| Literature DB >> 30899265 |
Yi Miao1,2,3, Hua-Yuan Zhu1,2,3, Chun Qiao1,2,3, Yi Xia1,2,3, Yiling Kong1,2,3, Yi-Xin Zou1,2,3, Yu-Qing Miao1,2,3, Xiao Chen1,2,3, Lei Cao1,2,3, Wei Wu1,2,3, Jin-Hua Liang1,2,3, Jia-Zhu Wu1,2,3, Li Wang1,2,3, Lei Fan1,2,3, Wei Xu1,2,3, Jian-Yong Li1,2,3.
Abstract
Hemophagocytic lymphohistiocytosis (HLH) can be classified into primary HLH and secondary HLH. Primary HLH usually occurs in infants and children with an underlying genetic defect, and there are also teens and occasional adults with primary HLH. Most cases with secondary HLH are adult patients with secondary triggers including infections, malignancies, and autoimmune diseases. The distinction between primary HLH and secondary HLH seems to be less straightforward, as patients with secondary HLH may also have genetic defects while primary HLH can be triggered by secondary causes. In this study, using amplicon-based targeted gene sequencing (TGS), we sequenced eighteen HLH-related genes in 112 adult HLH cases, which were mostly secondary HLH. Mutations or rare variants were identified in 48 cases (42.9%). All the variants except one were missense variants, and biallelic gene mutations were identified in 3 cases in which only one case harbored homogenous missense mutation. Recurrent variants including UNC13D p.G863D and AP3B1 p.T359A are much more prevalent in our cohort than in normal East Asian population, and in silico analysis predicted pathogenicity of these variants. In conclusion, according to our study, genetic defects may also contribute to the development of adult HLH cases or secondary HLH cases.Entities:
Keywords: AP3B1; ITK; LYST; PRF1; UNC13D; hemophagocytic lymphohistiocytosis; mutation; targeted gene sequencing
Year: 2019 PMID: 30899265 PMCID: PMC6416222 DOI: 10.3389/fimmu.2019.00395
Source DB: PubMed Journal: Front Immunol ISSN: 1664-3224 Impact factor: 7.561
Genes included in targeted sequencing panel.
| AP3B1 | 5q14.1 | 43 | Hermansky-Pudlak syndrome type 2 |
| ARF6 | 14q21.3 | 4 | Involved in cytotoxic granule secretion |
| CD27 | 12p13.31 | 11 | EBV infection including EBV-associated lymphoproliferative disease/hemophagocytic lymphohistiocytosis |
| CORO1A | 16p11.2 | 13 | EBV-associated B-cell lymphoproliferation |
| CTPS1 | 1p34.2 | 19 | Immunodeficiency associated with EBV infection |
| GNLY | 2p11.2 | 7 | Co-localizing with perforin in the lytic granules of cytotoxic T and NK cells |
| GZMB | 14q12 | 8 | Co-localizing with perforin in the lytic granules of cytotoxic T and NK cells |
| ITK | 5q33.3 | 20 | Inducible T-cell kinase deficiency |
| LAMP1 | 13q34 | 14 | Endosomal/lysosomal pathway |
| LYST | 1q42.3 | 103 | Chediak-Higashi syndrome |
| PRF1 | 10q22.1 | 12 | Familial hemophagocytic lymphohistiocytosis type 2 |
| RAB27A | 15q21.3 | 5 | Griscelli syndrome type 2 |
| SH2D1A | Xq25 | 5 | X-linked lymphoproliferative disease type 1 |
| SRGN | 10q22.1 | 4 | Binding to granzyme B and involved in the granule mediated apoptosis |
| STX11 | 6q24.2 | 5 | Familial hemophagocytic lymphohistiocytosis type 4 |
| STXBP2 | 19p13.2 | 30 | Familial hemophagocytic lymphohistiocytosis type 5 |
| UNC13D | 17q25.1 | 40 | Familial hemophagocytic lymphohistiocytosis type 3 |
| XIAP | Xq25 | 13 | X-linked lymphoproliferative disease type 2 |
Figure 1The numbers of cases with each mutated gene in our cohort.
