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Li H, Zhou Y, Zhao N, Wang Y, Lai Y, Zeng F, Yang F. ISMI-VAE: A deep learning model for classifying disease cells using gene expression and SNV data. Comput Biol Med 2024; 175:108485. [PMID: 38653063 DOI: 10.1016/j.compbiomed.2024.108485] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/03/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Various studies have linked several diseases, including cancer and COVID-19, to single nucleotide variations (SNV). Although single-cell RNA sequencing (scRNA-seq) technology can provide SNV and gene expression data, few studies have integrated and analyzed these multimodal data. To address this issue, we introduce Interpretable Single-cell Multimodal Data Integration Based on Variational Autoencoder (ISMI-VAE). ISMI-VAE leverages latent variable models that utilize the characteristics of SNV and gene expression data to overcome high noise levels and uses deep learning techniques to integrate multimodal information, map them to a low-dimensional space, and classify disease cells. Moreover, ISMI-VAE introduces an attention mechanism to reflect feature importance and analyze genetic features that could potentially cause disease. Experimental results on three cancer data sets and one COVID-19 data set demonstrate that ISMI-VAE surpasses the baseline method in terms of both effectiveness and interpretability and can effectively identify disease-causing gene features.
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Affiliation(s)
- Han Li
- Department of Automation, Xiamen University, Xiamen, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China; Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision Making, Xiamen university, Xiamen, 361000, China
| | - Yitao Zhou
- Department of Automation, Xiamen University, Xiamen, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China; Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision Making, Xiamen university, Xiamen, 361000, China
| | - Ningyuan Zhao
- Department of Automation, Xiamen University, Xiamen, China
| | - Ying Wang
- Department of Automation, Xiamen University, Xiamen, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China; Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision Making, Xiamen university, Xiamen, 361000, China
| | - Yongxuan Lai
- School of Informatics, Xiamen University, Xiamen, China
| | - Feng Zeng
- Department of Automation, Xiamen University, Xiamen, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China; Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision Making, Xiamen university, Xiamen, 361000, China; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, China; Research Unit of Cellular Stress of CAMS, Cancer Research Center, School of Medicine, Xiamen University, China.
| | - Fan Yang
- Department of Automation, Xiamen University, Xiamen, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China; Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision Making, Xiamen university, Xiamen, 361000, China.
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Seeger N, Gutknecht S, Zschokke I, Fleischmann I, Roth N, Metzger J, Weber M, Breitenstein S, Grochola LF. A Predictive Noninvasive Single-Nucleotide Variation-Based Biomarker Signature for Resectable Pancreatic Cancer: Protocol for a Prospective Validation Study. JMIR Res Protoc 2024; 13:e54042. [PMID: 38635586 DOI: 10.2196/54042] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/24/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Single-nucleotide variations (SNVs; formerly SNPs) are inherited genetic variants that can be easily determined in routine clinical practice using a simple blood or saliva test. SNVs have potential to serve as noninvasive biomarkers for predicting cancer-specific patient outcomes after resection of pancreatic ductal adenocarcinoma (PDAC). Two recent analyses led to the identification and validation of three SNVs in the CD44 and CHI3L2 genes (rs187115, rs353630, and rs684559), which can be used as predictive biomarkers to help select patients most likely to benefit from pancreatic resection. These variants were associated with an over 2-fold increased risk for tumor-related death in three independent PDAC study cohorts from Europe and the United States, including The Cancer Genome Atlas cohorts (reaching a P value of 1×10-8). However, these analyses were limited by the inherent biases of a retrospective study design, such as selection and publication biases, thereby limiting the clinical use of these promising biomarkers in guiding PDAC therapy. OBJECTIVE To overcome the limitations of previous retrospectively designed studies and translate the findings into clinical practice, we aim to validate the association of the identified SNVs with survival in a controlled setting using a prospective cohort of patients with PDAC following pancreatic resection. METHODS All patients with PDAC who will undergo pancreatic resection at three participating hospitals in Switzerland and fulfill the inclusion criteria will be included in the study consecutively. The SNV genotypes will be determined using standard genotyping techniques from patient blood samples. For each genotyped locus, log-rank and Cox multivariate regression tests will be performed, accounting for the relevant covariates American Joint Committee on Cancer stage and resection status. Clinical follow-up data will be collected for at least 3 years. Sample size calculation resulted in a required sample of 150 patients to sufficiently power the analysis. RESULTS The follow-up data collection started in August 2019 and the estimated end of data collection will be in May 2027. The study is still recruiting participants and 142 patients have been recruited as of November 2023. The DNA extraction and genotyping of the SNVs will be performed after inclusion of the last patient. Since no SNV genotypes have been determined, no data analysis has been performed to date. The results are expected to be published in 2027. CONCLUSIONS This is the first prospective study of the CD44 and CHI3L2 SNV-based biomarker signature in PDAC. A prospective validation of this signature would enable its clinical use as a noninvasive predictive biomarker of survival after pancreatic resection that is readily available at the time of diagnosis and can assist in guiding PDAC therapy. The results of this study may help to individualize treatment decisions and potentially improve patient outcomes. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/54042.
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Affiliation(s)
- Nico Seeger
- Department of Visceral and Thoracic Surgery, Cantonal Hospital of Winterthur, Winterthur, Switzerland
| | - Stefan Gutknecht
- Department of Visceral, Thoracic and Cardiovascular Surgery, Triemli Hospital, Zurich, Switzerland
| | - Irin Zschokke
- Department of General and Visceral Surgery, Cantonal Hospital of Lucerne, Lucerne, Switzerland
| | - Isabella Fleischmann
- Department of General and Visceral Surgery, Cantonal Hospital of Lucerne, Lucerne, Switzerland
| | - Nadja Roth
- Department of General and Visceral Surgery, Cantonal Hospital of Lucerne, Lucerne, Switzerland
| | - Jürg Metzger
- Department of General and Visceral Surgery, Cantonal Hospital of Lucerne, Lucerne, Switzerland
| | - Markus Weber
- Department of Visceral, Thoracic and Cardiovascular Surgery, Triemli Hospital, Zurich, Switzerland
| | - Stefan Breitenstein
- Department of Visceral and Thoracic Surgery, Cantonal Hospital of Winterthur, Winterthur, Switzerland
| | - Lukasz Filip Grochola
- Department of Visceral and Thoracic Surgery, Cantonal Hospital of Winterthur, Winterthur, Switzerland
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Chang X, Qu H, Liu Y, Glessner J, Hakonarson H. A Protective Role of Low Polygenic Risk Score in Healthy Individuals Carrying Attention-Deficit/Hyperactivity Disorder-Associated Copy Number Variations. Biol Psychiatry 2024; 95:881-887. [PMID: 37865391 DOI: 10.1016/j.biopsych.2023.10.011] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Previous studies have implicated both rare copy number variations (CNVs) and common variants in liability for attention-deficit/hyperactivity disorder (ADHD). However, how common and rare genetic variants jointly contribute to individual liability requires further investigation in larger cohorts. METHODS This study comprises 9385 participants of European descent and 7810 participants of African American ancestry who were recruited from the greater Philadelphia area by the Children's Hospital of Philadelphia. The polygenic risk score (PRS) of each participant was estimated by linkage disequilibrium pruning and p-value thresholding (P + T) methods using PRSice-2. We investigated whether the risk of ADHD follows a polygenic liability threshold model wherein 1) the risk of ADHD requires less contribution from common variants in the presence of a rare CNV, and 2) control carriers of ADHD-associated CNVs have lower common risk allele burden than noncarriers. RESULTS CNVs previously reported in ADHD cases were significantly associated with ADHD risk in both the European American cohort and the African American cohort. Healthy control participants carrying those same risk CNVs had lower PRSs than those without risk CNVs in the European American cohort. This result was replicated in the African American cohort. However, PRSs were not significantly different in case participants carrying risk CNVs versus those without risk CNVs. CONCLUSIONS These findings provide evidence in support of interactive effects of PRS and ADHD-associated CNVs on disease risk and add novel insights into the genetic basis of ADHD by highlighting a protective role of low PRS in ADHD.
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Affiliation(s)
- Xiao Chang
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong, China; Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
| | - Huiqi Qu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yichuan Liu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Joseph Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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Costanzi JM, Stosic MS, Løvestad AH, Ambur OH, Rounge TB, Christiansen IK. Changes in intrahost genetic diversity according to lesion severity in longitudinal HPV16 samples. J Med Virol 2024; 96:e29641. [PMID: 38708811 DOI: 10.1002/jmv.29641] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/07/2024]
Abstract
Human papillomavirus type 16 (HPV16) is the most common cause of cervical cancer, but most infections are transient with lesions not progressing to cancer. There is a lack of specific biomarkers for early cancer risk stratification. This study aimed to explore the intrahost HPV16 genomic variation in longitudinal samples from HPV16-infected women with different cervical lesion severity (normal, low-grade, and high-grade). The TaME-seq deep sequencing protocol was used to generate whole genome HPV16 sequences of 102 samples collected over time from 40 individuals. Single nucleotide variants (SNVs) and intrahost SNVs (iSNVs) were identified in the viral genomes. A majority of individuals had a unique set of SNVs and these SNVs were stable over time. Overall, the number of iSNVs and APOBEC3-induced iSNVs were significantly lower in high-grade relative to normal and low-grade samples. A significant increase in the number of APOBEC3-induced iSNVs over time was observed for normal samples when compared to high-grade. Our results indicates that the lower incidence of iSNVs and APOBEC3-induced iSNVs in high-grade lesions may have implications for novel biomarkers discoveries, potentially aiding early stratification of HPV-induced cervical precancerous lesions.
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Affiliation(s)
- Jean-Marc Costanzi
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Centre of Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Milan S Stosic
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Alexander H Løvestad
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, Oslo, Norway
- Clinical Molecular Biology (EpiGen), Akershus University Hospital Lørenskog, Norway and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ole H Ambur
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Trine B Rounge
- Centre of Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Irene K Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
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Deng X, Guo X, Chen X, Zeng X, Guo J, Bai X, Zhang P, Wang Y. ACE Gene Mutations (rs577350502) in Early-Onset and Recurrent Myocardial Infarction: A Case Report and Review. Pharmgenomics Pers Med 2024; 17:163-169. [PMID: 38659693 PMCID: PMC11042475 DOI: 10.2147/pgpm.s455740] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
Background Acute myocardial infarction (AMI) is a severe acute coronary syndrome, demonstrating a trend toward affecting younger individuals in recent years. The association between early-onset myocardial infarction and single nucleotide polymorphism necessitates further exploration and evaluation. Case description We present a case of a patient experiencing early-onset and recurrent myocardial infarction. The patient underwent stent implantation for myocardial infarction at the age of 53 and subsequently encountered two more myocardial infarctions within a span of 16 years. Following interventional therapy, genetic testing was conducted to assess the efficacy of subsequent anti-heart failure medications, with the aim to preemptively address heart failure risks. Genetic testing revealed a mutation in the angiotensin-converting enzyme (ACE) gene (rs577350502, g.63488533C>A), characterized by an intron-deletion single nucleotide variant. Conclusion While this variant has not been previously reported to be associated with any specific disease, we hypothesize that it may contribute to the susceptibility and risk of myocardial infarction and coronary heart disease in the patient under consideration. This observation underscores the significance of investigating the insertion/deletion polymorphisms of the ACE gene in the context of AMI and emphasizes the necessity for further validation of this variant and other genetic markers associated with AMI in related diseases.
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Affiliation(s)
- Xiaoxi Deng
- Department of Pathology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
| | - Xiaofei Guo
- Department of Pathology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
| | - Xiaojie Chen
- Department of Emergency, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
| | - Xinyu Zeng
- Department of Pathology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
| | - Jiamin Guo
- Department of Pathology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
| | - Xin Bai
- Department of Pathology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
| | - Ping Zhang
- Department of Pathology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
| | - Yuan Wang
- Department of Pathology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, People's Republic of China
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Chávez-Vélez E, Álvarez-Nava F, Torres-Vinueza A, Balarezo-Díaz T, Pilataxi K, Acosta-López C, Peña IZ, Narváez K. Single nucleotide variants in the CCL2, OAS1 and DPP9 genes and their association with the severity of COVID-19 in an Ecuadorian population. Front Cell Infect Microbiol 2024; 14:1322882. [PMID: 38694517 PMCID: PMC11061356 DOI: 10.3389/fcimb.2024.1322882] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/15/2024] [Indexed: 05/04/2024] Open
Abstract
COVID-19 has a broad clinical spectrum, ranging from asymptomatic-mild form to severe phenotype. The severity of COVID-19 is a complex trait influenced by various genetic and environmental factors. Ethnic differences have been observed in relation to COVID-19 severity during the pandemic. It is currently unknown whether genetic variations may contribute to the increased risk of severity observed in Latin-American individuals The aim of this study is to investigate the potential correlation between gene variants at CCL2, OAS1, and DPP9 genes and the severity of COVID-19 in a population from Quito, Ecuador. This observational case-control study was conducted at the Carrera de Biologia from the Universidad Central del Ecuador and the Hospital Quito Sur of the Instituto Ecuatoriano de Seguridad Social (Quito-SUR-IESS), Quito, Ecuador. Genotyping for gene variants at rs1024611 (A>G), rs10774671 (A>G), and rs10406145 (G>C) of CCL2, OAS1, and DPP9 genes was performed on 100 COVID-19 patients (43 with severe form and 57 asymptomatic-mild) using RFLP-PCR. The genotype distribution of all SNVs throughout the entire sample of 100 individuals showed Hardy Weinberg equilibrium (P=0.53, 0.35, and 0.4 for CCL2, OAS1, and DPP9, respectively). The HWE test did not find any statistically significant difference in genotype distribution between the study and control groups for any of the three SNVs. The multivariable logistic regression analysis showed that individuals with the GG of the CCL2 rs1024611 gene variant had an increased association with the severe COVID-19 phenotype in a recessive model (P = 0.0003, OR = 6.43, 95% CI 2.19-18.89) and for the OAS1 rs10774671 gene variant, the log-additive model showed a significant association with the severe phenotype of COVID-19 (P=0.0084, OR=3.85, 95% CI 1.33-11.12). Analysis of haplotype frequencies revealed that the coexistence of GAG at CCL2, OAS1, and DPP9 variants, respectively, in the same individual increased the presence of the severe COVID-19 phenotype (OR=2.273, 95% CI: 1.271-4.068, P=0.005305). The findings of the current study suggests that the ethnic background affects the allele and genotype frequencies of genes associated with the severity of COVID-19. The experience with COVID-19 has provided an opportunity to identify an ethnicity-based approach to recognize genetically high-risk individuals in different populations for emerging diseases.
