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Yeh PJ, Nash K, Charlesworth JEG, Collen LV, Snapper S, Uhlig HH. Catalyzing change: Implementing standardised reporting in monogenic inflammatory bowel disease research. J Pediatr Gastroenterol Nutr 2024; 78:759-762. [PMID: 38356297 DOI: 10.1002/jpn3.12147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Affiliation(s)
- Pai-Jui Yeh
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Katrina Nash
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James E G Charlesworth
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Lauren V Collen
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Scott Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
- Biomedical Research Centre, University of Oxford, Oxford, UK
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Li W, Huang X, Li D, Liu X, Jiang X, Bian X, Li X, Zhang J. A combination of genomics and transcriptomics provides insights into the distribution and differential mRNA expression of type VI secretion system in clinical Klebsiella pneumoniae. mSphere 2024; 9:e0082223. [PMID: 38436228 PMCID: PMC10964426 DOI: 10.1128/msphere.00822-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
The type VI secretion system (T6SS) serves as a crucial molecular weapon in interbacterial competition and significantly influences the adaptability of bacteria in their ecological niche. However, the distribution and function of T6SS in clinical Klebsiella pneumoniae, a common opportunistic nosocomial pathogen, have not been fully elucidated. Here, we conducted a genomic analysis of 65 clinical K. pneumoniae isolates obtained from patients with varying infections. Genes encoding a T6SS cluster present in all analyzed strains of K. pneumoniae, and strains with identical sequence type carried structurally and numerically identical T6SS. Our study also highlights the importance of selecting conserved regions within essential T6SS genes for PCR-based identification of T6SS in bacteria. Afterward, we utilized the predominant sequence type 11 (ST11) K. pneumoniae HS11286 to investigate the effect of knocking out T6SS marker genes hcp or vgrG. Transcriptome analysis identified a total of 1,298 co-upregulated and 1,752 co-downregulated differentially expressed genes in both mutants. Pathway analysis showed that only Δhcp mutant exhibited alterations in transport, establishment of localization, localization, and cell processes. The absence of hcp or vgrG gene suppressed the expression of other T6SS-related genes within the locus I cluster. Additionally, interbacterial competition experiments showed that hcp and vgrG are essential for competitive ability of ST11 K. pneumoniae HS11286. This study furthers our understanding of the genomic characteristics of T6SS in clinical K. pneumoniae and suggests the involvement of multiple genes in T6SS of strain HS11286. IMPORTANCE Gram-negative bacteria use type VI secretion system (T6SS) to deliver effectors that interact with neighboring cells for niche advantage. Klebsiella pneumoniae is an opportunistic nosocomial pathogen that often carries multiple T6SS loci, the function of which has not yet been elucidated. We performed a genomic analysis of 65 clinical K. pneumoniae strains isolated from various sources, confirming that all strains contained T6SS. We then used transcriptomics to further study changes in gene expression and its effect on interbacterial competition following the knockout of key T6SS genes in sequence type 11 (ST11) K. pneumoniae HS11286. Our findings revealed the distribution and genomic characteristics of T6SS in clinical K. pneumoniae. This study also described the overall transcriptional changes in the predominant Chinese ST11 strain HS11286 upon deletion of crucial T6SS genes. Additionally, this work provides a reference for future research on the identification of T6SS in bacteria.
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Affiliation(s)
- Wanzhen Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaolan Huang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Dan Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Shanghai, China
| | - Xiaofen Liu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaoying Jiang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Shanghai, China
| | - Xingchen Bian
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Clinical Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, China
| | - Xin Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Clinical Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, China
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3
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Handoko, Adham M, Rachmadi L, Wibowo H, Gondhowiardjo SA. Cold Tumour Phenotype Explained Through Whole Genome Sequencing in Clinical Nasopharyngeal Cancer: A Preliminary Study. Immunotargets Ther 2024; 13:173-182. [PMID: 38524775 PMCID: PMC10959245 DOI: 10.2147/itt.s452117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Nasopharyngeal cancer (NPC) is a complex cancer due to its unique genomic features and association with the Epstein-Barr virus (EBV). Despite therapeutic advancements, NPC prognosis remains poor, necessitating a deeper understanding of its genomics. Here, we present a comprehensive whole genome sequencing (WGS) view of NPC genomics and its correlation with the phenotype. Methods This study involved WGS of a clinical NPC biopsy specimen. Sequencing was carried out using a long read sequencer from Oxford Nanopore. Analysis of the variants involved correlation with the phenotype of NPC. Results A loss of genes within chromosome 6 from copy number variation (CNV) was found. The lost genes included HLA-A, HLA-B, and HLA-C, which work in the antigen presentation process. This loss of the major histocompatibility complex (MHC) apparatus resulted in the tumour's ability to evade immune recognition. The tumour exhibited an immunologically "cold" phenotype, with mild tumour-infiltrating lymphocytes, supporting the possible etiology of loss of antigen presentation capability. Furthermore, the driver mutation PIK3CA gene was identified along with various other gene variants affecting numerous signaling pathways. Discussion Comprehensive WGS was able to detect various mutations and genomic losses, which could explain tumour progression and immune evasion ability. Furthermore, the study identified the loss of other genes related to cancer and immune pathways, emphasizing the complexity of NPC genomics. In conclusion, this study underscores the significance of MHC class I gene loss and its probable correlation with the cold tumour phenotype observed in NPC.
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Affiliation(s)
- Handoko
- Department of Radiation Oncology, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Doctoral Program in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Marlinda Adham
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Otorhinolaryngology - Head and Neck Surgery Department, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia
| | - Lisnawati Rachmadi
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Anatomical Pathology, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia
| | - Heri Wibowo
- Integrated Laboratory, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Soehartati A Gondhowiardjo
- Department of Radiation Oncology, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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4
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Brown A, Batra S. Rare Hematologic Malignancies and Pre-Leukemic Entities in Children and Adolescents Young Adults. Cancers (Basel) 2024; 16:997. [PMID: 38473358 DOI: 10.3390/cancers16050997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
There are a variety of rare hematologic malignancies and germline predispositions syndromes that occur in children and adolescent young adults (AYAs). These entities are important to recognize, as an accurate diagnosis is essential for risk assessment, prognostication, and treatment. This descriptive review summarizes rare hematologic malignancies, myelodysplastic neoplasms, and germline predispositions syndromes that occur in children and AYAs. We discuss the unique biology, characteristic genomic aberrations, rare presentations, diagnostic challenges, novel treatments, and outcomes associated with these rare entities.
