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Rupar N, Šelb J, Košnik M, Zidarn M, Andrejević S, Čulav L, Grivčeva-Panovska V, Korošec P, Rijavec M. The CC2D2B is a novel genetic modifier of the clinical phenotype in patients with hereditary angioedema due to C1 inhibitor deficiency. Gene 2024; 919:148496. [PMID: 38679185 DOI: 10.1016/j.gene.2024.148496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
Hereditary angioedema due to C1 inhibitor deficiency (HAE-C1-INH) is a rare genetic disorder caused by pathogenic variants in the SERPING1 gene and characterised by swelling and a highly variable clinical phenotype. We aimed to identify novel modifying genetic factors predisposing to the clinical symptoms. We performed whole exome sequencing (WES) and comprehensive bioinformatic analysis in symptomatic and asymptomatic (three duos) family members with HAE-C1-INH. Selected variants identified using WES (present in all asymptomatic and absent in symptomatic patients) were determined using Sanger sequencing. We included 88 clinically well-characterised HAE-C1-INH patients from south-eastern Europe (nine asymptomatic) from 42 unrelated families. We identified 39 variants in 23 genes (ANKRD36C, ARGFX, CC2D2B, IL5RA, IRF2BP2, LGR6, MRPL45, MUC3A, NPIPA1, NRG1, OR5M1, OR5M3, OR5M10, OR8U3, PLCL1, PRSS3, PSKH2, PTPRA, RTP4, SEZ6, SLC25A5, VWA3A, and ZNF790). We selected variants in CC2D2B and PLCL1, which were analysed using Sanger sequencing in the entire group of HAE-C1-INH. We found significant differences in the frequencies of the CC2D2B c.190A>G (rs17383738) variant between symptomatic and asymptomatic patients, where heterozygotes were more common in asymptomatic HAE-C1-INH patients in comparison to symptomatic patients (55 % vs 23%; P = 0.049, OR = 4.24, 95% CI 1.07-14.69). Our study identified novel genetic factors that modify the clinical variability of HAE-C1-INH. We further demonstrated, in a large cohort, the importance of the CC2D2B gene as a disease-modifying factor. Based on linkage disequilibrium analysis, the CCNJ and ZNF518A genes might also be involved in the clinical variability of HAE-C1-INH.
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Affiliation(s)
- Nina Rupar
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
| | - Julij Šelb
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia; Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Mitja Košnik
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia; Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Mihaela Zidarn
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia; Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Slađana Andrejević
- Clinic of Allergology and Immunology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Ljerka Čulav
- General Hospital Šibenik, 22000 Šibenik, Croatia
| | - Vesna Grivčeva-Panovska
- Dermatology Clinic, School of Medicine, Ss. Cyril and Methodius University, 1000 Skopje, Republic of Macedonia
| | - Peter Korošec
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia; Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia; Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia; Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia.
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Dobner J, Nguyen T, Pavez-Giani MG, Cyganek L, Distelmaier F, Krutmann J, Prigione A, Rossi A. mtDNA analysis using Mitopore. Mol Ther Methods Clin Dev 2024; 32:101231. [PMID: 38572068 PMCID: PMC10988129 DOI: 10.1016/j.omtm.2024.101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
Mitochondrial DNA (mtDNA) analysis is crucial for the diagnosis of mitochondrial disorders, forensic investigations, and basic research. Existing pipelines are complex, expensive, and require specialized personnel. In many cases, including the diagnosis of detrimental single nucleotide variants (SNVs), mtDNA analysis is still carried out using Sanger sequencing. Here, we developed a simple workflow and a publicly available webserver named Mitopore that allows the detection of mtDNA SNVs, indels, and haplogroups. To simplify mtDNA analysis, we tailored our workflow to process noisy long-read sequencing data for mtDNA analysis, focusing on sequence alignment and parameter optimization. We implemented Mitopore with eliBQ (eliminate bad quality reads), an innovative quality enhancement that permits the increase of per-base quality of over 20% for low-quality data. The whole Mitopore workflow and webserver were validated using patient-derived and induced pluripotent stem cells harboring mtDNA mutations. Mitopore streamlines mtDNA analysis as an easy-to-use fast, reliable, and cost-effective analysis method for both long- and short-read sequencing data. This significantly enhances the accessibility of mtDNA analysis and reduces the cost per sample, contributing to the progress of mtDNA-related research and diagnosis.
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Affiliation(s)
- Jochen Dobner
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Thach Nguyen
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Mario Gustavo Pavez-Giani
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Lukas Cyganek
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jean Krutmann
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andrea Rossi
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
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Yi H, Yun Y, Choi WH, Hwang HY, Cha JH, Seok H, Song JJ, Lee JH, Lee SY, Kim D. CRISPR-based editing strategies to rectify EYA1 complex genomic rearrangement linked to haploinsufficiency. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102199. [PMID: 38766525 PMCID: PMC11101721 DOI: 10.1016/j.omtn.2024.102199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/21/2024] [Indexed: 05/22/2024]
Abstract
Pathogenic structure variations (SVs) are associated with various types of cancer and rare genetic diseases. Recent studies have used Cas9 nuclease with paired guide RNAs (gRNAs) to generate targeted chromosomal rearrangements, focusing on producing fusion proteins that cause cancer, whereas research on precision genome editing for rectifying SVs is limited. In this study, we identified a novel complex genomic rearrangement (CGR), specifically an EYA1 inversion with a deletion, implicated in branchio-oto-renal/branchio-oto syndrome. To address this, two CRISPR-based approaches were tested. First, we used Cas9 nuclease and paired gRNAs tailored to the patient's genome. The dual CRISPR-Cas9 system induced efficient correction of paracentric inversion in patient-derived fibroblast, and effectively restored the expression of EYA1 mRNA and protein, along with its transcriptional activity required to regulate the target gene expression. Additionally, we used CRISPR activation (CRISPRa), which leads to the upregulation of EYA1 mRNA expression in patient-derived fibroblasts. Moreover, CRISPRa significantly improved EYA1 protein expression and transcriptional activity essential for target gene expression. This suggests that CRISPRa-based gene therapies could offer substantial translational potential for approximately 70% of disease-causing EYA1 variants responsible for haploinsufficiency. Our findings demonstrate the potential of CRISPR-guided genome editing for correcting SVs, including those with EYA1 CGR linked to haploinsufficiency.
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Affiliation(s)
- Hwalin Yi
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Yejin Yun
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Won Hoon Choi
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Hye-Yeon Hwang
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Ju Hyuen Cha
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Heeyoung Seok
- Department of Transdisciplinary Research and Collaboration, Genomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, South Korea
| | - Jae-Jin Song
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, South Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
| | - Daesik Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
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Yi X, Kemppainen P, Merilä J. SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering. Mol Ecol Resour 2024:e13985. [PMID: 38850116 DOI: 10.1111/1755-0998.13985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024]
Abstract
Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.
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Affiliation(s)
- Xueling Yi
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Petri Kemppainen
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Juha Merilä
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme, University of Helsinki, Helsinki, Finland
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Choi YJ, Fischer K, Méité A, Koudou BG, Fischer PU, Mitreva M. Distinguishing recrudescence from reinfection in lymphatic filariasis. EBioMedicine 2024; 105:105188. [PMID: 38848649 DOI: 10.1016/j.ebiom.2024.105188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The Global Program to Eliminate Lymphatic Filariasis (GPELF) is the largest public health program based on mass drug administration (MDA). Despite decades of MDA, ongoing transmission in some countries remains a challenge. To optimise interventions, it is critical to differentiate between recrudescence and new infections. Since adult filariae are inaccessible in humans, deriving a method that relies on the offspring microfilariae (mf) is necessary. METHODS We developed a genome amplification and kinship analysis-based approach using Brugia malayi samples from gerbils, and applied it to analyse Wuchereria bancrofti mf from humans in Côte d'Ivoire. We examined the pre-treatment genetic diversity in 269 mf collected from 18 participants, and further analysed 1-year post-treatment samples of 74 mf from 4 participants. Hemizygosity of the male X-chromosome allowed for direct inference of haplotypes, facilitating robust maternal parentage inference. To enrich parasite DNA from samples contaminated with host DNA, a whole-exome capture panel was created for W. bancrofti. FINDINGS By reconstructing and temporally tracking sibling relationships across pre- and post-treatment samples, we differentiated between new and established maternal families, suggesting reinfection in one participant and recrudescence in three participants. The estimated number of reproductively active adult females ranged between 3 and 11 in the studied participants. Population structure analysis revealed genetically distinct parasites in Côte d'Ivoire compared to samples from other countries. Exome capture identified protein-coding variants with ∼95% genotype concordance rate. INTERPRETATION We have generated resources to facilitate the development of molecular genetic tools that can estimate adult worm burdens and monitor parasite populations, thus providing essential information for the successful implementation of GPELF. FUNDING This work was financially supported by the Bill and Melinda Gates Foundation (https://www.gatesfoundation.org) under grant OPP1201530 (Co-PIs PUF & Gary J. Weil). B. malayi parasite material was generated with support of the Foundation for Barnes Jewish Hospital (PUF). In addition, the development of computational methods was supported by the National Institutes of Health under grants AI144161 (MM) and AI146353 (MM). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Affiliation(s)
- Young-Jun Choi
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kerstin Fischer
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Aboulaye Méité
- Programme National de la Lutte Contre la Schistosomiase, Les Geohelminthiases et la Filariose Lymphatique, Abidjan, Côte d'Ivoire
| | - Benjamin G Koudou
- Centre Suisse de Recherche Scientifique en Côte d'Ivoire, Abidjan, Côte d'Ivoire; Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Peter U Fischer
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Makedonka Mitreva
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
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6
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Pujari AN, Cullen PJ. Modulators of MAPK pathway activity during filamentous growth in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2024; 14:jkae072. [PMID: 38560781 PMCID: PMC11152069 DOI: 10.1093/g3journal/jkae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 12/22/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Mitogen-activated protein kinase (MAPK) pathways control the response to intrinsic and extrinsic stimuli. In the budding yeast Saccharomyces cerevisiae, cells undergo filamentous growth, which is regulated by the fMAPK pathway. To better understand the regulation of the fMAPK pathway, a genetic screen was performed to identify spontaneous mutants with elevated activity of an fMAPK pathway-dependent growth reporter (ste4 FUS1-HIS3). In total, 159 mutants were isolated and analyzed by secondary screens for invasive growth by the plate-washing assay and filament formation by microscopy. Thirty-two mutants were selected for whole-genome sequencing, which identified new alleles in genes encoding known regulators of the fMAPK pathway. These included gain-of-function alleles in STE11, which encodes the MAPKKK, as well as loss-of-function alleles in KSS1, which encodes the MAP kinase, and loss-of-function alleles in RGA1, which encodes a GTPase-activating protein (GAP) for CDC42. New alleles in previously identified pathway modulators were also uncovered in ALY1, AIM44, RCK2, IRA2, REG1, and in genes that regulate protein folding (KAR2), glycosylation (MNN4), and turnover (BLM10). Mutations leading to C-terminal truncations in the transcription factor Ste12p were also uncovered that resulted in elevated reporter activity, identifying an inhibitory domain of the protein from residues 491 to 688. We also find that a diversity of filamentous growth phenotypes can result from combinatorial effects of multiple mutations and by loss of different regulators of the response. The alleles identified here expand the connections surrounding MAPK pathway regulation and reveal new features of proteins that function in the signaling cascade.
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Affiliation(s)
- Atindra N Pujari
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Paul J Cullen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
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Song X, Yao Z, Zhang Z, Lyu S, Chen N, Qi X, Liu X, Ma W, Wang W, Lei C, Jiang Y, Wang E, Huang Y. Whole-genome sequencing reveals genomic diversity and selection signatures in Xia'nan cattle. BMC Genomics 2024; 25:559. [PMID: 38840048 PMCID: PMC11151506 DOI: 10.1186/s12864-024-10463-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 05/28/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. Xia'nan cattle, a crossbreed of Charolais and Nanyang cattle, is China's first specialized beef cattle breed with independent intellectual property rights. After more than two decades of selective breeding, Xia'nan cattle exhibit a robust physique, good environmental adaptability, good tolerance to coarse feed, and high meat production rates. This study analyzed the population genetic structure, genetic diversity, and genomic variations of Xia'nan cattle using whole-genome sequencing data from 30 Xia'nan cattle and 178 published cattle genomic data. RESULT The ancestry estimating composition analysis showed that the ancestry proportions for Xia'nan cattle were mainly Charolais with a small amount of Nanyang cattle. Through the genetic diversity studies (nucleotide diversity and linkage disequilibrium decay), we found that the genomic diversity of Xia'nan cattle is higher than that of specialized beef cattle breeds in Europe but lower than that of Chinese native cattle. Then, we used four methods to detect genome candidate regions influencing the excellent traits of Xia'nan cattle. Among the detected results, 42 genes (θπ and CLR) and 131 genes (FST and XP-EHH) were detected by two different detection strategies. In addition, we found a region in BTA8 with strong selection signals. Finally, we conducted functional annotation on the detected genes and found that these genes may influence body development (NR6A1), meat quality traits (MCCC1), growth traits (WSCD1, TMEM68, MFN1, NCKAP5), and immunity (IL11RA, CNTFR, CCL27, SLAMF1, SLAMF7, NAA35, and GOLM1). CONCLUSION We elucidated the genomic features and population structure of Xia'nan cattle and detected some selection signals in genomic regions potentially associated with crucial economic traits in Xia'nan cattle. This research provided a basis for further breeding improvements in Xia'nan cattle and served as a reference for genetic enhancements in other crossbreed cattle.
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Affiliation(s)
- Xingya Song
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China
| | - Zhi Yao
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Shijie Lyu
- Institute of Animal Husbandry, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China
| | - Xingshan Qi
- Biyang County Xiananniu Technology Development Co., Ltd, Zhumadian, 463700, People's Republic of China
| | - Xian Liu
- Henan Provincial Livestock Technology Promotion Station, Zhengzhou, 450008, Henan, People's Republic of China
| | - Weidong Ma
- Shaanxi Agricultural and Animal Husbandry Seed Farm, Shaanxi Fufeng, 722203, People's Republic of China
| | - Wusheng Wang
- Shaanxi Agricultural and Animal Husbandry Seed Farm, Shaanxi Fufeng, 722203, People's Republic of China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China
| | - Eryao Wang
- Institute of Animal Husbandry, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, Shaanxi, People's Republic of China.
