Refractory nontuberculous mycobacterial infection and potential hidden immunodeficiency related to RAG mutation and production of anti-interferon-α autoantibodies: a case report

Abstract

Background

Nontuberculous mycobacterial infectious diseases are associated with host immunological status. Neutralizing anti-interferon (IFN)-γ autoantibodies have been considered as a significant cause of nontuberculous mycobacterial infections. However, another autoantibody specifically targeting interferon-α, occurring in patients with nontuberculous mycobacterial infection, has been rarely reported.

Case presentation

We report the case of a 23-year-old female who developed refractory nontuberculous mycobacterial infection and subsequently manifested skin lesions and motor disorder of muscles. The laboratory examination results showed elevated levels of globulin and immunoglobulin, as well as local deposits of amyloid material in pleural sections. Additionally, various tissue biopsies showed no evidence of malignancy. After 6 months of anti-nontuberculous mycobacterial therapy, the patient recovered normal temperature but developed progressive pulmonary lesions. The patient received steroids and methotrexate treatment and her skin lesions as well limitation of muscle movement improved. Further evaluation revealed a hidden immunodeficiency with positive anti-interferon-α autoantibodies and recombinase activating gene (RAG) mutation.

Conclusions

This case highlights alternation of infection and immune dysregulation, likely resulting from RAG mutation and production of anti-interferon-α autoantibodies.

Introduction

Nontuberculous mycobacteria (NTM) are widely existed in natural environment such as natural and drinking water and soil [1]. Their detection in human clinical specimens may represent neither colonization by environmental organisms or true opportunistic infection. Host susceptibility constitutes a major risk determinant for NTM disease, particularly among individuals with pre-existing structural lung pathologies such as chronic obstructive pulmonary disease, bronchiectasis, and cystic fibrosis. Additional predisposing factors encompass immunocompromised states, including HIV infection, cancer, alcoholism, and diabetes mellitus [2]. The interleukin-12/interferon (IFN)-γ pathway is crucial for host defences against NTM infection, and any defects in this pathway can predispose the host to NTM [3]. Case reports of NTM infection associated with anti-IFN-γ autoantibodies, which block the activity of interleukin-12/IFN-γ pathway, have been increasing worldwide. But another autoantibody specifically targeting interferon-α, potentially linked to NTM infectious disease, has been rarely reported. Herein, we described a young female diagnosed with disseminated NTM infection with occurrence of anti-IFN-α autoantibody, rather than the more commonly recognized anti- IFN-γ antibody.

Case presentation

A 23-year-old female was first admitted to respiratory department on May 20th, 2022, presenting with a six-month history of abdominal pain, fever, and arthrodynia. Prior to admission, she had been suspected of having tuberculosis, hematologic malignancies, or connective tissue disease, but no sufficient evidence supported these suspicions. Diagnostic antituberculosis therapy lasted for 12 days but failed to improve her abdominal pain and abnormal temperature. Physical examination revealed an appearance of cachexia, coarse breathing sounds and lower abdominal tenderness. The routine blood test showed normal counts for leukocytes, neutrophils, and lymphocytes, but the hemoglobin level was 62.10 g/L. The C-reactive protein and erythrocyte sedimentation rate were 149.94 mg/L and > 140 mm, respectively. Other remarkable results included elevated globulin (58.9 g/L), immunoglobulin (Ig) G (31.51 g/L), Ig M (1.87 g/L), and Ig E (215.6 IU/ml), and reduced albumin (20.1 g/L). The counts for CD4 +, CD8 + T-lymphocytes, and human immunodeficiency virus antibodies were normal. Echocardiography found a small amount of thick pericardial effusion. Computed tomography of the chest revealed solid nodules, one located in the dorsal segment (1.5 cm in diameter) and another in outer basal segment of the right lower lobe of the lung (Fig. 1: A and B). Gastroscopic biopsy showed chronic non-atrophic gastritis. Colonoscopy was aborted at 25 cm from the anal verge due to severe intestinal adhesions causing remarkable resistance to scope advancement, though no mucosal abnormalities were observed. Positron emission tomography-computed tomography showed bilateral pneumonia, splenomegaly and multiple lymph node enlargements with increased glucose metabolism, as well as mesenteric edema. The patient underwent a left cervical lymph node biopsy, which revealed multiple necrotic areas of varying sizes containing cholesterol crystals, extensive foam cell reaction in partial areas, and significant fibrous tissue proliferation around the necrotic foci (Fig. 2: A to D). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) confirmed the presence of Mycobacterium gordonae in the lymph node specimen. Given this finding, the diagnosis of disseminated Mycobacterium gordonae infection involving lymph nodes, lungs, abdominal and pericardial cavities, and sigmoid colon was established. The patient initially received empiric therapy with fluconazole and imipenem/cilastatin. After the pathogen was identified, the treatment regimen was changed to moxifloxacin, azithromycin, rifampicin, ethambutol, and cefoxitin for targeting NTM. She was discharged in stable condition and continued the regimen at a local hospital.