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Affiliation(s)
- Erik Chávez-Vélez
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Francisco Álvarez-Nava
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Alisson Torres-Vinueza
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Thalía Balarezo-Díaz
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Kathya Pilataxi
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Camila Acosta-López
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Ivonne Z. Peña
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
| | - Katherin Narváez
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
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Xiao Z, Ying W, Xing Z, Zhihui L, Qiuyu Z, Caijiao H, Changlong L, Shi H, Deng L, Zhenwen C, Jianquan N, Xueyun H, Xiaoyan D. Unexpected mutations occurred in CRISPR/Cas9 edited Drosophila analyzed by deeply whole genomic sequencing. Heliyon 2024; 10:e29061. [PMID: 38596060 PMCID: PMC11002691 DOI: 10.1016/j.heliyon.2024.e29061] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
CRISPR/Cas9 possesses the most promising prospects as a gene-editing tool in post-genomic researches. It becomes an epoch-marking technique for the features of speed and convenience of genomic modification. However, it is still unclear whether CRISPR/Cas9 gene editing can cause irreversible damage to the genome. In this study, we successfully knocked out the WHITE gene in Drosophila, which governs eye color, utilizing CRISPR/Cas9 technology. Subsequently, we conducted high-throughput sequencing to assess the impact of this editing process on the stability of the entire genomic profile. The results revealed the presence of numerous unexpected mutations in the Drosophila genome, including 630 SNVs (Single Nucleotide Variants), 525 Indels (Insertion and Deletion) and 425 MSIs (microsatellite instability). Although the KO (knockout) specifically occurred on chromosome X, the majority of mutations were observed on chromosome 3, indicating that this effect is genome-wide and associated with the spatial structure between chromosomes, rather than being solely limited to the location of the KO gene. It is worth noting that most of the mutations occurred in the intergenic and intron regions, without exerting any significant on the function or healthy of the animal. In addition, the mutations downstream of the knockout gene well beyond the upstream. This study has found that gene editing can lead to unexpected mutations in the genome, but most of these mutations are harmless. This research has deepened our understanding of CRISPR/Cas9 and broadened its application prospects.
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Affiliation(s)
- Zhu Xiao
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Wu Ying
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Zhang Xing
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Li Zhihui
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Zhang Qiuyu
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Hu Caijiao
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Li Changlong
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Hanping Shi
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Li Deng
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Chen Zhenwen
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Ni Jianquan
- Gene Regulatory Laboratory, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Huo Xueyun
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| | - Du Xiaoyan
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
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Tóth ÁV, Bartók Á. Reviewing critical TRPM2 variants through a structure-function lens. J Biotechnol 2024; 385:49-57. [PMID: 38442841 DOI: 10.1016/j.jbiotec.2024.02.017] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
The transient receptor potential melastatin 2 (TRPM2) channel plays a central role in connecting redox state with calcium signaling in living cells. This coupling makes TRPM2 essential for physiological functions such as pancreatic insulin secretion or cytokine production, but also allows it to contribute to pathological processes, including neuronal cell death or ischemia-reperfusion injury. Genetic deletion of the channel, albeit not lethal, alters physiological functions in mice. In humans, population genetic studies and whole-exome sequencing have identified several common and rare genetic variants associated with mental disorders and neurodegenerative diseases, including single nucleotide variants (SNVs) in exonic regions. In this review, we summarize available information on the four best-documented SNVs: one common (rs1556314) and three rare genetic variants (rs139554968, rs35288229, and rs145947009), manifested in amino acid substitutions D543E, R707C, R755C, and P1018L respectively. We discuss existing evidence supporting or refuting the associations between SNVs and disease. Furthermore, we aim to interpret the molecular impacts of these amino acid substitutions based on recently published structures of human TRPM2. Finally, we formulate testable hypotheses and suggest means to investigate them. Studying the function of proteins with rare mutations might provide insight into disease etiology and delineate new drug targets.
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Affiliation(s)
- Ádám V Tóth
- Department of Biochemistry, Semmelweis University, 37-47 Tűzoltó street, Budapest 1094, Hungary; HCEMM-SE Molecular Channelopathies Research Group, 37-47 Tűzoltó street, Budapest 1094, Hungary; HUN-REN-SE Ion Channel Research Group, 37-47 Tűzoltó street, Budapest 1094, Hungary
| | - Ádám Bartók
- Department of Biochemistry, Semmelweis University, 37-47 Tűzoltó street, Budapest 1094, Hungary; HCEMM-SE Molecular Channelopathies Research Group, 37-47 Tűzoltó street, Budapest 1094, Hungary; HUN-REN-SE Ion Channel Research Group, 37-47 Tűzoltó street, Budapest 1094, Hungary.
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Torres-Espíndola LM, Pérez-De Marcos JC, Castillejos-López M, Velasco-Hidalgo L, Cárdenas-Cardós R, De Uña-Flores A, Salinas-Lara C, Caballero-Salazar S, Fernández-Plata R, Aquíno-Gálvez A. Factors Influencing Mortality in Children with Central Nervous System Tumors: A Cohort Study on Clinical Characteristics and Genetic Markers. Genes (Basel) 2024; 15:473. [PMID: 38674407 PMCID: PMC11050576 DOI: 10.3390/genes15040473] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Multidrug resistance (MDR) commonly leads to cancer treatment failure because cancer cells often expel chemotherapeutic drugs using ATP-binding cassette (ABC) transporters, which reduce drug levels within the cells. This study investigated the clinical characteristics and single nucleotide variant (SNV) in ABCB1, ABCC1, ABCC2, ABCC4, and ABCG2, and their association with mortality in pediatric patients with central nervous system tumors (CNST). Using TaqMan probes, a real-time polymerase chain reaction genotyped 15 SNPs in 111 samples. Patients were followed up until death or the last follow-up day using the Cox proportional hazards model. An association was found between the rs1045642 (ABCB1) in the recessive model (HR = 2.433, 95% CI 1.098-5.392, p = 0.029), and the ICE scheme in the codominant model (HR = 9.810, 95% CI 2.74-35.06, p ≤ 0.001), dominant model (HR = 6.807, 95% CI 2.87-16.103, p ≤ 0.001), and recessive model (HR = 6.903, 95% CI 2.915-16.544, p = 0.038) significantly increased mortality in this cohort of patients. An association was also observed between the variant rs3114020 (ABCG2) and mortality in the codominant model (HR = 5.35, 95% CI 1.83-15.39, p = 0.002) and the dominant model (HR = 4.421, 95% CI 1.747-11.185, p = 0.002). A significant association between the ICE treatment schedule and increased mortality risk in the codominant model (HR = 6.351, 95% CI 1.831-22.02, p = 0.004, HR = 9.571, 95% CI 2.856-32.07, p ≤ 0.001), dominant model (HR = 6.592, 95% CI 2.669-16.280, p ≤ 0.001), and recessive model (HR = 5.798, 95% CI 2.411-13.940, p ≤ 0.001). The genetic variants rs3114020 in the ABCG2 gene and rs1045642 in the ABCB1 gene and the ICE chemotherapy schedule were associated with an increased mortality risk in this cohort of pediatric patients with CNST.
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Affiliation(s)
| | - Juan Carlos Pérez-De Marcos
- Pharmacology Laboratory, National Institute of Pediatrics, Mexico City 04530, Mexico;
- Oncology Service, National Institute of Pediatrics, Mexico City 04530, Mexico; (L.V.-H.); (R.C.-C.)
- Red MEDICI, FESI UNAM, Tlalnepantla Edo, Mexico City 54090, Mexico
| | - Manuel Castillejos-López
- Hospital Epidemiology and Infectology Unit, National Institute of Respiratory Diseases Ismael Cosío Villegas, Mexico City 14080, Mexico; (M.C.-L.); (R.F.-P.)
| | - Liliana Velasco-Hidalgo
- Oncology Service, National Institute of Pediatrics, Mexico City 04530, Mexico; (L.V.-H.); (R.C.-C.)
| | - Rocío Cárdenas-Cardós
- Oncology Service, National Institute of Pediatrics, Mexico City 04530, Mexico; (L.V.-H.); (R.C.-C.)
| | - Armando De Uña-Flores
- Radiology and Imaging Service, National Institute of Pediatrics, Mexico City 04530, Mexico;
| | - Citlaltepetl Salinas-Lara
- Department of Neuropathology, National Institute of Neurology and Neurosurgery, Manuel Velasco Suárez, Mexico City 14269, Mexico;
| | | | - Rosario Fernández-Plata
- Hospital Epidemiology and Infectology Unit, National Institute of Respiratory Diseases Ismael Cosío Villegas, Mexico City 14080, Mexico; (M.C.-L.); (R.F.-P.)
| | - Arnoldo Aquíno-Gálvez
- Molecular Biology Laboratory, Pulmonary Fibrosis Department, National Institute of Respiratory Diseases Ismael Cosío Villegas, Mexico City 14080, Mexico
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10
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Wang D, Chen W, Wang Y, Yu J, Bai Y, Luo S, Song C, Wang M, Yu Y, Li Z, Han Y, Zhen Q, Sun L. Genome-Wide Meta-Analysis Identifies 11 Susceptibility Variants of Vitiligo in the Chinese Han Population. J Invest Dermatol 2024:S0022-202X(24)00081-2. [PMID: 38286188 DOI: 10.1016/j.jid.2024.01.010] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
Vitiligo is an autoimmune disease involving loss of melanocytes. Although several genetic studies have confirmed that genetic factors play an important role, its pathogenesis remains incompletely characterized. In this study, a genome-wide meta-analysis was conducted to search for more susceptibility variants of vitiligo. Tang et al performed a GWAS for cohort I (1117 vitiligo cases and 1701 healthy controls) previously, and we conducted a GWAS for cohort II (3323 vitiligo cases and 7186 healthy controls) in this study, with the results subjected to a genome-wide meta-analysis and linkage disequilibrium analysis. We identify, to our knowledge, 11 previously unreported susceptibility variants, of which 6 variants are located in the intronic regions, and the remaining 5 variants are located within intergenic regions between genes. In addition, the results of polygenic risk score show that the best evaluated effect for target data is among significant SNVs of the base data. The susceptibility genes of vitiligo are mainly enriched in the immune-related functions and pathways. The susceptibility variants expand the role of genetic factors associated with vitiligo. The bioinformatics analysis for risk genes provides further insight into the pathogenesis of vitiligo.
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Affiliation(s)
- Daiyue Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Weiwei Chen
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yirui Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Jing Yu
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yuanming Bai
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Sihan Luo
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Can Song
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Minhao Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yanxia Yu
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Zhuo Li
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yang Han
- Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China; School of Public Health, North China University of Science and Technology, Tangshan, China; Health Science Center, North China University of Science and Technology, Tangshan, China
| | - Qi Zhen
- Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China; School of Public Health, North China University of Science and Technology, Tangshan, China; Health Science Center, North China University of Science and Technology, Tangshan, China.
| | - Liangdan Sun
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China; School of Public Health, North China University of Science and Technology, Tangshan, China; Health Science Center, North China University of Science and Technology, Tangshan, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China; Inflammation and Immune Diseases Laboratory, North China University of Science and Technology, Tangshan, China.
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11
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Merzah M, Natae S, Sándor J, Fiatal S. Single Nucleotide Variants ( SNVs) of the Mesocorticolimbic System Associated with Cardiovascular Diseases and Type 2 Diabetes: A Systematic Review. Genes (Basel) 2024; 15:109. [PMID: 38254998 PMCID: PMC10815084 DOI: 10.3390/genes15010109] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The mesocorticolimbic (MCL) system is crucial in developing risky health behaviors which lead to cardiovascular diseases (CVDs) and type 2 diabetes (T2D). Although there is some knowledge of the MCL system genes linked to CVDs and T2D, a comprehensive list is lacking, underscoring the significance of this review. This systematic review followed PRISMA guidelines and the Cochrane Handbook for Systematic Reviews of Interventions. The PubMed and Web of Science databases were searched intensively for articles related to the MCL system, single nucleotide variants (SNVs, formerly single nucleotide polymorphisms, SNPs), CVDs, T2D, and associated risk factors. Included studies had to involve a genotype with at least one MCL system gene (with an identified SNV) for all participants and the analysis of its link to CVDs, T2D, or associated risk factors. The quality assessment of the included studies was performed using the Q-Genie tool. The VEP and DAVID tools were used to annotate and interpret genetic variants and identify enriched pathways and gene ontology terms associated with the gene list. The review identified 77 articles that met the inclusion criteria. These articles provided information on 174 SNVs related to the MCL system that were linked to CVDs, T2D, or associated risk factors. The COMT gene was found to be significantly related to hypertension, dyslipidemia, insulin resistance, obesity, and drug abuse, with rs4680 being the most commonly reported variant. This systematic review found a strong association between the MCL system and the risk of developing CVDs and T2D, suggesting that identifying genetic variations related to this system could help with disease prevention and treatment strategies.
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Affiliation(s)
- Mohammed Merzah
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (M.M.)
- Doctoral School of Health Sciences, University of Debrecen, 4032 Debrecen, Hungary
| | - Shewaye Natae
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (M.M.)
- Doctoral School of Health Sciences, University of Debrecen, 4032 Debrecen, Hungary
| | - János Sándor
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (M.M.)
- ELKH-DE Public Health Research Group, Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Szilvia Fiatal
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (M.M.)
