Clinical Characteristics of PIK3R1 (APDS2) patients
Our clinical studies identified 4 Chinese APDS2 patients from 4 unrelated families. The clinical features of the 4 subjects are shown in Table 1. All patients experienced recurrent respiratory tract infections and lymphadenopathy, and lymph node biopsy revealed a high proliferation of lymphocytes. Lymphadenopathy was especially observed in cervical, mediastinal, intrathoracic, coeliac, and inguinal lymph nodes. Three subjects progressed to pneumonia, and growth retardation was found in two patients.
Furthermore, septic arthritis was diagnosed in three patients with a single knee joint. Three patients had persistent or recurrent splenomegaly or hepatomegaly. Persistent or recurrent EBV viraemia was detected in two patients. In addition, one patient exhibited cardiac anomalies, demonstrating tetralogy of Fallot.
Immunological profile of four PIK3R1 (APDS2) patients
We summarized the immune cells and immunoglobulin profiles of all four subjects in Table 2. Generally, they all had decreased IgG and IgA levels at the time of diagnosis. Reduced IgM levels were observed in two patients, while the other patients presented with higher IgM levels. All patients had normal IgE.
All patients showed decreased B lymphocytes, especially memory B cells. In contrast, they had an increased proportion of transitional B lymphocytes, which indicated an impairment of B-cell maturation. Most of our patients had a decreased number of naïve CD4+ T lymphocytes and CD8+ T lymphocytes but increased central memory CD4+ T cells and cytotoxic CD8+ T cells. Other CD4+ and CD8+ subsets were not consistently changed in all four patients. Given that PIK3R1 patients are characterized by inflammatory arthritis, elevated erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP), we evaluated the regulatory T cells (Tregs) of two patients (P1, P2). The percentage of Treg cells among total CD4+ T cells was 1.9% in P1 and 4% in P2, which was lower than that of age-matched healthy controls (Supplementary Fig. 1).
Genetic analysis of PIK3R1 (APDS2)
Genetic variations were analysed and confirmed by WES. In addition to PIK3R1 gene mutations, there were no other pathogenic gene mutations. All of these mutations were de novo (Fig. 1A). Three of 4 patients, P1, P2, and P4, carried the previously described mutation c.1425 + 1G > A on the PIK3R1 gene [3, 7], and patient P3 had the mutation c.1425 + 2T > G [11], resulting in skipping of exon 11 (Fig. 1B).
T-cell activation and the expression of T-cell exhaustion markers are not changed in APDS2 patients
Previous studies confirmed that PIK3CD patients exhibit upregulation of the immunosuppressive molecule PD-1 and reduced proliferative capacity of CD8+ T cells, which indicates an exhaustion phenotype[15]. We investigated whether PIK3R1 patients have similar characteristics.
We examined T-cell activation marker CD69 and interleukin (IL)-2 secretion after mitogen ConA stimulation and found slightly reduced CD69 in P1 and P2 compared with healthy controls (Fig. 2A). There was no difference in the effector cytokine IL-2 between P1 and healthy control. Moreover, P1 cells exhibited even higher TNF-α secretion than control T cells (Fig. 2B). In addition, we evaluated the T-cell exhaustion marker PD-1, T-cell immunoglobulin domain and mucin domain-3 (Tim-3), and TCF-1 in PIK3R1 patients (P1, P2). Nevertheless, PD-1 and Tim-3 expression were equal between APDS2 patients and healthy controls in both CD4+ T (Fig. 2C) and CD8+ T cells (Fig. 2D).