Fig. 1

Chest computed tomography revealed solid nodules in the dorsal and outer basal segment of the right lower lobe of the lung (A and B, first hospitalization in May 2022) and lung lesions progressed following six months of NTM-targeting treatment (C to F, December 2022)

Fig. 2

Histopathological features of a lymph node: low-power histological overview (A, × 40), significant fibrous tissue proliferation (B, × 100), necrotic areas containing cholesterol crystals (C, × 100), and foam cell reaction (D, × 200). Lung biopsy showed infiltration of inflammatory cells and granulation tissue proliferation (E, ×100). Histological examination of a skin biopsy sample showed dermal nerve endings (red arrow) along with lymphocyte and histiocyte infiltration (G, ×100), collagen proliferation (H, ×100) and suspected bacilli (I, anti-acid staining, ×600, red arrow). Muscle biopsy demonstrated swollen muscle fibers and indistinct striations (F, ×200), as well as scattered inflammatory cell infiltration (J, ×200)

The patient experienced eight hospitalizations between June 2022 and July 2023, primarily due to recurrent edema and abdominal pain. Pathogen identification detected both conventional and atypical microorganisms through advanced diagnostic methods. Next-generation sequencing of bronchoalveolar lavage fluid detected multiple pathogens including Haemophilus parainfluenzae (71,951 reads), Haemophilus influenzae (6,967 reads), Klebsiella pneumoniae (68,532 reads), Escherichia coli (37,456 reads), Enterobacter cloacae (15,234 reads), and Candida tropicalis (10,745 reads). Notably, blood analysis identified Mycobacterium intracellulare (1 read), while ascitic fluid analysis through MALDI-TOF-MS confirmed the presence of Mycobacterium tuberculosis. A lung biopsy was conducted in December 2022 to determine the pathological changes, which indicated chronic suppurative inflammation (Fig. 2E). Prior to the identification of Mycobacterium tuberculosis, the primary therapeutic regimen was adjusted based on microbiological findings and comprised anti-NTM therapy (including linezolid, clarithromycin, moxifloxacin, rifampicin and ethambutol) along with voriconazole for suspected fungal infection. The patient’s temperature returned to normal after six months of persistent treatment, but her condition did not completely improve, with abdominal pain persisting and lung lesions progressing (Fig. 1: C-F). She was hospitalized once due to intestinal obstruction. Following the identification of Mycobacterium tuberculosis, the patient received antituberculosis therapy on a regimen of pyrazinamide 0.5 g daily, rifampin 0.5 g twice weekly, isoniazid 0.15 g daily, and moxifloxacin 0.4 g daily, considering resistance to ethambutol. However, repeated ascites analysis for tuberculosis confirmation was not performed. In view of the persistent ascites, methylprednisolone 20 mg daily was added to reduce inflammation reaction and maintained over a period of 2.5 months. The patient’s clinical condition improved compared to previous and kept a relatively stable period with the initiation of glucocorticoid treatment.

Subsequently, skin and muscle symptoms emerged as prominent manifestations. The patient developed limited mobility in the right upper limb and mouth opening, neck stiffness and red, well-defined and painful rash on the extensor side of her left lower leg in February 2024 (Fig. 3). A skin biopsy showed degeneration of dermal nerve endings, with suspected bacilli and surrounding lymphocyte and histiocyte infiltration (Fig. 2: G, H, and I). A muscle biopsy indicated swollen muscle fibers, indistinct striations, and scattered inflammatory cell infiltration (Fig. 2: F and J). Consultation on external pleural pathological sections revealed focal amyloid deposits, positive for κ light chains and Congo red stain. The patient received methotrexate 10 mg weekly and anti-infection treatment, and methotrexate appeared to relieve the limitations in limb and mouth movement and improve skin lesions. The patient’s last medical record was documented in May 2024. The patient was presumed deceased as attempts to follow up on her clinical condition by telephone failed due to no reply. The clinical details in the disease course were summarized in Table 1.