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12
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Cooper SE, Coelho MA, Strauss ME, Gontarczyk AM, Wu Q, Garnett MJ, Marioni JC, Bassett AR. sc SNV-seq: high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics. Genome Biol 2024; 25:20. [PMID: 38225637 PMCID: PMC10789043 DOI: 10.1186/s13059-024-03169-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024] Open
Abstract
CRISPR screens with single-cell transcriptomic readouts are a valuable tool to understand the effect of genetic perturbations including single nucleotide variants (SNVs) associated with diseases. Interpretation of these data is currently limited as genotypes cannot be accurately inferred from guide RNA identity alone. scSNV-seq overcomes this limitation by coupling single-cell genotyping and transcriptomics of the same cells enabling accurate and high-throughput screening of SNVs. Analysis of variants across the JAK1 gene with scSNV-seq demonstrates the importance of determining the precise genetic perturbation and accurately classifies clinically observed missense variants into three functional categories: benign, loss of function, and separation of function.
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Affiliation(s)
- Sarah E Cooper
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthew A Coelho
- Translational Cancer Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Magdalena E Strauss
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Aleksander M Gontarczyk
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Qianxin Wu
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Mathew J Garnett
- Translational Cancer Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - John C Marioni
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Cellular Genetics, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Present Address: Genentech, South San Francisco, CA, USA
| | - Andrew R Bassett
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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13
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Cabello-Aguilar S, Vendrell JA, Solassol J. A Bioinformatics Toolkit for Next-Generation Sequencing in Clinical Oncology. Curr Issues Mol Biol 2023; 45:9737-9752. [PMID: 38132454 PMCID: PMC10741970 DOI: 10.3390/cimb45120608] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023] Open
Abstract
Next-generation sequencing (NGS) has taken on major importance in clinical oncology practice. With the advent of targeted therapies capable of effectively targeting specific genomic alterations in cancer patients, the development of bioinformatics processes has become crucial. Thus, bioinformatics pipelines play an essential role not only in the detection and in identification of molecular alterations obtained from NGS data but also in the analysis and interpretation of variants, making it possible to transform raw sequencing data into meaningful and clinically useful information. In this review, we aim to examine the multiple steps of a bioinformatics pipeline as used in current clinical practice, and we also provide an updated list of the necessary bioinformatics tools. This resource is intended to assist researchers and clinicians in their genetic data analyses, improving the precision and efficiency of these processes in clinical research and patient care.
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Affiliation(s)
- Simon Cabello-Aguilar
- Montpellier BioInformatics for Clinical Diagnosis (MOBIDIC), Molecular Medicine and Genomics Platform (PMMG), CHU Montpellier, 34295 Montpellier, France
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (J.A.V.); (J.S.)
| | - Julie A. Vendrell
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (J.A.V.); (J.S.)
| | - Jérôme Solassol
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (J.A.V.); (J.S.)
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14
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Boutros A, Carosio R, Campanella D, Spagnolo F, Banelli B, Morabito A, Pistillo M, Croce E, Cecchi F, Pronzato P, Queirolo P, Raposio E, Fontana V, Tanda E. The predictive and prognostic role of single nucleotide gene variants of PD-1 and PD-L1 in patients with advanced melanoma treated with PD-1 inhibitors. Immunooncol Technol 2023; 20:100408. [PMID: 38192613 PMCID: PMC10772261 DOI: 10.1016/j.iotech.2023.100408] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Background Despite having revolutionized the treatment paradigm for advanced melanoma, not all patients benefit from immune checkpoint inhibitor therapy. To date, there are no predictive biomarkers for response or the occurrence of immune-related adverse events (irAEs) to programmed cell death protein 1 (PD-1) inhibitors. Our aim was to investigate the predictive and prognostic role of single nucleotide variants (SNVs) of genes involved in the PD-1 axis. Methods We analysed, in metastatic melanoma patients treated with nivolumab or pembrolizumab, five PD-1 SNVs, namely PD1.3 G>A (rs11568821), PD1.5 C>T (rs2227981), PD1.6 G>A (rs10204525), PD1.7 T>C(rs7421861), PD1.10 C>G (rs5582977) and three programmed death-ligand 1 (PD-L1) SNVs: +8293 C>A (rs2890658), PD-L1 C>T (rs2297136) and PD-L1 G>C (rs4143815). Association of SNV genotypic frequencies with best overall response to PD-1 inhibitors and development of irAEs were estimated through a modified Poisson regression. A Cox regression modelling approach was applied to evaluate the SNV association with OS. Results A total of 125 patients with advanced melanoma were included in the analysis. A reduction in irAEs risk was observed in patients carrying the PD-L1 +8293 C/A genotype compared with those carrying the C/C genotype (risk ratio = 0.45; 95% CL 0.22-0.93; P = 0.031). A trend for a reduction in irAEs was also observed with the PD1.5 T allele (risk ratio = 0.70, 95% confidence limits 0.48-1.01 versus C allele). None of the SNVs was associated with response to therapy. Finally, a survival benefit was observed in patients harbouring the PD1.7 C/C genotype (hazard ratio = 0.37; 95% confidence limits 0.14-0.96; P = 0.028) in the homozygous model. Conclusions Our study showed that PD-1.5 and PD-L1 +8293 SNVs may play a role as a predictive biomarker of development of irAEs to PD-1 inhibitors. PD1.7 SNV may also be associated with a reduction of the risk of death, although further translational research is needed to confirm these results.
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Affiliation(s)
- A. Boutros
- Skin Cancer Unit, Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, Genoa
- Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genoa
| | - R. Carosio
- Tumor Epigenetics Unit, IRCCS Ospedale Policlinico San Martino, Genoa
| | - D. Campanella
- Clinical Epidemiology Unit, IRCCS Ospedale Policlinico San Martino, Genoa
| | - F. Spagnolo
- Skin Cancer Unit, Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, Genoa
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Plastic Surgery Division, University of Genova, Genoa
| | - B. Banelli
- Tumor Epigenetics Unit, IRCCS Ospedale Policlinico San Martino, Genoa
| | - A. Morabito
- Tumor Epigenetics Unit, IRCCS Ospedale Policlinico San Martino, Genoa
| | - M.P. Pistillo
- Tumor Epigenetics Unit, IRCCS Ospedale Policlinico San Martino, Genoa
| | - E. Croce
- Skin Cancer Unit, Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, Genoa
- Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genoa
| | - F. Cecchi
- Skin Cancer Unit, Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, Genoa
| | - P. Pronzato
- Skin Cancer Unit, Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, Genoa
| | - P. Queirolo
- Division of Melanoma Sarcoma and Rare Tumors, IRCCS European Institute of Oncology, Milan, Italy
| | - E. Raposio
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Plastic Surgery Division, University of Genova, Genoa
| | - V. Fontana
- Clinical Epidemiology Unit, IRCCS Ospedale Policlinico San Martino, Genoa
| | - E.T. Tanda
- Skin Cancer Unit, Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, Genoa
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15
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Rojas Velazquez MN, Therkelsen S, Pandey AV. Exploring Novel Variants of the Cytochrome P450 Reductase Gene ( POR) from the Genome Aggregation Database by Integrating Bioinformatic Tools and Functional Assays. Biomolecules 2023; 13:1728. [PMID: 38136599 PMCID: PMC10741880 DOI: 10.3390/biom13121728] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Cytochrome P450 oxidoreductase (POR) is an essential redox partner for steroid and drug-metabolizing cytochromes P450 located in the endoplasmic reticulum. Mutations in POR lead to metabolic disorders, including congenital adrenal hyperplasia, and affect the metabolism of steroids, drugs, and xenobiotics. In this study, we examined approximately 450 missense variants of the POR gene listed in the Genome Aggregation Database (gnomAD) using eleven different in silico prediction tools. We found that 64 novel variants were consistently predicted to be disease-causing by most tools. To validate our findings, we conducted a population analysis and selected two variations in POR for further investigation. The human POR wild type and the R268W and L577P variants were expressed in bacteria and subjected to enzyme kinetic assays using a model substrate. We also examined the activities of several cytochrome P450 proteins in the presence of POR (WT or variants) by combining P450 and reductase proteins in liposomes. We observed a decrease in enzymatic activities (ranging from 35% to 85%) of key drug-metabolizing enzymes, supported by POR variants R288W and L577P compared to WT-POR. These results validate our approach of curating a vast amount of data from genome projects and provide an updated and reliable reference for diagnosing POR deficiency.
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Affiliation(s)
- Maria Natalia Rojas Velazquez
- Division of Pediatric Endocrinology, Department of Pediatrics, University Children’s Hospital Bern, 3010 Bern, Switzerland; (M.N.R.V.); (S.T.)
- Translational Hormone Research, Department of Biomedical Research, University of Bern, 3010 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010 Bern, Switzerland
| | - Søren Therkelsen
- Division of Pediatric Endocrinology, Department of Pediatrics, University Children’s Hospital Bern, 3010 Bern, Switzerland; (M.N.R.V.); (S.T.)
- Translational Hormone Research, Department of Biomedical Research, University of Bern, 3010 Bern, Switzerland
- Department of Drug Design and Pharmacology, University of Copenhagen, 1172 Copenhagen, Denmark
| | - Amit V. Pandey
- Division of Pediatric Endocrinology, Department of Pediatrics, University Children’s Hospital Bern, 3010 Bern, Switzerland; (M.N.R.V.); (S.T.)
- Translational Hormone Research, Department of Biomedical Research, University of Bern, 3010 Bern, Switzerland
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16
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Kereszturi É. Diversity and Classification of Genetic Variations in Autism Spectrum Disorder. Int J Mol Sci 2023; 24:16768. [PMID: 38069091 PMCID: PMC10706722 DOI: 10.3390/ijms242316768] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 10/30/2023] [Revised: 11/19/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition with symptoms that affect the whole personality and all aspects of life. Although there is a high degree of heterogeneity in both its etiology and its characteristic behavioral patterns, the disorder is well-captured along the autistic triad. Currently, ASD status can be confirmed following an assessment of behavioral features, but there is a growing emphasis on conceptualizing autism as a spectrum, which allows for establishing a diagnosis based on the level of support need, free of discrete categories. Since ASD has a high genetic predominance, the number of genetic variations identified in the background of the condition is increasing exponentially as genetic testing methods are rapidly evolving. However, due to the huge amount of data to be analyzed, grouping the different DNA variations is still challenging. Therefore, in the present review, a multidimensional classification scheme was developed to accommodate most of the currently known genetic variants associated with autism. Genetic variations have been grouped according to six criteria (extent, time of onset, information content, frequency, number of genes involved, inheritance pattern), which are themselves not discrete categories, but form a coherent continuum in line with the autism spectrum approach.
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Affiliation(s)
- Éva Kereszturi
- Department of Molecular Biology, Semmelweis University, H-1085 Budapest, Hungary
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17
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Neupane A, Chariker JH, Rouchka EC. Analysis of Nucleotide Variations in Human G-Quadruplex Forming Regions Associated with Disease States. Genes (Basel) 2023; 14:2125. [PMID: 38136947 PMCID: PMC10742762 DOI: 10.3390/genes14122125] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
While the role of G quadruplex (G4) structures has been identified in cancers and metabolic disorders, single nucleotide variations (SNVs) and their effect on G4s in disease contexts have not been extensively studied. The COSMIC and CLINVAR databases were used to detect SNVs present in G4s to identify sequence level changes and their effect on the alteration of the G4 secondary structure. A total of 37,515 G4 SNVs in the COSMIC database and 2378 in CLINVAR were identified. Of those, 7236 COSMIC (19.3%) and 457 (19%) of the CLINVAR variants result in G4 loss, while 2728 (COSMIC) and 129 (CLINVAR) SNVs gain a G4 structure. The remaining variants potentially affect the folding energy without affecting the presence of a G4. Analysis of mutational patterns in the G4 structure shows a higher selective pressure (3-fold) in the coding region on the template strand compared to the reverse strand. At the same time, an equal proportion of SNVs were observed among intronic, promoter, and enhancer regions across strands.
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Affiliation(s)
- Aryan Neupane
- School of Graduate and Interdisciplinary Studies, University of Louisville, Louisville, KY 40292, USA;
| | - Julia H. Chariker
- Department of Neuroscience Training, University of Louisville, Louisville, KY 40292, USA;
- Kentucky IDeA Network of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
| | - Eric C. Rouchka
- Kentucky IDeA Network of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA
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18
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Leal VNC, Paulino LM, Cambui RAG, Zupelli TG, Yamada SM, Oliveira LAT, Dutra VDF, Bub CB, Sakashita AM, Yokoyama APH, Kutner JM, Vieira CA, Santiago WMDS, Andrade MMS, Teixeira FME, Alberca RW, Gozzi-Silva SC, Yendo TM, Netto LC, Duarte AJS, Sato MN, Venturini J, Pontillo A. A common variant close to the "tripwire" linker region of NLRP1 contributes to severe COVID-19. Inflamm Res 2023; 72:1933-1940. [PMID: 36416944 PMCID: PMC9684769 DOI: 10.1007/s00011-022-01670-3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/26/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE AND DESIGN The heterogeneity of response to SARS-CoV-2 infection is directly linked to the individual genetic background. Genetic variants of inflammasome-related genes have been pointed as risk factors for several inflammatory sterile and infectious disease. In the group of inflammasome receptors, NLRP1 stands out as a good novel candidate as severity factor for COVID-19 disease. METHODS To address this question, we performed an association study of NLRP1, DPP9, CARD8, IL1B, and IL18 single nucleotide variants (SNVs) in a cohort of 945 COVID-19 patients. RESULTS The NLRP1 p.Leu155His in the linker region, target of viral protease, was significantly associated to COVID-19 severity, which could contribute to the excessive cytokine release reported in severe cases. CONCLUSION Inflammasome genetic background contributes to individual response to SARS-CoV-2.