Summary of variants detected in our cohort.
| AP3B1 p.Q891X | NM_003664 | 1 | Not pathogenic | NA | Pathogenic | 0 | – | NA | No |
| AP3B1 p.T359A | NM_003664 | 3 | Pathogenic | Possibly pathogenic | Pathogenic | 0.0002 | 0.0001997 | ( | No |
| CORO1A p.A88T | NM_007074 | 1 | Not pathogenic | Pathogenic | Pathogenic | – | – | NA | No |
| CORO1A p.R199H | NM_007074 | 1 | Pathogenic | Not pathogenic | Polymorphism | – | – | NA | No |
| CORO1A:p.L235V | NM_007074 | 1 | Not pathogenic | Not pathogenic | Pathogenic | – | – | NA | No |
| CORO1A:p.P277R | NM_007074 | 1 | Pathogenic | Not pathogenic | Pathogenic | – | – | NA | No |
| CTPS1 p.K460R | NM_001905 | 1 | Not pathogenic | Not pathogenic | Pathogenic | 0.0005 | 0.0003994 | NA | No |
| CTPS1 p.M283V | NM_001905 | 1 | Not pathogenic | Not pathogenic | Pathogenic | 0.0005 | – | NA | No |
| GNLY:p.H35D | NM_006433 | 1 | Not pathogenic | Not pathogenic | Polymorphism | 0.0003 | 0.000399 | NA | No |
| GZMB p.R120Q | NM_006433 | 1 | Not pathogenic | Not pathogenic | Polymorphism | 0 | 0.0003994 | NA | No |
| ITK p.R581W | NM_005546 | 4 | Pathogenic | Pathogenic | Pathogenic | 0.0081 | 0.0009984 | ( | Conditions: lymphoproliferative syndrome 1, lymphoproliferative syndrome; clinical significance: conflicting interpretations of pathogenicity |
| LAMP1 p.P196L | NM_005561 | 1 | Pathogenic | Pathogenic | Polymorphism | – | – | NA | No |
| LYST p.D2665G | NM_000081 | 1 | Not pathogenic | Possibly pathogenic | Pathogenic | 0.0009 | 0.0009984 | NA | No |
| LYST p.E1036A | NM_000081 | 1 | Not pathogenic | Not pathogenic | Polymorphism | 0.0008 | 0.0001997 | NA | No |
| LYST p.H123R | NM_000081 | 2 | Not pathogenic | Possibly pathogenic | Polymorphism | 0.0095 | 0.0021965 | ( | Conditions: Chédiak-Higashi syndrome, not specified; clinical significance: conflicting interpretations of pathogenicity |
| LYST p.H151R | NM_000081 | 1 | Pathogenic | Pathogenic | Pathogenic | 0.0009 | 0.0003994 | ( | No |
| LYST p.I724M | NM_000081 | 1 | Not pathogenic | Possibly pathogenic | Polymorphism | 0.0006 | – | NA | No |
| LYST p.K3626N | NM_000081 | 1 | Not pathogenic | Pathogenic | Pathogenic | – | – | NA | No |
| LYST p.M1860V | NM_000081 | 1 | Pathogenic | Not pathogenic | Pathogenic | – | – | NA | No |
| PRF1 p.A196P | NM_001083116 | 1 | Pathogenic | Pathogenic | Pathogenic | – | – | NA | No |
| PRF1 p.R33H | NM_001083116 | 1 | Pathogenic | Not pathogenic | Polymorphism | 0.0002 | 0.0001997 | ( | No |
| PRF1 p.R4C | NM_001083116 | 1 | Not pathogenic | Not pathogenic | Polymorphism | 0.008 | 0.0027955 | ( | Conditions: aplastic anemia, hemophagocytic lymphohistiocytosis, familial, 2, familial hemophagocytic lymphohistiocytosis, not specified, not provided; clinical significance: conflicting interpretations of pathogenicity |
| RAB27A p.T85M | NM_004580 | 1 | Pathogenic | Pathogenic | Pathogenic | 0.0001 | – | NA | No |
| STX11 p.F281C | NM_003764 | 2 | Not pathogenic | Not pathogenic | Polymorphism | 0.0001 | 0.0001997 | NA | No |
