Abstract
Tyrosine kinase 2 (TYK2) deficiency is a rare primary immunodeficiency disease (PID). Patients carry TYK2 gene mutations and suffer from recurrent infections by intracellular pathogens, including mycobacteria. Delayed diagnosis often hinders timely and effective treatment, resulting in poor prognosis. In this study, we report a newly discovered TYK2 deficiency patient with recurrent pulmonary infections. The patient, a 27-year-old Chinese man with a history of tuberculosis, presented with recurrent cough, phlegm, and purulent sputum. Lung CT scan showed bronchiectasis with concomitant infection. Next-generation sequencing (NGS) identified Mycobacterium gordonae and Mycobacterium chelonae in lung, along with heterozygous c.997G>A&c.10C>T (p.V333M&p.R4C) mutation in TYK2. Further pathogenicity prediction analysis via dbNSFP (v5.1a) suggested the potential pathogenicity of this genetic variant. Additionally, TYK2 mRNA expression in peripheral blood mononuclear cells (PBMCs) also decreased significantly. Following anti-infective treatment, the patient improved and was discharged with regular human immunoglobulin infusion. However, the patient unfortunately succumbed to disease exacerbation in October 2021, 15 months after diagnosis. Furthermore, a literature review was conducted on cases of TYK2 deficiency. Previous studies have identified 24 mutation sites within TYK2 gene, which impair immune function and lead to early-onset recurrent infections. These mutations contribute to clinical heterogeneity, with the most common manifestation being recurrent infections by opportunistic pathogens, particularly mycobacteria. Our discovery of a novel TYK2 mutation expands the gene’s mutation spectrum. Analyzing the characteristics of reported cases enhances understanding of TYK2 deficiency’s clinical manifestations and facilitates early diagnosis of this rare condition.
Introduction
Tyrosine kinase 2 (TYK2) deficiency is a rare primary immunodeficiency disease (PID) caused by mutations in the TYK2 gene, inherited as an autosomal recessive (AR) trait. As a member of the Janus kinase (JAK) family, TYK2 mediates the phosphorylation of signal transducer and activator of transcription (STAT) proteins, which regulate downstream immune-related genes and modulate immune responses. 1 TYK2 is crucial in cytokine signaling pathways involved in both innate and acquired immunity including IL-12, IL-23, IFN-α/β, IL-6, and IL-10 signaling.1,2 Specifically, IL-12 and IL-23 drive the differentiation of T-helper cells into Th1 cells, which produce IFN-γ—a critical cytokine for macrophage activation and the clearance of intracellular bacteria.3–6 Moreover, IFN-α/β are critical for the transcription of antiviral immune factors. 7 The first case of TYK2 deficiency, defined as autosomal recessive hyper-IgE syndrome (AR-HIES), was reported by Minegishi et al. in 2006. 8 Since then, reports of TYK2 gene mutations have increased, with studies linking these mutations to a spectrum of diseases, including autoimmune and inflammatory disorders, infections, and certain cancers.9–12 To date, 41 TYK2-deficient patients and 24 pathogenic mutation sites have been reported.13,14 These mutations dysregulate cytokine signaling pathways, impairing host defense mechanisms.14–16 Clinically, TYK2-deficient patients commonly present with intracellular bacterial infections (e.g., mycobacterial infections) and viral infections. Some patients may appear fungal infections, allergic diseases (e.g., eczema or atopic dermatitis), and complications related to Bacillus Calmette-Guérin (BCG) vaccination.17,18 In this study, we investigated a patient with non-tuberculous mycobacterial disease carrying a new TYK2 gene mutation and reviewed the literature related to cases of TYK2 deficiency.
Materials and methods
Subjects
Our patient was diagnosed at Xiangya Hospital, Central South University (China). The heathy control was recruited from the health examination center of Xiangya Hospital. Written informed consents were obtained from the subjects. This study was approved by the Ethics Committee of Xiangya Hospital, Central South University (No: 202103133).
Genetic testing
Whole blood samples from patients and their parents underwent comprehensive mutational analysis employing Next-generation sequencing (NGS) with confirmatory Sanger sequencing, performed at Zhenyuan Medical Laboratory (Hangzhou, China).
Bioinformatics analysis
To evaluate the functional impact of the identified variants, we performed comprehensive in silico analyses using dbNSFP (v5.1a), integrating multiple prediction algorithms. Variants were annotated with SIFT, Polyphen2-HDIV, Polyphen2-HVAR, FATHMM-XF, MutationTaster, MutationAssessor, CADD, and M-CAP. As previously reported, a variant was considered potentially deleterious if predicted as harmful by at least one algorithm.19,20 Evolutionary conservation was assessed using GERP++ RS and phyloP100way vertebrate. The deleterious thresholds were as follows: SIFT < 0.05, Polyphen2-HDIV ⩾ 0.454, Polyphen2-HVAR ⩾ 0.447, FATHMM-XF > 0.5, MutationTaster > 0.5, MutationAssessor > 1.935, CADD ⩾ 20, M-CAP > 0.025, GERP++ RS > 2, and phyloP100way vertebrate > 2. Population frequencies of all variants were verified against the whole gnomAD genome samples (v4.1) (exclusion threshold: AF ⩾ 0.1%).