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Affiliation(s)
- Vinicius N C Leal
- Laboratório de Imunogenética, Departamento de Imunologia, Instituto de Ciências Biomédicas/ICB, Universidade de São Paulo/USP, São Paulo, SP, Brasil
| | - Leandro M Paulino
- Faculdade de Medicina, Universidade Federal de Mato Grosso do Sul, Campo grande, Mato Grosso do Sul, Brasil
| | - Raylane A G Cambui
- Laboratório de Imunogenética, Departamento de Imunologia, Instituto de Ciências Biomédicas/ICB, Universidade de São Paulo/USP, São Paulo, SP, Brasil
| | - Thiago G Zupelli
- Laboratório de Imunogenética, Departamento de Imunologia, Instituto de Ciências Biomédicas/ICB, Universidade de São Paulo/USP, São Paulo, SP, Brasil
| | - Suemy M Yamada
- Laboratório de Imunogenética, Departamento de Imunologia, Instituto de Ciências Biomédicas/ICB, Universidade de São Paulo/USP, São Paulo, SP, Brasil
| | - Leonardo A T Oliveira
- Laboratório de Imunogenética, Departamento de Imunologia, Instituto de Ciências Biomédicas/ICB, Universidade de São Paulo/USP, São Paulo, SP, Brasil
| | - Valéria de F Dutra
- Departamento de Hemoterapia, Hospital Israelita Albert Einstein, São Paulo, SP, Brasil
| | - Carolina B Bub
- Departamento de Hemoterapia, Hospital Israelita Albert Einstein, São Paulo, SP, Brasil
| | - Araci M Sakashita
- Departamento de Hemoterapia, Hospital Israelita Albert Einstein, São Paulo, SP, Brasil
| | - Ana Paula H Yokoyama
- Departamento de Hemoterapia, Hospital Israelita Albert Einstein, São Paulo, SP, Brasil
| | - José M Kutner
- Departamento de Hemoterapia, Hospital Israelita Albert Einstein, São Paulo, SP, Brasil
| | - Camila A Vieira
- Faculdade de Medicina, Universidade Federal de Mato Grosso do Sul, Campo grande, Mato Grosso do Sul, Brasil
| | - Wellyngton M de S Santiago
- Faculdade de Medicina, Universidade Federal de Mato Grosso do Sul, Campo grande, Mato Grosso do Sul, Brasil
| | - Milena M S Andrade
- Laboratório de Investigação Médica em Dermatologia e Imunodeficiências (LIM-56, Departamento de Dermatologia, Hospital das Clínicas E Faculdade de Medicina/HCFMUSP, São Paulo, Brasil
| | - Franciane M E Teixeira
- Laboratório de Investigação Médica em Dermatologia e Imunodeficiências (LIM-56, Departamento de Dermatologia, Hospital das Clínicas E Faculdade de Medicina/HCFMUSP, São Paulo, Brasil
| | - Ricardo W Alberca
- Laboratório de Investigação Médica em Dermatologia e Imunodeficiências (LIM-56, Departamento de Dermatologia, Hospital das Clínicas E Faculdade de Medicina/HCFMUSP, São Paulo, Brasil
| | - Sarah C Gozzi-Silva
- Laboratório de Investigação Médica em Dermatologia e Imunodeficiências (LIM-56, Departamento de Dermatologia, Hospital das Clínicas E Faculdade de Medicina/HCFMUSP, São Paulo, Brasil
| | - Tatiana M Yendo
- Departamento de Dermatologia, Faculdade de Medicina, Instituto de Medicina Tropical, Universidade de São Paulo/FMUSP, São Paulo, Brasil
| | - Lucas C Netto
- Unidade Terapia Intensiva, Hospital das Clínicas/FMUSP, São Paulo, Brasil
| | - Alberto J S Duarte
- Laboratório de Investigação Médica em Dermatologia e Imunodeficiências (LIM-56, Departamento de Dermatologia, Hospital das Clínicas E Faculdade de Medicina/HCFMUSP, São Paulo, Brasil
- Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo/FMUSP, São Paulo, Brasil
| | - Maria N Sato
- Laboratório de Investigação Médica em Dermatologia e Imunodeficiências (LIM-56, Departamento de Dermatologia, Hospital das Clínicas E Faculdade de Medicina/HCFMUSP, São Paulo, Brasil
| | - James Venturini
- Faculdade de Medicina, Universidade Federal de Mato Grosso do Sul, Campo grande, Mato Grosso do Sul, Brasil
| | - Alessandra Pontillo
- Laboratório de Imunogenética, Departamento de Imunologia, Instituto de Ciências Biomédicas/ICB, Universidade de São Paulo/USP, São Paulo, SP, Brasil.
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19
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Jakab S, Bali K, Freytag C, Pataki A, Fehér E, Halas M, Jerzsele Á, Szabó I, Szarka K, Bálint Á, Bányai K. Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance. Animals (Basel) 2023; 13:3223. [PMID: 37893946 PMCID: PMC10603690 DOI: 10.3390/ani13203223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major concern worldwide. Control of PRRSV is a challenging task due to various factors, including the viral diversity and variability. In this study, we evaluated an amplicon library preparation protocol targeting the ORF7 region of both PRRSV species, Betaarterivirus suid 1 and Betaarterivirus suid 2. We designed tailed primers for a two-step PCR procedure that generates ORF7-specific amplicon libraries suitable for use on Illumina sequencers. We tested the method with serum samples containing common laboratory strains and with pooled serum samples (n = 15) collected from different pig farms during 2019-2021 in Hungary. Testing spiked serum samples showed that the newly designed method is highly sensitive and detects the viral RNA even at low copy numbers (corresponding to approx. Ct 35). The ORF7 sequences were easily assembled even from clinical samples. Two different sequence variants were identified in five samples, and the Porcilis MLV vaccine strain was identified as the minor variant in four samples. An in-depth analysis of the deep sequencing results revealed numerous polymorphic sites along the ORF7 gene in a total of eight samples, and some sites (positions 12, 165, 219, 225, 315, 345, and 351) were found to be common in several clinical specimens. We conclude that amplicon deep sequencing of a highly conserved region of the PRRSV genome could support both laboratory diagnosis and epidemiologic surveillance of the disease.
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Affiliation(s)
- Szilvia Jakab
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
| | - Krisztina Bali
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
| | - Csongor Freytag
- Department of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (C.F.); (K.S.)
| | - Anna Pataki
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
| | - Enikő Fehér
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
| | | | - Ákos Jerzsele
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István u 2, H-1078 Budapest, Hungary;
| | - István Szabó
- National PRRS Eradication Committee, Keleti Károly u. 24., H-1024 Budapest, Hungary;
| | - Krisztina Szarka
- Department of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (C.F.); (K.S.)
| | - Ádám Bálint
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, H-1143 Budapest, Hungary;
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István u 2, H-1078 Budapest, Hungary;
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20
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El-Haddad K, Adhikari TM, Tu ZJ, Cheng YW, Leng X, Zhang X, Rhoads D, Ko JS, Worley S, Li J, Rubin BP, Esper FP. Intra-host mutation rate of acute SARS-CoV-2 infection during the initial pandemic wave. Virus Genes 2023; 59:653-661. [PMID: 37310519 DOI: 10.1007/s11262-023-02011-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2 mutation is minimized through a proofreading function encoded by NSP-14. Most estimates of the SARS-CoV-2 mutation rate are derived from population based sequence data. Our understanding of SARS-CoV-2 evolution might be enhanced through analysis of intra-host viral mutation rates in specific populations. Viral genome analysis was performed between paired samples and mutations quantified at allele frequencies (AF) ≥ 0.25, ≥ 0.5 and ≥ 0.75. Mutation rate was determined employing F81 and JC69 evolution models and compared between isolates with (ΔNSP-14) and without (wtNSP-14) non-synonymous mutations in NSP-14 and by patient comorbidity. Forty paired samples with median interval of 13 days [IQR 8.5-20] were analyzed. The estimated mutation rate by F81 modeling was 93.6 (95%CI 90.8-96.4], 40.7 (95%CI 38.9-42.6) and 34.7 (95%CI 33.0-36.4) substitutions/genome/year at AF ≥ 0.25, ≥ 0.5, ≥ 0.75 respectively. Mutation rate in ΔNSP-14 were significantly elevated at AF ≥ 0.25 vs wtNSP-14. Patients with immune comorbidities had higher mutation rate at all allele frequencies. Intra-host SARS-CoV-2 mutation rates are substantially higher than those reported through population analysis. Virus strains with altered NSP-14 have accelerated mutation rate at low AF. Immunosuppressed patients have elevated mutation rate at all AF. Understanding intra-host virus evolution will aid in current and future pandemic modeling.
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Affiliation(s)
- Kim El-Haddad
- Center for Pediatric Infectious Disease, Cleveland Clinic Children's, R3, 9500 Euclid Avenue, Cleveland, 44195 , OH, USA.
| | - Thamali M Adhikari
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Zheng Jin Tu
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yu-Wei Cheng
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaoyi Leng
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Xiangyi Zhang
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Daniel Rhoads
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jennifer S Ko
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sarah Worley
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Jing Li
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Frank P Esper
- Center for Pediatric Infectious Disease, Cleveland Clinic Children's, R3, 9500 Euclid Avenue, Cleveland, 44195 , OH, USA.
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21
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Li G, Zhu X, Wang Y, Ma H, Wang Y, Wu H, Li X, Wang Y, Gao J, Chen X, Huang X, Yao Y, Hu X. Transcription-wide impact by RESCUE-induced off-target single-nucleotide variants in mammalian cells. J Mol Cell Biol 2023; 15:mjad011. [PMID: 36822625 PMCID: PMC10485882 DOI: 10.1093/jmcb/mjad011] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
RNA base editing is a promising tool in precise molecular therapy. Currently, there are two widely used RNA base editors, REPAIR and RESCUE. REPAIR only facilitates A-to-I conversions, while RESCUE performs both A-to-I and C-to-U conversions. Thus, RESCUE can generate twice the number of mutations compared to REPAIR. However, transcription-wide impact due to RESCUE-induced off-target single-nucleotide variants (SNVs) is not fully appreciated. Therefore, to determine the off-target effects of RESCUE-mediated editing, we employed transcription-wide sequencing on cells edited by RESCUE. The SNVs showed different off-target effects on mRNA, circRNA, lncRNA, and miRNA expression patterns and their interacting networks. Our results illustrate the transcription-wide impact of RESCUE-induced off-target SNVs and highlight the need for careful characterization of the off-target impact by this editing platform.
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Affiliation(s)
- Guo Li
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yihan Wang
- National Research Institute for Family Planning, Beijing 100081, China
| | - Hongru Ma
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Yuzhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hanyu Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yiling Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Jianen Gao
- National Research Institute for Family Planning, Beijing 100081, China
| | - Xuexin Chen
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | | | - Yuan Yao
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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22
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Németh ZI, Rákosa R. Congruence Concept for Comparison of Spectra. Appl Spectrosc 2023; 77:350-359. [PMID: 36609191 DOI: 10.1177/00037028231152497] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This paper introduces an alternative, easy-to-implement spectrum comparison concept. The evaluation procedure is illustrated by artificial and attenuated total reflection Fourier transform infrared (ATR FT-IR) spectra, which it can also be extended to other spectrometries (e.g., ultraviolet-visible or UV-Vis and Raman). The evaluation for the comparison of two spectra is divided into four phases: (i) spectrum pre-treatment (e.g., smoothing and background correction), (ii) standard normal variate (SNV) transformation, (iii) regression analysis of SNV spectra, and (iv) calculation of the quantification index (FG). The FG is derived from the formula of R2. It characterizes and quantifies the identity and/or similarity of the compared spectra.
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Affiliation(s)
- Zsolt I Németh
- Spectrometry Laboratory, Investigating Team Ltd., Sopron, Hungary
| | - Rita Rákosa
- Spectrometry Laboratory, Investigating Team Ltd., Sopron, Hungary
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23
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Yunis LK, Linares-Ballesteros A, Aponte N, Barros G, García J, Niño L, Uribe G, Quintero E, Yunis JJ. Pharmacogenetics of ABCB1, CDA, DCK, GSTT1, GSTM1 and outcomes in a cohort of pediatric acute myeloid leukemia patients from Colombia. Cancer Rep (Hoboken) 2023; 6:e1744. [PMID: 36316809 PMCID: PMC10026301 DOI: 10.1002/cnr2.1744] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND AND AIM Different studies have shown pharmacogenetic variants related to drug toxicity in acute myeloid leukemia (AML) patients. Our aim was to identify the association between ABCB1, CDA, DCK, GSTT1, and GSTM1 variants with clinical outcomes and toxicity in pediatric patients with AML. METHODS Fifty-one confirmed de novo AML pediatric patients were included. A SNaPshot™ assay and conventional PCR were used to evaluate ABCB1, CDA, DCK, GSTT1, and GSTM1 variants. Clinical outcomes and toxicity associations were evaluated using odds ratios and Chi-square analysis. RESULTS Patients carrying ABCB1 (1236C > T, rs1128503) GG genotype in had a 6.8 OR (CI 95% 1.08-42.73, p = .044) for cardiotoxicity as compared to patients carrying either AA or GA genotypes 0.14 OR (CI 95% 0.023-0.92, p = .044). For ABCB1 (1236G > A rs1128503/2677C > A/T rs2032582/3435G > A rs1045642) AA/AA/AA combined genotypes had a strong association with death after HSTC OR 13.73 (CI 95% 1.94-97.17, p = .009). Combined genotypes GG/CC/GG with CDA (79A > C, rs2072671) CA genotype or CDA (-451G > A, rs532545) CT genotype, had a 4.11 OR (CI 95% 2.32-725, p = .007) and 3.8 OR (CI 95% 2.23-6.47, p = .027) with MRD >0.1% after first chemotherapy cycle, respectively. CONCLUSION Our results highlight the importance of pharmacogenetic analysis in pediatric AML, particularly in populations with a high degree of admixture, and might be useful as a future tool for patient stratification for treatment.