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Affiliation(s)
- Amber Brown
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Department of Pediatrics, Riley Hospital for Children, 705 Riley Hospital Drive, Indianapolis, IN 46202, USA
| | - Sandeep Batra
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Department of Pediatrics, Riley Hospital for Children, 705 Riley Hospital Drive, Indianapolis, IN 46202, USA
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Suryani L, Lee HPY, Teo WK, Chin ZK, Loh KS, Tay JK. Precision Medicine for Nasopharyngeal Cancer-A Review of Current Prognostic Strategies. Cancers (Basel) 2024; 16:918. [PMID: 38473280 DOI: 10.3390/cancers16050918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV) driven malignancy arising from the nasopharyngeal epithelium. Current treatment strategies depend on the clinical stage of the disease, including the extent of the primary tumour, the extent of nodal disease, and the presence of distant metastasis. With the close association of EBV infection with NPC development, EBV biomarkers have shown promise in predicting treatment outcomes. Among the omic technologies, RNA and miRNA signatures have been widely studied, showing promising results in the research setting to predict treatment response. The transformation of radiology images into measurable features has facilitated the use of radiomics to generate predictive models for better prognostication and treatment selection. Nonetheless, much of this work remains in the research realm, and challenges remain in clinical implementation.
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Affiliation(s)
- Luvita Suryani
- Department of Otolaryngology-Head & Neck Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Hazel P Y Lee
- Department of Otolaryngology-Head & Neck Surgery, National University Hospital, Singapore 119228, Singapore
| | - Wei Keat Teo
- Department of Otolaryngology-Head & Neck Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Zhi Kang Chin
- Department of Otolaryngology-Head & Neck Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Kwok Seng Loh
- Department of Otolaryngology-Head & Neck Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Joshua K Tay
- Department of Otolaryngology-Head & Neck Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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Yaglom HD, Bhattarai R, Lemmer D, Rust L, Ridenour C, Chorbi K, Kim E, Centner H, Sheridan K, Jasso-Selles D, Erickson DE, French C, Bowers JR, Valentine M, Francis D, Hepp CM, Brady S, Komatsu KK, Engelthaler DM. Large Clusters of Invasive emm49 Group A Streptococcus Identified within and across Arizona Healthcare Facilities through Statewide Genomic Surveillance System, 2019-2021. J Infect Dis 2024:jiae086. [PMID: 38373258 DOI: 10.1093/infdis/jiae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/03/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024] Open
Abstract
A statewide genomic surveillance system for invasive Group A Streptococcus was implemented in Arizona in June 2019, resulting in 1,046 isolates being submitted for genomic analysis to characterize emm-types and identify transmission clusters. Eleven of the 32 identified distinct emm-types comprised >80% of samples, with 29.7% of all isolates being typed as emm49 (and its genetic derivative emm151). Phylogenetic analysis initially identified an emm49 genomic cluster of four isolates that rapidly expanded over subsequent months (June 2019-February 2020). Public health investigations identified epidemiologic links with three different long-term care facilities, resulting in specific interventions. Unbiased genomic surveillance allowed for identification and response to clusters that would have otherwise remained undetected.
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Affiliation(s)
- Hayley D Yaglom
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Rachana Bhattarai
- Arizona Department of Health Services, Bureau of Infectious Disease and Services, Phoenix, Arizona, USA
| | - Darrin Lemmer
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Laura Rust
- Arizona Department of Health Services, Bureau of Infectious Disease and Services, Phoenix, Arizona, USA
| | - Chase Ridenour
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Kaitlyn Chorbi
- Arizona Department of Health Services, Bureau of Infectious Disease and Services, Phoenix, Arizona, USA
| | - Elizabeth Kim
- Arizona Department of Health Services, Bureau of Infectious Disease and Services, Phoenix, Arizona, USA
| | - Heather Centner
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Krystal Sheridan
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Daniel Jasso-Selles
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Daryn E Erickson
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Chris French
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Jolene R Bowers
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Michael Valentine
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Drew Francis
- Arizona State Public Health Laboratory, Phoenix, Arizona, USA
| | - Crystal M Hepp
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
| | - Shane Brady
- Arizona Department of Health Services, Public Health Preparedness Services, Phoenix, Arizona, USA
| | - Kenneth K Komatsu
- Arizona Department of Health Services, Public Health Services, Phoenix, Arizona, USA
| | - David M Engelthaler
- Translational Genomics Research Institute, Pathogen and Microbiome Division, Flagstaff, Arizona, USA
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Misas E, Seagle E, Jenkins EN, Rajeev M, Hurst S, Nunnally NS, Bentz ML, Lyman MM, Berkow E, Harrison LH, Schaffner W, Markus TM, Pierce R, Farley MM, Chow NA, Lockhart SR, Litvintseva AP. Genomic description of acquired fluconazole- and echinocandin-resistance in patients with serial Candida glabrata isolates. J Clin Microbiol 2024; 62:e0114023. [PMID: 38265207 PMCID: PMC10865870 DOI: 10.1128/jcm.01140-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/29/2023] [Indexed: 01/25/2024] Open
Abstract
Candida glabrata is one of the most common causes of systemic candidiasis, often resistant to antifungal medications. To describe the genomic context of emerging resistance, we conducted a retrospective analysis of 82 serially collected isolates from 33 patients from population-based candidemia surveillance in the United States. We used whole-genome sequencing to determine the genetic relationships between isolates obtained from the same patient. Phylogenetic analysis demonstrated that isolates from 29 patients were clustered by patient. The median SNPs between isolates from the same patient was 30 (range: 7-96 SNPs), while unrelated strains infected four patients. Twenty-one isolates were resistant to echinocandins, and 24 were resistant to fluconazole. All echinocandin-resistant isolates carried a mutation either in the FKS1 or FKS2 HS1 region. Of the 24 fluconazole-resistant isolates, 17 (71%) had non-synonymous polymorphisms in the PDR1 gene, which were absent in susceptible isolates. In 11 patients, a genetically related resistant isolate was collected after recovering susceptible isolates, indicating in vivo acquisition of resistance. These findings allowed us to estimate the intra-host diversity of C. glabrata and propose an upper boundary of 96 SNPs for defining genetically related isolates, which can be used to assess donor-to-host transmission, nosocomial transmission, or acquired resistance. IMPORTANCE In our study, mutations associated to azole resistance and echinocandin resistance were detected in Candida glabrata isolates using a whole-genome sequence. C. glabrata is the second most common cause of candidemia in the United States, which rapidly acquires resistance to antifungals, in vitro and in vivo.
