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Leimi L, Koski JR, Kilpivaara O, Vettenranta K, Lokki AI, Meri S. Rare variants in complement system genes associate with endothelial damage after pediatric allogeneic hematopoietic stem cell transplantation. Front Immunol 2023; 14:1249958. [PMID: 37771589 PMCID: PMC10525714 DOI: 10.3389/fimmu.2023.1249958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
Introduction Complement system has a postulated role in endothelial problems after hematopoietic stem cell transplantation (HSCT). In this retrospective, singlecenter study we studied genetic complement system variants in patients with documented endotheliopathy. In our previous study among pediatric patients with an allogeneic HSCT (2001-2013) at the Helsinki University Children´s Hospital, Finland, we identified a total of 19/122 (15.6%) patients with vascular complications, fulfilling the criteria of capillary leak syndrome (CLS), venoocclusive disease/sinusoidal obstruction syndrome (VOD/SOS) or thrombotic microangiopathy (TMA). Methods We performed whole exome sequencing (WES) on 109 patients having an adequate pre-transplantation DNA for the analysis to define possible variations and mutations potentially predisposing to functional abnormalities of the complement system. In our data analysis, we focused on 41 genes coding for complement components. Results 50 patients (45.9%) had one or several, nonsynonymous, rare germline variants in complement genes. 21/66 (31.8%) of the variants were in the terminal pathway. Patients with endotheliopathy had variants in different complement genes: in the terminal pathway (C6 and C9), lectin pathway (MASP1) and receptor ITGAM (CD11b, part of CR3). Four had the same rare missense variant (rs183125896; Thr279Ala) in the C9 gene. Two of these patients were diagnosed with endotheliopathy and one with capillary leak syndrome-like problems. The C9 variant Thr279Ala has no previously known disease associations and is classified by the ACMG guidelines as a variant of uncertain significance (VUS). We conducted a gene burden test with gnomAD Finnish (fin) as the reference population. Complement gene variants seen in our patient population were investigated and Total Frequency Testing (TFT) was used for execution of burden tests. The gene variants seen in our patients with endotheliopathy were all significantly (FDR < 0.05) enriched compared to gnomAD. Overall, 14/25 genes coding for components of the complement system had an increased burden of missense variants among the patients when compared to the gnomAD Finnish population (N=10 816). Discussion Injury to the vascular endothelium is relatively common after HSCT with different phenotypic appearances suggesting yet unidentified underlying mechanisms. Variants in complement components may be related to endotheliopathy and poor prognosis in these patients.
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Affiliation(s)
- Lilli Leimi
- Pediatric Research Center, Children’s Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Jessica R. Koski
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Kim Vettenranta
- Pediatric Research Center, Children’s Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - A. Inkeri Lokki
- Department of Bacteriology and Immunology and Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Seppo Meri
- Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- Department of Bacteriology and Immunology and Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
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Hakkarainen M, Koski JR, Heckman CA, Anttila P, Silvennoinen R, Lievonen J, Kilpivaara O, Wartiovaara‐Kautto U. A germline exome analysis reveals harmful POT1 variants in multiple myeloma patients and families. EJHaem 2022; 3:1352-1357. [PMID: 36467798 PMCID: PMC9713058 DOI: 10.1002/jha2.557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 06/17/2023]
Abstract
Observations of inherited susceptibility to multiple myeloma have led to active research in defining predisposing genes to the disease. Here, we analysed 128 plasma cell dyscrasia patients' germline whole-exome sequencing data. Rare dominantly inherited pathogenic or likely pathogenic (P/LP) variant was found in 9.4% of the patients. Among the P/LP variants, CHEK2 (p. Thr410MetfsTer15) was the most prevalent (n = 5, 3.9%). Interestingly, P/LP variants in POT1 were identified in three patients (2.3%). Our findings broaden the spectrum of POT1-related cancers and demonstrate the importance of the germline genetic analysis in hematological malignancies.