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Affiliation(s)
- Luz K Yunis
- Grupo de Patología Molecular, Universidad Nacional de Colombia, Bogotá, Colombia
- Servicios Médicos Yunis Turbay y Cía S.A.S, Instituto de Genética, Bogotá, Colombia
| | - Adriana Linares-Ballesteros
- Unidad de Oncología/Hematología Pediátrica, HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
- Grupo de Oncohematología Pediátrica, Universidad Nacional de Colombia-HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
| | - Nelson Aponte
- Unidad de Oncología/Hematología Pediátrica, HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
- Grupo de Oncohematología Pediátrica, Universidad Nacional de Colombia-HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
| | - Gisela Barros
- Unidad de Oncología/Hematología Pediátrica, HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
- Grupo de Oncohematología Pediátrica, Universidad Nacional de Colombia-HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
| | - Johnny García
- Unidad de Oncología/Hematología Pediátrica, HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
- Grupo de Oncohematología Pediátrica, Universidad Nacional de Colombia-HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
| | - Laura Niño
- Unidad de Oncología/Hematología Pediátrica, HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
- Grupo de Oncohematología Pediátrica, Universidad Nacional de Colombia-HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
| | - Gloria Uribe
- Unidad de Patología, HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
| | - Edna Quintero
- Unidad de Patología, HOMI Fundación Hospital Pediátrico La Misericordia, Bogotá, Colombia
| | - Juan J Yunis
- Grupo de Patología Molecular, Universidad Nacional de Colombia, Bogotá, Colombia
- Servicios Médicos Yunis Turbay y Cía S.A.S, Instituto de Genética, Bogotá, Colombia
- Departamento de Patología, Facultad de Medicina e Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
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24
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Behera S, LeFaive J, Orchard P, Mahmoud M, Paulin LF, Farek J, Soto DC, Parker SCJ, Smith AV, Dennis MY, Zook JM, Sedlazeck FJ. FixItFelix: improving genomic analysis by fixing reference errors. Genome Biol 2023; 24:31. [PMID: 36810122 PMCID: PMC9942314 DOI: 10.1186/s13059-023-02863-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/20/2023] [Indexed: 02/23/2023] Open
Abstract
The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical relevance. Here, we present FixItFelix, an efficient remapping approach, together with a modified version of the GRCh38 reference genome that improves the subsequent analysis across these genes within minutes for an existing alignment file while maintaining the same coordinates. We showcase these improvements over multi-ethnic control samples, demonstrating improvements for population variant calling as well as eQTL studies.
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Affiliation(s)
- Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jonathon LeFaive
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jesse Farek
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Daniela C Soto
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Megan Y Dennis
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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25
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Kumari I, Lakhanpal D, Swargam S, Nath Jha A. Leishmaniasis: Omics approaches to understand its biology from molecule to cell level. Curr Protein Pept Sci 2023; 24:229-239. [PMID: 36809951 DOI: 10.2174/1389203724666230210123147] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/12/2022] [Accepted: 01/03/2023] [Indexed: 02/17/2023]
Abstract
Leishmaniasis is the second deadliest vector-borne, neglected tropical zoonotic disease and is found in a variety of clinical forms based on genetic background. Its endemic type is present in tropical, sub-tropical and Mediterranean areas around the world which accounts for a lot of deaths every year. Currently, a variety of techniques are present to detect leishmaniasis with advantages and disadvantages. The advancing next-generation sequencing (NGS) techniques are employed to find out novel diagnostic markers based on single nucleotide variants. Total 274 NGS studies are available in European Nucleotide Archive (ENA) portal (https://www.ebi.ac.uk/ena/browser/home) that focused on wild-type and mutated Leishmania, differential gene expression, miRNA expression, and detection of aneuploidy mosaicism by omics approaches. These studies have provided insights into the population structure, virulence, and extensive structural variation, including known and suspected drug resistance loci, mosaic aneuploidy and hybrid formation under stressed conditions and inside the midgut of the sandfly. The complex interactions occurring within the parasite-host-vector triangle can be better understood by omics approaches. Further, advanced CRISPR technology allows researchers to delete and modify each gene individually to know the importance of genes in the virulence and survival of the disease-causing protozoa. In vitro Generation of Leishmania, hybrids are helping to understand the mechanism of disease progression in its different stages of infection. This review will give a comprehensive picture of the available omics data of various Leishmania spp. which helped to reveal the effect of climate change on the spread of its vector, the pathogen survival strategies, emerging antimicrobial resistance and its clinical importance.
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Affiliation(s)
- Indu Kumari
- Indian Biological Data Centre, Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Dinesh Lakhanpal
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Shahpur (Temporary Academic Block) and Dharmashala, Himachal Pradesh, India
| | - Sandeep Swargam
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Shahpur (Temporary Academic Block) and Dharmashala, Himachal Pradesh, India
| | - Anupam Nath Jha
- Computational Biophysics Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
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26
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Ansari AH, Kumar M, Sarkar S, Maiti S, Chakraborty D. CriSNPr, a single interface for the curated and de novo design of gRNAs for CRISPR diagnostics using diverse Cas systems. eLife 2023; 12:77976. [PMID: 36752591 PMCID: PMC9940907 DOI: 10.7554/elife.77976] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 02/07/2023] [Indexed: 02/09/2023] Open
Abstract
CRISPR-based diagnostics (CRISPRDx) have improved clinical decision-making, especially during the COVID-19 pandemic, by detecting nucleic acids and identifying variants. This has been accelerated by the discovery of new and engineered CRISPR effectors, which have expanded the portfolio of diagnostic applications to include a broad range of pathogenic and non-pathogenic conditions. However, each diagnostic CRISPR pipeline necessitates customized detection schemes based on the fundamental principles of the Cas protein used, its guide RNA (gRNA) design parameters, and the assay readout. This is especially relevant for variant detection, a low-cost alternative to sequencing-based approaches for which no in silico pipeline for the ready-to-use design of CRISPRDx currently exists. In this manuscript, we fill this lacuna using a unified web server, CriSNPr (CRISPR-based SNP recognition), which provides the user with the opportunity to de novo design gRNAs based on six CRISPRDx proteins of choice (Fn/enFnCas9, LwCas13a, LbCas12a, AaCas12b, and Cas14a) and query for ready-to-use oligonucleotide sequences for validation on relevant samples. Furthermore, we provide a database of curated pre-designed gRNAs as well as target/off-target for all human and SARS-CoV-2 variants reported thus far. CriSNPr has been validated on multiple Cas proteins, demonstrating its broad and immediate applicability across multiple detection platforms. CriSNPr can be found at http://crisnpr.igib.res.in/.
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Affiliation(s)
- Asgar H Ansari
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Manoj Kumar
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Sajal Sarkar
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
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27
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Gu X, Wang L, Coates PJ, Gnanasundram SV, Sgaramella N, Sörlin J, Erdogan B, Magan M, Nylander K. Evidence for etiologic field changes in tongue distant from tumor in patients with squamous cell carcinoma of the oral tongue. J Pathol 2023; 259:93-102. [PMID: 36314576 PMCID: PMC10108103 DOI: 10.1002/path.6025] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/07/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Oral cancer is a paradigm of Slaughter's concept of field cancerization, where tumors are thought to originate within an area of cells containing genetic alterations that predispose to cancer development. The field size is unclear but may represent a large area of tissue, and the origin of mutations is also unclear. Here, we analyzed whole exome and transcriptome features in contralateral tumor-distal tongue (i.e. distant from the tumor, not tumor-adjacent) and corresponding tumor tissues of 15 patients with squamous cell carcinoma of the oral tongue. The number of point mutations ranged from 41 to 237 in tumors and from one to 78 in tumor-distal samples. Tumor-distal samples showed mainly clock-like (associated with aging) or tobacco smoking mutational signatures. Tumors additionally showed mutations that associate with cytidine deaminase AID/APOBEC enzyme activities or a UV-like signature. Importantly, no point mutations were shared between a tumor and the matched tumor-distal sample in any patient. TP53 was the most frequently mutated gene in tumors (67%), whereas a TP53 mutation was detected in only one tumor-distal sample, and this mutation was not shared with the matched tumor. Arm-level copy number variation (CNV) was found in 12 tumors, with loss of chromosome (Chr) 8p or gain of 8q being the most frequent events. Two tumor-distal samples showed a gain of Chr8, which was associated with increased expression of Chr8-located genes in these samples, although gene ontology did not show a role for these genes in oncogenic processes. In situ hybridization revealed a mixed pattern of Chr8 gain and neutral copy number in both tumor cells and adjacent nontumor epithelium in one patient. We conclude that distant field cancerization exists but does not present as tumor-related mutational events. The data are compatible with etiologic field effects, rather than classical monoclonal field cancerization theory. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Xiaolian Gu
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
| | - Lixiao Wang
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
| | - Philip J Coates
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | | | - Nicola Sgaramella
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
| | - Jonas Sörlin
- Clinical Genetics, Laboratory Medicine, Norrlands Universitetssjukhus, Umeå, Sweden
| | - Baris Erdogan
- Department of Clinical Sciences/ENT, Umeå University, Umeå, Sweden
| | - Mustafa Magan
- Department of Clinical Sciences/ENT, Umeå University, Umeå, Sweden
| | - Karin Nylander
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
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Saghaug CS, Gamlem AL, Hauge KB, Vahokoski J, Klotz C, Aebischer T, Langeland N, Hanevik K. Genetic diversity in the metronidazole metabolism genes nitroreductases and pyruvate ferredoxin oxidoreductases in susceptible and refractory clinical samples of Giardia lamblia. Int J Parasitol Drugs Drug Resist 2022; 21:51-60. [PMID: 36682328 PMCID: PMC9871439 DOI: 10.1016/j.ijpddr.2022.12.003] [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: 03/04/2022] [Revised: 11/30/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
The effectiveness of metronidazole against the tetraploid intestinal parasite Giardia lamblia is dependent on its activation/inactivation within the cytoplasm. There are several activating enzymes, including pyruvate ferredoxin reductase (PFOR) and nitroreductase (NR) 1 which metabolize metronidazole into toxic forms, while NR2 on the other hand inactivates it. Metronidazole treatment failures have been increasing rapidly over the last decade, indicating genetic resistance mechanisms. Analyzing genetic variation in the PFOR and NR genes in susceptible and refractory Giardia isolates may help identify potential markers of resistance. Full length PFOR1, PFOR2, NR1 and NR2 genes from clinical culturable isolates and non-cultured clinical Giardia assemblage B samples were cloned, sequenced and single nucleotide variants (SNVs) were analyzed to assess genetic diversity and alleles. A similar ratio of amino acid changing SNVs per gene length was found for the NRs; 4.2% for NR1 and 6.4% for NR2, while the PFOR1 and PFOR2 genes had less variability with a ratio of 1.1% and 1.6%, respectively. One of the samples from a refractory case had a nonsense mutation which caused a truncated NR1 gene in one out of six alleles. Further, we found three NR2 alleles with frameshift mutations, possibly causing a truncated protein in two susceptible isolates. One of these isolates was homozygous for the affected NR2 allele. Three nsSNVs with potential for affecting protein function were found in the ferredoxin domain of the PFOR2 gene. The considerable variation and discovery of mutations possibly causing dysfunctional NR proteins in clinical Giardia assemblage B isolates, reveal a potential for genetic link to metronidazole susceptibility and resistance.
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Affiliation(s)
- Christina S Saghaug
- Department of Clinical Science, University of Bergen, Bergen, Norway; Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway.
| | - Astrid L Gamlem
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kirsti B Hauge
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Juha Vahokoski
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Christian Klotz
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Toni Aebischer
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway; Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway; Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
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29
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Mukai-Sasaki Y, Liao Z, Yang D, Inoue T. Modulators of radiation-induced cardiopulmonary toxicities for non-small cell lung cancer: Integrated cytokines, single nucleotide variants, and HBP systems imaging. Front Oncol 2022; 12:984364. [PMID: 36591530 PMCID: PMC9797663 DOI: 10.3389/fonc.2022.984364] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022] Open
Abstract
Radiation therapy (RT)-induced cardiopulmonary toxicities remain dose-limiting toxicities for patients receiving radiation dosages to the thorax, especially for lung cancer. Means of monitoring and predicting for those receiving RT or concurrent chemoradiation therapy before treatment begins in individual patients could benefit early intervention to prevent or minimize RT-induced side effects. Another aspect of an individual's susceptibility to the adverse effects of thoracic irradiation is the immune system as reflected by phenotypic factors (patterns of cytokine expressions), genotypic factors (single nucleotide variants SNVs; formerly single nucleotide polymorphisms [SNPs]), and aspects of quantitative cellular imaging. Levels of transcription, production, and functional activity of cytokines are often influenced by SNVs that affect coding regions in the promoter or regulatory regions of cytokine genes. SNVs can also lead to changes in the expression of the inflammatory cytokines, interferons, interleukins (IL-6, IL-17) and tumor necrosis factors (TNF-α) at the protein level. RT-induced cardiopulmonary toxicities could be quantified by the uptake of 18F-fluorodeoxyglucose (FDG), however, FDG is a sensitive but not specific biomarker in differential diagnosis between inflammation/infection and tumor recurrence. FDG is suitable for initial diagnosis of predisposed tissue injuries in non-small cell lung cancer (NSCLC). 99mTc-ethylenedicysteine-glucosamine (99mTc-EC-G) was able to measure tumor DNA proliferation and myocardial ischemia via hexosamine biosynthetic pathways (HBP). Thus, 99mTc-EC-G could be an alternative to FDG in the assessment of RT doses and select patients in HBP-directed targets for optimal outcomes. This article reviewed correlative analyses of pro-inflammatory cytokines, genotype SNVs, and cellular imaging to improve the diagnosis, prognosis, monitoring, and prediction of RT-induced cardiopulmonary toxicities in NSCLC.