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Affiliation(s)
- E. Misas
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - E. Seagle
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - E. N. Jenkins
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- ASRT, Inc., Atlanta, Georgia, USA
| | - M. Rajeev
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - S. Hurst
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - N. S. Nunnally
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M. L. Bentz
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M. M. Lyman
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - E. Berkow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - L. H. Harrison
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - W. Schaffner
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - T. M. Markus
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - R. Pierce
- Oregon Public Health Division, Oregon Health Authority, Portland, USA
| | - M. M. Farley
- Emory University School of Medicine, Decatur, Georgia, USA
| | - N. A. Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - S. R. Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - A. P. Litvintseva
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Ahmadi S, Landa I. The prognostic power of gene mutations in thyroid cancer. Endocr Connect 2024; 13:e230297. [PMID: 38078934 PMCID: PMC10831542 DOI: 10.1530/ec-23-0297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
The introduction and generalization of next-generation sequencing techniques have significantly increased the identification of mutations in thyroid tumors from multiple patient cohorts. The understanding of the association between specific mutations and clinical outcomes is gradually leading to individualizing the care of patients with thyroid cancer. BRAFV600 is the most common mutation seen in thyroid cancer patients and unequivocally predicts malignancy, but when considered in isolation, it is not recommended to be used as an independent prognostic factor. Mutations in RAS are the second most common alterations in thyroid cancer but can be found in benign and malignant lesions. Rearrangements involving receptor tyrosine kinases, primarily RET, are found in a subset of thyroid tumors without mutations in either BRAF or RAS. The assessment of additional mutations is increasingly employed in thyroid cancer prognostication. The coexistence of BRAF with alterations in genes such as PIK3CA, TERT promoter, or TP53 is associated with less favorable outcomes. Similar studies have also shown that additional oncogenic mutations in RAS-mutant thyroid carcinoma, such as those affecting the EIF1AX gene, likely predict a more aggressive clinicopathologic behavior. Overall, emerging evidence suggests that the co-occurrence of specific alterations in defined genes with BRAF or RAS mutations can become prognostic tools and useful predictors of thyroid tumor aggressiveness.
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Affiliation(s)
- Sara Ahmadi
- Division of Endocrinology, Thyroid Section, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Iñigo Landa
- Division of Endocrinology, Thyroid Section, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Collins K, Acosta AM, Siegmund SE, Cheng L, Hirsch MS, Idrees MT. Genetic Profiling Uncovers Genome-Wide Loss of Heterozygosity and Provides Insight into Mechanisms of Sarcomatoid Transformation in Chromophobe Renal Cell Carcinoma. Mod Pathol 2024; 37:100396. [PMID: 38043790 DOI: 10.1016/j.modpat.2023.100396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/07/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
Sarcomatoid transformation occurs in ∼8% of chromophobe renal cell carcinoma (chRCC) and is associated with aggressive clinical behavior. In recent years, several studies have identified genomic, transcriptomic, and epigenomic correlates of aggressive behavior in chRCC; however, the molecular mechanisms associated with sarcomatoid transformation remain incompletely understood. In this study, we analyzed paired conventional and sarcomatoid histologic components of individual chRCC to elucidate the genomic alterations that underlie sarcomatoid transformation in this tumor type. Massively parallel sequencing was performed on paired (conventional and sarcomatoid) components from 8 chRCCs. All cases harbored TP53 variants (87.5% showing TP53 variants in both components and 12.5% only in the sarcomatoid component). Intratumor comparisons revealed that TP53 variants were concordant in 71% and discordant in 29% of cases. Additional recurrent single-nucleotide variants were found in RB1 (37.5% of cases) and PTEN (25% of cases), with the remaining single-nucleotide variants detected in these tumors (PBRM1, NF1, and ASXL1) being nonrecurrent. Copy number variant analysis showed the characteristic pattern of chromosomal losses associated with chRCC (1, 2, 6, 10, 13, 17, and 21) in the conventional histologic components only. Interestingly, the sarcomatoid components of these tumors demonstrated widespread loss of heterozygosity but lacked the above chromosomal losses, likely as a consequence of whole-genome duplication/imbalanced chromosomal duplication events. Overall, the findings suggest that TP53 variants followed by whole-genome duplication/imbalanced chromosomal duplication events underlie sarcomatoid transformation in chRCC.
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Affiliation(s)
- Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Andres M Acosta
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Stephanie E Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Liang Cheng
- Department of Pathology, Warren Alpert Medical School of Brown University, Lifespan Academic Medical Center, Providence, Rhode Island
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
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Stracquadanio S, Nicolosi A, Privitera GF, Massimino M, Marino A, Bongiorno D, Stefani S. Role of transcriptomic and genomic analyses in improving the comprehension of cefiderocol activity in Acinetobacter baumannii. mSphere 2024; 9:e0061723. [PMID: 38078714 PMCID: PMC10826366 DOI: 10.1128/msphere.00617-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/05/2023] [Indexed: 01/31/2024] Open
Abstract
The mechanisms of action and resistance of cefiderocol (FDC) in Acinetobacter baumannii are still not fully elucidated, but iron transport systems have been evoked in its entry into the cell to reach the penicillin-binding proteins (PBPs). To capture the dynamics of gene expression related to FDC action in various conditions, we report on the genomic and transcriptomic features of seven A. baumannii strains with different FDC susceptibility, focusing on the variants in genes associated with β-lactam resistance and the expression of the siderophore biosynthesis and transport systems acinetobactin and baumannoferrin. We also investigated the expression of the TonB energy transduction system (ETS) and siderophore receptors piuA and pirA. The four clinical samples belonged to the same clonal complex (CC2), and the two strains with the highest FDC MICs showed peculiar variants in PBP2 and ampC. Similarly, the two clinical strains with the lowest MICs shared variants in an outer membrane protein as well as ampC. Gene expression analyses highlighted the up-regulation of the acinetobactin and baumannoferrin genes in response to iron depletion and a down-regulation in the presence of high iron concentrations. In response to FDC, gene expression seemed strain-dependent, probably due to the different metabolic features of each strain. Overall, FDC activates the ETS, confirming the active import of the drug; baumannoferrin, more than acinetobactin, appeared stimulated by FDC in an iron-depleted medium. In conclusion, iron transport systems play a clear role in the FDC uptake, and their expression likely contributes to MIC variation together with β-lactam resistance determinants.IMPORTANCEAcinetobacter baumannii poses a threat to healthcare due to its ability to give difficult-to-treat infections as a consequence of our shortage of antibiotic molecules active on this multidrug-resistant bacterium. Cefiderocol (FDC) represents one of the few drugs active on A. baumannii, and to preserve its activity, this study explored the transcriptomic and genomic features of seven strains with varying susceptibility to FDC. Transcriptomic analyses revealed the different effects of FDC on iron transport systems, promoting mainly baumannoferrin expression-thus more likely related to FDC entry-and the energy transduction systems. These findings suggest that not all iron transport systems are equally involved in FDC entry into A. baumannii cells. Finally, mutations in PBPs and β-lactamases may contribute to the resistance onset. Overall, the study sheds light on the importance of iron availability and metabolic differences in FDC resistance, offering insights into understanding the evolution of resistance in A. baumannii strains.
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Affiliation(s)
- Stefano Stracquadanio
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, Catania, Italy
| | - Alice Nicolosi
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, Catania, Italy
| | - Grete Francesca Privitera
- Department of Clinical and Experimental Medicine, Unit of Math and Comp Science, University of Catania, Catania, Italy
| | - Mariacristina Massimino
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Andrea Marino
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, Catania, Italy
| | - Dafne Bongiorno
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, Catania, Italy
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11
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Piszczek L, Kaczanowska J, Haubensak W. Towards correlative archaeology of the human mind. Biol Chem 2024; 405:5-12. [PMID: 37819768 PMCID: PMC10687516 DOI: 10.1515/hsz-2023-0199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023]
Abstract
Retracing human cognitive origins started out at the systems level with the top-down interpretation of archaeological records spanning from man-made artifacts to endocasts of ancient skulls. With emerging evolutionary genetics and organoid technologies, it is now possible to deconstruct evolutionary processes on a molecular/cellular level from the bottom-up by functionally testing archaic alleles in experimental models. The current challenge is to complement these approaches with novel strategies that allow a holistic reconstruction of evolutionary patterns across human cognitive domains. We argue that computational neuroarcheology can provide such a critical mesoscale framework at the brain network-level, linking molecular/cellular (bottom-up) to systems (top-down) level data for the correlative archeology of the human mind.
