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Gracheva AS, Kashatnikova DA, Redkin IV, Zakharchenko VE, Kuzovlev AN, Salnikova LE. Genetics and Traumatic Brain Injury: Findings from an Exome-Based Study of a 50-Patient Case Series. Curr Issues Mol Biol 2024; 46:10351-10368. [PMID: 39329968 PMCID: PMC11430351 DOI: 10.3390/cimb46090616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 09/14/2024] [Accepted: 09/16/2024] [Indexed: 09/28/2024] Open
Abstract
Traumatic brain injury (TBI) is the leading cause of global mortality and morbidity. Because TBI is accident-related, the role of genetics in predisposing to TBI has been largely unexplored. However, the likelihood of injury may not be entirely random and may be associated with certain physical and mental characteristics. In this study, we analyzed the exomes of 50 patients undergoing rehabilitation after TBI. Patients were divided into three groups according to rehabilitation outcome: improvement, no change, and deterioration/death. We focused on rare, potentially functional missense and high-impact variants in genes intolerant to these variants. The concordant results from the three independent groups of patients allowed for the suggestion of the existence of a genetic predisposition to TBI, associated with rare functional variations in intolerant genes, with a prevalent dominant mode of inheritance and neurological manifestations in the genetic phenotypes according to the OMIM database. Forty-four of the 50 patients had one or more rare, potentially deleterious variants in one or more neurological genes. Comparison of these results with those of a 50-sampled matched non-TBI cohort revealed significant differences: P = 2.6 × 10-3, OR = 4.89 (1.77-13.47). There were no differences in the distribution of the genes of interest between the TBI patient groups. Our exploratory study provides new insights into the impact of genetics on TBI risk and is the first to address potential genetic susceptibility to TBI.
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Affiliation(s)
- Alesya S Gracheva
- The Department of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Darya A Kashatnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- The Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Ivan V Redkin
- The Laboratory of Organoprotection in Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Vladislav E Zakharchenko
- The Department of Clinical Laboratory Diagnostics, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Artem N Kuzovlev
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
| | - Lyubov E Salnikova
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- The Laboratory of Molecular Immunology, National Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
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2
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Liu X, Pang Y, Shan J, Wang Y, Zheng Y, Xue Y, Zhou X, Wang W, Sun Y, Yan X, Shi J, Wang X, Gu H, Zhang F. Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies. Brief Bioinform 2024; 25:bbae440. [PMID: 39256199 PMCID: PMC11387064 DOI: 10.1093/bib/bbae440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/28/2024] [Accepted: 08/21/2024] [Indexed: 09/12/2024] Open
Abstract
Deoxyribonucleic acid (DNA) methylation plays a key role in gene regulation and is critical for development and human disease. Techniques such as whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) allow DNA methylation analysis at the genome scale, with Illumina NovaSeq 6000 and MGI Tech DNBSEQ-T7 being popular due to their efficiency and affordability. However, detailed comparative studies of their performance are not available. In this study, we constructed 60 WGBS and RRBS libraries for two platforms using different types of clinical samples and generated approximately 2.8 terabases of sequencing data. We systematically compared quality control metrics, genomic coverage, CpG methylation levels, intra- and interplatform correlations, and performance in detecting differentially methylated positions. Our results revealed that the DNBSEQ platform exhibited better raw read quality, although base quality recalibration indicated potential overestimation of base quality. The DNBSEQ platform also showed lower sequencing depth and less coverage uniformity in GC-rich regions than did the NovaSeq platform and tended to enrich methylated regions. Overall, both platforms demonstrated robust intra- and interplatform reproducibility for RRBS and WGBS, with NovaSeq performing better for WGBS, highlighting the importance of considering these factors when selecting a platform for bisulfite sequencing.