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Kase AM, Gleba J, Miller JL, Miller E, Petit J, Barrett MT, Zhou Y, Parent EE, Cai H, Knight JA, Orme J, Reynolds J, Durham WF, Metz TM, Meurice N, Edenfield B, Alasonyalilar Demirer A, Bilgili A, Hickman PG, Pawlush ML, Marlow L, Wickland DP, Tan W, Copland JA. Patient-Derived Tumor Xenograft Study with CDK4/6 Inhibitor Plus AKT Inhibitor for the Management of Metastatic Castration-Resistant Prostate Cancer. Mol Cancer Ther 2024; 23:823-835. [PMID: 38442920 DOI: 10.1158/1535-7163.mct-23-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/04/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
Metastatic castration-resistant prostate cancer (mCRPC) is an aggressive malignancy with poor outcomes. To investigate novel therapeutic strategies, we characterized three new metastatic prostate cancer patient derived-tumor xenograft (PDTX) models and developed 3D spheroids from each to investigate molecular targeted therapy combinations including CDK4/6 inhibitors (CDK4/6i) with AKT inhibitors (ATKi). Metastatic prostate cancer tissue was collected and three PDTX models were established and characterized using whole-exome sequencing. PDTX 3D spheroids were developed from these three PDTXs to show resistance patterns and test novel molecular-targeted therapies. CDK4/6i's were combined with AKTi's to assess synergistic antitumor response to prove our hypothesis that blockade of AKT overcomes drug resistance to CDK4/6i. This combination was evaluated in PDTX three-dimensional (3D) spheroids and in vivo experiments with responses measured by tumor volumes, PSA, and Ga-68 PSMA-11 PET-CT imaging. We demonstrated CDK4/6i's with AKTi's possess synergistic antitumor activity in three mCRPC PDTX models. These models have multiple unique pathogenic and deleterious genomic alterations with resistance to single-agent CDK4/6i's. Despite this, combination therapy with AKTi's was able to overcome resistance mechanisms. The IHC and Western blot analysis confirmed on target effects, whereas tumor volume, serum PSA ELISA, and radionuclide imaging demonstrated response to therapy with statistically significant SUV differences seen with Ga-68 PSMA-11 PET-CT. These preclinical data demonstrating antitumor synergy by overcoming single-agent CDK 4/6i as well as AKTi drug resistance provide the rational for a clinical trial combining a CDK4/6i with an AKTi in patients with mCRPC whose tumor expresses wild-type retinoblastoma 1.
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Affiliation(s)
- Adam M Kase
- Division of Hematology-Oncology, Mayo Clinic Jacksonville, Florida
| | - Justyna Gleba
- Cancer Biology Department, Mayo Clinic Jacksonville, Florida
| | - James L Miller
- Cancer Biology Department, Mayo Clinic Jacksonville, Florida
| | - Erin Miller
- Cancer Biology Department, Mayo Clinic Jacksonville, Florida
| | - Joachim Petit
- Division of Hematology-Oncology, Mayo Clinic Scottsdale, Arizona
| | | | - Yumei Zhou
- Division of Hematology-Oncology, Mayo Clinic Scottsdale, Arizona
| | | | - Hancheng Cai
- Radiology Department, Mayo Clinic Jacksonville, Florida
| | - Joshua A Knight
- Cancer Biology Department, Mayo Clinic Jacksonville, Florida
| | - Jacob Orme
- Division of Hematology-Oncology, Mayo Clinic Rochester, Minnesota
| | - Jordan Reynolds
- Department of Laboratory Medicine and Pathology, Mayo Clinic Jacksonville, Florida
| | | | - Thomas M Metz
- Charles River Discovery Research Services Germany, Freiburg, Germany
| | - Nathalie Meurice
- Division of Hematology-Oncology, Mayo Clinic Scottsdale, Arizona
| | | | | | - Ahmet Bilgili
- Cancer Biology Department, Mayo Clinic Jacksonville, Florida
| | | | | | - Laura Marlow
- Cancer Biology Department, Mayo Clinic Jacksonville, Florida
| | - Daniel P Wickland
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic Jacksonville, Florida
| | - Winston Tan
- Division of Hematology-Oncology, Mayo Clinic Jacksonville, Florida
| | - John A Copland
- Cancer Biology Department, Mayo Clinic Jacksonville, Florida
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Choudhury AD, Kwak L, Cheung A, Allaire KM, Marquez J, Yang DD, Tripathi A, Kilar JM, Flynn M, Maynard B, Reichel R, Pace AF, Chen BK, Van Allen EM, Kilbridge K, Wei XX, McGregor BA, Pomerantz MM, Bhatt RS, Sweeney CJ, Bubley GJ, Jacene HA, Taplin ME, Huang FW, Harshman LC, Fong L. Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer. Cancer Immunol Res 2024; 12:704-718. [PMID: 38552171 PMCID: PMC11148544 DOI: 10.1158/2326-6066.cir-22-0306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/15/2023] [Accepted: 03/08/2024] [Indexed: 06/05/2024]
Abstract
The checkpoint immunotherapeutic pembrolizumab induces responses in a small minority of patients with metastatic castration-resistant prostate cancer (mCRPC). Radium-223 (R223) may increase immunogenicity of bone metastases and increase pembrolizumab (P) activity. In a randomized phase II study, we assessed the effect of R223+P compared with R223 on tumor immune infiltration, safety, and clinical outcomes in patients with mCRPC. The primary endpoint was differences in CD4+ and CD8+ T-cell infiltrate in 8-week versus baseline bone metastasis biopsies; secondary endpoints were safety, radiographic progression-free survival (rPFS), and overall survival (OS). Of the 42 treated patients (29 R223+P, 13 R223), 18 R223+P and 8 R223 patients had evaluable paired tumor biopsies. Median fold-change of CD4+ T cells was -0.7 (range: -9.3 to 4.7) with R223+P and 0.1 (-11.1 to 3.7) with R223 (P = 0.66); for CD8+ T cells, median fold-change was -0.6 (-7.4 to 5.3) with R223+P and -1.3 (-3.1 to 4.8) with R223 (P = 0.66). Median rPFS and OS was 6.1 (95% confidence interval: 2.7-11.0) and 16.9 months [12.7-not reached (NR)], respectively, with R223+P and 5.7 (2.6-NR) and 16.0 (9.0-NR), respectively, with R223. Although R223+P was well tolerated with no unexpected toxicity, the combination did not improve efficacy. High-dimensional flow cytometry demonstrated minimal immune modulation with R223, whereas R223+P induced CTLA-4 expression on circulating CD4+ T cells. Clinical responders possessed lower circulating frequencies of Ki67+ T and myeloid cells at baseline and higher circulating frequencies of TIM-3+ T and myeloid cells by week 9. Although R223+P did not induce T-cell infiltration into the tumor microenvironment, exhaustion of induced peripheral T-cell immune responses may dampen the combination's clinical activity.
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Affiliation(s)
- Atish D Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Lucia Kwak
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alexander Cheung
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Kathryn M Allaire
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Jaqueline Marquez
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - David D Yang
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | | | | | | | | | - Rebecca Reichel
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Brandon K Chen
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Eliezer M Van Allen
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Kerry Kilbridge
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Xiao X Wei
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Bradley A McGregor
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Mark M Pomerantz
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Rupal S Bhatt
- Harvard Medical School, Boston, Massachusetts
- Beth-Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Glenn J Bubley
- Harvard Medical School, Boston, Massachusetts
- Beth-Israel Deaconess Medical Center, Boston, Massachusetts
| | - Heather A Jacene
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Franklin W Huang
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | | | - Lawrence Fong
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
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10
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Shrestha H, McCulloch K, Chisholm RH, Armoo SK, Veriegh F, Sirwani N, Crawford KE, Osei-Atweneboana MY, Grant WN, Hedtke SM. Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination. Mol Ecol 2024; 33:e17357. [PMID: 38683054 DOI: 10.1111/mec.17357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 05/01/2024]
Abstract
We present a framework for identifying when conditions are favourable for transmission of vector-borne diseases between communities by incorporating predicted disease prevalence mapping with landscape analysis of sociological, environmental and host/parasite genetic data. We explored the relationship between environmental features and gene flow of a filarial parasite of humans, Onchocerca volvulus, and its vector, blackflies in the genus Simulium. We generated a baseline microfilarial prevalence map from point estimates from 47 locations in the ecological transition separating the savannah and forest in Ghana, where transmission of O. volvulus persists despite onchocerciasis control efforts. We generated movement suitability maps based on environmental correlates with mitochondrial population structure of 164 parasites from 15 communities and 93 vectors from only four sampling sites, and compared these to the baseline prevalence map. Parasite genetic distance between sampling locations was significantly associated with elevation (r = .793, p = .005) and soil moisture (r = .507, p = .002), while vector genetic distance was associated with soil moisture (r = .788, p = .0417) and precipitation (r = .835, p = .0417). The correlation between baseline prevalence and parasite resistance surface maps was stronger than that between prevalence and vector resistance surface maps. The centre of the study area had high prevalence and suitability for parasite and vector gene flow, potentially contributing to persistent transmission and suggesting the importance of re-evaluating transmission zone boundaries. With suitably dense sampling, this framework can help delineate transmission zones for onchocerciasis and would be translatable to other vector-borne diseases.
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Affiliation(s)
- Himal Shrestha
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Karen McCulloch
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Rebecca H Chisholm
- Department of Mathematical and Physical Sciences, La Trobe University, Bundoora, Victoria, Australia
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Samuel K Armoo
- Biomedical and Public Health Research Unit, CSIR-Water Research Institute, Accra, Ghana
| | - Francis Veriegh
- Biomedical and Public Health Research Unit, CSIR-Water Research Institute, Accra, Ghana
| | - Neha Sirwani
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Katie E Crawford
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | | | - Warwick N Grant
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Shannon M Hedtke
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
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11
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Lin X, Feng M, Li Y, Liu Y, Wang M, Li Y, Yang T, Zhao C. Study on the origin of the Baise horse based on whole-genome resequencing. Anim Genet 2024; 55:410-419. [PMID: 38584302 DOI: 10.1111/age.13424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 03/09/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024]
Abstract
The Baise horse, an indigenous horse breed mainly distributed in the Baise region of Guangxi province in southwest China, has a long history as draft animal. However, there is a lack of research regarding the origin and ancestral composition of the Baise horse. In this study, whole-genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chakouyi horse into the Baise horse. In summary, our results confirm that the formation of the Baise horse did not involve participation from foreign breeds. Geographical distance emerges as a crucial factor in determining the genetic relationships with the Baise horse. Gene flows of indigenous horse breeds along ancient routes of trade activities had played a role in the formation of the Baise horse.
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Affiliation(s)
- Xiaoran Lin
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- Beijing General Station of Animal Husbandry, Beijing, China
| | - Mo Feng
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Li
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yu Liu
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Min Wang
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuanyuan Li
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Tao Yang
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunjiang Zhao
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China
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12
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Pang R, Li S, Chen W, Yuan L, Xiao H, Xing K, Li Y, Zhang Z, He X, Zhang W. Insecticide resistance reduces the profitability of insect-resistant rice cultivars. J Adv Res 2024; 60:1-12. [PMID: 37499938 PMCID: PMC11156607 DOI: 10.1016/j.jare.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/02/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023] Open
Abstract
INTRODUCTION Preventing crop yield loss caused by pests is critical for global agricultural production. Agricultural pest control has largely relied on chemical pesticides. The interaction between insecticide resistance and the adaptation of herbivorous pests to host plants may represent an emerging threat to future food security. OBJECTIVES This study aims to unveil genetic evidence for the reduction in the profitability of resistant cultivars derived from insecticide resistance in target pest insects. METHODS An experimental evolution system encompassing resistant rice and its major monophagous pest, the brown planthopper Nilaparvata lugens, was constructed. Whole genome resequencing and selective sweep analysis were utilized to identify the candidate gene loci related to the adaptation. RNA interference and induced expression assay were conducted to validate the function of the candidate loci. RESULTS We found that the imidacloprid-resistant population of N. lugens rapidly adapted to resistant rice IR36. Gene loci related to imidacloprid resistance may contribute to this phenomenon. Multiple alleles in the nicotinic acetylcholine receptor (nAChR)-7-like and P450 CYP4C61 were significantly correlated with changes in virulence to IR36 rice and insecticide resistance of N. lugens. One avirulent/susceptible genotype and two virulent/resistant genotypes could be inferred from the corresponding alleles. Importantly, we found that the virulent/resistant genotypes already exist in the wild in China, exhibiting increasing frequencies along with insecticide usage. We validated the relevance of these genotypes and the virulence to three more resistant rice cultivars. Knockdown of the above two genes in N. lugens significantly decreased both the resistance to imidacloprid and the virulence towards resistant rice. CONCLUSION Our findings provide direct genetic evidence to the eco-evolutionary consequence of insecticide resistance, and suggest an urgent need for the implementation of predictably sustainable pest management.
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Affiliation(s)
- Rui Pang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China; National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shihui Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weiwen Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Longyu Yuan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Hanxiang Xiao
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Ke Xing
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanfang Li
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Zhenfei Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
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13
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Duman ET, Sitte M, Conrads K, Mackay A, Ludewig F, Ströbel P, Ellenrieder V, Hessmann E, Papantonis A, Salinas G. A single-cell strategy for the identification of intronic variants related to mis-splicing in pancreatic cancer. NAR Genom Bioinform 2024; 6:lqae057. [PMID: 38800828 PMCID: PMC11127633 DOI: 10.1093/nargab/lqae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/24/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024] Open
Abstract
Most clinical diagnostic and genomic research setups focus almost exclusively on coding regions and essential splice sites, thereby overlooking other non-coding variants. As a result, intronic variants that can promote mis-splicing events across a range of diseases, including cancer, are yet to be systematically investigated. Such investigations would require both genomic and transcriptomic data, but there currently exist very few datasets that satisfy these requirements. We address this by developing a single-nucleus full-length RNA-sequencing approach that allows for the detection of potentially pathogenic intronic variants. We exemplify the potency of our approach by applying pancreatic cancer tumor and tumor-derived specimens and linking intronic variants to splicing dysregulation. We specifically find that prominent intron retention and pseudo-exon activation events are shared by the tumors and affect genes encoding key transcriptional regulators. Our work paves the way for the assessment and exploitation of intronic mutations as powerful prognostic markers and potential therapeutic targets in cancer.