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Affiliation(s)
- Lukasz Piszczek
- Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, A-Vienna, Austria
| | | | - Wulf Haubensak
- Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, A-Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, A-1030Vienna, Austria
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12
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Kaur P, Ring A, Porras TB, Zhou G, Lu J, Kang I, Lang JE. Integrated Proteo genomic Analysis Reveals Distinct Potentially Actionable Therapeutic Vulnerabilities in Triple-Negative Breast Cancer Subtypes. Cancers (Basel) 2024; 16:516. [PMID: 38339267 PMCID: PMC10854633 DOI: 10.3390/cancers16030516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is characterized by an aggressive clinical presentation and a paucity of clinically actionable genomic alterations. Here, we utilized the Cancer Genome Atlas (TCGA) to explore the proteogenomic landscape of TNBC subtypes to see whether genomic alterations can be inferred from proteomic data. We found only 4% of the protein level changes are explained by mutations, while 21% of the protein and 35% of the transcriptomics changes were determined by copy number alterations (CNAs). We found tighter coupling between proteome and genome in some genes that are predicted to be the targets of drug inhibitors, including CDKs, PI3K, tyrosine kinase (TKI), and mTOR. The validation of our proteogenomic workflow using mass spectrometry Clinical Proteomic Tumor Analysis Consortium (MS-CPTAC) data also demonstrated the highest correlation between protein-RNA-CNA. The integrated proteogenomic approach helps to prioritize potentially actionable targets and may enable the acceleration of personalized cancer treatment.
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Affiliation(s)
- Pushpinder Kaur
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Alexander Ring
- Department of Medical Oncology and Hematology, University Hospital Zürich, 8091 Zurich, Switzerland
| | - Tania B. Porras
- Cancer and Blood Disease Institute, Children Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA
| | - Guang Zhou
- Division of Breast Services, Department of General Surgery, Digestive Disease and Surgery Institute, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Janice Lu
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Medical Oncology, Department of Medicine, University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Irene Kang
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Medical Oncology, Department of Medicine, University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Julie E. Lang
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Breast Services, Department of General Surgery, Digestive Disease and Surgery Institute, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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13
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Marani M, Madan V, Le TK, Deng J, Lee KK, Ma EZ, Kwatra SG. Dysregulation of the Skin-Liver Axis in Prurigo Nodularis: An Integrated Genomic, Transcriptomic, and Population-Based Analysis. Genes (Basel) 2024; 15:146. [PMID: 38397136 PMCID: PMC10887737 DOI: 10.3390/genes15020146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/06/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Pruritus has long been linked to hepatic dysfunction; however, there are limited data characterizing the association between liver disease and prurigo nodularis (PN), a chronic inflammatory skin disease featuring severe pruritis. We thus conducted a cross-sectional analysis of hepatic comorbidities in PN patients using TriNetX, a large global health research network. This analysis revealed that PN patients had a higher risk (p < 0.001) of developing liver cirrhosis, acute and subacute hepatic failure, inflammatory liver disease, chronic hepatitis, nonalcoholic steatohepatitis, portal hypertension, fatty liver, chronic passive congestion of the liver, and hepatocellular carcinoma compared with healthy controls. The cumulative incidence of liver disease was about three times higher in PN patients compared with healthy controls. These findings provided the basis for translational studies to investigate a genetic mechanism for this association. Cutaneous transcriptomic analysis performed on PN patients revealed the dysregulation of genes related to hepatic failure in lesional PN compared with both nonlesional PN and control skin. Similarly, gene set variation analysis (GSVA) revealed a significantly increased (p < 0.05) activation of liver metabolism, chronic hepatic failure, acute hepatic failure, cholestatic liver disease, polycystic liver disease, and hepatocellular carcinoma pathways in lesional PN compared with control skin. A subsequent genome-wide association study (GWAS) identified shared single-nucleotide polymorphisms (SNPs) in the genes AR, EDIL3, MACROD2, PCSK5, RUNX1T1, TENM4, and ZEB2 between PN and liver disease from the FinnGen cohort. Significant dysregulation of the skin-liver axis in PN patients may explain the increased incidence and severity of hepatic comorbidities and help identify future therapeutic targets for PN.
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Affiliation(s)
| | | | | | | | | | | | - Shawn G. Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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14
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Halvorsen M, de Schipper E, Boberg J, Strom N, Hagen K, Lindblad-Toh K, Karlsson E, Pedersen N, Bulik C, Fundín B, Landén M, Kvale G, Hansen B, Haavik J, Mattheisen M, Rück C, Mataix-Cols D, Crowley J. A Burden of Rare Copy Number Variants in Obsessive-Compulsive Disorder. Res Sq 2024:rs.3.rs-3749504. [PMID: 38260575 PMCID: PMC10802697 DOI: 10.21203/rs.3.rs-3749504/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Current genetic research on obsessive-compulsive disorder (OCD) supports contributions to risk specifically from common single nucleotide variants (SNVs), along with rare coding SNVs and small insertion-deletions (indels). The contribution to OCD risk from large, rare copy number variants (CNVs), however, has not been formally assessed at a similar scale. Here we describe an analysis of rare CNVs called from genotype array data in 2,248 deeply phenotyped OCD cases and 3,608 unaffected controls from Sweden and Norway. We found that in general cases carry an elevated burden of large (>30kb, at least 15 probes) CNVs (OR=1.12, P=1.77×10-3). The excess rate of these CNVs in cases versus controls was around 0.07 (95% CI 0.02-0.11, P=2.58×10-3). This signal was largely driven by CNVs overlapping protein-coding regions (OR=1.19, P=3.08×10-4), particularly deletions impacting loss-of-function intolerant genes (pLI>0.995, OR=4.12, P=2.54×10-5). We did not identify any specific locus where CNV burden was associated with OCD case status at genome-wide significance, but we noted non-random recurrence of CNV deletions in cases (permutation P = 2.60×10-3). In cases where sufficient clinical data were available (n=1612) we found that carriers of neurodevelopmental duplications were more likely to have comorbid autism (P<0.001), and that carriers of deletions overlapping neurodevelopmental genes had lower treatment response (P=0.02). The results demonstrate a contribution of large, rare CNVs to OCD risk, and suggest that studies of rare coding variation in OCD would have increased power to identify risk genes if this class of variation were incorporated into formal tests.