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Affiliation(s)
- Xin Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Junqi Shan
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Yunfei Wang
- Hangzhou ShengTing Biotech Co. Ltd, Hangzhou, Zhejiang Province 310018, China
| | - Yanhua Zheng
- Department of Hematology, The First Hospital of China Medical University, Shenyang, Liaoning, Shenyang, Liaoning province 110001, China
| | - Yuhang Xue
- Department of Hematology, The First Hospital of China Medical University, Shenyang, Liaoning, Shenyang, Liaoning province 110001, China
| | - Xuerong Zhou
- Department of Hematology, The First Hospital of China Medical University, Shenyang, Liaoning, Shenyang, Liaoning province 110001, China
| | - Wenjun Wang
- Hangzhou ShengTing Biotech Co. Ltd, Hangzhou, Zhejiang Province 310018, China
| | - Yanlai Sun
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Xiaojing Yan
- Department of Hematology, The First Hospital of China Medical University, Shenyang, Liaoning, Shenyang, Liaoning province 110001, China
| | - Jiantao Shi
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoxue Wang
- Department of Hematology, The First Hospital of China Medical University, Shenyang, Liaoning, Shenyang, Liaoning province 110001, China
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
| | - Fan Zhang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
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3
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Danilov SM, Adzhubei IA, Kozuch AJ, Petukhov PA, Popova IA, Choudhury A, Sengupta D, Dudek SM. Carriers of Heterozygous Loss-of-Function ACE Mutations Are at Risk for Alzheimer's Disease. Biomedicines 2024; 12:162. [PMID: 38255267 PMCID: PMC10813023 DOI: 10.3390/biomedicines12010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
We hypothesized that subjects with heterozygous loss-of-function (LoF) ACE mutations are at risk for Alzheimer's disease because amyloid Aβ42, a primary component of the protein aggregates that accumulate in the brains of AD patients, is cleaved by ACE (angiotensin I-converting enzyme). Thus, decreased ACE activity in the brain, either due to genetic mutation or the effects of ACE inhibitors, could be a risk factor for AD. To explore this hypothesis in the current study, existing SNP databases were analyzed for LoF ACE mutations using four predicting tools, including PolyPhen-2, and compared with the topology of known ACE mutations already associated with AD. The combined frequency of >400 of these LoF-damaging ACE mutations in the general population is quite significant-up to 5%-comparable to the frequency of AD in the population > 70 y.o., which indicates that the contribution of low ACE in the development of AD could be under appreciated. Our analysis suggests several mechanisms by which ACE mutations may be associated with Alzheimer's disease. Systematic analysis of blood ACE levels in patients with all ACE mutations is likely to have clinical significance because available sequencing data will help detect persons with increased risk of late-onset Alzheimer's disease. Patients with transport-deficient ACE mutations (about 20% of damaging ACE mutations) may benefit from preventive or therapeutic treatment with a combination of chemical and pharmacological (e.g., centrally acting ACE inhibitors) chaperones and proteosome inhibitors to restore impaired surface ACE expression, as was shown previously by our group for another transport-deficient ACE mutation-Q1069R.
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Affiliation(s)
- Sergei M. Danilov
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois Chicago, Chicago, IL 60612, USA; (A.J.K.); (S.M.D.)
| | - Ivan A. Adzhubei
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA;
| | - Alexander J. Kozuch
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois Chicago, Chicago, IL 60612, USA; (A.J.K.); (S.M.D.)
| | - Pavel A. Petukhov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL 60612, USA;
| | - Isolda A. Popova
- Toxicology Research Laboratory, University of Illinois Chicago, IL 60612, USA;
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg 2193, South Africa; (A.C.); (D.S.)
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg 2193, South Africa; (A.C.); (D.S.)
| | - Steven M. Dudek
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois Chicago, Chicago, IL 60612, USA; (A.J.K.); (S.M.D.)
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Buianova AA, Proskura MV, Cheranev VV, Belova VA, Shmitko AO, Pavlova AS, Vasiliadis IA, Suchalko ON, Rebrikov DV, Petrosyan EK, Korostin DO. Candidate Genes for IgA Nephropathy in Pediatric Patients: Exome-Wide Association Study. Int J Mol Sci 2023; 24:15984. [PMID: 37958966 PMCID: PMC10647220 DOI: 10.3390/ijms242115984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
IgA nephropathy (IgAN) is an autoimmune disorder which is believed to be non-monogenic. We performed an exome-wide association study of 70 children with IgAN and 637 healthy donors. The HLA allele frequencies were compared between the patients and healthy donors from the bone marrow registry of the Pirogov University. We tested 78,020 gene markers for association and performed functional enrichment analysis and transcription factor binding preference detection. We identified 333 genetic variants, employing three inheritance models. The most significant association with the disorder was observed for rs143409664 (PRAG1) in the case of the additive and dominant models (PBONF = 1.808 × 10-15 and PBONF = 1.654 × 10-15, respectively), and for rs13028230 (UBR3) in the case of the recessive model (PBONF = 1.545 × 10-9). Enrichment analysis indicated the strongly overrepresented "immune system" and "kidney development" terms. The HLA-DQA1*01:01:01G allele (p = 0.0076; OR, 2.021 [95% CI, 1.322-3.048]) was significantly the most frequent among IgAN patients. Here, we characterized, for the first time, the genetic background of Russian IgAN patients, identifying the risk alleles typical of the population. The most important signals were detected in previously undescribed loci.