Real-time quantitative PCR analysis
RNA was extracted using TRIzol Reagent according to the manufacturer’s instructions (ECOTOP Biotechnology, GuangZhou, China). cDNA synthesis was performed with 2 × Hieff® PCR Master Mix (Yeasen Biotechnology, Shanghai, China). Quantitative RT-PCR was performed with Hieff® qPCR SYBR Green Master Mix (Yeasen Biotechnology, Shanghai, China). The relative interest mRNA expression was normalized to GAPDH using the ΔΔCt method. The primer sequences are: TYK2 forward primer GAGATGCAAGCCTGATGCTAT, reverse primer GGTTCCCGAGGATTCATGCC; GAPDH forward primer AGAAGGCTGGGGCTCATTTG, reverse primer GGGGCCATCCACAGTCTTC.
Literature review and data acquisition
To identify published cases on TYK2 deficiency, we conducted a systematic literature search in PubMed and Web of Science (WoS) databases. We searched the case reports published in English from 2006 to April 2024 using the following search terms: “TYK2 deficiency” or “TYK2 mutation”. We retrieved a total of 34 English literatures. After screening of titles and abstracts, 12 repetitive and 3 irrelevant ones were excluded. Then, we checked reference lists of retrieved articles for additional relevant reports. Finally, 42 relevant cases including our patient were included for this review.
Results
Case presentation
History
A 27-year-old Chinese man was admitted to our hospital in 2021 due to recurrent cough, phlegm, and purulent sputum for over 20 years. In 2011, the patient was diagnosed with tuberculosis because of pulmonary nodules and received anti-tuberculosis treatment for 7 months. During the next several years, he was hospitalized several times for coughing, exercise-induced dyspnea, skin erythema nodules, and fever. The patient had received multiple rounds of anti-infective and anti-tuberculosis treatments; however, the response was suboptimal. In 2021, the patient was referred to our hospital again due to cough, phlegm, and purulent sputum. The family history of the patient was not contributory.
Physical examination
After admission, physical examination revealed that the patient had an anemic appearance and cachexia. There were erythema nodosum and enlarged superficial lymph nodes. The lung auscultation found decreased bilateral breath sound and a lot of moist rales (crackles). Besides, we found shifting dullness indicating the presence of ascites. The remainder of the examination was normal.
Laboratory findings
These data were collected after the patient was hospitalized. Blood routine examination revealed the WBC count of 10.9 × 109/L and the Hb value of 86 g/L. Urine and fecal routine examination showed no abnormalities. Biochemical routine test showed the albumin level was 30.2 to 34.6 g/L. Increased erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) and procalcitonin (PCT). His immunological evaluations and lymphocytes subsets (TBNK) were normal. Lung CT scan revealed bronchiectasis with concurrent infection (Figure 1). No bacterial growth was found in multiple pathological examinations of the bronchial biopsy sample. However, NGS of the lung tissue suggested infection of Mycobacterium gordonae and Mycobacterium chelonae. Metagenomic next-generation sequencing (mNGS) of blood detected the presence of Epstein-Barr virus (EBV). Other examinations were normal.

Lung CT findings of the patient. (a–f) The Lung CT scan revealed thickening of the bronchial walls, multiple scattered ground-glass nodules, and strip opacities within the lungs.
Gene mutation screening
We investigated the TYK2 gene mutation of the patient and his parents by NGS and Sanger sequencing. Results showed that the patient carried the heterozygous c.997G>A&c.10C>T (p.V333M& p.R4C) mutation in TYK2, which were respectively inherited from his mother and father (Figure 2).

The heterozygous mutations in exon7 and exon3 of the TYK2 gene in the patient. We identified the TYK2 gene mutation of the patient and his parents by NGS and Sanger sequencing. (a) The heterozygous TYK2 c.997G>A mutation that was inherited from his mother. (b) The heterozygous TYK2 c.10C>T mutation that was inherited from his father. (c) Pedigree of a family in our patient.