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Affiliation(s)
- Yuki Mukai-Sasaki
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States,Advanced Medical Center, Shonan Kamakura General Hospital, Kamakura, Japan,*Correspondence: Yuki Mukai-Sasaki,
| | - Zhongxing Liao
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - David Yang
- Advanced Medical Center, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Tomio Inoue
- Advanced Medical Center, Shonan Kamakura General Hospital, Kamakura, Japan
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30
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Landeros N, Gonzalez-Hormazabal P, Pérez-Moreno P, Tapia JC, Jara L. A Single Variant in Pri-miRNA-155 Associated with Susceptibility to Hereditary Breast Cancer Promotes Aggressiveness in Breast Cancer Cells. Int J Mol Sci 2022; 23:ijms232315418. [PMID: 36499743 PMCID: PMC9735695 DOI: 10.3390/ijms232315418] [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: 10/18/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Variants in genes encoding for microRNAs have been associated with their deregulation in breast cancer (BC). Sequencing of microRNAs deregulated in BC was performed using DNA from Chilean patients with a strong family history and negative for mutations in BRCA1/BRCA2. Seventeen variants were identified, three of which were selected for a case-control association study: rs376491654 (miR-335), rs755634302 (miR-497), and rs190708267 (miR-155). For rs190708267 C>T, the heterozygous T allele was detected in four BC cases and absent in controls, while homozygous TT cases were not detected. Variants were modelled in silico, cloned in a plasmid, expressed in BC cell lines, and functional in vitro assays were performed. Overexpression of the miR-155-T allele increased mature miR-155-5p levels in both BC cell lines, suggesting that its presence alters pre-miR-155 processing. Moreover, BC cells overexpressing the miR-155-T allele showed increased proliferation, migration, and resistance to cisplatin-induced death compared to miR-155-C overexpressing cells. Of note, the 3′UTR of APC, GSK3β, and PPP1CA genes, all into the canonical Wnt signaling pathway, were identified as direct targets. APC and GSK3β mRNA levels decreased while PP1 levels increased. These results suggest a pathogenic role of the variant rs190708267 (miR-155) in BRCA 1/2 negative BC, conferring susceptibility and promoting traits of aggressiveness.
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Affiliation(s)
- Natalia Landeros
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
| | - Patricio Gonzalez-Hormazabal
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
| | - Pablo Pérez-Moreno
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
| | - Julio C Tapia
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
| | - Lilian Jara
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
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31
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Wei X, Zheng J, Evans JD, Huang Q. Transgenerational genomic analyses reveal allelic oscillation and purifying selection in a gut parasite Nosema ceranae. Front Microbiol 2022; 13:927892. [PMID: 36386715 PMCID: PMC9664190 DOI: 10.3389/fmicb.2022.927892] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Standing genetic variation is the predominant source acted on by selection. Organisms with high genetic diversity generally show faster responses toward environmental change. Nosema ceranae is a microsporidian parasite of honey bees, infecting midgut epithelial cells. High genetic diversity has been found in this parasite, but the mechanism for the parasite to maintain this diversity remains unclear. This study involved continuous inoculation of N. ceranae to honey bees. We found that the parasites slowly increased genetic diversity over three continuous inoculations. The number of lost single nucleotide variants (SNVs) was balanced with novel SNVs, which were mainly embedded in coding regions. Classic allele frequency oscillation was found at the regional level along the genome, and the associated genes were enriched in apoptosis regulation and ATP binding. The ratio of synonymous and non-synonymous substitution suggests a purifying selection, and our results provide novel insights into the evolutionary dynamics in microsporidian parasites.
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Affiliation(s)
- Xiuxiu Wei
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang, China,Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
| | - Jialan Zheng
- College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Jay D. Evans
- USDA-ARS Bee Research Laboratory, Beltsville, MD, United States
| | - Qiang Huang
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang, China,Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China,*Correspondence: Qiang Huang,
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Kumar P, Oraon PK, Yadav P, Roy A, Goel S, Reddy MK, Mukherjee SK, Mandal B. Random distribution of nucleotide polymorphism throughout the genome of tomato-infecting begomovirus species occurring in India: implication in PCR based diagnosis. Virusdisease 2022; 33:270-283. [PMID: 36277410 PMCID: PMC9481814 DOI: 10.1007/s13337-022-00785-9] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/29/2022] [Indexed: 10/14/2022] Open
Abstract
Multiple begomovirus species are known to cause leaf curl disease in tomato in India. In order to develop specific and generic PCR based diagnostics for the tomato-infecting begomoviruses, in this study, we attempted to design primers initially based on the multiple alignment of the complete genome sequence of DNA-A component. However, the specific nucleotide stretches adequate for preparing specific primers could not be obtained. Alternatively, the online Primer-BLAST tool that offers designing of target-specific PCR primers was attempted to prepare specific primers targeting three clones (DNA-A) of tomato-infecting begomovirus species (Tomato leaf curl New Delhi virus, Tomato leaf curl Palampur virus and Tomato leaf curl Joydebpur virus) selected based on their sequence identity and phylogenetic relatedness. The primers derived from Primer-BLAST tool showed high level of cross-reaction among these begomovirus species and therefore were not able to differentiate these target begomovirus species. In order to understand the reason of cross-reactivity further sequence analysis revealed the high occurrence of single nucleotide variations (SNVs) compared to the multi-nucleotide stretches. There was no SNV hot-spot in the genome, rather the SNVs were randomly distributed throughout the genome of these begomovirus species. This pattern of nucleotide diversities among these tomato-infecting begomoviruses seriously implicated on developing specific PCR diagnostics. On the contrary, sequence analysis showed high sequence conservancy, which enabled to develop a generic PCR diagnostic for these begomoviruses. Our study, thus showed that the genome sequence diversity pattern among the tomato-infecting begomoviruses in India poses challenges in developing PCR based specific diagnostics. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-022-00785-9.
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Affiliation(s)
- Pradeep Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | | | - Pragati Yadav
- Department of Botany, University of Delhi, Delhi, India
| | - Anirban Roy
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | | | - M. Krishna Reddy
- Division of Crop Protection, Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, India
| | - Sunil Kumar Mukherjee
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
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Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E, Paul Flicek, Germer S, Brand H, Hall IM, Talkowski ME, Narzisi G, Zody MC. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell 2022; 185:3426-3440.e19. [PMID: 36055201 PMCID: PMC9439720 DOI: 10.1016/j.cell.2022.08.004] [Citation(s) in RCA: 201] [Impact Index Per Article: 100.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/21/2022] [Accepted: 08/03/2022] [Indexed: 01/05/2023]
Abstract
The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-genome sequencing (WGS) data consented for public distribution without access or use restrictions. The final, phase 3 release of the 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low-coverage WGS. Here, we present a high-coverage 3,202-sample WGS 1kGP resource, which now includes 602 complete trios, sequenced to a depth of 30X using Illumina. We performed single-nucleotide variant (SNV) and short insertion and deletion (INDEL) discovery and generated a comprehensive set of structural variants (SVs) by integrating multiple analytic methods through a machine learning model. We show gains in sensitivity and precision of variant calls compared to phase 3, especially among rare SNVs as well as INDELs and SVs spanning frequency spectrum. We also generated an improved reference imputation panel, making variants discovered here accessible for association studies.
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Affiliation(s)
| | | | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Haley J. Abel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Allison A. Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Wayne E. Clarke
- New York Genome Center, New York, NY 10013, USA,Outlier Informatics Inc., Saskatoon, SK S7H 1L4, Canada
| | | | | | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | | | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ira M. Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA,Center for Genomic Health, Yale University School of Medicine, New Haven, CT 06510, USA,Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael E. Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michael C. Zody
- New York Genome Center, New York, NY 10013, USA,Corresponding author
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Wan R, Schieck M, Caballero-Oteyza A, Hofmann W, Cochino AV, Shcherbina A, Sherkat R, Wache-Mainier C, Fernandez A, Sultan M, Illig T, Grimbacher B, Proietti M, Steinemann D. Copy Number Analysis in a Large Cohort Suggestive of Inborn Errors of Immunity Indicates a Wide Spectrum of Relevant Chromosomal Losses and Gains. J Clin Immunol 2022; 42:1083-92. [PMID: 35486341 DOI: 10.1007/s10875-022-01276-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 12/20/2022]
Abstract
Inborn errors of immunity (IEI) are genetically driven disorders. With the advancement of sequencing technologies, a rapidly increasing number of gene defects has been identified, thereby mirroring the high heterogeneity in immunological and clinical presentations observed in patients. However, for a large majority of patients, no causative single nucleotide variant (SNV) or small indel can be identified using next-generation sequencing. First studies have shown that also copy number variants (CNVs) can cause IEI. Unfortunately, CNVs are not well examined in many routine diagnostic settings and the aim of this study was to assess the number of clinically relevant chromosomal losses and gains in a large cohort. We identified a total of 20 CNVs using whole exome sequencing data of a cohort of 191 patients with a suspected IEI. A definite molecular diagnosis could be made in five patients (2.6%), including pathogenic deletions affecting ICOS, TNFAIP3, and 22q11.2. CNVs of uncertain significance were observed in fifteen patients (7.9%), including deletions of 11q22.1q22.3 and 16p11.2 but also duplications affecting entire or parts of genes previously associated with IEI. Importantly, five patients carrying a CNV of uncertain significance also carried pathogenic or likely pathogenic SNVs (PIK3R1, NFKB1, NLRC4, DOCK2), or SNVs of unknown significance (NFKB2). This cooccurrence of SNVs and CNVs suggests modifying effects in some patients, and functional follow-up is warranted now in order to better understand phenotypic heterogeneity. In summary, the diagnostic yield of IEI can be increased substantially by evaluating CNVs, which allows an improved therapeutic management in those patients.
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Akiyama Y, Kondou R, Iizuka A, Miyata H, Maeda C, Kanematsu A, Ashizawa T, Nagashima T, Urakami K, Shimoda Y, Ohshima K, Shiomi A, Ohde Y, Terashima M, Uesaka K, Hirashima Y, Kiyohara Y, Katagiri H, Sugino T, Notsu A, Mori K, Takahashi M, Kenmotsu H, Yamaguchi K. Characterization of the Immunological Status of Hypermutated Solid Tumors in the Cancer Genome Analysis Project HOPE. Anticancer Res 2022; 42:3537-3549. [PMID: 35790264 DOI: 10.21873/anticanres.15840] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 03/31/2022] [Accepted: 06/02/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Many reports demonstrate that a high tumor mutation burden (TMB-H) is closely associated with good prognosis of cancer. However, specific studies investigating the association of various TMB statuses with overall survival in patients with solid tumors are scarce. PATIENTS AND METHODS In the present study, we investigated the association of TMB status with overall survival in 5,072 patients with cancer from the HOPE project and clarified the specific mechanism responsible for the good prognosis of the TMB-H group. All tumors were classified into one of four groups based on TMB: ultralow (UL), low (L), intermediate (I) and high (H). RESULTS The TMB-H group had a better prognosis than the TMB-I and TMB-L groups, but not than the TMB-UL group. Analyzing the expression of 293 immune response-associated genes, 17 genes were up-regulated in the TMB-H group compared to the TMB-I and TNB-L groups, and two genes [CD274 and interferon-γ (IFNG)] were identified as good prognostic factors. Analysis of immune cell populations inside tumors demonstrated that the frequencies of exhausted CD8+ T-cells, activated effector CD8+ T-cells and natural killer cells were significantly higher in the TMB-H group. The T-cell receptor repertoire numbers and the diversity evenness score (DE50) were lower in the TMB-H group than in TMB-UL group; however, no association of the DE50 value with the binding or elution affinity of epitope peptides from neoantigens was found. CONCLUSION One possible mechanism for the good prognosis of the TMB-UL group compared to the TMB-H group might be that the TMB-UL group features a balance between immunosuppression and immunostimulation.
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Affiliation(s)
- Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan;
| | - Ryota Kondou
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akira Iizuka
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Haruo Miyata
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Chie Maeda
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akari Kanematsu
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Tadashi Ashizawa
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Tokyo, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Tokyo, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yasuhisa Ohde
- Division of Thoracic Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Masanori Terashima
- Division of Gastric Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yasuyuki Hirashima
- Division of Gynecology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yoshio Kiyohara
- Division of Dermatology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Hirohisa Katagiri
- Division of Orthopedic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Akifumi Notsu
- Clinical Research Center, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Keita Mori
- Clinical Research Center, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Mitsuru Takahashi
- Division of Orthopedic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
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Chen J, He J, Luo J, Zhong S. Corrigendum: Association of αENaC p. Ala663Thr Gene Polymorphism With Sudden Sensorineural Hearing Loss. Front Genet 2022; 13:931037. [PMID: 35754831 PMCID: PMC9219908 DOI: 10.3389/fgene.2022.931037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jialei Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing He
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Luo
- Department of Pathology and Pathophysiology, Chongqing Medical University, Chongqing, China
| | - Shixun Zhong
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Zeng C, Long J, Deng C, Xie L, Ma H, Guo Y, Liu S, Deng M. Genetic Alterations in Papillary Thyroid Carcinoma With Hashimoto 's Thyroiditis: ANK3, an Indolent Maintainer of Papillary Thyroid Carcinoma. Front Oncol 2022; 12:894786. [PMID: 35646694 PMCID: PMC9133634 DOI: 10.3389/fonc.2022.894786] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/11/2022] [Indexed: 11/15/2022] Open
Abstract
Hashimoto’s thyroiditis (TH) is a risk factor for the occurrence of papillary thyroid carcinoma (PTC), which is considered to be the most common type of thyroid cancer. In recent years, the prevalence of PTC with TH has been increasing, but little is known about the genetic alteration in PTC with TH. This study analyzed the mutation spectrum and mutation signature of somatic single nucleotide variants (SNV) for 10 non-tumor and tumor pair tissues of PTC with TH using whole-exome sequencing. The ANK3 protein expression was evaluated by immunohistochemistry in PTC with TH and PTC samples. Moreover, the functional role of ANK3 in PTC cells was determined by CCK-8 proliferation assay, colony formation assays, cell cycle analysis, cell invasion and migration and in vivo study through overexpression assay. Our results showed three distinct mutational signatures and the C>T/G>A substitution was the most common type of SNV. Gene-set enrichment analysis showed that most of the significantly mutated genes were enriched in the regulation of actin cytoskeleton signaling. Moreover, NCOR2, BPTF, ANK3, and PCSK5 were identified as the significantly mutated genes in PTC with TH, most of which have not been previously characterized. Unexpectedly, it was found that ANK3 was overexpressed in cytoplasm close to the membrane of PTC cells with TH and in almost all PTC cases, suggesting its role as a diagnostic marker of PTC. Ectopic expression of ANK3 suppressed invasion and migration, increased apoptosis of B-CPAP and TPC-1 cells. Moreover, our findings revealed that enhanced ANK3 expression inhibits growth of PTC cells both in vitro and in vivo. Ectopic expression of ANK3 significantly enhanced E-cadherin protein expression and inhibited PTC progression, at least in part, by suppression of epithelial-mesenchymal transition (EMT). Our study shows that ANK3 exerts an anti-oncogenic role in the development of PTC and might be an indolent maintainer of PTC.