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Affiliation(s)
- Emre Taylan Duman
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Maren Sitte
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Karly Conrads
- Clinic of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - Adi Mackay
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Fabian Ludewig
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Philipp Ströbel
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Volker Ellenrieder
- Clinic of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Comprehensive Cancer Center Lower Saxony (CCC-N), Göttingen, Germany
| | - Elisabeth Hessmann
- Clinic of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Comprehensive Cancer Center Lower Saxony (CCC-N), Göttingen, Germany
| | - Argyris Papantonis
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
- Institute of Pathology, University Medical Center, Göttingen, Germany
- Comprehensive Cancer Center Lower Saxony (CCC-N), Göttingen, Germany
| | - Gabriela Salinas
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center, Göttingen, Germany
- Clinical Research Unit 5002 (CRU5002), University Medical Center, Göttingen, Germany
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14
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Martinez-Mayer J, Brinkmeier ML, O'Connell SP, Ukagwu A, Marti MA, Miras M, Forclaz MV, Benzrihen MG, Cheung LYM, Camper SA, Ellsworth BS, Raetzman LT, Pérez-Millán MI, Davis SW. Knockout mice with pituitary malformations help identify human cases of hypopituitarism. Genome Med 2024; 16:75. [PMID: 38822427 PMCID: PMC11140907 DOI: 10.1186/s13073-024-01347-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 05/20/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Congenital hypopituitarism (CH) and its associated syndromes, septo-optic dysplasia (SOD) and holoprosencephaly (HPE), are midline defects that cause significant morbidity for affected people. Variants in 67 genes are associated with CH, but a vast majority of CH cases lack a genetic diagnosis. Whole exome and whole genome sequencing of CH patients identifies sequence variants in genes known to cause CH, and in new candidate genes, but many of these are variants of uncertain significance (VUS). METHODS The International Mouse Phenotyping Consortium (IMPC) is an effort to establish gene function by knocking-out all genes in the mouse genome and generating corresponding phenotype data. We used mouse embryonic imaging data generated by the Deciphering Mechanisms of Developmental Disorders (DMDD) project to screen 209 embryonic lethal and sub-viable knockout mouse lines for pituitary malformations. RESULTS Of the 209 knockout mouse lines, we identified 51 that have embryonic pituitary malformations. These genes not only represent new candidates for CH, but also reveal new molecular pathways not previously associated with pituitary organogenesis. We used this list of candidate genes to mine whole exome sequencing data of a cohort of patients with CH, and we identified variants in two unrelated cases for two genes, MORC2 and SETD5, with CH and other syndromic features. CONCLUSIONS The screening and analysis of IMPC phenotyping data provide proof-of-principle that recessive lethal mouse mutants generated by the knockout mouse project are an excellent source of candidate genes for congenital hypopituitarism in children.
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Affiliation(s)
- Julian Martinez-Mayer
- Institute of Biosciences, Biotechnology and Translational Biology (iB3), University of Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
| | - Michelle L Brinkmeier
- Department of Human Genetics, University of Michigan, 1241 Catherine St., Ann Arbor, MI, 48109-5618, USA
| | - Sean P O'Connell
- Department of Biological Sciences, University of South Carolina, 715 Sumter St., Columbia, SC, 29208, USA
| | - Arnold Ukagwu
- Department of Physiology, Southern Illinois University, 1135 Lincoln Dr, Carbondale, IL, 62901, USA
| | - Marcelo A Marti
- Instituto de Química Biológica de La Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mirta Miras
- Hospital De Niños de La Santísima Trinidad, Córdoba, Argentina
| | - Maria V Forclaz
- Servicio de Endocrinología, Hospital Posadas, Buenos Aires, Argentina
| | - Maria G Benzrihen
- Servicio de Endocrinología, Hospital Posadas, Buenos Aires, Argentina
| | - Leonard Y M Cheung
- Department of Human Genetics, University of Michigan, 1241 Catherine St., Ann Arbor, MI, 48109-5618, USA
- Department of Physiology and Biophyscis, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Sally A Camper
- Department of Human Genetics, University of Michigan, 1241 Catherine St., Ann Arbor, MI, 48109-5618, USA
| | - Buffy S Ellsworth
- Department of Physiology, Southern Illinois University, 1135 Lincoln Dr, Carbondale, IL, 62901, USA
| | - Lori T Raetzman
- Department of Molecular and Integrative Physiology, University of Illinois, Champaign-Urbana, Urbana, IL, 61801, USA
| | - Maria I Pérez-Millán
- Institute of Biosciences, Biotechnology and Translational Biology (iB3), University of Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina.
| | - Shannon W Davis
- Department of Biological Sciences, University of South Carolina, 715 Sumter St., Columbia, SC, 29208, USA.
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15
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June V, Song X, Chen ZJ. Imprinting but not cytonuclear interactions determines seed size heterosis in Arabidopsis hybrids. PLANT PHYSIOLOGY 2024; 195:1214-1228. [PMID: 38319651 PMCID: PMC11142339 DOI: 10.1093/plphys/kiae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024]
Abstract
The parent-of-origin effect on seeds can result from imprinting (unequal expression of paternal and maternal alleles) or combinational effects between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding factors, we produced cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in Arabidopsis (Arabidopsis thaliana) ecotypes Col-0 and C24. These CNS lines differed only in the nuclear genome (imprinting) or cytoplasm. The CNS reciprocal hybrids with the same cytoplasm displayed ∼20% seed size difference, whereas the seed size was similar between the reciprocal hybrids with fixed imprinting. Transcriptome analyses in the endosperm of CNS hybrids using laser-capture microdissection identified 104 maternally expressed genes (MEGs) and 90 paternally expressed genes (PEGs). These imprinted genes were involved in pectin catabolism and cell wall modification in the endosperm. Homeodomain Glabrous9 (HDG9), an epiallele and one of 11 cross-specific imprinted genes, affected seed size. In the embryo, there were a handful of imprinted genes in the CNS hybrids but only 1 was expressed at higher levels than in the endosperm. AT4G13495 was found to encode a long-noncoding RNA (lncRNA), but no obvious seed phenotype was observed in lncRNA knockout lines. Nuclear RNA Polymerase D1 (NRPD1), encoding the largest subunit of RNA Pol IV, was involved in the biogenesis of small interfering RNAs. Seed size and embryos were larger in the cross using nrpd1 as the maternal parent than in the reciprocal cross, supporting a role of the maternal NRPD1 allele in seed development. Although limited ecotypes were tested, these results suggest that imprinting and the maternal NRPD1-mediated small RNA pathway play roles in seed size heterosis in plant hybrids.
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Affiliation(s)
- Viviana June
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xiaoya Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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16
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Devins KM, Baranov E, Hung YP, Dickson BC, Oliva E, Deshpande V. Large and Extensive Multilocular Peritoneal Inclusion Cysts Lack Genomic Alterations and Follow an Indolent Clinical Course Despite Rare Recurrences. Am J Surg Pathol 2024:00000478-990000000-00362. [PMID: 38813820 DOI: 10.1097/pas.0000000000002249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Peritoneal inclusion cysts (PICs) are unilocular or multilocular cystic lesions lined by bland mesothelial cells. While most are small and localized, rare examples may be large or multifocal with diffuse peritoneal involvement, causing clinical and even pathologic concern for malignancy. We examined 20 PIC, including 8 large solitary and 12 multifocal lesions. Solitary PIC were found in 7 female and 1 male patients ranging from 19 to 55 (median: 37) years. Expanded collagenous (n=2) or edematous (n=1) areas were occasionally seen in the septae, and 1 had microscopic foci of myxoid stroma. Four had hobnail cells, and 1 had minor areas of papillary mesothelial hyperplasia. Multifocal PICs occurred in 9 female and 3 male patients ranging from 26 to 80 (median: 53) years. Three showed extensive associated fibrosis with entrapment of preexisting adipose tissue, 2 had areas resembling granulation tissue, and 3 had scattered foci of myxoid stroma. Hobnail cells were present in 9, papillary mesothelial hyperplasia in 2, entrapped single cells in 1, and 2 had areas resembling adenomatoid tumors. Two of the multifocal PICs had limited local recurrences at 18 and 21 months. No patients died of disease. Clonal alterations were not identified in any of the tested PICs (mutational and fusion analysis in 5, chromosomal microarray in 1). Despite limited local recurrences, we demonstrate that even large and multifocal PICs may lack identifiable genomic alterations and are associated with benign outcomes.
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Affiliation(s)
- Kyle M Devins
- James Homer Wright Pathology Laboratories, Massachusetts General Hospital
| | - Esther Baranov
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Yin P Hung
- James Homer Wright Pathology Laboratories, Massachusetts General Hospital
| | - Brendan C Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital
- Department of Laboratory Medicine and Pathobiology, University of Toronto; Toronto, Ontario, Canada
| | - Esther Oliva
- James Homer Wright Pathology Laboratories, Massachusetts General Hospital
| | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
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17
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Riley LG, Sabui S, Said HM, Niaz A, Girisha KM, Radhakrishnan P, Nampoothiri S, Yesodharan D, Kilo T, Smith J, Wong RSH, Menezes MP, Gupta S, Cooper ST, Balasubramaniam S. Genome sequencing enables diagnosis and treatment of SLC5A6 neuropathy. Eur J Hum Genet 2024:10.1038/s41431-024-01641-8. [PMID: 38816490 DOI: 10.1038/s41431-024-01641-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/29/2024] [Accepted: 05/16/2024] [Indexed: 06/01/2024] Open
Abstract
The sodium-dependent multivitamin transporter encoded by SLC5A6 is responsible for uptake of biotin, pantothenic acid, and α-lipoic acid. Thirteen individuals from eight families are reported with pathogenic biallelic SLC5A6 variants. Phenotype ranges from multisystem metabolic disorder to childhood-onset peripheral motor neuropathy. We report three additional affected individuals with biallelic SLC5A6 variants. In Family A, a male proband (AII:1) presenting in early childhood with gross motor regression, motor axonal neuropathy, recurrent cytopenia and infections, and failure to thrive was diagnosed at 12 years of age via genome sequencing (GS) with a paternal NM_021095.4:c.393+2T>C variant and a maternal c.1285A>G p.(Ser429Gly) variant. An uncle with recurrent cytopenia and peripheral neuropathy was subsequently found to have the same genotype. We also report an unrelated female with peripheral neuropathy homozygous for the c.1285A>G p.(Ser429Gly) recurrent variant identified in seven reported cases, including this study. RT-PCR studies on blood mRNA from AII:1 showed c.393+2T>C caused mis-splicing with all canonically spliced transcripts in AII:1 containing the c.1285A>G variant. SLC5A6 mRNA expression in AII:1 fibroblasts was ~50% of control levels, indicative of nonsense-mediated decay of mis-spliced transcripts. Biotin uptake studies on AII:1 fibroblasts, expressing the p.(Ser429Gly) variant, showed an ~90% reduction in uptake compared to controls. Targeted treatment of AII:1 with biotin, pantothenic acid, and lipoic acid resulted in clinical improvement. Health Economic analyses showed implementation of GS as an early investigation could have saved $ AUD 105,988 and shortened diagnostic odyssey and initiation of treatment by up to 7 years.
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Affiliation(s)
- Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and The Children's Medical Research Institute, Sydney, NSW, Australia.
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia.
| | - Subrata Sabui
- Department of Physiology/Biophysics, University of California, Irvine, CA, USA
- Department of Research, Veterans Affairs Medical Center, Long Beach, CA, USA
| | - Hamid M Said
- Department of Physiology/Biophysics, University of California, Irvine, CA, USA
- Department of Research, Veterans Affairs Medical Center, Long Beach, CA, USA
- Department of Medicine, University of California, Irvine, CA, USA
| | - Aram Niaz
- Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and The Children's Medical Research Institute, Sydney, NSW, Australia
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Suma Genomics Private Limited and Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
| | - Periyasamy Radhakrishnan
- Suma Genomics Private Limited and Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Division of Reproductive Genetics, Department of Reproductive Science, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Cochin, Kerala, India
| | - Dhanya Yesodharan
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Cochin, Kerala, India
| | - Tatjana Kilo
- Haematology Department, Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Janine Smith
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, NSW, 2145, Australia
- Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Rachel S H Wong
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Manoj P Menezes
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Sachin Gupta
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Sandra T Cooper
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
- The Children's Medical Research Institute, Westmead, NSW, Australia
| | - Shanti Balasubramaniam
- Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, NSW, Australia
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18
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Basharat R, de Bruijn SE, Zahid M, Rodenburg K, Hitti-Malin RJ, Rodríguez-Hidalgo M, Boonen EGM, Jarral A, Mahmood A, Corominas J, Khalil S, Zai JA, Ali G, Ruiz-Ederra J, Gilissen C, Cremers FPM, Ansar M, Panneman DM, Roosing S. Next-generation sequencing to genetically diagnose a diverse range of inherited eye disorders in 15 consanguineous families from Pakistan. Exp Eye Res 2024; 244:109945. [PMID: 38815792 DOI: 10.1016/j.exer.2024.109945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/19/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Inherited retinal dystrophies (IRDs) are characterized by photoreceptor dysfunction or degeneration. Clinical and phenotypic overlap between IRDs makes the genetic diagnosis very challenging and comprehensive genomic approaches for accurate diagnosis are frequently required. While there are previous studies on IRDs in Pakistan, causative genes and variants are still unknown for a significant portion of patients. Therefore, there is a need to expand the knowledge of the genetic spectrum of IRDs in Pakistan. Here, we recruited 52 affected and 53 normal individuals from 15 consanguineous Pakistani families presenting non-syndromic and syndromic forms of IRDs. We employed single molecule Molecular Inversion Probes (smMIPs) based panel sequencing and whole genome sequencing to identify the probable disease-causing variants in these families. Using this approach, we obtained a 93% genetic solve rate and identified 16 (likely) causative variants in 14 families, of which seven novel variants were identified in ATOH7, COL18A1, MERTK, NDP, PROM1, PRPF8 and USH2A while nine recurrent variants were identified in CNGA3, CNGB1, HGSNAT, NMNAT1, SIX6 and TULP1. The novel MERTK variant and one recurrent TULP1 variant explained the intra-familial locus heterogeneity in one of the screened families while two recurrent CNGA3 variants explained compound heterozygosity in another family. The identification of variants in known disease-associated genes emphasizes the utilization of time and cost-effective screening approaches for rapid diagnosis. The timely genetic diagnosis will not only identify any associated systemic issues in case of syndromic IRDs, but will also aid in the acceleration of personalized medicine for patients affected with IRDs.