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Garcia-Quiñones JA, Sánchez-Domínguez CN, Serna-Rodríguez MF, Marino-Martínez IA, Rivas-Estilla AM, Pérez-Maya AA. Genetic Variants Associated with Suicide Risk in the Mexican Population: A Systematic Literature Review. Arch Suicide Res 2024; 28:71-89. [PMID: 36772904 DOI: 10.1080/13811118.2023.2176269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Suicide is defined as the action of harming oneself with the intention of dying. It is estimated that worldwide, one person dies by suicide every 40 s, making it a major health problem. Studies in families have suggested that suicide has a genetic component, so the search for genetic variants associated with suicidal behavior could be useful as potential biomarkers to identify people at risk of suicide. In Mexico, some studies of gene variants related to neurotransmission and other important pathways have been carried out and potential association of variants located in the following genes has been suggested: SLC6A4, SAT-1, TPH-2, ANKK1, GSHR, SCARA50, RGS10, STK33, COMT, and FKBP5. This systematic review shows the genetic studies conducted on the Mexican population. This article contributes by compiling the existing information on genetic variants and genes associated with suicidal behavior, in the future could be used as potential biomarkers to identify people at risk of suicide.
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Dias De Castro LL, Oliveira Júnior GA, Perez BC, Carvalho ME, De Souza Ramos EA, Ferraz JBS, Molento MB. Genome-wide association study in thoroughbred horses naturally infected with cyathostomins. Anim Biotechnol 2023; 34:2467-2479. [PMID: 35856721 DOI: 10.1080/10495398.2022.2099880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Cyathostomins are considered one of the most important parasites of horses. A group of horses within a herd can be responsible for eliminating the majority of parasite eggs. This phenotype might be explained by genetic factors. This study aimed to identify genomic regions associated with fecal egg count (FEC) and hematological parameters by performing a genomic-wide association study (GWAS) in Thoroughbred horses naturally infected with cyathostomins. Packed cell volume (PCV), differential leukocyte, and FEC were determined from 90 horses. All animals were genotyped using the Illumina Equine 70 K BeadChip panel containing 65,157 SNP markers. The five genomic windows that have explained the highest percentage of the additive genetic variance of a specific trait (top 5) were further explored to identify candidate genes. A total of 33, 21, 30, 21, and 19 genes were identified for FEC, PCV, eosinophils, neutrophils, and lymphocyte count, respectively. The top 5 marker regions explained 2.86, 2.56, 2.73, 2.33, and 2.37% of the additive genetic variation of FEC, PCV, eosinophils, neutrophils, and lymphocytes count, respectively. This is the first study correlating phenotypic horse health traits to GWAS analysis, which may be used for animal breeding activities, reducing losses due to parasite infections.
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Affiliation(s)
- Luciana L Dias De Castro
- Laboratory of Parasitology, Department of Veterinary Medicine, University of Caxias do Sul. R: Francisco Getúlio Vargas, Caxias do Sul, Brazil
| | - Gerson A Oliveira Júnior
- College of Animal Science and Food Science, University of São Paulo, Pirassununga, Brazil
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Canada
| | - Bruno Costa Perez
- College of Animal Science and Food Science, University of São Paulo, Pirassununga, Brazil
| | - Minos E Carvalho
- College of Animal Science and Food Science, University of São Paulo, Pirassununga, Brazil
| | - Edneia A De Souza Ramos
- Laboratory of Epigenetics, Department of Pathology, Federal University of Parana, Curitiba, Brazil
| | - José Bento S Ferraz
- College of Animal Science and Food Science, University of São Paulo, Pirassununga, Brazil
| | - Marcelo Beltrão Molento
- Laboratory of Veterinary Clinical Parasitology, Department of Veterinary Medicine, Federal University of Parana, Curitiba, Brazil
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Martín-Valmaseda M, Devin SR, Ortuño-Hernández G, Pérez-Caselles C, Mahdavi SME, Bujdoso G, Salazar JA, Martínez-Gómez P, Alburquerque N. CRISPR/Cas as a Genome-Editing Technique in Fruit Tree Breeding. Int J Mol Sci 2023; 24:16656. [PMID: 38068981 PMCID: PMC10705926 DOI: 10.3390/ijms242316656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
CRISPR (short for "Clustered Regularly Interspaced Short Palindromic Repeats") is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from the naturally occurring genome-editing systems found in bacteria. In this work, we reviewed the methods used to introduce CRISPR/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out target genes in different fruit tree species, including on tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses. The application of this gene-editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits into elite cultivars without changing other traits. However, currently, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are genotype-dependent, and the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, the latest news on the legislation and regulations about the use of plants modified using CRISPR/Cas systems has been also discussed.
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Affiliation(s)
- Marina Martín-Valmaseda
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sama Rahimi Devin
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Germán Ortuño-Hernández
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Cristian Pérez-Caselles
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sayyed Mohammad Ehsan Mahdavi
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Geza Bujdoso
- Research Centre for Fruit Growing, Hungarian University of Agriculture and Life Sciences, 1223 Budapest, Hungary;
| | - Juan Alfonso Salazar
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Pedro Martínez-Gómez
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Nuria Alburquerque
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
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Galiero R, Caturano A, Vetrano E, Monda M, Marfella R, Sardu C, Salvatore T, Rinaldi L, Sasso FC. Precision Medicine in Type 2 Diabetes Mellitus: Utility and Limitations. Diabetes Metab Syndr Obes 2023; 16:3669-3689. [PMID: 38028995 PMCID: PMC10658811 DOI: 10.2147/dmso.s390752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is one of the most widespread diseases in Western countries, and its incidence is constantly increasing. Epidemiological studies have shown that in the next 20 years. The number of subjects affected by T2DM will double. In recent years, owing to the development and improvement in methods for studying the genome, several authors have evaluated the association between monogenic or polygenic genetic alterations and the development of metabolic diseases and complications. In addition, sedentary lifestyle and socio-economic and pandemic factors have a great impact on the habits of the population and have significantly contributed to the increase in the incidence of metabolic disorders, obesity, T2DM, metabolic syndrome, and liver steatosis. Moreover, patients with type 2 diabetes appear to respond to antihyperglycemic drugs. Only a minority of patients could be considered true non-responders. Thus, it appears clear that the main aim of precision medicine in T2DM is to identify patients who can benefit most from a specific drug class more than from the others. Precision medicine is a discipline that evaluates the applicability of genetic, lifestyle, and environmental factors to disease development. In particular, it evaluated whether these factors could affect the development of diseases and their complications, response to diet, lifestyle, and use of drugs. Thus, the objective is to find prevention models aimed at reducing the incidence of pathology and mortality and therapeutic personalized approaches, to obtain a greater probability of response and efficacy. This review aims to evaluate the applicability of precision medicine for T2DM, a healthcare burden in many countries.