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Affiliation(s)
- Anastasiia A. Buianova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Mariia V. Proskura
- Nephrology Department, Russian Children’s Clinical Hospital, Leninsky Prospect 117, 119571 Moscow, Russia; (M.V.P.); (E.K.P.)
| | - Valery V. Cheranev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Vera A. Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Anna O. Shmitko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Anna S. Pavlova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Iuliia A. Vasiliadis
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Oleg N. Suchalko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Denis V. Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Edita K. Petrosyan
- Nephrology Department, Russian Children’s Clinical Hospital, Leninsky Prospect 117, 119571 Moscow, Russia; (M.V.P.); (E.K.P.)
| | - Dmitriy O. Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
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5
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Belova V, Shmitko A, Pavlova A, Afasizhev R, Cheranev V, Tabanakova A, Ponikarovskaya N, Rebrikov D, Korostin D. Performance comparison of Agilent new SureSelect All Exon v8 probes with v7 probes for exome sequencing. BMC Genomics 2022; 23:582. [PMID: 35962321 PMCID: PMC9375261 DOI: 10.1186/s12864-022-08825-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
Exome sequencing is becoming a routine in health care, because it increases the chance of pinpointing the genetic cause of an individual patient's condition and thus making an accurate diagnosis. It is important for facilities providing genetic services to keep track of changes in the technology of exome capture in order to maximize throughput while reducing cost per sample. In this study, we focused on comparing the newly released exome probe set Agilent SureSelect Human All Exon v8 and the previous probe set v7. In preparation for higher throughput of exome sequencing using the DNBSEQ-G400, we evaluated target design, coverage statistics, and variants across these two different exome capture products. Although the target size of the v8 design has not changed much compared to the v7 design (35.24 Mb vs 35.8 Mb), the v8 probe design allows you to call more of SNVs (+ 3.06%) and indels (+ 8.49%) with the same number of raw reads per sample on the common target regions (34.84 Mb). Our results suggest that the new Agilent v8 probe set for exome sequencing yields better data quality than the current Agilent v7 set.
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Affiliation(s)
- Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation.
| | - Anna Shmitko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Anna Pavlova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Robert Afasizhev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Valery Cheranev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Anastasia Tabanakova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Natalya Ponikarovskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Denis Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Dmitriy Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
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Tan M, Wang X, Liu H, Peng X, Yang Y, Yu H, Xu L, Li J, Cao H. Genetic Diagnostic Yield and Novel Causal Genes of Congenital Heart Disease. Front Genet 2022; 13:941364. [PMID: 35910219 PMCID: PMC9326225 DOI: 10.3389/fgene.2022.941364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Congenital heart disease (CHD) is the most common congenital malformation in fetuses and neonates, which also represents a leading cause of mortality. Although significant progress has been made by emerging advanced technologies in genetic etiology diagnosis, the causative genetic mechanisms behind CHD remain poorly understood and more than half of CHD patients lack a genetic diagnosis. Unlike carefully designed large case-control cohorts by multicenter trials, we designed a reliable strategy to analyze case-only cohorts to utilize clinical samples sufficiently. Combined low-coverage whole-genome sequencing (WGS) and whole-exome sequencing (WES) were simultaneously conducted in a patient-only cohort for identifying genetic etiologies and exploring candidate, or potential causative CHD-related genes. A total of 121 sporadic CHD patients were recruited and 34.71% (95% CI, 26.80 to 43.56) was diagnosed with genetic etiologies by low-coverage WGS and WES. Chromosomal abnormalities and damaging variants of CHD-related genes could explain 24.79% (95% CI, 17.92 to 33.22) and 18.18% (95% CI, 12.26 to 26.06) of CHD patients, separately, and 8.26% (95% CI, 4.39 to 14.70) of them have simultaneously detected two types of variants. Deletion of chromosome 22q11.2 and pathogenic variants of the COL3A1 gene were the most common recurrent variants of chromosomal abnormalities and gene variants, respectively. By in-depth manual interpretation, we identified eight candidate CHD-causing genes. Based on rare disease-causing variants prediction and interaction analysis with definitive CHD association genes, we proposed 86 genes as potential CHD-related genes. Gene Ontology (GO) enrichment analysis of the 86 genes revealed regulation-related processes were significantly enriched and processes response to regulation of muscle adaptation might be one of the underlying molecular mechanisms of CHD. Our findings and results provide new insights into research strategies and underlying mechanisms of CHD.