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Affiliation(s)
- Rabia Basharat
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Zahid
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rebekkah J Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - María Rodríguez-Hidalgo
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Erica G M Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Afeefa Jarral
- Department of Biotechnology, Mirpur University of Science and Technology, Mirpur, (AJK), Pakistan
| | - Arif Mahmood
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sharqa Khalil
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jawaid Ahmed Zai
- Department of Physiology and MLT, University of Sindh, Jamshoro, Pakistan
| | - Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Ansar
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Daan M Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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19
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Pérez-Gutiérrez AM, Carmona R, Loucera C, Cervilla JA, Gutiérrez B, Molina E, Lopez-Lopez D, Pérez-Florido J, Zarza-Rebollo JA, López-Isac E, Dopazo J, Martínez-González LJ, Rivera M. Mutational landscape of risk variants in comorbid depression and obesity: a next-generation sequencing approach. Mol Psychiatry 2024:10.1038/s41380-024-02609-2. [PMID: 38806690 DOI: 10.1038/s41380-024-02609-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024]
Abstract
Major depression (MD) and obesity are complex genetic disorders that are frequently comorbid. However, the study of both diseases concurrently remains poorly addressed and therefore the underlying genetic mechanisms involved in this comorbidity remain largely unknown. Here we examine the contribution of common and rare variants to this comorbidity through a next-generation sequencing (NGS) approach. Specific genomic regions of interest in MD and obesity were sequenced in a group of 654 individuals from the PISMA-ep epidemiological study. We obtained variants across the entire frequency spectrum and assessed their association with comorbid MD and obesity, both at variant and gene levels. We identified 55 independent common variants and a burden of rare variants in 4 genes (PARK2, FGF21, HIST1H3D and RSRC1) associated with the comorbid phenotype. Follow-up analyses revealed significantly enriched gene-sets associated with biological processes and pathways involved in metabolic dysregulation, hormone signaling and cell cycle regulation. Our results suggest that, while risk variants specific to the comorbid phenotype have been identified, the genes functionally impacted by the risk variants share cell biological processes and signaling pathways with MD and obesity phenotypes separately. To the best of our knowledge, this is the first study involving a targeted sequencing approach toward the study of the comorbid MD and obesity. The framework presented here allowed a deep characterization of the genetics of the co-occurring MD and obesity, revealing insights into the mutational and functional profile that underlies this comorbidity and contributing to a better understanding of the relationship between these two disabling disorders.
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Affiliation(s)
- Ana M Pérez-Gutiérrez
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
| | - Rosario Carmona
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
| | - Carlos Loucera
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Jorge A Cervilla
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
- Department of Psychiatry, Faculty of Medicine, University of Granada, Granada, Spain
| | - Blanca Gutiérrez
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
- Department of Psychiatry, Faculty of Medicine, University of Granada, Granada, Spain
| | - Esther Molina
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
- Department of Nursing, Faculty of Health Sciences, University of Granada, Granada, Spain
| | - Daniel Lopez-Lopez
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Javier Pérez-Florido
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
| | - Juan Antonio Zarza-Rebollo
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
| | - Elena López-Isac
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
| | - Joaquín Dopazo
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
| | - Luis Javier Martínez-González
- Genomics Unit, Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Margarita Rivera
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain.
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain.
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain.
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20
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Lin R, Li H, Lin W, Yang F, Bao X, Pan C, Lai L, Lin W. Whole-genome selection signature differences between Chaohu and Ji'an red ducks. BMC Genomics 2024; 25:522. [PMID: 38802792 PMCID: PMC11131323 DOI: 10.1186/s12864-024-10339-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.
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Affiliation(s)
- Ruiyi Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Huihuang Li
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Weilong Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Fan Yang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Xinguo Bao
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Chengfu Pan
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Lianjie Lai
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Weimin Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
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21
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Li MD, Liu Q, Shi X, Wang Y, Zhu Z, Guan Y, He J, Han H, Mao Y, Ma Y, Yuan W, Yao J, Yang Z. Integrative analysis of genetics, epigenetics and RNA expression data reveal three susceptibility loci for smoking behavior in Chinese Han population. Mol Psychiatry 2024:10.1038/s41380-024-02599-1. [PMID: 38789676 DOI: 10.1038/s41380-024-02599-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/18/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Despite numerous studies demonstrate that genetics and epigenetics factors play important roles on smoking behavior, our understanding of their functional relevance and coordinated regulation remains largely unknown. Here we present a multiomics study on smoking behavior for Chinese smoker population with the goal of not only identifying smoking-associated functional variants but also deciphering the pathogenesis and mechanism underlying smoking behavior in this under-studied ethnic population. After whole-genome sequencing analysis of 1329 Chinese Han male samples in discovery phase and OpenArray analysis of 3744 samples in replication phase, we discovered that three novel variants located near FOXP1 (rs7635815), and between DGCR6 and PRODH (rs796774020), and in ARVCF (rs148582811) were significantly associated with smoking behavior. Subsequently cis-mQTL and cis-eQTL analysis indicated that these variants correlated significantly with the differential methylation regions (DMRs) or differential expressed genes (DEGs) located in the regions where these variants present. Finally, our in silico multiomics analysis revealed several hub genes, like DRD2, PTPRD, FOXP1, COMT, CTNNAP2, to be synergistic regulated each other in the etiology of smoking.
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Affiliation(s)
- Ming D Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China.
| | - Qiang Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqiang Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhouhai Zhu
- Joint Institute of Tobacco and Health, Kunming, Yunnan, China
| | - Ying Guan
- Joint Institute of Tobacco and Health, Kunming, Yunnan, China
| | - Jingmin He
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- College of Biological Sciences, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Haijun Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Mao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunlong Ma
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenji Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianhua Yao
- Joint Institute of Tobacco and Health, Kunming, Yunnan, China
| | - Zhongli Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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22
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Josić D, Çoraman E, Waurick I, Franzenburg S, Ancillotto L, Bajić B, Budinski I, Dietz C, Görföl T, Hayden Bofill SI, Presetnik P, Russo D, Spada M, Zrnčić V, Blom MPK, Mayer F. Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri). Mol Ecol 2024:e17411. [PMID: 38785347 DOI: 10.1111/mec.17411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/16/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
Studying hybrid zones that form between morphologically cryptic taxa offers valuable insights into the mechanisms of cryptic speciation and the evolution of reproductive barriers. Although hybrid zones have long been the focus of evolutionary studies, the awareness of cryptic hybrid zones increased recently due to rapidly growing evidence of biological diversity lacking obvious phenotypic differentiation. The characterization of cryptic hybrid zones with genome-wide analysis is in its early stages and offers new perspectives for studying population admixture and thus the impact of gene flow. In this study, we investigate the population genomics of the Myotis nattereri complex in one of its secondary contact zones, where a putative hybrid zone is formed between two of its cryptic lineages. By utilizing a whole-genome shotgun sequencing approach, we aim to characterize this cryptic hybrid zone in detail. Demographic analysis suggests that the cryptic lineages diverged during the Pliocene, c. 3.6 million years ago. Despite this ancient separation, the populations in the contact zone exhibit mitochondrial introgression and a considerable amount of mixing in nuclear genomes. The genomic structure of the populations corresponds to geographic locations and the genomic admixture changes along a geographic gradient. These findings suggest that there is no effective hybridization barrier between both lineages, nevertheless, their population structure is shaped by dispersal barriers. Our findings highlight how such deeply diverged cryptic lineages can still readily hybridize in secondary contact.
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Affiliation(s)
- Darija Josić
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Emrah Çoraman
- Department of Ecology and Evolution, Eurasia Institute of Earth Sciences, Istanbul Technical University, İstanbul, Türkiye
| | - Isabelle Waurick
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Sören Franzenburg
- IKMB, Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Leonardo Ancillotto
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Universita degli Studi di Napoli Federico II, Portici, Italy
| | - Branka Bajić
- Department of Genetic Research, Institute for Biological Research 'Siniša Stanković' - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ivana Budinski
- Department of Genetic Research, Institute for Biological Research 'Siniša Stanković' - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Tamás Görföl
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | - Sofia I Hayden Bofill
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Primož Presetnik
- Centre for Cartography of Fauna and Flora, Miklavž na Dravskem Polju, Slovenia
| | - Danillo Russo
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Universita degli Studi di Napoli Federico II, Portici, Italy
| | - Martina Spada
- Dipartimento Ambiente-Salute-Sicurezza, Universita degli Studi dell'Insubria, Varese, Italy
| | - Vida Zrnčić
- Croatian Biospeleogical Society Zagreb, Zagreb, Croatia
| | - Mozes P K Blom
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Frieder Mayer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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23
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Yasin M, Licchetta L, Khan N, Ullah I, Jan Z, Dawood M, Ahmed AN, Azeem A, Minardi R, Carelli V, Saleha S. Genetic heterogeneity in epilepsy and comorbidities: insights from Pakistani families. BMC Neurol 2024; 24:172. [PMID: 38783254 PMCID: PMC11112905 DOI: 10.1186/s12883-024-03671-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Epilepsy, a challenging neurological condition, is often present with comorbidities that significantly impact diagnosis and management. In the Pakistani population, where financial limitations and geographical challenges hinder access to advanced diagnostic methods, understanding the genetic underpinnings of epilepsy and its associated conditions becomes crucial. METHODS This study investigated four distinct Pakistani families, each presenting with epilepsy and a spectrum of comorbidities, using a combination of whole exome sequencing (WES) and Sanger sequencing. The epileptic patients were prescribed multiple antiseizure medications (ASMs), yet their seizures persist, indicating the challenging nature of ASM-resistant epilepsy. RESULTS Identified genetic variants contributed to a diverse range of clinical phenotypes. In the family 1, which presented with epilepsy, developmental delay (DD), sleep disturbance, and aggressive behavior, a homozygous splice site variant, c.1339-6 C > T, in the COL18A1 gene was detected. The family 2 exhibited epilepsy, intellectual disability (ID), DD, and anxiety phenotypes, a homozygous missense variant, c.344T > A (p. Val115Glu), in the UFSP2 gene was identified. In family 3, which displayed epilepsy, ataxia, ID, DD, and speech impediment, a novel homozygous frameshift variant, c.1926_1941del (p. Tyr643MetfsX2), in the ZFYVE26 gene was found. Lastly, family 4 was presented with epilepsy, ID, DD, deafness, drooling, speech impediment, hypotonia, and a weak cry. A homozygous missense variant, c.1208 C > A (p. Ala403Glu), in the ATP13A2 gene was identified. CONCLUSION This study highlights the genetic heterogeneity in ASM-resistant epilepsy and comorbidities among Pakistani families, emphasizing the importance of genotype-phenotype correlation and the necessity for expanded genetic testing in complex clinical cases.
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Affiliation(s)
- Muhammad Yasin
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Laura Licchetta
- RCCS, Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Irfan Ullah
- Department of Neurology, Khyber Teaching Hospital, Peshawar, Khyber Pakhtunkhwa, 25000, Pakistan
| | - Zakir Jan
- Department of Neurology, Pakistan Institute of Medical Science, Islamabad, 44000, Pakistan
| | - Muhammad Dawood
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Asif Naveed Ahmed
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Arfa Azeem
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Raffaella Minardi
- RCCS, Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Valerio Carelli
- RCCS, Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy.
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan.
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24
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Lin L, Andersen MK, Stæger FF, Li Z, Hanghøj K, Linneberg A, Grarup N, Jørgensen ME, Hansen T, Moltke I, Albrechtsen A. Analysis of admixed Greenlandic siblings shows that the mean genotypic values for metabolic phenotypes differ between Inuit and Europeans. Genome Med 2024; 16:71. [PMID: 38778393 PMCID: PMC11112775 DOI: 10.1186/s13073-024-01326-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 03/28/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Disease prevalence and mean phenotype values differ between many populations, including Inuit and Europeans. Whether these differences are partly explained by genetic differences or solely due to differences in environmental exposures is still unknown, because estimates of the genetic contribution to these means, which we will here refer to as mean genotypic values, are easily confounded, and because studies across genetically diverse populations are lacking. METHODS Leveraging the unique genetic properties of the small, admixed and historically isolated Greenlandic population, we estimated the differences in mean genotypic value between Inuit and European genetic ancestry using an admixed sibling design. Analyses were performed across 26 metabolic phenotypes, in 1474 admixed sibling pairs present in a cohort of 5996 Greenlanders. RESULTS After FDR correction for multiple testing, we found significantly lower mean genotypic values in Inuit genetic ancestry compared to European genetic ancestry for body weight (effect size per percentage of Inuit genetic ancestry (se), -0.51 (0.16) kg/%), body mass index (-0.20 (0.06) kg/m2/%), fat percentage (-0.38 (0.13) %/%), waist circumference (-0.42 (0.16) cm/%), hip circumference (-0.38 (0.11) cm/%) and fasting serum insulin levels (-1.07 (0.51) pmol/l/%). The direction of the effects was consistent with the observed mean phenotype differences between Inuit and European genetic ancestry. No difference in mean genotypic value was observed for height, markers of glucose homeostasis, or circulating lipid levels. CONCLUSIONS We show that mean genotypic values for some metabolic phenotypes differ between two human populations using a method not easily confounded by possible differences in environmental exposures. Our study illustrates the importance of performing genetic studies in diverse populations.
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Affiliation(s)
- Long Lin
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Mette K Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Frederik Filip Stæger
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Zilong Li
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Kristian Hanghøj
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Allan Linneberg
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region of Denmark, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Marit Eika Jørgensen
- Centre for Public Health in Greenland, National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Clinical Research, Copenhagen University Hospital - Steno Diabetes Center Copenhagen, Herlev, Denmark
- Steno Diabetes Center Greenland, Nuuk, Greenland
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
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25
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Wade KJ, Suseno R, Kizer K, Williams J, Boquett J, Caillier S, Pollock NR, Renschen A, Santaniello A, Oksenberg JR, Norman PJ, Augusto DG, Hollenbach JA. MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.595060. [PMID: 38826378 PMCID: PMC11142050 DOI: 10.1101/2024.05.20.595060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short read de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target-capture short read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short read data. MHConstructor facilitates wide-spread access to high quality, alignment-free MHC sequence analysis.
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Affiliation(s)
- Kristen J. Wade
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Rayo Suseno
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Kerry Kizer
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jacqueline Williams
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Juliano Boquett
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stacy Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Nicholas R. Pollock
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Adam Renschen
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Danillo G. Augusto
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, United States
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
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26
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Afridi TUK, Fatima A, Satti HS, Akram Z, Yousafzai IK, Naeem WB, Fatima N, Ali A, Iqbal Z, Khan A, Shahzad M, Liu C, Toft M, Zhang F, Tariq M, Davis EE, Khan TN. Exome sequencing in four families with neurodevelopmental disorders: genotype-phenotype correlation and identification of novel disease-causing variants in VPS13B and RELN. Mol Genet Genomics 2024; 299:55. [PMID: 38771357 DOI: 10.1007/s00438-024-02149-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/30/2024] [Indexed: 05/22/2024]
Abstract
Neurodevelopmental disorders (NDDs) are a clinically and genetically heterogeneous group of early-onset pediatric disorders that affect the structure and/or function of the central or peripheral nervous system. Achieving a precise molecular diagnosis for NDDs may be challenging due to the diverse genetic underpinnings and clinical variability. In the current study, we investigated the underlying genetic cause(s) of NDDs in four unrelated Pakistani families. Using exome sequencing (ES) as a diagnostic approach, we identified disease-causing variants in established NDD-associated genes in all families, including one hitherto unreported variant in RELN and three recurrent variants in VPS13B, DEGS1, and SPG11. Overall, our study highlights the potential of ES as a tool for clinical diagnosis.