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Affiliation(s)
- Chao Zeng
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jiali Long
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Chunmiao Deng
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Linying Xie
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hongmei Ma
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yimin Guo
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shuguang Liu
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Min Deng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
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38
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Liu Z, Gao Q, Wang T, Chai W, Zhan Y, Akhtar F, Zhang Z, Li Y, Shi X, Wang C. Multi-Thoracolumbar Variations and NR6A1 Gene Polymorphisms Potentially Associated with Body Size and Carcass Traits of Dezhou Donkey. Animals (Basel) 2022; 12:ani12111349. [PMID: 35681814 PMCID: PMC9179361 DOI: 10.3390/ani12111349] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
The number of thoracolumbar vertebrae is a quantitative trait positively correlated with the economic traits of livestock. More thoracolumbar vertebrae individuals could genetically be used to improve the livestock population, as more thoracolumbar vertebrae means a longer carcass, which could bring more meat production. Nuclear receptor subfamily 6 group A member 1 (NR6A1) is considered a strong candidate gene for effecting the number of vertebrae in livestock. The purposes of this study are as follows: (a) Analyzing the effect of TLN variation on body size and carcass traits of Dezhou donkey; (b) Studying the distribution of seven single nucleotide variants (SNVs) in NR6A1 gene of Dezhou donkey; (c) Exploring the relationship between latent SNVs and TLN, the body size and carcass traits. We examined the thoracic and lumbar vertebrae number and seven SNVs in NR6A1 gene of 455 Dezhou donkeys, and analyzed the relationships between them. Five types of thoracolumbar combinations (T17L5 (individual with 17 thoracic and five lumbar vertebrae) 2.4%, T18L5 75.8%, T19L5 1.1%, T17L6 11.9%, and T18L6 8.8%) of Dezhou donkeys were detected in this study. For one thoracolumbar vertebra added, the body length of Dezhou donkey increases by 3 cm and the carcass weight increases by 6 kg. Seven SNVs (g.18093100G > T, g.18094587G > T, g.18106043G > T, g.18108764G > T, g.18110615T > G, g.18112000C > T and g.18114954T > G) of the NR6A1 gene were found to have a significant association with the TLN, body size and carcass traits of Dezhou donkey (p < 0.05), respectively. For instance, g.18114954C > T is significantly associated with lumber vertebrae number, the total number of thoracolumbar, and carcass weight, and individuals with TT genotype had significantly larger value than CC genotype (p < 0.05). Using these 7SNVs, 16 different haplotypes were estimated. Compared to Hap3Hap3, individuals homozygous for Hap2Hap2 showed significantly longer length in one thoracic spine (STL), the total thoracic vertebrae and one thoracolumbar spine. Our study will not only extend the understanding of genetic variation in the NR6A1 gene of Dezhou donkey, but also provide useful information for marker assisted selection in donkey breeding program.
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Affiliation(s)
- Ziwen Liu
- Liao Cheng Reaserch Inisitute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng 252059, China; (Z.L.); (T.W.); (W.C.); (Y.Z.); (F.A.); (Z.Z.); (Y.L.); (X.S.)
| | - Qican Gao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China;
| | - Tianqi Wang
- Liao Cheng Reaserch Inisitute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng 252059, China; (Z.L.); (T.W.); (W.C.); (Y.Z.); (F.A.); (Z.Z.); (Y.L.); (X.S.)
| | - Wenqiong Chai
- Liao Cheng Reaserch Inisitute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng 252059, China; (Z.L.); (T.W.); (W.C.); (Y.Z.); (F.A.); (Z.Z.); (Y.L.); (X.S.)
| | - Yandong Zhan
- Liao Cheng Reaserch Inisitute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng 252059, China; (Z.L.); (T.W.); (W.C.); (Y.Z.); (F.A.); (Z.Z.); (Y.L.); (X.S.)
| | - Faheem Akhtar
- Liao Cheng Reaserch Inisitute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng 252059, China; (Z.L.); (T.W.); (W.C.); (Y.Z.); (F.A.); (Z.Z.); (Y.L.); (X.S.)
| | - Zhenwei Zhang
- Liao Cheng Reaserch Inisitute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng 252059, China; (Z.L.); (T.W.); (W.C.); (Y.Z.); (F.A.); (Z.Z.); (Y.L.); (X.S.)
| | - Yuhua Li
- Liao Cheng Reaserch Inisitute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng 252059, China; (Z.L.); (T.W.); (W.C.); (Y.Z.); (F.A.); (Z.Z.); (Y.L.); (X.S.)
| | - Xiaoyuan Shi
- Liao Cheng Reaserch Inisitute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng 252059, China; (Z.L.); (T.W.); (W.C.); (Y.Z.); (F.A.); (Z.Z.); (Y.L.); (X.S.)
| | - Changfa Wang
- Liao Cheng Reaserch Inisitute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng 252059, China; (Z.L.); (T.W.); (W.C.); (Y.Z.); (F.A.); (Z.Z.); (Y.L.); (X.S.)
- Correspondence:
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39
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Li Q, Meng Y, Wang J, Xie Y, Li T, Sun W. A Systematic Screening of ADHD-Susceptible Variants From 25 Chinese Parents-Offspring Trios. Front Genet 2022; 13:878036. [PMID: 35559026 PMCID: PMC9087589 DOI: 10.3389/fgene.2022.878036] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is one of the most prevalent and heritable childhood behavioral disorders. Although a number of ADHD-susceptible regions had been identified, details about the variations of genes and their related patterns involved in ADHD are still lacking. In this study, we collected 25 Chinese parents-offspring trios, each of which consisted of a child diagnosed with ADHD and his/her unaffected parents, and analyzed the variations from whole-genome sequencing data. SNVs in reported ADHD-susceptible regions and on the genes whose functions were related to dopamine were screened, and we identified a set of variants with functional annotations which were specifically detected in ADHD children, including most SNVs in the gene coding region that might impair protein functions and a few SNVs in promoter or 3' untranslated region (3'-UTR) that might affect the regulation of relative gene expression in a transcriptional or posttranscriptional level. All the information may further contribute to the understanding, prediction, prevention, and treatment of ADHD in clinical.
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Affiliation(s)
- Qianqian Li
- Department of Psychological Counseling, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yingying Meng
- School of Medicine, Nankai University, Tianjin, China
| | - Jingyang Wang
- School of Medicine, Nankai University, Tianjin, China
| | - Yuhang Xie
- School of Medicine, Nankai University, Tianjin, China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Wei Sun
- School of Medicine, Nankai University, Tianjin, China
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40
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Zhou C, Sun Y, Gong Z, Li J, Zhao X, Yang Q, Yu H, Ye J, Liang J, Jiang L, Zhang D, Shen Z, Zheng S. FAT1 and MSH2 Are Predictive Prognostic Markers for Chinese Osteosarcoma Patients Following Chemotherapeutic Treatment. J Bone Miner Res 2022; 37:885-895. [PMID: 35279875 DOI: 10.1002/jbmr.4545] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/24/2022] [Accepted: 03/09/2022] [Indexed: 11/10/2022]
Abstract
Osteosarcoma is characterized by diverse genetic mutations, including single-nucleotide variants (SNVs), which can complicate clinical outcomes of the treatment. This study identified key mutations or polymorphisms in genes that correlate with osteosarcoma prognoses. A total of 110 patients with osteosarcoma were assigned to "good" or "poor" cohorts depending on their 5-year disease-free survival (DFS) after surgery and chemotherapeutic treatment. We performed next-generation sequencing analysis of tumor tissues for prognosis-associated SNVs in 315 tumorigenesis-related genes, followed by modeling of clinical outcomes for these patients using random forest classification via a support vector machine (SVM). Data from the Chinese Millionome Database were used to compare SNV frequency in osteosarcoma patients and healthy people. SVM screening identified 17 nonsynonymous SNVs located in 15 genes, of which rs17224367 and rs3733406 (located in MSH2 and FAT1, respectively) were strongly correlated with osteosarcoma prognosis. These results were verified in a 26-patient validation cohort, confirming that these SNVs could be used to predict prognosis. These results demonstrated that two SNVs located in MSH2 and FAT1 are associated with prognosis of osteosarcoma patients. © 2022 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Chenliang Zhou
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yong Sun
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Ziying Gong
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, China.,Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing, China
| | - Jieyi Li
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, China.,Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing, China
| | - Xiaokai Zhao
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, China.,Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing, China
| | - Quanjun Yang
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Hongjie Yu
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, China.,Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing, China
| | - Jianwei Ye
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, China.,Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing, China
| | - Jinrong Liang
- Medical School, Anhui University of Science and Technology, Huainan, China
| | - Linlan Jiang
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Daoyun Zhang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, China.,Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing, China
| | - Zan Shen
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shuier Zheng
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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41
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Rath D, Rapp V, Schwartz J, Winter S, Emschermann F, Arnold D, Rheinlaender J, Büttcher M, Strebl M, Braun MB, Altgelt K, Uribe ÁP, Schories C, Canjuga D, Schaeffeler E, Borst O, Schäffer TE, Langer H, Stehle T, Schwab M, Geisler T, Gawaz M, Chatterjee M. Homophilic Interaction Between Transmembrane-JAM-A and Soluble JAM-A Regulates Thrombo-Inflammation: Implications for Coronary Artery Disease. JACC Basic Transl Sci 2022; 7:445-461. [PMID: 35663628 PMCID: PMC9156439 DOI: 10.1016/j.jacbts.2022.03.003] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 11/02/2022]
Abstract
Genetic predisposition through F11R-single-nucleotide variation (SNV) influences circulatory soluble junctional adhesion molecule-A (sJAM-A) levels in coronary artery disease (CAD) patients. Homozygous carriers of the minor alleles (F11R-SNVs rs2774276, rs790056) show enhanced levels of thrombo-inflammatory sJAM-A. Both F11R-SNVs and sJAM-A are associated with worse prognosis for recurrent myocardial infarction in CAD patients. Platelet surface-associated JAM-A correlate with platelet activation markers in CAD patients. Activated platelets shed transmembrane-JAM-A, generating proinflammatory sJAM-A and JAM-A-bearing microparticles. Platelet transmembrane-JAM-A and sJAM-A as homophilic interaction partners exaggerate thrombotic and thrombo-inflammatory platelet monocyte interactions. Therapeutic strategies interfering with this homophilic interface may regulate thrombotic and thrombo-inflammatory platelet response in cardiovascular pathologies where circulatory sJAM-A levels are elevated.
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Key Words
- ACM, all-cause mortality
- ACS, acute coronary syndrome
- ADP, adenosine diphosphate
- CAD, coronary artery disease
- CCS, chronic coronary syndrome
- CE, combined endpoint
- HC, homozygous carriers
- IS, ischemic stroke
- JAM-A
- JAM-A, junctional adhesion molecule-A
- MI, myocardial infarction
- SNV
- SNV, single-nucleotide variation
- TRAP, thrombin receptor activating peptide
- coronary artery disease
- platelet
- sJAM-A, soluble junctional adhesion molecule-A
- smJAM-A, soluble murine junctional adhesion molecule-A
- thrombo-inflammation
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Affiliation(s)
- Dominik Rath
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Vera Rapp
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Jessica Schwartz
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Winter
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Tübingen, Germany
| | - Frederic Emschermann
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Daniel Arnold
- Institute of Applied Physics, University of Tübingen, Tübingen, Germany
| | | | - Manuela Büttcher
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Michael Strebl
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Michael B. Braun
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Konstanze Altgelt
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Álvaro Petersen Uribe
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Christoph Schories
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Denis Canjuga
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Elke Schaeffeler
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Tübingen, Germany
| | - Oliver Borst
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
- DFG Heisenberg Group Thrombocardiology, Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | | | - Harald Langer
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Tübingen, Germany
- Department of Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany
- Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Tobias Geisler
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Meinrad Gawaz
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Madhumita Chatterjee
- Department of Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
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Spurna Z, Capkova P, Srovnal J, Duchoslavova J, Punova L, Aleksijevic D, Vrtel R. Clinical impact of variants in non-coding regions of SHOX - Current knowledge. Gene 2022; 818:146238. [PMID: 35074420 DOI: 10.1016/j.gene.2022.146238] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 01/21/2023]
Abstract
The short stature homeobox-containing (SHOX) is the most frequently analysed gene in patients classified as short stature patients (ISS) or diagnosed with Leri-Weill dyschondrosteosis (LWD), Langer mesomelic dysplasia (LMD), or Madelung deformity (MD). However, clinical testing of this gene focuses primarily on single nucleotide variants (SNV) in its coding sequences and copy number variants (CNV) overlapping SHOX gene. This review summarizes the clinical impact of variants in noncoding regions of SHOX. RECENT FINDINGS: CNV extending exclusively into the regulatory elements (i.e., not interrupting the coding sequence) are found more frequently in downstream regulatory elements of SHOX. Further, duplications are more frequent than deletions. Interestingly, downstream duplications are more common than deletions in patients with ISS or LWD but no such differences exist for upstream CNV. Moreover, the presence of specific CNVs in the patient population suggests the involvement of additional unknown factors. Some of its intronic variants, notably NM_000451.3(SHOX):c.-9delG and c.-65C>A in the 5'UTR, have unclear clinical roles. However, these intronic SNV may increase the probability that other CNV will arise de novo in the SHOX gene based on homologous recombination or incorrect splicing of mRNA. SUMMARY: This review highlights the clinical impact of noncoding changes in the SHOX gene and the need to apply new technologies and genotype-phenotype correlation in their analysis.