| STXBP2 p.G270W | NM_006949 | 1 | Pathogenic | Pathogenic | Pathogenic | 0.0005 | 0.0003994 | NA | No |
| STXBP2 p.P391L | NM_006949 | 1 | Pathogenic | Pathogenic | Pathogenic | – | – | NA | No |
| STXBP2 p.R192H | NM_006949 | 1 | Pathogenic | Pathogenic | Pathogenic | – | – | ( | No |
| STXBP2 p.R465C | NM_006949 | 1 | Pathogenic | Pathogenic | Pathogenic | 0 | 0.0001997 | NA | Condition: familial hemophagocytic lymphohistiocytosis type 5; clinical significance: uncertain significance |
| STXBP2 p.T166M | NM_006949 | 4 | Not pathogenic | Not pathogenic | Polymorphism | 0.0076 | 0.0025959 | ( | Condition: not specified; clinical significance: Likely benign |
| STXBP2 p.T318M | NM_006949 | 1 | Not pathogenic | Pathogenic | Pathogenic | 0.005 | 0.0011981 | ( | No |
| UNC13D p.A2V | NM_199242 | 1 | Pathogenic | Possibly pathogenic | Polymorphism | 0 | – | NA | No |
| UNC13D p.E57K | NM_199242 | 1 | Not pathogenic | Not pathogenic | Polymorphism | 0 | – | NA | |
| UNC13D p.G863D | NM_199242 | 4 | Pathogenic | Pathogenic | Pathogenic | 0.0043 | 0.0013978 | ( | Condition: hemophagocytic lymphohistiocytosis, familial, 3; clinical significance: uncertain significance |
| UNC13D p.R266P | NM_199242 | 1 | Pathogenic | Pathogenic | Pathogenic | – | – | NA | No |
| UNC13D p.R411Q | NM_199242 | 2 | Not pathogenic | Possibly pathogenic | Pathogenic | 0.008 | 0.0007987 | ( | No |
| UNC13D p.R427Q | NM_199242 | 1 | Not pathogenic | Pathogenic | Pathogenic | 0.0003 | 0.0001997 | ( | No |
| UNC13D p.T1045M | NM_199242 | 1 | Not pathogenic | Possibly pathogenic | Pathogenic | 0 | 0.0001997 | ( | No |
| UNC13D p.V1037M | NM_199242 | 1 | Not pathogenic | Possibly pathogenic | Pathogenic | – | – | NA | No |
| XIAP p.A321G | NM_001167 | 1 | Pathogenic | Pathogenic | Pathogenic | 0.0046 | 0.0007947 | NA | No |
From the ExAC database. “–”indicated no data; NA, not available.
Figure 2Mutations in UNC13D, LYST, STXBP2, ITK, and AP3B1.
Figure 3(A) the numbers of cases with mutations according to underlying causes; (B) the impact of presence of mutations on short-term survival; (C,D) the impact of homozygous/compound heterozygous mutations or double heterozygous mutations on short-term survival; (E) the short term survival of patients with pathogenic variants, patients with benign variants and patients with variants of uncertain significance.
Mutation rate of UNC13D, STXBP2, LYST, ITK, CORO1A, and AP3B1 in different groups.
| UNC13D | 10/66 (15.2%) | 0/23 (0%) | 2/19 (10.5%) | 0/4 (0%) | 0.2036 |
| STXBP2 | 6/66 (9.1%) | 1/23 (4.3%) | 2/19 (10.5%) | 0/4 (0%) | 0.7936 |
| LYST | 2/66 (3.0%) | 3/23 (13.0%) | 3/19 (15.8%) | 0/4 (0%) | 0.1485 |
| ITK | 1/66 (1.5%) | 2/23 (8.7%) | 1/19 (5.3%) | 0/4 (0%) | 0.4241 |
| CORO1A | 2/66 (3.0%) | 1/23 (4.3%) | 0/19 (0%) | 0/4 (0%) | 0.8230 |
| AP3B1 | 3/66 (4.5%) | 0/23 (0%) | 0/19 (0%) | 1/4 (25.0%) | 0.0697 |
| At least one of UNC13D, STXBP2, LYST, or AP3B1 | 21/66 | 4/23 (17.4%) | 7/19 (36.8%) | 1/4 (25.0%) | |
| (31.8%) | 0.5077 |