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Affiliation(s)
- Tehseen Ullah Khan Afridi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Ambrin Fatima
- Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, 74800, Pakistan
| | - Humayoon Shafique Satti
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Zaineb Akram
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Imran Khan Yousafzai
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Wajahat Bin Naeem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Nasreen Fatima
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Asmat Ali
- Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, 74800, Pakistan
| | - Zafar Iqbal
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Ayaz Khan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Shahzad
- Department of Neurosurgery, District Headquarter Hospital, Kohat, Pakistan
| | - Chunyu Liu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Feng Zhang
- Institute of Medical Genetics and Genomics, Fudan University, Shanghai, 200438, China
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.
- Department of Pediatrics and Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Tahir N Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan.
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.
- Department of Pediatrics and Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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27
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Sendecki A, Ledwoń D, Nycz J, Wąsowska A, Boguszewska-Chachulska A, Mitas AW, Wylęgała E, Teper S. A deep learning approach to explore the association of age-related macular degeneration polygenic risk score with retinal optical coherence tomography: A preliminary study. Acta Ophthalmol 2024. [PMID: 38761033 DOI: 10.1111/aos.16710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024]
Abstract
PURPOSE Age-related macular degeneration (AMD) is a complex eye disorder affecting millions worldwide. This article uses deep learning techniques to investigate the relationship between AMD, genetics and optical coherence tomography (OCT) scans. METHODS The cohort consisted of 332 patients, of which 235 were diagnosed with AMD and 97 were controls with no signs of AMD. The genome-wide association studies summary statistics utilized to establish the polygenic risk score (PRS) in relation to AMD were derived from the GERA European study. A PRS estimation based on OCT volumes for both eyes was performed using a proprietary convolutional neural network (CNN) model supported by machine learning models. The method's performance was assessed using numerical evaluation metrics, and the Grad-CAM technique was used to evaluate the results by visualizing the features learned by the model. RESULTS The best results were obtained with the CNN and the Extra Tree regressor (MAE = 0.55, MSE = 0.49, RMSE = 0.70, R2 = 0.34). Extending the feature vector with additional information on AMD diagnosis, age and smoking history improved the results slightly, with mainly AMD diagnosis used by the model (MAE = 0.54, MSE = 0.44, RMSE = 0.66, R2 = 0.42). Grad-CAM heatmap evaluation showed that the model decisions rely on retinal morphology factors relevant to AMD diagnosis. CONCLUSION The developed method allows an efficient PRS estimation from OCT images. A new technique for analysing the association of OCT images with PRS of AMD, using a deep learning approach, may provide an opportunity to discover new associations between genotype-based AMD risk and retinal morphology.
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Affiliation(s)
- Adam Sendecki
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Daniel Ledwoń
- Faculty of Biomedical Engineering, Silesian University of Technology, Zabrze, Poland
| | - Julia Nycz
- Institute of Biomedical Engineering and Informatics, Technische Universität Ilmenau, Ilmenau, Germany
| | - Anna Wąsowska
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland
- Genomed S.A., Warszawa, Poland
| | | | - Andrzej W Mitas
- Faculty of Biomedical Engineering, Silesian University of Technology, Zabrze, Poland
| | - Edward Wylęgała
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Sławomir Teper
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland
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28
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Dunstan-Harrison C, Morison IM, Ledgerwood EC. Inherited thrombocytopenia associated with a variant in the FLI1 binding site in the 5' UTR of ANKRD26. Clin Genet 2024. [PMID: 38757516 DOI: 10.1111/cge.14547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Variants in the 5' UTR of ANKRD26 are a common cause of inherited thrombocytopenia (ANKRD26-RT), and are associated with sustained ANKRD26 expression, which inhibits megakaryocyte maturation and proplatelet formation. ANKRD26 expression is controlled by the binding of a RUNX1/FLI1 complex to the 5' UTR. To date, all reported ANKRD26-RD associated variants have been within the RUNX1 binding site and a 22 base pair flanking region. Here, we report a novel variant in the 5' UTR of ANKRD26, c.-107C>T. This variant is in the FLI1 binding site, and is predicted to disrupt FLI1 binding due to loss of a hydrogen bond with FLI1. Differentiated PBMCs from affected family members showed impaired megakaryocyte maturation and proplatelet formation and sustained expression of ANKRD26, and platelets from affected family members had higher ANKRD26 expression than control platelets. The variant increased activity of the ANKRD26 promotor in a reporter assay. We also provide evidence that the previously reported c.-140C>G ANKRD26 5' UTR variant is benign and not associated with thrombocytopenia. Identification of the c.-107C>T variant extends the range of the regulatory region in the 5' UTR of ANKRD26 that is associated with ANKRD26-RT.
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Affiliation(s)
- Caitlin Dunstan-Harrison
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ian M Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Elizabeth C Ledgerwood
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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29
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Lin AL, Rudneva VA, Richards AL, Zhang Y, Woo HJ, Cohen M, Tisnado J, Majd N, Wardlaw SL, Page-Wilson G, Sengupta S, Chow F, Goichot B, Ozer BH, Dietrich J, Nachtigall L, Desai A, Alano T, Ogilive S, Solit DB, Bale TA, Rosenblum M, Donoghue MTA, Geer EB, Tabar V. Genome-wide loss of heterozygosity predicts aggressive, treatment-refractory behavior in pituitary neuroendocrine tumors. Acta Neuropathol 2024; 147:85. [PMID: 38758238 PMCID: PMC11101347 DOI: 10.1007/s00401-024-02736-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
Abstract
Pituitary neuroendocrine tumors (PitNETs) exhibiting aggressive, treatment-refractory behavior are the rare subset that progress after surgery, conventional medical therapies, and an initial course of radiation and are characterized by unrelenting growth and/or metastatic dissemination. Two groups of patients with PitNETs were sequenced: a prospective group of patients (n = 66) who consented to sequencing prior to surgery and a retrospective group (n = 26) comprised of aggressive/higher risk PitNETs. A higher mutational burden and fraction of loss of heterozygosity (LOH) was found in the aggressive, treatment-refractory PitNETs compared to the benign tumors (p = 1.3 × 10-10 and p = 8.5 × 10-9, respectively). Within the corticotroph lineage, a characteristic pattern of recurrent chromosomal LOH in 12 specific chromosomes was associated with treatment-refractoriness (occurring in 11 of 14 treatment-refractory versus 1 of 14 benign corticotroph PitNETs, p = 1.7 × 10-4). Across the cohort, a higher fraction of LOH was identified in tumors with TP53 mutations (p = 3.3 × 10-8). A machine learning approach identified loss of heterozygosity as the most predictive variable for aggressive, treatment-refractory behavior, outperforming the most common gene-level alteration, TP53, with an accuracy of 0.88 (95% CI: 0.70-0.96). Aggressive, treatment-refractory PitNETs are characterized by significant aneuploidy due to widespread chromosomal LOH, most prominently in the corticotroph tumors. This LOH predicts treatment-refractoriness with high accuracy and represents a novel biomarker for this poorly defined PitNET category.
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Affiliation(s)
- Andrew L Lin
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vasilisa A Rudneva
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hyung Jun Woo
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Cohen
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamie Tisnado
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nazanin Majd
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon L Wardlaw
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Gabrielle Page-Wilson
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Soma Sengupta
- Department of Neurology and Neurosurgery, University of North Carolina, Chapel Hill, NC, USA
| | - Frances Chow
- Department of Neurology, Keck School of Medicine at University of Southern California Medical Center, Los Angeles, CA, USA
| | - Bernard Goichot
- Department of Endocrinology, Les Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Byram H Ozer
- Department of Oncology, Sibley Memorial Hospital/Johns Hopkins, Washington, DC, USA
| | - Jorg Dietrich
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Lisa Nachtigall
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Arati Desai
- Department of Medicine, University of Pennsylvania Medical Center, Philadelphia, PA, USA
| | - Tina Alano
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shahiba Ogilive
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tejus A Bale
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Rosenblum
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eliza B Geer
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Viviane Tabar
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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30
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Engvall K, Uvdal H, Björn N, Åvall-Lundqvist E, Gréen H. Prediction models of persistent taxane-induced peripheral neuropathy among breast cancer survivors using whole-exome sequencing. NPJ Precis Oncol 2024; 8:102. [PMID: 38755266 PMCID: PMC11099113 DOI: 10.1038/s41698-024-00594-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
Persistent taxane-induced peripheral neuropathy (TIPN) is highly prevalent among early-stage breast cancer survivors (ESBCS) and has detrimental effect on quality of life. We leveraged logistic regression models to develop and validate polygenic prediction models to estimate the risk of persistent PN symptoms in a training cohort and validation cohort taking clinical risk factors into account. Based on 337 whole-exome sequenced ESBCS two of five prediction models for individual PN symptoms obtained AUC results above 60% when validated. Using the model for numbness in feet (35 SNVs) in the test cohort, 73% survivors were correctly predicted. For tingling in feet (55 SNVs) 70% were correctly predicted. Both models included SNVs from the ADAMTS20, APT6V0A2, CCDC88C, CYP2C8, EPHA5, NR1H3, PSKH2/APTV0D2, and SCN10A genes. For cramps in feet, difficulty climbing stairs and difficulty opening a jar the validation was unsuccessful. Polygenic prediction models including clinical risk factors can estimate the risk of persistent taxane-induced numbness in feet and tingling in feet in ESBCS.
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Affiliation(s)
- Kristina Engvall
- Department of Oncology, Jönköping, Region Jönköping County, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
| | - Hanna Uvdal
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Niclas Björn
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Elisabeth Åvall-Lundqvist
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Henrik Gréen
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
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Flannery KP, Safwat S, Matsell E, Battula N, Hamed AAA, Mohamed IN, Elseed MA, Koko M, Abubaker R, Abozar F, Elsayed LEO, Bhise V, Molday RS, Salih MA, Yahia A, Manzini MC. A novel missense variant in the ATPase domain of ATP8A2 and review of phenotypic variability of ATP8A2-related disorders caused by missense changes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24306843. [PMID: 38798571 PMCID: PMC11118633 DOI: 10.1101/2024.05.15.24306843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
ATPase, class 1, type 8A, member 2 (ATP8A2) is a P4-ATPase with a critical role in phospholipid translocation across the plasma membrane. Pathogenic variants in ATP8A2 are known to cause cerebellar ataxia, mental retardation, and disequilibrium syndrome 4 (CAMRQ4) which is often associated with encephalopathy, global developmental delay, and severe motor deficits. Here, we present a family with two siblings presenting with global developmental delay, intellectual disability, spasticity, ataxia, nystagmus, and thin corpus callosum. Whole exome sequencing revealed a homozygous missense variant in the nucleotide binding domain of ATP8A2 (p.Leu538Pro) that results in near complete loss of protein expression. This is in line with other missense variants in the same domain leading to protein misfolding and loss of ATPase function. In addition, by performing diffusion-weighted imaging, we identified bilateral hyperintensities in the posterior limbs of the internal capsule suggesting possible microstructural changes in axon tracts that had not been appreciated before and could contribute to the sensorimotor deficits in these individuals.
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Affiliation(s)
- Kyle P. Flannery
- Department of Neuroscience & Cell Biology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Sylvia Safwat
- Department of Neuroscience & Cell Biology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Eli Matsell
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| | - Namarata Battula
- Department of Neuroscience & Cell Biology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | | | | | - Maha A. Elseed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mahmoud Koko
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Rayan Abubaker
- Sudanese Neurogenetics Research group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Fatima Abozar
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Liena E. O. Elsayed
- Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, P.O.Box 84428, Riyadh 11671, Saudi Arabia
| | - Vikram Bhise
- Department of Pediatrics and Neurology, Rutgers – Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Robert S. Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| | - Mustafa A. Salih
- Consultant Pediatric Neurologist, Health Sector, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Ashraf Yahia
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women’s and Children’s Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Solna, Sweden
| | - M. Chiara Manzini
- Department of Neuroscience & Cell Biology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901
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Veyssiere M, Rodriguez Ordonez MDP, Chalabi S, Michou L, Cornelis F, Boland A, Olaso R, Deleuze JF, Petit-Teixeira E, Chaudru V. MYLK* FLNB and DOCK1* LAMA2 gene-gene interactions associated with rheumatoid arthritis in the focal adhesion pathway. Front Genet 2024; 15:1375036. [PMID: 38803542 PMCID: PMC11128622 DOI: 10.3389/fgene.2024.1375036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/18/2024] [Indexed: 05/29/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease caused by a combination of genetic and environmental factors. Rare variants with low predicted effects in genes participating in the same biological function might be involved in developing complex diseases such as RA. From whole-exome sequencing (WES) data, we identified genes containing rare non-neutral variants with complete penetrance and no phenocopy in at least one of nine French multiplex families. Further enrichment analysis highlighted focal adhesion as the most significant pathway. We then tested if interactions between the genes participating in this function would increase or decrease the risk of developing RA disease. The model-based multifactor dimensionality reduction (MB-MDR) approach was used to detect epistasis in a discovery sample (19 RA cases and 11 healthy individuals from 9 families and 98 unrelated CEU controls from the International Genome Sample Resource). We identified 9 significant interactions involving 11 genes (MYLK, FLNB, DOCK1, LAMA2, RELN, PIP5K1C, TNC, PRKCA, VEGFB, ITGB5, and FLT1). One interaction (MYLK*FLNB) increasing RA risk and one interaction decreasing RA risk (DOCK1*LAMA2) were confirmed in a replication sample (200 unrelated RA cases and 91 GBR unrelated controls). Functional and genomic data in RA samples or relevant cell types argue the key role of these genes in RA.