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Affiliation(s)
- Meihua Tan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Genomics Co., Ltd, Shenzhen, China
| | - Xinrui Wang
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Hongjie Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyan Peng
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - You Yang
- BGI Genomics Co., Ltd, Shenzhen, China
| | - Haifei Yu
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Fuzhou, China
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Affiliated Hospital of Fujian Medical University, Fujian Maternity and Child Health Hospital, Fuzhou, China
- *Correspondence: Liangpu Xu, ; Jia Li, ; Hua Cao,
| | - Jia Li
- BGI Genomics Co., Ltd, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang BGI Genomics Co., Ltd, Shijiazhuang, China
- *Correspondence: Liangpu Xu, ; Jia Li, ; Hua Cao,
| | - Hua Cao
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- *Correspondence: Liangpu Xu, ; Jia Li, ; Hua Cao,
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7
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Semchenkova A, Mikhailova E, Komkov A, Gaskova M, Abasov R, Matveev E, Kazanov M, Mamedov I, Shmitko A, Belova V, Miroshnichenkova A, Illarionova O, Olshanskaya Y, Tsaur G, Verzhbitskaya T, Ponomareva N, Bronin G, Kondratchik K, Fechina L, Diakonova Y, Vavilova L, Myakova N, Novichkova G, Maschan A, Maschan M, Zerkalenkova E, Popov A. Lineage Conversion in Pediatric B-Cell Precursor Acute Leukemia under Blinatumomab Therapy. Int J Mol Sci 2022; 23:4019. [PMID: 35409391 PMCID: PMC8999738 DOI: 10.3390/ijms23074019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/24/2022] [Accepted: 04/02/2022] [Indexed: 12/28/2022] Open
Abstract
We report incidence and deep molecular characteristics of lineage switch in 182 pediatric patients affected by B-cell precursor acute lymphoblastic leukemia (BCP-ALL), who were treated with blinatumomab. We documented six cases of lineage switch that occurred after or during blinatumomab exposure. Therefore, lineage conversion was found in 17.4% of all resistance cases (4/27) and 3.2% of relapses (2/63). Half of patients switched completely from BCP-ALL to CD19-negative acute myeloid leukemia, others retained CD19-positive B-blasts and acquired an additional CD19-negative blast population: myeloid or unclassifiable. Five patients had KMT2A gene rearrangements; one had TCF3::ZNF384 translocation. The presented cases showed consistency of gene rearrangements and fusion transcripts across initially diagnosed leukemia and lineage switch. In two of six patients, the clonal architecture assessed by IG/TR gene rearrangements was stable, while in others, loss of clones or gain of new clones was noted. KMT2A-r patients demonstrated very few additional mutations, while in the TCF3::ZNF384 case, lineage switch was accompanied by a large set of additional mutations. The immunophenotype of an existing leukemia sometimes changes via different mechanisms and with different additional molecular changes. Careful investigation of all BM compartments together with all molecular -minimal residual disease studies can lead to reliable identification of lineage switch.
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Affiliation(s)
- Alexandra Semchenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Ekaterina Mikhailova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Alexander Komkov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117998 Moscow, Russia
| | - Marina Gaskova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Ruslan Abasov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Evgenii Matveev
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Institute for Information Transmission Problems (the Kharkevich Institute, RAS), 127051 Moscow, Russia
| | - Marat Kazanov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Institute for Information Transmission Problems (the Kharkevich Institute, RAS), 127051 Moscow, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Ilgar Mamedov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117998 Moscow, Russia
| | - Anna Shmitko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 119334 Moscow, Russia; (A.S.); (V.B.)
| | - Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 119334 Moscow, Russia; (A.S.); (V.B.)
| | - Anna Miroshnichenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Olga Illarionova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Grigory Tsaur
- Regional Clinical Children Hospital, 620149 Ekaterinburg, Russia; (G.T.); (T.V.); (L.F.)
- Research Institute of Medical Cell Technologies, 620026 Ekaterinburg, Russia
| | - Tatiana Verzhbitskaya
- Regional Clinical Children Hospital, 620149 Ekaterinburg, Russia; (G.T.); (T.V.); (L.F.)
- Research Institute of Medical Cell Technologies, 620026 Ekaterinburg, Russia
| | | | - Gleb Bronin
- Morozov City Children Clinical Hospital, 119049 Moscow, Russia; (G.B.); (K.K.)
| | | | - Larisa Fechina
- Regional Clinical Children Hospital, 620149 Ekaterinburg, Russia; (G.T.); (T.V.); (L.F.)
- Research Institute of Medical Cell Technologies, 620026 Ekaterinburg, Russia
| | - Yulia Diakonova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Liudmila Vavilova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Natalia Myakova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Alexey Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Michael Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Elena Zerkalenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
| | - Alexander Popov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117998 Moscow, Russia; (A.S.); (E.M.); (A.K.); (M.G.); (R.A.); (E.M.); (M.K.); (I.M.); (A.M.); (O.I.); (Y.O.); (Y.D.); (L.V.); (N.M.); (G.N.); (A.M.); (M.M.); (E.Z.)
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