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Affiliation(s)
- Zuzana Spurna
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic.
| | - Pavlina Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Josef Srovnal
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jana Duchoslavova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Lucia Punova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Darina Aleksijevic
- Department of Paediatrics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Radek Vrtel
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
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Li K, Wang AKY, Liu S, Fang S, Lu AZ, Shen J, Yang L, Hu CD, Yang K, Wan J. Advanced Functions Embedded in the Second Version of Database, Global Evaluation of SARS-CoV-2/hCoV-19 Sequences 2. Front Med (Lausanne) 2022; 9:813964. [PMID: 35479940 PMCID: PMC9037956 DOI: 10.3389/fmed.2022.813964] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/07/2022] [Indexed: 11/22/2022] Open
Abstract
The Global Evaluation of SARS-CoV-2/hCoV-19 Sequences 2 (GESS v2 https://shiny.ph.iu.edu/GESS_v2/) is an updated version of GESS, which has offered a handy query platform to analyze single-nucleotide variants (SNVs) on millions of high coverages and high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) complete genomes provided by the Global Initiative on Sharing Avian Influenza Data (GISAID). Including the tools in the first version, the GESS v2 is embedded with new functions, which allow users to search SNVs, given the viral nucleotide or amino acid sequence. The GESS v2 helps users to identify SNVs or SARS-CoV-2 lineages enriched in countries of user's interest and show the migration path of a selected lineage on a world map during specific time periods chosen by the users. In addition, the GESS v2 can recognize the dynamic variations of newly emerging SNVs in each month to help users monitor SNVs, which will potentially become dominant soon. More importantly, multiple sets of analyzed results about SNVs can be downloaded directly from the GESS v2 by which users can conduct their own independent research. With these significant updates, the GESS v2 will continue to serve as a public open platform for researchers to explore SARS-CoV-2 evolutionary patterns from the perspectives of the prevalence and impact of SNVs.
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Affiliation(s)
- Kailing Li
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | | | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
- Collaborative Core for Cancer Bioinformatics (CB) shared by Indiana University Simon Comprehensive Cancer Center and Purdue University Center for Cancer Research, West Lafayette, IN, United States
| | - Shuyi Fang
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Alex Z. Lu
- Park Tudor School, Indianapolis, IN, United States
| | - Jikui Shen
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lei Yang
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Chang-Deng Hu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Kai Yang
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jun Wan
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
- Collaborative Core for Cancer Bioinformatics (CB) shared by Indiana University Simon Comprehensive Cancer Center and Purdue University Center for Cancer Research, West Lafayette, IN, United States
- The Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
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Abstract
Single-cell sequencing technologies are revolutionizing cancer research and are poised to become the standard for translational cancer studies. Rapidly decreasing costs and increasing throughput and resolution are paving the way for the adoption of single-cell technologies in clinical settings for personalized medicine applications. In this chapter, we review the state of the art of single-cell DNA and RNA sequencing technologies, the computational tools to analyze the data, and their potential application to precision oncology. We also discuss the advantages of single-cell over bulk sequencing for the dissection of intra-tumor heterogeneity and the characterization of subclonal cell populations, the implementation of targeted drug repurposing approaches, and describe advanced methodologies for multi-omics data integration and to assess cell signaling at single-cell resolution.
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Affiliation(s)
- David T Melnekoff
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alessandro Laganà
- Department of Genetics and Genomic Sciences, Department of Oncological Sciences, Mount Sinai Icahn School of Medicine, New York, NY, USA.
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Dugan AJ, Nelson PT, Katsumata Y, Shade LMP, Teylan MA, Boehme KL, Mukherjee S, Kauwe JSK, Hohman TJ, Schneider JA, Fardo DW. Association between WWOX/MAF variants and dementia-related neuropathologic endophenotypes. Neurobiol Aging 2022; 111:95-106. [PMID: 34852950 PMCID: PMC8761217 DOI: 10.1016/j.neurobiolaging.2021.10.011] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/30/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022]
Abstract
The genetic locus containing the WWOX and MAF genes was implicated as a clinical Alzheimer's disease (AD) risk locus in two recent large meta-analytic genome wide association studies (GWAS). In a prior GWAS, we identified a variant in WWOX as a suggestive risk allele for hippocampal sclerosis. We hypothesized that the WWOX/MAF locus may be preferentially associated with non-plaque- and non-tau-related neuropathological changes (NC). Data from research participants with GWAS and autopsy measures from the National Alzheimer's Coordinating Center and the Religious Orders Study and the Rush Memory and Aging Project were meta-analyzed. Notably, no variants in the locus were significantly associated with ADNC. However, several WWOX/MAF variants had significant adjusted associations with limbic-predominant age-related TDP-43 encephalopathy NC (LATE-NC), HS, and brain arteriolosclerosis. These associations remained largely unchanged after adjustment for ADNC (operationalized with standard semiquantitative staging), suggesting that these associations are independent of ADNC. Thus, WWOX genetic variants were associated pathologically with LATE-NC, not ADNC.
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Affiliation(s)
- Adam J Dugan
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA; Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | - Yuriko Katsumata
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA; Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA
| | - Lincoln M P Shade
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Merilee A Teylan
- National Alzheimer's Coordinating Center, Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Kevin L Boehme
- Department of Biology, Brigham Young University, Provo, UT, USA
| | | | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | - Timothy J Hohman
- Vanderbilt Memory & Alzheimer's Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julie A Schneider
- Departments of Neurology and Pathology, Rush University Medical Center, Chicago, IL, USA
| | - David W Fardo
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA; Sanders-Brown Center on Aging and Alzheimer's Disease Research Center, University of Kentucky, Lexington, KY, USA.
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46
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Benet-Pagès A, Rosenbloom KR, Nassar LR, Lee CM, Raney BJ, Clawson H, Schmelter D, Casper J, Gonzalez JN, Perez G, Lee BT, Zweig AS, James Kent W, Haeussler M, Kuhn RM. Variant Interpretation: UCSC Genome Browser Recommended Track Sets. Hum Mutat 2022; 43:998-1011. [PMID: 35088925 PMCID: PMC9288501 DOI: 10.1002/humu.24335] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/30/2021] [Accepted: 01/25/2022] [Indexed: 11/11/2022]
Abstract
The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of the human genome was first released in 2000. As it has grown in scope to display more types of data it has also grown more complicated. The data, which are dispersed at many locations worldwide, are collected into one view on the Browser, where the graphical interface presents the data in one location. This supports the expertise of the researcher to interpret variants in the genome. Because the analysis of Single Nucleotide Variants (SNVs) and Copy Number Variants (CNVs) require interpretation of data at very different genomic scales, different data resources are required. We present here several Recommended Track Sets designed to facilitate the interpretation of variants in the clinic, offering quick access to datasets relevant to the appropriate scale. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Anna Benet-Pagès
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Medical Genetics Center (MGZ), Munich, Germany
| | - Kate R Rosenbloom
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Luis R Nassar
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Christopher M Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Brian J Raney
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Hiram Clawson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Daniel Schmelter
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jonathan Casper
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | - Gerardo Perez
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Brian T Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Ann S Zweig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - W James Kent
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | - Robert M Kuhn
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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47
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Chen J, He J, Luo J, Zhong S. Association of αENaC p. Ala663Thr Gene Polymorphism With Sudden Sensorineural Hearing Loss. Front Genet 2022; 12:659517. [PMID: 35024042 PMCID: PMC8744410 DOI: 10.3389/fgene.2021.659517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 12/08/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: The etiology of sudden sensorineural hearing loss (SSNHL) is still unknown. It has been demonstrated that normal endolymph metabolism is essential for inner ear function and that epithelial sodium channels (ENaC) may play an important role in the regulation of endolymphatic Na+. This study aimed to explore the potential association between αENaC p. Ala663Thr gene polymorphism and SSNHL. Methods: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to examine the genotype and allele frequency of the αENaC p. Ala663Thr polymorphism in 20 cases of low-frequency SSNHL (LF-SSNHL), 19 cases of high-frequency SSNHL (HF-SSNHL), 31 cases of all frequency SSNHL (AF-SSNHL), 42 cases of profound deafness SSNHL (PD-SSNHL), and 115 normal controls. Results: The T663 allele was found to be significantly associated with an increased risk of LF-SSNHL (p = 0.046, OR = 2.16, 95% CI = 1.01-4.62). The TT genotype and T663 allele, on the other hand, conferred a protective effect for PD-SSNHL (AA vs. TT: p = 0.012, OR = 0.25, 95% CI = 0.08-0.74; A vs. T: p = 0.001, OR = 0.36, 95% CI = 0.21-0.61). However, there was no statistically significant difference in genotype or allele frequency between the two groups (HF-SSNHL and AF-SSNHL) and the control group. Conclusion: The αENaC p. Ala663Thr gene polymorphism plays different roles in different types of SSNHL.
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Affiliation(s)
- Jialei Chen
- Department of Pathology and Pathophysiology, Chongqing Medical University, Chongqing, China
| | - Jing He
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Luo
- Department of Pathology and Pathophysiology, Chongqing Medical University, Chongqing, China
| | - Shixun Zhong
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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48
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Abstract
High-throughput sequencing (HTS) technologies have contributed to expand current knowledge of the biology of complex diseases, including nonalcoholic fatty liver disease (NAFLD). Genome-wide association studies, whole exome sequencing, and sequencing of entire genes are used to identify variants and/or mutations that predispose to the disease pathogenesis. Here, we present a tutorial that may guide readers to manage high volume of genetics data in the context of Next-Generation Sequencing (NGS) studies.
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Affiliation(s)
- Adrian Salatino
- School of Medicine, Institute of Medical Research A Lanari, University of Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Department of Molecular Genetics and Biology of Complex Diseases, Institute of Medical Research (IDIM), National Scientific and Technical Research Council (CONICET)-University of Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Silvia Sookoian
- School of Medicine, Institute of Medical Research A Lanari, University of Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
- Department of Clinical and Molecular Hepatology, Institute of Medical Research (IDIM), National Scientific and Technical Research Council (CONICET)-University of Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Carlos J Pirola
- School of Medicine, Institute of Medical Research A Lanari, University of Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
- Department of Molecular Genetics and Biology of Complex Diseases, Institute of Medical Research (IDIM), National Scientific and Technical Research Council (CONICET)-University of Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
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49
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Ruff DW, Dhingra DM, Thompson K, Marin JA, Ooi AT. High-Throughput Multimodal Single-Cell Targeted DNA and Surface Protein Analysis Using the Mission Bio Tapestri Platform. Methods Mol Biol 2022; 2386:171-188. [PMID: 34766272 DOI: 10.1007/978-1-0716-1771-7_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An important aspect of understanding cancer biology is to connect the diverse repertoire of genotype-to-phenotype displays in individual specimens and ultimately resolve disease course outcome through informative datasets. A focus of cancer genomics has strived to provide predictive capabilities using genomic information to further inform therapeutic strategies. The advent of single-cell sequencing and analysis now provides a route to decipher high-resolution genomic diversity in individual samples and facilitate detailed understanding of clonal evolution in clinical research settings. In addition to generating high-throughput single-cell genomic SNV and CNV data, this protocol describes a new analytical ability that adds a second dimension which provides for interrogation of surface protein marker expression. The first immediate application of this technology is quite suitable to heme cancer cell studies. This multimodal approach allows for correlation of diverse genomic signatures to key phenotypic biomarkers such as immunophenotypes in leukemic diseases.
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Affiliation(s)
| | | | | | | | - Aik T Ooi
- Mission Bio, Inc., South San Francisco, CA, USA.
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50
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Zhu W, Zhang J, Yuan X, Liu X, Zhang Z, Mao Y, Feng Y, Yue A, Sun J, Wen C, Xu J, Shen Y, Che Y, Du J. Whole-exome sequencing reveals novel candidate single nucleotide variations for preventing adverse effects of levonorgestrel implantation. Pharmacogenomics 2021; 22:1185-1199. [PMID: 34783250 DOI: 10.2217/pgs-2021-0105] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To identify novel genes associated with adverse effects of levonorgestrel (LNG) implants based on comparative whole-exome sequencing. Materials & methods: A cohort comprising 104 participants, including 52 controls and 52 women with LNG-related adverse effects, was recruited. Seven cases and eight controls were selected for whole-exome sequencing. We verified 13 single nucleotide variations (SNVs) related with integrin-mediated signaling pathway and cell proliferation using the MassARRAY platform. Results: Finally, we screened 49 cases and 52 controls for analyses. Two SNVs (rs7255721 and rs1042522) were located in ADAMTS10 and TP53, respectively, and significantly different between two groups. These two SNVs lead to changes in protein structure and physicochemical parameters. Conclusion: Here, we defined two pathogenic mutations related to adverse LNG effects.
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Affiliation(s)
- Weiqiang Zhu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Junxian Zhang
- Department of Family Planning, Maternal & Child Health Care Hospital of Xinjiang Uygur Autonomous Region, Xinjiang 830001, China
| | - Xuelian Yuan
- Hami Central Hospital, Xinjiang Medical University, Xinjiang 830099, China
| | - Xiaoli Liu
- Chongqing Health Center for Women & Children, Chongqing 400010, China
| | - Zhaofeng Zhang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Yanyan Mao
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Ying Feng
- Department of Family Planning, Maternal & Child Health Care Hospital of Xinjiang Uygur Autonomous Region, Xinjiang 830001, China
| | - Ailing Yue
- Hami Central Hospital, Xinjiang Medical University, Xinjiang 830099, China
| | - Junjie Sun
- Chongqing Health Center for Women & Children, Chongqing 400010, China
| | - Chuan Wen
- Hami Central Hospital, Xinjiang Medical University, Xinjiang 830099, China
| | - Jianhua Xu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Yupei Shen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Yan Che
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Jing Du
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
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