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Affiliation(s)
- Maëva Veyssiere
- Institut National de la Santé et de la Recherche Médicale, Université de Paris, Paris, France
| | | | - Smahane Chalabi
- GenHotel—Univ Evry, University of Paris Saclay, Evry, France
| | - Laetitia Michou
- Division of Rheumatology, Department of Medicine, CHU de Québec-Université Laval, Québec City, QC, Canada
| | - François Cornelis
- Génétiqe-Oncogénétique Adulte-Prévention, Institut National de la Santé et de la Recherche Médicale, Clermont-Auvergne University and CHU, Clermont-Ferrand, France
| | - Anne Boland
- Commissariat à l'Energie Atomique, Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
| | - Robert Olaso
- Commissariat à l'Energie Atomique, Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Commissariat à l'Energie Atomique, Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
| | | | - Valérie Chaudru
- Institut National de la Santé et de la Recherche Médicale, Université de Paris, Paris, France
- GenHotel—Univ Evry, University of Paris Saclay, Evry, France
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Ou JH, Rönneburg T, Carlborg Ö, Honaker CF, Siegel PB, Rubin CJ. Complex genetic architecture of the chicken Growth1 QTL region. PLoS One 2024; 19:e0295109. [PMID: 38739572 PMCID: PMC11090294 DOI: 10.1371/journal.pone.0295109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
The genetic complexity of polygenic traits represents a captivating and intricate facet of biological inheritance. Unlike Mendelian traits controlled by a single gene, polygenic traits are influenced by multiple genetic loci, each exerting a modest effect on the trait. This cumulative impact of numerous genes, interactions among them, environmental factors, and epigenetic modifications results in a multifaceted architecture of genetic contributions to complex traits. Given the well-characterized genome, diverse traits, and range of genetic resources, chicken (Gallus gallus) was employed as a model organism to dissect the intricate genetic makeup of a previously identified major Quantitative Trait Loci (QTL) for body weight on chromosome 1. A multigenerational advanced intercross line (AIL) of 3215 chickens whose genomes had been sequenced to an average of 0.4x was analyzed using genome-wide association study (GWAS) and variance-heterogeneity GWAS (vGWAS) to identify markers associated with 8-week body weight. Additionally, epistatic interactions were studied using the natural and orthogonal interaction (NOIA) model. Six genetic modules, two from GWAS and four from vGWAS, were strongly associated with the studied trait. We found evidence of both additive- and non-additive interactions between these modules and constructed a putative local epistasis network for the region. Our screens for functional alleles revealed a missense variant in the gene ribonuclease H2 subunit B (RNASEH2B), which has previously been associated with growth-related traits in chickens and Darwin's finches. In addition, one of the most strongly associated SNPs identified is located in a non-coding region upstream of the long non-coding RNA, ENSGALG00000053256, previously suggested as a candidate gene for regulating chicken body weight. By studying large numbers of individuals from a family material using approaches to capture both additive and non-additive effects, this study advances our understanding of genetic complexities in a highly polygenic trait and has practical implications for poultry breeding and agriculture.
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Affiliation(s)
- Jen-Hsiang Ou
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tilman Rönneburg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Örjan Carlborg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Christa Ferst Honaker
- Virginia Polytechnic Institute and State University, School of Animal Sciences, Blacksburg, Virginia, United States of America
| | - Paul B. Siegel
- Virginia Polytechnic Institute and State University, School of Animal Sciences, Blacksburg, Virginia, United States of America
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Institute of Marine Research, Bergen, Norway
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Shen Z, Zhang T, Twumasi G, Zhang J, Wang J, Xi Y, Wang R, Wang J, Zhang R, Liu H. Genetic analysis of a Kaijiang duck conservation population through genome-wide scan. Br Poult Sci 2024:1-9. [PMID: 38738932 DOI: 10.1080/00071668.2024.2335937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 03/08/2024] [Indexed: 05/14/2024]
Abstract
1. The Kaijiang duck is a native Chinese breed known for its excellent egg laying performance, killing-out percentage (88.57%), and disease resistance. The assessment of population genetic structure is the basis for understanding the genetics of indigenous breeds and for their protection and management.2. In this study, whole-genome sequencing was performed on 60 Kaijiang ducks to identify genetic variations and investigate the population structure. Homozygosity (ROH) analysis was conducted to assess inbreeding levels in the population.3. The study revealed a moderate level of inbreeding, indicated by an average inbreeding coefficient of 0.1043. This may impact the overall genetic diversity.4. Genomic Regions of Interest identified included 168 genomic regions exhibiting high levels of autozygosity. These regions were associated with processes including muscle growth, pigmentation, neuromodulation, and growth and reproduction.5. The significance of these pathways indicated their potential role in shaping the desirable traits of the Kaijiang duck. These findings provide insights into the genetic basis of the Kaijiang duck's desirable traits and can inform future breeding and conservation efforts.
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Affiliation(s)
- Z Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - T Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - G Twumasi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Y Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - R Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - R Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - H Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Sahu TK, Verma SK, Gayacharan, Singh NP, Joshi DC, Wankhede DP, Singh M, Bhardwaj R, Singh B, Parida SK, Chattopadhyay D, Singh GP, Singh AK. Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata). BMC PLANT BIOLOGY 2024; 24:379. [PMID: 38720284 PMCID: PMC11077894 DOI: 10.1186/s12870-024-04976-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank. RESULTS The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo-keto-reductase with flowering and maturity were revealed. CONCLUSION This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.
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Affiliation(s)
- Tanmaya Kumar Sahu
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, Uttar Pradesh, India
| | - Sachin Kumar Verma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | | | - Dinesh Chandra Joshi
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - D P Wankhede
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Mohar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Rakesh Bhardwaj
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Badal Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | | | | | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India.
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Al-Yazeedi T, Adams S, Tandonnet S, Turner A, Kim J, Lee J, Pires-daSilva A. The contribution of an X chromosome QTL to non-Mendelian inheritance and unequal chromosomal segregation in Auanema freiburgense. Genetics 2024; 227:iyae032. [PMID: 38431281 DOI: 10.1093/genetics/iyae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Auanema freiburgense is a nematode with males, females, and selfing hermaphrodites. When XO males mate with XX females, they typically produce a low proportion of XO offspring because they eliminate nullo-X spermatids. This process ensures that most sperm carry an X chromosome, increasing the likelihood of X chromosome transmission compared to random segregation. This occurs because of an unequal distribution of essential cellular organelles during sperm formation, likely dependent on the X chromosome. Some sperm components are selectively segregated into the X chromosome's daughter cell, while others are discarded with the nullo-X daughter cell. Intriguingly, the interbreeding of 2 A. freiburgense strains results in hybrid males capable of producing viable nullo-X sperm. Consequently, when these hybrid males mate with females, they yield a high percentage of male offspring. To uncover the genetic basis of nullo-spermatid elimination and X chromosome drive, we generated a genome assembly for A. freiburgense and genotyped the intercrossed lines. This analysis identified a quantitative trait locus spanning several X chromosome genes linked to the non-Mendelian inheritance patterns observed in A. freiburgense. This finding provides valuable clues to the underlying factors involved in asymmetric organelle partitioning during male meiotic division and thus non-Mendelian transmission of the X chromosome and sex ratios.
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Affiliation(s)
- Talal Al-Yazeedi
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sally Adams
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sophie Tandonnet
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Anisa Turner
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Jun Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Junho Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
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Yang L, Yi L, Yang J, Zhang R, Xie Z, Wang H. Temporal landscape and translational regulation of A-to-I RNA editing in mouse retina development. BMC Biol 2024; 22:106. [PMID: 38715001 PMCID: PMC11077751 DOI: 10.1186/s12915-024-01908-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 05/01/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The significance of A-to-I RNA editing in nervous system development is widely recognized; however, its influence on retina development remains to be thoroughly understood. RESULTS In this study, we performed RNA sequencing and ribosome profiling experiments on developing mouse retinas to characterize the temporal landscape of A-to-I editing. Our findings revealed temporal changes in A-to-I editing, with distinct editing patterns observed across different developmental stages. Further analysis showed the interplay between A-to-I editing and alternative splicing, with A-to-I editing influencing splicing efficiency and the quantity of splicing events. A-to-I editing held the potential to enhance translation diversity, but this came at the expense of reduced translational efficiency. When coupled with splicing, it could produce a coordinated effect on gene translation. CONCLUSIONS Overall, this study presents a temporally resolved atlas of A-to-I editing, connecting its changes with the impact on alternative splicing and gene translation in retina development.
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Affiliation(s)
- Ludong Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Liang Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Jiaqi Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Rui Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
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Lan D, Fu W, Ji W, Mipam TD, Xiong X, Ying S, Xiong Y, Sheng P, Ni J, Bai L, Shan T, Kong X, Li J. Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks. J Anim Sci Biotechnol 2024; 15:64. [PMID: 38706000 PMCID: PMC11071219 DOI: 10.1186/s40104-024-01027-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND The genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes. RESULTS We discovered 290 Mb of nonreference sequences and 504 new genes. Our pangenome-wide presence and absence variation (PAV) analysis revealed 5,120 PAV-related genes, highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations. Principal component analysis (PCA) based on binary gene PAV data classified yaks into three new groups: wild, domestic, and Jinchuan. Moreover, we proposed a 'two-haplotype genomic hybridization model' for understanding the hybridization patterns among breeds by integrating gene frequency, heterozygosity, and gene PAV data. A gene PAV-GWAS identified a novel gene (BosGru3G009179) that may be associated with the multirib trait in Jinchuan yaks. Furthermore, an integrated transcriptome and pangenome analysis highlighted the significant differences in the expression of core genes and the mutational burden of differentially expressed genes between yaks from high and low altitudes. Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed mRNAs and lncRNAs (between high- and low-altitude regions), especially in the heart and lungs, when comparing high- and low-altitude adaptations. CONCLUSIONS The yak pangenome offers a comprehensive resource and new insights for functional genomic studies, supporting future biological research and breeding strategies.
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Affiliation(s)
- Daoliang Lan
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China.
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China.
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China.
| | - Wei Fu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Wenhui Ji
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Tserang-Donko Mipam
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Xianrong Xiong
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Shi Ying
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Yan Xiong
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Peng Sheng
- Jiguang Gene Biotechnology Co., Ltd., Nanjing, China
| | - Jiangping Ni
- Jiguang Gene Biotechnology Co., Ltd., Nanjing, China
| | - Lijun Bai
- Chengdu Genepre Technology Co., Ltd., Chengdu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | | | - Jian Li
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
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Šimon M, Mikec Š, Atanur SS, Konc J, Morton NM, Horvat S, Kunej T. Whole genome sequencing of mouse lines divergently selected for fatness (FLI) and leanness (FHI) revealed several genetic variants as candidates for novel obesity genes. Genes Genomics 2024; 46:557-575. [PMID: 38483771 PMCID: PMC11024027 DOI: 10.1007/s13258-024-01507-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 02/25/2024] [Indexed: 04/18/2024]
Abstract
BACKGROUND Analysing genomes of animal model organisms is widely used for understanding the genetic basis of complex traits and diseases, such as obesity, for which only a few mouse models exist, however, without their lean counterparts. OBJECTIVE To analyse genetic differences in the unique mouse models of polygenic obesity (Fat line) and leanness (Lean line) originating from the same base population and established by divergent selection over more than 60 generations. METHODS Genetic variability was analysed using WGS. Variants were identified with GATK and annotated with Ensembl VEP. g.Profiler, WebGestalt, and KEGG were used for GO and pathway enrichment analysis. miRNA seed regions were obtained with miRPathDB 2.0, LncRRIsearch was used to predict targets of identified lncRNAs, and genes influencing adipose tissue amount were searched using the IMPC database. RESULTS WGS analysis revealed 6.3 million SNPs, 1.3 million were new. Thousands of potentially impactful SNPs were identified, including within 24 genes related to adipose tissue amount. SNP density was highest in pseudogenes and regulatory RNAs. The Lean line carries SNP rs248726381 in the seed region of mmu-miR-3086-3p, which may affect fatty acid metabolism. KEGG analysis showed deleterious missense variants in immune response and diabetes genes, with food perception pathways being most enriched. Gene prioritisation considering SNP GERP scores, variant consequences, and allele comparison with other mouse lines identified seven novel obesity candidate genes: 4930441H08Rik, Aff3, Fam237b, Gm36633, Pced1a, Tecrl, and Zfp536. CONCLUSION WGS revealed many genetic differences between the lines that accumulated over the selection period, including variants with potential negative impacts on gene function. Given the increasing availability of mouse strains and genetic polymorphism catalogues, the study is a valuable resource for researchers to study obesity.
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Affiliation(s)
- Martin Šimon
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia.
| | - Špela Mikec
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
| | - Santosh S Atanur
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, SW7 2AZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Janez Konc
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, 1000, Slovenia
| | - Nicholas M Morton
- The Queen's Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Simon Horvat
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
| | - Tanja Kunej
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia.
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40
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Hadar N, Dolgin V, Oustinov K, Yogev Y, Poleg T, Safran A, Freund O, Agam N, Jean MM, Proskorovski-Ohayon R, Wormser O, Drabkin M, Halperin D, Eskin-Schwartz M, Narkis G, Sued-Hendrickson S, Aminov I, Gombosh M, Aharoni S, Birk OS. VARista: a free web platform for streamlined whole-genome variant analysis across T2T, hg38, and hg19. Hum Genet 2024; 143:695-701. [PMID: 38607411 DOI: 10.1007/s00439-024-02671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
Abstract
With the increasing importance of genomic data in understanding genetic diseases, there is an essential need for efficient and user-friendly tools that simplify variant analysis. Although multiple tools exist, many present barriers such as steep learning curves, limited reference genome compatibility, or costs. We developed VARista, a free web-based tool, to address these challenges and provide a streamlined solution for researchers, particularly those focusing on rare monogenic diseases. VARista offers a user-centric interface that eliminates much of the technical complexity typically associated with variant analysis. The tool directly supports VCF files generated using reference genomes hg19, hg38, and the emerging T2T, with seamless remapping capabilities between them. Features such as gene summaries and links, tissue and cell-specific gene expression data for both adults and fetuses, as well as automated PCR design and integration with tools such as SpliceAI and AlphaMissense, enable users to focus on the biology and the case itself. As we demonstrate, VARista proved effective in narrowing down potential disease-causing variants, prioritizing them effectively, and providing meaningful biological context, facilitating rapid decision-making. VARista stands out as a freely available and comprehensive tool that consolidates various aspects of variant analysis into a single platform that embraces the forefront of genomic advancements. Its design inherently supports a shift in focus from technicalities to critical thinking, thereby promoting better-informed decisions in genetic disease research. Given its unique capabilities and user-centric design, VARista has the potential to become an essential asset for the genomic research community. https://VARista.link.