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Affiliation(s)
- Marja Hakkarainen
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Medical and Clinical Genetics/Medium, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of HematologyHelsinki University Hospital Comprehensive Cancer Center, University of HelsinkiHelsinkiFinland
| | - Jessica R. Koski
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Medical and Clinical Genetics/Medium, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Caroline A. Heckman
- Institute for Molecular Medicine Finland ‐ FIMM, HiLIFE ‐ Helsinki institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipUniversity of HelsinkiHelsinkiFinland
| | - Pekka Anttila
- Department of HematologyHelsinki University Hospital Comprehensive Cancer Center, University of HelsinkiHelsinkiFinland
| | - Raija Silvennoinen
- Department of HematologyHelsinki University Hospital Comprehensive Cancer Center, University of HelsinkiHelsinkiFinland
| | - Juha Lievonen
- Department of HematologyHelsinki University Hospital Comprehensive Cancer Center, University of HelsinkiHelsinkiFinland
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Medical and Clinical Genetics/Medium, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipUniversity of HelsinkiHelsinkiFinland
- HUS Diagnostic Center (Helsinki University Hospital), HUSLAB Laboratory of GeneticsHelsinkiFinland
| | - Ulla Wartiovaara‐Kautto
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of HematologyHelsinki University Hospital Comprehensive Cancer Center, University of HelsinkiHelsinkiFinland
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Douglas SPM, Lahtinen AK, Koski JR, Leimi L, Keränen MAI, Koskenvuo M, Heckman CA, Jahnukainen K, Pitkänen E, Wartiovaara-Kautto U, Kilpivaara O. Enrichment of cancer-predisposing germline variants in adult and pediatric patients with acute lymphoblastic leukemia. Sci Rep 2022; 12:10670. [PMID: 35739278 PMCID: PMC9225984 DOI: 10.1038/s41598-022-14364-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/06/2022] [Indexed: 11/10/2022] Open
Abstract
Despite recent progress in acute lymphoblastic leukemia (ALL) therapies, a significant subset of adult and pediatric ALL patients has a dismal prognosis. Better understanding of leukemogenesis and recognition of germline genetic changes may provide new tools for treating patients. Given that hematopoietic stem cell transplantation, often from a family member, is a major form of treatment in ALL, acknowledging the possibility of hereditary predisposition is of special importance. Reports of comprehensive germline analyses performed in adult ALL patients are scarce. Aiming at fulfilling this gap of knowledge, we investigated variants in 93 genes predisposing to hematologic malignancies and 70 other cancer-predisposing genes from exome data obtained from 61 adult and 87 pediatric ALL patients. Our results show that pathogenic (P) or likely pathogenic (LP) germline variants in genes associated with predisposition to ALL or other cancers are prevalent in ALL patients: 8% of adults and 11% of children. Comparison of P/LP germline variants in patients to population-matched controls (gnomAD Finns) revealed a 2.6-fold enrichment in ALL cases (CI 95% 1.5–4.2, p = 0.00071). Acknowledging inherited factors is crucial, especially when considering hematopoietic stem cell transplantation and planning post-therapy follow-up. Harmful germline variants may also predispose patients to excessive toxicity potentially compromising the outcome. We propose integrating germline genetics into precise ALL patient care and providing families genetic counseling.
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Affiliation(s)
- Suvi P M Douglas
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Atte K Lahtinen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jessica R Koski
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lilli Leimi
- Children's Hospital, and Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mikko A I Keränen
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, University of Helsinki, Helsinki, Finland
| | - Minna Koskenvuo
- Division of Hematology-Oncology and Stem Cell Transplantation, New Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Kirsi Jahnukainen
- Children's Hospital, and Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Women's and Children's Health, Karolinska Institutet and University Hospital, Solna, Sweden
| | - Esa Pitkänen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Ulla Wartiovaara-Kautto
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland.
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,HUSLAB Laboratory of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland.
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