testing is recommended^[13] in patients with (1) severe unexplained lung disease in newborn period; (2) diffuse disease involving the entire lung on HRCT; (3) if lung biopsy is performed, histopathology that demonstrates findings of congenital PAP, desquamative interstitial pneumonia, nonspecific interstitial pneumonia, or chronic pneumonitis of infancy; and (4) Electron microscopy demonstrating abnormal or absent lamellar bodies.

Whole lung lavage is considered the standard of care in the management of pediatric PAP.^[14] This involves sequential clearing of the surfactant-rich proteinaceous secretions from each segment of both lungs. Children undergoing WLL have significantly better oxygenation and 5-year survival than those without WLL.^[14],[15] Long-term outcomes, however, are variable, as some children undergo prolonged remission with a single WLL, whereas others require repeated cycles to control symptoms.^[2] Moreover, WLL is not useful in certain situations such as congenital PAP wherein lung transplantation has been reported to have better success and acquired cases of PAP like those secondary to hematological malignancy.^[2] Overall, therapy for secondary PAP generally involves WLL and the treatment of the underlying condition. Other therapeutic options include GM-CSF, steroids, bone marrow transplant, and lung transplant in certain variants of PAP. The MARS mutation results in a severe phenotype, with a reported mortality of 46%, most during infancy^[10] and without much benefit from WLL.^[8] However, our child had a comparatively milder course without multisystem involvement, and is currently doing well after WLL, 3 years postdiagnosis.

This is perhaps one of the initial reports of PAP due to MARS mutation in a child from India. In contrast to the few reports published in the literature, the case presented by us, responded well to therapy, and is thriving symptom-free over the last 3 years.

Declaration of patient consent

The authors certify that they have obtained all appropriate patient consent forms. In the form the patient(s) has/have given his/her/their consent for his/her/their images and other clinical information to be reported in the journal. The patients understand that their names and initials will not be published and due efforts will be made to conceal their identity, but anonymity cannot be guaranteed.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.

References

1.	Borie R, Danel C, Debray MP, et al. Pulmonary alveolar proteinosis. Eur Respir Rev 2011;20:98-107.
2.	Bush A, Pabary R. Pulmonary alveolarproteinosis in children. Breathe (Sheff) 2020;16:200001.
3.	Alasiri AM, Alasbali RA, Alaqil MA, et al. Autoimmune pulmonary alveolar proteinosis successfully treated with lung lavage in an adolescent patient: A case report. J Med Case Rep 2021;15:340.
4.	Griese M. Pulmonary alveolar proteinosis: A comprehensive clinical perspective. Pediatrics 2017;140:e20170610.
5.	Hadchouel A, Drummond D, Abou Taam R, et al. Alveolar proteinosis of genetic origins. Eur Respir Rev 2020;29:190187.
6.	Punatar AD, Kusne S, Blair JE, et al. Opportunistic infections in patients with pulmonary alveolar proteinosis. J Infect 2012;65:173-9.
7.	Spinner MA, Sanchez LA, Hsu AP, et al. GATA2 deficiency: A protean disorder of hematopoiesis, lymphatics, and immunity. Blood 2014;123:809-21.
8.	Hadchouel A, Wieland T, Griese M, et al. Biallelic mutations of methionyl-tRNA synthetase cause a specific type of pulmonary alveolar proteinosis prevalent on Réunion Island. Am J Hum Genet 2015;96:826-31.
9.	van Meel E, Wegner DJ, Cliften P, et al. Rare recessive loss-of-function methionyl-tRNA synthetase mutations presenting as a multi-organ phenotype. BMC Med Genet 2013;14:106.
10.	Enaud L, Hadchouel A, Coulomb A, et al. Pulmonary alveolar proteinosis in children on La Réunion Island: A new inherited disorder? Orphanet J Rare Dis 2014;9:85.
11.	Bansal A, Sikri V. A case of pulmonary alveolar proteinosis treated with whole lung lavage. Indian J Crit Care Med 2013;17:314-7. [PUBMED] [Full text]
12.	Hildebrandt J, Yalcin E, Bresser HG, et al. Characterization of CSF2RA mutation related juvenile pulmonary alveolar proteinosis. Orphanet J Rare Dis 2014;9:171.
13.	Kurland G, Deterding RR, Hagood JS, et al. An official American thoracic society clinical practice guideline: Classification, evaluation, and management of childhood interstitial lung disease in infancy. Am J Respir Crit Care Med 2013;188:376-94.
14.	Awab A, Khan MS, Youness HA. Whole lung lavage-technical details, challenges and management of complications. J Thorac Dis 2017;9:1697-706.
15.	Seymour JF, Presneill JJ. Pulmonary alveolar proteinosis: Progress in the first 44 years. Am J Respir Crit Care Med 2002;166:215-35.