We also performed pathogenicity prediction analysis for the gene mutations. The c.10C>T (p.R4C) variant exhibited consistent deleterious predictions (Polyphen2 HDIV = 0.468, FATHMM-XF = 0.522963, M-CAP = 0.063591), high evolutionary conservation (GERP++ RS = 4.63, phyloP100way vertebrate = 4.287), and extreme rarity in gnomAD v4.1 joint data (AF = 0.00000309783). Similarly, the c.997G>A (p.V333M) variant was predicted as damaging (M-CAP = 0.02964), with elevated conservation scores (GERP++ RS = 2.28, phyloP100way vertebrate = 2.377) and an extremely low population frequency in gnomAD v4.1 joint data (AF = 0.0000782522).
Gene expression in vivo
We detected the TYK2 mRNA expression of the patient-derived peripheral blood mononuclear cells (PBMCs) by qRT-PCR. Unsurprisingly, compared with healthy control, the expression of TYK2 significantly decreased in the patient (Figure 3). This result revealed that the patient displayed defective TYK2 mRNA expression caused by gene mutation.

The mRNA expression of TYK2 in PBMCs from our patient.
Literature review
The first TYK2-deficient patient (P1) was reported in 2006, which showed infections with intracellular bacteria and viruses, atopic dermatitis-like skin inflammation, and a high amount of serum IgE. 8 In recent years, with the progress of immunology and gene detection technology, cases of TYK2 deficiency have been reported continuously. So far, including our patient, there were 42 patients reported with TYK2 deficiency caused by gene mutation. The clinical features and genetic information of 42 patients are shown in Table 1.
Clinical and genetic characteristics of 42 patients with TYK2 deficiency.
BCG, Bacillus Calmette-Guerin; HSV, herpes simplex virus; PIV3, human parainfluenza virus type 3; VZV, varicella-zoster virus; EBV, Epstein-Barr virus; RSV, respiratory syncytial virus; MMR, Measles, Mumps, and Rubella; COVID-19, Corona Virus Disease 2019; CMV, Cytomegalovirus; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
Of all 42 cases, 25 (60%) patients were male. All patients were under 40 years old. And juvenile patients aged less than 18 years were 31 (74%). All patients had recurrent infections. Mycobacterial infections were found in 27 (64%) cases, including 12 cases of mycobacterium tuberculosis, 11 cases of BCG, and 4 cases of non-tuberculous mycobacteria infection (Mycobacterium avium complex, Mycobacterium intracellulare, Mycobacterium fortuitum, Mycobacterium gordonae, and Mycobacterium chelonae). Viral infections were identified in 22 (52%) patients. There were 7 (17%) patients with fungal infections, most commonly Candida, and 6 (14%) patients had other infections. In addition, a small proportion of patients had signs of eczema or atopic dermatitis. In all 24 reported mutation sites, P1104A mutation was found in 10 patients (42%), all of whom suffered with mycobacterial infections (7 with M. tuberculosis, 2 with BCG, and 1 with M. avium complex). This result shows that P1104A may be an important reminder of mycobacterial infections in TYK2-deficient patients.
Unsurprisingly, the role of TYK2 mutations in various diseases has also attracted significant attention in recent years. For instance, Motegi et al. identified the rs201917359 variant (TYK2Arg231Trp) as a gain-of-function mutation in the Japanese population, which could enhance TYK2 signaling and contribute to the pathogenesis of Rheumatoid Arthritis. 21 Similarly, in a newly report by Yang et al., the TYK2 gene mutations (rs2304256, rs280519, and rs12720270) may be associated with a reduced risk of microscopic polyangiitis (MPA) in the male population in Guangxi, China. 22 Moreover, genome-wide association studies (GWAS) have found that loss-of-function mutations in TYK2 were associated with a reduced risk of immune diseases including multiple sclerosis, inflammatory bowel disease, ankylosing spondylitis, and psoriasis. 23 Beyond autoimmune and inflammatory conditions, TYK2 mutations have been found in various cancers. In 2013, the first TYK2 GOF point mutations were found in T-cell acute lymphoblastic leukemia (T-ALL) cell lines 24 ; two GOF TYK2 germline mutations (p.Pro760Leu and p.Gly761Val) were found in pediatric patients with primary acute lymphoblastic leukemia. 25 These reports underscored the diverse impact of TYK2 mutations on disease susceptibility and hinted at the potential of TYK2 as a therapeutic target across multiple conditions.
Discussion
We identified a novel heterozygous TYK2 mutation (c.997G>A&c.10C>T) in a patient with recurrent lung infections. Subsequently, we performed pathogenicity prediction of the mutation site through bioinformatics analysis and found that the mutation exhibited potential pathogenicity. Furthermore, we isolated PBMCs from the patient and used RT-qPCR to demonstrate a significant decrease in TYK2 mRNA. To the best of our knowledge, this heterozygous mutation of TYK2 has not been previously reported.