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Affiliation(s)
- Noam Hadar
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Vadim Dolgin
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Katya Oustinov
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tomer Poleg
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Amit Safran
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ofek Freund
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Nadav Agam
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Matan M Jean
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Regina Proskorovski-Ohayon
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ohad Wormser
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Max Drabkin
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Daniel Halperin
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Marina Eskin-Schwartz
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Genetics Institute, Soroka University Medical Center, Beer-Sheva, Israel
| | - Ginat Narkis
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Genetics Institute, Soroka University Medical Center, Beer-Sheva, Israel
| | - Sufa Sued-Hendrickson
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ilana Aminov
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Maya Gombosh
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sarit Aharoni
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
- Genetics Institute, Soroka University Medical Center, Beer-Sheva, Israel.
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Wan JN, Wang SW, Leitch AR, Leitch IJ, Jian JB, Wu ZY, Xin HP, Rakotoarinivo M, Onjalalaina GE, Gituru RW, Dai C, Mwachala G, Bai MZ, Zhao CX, Wang HQ, Du SL, Wei N, Hu GW, Chen SC, Chen XY, Wan T, Wang QF. The rise of baobab trees in Madagascar. Nature 2024; 629:1091-1099. [PMID: 38750363 PMCID: PMC11136661 DOI: 10.1038/s41586-024-07447-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
The baobab trees (genus Adansonia) have attracted tremendous attention because of their striking shape and distinctive relationships with fauna1. These spectacular trees have also influenced human culture, inspiring innumerable arts, folklore and traditions. Here we sequenced genomes of all eight extant baobab species and argue that Madagascar should be considered the centre of origin for the extant lineages, a key issue in their evolutionary history2,3. Integrated genomic and ecological analyses revealed the reticulate evolution of baobabs, which eventually led to the species diversity seen today. Past population dynamics of Malagasy baobabs may have been influenced by both interspecific competition and the geological history of the island, especially changes in local sea levels. We propose that further attention should be paid to the conservation status of Malagasy baobabs, especially of Adansonia suarezensis and Adansonia grandidieri, and that intensive monitoring of populations of Adansonia za is required, given its propensity for negatively impacting the critically endangered Adansonia perrieri.
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Affiliation(s)
- Jun-Nan Wan
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Sheng-Wei Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Jian-Bo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Hai-Ping Xin
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | | | | | - Robert Wahiti Gituru
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Can Dai
- School of Resources and Environmental Science, Hubei University, Wuhan, China
| | | | - Ming-Zhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Sheng-Lan Du
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Neng Wei
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Guang-Wan Hu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Si-Chong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Ya Chen
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
- Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Tao Wan
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China.
| | - Qing-Feng Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China.
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Reda Del Barrio S, de Vergas Gutiérrez J, Quesada-Espinosa JF, Sánchez-Calvín MT, Gómez-Manjón I, Sierra-Tomillo O, Juárez-Rufián A, García Fernández A. Diagnostic yield of genetic testing in adults with sensorineural hearing loss. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2024; 75:185-191. [PMID: 38346493 DOI: 10.1016/j.otoeng.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/06/2023] [Indexed: 02/19/2024]
Abstract
INTRODUCTION The contribution of genetic causes to sensorineural hearing loss (SNHL) in adults is less clear than in children, and genetic diagnosis is still not standardized in adults. In this study we present the genetic results obtained in a cohort of adult patients with SNHL. MATERIALS AND METHODS We included 63 adults with SNHL that received genetic testing between 2019 and 2022. Whole exome sequencing was performed and variants in genes related to hearing loss (virtual panel with 244 genes) were prioritised and analysed. RESULTS 24% (15/63) of patients were genetically diagnosed: 87% (13/15) of patients had non-syndromic hearing loss and 13% (2/15) had syndromic hearing loss. We identified pathogenic and likely pathogenic variants in 11 different genes. CONCLUSIONS Our results show that a significant proportion of adults with SNHL have a genetic origin, and that implementation of genetic testing improves diagnostic accuracy and allows personalized management of these patients.
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Affiliation(s)
- Sara Reda Del Barrio
- Department of Otolaryngology-Head and Neck Surgery, Hospital Universitario 12 de Octubre, Madrid, Spain.
| | | | | | | | - Irene Gómez-Manjón
- Department of Genetics, Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | | | - Alfredo García Fernández
- Department of Otolaryngology-Head and Neck Surgery, Hospital Universitario 12 de Octubre, Madrid, Spain
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43
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Bolivar AM, Duzagac F, Deng N, Reyes-Uribe L, Chang K, Wu W, Bowen CM, Taggart MW, Thirumurthi S, Lynch PM, You YN, Rodriguez-Pascual J, Lipkin SM, Kopetz S, Scheet P, Lizee GA, Reuben A, Sinha KM, Vilar E. Genomic Landscape of Lynch Syndrome Colorectal Neoplasia Identifies Shared Mutated Neoantigens for Immunoprevention. Gastroenterology 2024; 166:787-801.e11. [PMID: 38244726 PMCID: PMC11034773 DOI: 10.1053/j.gastro.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/18/2023] [Accepted: 01/07/2024] [Indexed: 01/22/2024]
Abstract
BACKGROUND & AIMS Lynch syndrome (LS) carriers develop mismatch repair-deficient neoplasia with high neoantigen (neoAg) rates. No detailed information on targetable neoAgs from LS precancers exists, which is crucial for vaccine development and immune-interception strategies. We report a focused somatic mutation and frameshift-neoAg landscape of microsatellite loci from colorectal polyps without malignant potential (PWOMP), precancers, and early-stage cancers in LS carriers. METHODS We generated paired whole-exome and transcriptomic sequencing data from 8 colorectal PWOMP, 41 precancers, 8 advanced precancers, and 12 early-stage cancers of 43 LS carriers. A computational pipeline was developed to predict, rank, and prioritize the top 100 detected mutated neoAgs that were validated in vitro using ELISpot and tetramer assays. RESULTS Mutation calling revealed >10 mut/Mb in 83% of cancers, 63% of advanced precancers, and 20% of precancers. Cancers displayed an average of 616 MHC-I neoAgs/sample, 294 in advanced precancers, and 107 in precancers. No neoAgs were detected in PWOMP. A total of 65% of our top 100 predicted neoAgs were immunogenic in vitro, and were present in 92% of cancers, 50% of advanced precancers, and 29% of precancers. We observed increased levels of naïve CD8+ and memory CD4+ T cells in mismatch repair-deficient cancers and precancers via transcriptomics analysis. CONCLUSIONS Shared frameshift-neoAgs are generated within unstable microsatellite loci at initial stages of LS carcinogenesis and can induce T-cell responses, generating opportunities for vaccine development, targeting LS precancers and early-stage cancers.
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Affiliation(s)
- Ana M Bolivar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fahriye Duzagac
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nan Deng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Laura Reyes-Uribe
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle Chang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wenhui Wu
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Charles M Bowen
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Melissa W Taggart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Selvi Thirumurthi
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas; Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick M Lynch
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas; Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y Nancy You
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Colorectal Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Steven M Lipkin
- Division of Gastroenterology and Hepatology, Weill Cornell University, New York, New York
| | - Scott Kopetz
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory A Lizee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Krishna M Sinha
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas; Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Pineau RM, Libby E, Demory D, Lac DT, Day TC, Bravo P, Yunker PJ, Weitz JS, Bozdag GO, Ratcliff WC. Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment. Nat Ecol Evol 2024; 8:1010-1020. [PMID: 38486107 PMCID: PMC11090753 DOI: 10.1038/s41559-024-02367-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
Abstract
The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth's ecosystems. Yet little is known about how early steps in the evolution of multicellularity affect eco-evolutionary dynamics. Through long-term experimental evolution, we observed niche partitioning and the adaptive divergence of two specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subjected to selection for rapid growth, followed by selection favouring larger group size. Small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations, specializing on divergent aspects of a trade-off between growth rate and survival. Through modelling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically impactful emergent properties of this evolutionary transition.
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Affiliation(s)
- Rozenn M Pineau
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eric Libby
- Integrated Science Lab, Umeå university, Umeå, Sweden.
- Department of Mathematics and Mathematical Statistics, Umeå university, Umeå, Sweden.
| | - David Demory
- CNRS, Sorbonne Université, USR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Dung T Lac
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Thomas C Day
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Pablo Bravo
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Peter J Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
| | - G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Biology, University of Maryland, College Park, MD, USA.
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Gudra D, Valdovska A, Jonkus D, Kairisa D, Galina D, Ustinova M, Viksne K, Fridmanis D, Kalnina I. Genetic characterization of the Latvian local goat breed and genetic traits associated with somatic cell count. Animal 2024; 18:101154. [PMID: 38703755 DOI: 10.1016/j.animal.2024.101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 05/06/2024] Open
Abstract
The Latvian local goat (LVK) breed represents the only native domestic goat breed in Latvia, but its limited population places it within the endangered category. However, the LVK breed has not yet undergone a comprehensive genetic characterization. Therefore, we completed whole genome sequencing to reveal the genetic foundation of the LVK breed while identifying genetic traits linked to the somatic cell count (SCC) levels. The study included 40 genomes of LVK goats sequenced to acquire at least 35x or 10x coverage. A Principal component analysis, a genetic distance tree, and an admixture analysis showed LVK's similarity to some European breeds, such as Finnish Landrace, Alpine, and Saanen, which aligns with the breed's history. An analysis of genome-wide heterozygosity, nucleotide diversity, and LD analysis indicated that the LVK population exhibits substantial levels of genetic diversity. LVK genome was dominated by short runs of homozygosity (ROHs, ≤ 500 kb) with a median length of 25 kb. With FROH 2.49%, average inbreeding levels were low; however, FROH ranged broadly from 0.13 to 12.2%. With the exception of one pure-blood breeding buck exhibiting FROH of 9.3% and FSNP of 8.5%, animals with at least 66% LVK ancestry showed moderate or no inbreeding. Overall, this study demonstrated that the LVK goats can be differentiated from imported breeds, although the population has a complex genetic structure. We were able to identify potential genetic traits associated with SCC levels, although the kinship of the animals and the heterogenic substructure of the population might have largely influenced the association analysis. We identified 26 genetic variants associated with SCC levels, which included the potentially relevant SNP rs662053371 in the OSBPL8 gene, indicating a potential signal linked to lipid metabolism in goats. To conclude, these findings present valuable insight into the genetic structure of the LVK breed for the conservation of local genetic resources.
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Affiliation(s)
- D Gudra
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - A Valdovska
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, Helmana iela 8 K, LV-3004 Jelgava, Latvia; Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia.
| | - D Jonkus
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - D Kairisa
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - D Galina
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, Helmana iela 8 K, LV-3004 Jelgava, Latvia; Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - M Ustinova
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - K Viksne
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - D Fridmanis
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - I Kalnina
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
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Kyriazis CC, Serieys LE, Bishop JM, Drouilly M, Viljoen S, Wayne RK, Lohmueller KE. The influence of gene flow on population viability in an isolated urban caracal population. Mol Ecol 2024; 33:e17346. [PMID: 38581173 PMCID: PMC11035096 DOI: 10.1111/mec.17346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Laurel E.K. Serieys
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Marine Drouilly
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
- Centre for Social Science Research, University of Cape Town, Rondebosch, 7701, South Africa
| | - Storme Viljoen
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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47
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Lenz D, Schlieben LD, Shimura M, Bianzano A, Smirnov D, Kopajtich R, Berutti R, Adam R, Aldrian D, Baric I, Baumann U, Bozbulut NE, Brugger M, Brunet T, Bufler P, Burnytė B, Calvo PL, Crushell E, Dalgiç B, Das AM, Dezsőfi A, Distelmaier F, Fichtner A, Freisinger P, Garbade SF, Gaspar H, Goujon L, Hadzic N, Hartleif S, Hegen B, Hempel M, Henning S, Hoerning A, Houwen R, Hughes J, Iorio R, Iwanicka-Pronicka K, Jankofsky M, Junge N, Kanavaki I, Kansu A, Kaspar S, Kathemann S, Kelly D, Kirsaçlioğlu CT, Knoppke B, Kohl M, Kölbel H, Kölker S, Konstantopoulou V, Krylova T, Kuloğlu Z, Kuster A, Laass MW, Lainka E, Lurz E, Mandel H, Mayerhanser K, Mayr JA, McKiernan P, McClean P, McLin V, Mention K, Müller H, Pasquier L, Pavlov M, Pechatnikova N, Peters B, Petković Ramadža D, Piekutowska-Abramczuk D, Pilic D, Rajwal S, Rock N, Roetig A, Santer R, Schenk W, Semenova N, Sokollik C, Sturm E, Taylor RW, Tschiedel E, Urbonas V, Urreizti R, Vermehren J, Vockley J, Vogel GF, Wagner M, van der Woerd W, Wortmann SB, Zakharova E, Hoffmann GF, Meitinger T, Murayama K, Staufner C, Prokisch H. Genetic landscape of pediatric acute liver failure of indeterminate origin. Hepatology 2024; 79:1075-1087. [PMID: 37976411 PMCID: PMC11020061 DOI: 10.1097/hep.0000000000000684] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/23/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND AND AIMS Pediatric acute liver failure (PALF) is a life-threatening condition. In Europe, the main causes are viral infections (12%-16%) and inherited metabolic diseases (14%-28%). Yet, in up to 50% of cases the underlying etiology remains elusive, challenging clinical management, including liver transplantation. We systematically studied indeterminate PALF cases referred for genetic evaluation by whole-exome sequencing (WES), and analyzed phenotypic and biochemical markers, and the diagnostic yield of WES in this condition. APPROACH AND RESULTS With this international, multicenter observational study, patients (0-18 y) with indeterminate PALF were analyzed by WES. Data on the clinical and biochemical phenotype were retrieved and systematically analyzed. RESULTS In total, 260 indeterminate PALF patients from 19 countries were recruited between 2011 and 2022, of whom 59 had recurrent PALF. WES established a genetic diagnosis in 37% of cases (97/260). Diagnostic yield was highest in children with PALF in the first year of life (41%), and in children with recurrent acute liver failure (64%). Thirty-six distinct disease genes were identified. Defects in NBAS (n=20), MPV17 (n=8), and DGUOK (n=7) were the most frequent findings. When categorizing, the most frequent were mitochondrial diseases (45%), disorders of vesicular trafficking (28%), and cytosolic aminoacyl-tRNA synthetase deficiencies (10%). One-third of patients had a fatal outcome. Fifty-six patients received liver transplantation. CONCLUSIONS This study elucidates a large contribution of genetic causes in PALF of indeterminate origin with an increasing spectrum of disease entities. The high proportion of diagnosed cases and potential treatment implications argue for exome or in future rapid genome sequencing in PALF diagnostics.