LOF mutation in PIK3R1 downregulated TCF-1 expression through a PI3K-AKT-Foxo1 signalling axis
Hyperactivated PI3K enhances downstream AKT phosphorylation, which activates mTOR and Foxo1/3 to promote cell growth, proliferation, and survival [1, 3, 7, 27]. We detected the phosphorylation of AKT (pAKT S473) and total Foxo1 in PBMCs from P1 and healthy control. The AKT phosphorylation (pAKT S473) was increased (Fig. 3A) and total Foxo1 expression was decreased in P1 compared with healthy control (Fig. 3B). Foxo1 is the upstream regulator of TCF-1 [12]. We found normal TCF-1 expression in CD4+ T cells (Fig. 3C) but reduced TCF-1 in CD8+ T cells from PIK3R1 patients (Fig. 3D). Consistent with the protein expression level, TCF-1 transcription in CD8+ T cells of P1 and P2 was lower than that in the healthy controls (Fig. 3E). Therefore, we speculated that the aberrant PI3K-AKT-Foxo1 pathway may deregulate TCF-1 expression in CD8+ T cells.
The expression of the T-cell senescence marker CD57 was increased on CD8+ T lymphocytes but not on CD4+ T lymphocytes in PIK3R1 patients (P1, P2, P3) compared with healthy controls (Fig. 3F), which suggested that PIK3R1 mutations resulted in CD8+ T-cell senescence specifically. Furthermore, CD57 expression in T cells negatively correlated with TCF-1 expression. In healthy controls (Fig. 3G), P1 and P2 (Fig. 3H), the expression of CD57 in TCF-1low CD8+ T cells was higher than that in TCF-1hi CD8+ T cells. This finding indicates that CD57 expression is tightly correlated with TCF-1 expression. Further assessment of TCF-1 expression in CD8+ T-cell subsets of healthy controls revealed that TCF-1 expression was higher in naïve CD8+ and CD8+ TCM cells but lower in CD8+ effector memory T cells (TEM) and terminal effector memory cytotoxic T cells (TEMRA) (Fig. 3I). There was no significant difference in TCF-1 expression in CD8 + T-cell subsets between patients (P1 and P2) and healthy controls (Fig. 3J). Contrary to TCF-1, CD57 expression was lower in naïve CD8 and CD8+ TCM cells but higher in CD8+ TEM and CD8+ TEMRA cells of healthy controls (Fig. 3K). CD57 expression in CD8+ T-cell subsets exhibited no difference between P1, P2 and healthy controls (Fig. 3L).
Efficacy of Treatment
To prevent recurrent infections, the APDS2 patients received anti-infection prophylaxis and immunoglobulin replacement therapy due to hypogammaglobulinemia and decreased B lymphocytes. Two patients (P1 and P2) received mTOR inhibitor rapamycin treatment at 1 mg/m2 once daily. Both patients exhibited benefits. After rapamycin treatment, the patients presented with a reduced sinopulmonary infection frequency and decreased cervical lymph node size. The infection frequency in P1 was reduced from 2–3 times a month to once in 3–4 months, and for P2, it was reduced from once every six months to once a year. The total B-cell counts were not increased in treated PIK3R1 patients (P1, P2) (Fig. 4A), and the cell counts of whole T cells (Fig. 4B) and the inversion of the CD4/CD8 T-cell ratio (Fig. 4C) were not improved. Naïve T cells were not significantly increased in P2 but were slightly increased in P1 after treatment (Fig. 4D, Fig. 4E). Moreover, the proportion of CD8+ TCM cells increased at both P1 and P2 (Fig. 4F), and CD8+ TEM (Fig. 4G) and CD8 + TEMRA (Fig. 4H) decreased at P1, especially at 15 months. P2 exhibited decreased CD8+ TCM within four months of rapamycin treatment. Meanwhile, the proportion of senescent CD8+ CD57+ T cells was reduced in both treated patients (Fig. 4I). Consistent with the clinical and immunological improvements, the expression of TCF-1 in patients’ cells increased after rapamycin treatment (Fig. 4J). Furthermore, we found reduced phosphorylation of AKT (pAKT S473) (Fig. 4K) after rapamycin treatment at P1. We observed the same effects when cells were treated with a PI3K α/δ inhibitor. Increased Foxo1 and TCF-1 expression and decreased phosphorylation of AKT (pAKT S473) were observed after PI3K α/δ inhibitor treatment in T cells at P1 (Fig. 4L).