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Affiliation(s)
- Raffaele Galiero
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Alfredo Caturano
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Erica Vetrano
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Marcellino Monda
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Raffaele Marfella
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Celestino Sardu
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Teresa Salvatore
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Luca Rinaldi
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Ferdinando Carlo Sasso
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
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Weiler M, Stieger KC, Shroff K, Klein JP, Wood WH, Zhang Y, Chandrasekaran P, Lehrmann E, Camandola S, Long JM, Mattson MP, Becker KG, Rapp PR. Transcriptional changes in the rat brain induced by repetitive transcranial magnetic stimulation. Front Hum Neurosci 2023; 17:1215291. [PMID: 38021223 PMCID: PMC10679736 DOI: 10.3389/fnhum.2023.1215291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Transcranial Magnetic Stimulation (TMS) is a noninvasive technique that uses pulsed magnetic fields to affect the physiology of the brain and central nervous system. Repetitive TMS (rTMS) has been used to study and treat several neurological conditions, but its complex molecular basis is largely unexplored. Methods Utilizing three experimental rat models (in vitro, ex vivo, and in vivo) and employing genome-wide microarray analysis, our study reveals the extensive impact of rTMS treatment on gene expression patterns. Results These effects are observed across various stimulation protocols, in diverse tissues, and are influenced by time and age. Notably, rTMS-induced alterations in gene expression span a wide range of biological pathways, such as glutamatergic, GABAergic, and anti-inflammatory pathways, ion channels, myelination, mitochondrial energetics, multiple neuron-and synapse-specific genes. Discussion This comprehensive transcriptional analysis induced by rTMS stimulation serves as a foundational characterization for subsequent experimental investigations and the exploration of potential clinical applications.
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Affiliation(s)
- Marina Weiler
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Kevin C. Stieger
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Kavisha Shroff
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Jessie P. Klein
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - William H. Wood
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Prabha Chandrasekaran
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Elin Lehrmann
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Simonetta Camandola
- Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Jeffrey M. Long
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Mark P. Mattson
- Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Kevin G. Becker
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Peter R. Rapp
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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20
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Masamu U, Sangeda RZ, Mgaya J, Nkya S, Octavian B, Mtiiye FR, Nduguru J, Jonathan A, Kandonga D, Minja IK, Rugajo P, Balandya E, Makani J. Improved Biorepository to Support Sickle Cell Disease Genomics and Clinical Research: A Practical Approach to Link Patient Data and Biospecimens from Muhimbili Sickle Cell Program, Tanzania. Biopreserv Biobank 2023. [PMID: 37943607 DOI: 10.1089/bio.2023.0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
In Africa, sickle cell disease phenotypes' genetic contributors remain understudied due to the dearth of databases that pair biospecimens with demographic and clinical details. The absence of biorepositories in these settings can exacerbate this issue. This article documents the physical verification process of biospecimens in the biorepository, connecting them to patient clinical and demographic data and aiding in the planning of future genomic and clinical research studies' experience from the Muhimbili Sickle Cell Program in Dar es Salaam, Tanzania. The biospecimen database was updated with the current biospecimen position following the physical verification and then mapping this information to its demographic and clinical data using demographic identifiers. The biorepository stored 74,079 biospecimens in three -80°C freezers, including 63,345 from 5159 patients enrolled in the cohort between 2004 and 2016. Patients were identified by a control (first visit), entry (when confirmed sickle cell homozygous), admission (when hospitalized), and follow-up numbers (subsequent visits). Of 63,345 biospecimens, follow-ups were 46,915 (74.06%), control 8067 (12.74%), admission 5517 (8.71%), and entry 2846 (4.49%). Of these registered patients, females were 2521 (48.87%) and males were 2638 (51.13%). The age distribution was 1-59 years, with those older than 18 years being 577 (11.18%) and children 4582 (88.82%) of registered patients. The notable findings during the process include a lack of automated biospecimen checks, laboratory information management system, and tubes with volume calibration; this caused the verification process to be tedious and manual. Biospecimens not linked to clinical and demographic data, date format inconsistencies, and lack of regular updating of a database on exhausted biospecimens and updates when biospecimens are moved between positions within freezers were other findings that were found. A well-organized biorepository plays a crucial role in answering future research questions. Enforcing standard operating procedures and quality control will ensure that laboratory users adhere to the best biospecimen management procedures.
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Affiliation(s)
- Upendo Masamu
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Raphael Z Sangeda
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Josephine Mgaya
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Siana Nkya
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Beatrice Octavian
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Frank R Mtiiye
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Joyce Nduguru
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Agnes Jonathan
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Daniel Kandonga
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Irene K Minja
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Restorative Dentistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Paschal Rugajo
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Internal Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Emmanuel Balandya
- Department of Physiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Julie Makani