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Affiliation(s)
- Dominic Lenz
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Lea D. Schlieben
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
| | - Masaru Shimura
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
- Department of Metabolism, Chiba Children’s Hospital, Centre for Medical Genetics, Chiba, Japan
| | - Alyssa Bianzano
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Dmitrii Smirnov
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
| | - Robert Kopajtich
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
| | - Riccardo Berutti
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
| | - Rüdiger Adam
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, University Children’s Hospital, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Denise Aldrian
- Paediatrics I, Medical University of Innsbruck, Innsbruck, Austria
| | - Ivo Baric
- Department of Paediatrics, University Hospital Centre Zagreb, University of Zagreb, School of Medicine, Zagreb, Croatia
| | - Ulrich Baumann
- Department of Peadiatric Kidney, Liver, and Metabolic Diseases, Division for Paediatric Gastroenterology and Hepatology, Hannover Medical School, Hannover, Germany
| | - Neslihan E. Bozbulut
- Department of Paediatric Gastroenterology, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Melanie Brugger
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Theresa Brunet
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Philip Bufler
- Department of Paediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Birutė Burnytė
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Pier L. Calvo
- Regina Margherita Children’s Hospital, Paediatic Gastroenterology Unit, Torino, Italy
| | - Ellen Crushell
- National Centre for Inherited Metabolic Disorders, Children’s Health Ireland, Dublin, Ireland
| | - Buket Dalgiç
- Department of Paediatric Gastroenterology, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Anibh M. Das
- Hannover Medical School, Clinic for Paediatric Kidney, Liver, and Metabolic Diseases, Hannover, Germany
| | - Antal Dezsőfi
- First Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Felix Distelmaier
- Department of General Paediatrics, Neonatology and Paediatric Cardiology, University Children’s Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexander Fichtner
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Peter Freisinger
- Department of Paediatrics, Hospital Reutlingen, Reutlingen, Germany
| | - Sven F. Garbade
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Harald Gaspar
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Louise Goujon
- CLAD Ouest CHU Hôpital Sud, CRMR Déficiences intellectuelles, Service de Génétique Médicale, Rennes, France
| | - Nedim Hadzic
- King’s College Hospital, Paediatric Liver, GI & Nutrition Centre, London, United Kingdom
| | - Steffen Hartleif
- Eberhard Karls University Tuebingen, Paediatric Gastroenterology and Hepatology, Tuebingen, Germany
| | - Bianca Hegen
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, Institute of Human Genetics, Hamburg
| | - Stephan Henning
- Department of Paediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Andre Hoerning
- Department of Paediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Roderick Houwen
- Paediatric Gastroenterology, UMC Utrecht, Utrecht, The Netherlands
| | - Joanne Hughes
- Children’s Health Ireland, Temple Street Hospital, Dublin, Ireland
| | - Raffaele Iorio
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | | | - Martin Jankofsky
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Norman Junge
- Department of Peadiatric Kidney, Liver, and Metabolic Diseases, Division for Paediatric Gastroenterology and Hepatology, Hannover Medical School, Hannover, Germany
| | - Ino Kanavaki
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Third Department of Paediatrics, Attikon University General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Aydan Kansu
- Department of Paediatric Gastroenterology, Ankara University, School of Medicine, Ankara, Turkey
| | - Sonja Kaspar
- Department of Paediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Simone Kathemann
- Department of Paediatrics II, Paediatric Gastroenterology, Hepatology and Liver Transplantation, University Hospital Essen, Essen, Germany
| | - Deidre Kelly
- Birmingham Children’s Hospital NHS Trust, Liver Unit, Birmingham, UK
| | - Ceyda T. Kirsaçlioğlu
- Department of Paediatric Gastroenterology, Ankara University, School of Medicine, Ankara, Turkey
| | - Birgit Knoppke
- University Hospital Regensburg, KUNO University Children’s Hospital, Regensburg, Germany
| | - Martina Kohl
- Department of General Paediatrics, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Heike Kölbel
- Department of Paediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro and Behavioral Sciences, University Duisburg-Essen, Essen, Germany
| | - Stefan Kölker
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | | | - Tatiana Krylova
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Zarife Kuloğlu
- Department of Paediatric Gastroenterology, Ankara University, School of Medicine, Ankara, Turkey
| | - Alice Kuster
- Department of Neurometabolism, University Hospital of Nantes, Nantes, France
| | - Martin W. Laass
- Department of Pediatrics, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Elke Lainka
- Department of Paediatrics II, Paediatric Gastroenterology, Hepatology and Liver Transplantation, University Hospital Essen, Essen, Germany
| | - Eberhard Lurz
- Department of Paediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Hanna Mandel
- Department of Paediatrics, Rambam Medical Centre, Meyer Children’s Hospital, Metabolic Unit, Haifa, Israel
| | - Katharina Mayerhanser
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Johannes A. Mayr
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Patrick McKiernan
- University of Pittsburgh and Children’s Hospital of Pittsburgh of UPMC, Pittsburgh Liver Research Centre, Pittsburgh, Pennsylvania, USA
| | | | - Valerie McLin
- Department of Paediatrics, Gynecology, and Obstetrics, Division of Paediatric Subspecialities, Swiss Paediatric Liver Centre, Paediatric Gastroenterology, Hepatology and Nutrition Unit, University of Geneva, Geneva, Switzerland
| | - Karine Mention
- Jeanne de Flandres Hospital, Reference Centre for Inherited Metabolic Diseases, Lille, France
| | - Hanna Müller
- Department of Paediatrics, Division of Neonatology and Paediatric Intensive Care, University Hospital Marburg, Marburg, Germany
| | - Laurent Pasquier
- CLAD Ouest CHU Hôpital Sud, CRMR Déficiences intellectuelles, Service de Génétique Médicale, Rennes, France
| | - Martin Pavlov
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
| | - Natalia Pechatnikova
- Healthcare Department Morozov Children’s City Clinical Hospital, Moscow City, Moscow
| | - Bianca Peters
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Danijela Petković Ramadža
- Department of Paediatrics, University Hospital Centre Zagreb, University of Zagreb, School of Medicine, Zagreb, Croatia
| | | | - Denisa Pilic
- Department of Paediatrics II, Paediatric Gastroenterology, Hepatology and Liver Transplantation, University Hospital Essen, Essen, Germany
| | - Sanjay Rajwal
- Department of Paediatrics, Gynecology, and Obstetrics, Division of Paediatric Subspecialities, Swiss Paediatric Liver Centre, Paediatric Gastroenterology, Hepatology and Nutrition Unit, University of Geneva, Geneva, Switzerland
| | - Nathalie Rock
- Department of Paediatrics, Gynecology, and Obstetrics, Division of Paediatric Subspecialities, Swiss Paediatric Liver Centre, Paediatric Gastroenterology, Hepatology and Nutrition Unit, University of Geneva, Geneva, Switzerland
| | - Agnès Roetig
- Laboratory of Genetics of Mitochondrial Diseases, Imagine Institute, University Paris Cité, INSERM UMR, Paris, France
| | - René Santer
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Wilfried Schenk
- Department of Paediatrics, University Hospital Augsburg, Augsburg, Germany
| | - Natalia Semenova
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Christiane Sokollik
- Department of Paediatrics, Division of Paediatric Gastroenterology, Hepatology and Nutrition, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ekkehard Sturm
- Eberhard Karls University Tuebingen, Paediatric Gastroenterology and Hepatology, Tuebingen, Germany
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Eva Tschiedel
- Department of Paediatrics I, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Vaidotas Urbonas
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Roser Urreizti
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, IRSJD, Esplugues de Llobregat, Barcelona, Spain and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)- Instituto de Salud Carlos III, Spain
| | - Jan Vermehren
- University Hospital Regensburg, KUNO University Children’s Hospital, Regensburg, Germany
| | - Jerry Vockley
- University of Pittsburgh and Children’s Hospital of Pittsburgh of UPMC, Pittsburgh Liver Research Centre, Pittsburgh, Pennsylvania, USA
| | - Georg-Friedrich Vogel
- Paediatrics I, Medical University of Innsbruck, Innsbruck, Austria
- Institute of Cell Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Matias Wagner
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | - Saskia B. Wortmann
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
| | | | - Georg F. Hoffmann
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Thomas Meitinger
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Kei Murayama
- Department of Metabolism, Chiba Children’s Hospital, Centre for Medical Genetics, Chiba, Japan
| | - Christian Staufner
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
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48
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Kumar KR, Cowley MJ, Davis RL. Next-Generation Sequencing and Emerging Technologies. Semin Thromb Hemost 2024. [PMID: 38692283 DOI: 10.1055/s-0044-1786397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.
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Affiliation(s)
- Kishore R Kumar
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Sydney, Australia
| | - Mark J Cowley
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Computational Biology Group, Children's Cancer Institute, University of New South Wales, Randwick, New South Wales, Australia
| | - Ryan L Davis
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
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49
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Kroeze E, Weijers DD, Kleisman MM, Ilan U, Bladergroen RS, Hagelaar R, Meijerink JPP, Jongmans MCJ, Loeffen JLC, Kuiper RP. T-cell lymphoblastic lymphoma in constitutional mismatch repair deficiency (CMMRD): Exploring treatment opportunities. Hemasphere 2024; 8:e73. [PMID: 38741596 PMCID: PMC11089271 DOI: 10.1002/hem3.73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Affiliation(s)
- Emma Kroeze
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Dilys D. Weijers
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | | | - Uri Ilan
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | | | - Rico Hagelaar
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Jules P. P. Meijerink
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Present address:
Acerta‐Pharma (AstraZeneca)OssThe Netherlands
| | - Marjolijn C. J. Jongmans
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Department of Genetics, Utrecht University Medical CenterUtrecht UniversityUtrechtThe Netherlands
| | | | - Roland P. Kuiper
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Department of Genetics, Utrecht University Medical CenterUtrecht UniversityUtrechtThe Netherlands
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50
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Prabhash K, Saldanha E, Patil V, Bal M, Reddy P S, Sanjeev A, Kumar R, Poojary D, Noronha V, Menon N, Mittal N, Trivedi V, Nambiar K, Mishra R, Tanwar N, Malhotra R, Pange P, Gupta V, Veldore VH, Chougule A, Chaturvedi P, Dutt A, Chandrani P. RET Alterations Differentiate Molecular Profile of Medullary Thyroid Cancer. JCO Precis Oncol 2024; 8:e2300622. [PMID: 38754058 DOI: 10.1200/po.23.00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/31/2024] [Accepted: 03/19/2024] [Indexed: 05/18/2024] Open
Abstract
PURPOSE Medullary thyroid cancer (MTC) is a rare cancer originating from parafollicular C cells of the thyroid gland. Therapeutically relevant alterations in MTC are predominantly reported in RET oncogene, and lower-frequency alterations are reported in KRAS and BRAF. Nevertheless, there is an unmet need existing to analyze the MTC in the Indian cohort by using in-depth sequencing techniques that go beyond the identification of known therapeutic biomarkers. MATERIALS AND METHODS Here, we characterize MTC using integrative whole-exome and whole-transcriptome sequencing of 32 MTC tissue samples. We performed clinically relevant variant analysis, molecular pathway analysis, tumor immune-microenvironment analysis, and structural characterization of RET novel mutation. RESULTS Mutational landscape analysis shows expected RET mutations in 50% of the cases. Furthermore, we observed mutations in known cancer genes like KRAS, HRAS, SF3B1, and BRAF to be altered only in the RET-negative cohort. Pathway analysis showed differential enrichment of mutations in transcriptional deregulation genes in the RET-negative cohort. Furthermore, we observed novel RET kinase domain mutation Y900S showing affinity to RET inhibitors accessed via molecular docking and molecular dynamics simulation. CONCLUSION Altogether, this study provides a detailed genomic characterization of patients with MTC of Indian origin, highlighting the possible utility of targeted therapies in this disease.
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Affiliation(s)
- Kumar Prabhash
- Homi Bhabha National Institute (HBNI), Mumbai, India
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
| | - Elveera Saldanha
- Homi Bhabha National Institute (HBNI), Mumbai, India
- Medical Oncology Molecular Laboratory, Tata Memorial Hospital, Mumbai, India
- Computational Biology, Bioinformatics and Crosstalk Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | - Vijay Patil
- Homi Bhabha National Institute (HBNI), Mumbai, India
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
| | - Munita Bal
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Sreekanth Reddy P
- 4baseCare Onco Solutions Pvt Ltd, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Airy Sanjeev
- Medical Oncology Molecular Laboratory, Tata Memorial Hospital, Mumbai, India
- Computational Biology, Bioinformatics and Crosstalk Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | - Raunak Kumar
- Medical Oncology Molecular Laboratory, Tata Memorial Hospital, Mumbai, India
- Computational Biology, Bioinformatics and Crosstalk Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | - Disha Poojary
- Medical Oncology Molecular Laboratory, Tata Memorial Hospital, Mumbai, India
- Computational Biology, Bioinformatics and Crosstalk Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | - Vanita Noronha
- Homi Bhabha National Institute (HBNI), Mumbai, India
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
| | - Nandini Menon
- Homi Bhabha National Institute (HBNI), Mumbai, India
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
| | - Neha Mittal
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Vaishakhi Trivedi
- Homi Bhabha National Institute (HBNI), Mumbai, India
- Medical Oncology Molecular Laboratory, Tata Memorial Hospital, Mumbai, India
| | - Kavya Nambiar
- Medical Oncology Molecular Laboratory, Tata Memorial Hospital, Mumbai, India
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | - Nishtha Tanwar
- 4baseCare Onco Solutions Pvt Ltd, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Richa Malhotra
- 4baseCare Onco Solutions Pvt Ltd, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Priyanka Pange
- Medical Oncology Molecular Laboratory, Tata Memorial Hospital, Mumbai, India
| | - Vinod Gupta
- Medical Oncology Molecular Laboratory, Tata Memorial Hospital, Mumbai, India
| | - Vidya H Veldore
- 4baseCare Onco Solutions Pvt Ltd, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Anuradha Chougule
- Homi Bhabha National Institute (HBNI), Mumbai, India
- Medical Oncology Molecular Laboratory, Tata Memorial Hospital, Mumbai, India
| | - Pankaj Chaturvedi
- Homi Bhabha National Institute (HBNI), Mumbai, India
- Department of Head and Neck Surgery, Tata Memorial Hospital, Mumbai, India
| | - Amit Dutt
- Homi Bhabha National Institute (HBNI), Mumbai, India
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | - Pratik Chandrani
- Homi Bhabha National Institute (HBNI), Mumbai, India
- Medical Oncology Molecular Laboratory, Tata Memorial Hospital, Mumbai, India
- Computational Biology, Bioinformatics and Crosstalk Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
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