Firstly, the patient reported in this study had the same young age of onset as the previously reported cases. It hints that a younger age of onset is one of the clinical features of TYK2 deficiency. Based on this characteristic, it is important to distinguish TYK2 deficiency from other PID with similar young onset features, such as severe combined immunodeficiency (SCID) and X-linked agammaglobulinemia.26,27 Given the unique immunological profiles and clinical implications of these disorders, recognizing the distinctions among them is crucial for accurate diagnosis and tailored treatment strategies.
Except common tuberculous mycobacteria, our patient was also infected with non-tuberculous mycobacteria, a condition previously reported in 3 other patients (P13, P24, and P28).18,28,29 Analysis of all cases revealed that the most common symptom of TYK2 deficiency is susceptibility to opportunistic pathogens, especially intracellular bacteria like mycobacteria. TYK2 deficiency significantly contributes to impaired immune responses in mycobacterial infections.28,30 It has been reported that TYK2 mutation can weaken Natural Killer (NK) cell and T cell responses to IL-12 and IL-23 and lead to insufficient IFN-γ production, thereby increasing susceptibility to mycobacteria.31–33 Furthermore, the common pathogenic TYK2 variant (P1104A) has been proven to be associated with mycobacterial infections.18,34 As for the potential association between the c.997G>A & c.10C>T mutation and mycobacterial infection, it requires further experimental validation and additional case studies for confirmation in future, which is a limitation of this study. In a word, when encountering young patients with recurrent mycobacterium infections in clinical practice, we should consider the possibility of TYK2 deficiency and conduct genetic testing promptly.
It is also worth noting that BCG-related mycobacterial infections were found in 11 patients, as shown in Table 1. These patients quickly developed BCG-related adverse reactions following vaccination in infancy. Most of them showed lymphadenitis that was the main adverse event after BCG vaccination. 35 A smaller subset (only four patients) displayed more severe disseminated BCG disease. According to reported literature, disseminated BCG disease can be more pronounced in individuals with primary immunodeficiencies, leading to complications such as uncontrolled mycobacterial replication and a high incidence of fatal outcomes.36–38 Therefore, infants who quickly develop infections or severe disseminated BCG disease after vaccination should be vigilant for PID like TYK2 deficiency.
Our patient did not exhibit a high level of IgE or atopic dermatitis, which were reported in the first TYK2 deficiency case with Hyper IgE syndrome (HIES). 8 Apart from the initial case, these HIES-related phenotypes were also observed in P9 (eczema and highly elevated IgE) and P26 (allergic dermatitis).14,39 Researchers found impaired IL-6-mediated STAT3 phosphorylation in P1, but not in other reported patients.8,14,31 It was also observed that response to IL-6 was independent of TYK2. And studies have revealed that abnormalities in the IL-6 pathway can lead to elevated IgE levels and atopic dermatitis. 40 Therefore, those HIES-phenotype may not be associated with TYK2 but rather with other undetected mutations affecting IL-6 signaling. Overall, the underlying reasons and mechanisms of these phenotypes remain undetermined and require further study.
Based on reported cases of TYK2 deficiency, we summarize the main characteristics of TYK2 deficiency as follows: (A) TYK2 gene mutation and autosomal recessive inheritance; (B) young age of onset; (C) susceptibility to opportunistic pathogens, especially intracellular bacteria; (D) prone to adverse reactions following BCG vaccination. Therefore, in young patients suffering from recurrent mycobacterial or other opportunistic pathogen infections, congenital immunodeficiency diseases, including TYK2 deficiency, should be considered.
Conclusion
In this study, we identified a new patient with TYK2 mutation. The pathogenic mutation of c.997G>A& c.10C>T (p.V333M&p.R4C) in the TYK2 gene is novel, which enlarges the mutation spectrum of the TKY2 gene. Also, we analyzed the clinical manifestations and genetic information of previously reported cases to enhance understanding of the clinical characteristics of TYK2 deficiency and to promote the early diagnosis of this rare disease.
Footnotes
Acknowledgements
None.
Author Contributions
LX and HW collected the data. XH contributed to verification experiment. XG conducted the bioinformatics analysis. LX wrote the draft of the manuscript. JF conducted the study. RH conducted the study and edited the manuscript. All authors contributed to the article and approved the submitted version.
Data Availability
All datasets presented in the study are included in the article.
Declaration of conflicting interests
The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
Funding
The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by the Natural Science Foundation of Hunan Province (Grant numbers: 2023JJ30882).
Ethics Approval
This study was performed in line with the principles of the Declaration of Helsinki. Approval was granted by the Ethics Committee of Xiangya Hospital, Central South University (No: 202103133).
Informed consent
Written informed consent was obtained from all subjects before the study.
Consent to Participate
The human research participants in Xiangya Hospital provided written informed consent to participate in the study.
Consent to Publication
The authors affirm that the participants provided written informed consent for the publication of any potentially identifiable images or data included in this article.
Trial registration
Not applicable.