- Muhimbili Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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Crowley JJ, Cappi C, Ochoa-Panaifo ME, Frederick RM, Kook M, Wiese AD, Rancourt D, Atkinson EG, Giusti-Rodriguez P, Anderberg JL, Abramowitz JS, Adorno VR, Aguirre C, Alves GS, Alves GS, Ancalade N, Arellano Espinosa AA, Arnold PD, Ayton DM, Barbosa IG, Castano LMB, Barrera CN, Berardo MC, Berrones D, Best JR, Bigdeli TB, Burton CL, Buxbaum JD, Callahan JL, Carneiro MCB, Cepeda SL, Chazelle E, Chire JM, Munoz MC, Quiroz PC, Cobite J, Comer JS, Costa DL, Crosbie J, Cruz VO, Dager G, Daza LF, de la Rosa-Gómez A, Del Río D, Delage FZ, Dreher CB, Fay L, Fazio T, Ferrão YA, Ferreira GM, Figueroa EG, Fontenelle LF, Forero DA, Fragoso DTH, Gadad BS, Garrison SR, González A, Gonzalez LD, González MA, Gonzalez-Barrios P, Goodman WK, Grice DE, Guintivano J, Guttfreund DG, Guzick AG, Halvorsen MW, Hovey JD, Huang H, Irreño-Sotomonte J, Janssen-Aguilar R, Jensen M, Jimenez Reynolds AZ, Lujambio JAJ, Khalfe N, Knutsen MA, Lack C, Lanzagorta N, Lima MO, Longhurst MO, Lozada Martinez DA, Luna ES, Marques AH, Martinez MS, de Los Angeles Matos M, Maye CE, McGuire JF, Menezes G, Minaya C, Miño T, Mithani SM, de Oca CM, Morales-Rivero A, Moreira-de-Oliveira ME, Morris OJ, Muñoz SI, Naqqash Z, Núñez Bracho AA, Núñez Bracho BE, Rojas MCO, Olavarria Castaman LA, Balmaceda TO, Ortega I, Patel DI, Patrick AK, Paz Y Mino M, Perales Orellana JL, Stumpf BP, Peregrina T, Duarte TP, Piacsek KL, Placencia M, Prieto MB, Quarantini LC, Quarantini-Alvim Y, Ramos RT, Ramos IC, Ramos VR, Ramsey KA, Ray EV, Richter MA, Riemann BC, Rivas JC, Rosario MC, Ruggero CJ, Ruiz-Chow AA, Ruiz-Velasco A, Sagarnaga MN, Sampaio AS, Saraiva LC, Schachar RJ, Schneider SC, Schweissing EJ, Seligman LD, Shavitt RG, Soileau KJ, Stewart SE, Storch SB, Strouphauer ER, Cuevas VT, Timpano KR, la Garza BTD, Vallejo-Silva A, Vargas-Medrano J, Vásquez MI, Martinez GV, Weinzimmer SA, Yanez MA, Zai G, Zapata-Restrepo LM, Zappa LM, Zepeda-Burgos RM, Zoghbi AW, Miguel EC, Rodriguez CI, Martinez Mallen MC, Moya PR, Borda T, Moyano MB, Mattheisen M, Pereira S, Lázaro-Muñoz G, Martinez-Gonzalez KG, Pato MT, Nicolini H, Storch EA. Latin American Trans-ancestry INitiative for OCD genomics (LATINO): Study protocol. Am J Med Genet B Neuropsychiatr Genet 2023:e32962. [PMID: 37946624 DOI: 10.1002/ajmg.b.32962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/26/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
Obsessive-compulsive disorder (OCD) is a debilitating psychiatric disorder. Worldwide, its prevalence is ~2% and its etiology is mostly unknown. Identifying biological factors contributing to OCD will elucidate underlying mechanisms and might contribute to improved treatment outcomes. Genomic studies of OCD are beginning to reveal long-sought risk loci, but >95% of the cases currently in analysis are of homogenous European ancestry. If not addressed, this Eurocentric bias will result in OCD genomic findings being more accurate for individuals of European ancestry than other ancestries, thereby contributing to health disparities in potential future applications of genomics. In this study protocol paper, we describe the Latin American Trans-ancestry INitiative for OCD genomics (LATINO, https://www.latinostudy.org). LATINO is a new network of investigators from across Latin America, the United States, and Canada who have begun to collect DNA and clinical data from 5000 richly phenotyped OCD cases of Latin American ancestry in a culturally sensitive and ethical manner. In this project, we will utilize trans-ancestry genomic analyses to accelerate the identification of OCD risk loci, fine-map putative causal variants, and improve the performance of polygenic risk scores in diverse populations. We will also capitalize on rich clinical data to examine the genetics of treatment response, biologically plausible OCD subtypes, and symptom dimensions. Additionally, LATINO will help elucidate the diversity of the clinical presentations of OCD across cultures through various trainings developed and offered in collaboration with Latin American investigators. We believe this study will advance the important goal of global mental health discovery and equity.
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Affiliation(s)
- James J Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Carolina Cappi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Departamento de Psiquiatria, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Renee M Frederick
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Minjee Kook
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Andrew D Wiese
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Diana Rancourt
- Department of Psychology, University of South Florida, Tampa, Florida, USA
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Paola Giusti-Rodriguez
- Department of Psychiatry, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jacey L Anderberg
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Jonathan S Abramowitz
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Victor R Adorno
- Hospital Psiquiátrico de Asunción, Direccion General, Asuncion, Central, Paraguay
| | - Cinthia Aguirre
- Departamento de Psiquiatría, Hospital Psiquiátrico de Asunción, Asuncion, Central, Paraguay
| | - Gilberto S Alves
- Hospital Nina Rodrigues/Universidade Federal do Maranhão (UFMA), Sao Luis do Maranhao, Maranhao, Brazil
| | - Gustavo S Alves
- Hospital Universitário Professor Edgard Santos, Serviço de Psiquiatria, Laboratório de Neuropsicofarmacologia-LANP, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Pós-Graduação em Medicina e Saúde, Salvador, Bahia, Brazil
| | - NaEshia Ancalade
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Paul D Arnold
- The Mathison Centre for Mental Health Research & Education, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Daphne M Ayton
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Izabela G Barbosa
- Departamento de Saúde Mental da Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - María Celeste Berardo
- Centro Interdisciplinario de Tourette, TOC, TDAH y Trastornos Asociados (CITA), Buenos Aires, Buenos Aires, Argentina
| | - Dayan Berrones
- Department of Psychology, Rice University, Houston, Texas, USA
| | - John R Best
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, New York, USA
- VA New York Harbor Healthcare System, Brooklyn, New York, USA
| | - Christie L Burton
- Department of Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Maria Cecília B Carneiro
- Departamento de Psiquiatria e Medicina Legal, Universidade Federal do Paraná, Curitiba, Parana, Brazil
| | - Sandra L Cepeda
- Department of Psychology, University of Miami, Coral Gables, Florida, USA
| | - Evelyn Chazelle
- Centro Interdisciplinario de Tourette, TOC, TDAH y Trastornos Asociados (CITA), Buenos Aires, Buenos Aires, Argentina
| | - Jessica M Chire
- Instituto Nacional de Salud Mental "Honorio Delgado-Hideyo Noguchi", Dirección de Niños y Adolescentes Lima, Lima, Peru
| | | | | | - Journa Cobite
- Department of Counseling Psychology, University of Houston, Houston, Texas, USA
| | - Jonathan S Comer
- Department of Psychology, Florida International University, Miami, Florida, USA
| | - Daniel L Costa
- Departamento de Psiquiatria, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Jennifer Crosbie
- Department of Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Victor O Cruz
- Instituto Nacional de Salud Mental "Honorio Delgado-Hideyo Noguchi", Oficina Ejecutiva de Investigación, Lima, Lima, Peru
- School of Medicine, Universidad San Martin de Porres, Lima, Lima, Peru
| | - Guillermo Dager
- Corporación Universitaria Rafael Nuñez, Cartagena, Bolivar, Colombia
| | - Luisa F Daza
- Hospital Psiquiátrico Universitario Del Valle, Cali, Valle del Cauca, Colombia
| | - Anabel de la Rosa-Gómez
- Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | | | - Fernanda Z Delage
- Departamento de Medicina Forense e Psiquiatria, Universidade Federal do Paraná, Curitiba, Parana, Brazil
| | - Carolina B Dreher
- Departamento de Psiquiatria, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Psiquiatria, Clínica Médica, Porto Alegre, Rio Grande do Sul, Brazil
| | - Lucila Fay
- Centro Interdisciplinario de Tourette, TOC, TDAH y Trastornos Asociados (CITA), Buenos Aires, Buenos Aires, Argentina
| | - Tomas Fazio
- Centro Interdisciplinario de Tourette, TOC, TDAH y Trastornos Asociados (CITA), Buenos Aires, Buenos Aires, Argentina
| | - Ygor A Ferrão
- Departamento de Psiquiatria, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriela M Ferreira
- Departamento de Medicina Forense e Psiquiatria, Universidade Federal do Paraná, Curitiba, Parana, Brazil