Fig. 3

Red, well-defined and painful rash on the extensor side of left lower leg in February 2024

Table 1 Clinical details in the disease course

Given the remarkable features of infection and immune disorder, the following tests were carried out to explore whether there is a hidden immunodeficiency disease. The blood test for anti-IFN-α autoantibodies was positive (α1 subtype titer 1:2500; α2 subtype titer 1:500), but negative for anti-IFN-γ autoantibodies. Exome sequencing was conducted, finding abnormal mutations in RAG1, RAG2, USP8, USF3, PIK3CA, and IL6ST. The detailed defects in RAG1 were NM_000448: exon2: c.A746G: p.H249R, NM_000448: exon2: c.A1632G: p.L544L, and NM_000448: exon2: c.A2459G: p.K820R; while the defect in RAG2 was NM_000536: exon2: c.T1443C: p.H481H.

Discussion and conclusions

We described a female patient with intractable disseminated NTM infection, which was considered an external manifestation of a hidden immunodeficiency disease. A less common but not well-recognized cause related to anti-IFN-α autoantibodies emerged. These autoantibodies were found in patients with COVID-19 disease and accounted for the severity of disease [4, 5]. However, the relationship between anti-IFN-α autoantibodies and bacteria like NTM, rather than viruses, has rarely been reported. IFNs are categorized into three families. All IFNs signal through the JAK-STAT signaling pathway, and the signaling triggered by these three IFN types elicits important and distinct outcomes, including the induction of numerous IFN-stimulated genes (ISGs) [6]. ISGs generate antimicrobial effectors by enhancing innate pathogen-sensing capabilities, producing toxic antimicrobial products, interfering with nutrient acquisition, blocking the entry or promoting the exit of microorganisms [7]. This case should emphasize two characteristics: firstly, the clear identification of NTM infection and the effect of anti-NTM treatment is inferior to anti-IFN-γ autoantibody positivity; secondly, it exhibits features associated with immune dysregulation, including elevated Ig G, Ig E and globulin, migratory muscle pain, skin lesions as well as effective response to steroids and methotrexate. Whether the presence of anti-IFN-α autoantibodies can explain these manifestations remains unknown, but it provides a special aspect into comparison with the immunodeficiency disease caused by anti-IFN-γ autoantibodies.

Recombinase activating genes 1 and 2 (RAG1, RAG2) participate in the process of rearrangement of variable, diversity, and joining gene segment (VDJ) and are essential for lymphocyte development [8]. RAG expression is activated during the development of hematopoietic stem cells into mature B cells and T cells. RAG null mutations, complete absence of functional RAG, lead to the absence of mature T and B cells and severe combined immunodeficiency. While hypomorphic RAG defects with residual function cause inefficient generation of T and B cells and immune dysregulation resulting from the disruption of both T- and B-cell tolerance [9]. This may clarify why infections are more easily acquired and the why immune dysregulation occurs. RAG1 and RAG2 defects lead to a broad spectrum of clinical phenotypes, with combined immunodeficiency with granulomas and/or autoimmunity (CID-G/AI) being one of them. CID-G/AI is characterized by a milder clinical course, delayed onset, granuloma, and autoimmune phenomena [10]. Plasma from patients with RAG deficiency produces a broad spectrum of autoantibodies, including anti-IFN-α autoantibodies with neutralizing activity but anti-IFN-γ autoantibodies without neutralizing ability [11], which are in accordance with our case. The presence of anti-IFN-α autoantibodies is the consequence of immune dysregulation, but its production mechanism and function remain to be elucidated. Though the patient did not completely match the autoimmune phenomena described in the previous study, we suggest the late-onset age, refractory NTM infection, cutaneous and muscular manifestations, effective response to steroids and methotrexate, production antibodies targeting IFN-α and RAG mutation are likely to correspond to CID-G/AI. Upon exome sequencing for genes PIK3CA, IL6ST, USF3, and USP8, this case exhibited no clinical manifestations consistent with those reported in the current literature for human diseases.

Differential diagnosis should include malignant diseases and amyloidosis. The patient exhibited cachexia, but repeated biopsies revealed no evidence of tumor, including lymphoma. A muscle biopsy showed localized amyloid deposition, supporting a diagnosis of localized amyloidosis. It remains uncertain whether the patient’s history of intestinal obstruction indicates gastrointestinal involvement in amyloidosis. The kidneys, heart and gastrointestinal tract are commonly involved organs in systemic amyloidosis [12, 13]. However, the patient showed no clinical abnormalities related to the kidneys and heart. Due to economic reasons, the patient refused to undergo blood and urine light chain tests as well as bone marrow FISH examination.

This case was relatively complicated and subject to limitations. The diagnosis of NTM infection is intrinsically challenging in clinical practice. Since different NTM species (Mycobacterium gordonae and Mycobacterium intracellulare) were detected at different time, this may diminish diagnostic confidence. On the other hand, the role of RAG gene in the disease remains unclear. In summary, we emphasized that RAG mutation is potential underlying cause associated with refractory NTM infection and the production of anti-IFN-α autoantibodies.