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba, Parana, Brazil
| | - Edith G Figueroa
- Departamento de Psiquiatría de Adultos, Instituto Nacional de Salud Mental "Honorio Delgado-Hideyo Noguchi", Lima, Lima, Peru
| | - Leonardo F Fontenelle
- Departamento de Psiquiatria e Medicina Legal, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Psiquiatria, Instituto D'Or de Pesquisa e Ensino, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diego A Forero
- Fundación Universitaria del Área Andina, Escuela de Salud y Ciencias del Deporte, Bogota, Bogota, Colombia
| | - Daniele T H Fragoso
- Departamento de Medicina Forense e Psiquiatria, Universidade Federal do Paraná, Curitiba, Parana, Brazil
| | - Bharathi S Gadad
- Department of Psychiatry, Texas Tech University Health Sciences Center El Paso, El Paso, Texas, USA
| | | | | | - Laura D Gonzalez
- Centro Interdisciplinario de Tourette, TOC, TDAH y Trastornos Asociados (CITA), Buenos Aires, Buenos Aires, Argentina
| | - Marco A González
- Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Polaris Gonzalez-Barrios
- Departamento de Psiquiatría, Universidad de Puerto Rico, San Juan, Puerto Rico, USA
- Universidad de Puerto Rico Campus de Ciências Médicas, San Juan, Puerto Rico, USA
| | - Wayne K Goodman
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Dorothy E Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jerry Guintivano
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Andrew G Guzick
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Matthew W Halvorsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joseph D Hovey
- Department of Psychological Science, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Hailiang Huang
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA
| | - Jonathan Irreño-Sotomonte
- Center for Mental Health-Cersame, School of Medicine and Health Sciences, Universidad del Rosario, Bogota, District of Colombia, Colombia
| | - Reinhard Janssen-Aguilar
- Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suarez, Subdirección de Psiquiatría, Ciudad de México, Ciudad de Mexico, Mexico
| | - Matias Jensen
- Centro de Neurociencias, Universidad de Valparaíso, Valparaiso, Chile
| | | | | | - Nasim Khalfe
- Baylor College of Medicine, School of Medicine, Houston, Texas, USA
| | - Madison A Knutsen
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
- Department of Psychology, Augustana College, Rock Island, Illinois, USA
| | - Caleb Lack
- Department of Psychology, University of Central Oklahoma, Edmond, Oklahoma, USA
| | - Nuria Lanzagorta
- Departamento de Investigación Clínica, Grupo Médico Carracci, Ciudad de México, Ciudad de Mexico, Mexico
| | - Monicke O Lima
- Departamento de Psiquiatria, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Melanie O Longhurst
- Department of Psychiatry, Texas Tech University Health Sciences Center El Paso, El Paso, Texas, USA
| | | | - Elba S Luna
- Instituto Nacional de Salud Mental "Honorio Delgado-Hideyo Noguchi", Oficina Ejecutiva de Investigación, Lima, Lima, Peru
| | - Andrea H Marques
- National Institute of Mental Heatlh (NIMH), Bethesda, Maryland, USA
| | - Molly S Martinez
- DFW OCD Treatment Specialists, Richardson, Texas, USA
- Specialists in OCD and Anxiety Recovery (SOAR), Richardson, Texas, USA
| | - Maria de Los Angeles Matos
- Centro Interdisciplinario de Tourette, TOC, TDAH y Trastornos Asociados (CITA), Buenos Aires, Buenos Aires, Argentina
| | - Caitlyn E Maye
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph F McGuire
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Gabriela Menezes
- Programa de Ansiedade, Obsessões e Compulsões, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Charlene Minaya
- Department of Psychology, Fordham University, New York, New York, USA
| | - Tomás Miño
- Centro de Neurociencias, Universidad de Valparaíso, Valparaiso, Chile
| | - Sara M Mithani
- School of Nursing, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | | | | | - Maria E Moreira-de-Oliveira
- Programa de Ansiedade, Obsessões e Compulsões, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Olivia J Morris
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Sandra I Muñoz
- Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Zainab Naqqash
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | | | | | - Trinidad Olivos Balmaceda
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaiso, Valparaiso, Chile
| | - Iliana Ortega
- The Mathison Centre for Mental Health Research & Education, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Darpan I Patel
- School of Nursing, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Ainsley K Patrick
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mariel Paz Y Mino
- Clínica de Salud Mental USFQ, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
- Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Jose L Perales Orellana
- Universidad Tegnológica Privada de Santa Cruz (UTEPSA), Santa Cruz de la Sierra, Andres Ibañez, Bolivia
| | - Bárbara Perdigão Stumpf
- Departamento de Saúde Mental da Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | - Maritza Placencia
- Departamento Académico de Ciencias Dinámicas, Universidad Nacional Mayor de San Marcos, Lima, Lima, Peru
| | - María Belén Prieto
- Centro Interdisciplinario de Tourette, TOC, TDAH y Trastornos Asociados (CITA), Buenos Aires, Buenos Aires, Argentina
| | - Lucas C Quarantini
- Hospital Universitário Professor Edgard Santos, Serviço de Psiquiatria, Laboratório de Neuropsicofarmacologia-LANP, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Departamento de Neurociências e Saúde Mental, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Yana Quarantini-Alvim
- Hospital Universitário Professor Edgard Santos, Serviço de Psiquiatria, Laboratório de Neuropsicofarmacologia-LANP, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Faculdade Santa Casa, Faculdade de Psicologia, Salvador, Bahia, Brazil
| | - Renato T Ramos
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Iaroslava C Ramos
- Department of Psychiatry, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Psychiatry, Frederick Thompson Anxiety Disorders Centre, Toronto, Ontario, Canada
| | - Vanessa R Ramos
- Departamento de Psiquiatria, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Kesley A Ramsey
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elise V Ray
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Margaret A Richter
- Department of Psychiatry, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Juan C Rivas
- Hospital Psiquiátrico Universitario Del Valle, Cali, Valle del Cauca, Colombia
- Departamento de Psiquiatría, Universidad del Valle, Cali, Valle del Cauca, Colombia
- Departamento de Psiquiatria, Universidad ICESI, Cali, Valle del Cauca, Colombia
- Departamento de Psiquiatria, Fundación Valle del Lili, Cali, Valle del Cauca, Colombia
| | - Maria C Rosario
- Departamento de Psiquiatria da, Universidade Federal de São Paulo (UNIFESP), Sao Paulo, Sao Paulo, Brazil
| | - Camilo J Ruggero
- Department of Psychology, University of North Texas, Denton, Texas, USA
| | | | - Alejandra Ruiz-Velasco
- Department of Psychiatry, Texas Tech University Health Sciences Center El Paso, El Paso, Texas, USA
| | - Melisa N Sagarnaga
- Facultad de Psicología, Universidad de Buenos Aires, Buenos Aires, Buenos Aires, Argentina
| | - Aline S Sampaio
- Hospital Universitário Professor Edgard Santos, Serviço de Psiquiatria, Laboratório de Neuropsicofarmacologia-LANP, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Pós-Graduação em Medicina e Saúde, Salvador, Bahia, Brazil
- Departamento de Neurociências e Saúde Mental, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Leonardo C Saraiva
- Departamento de Psiquiatria, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Russell J Schachar
- Department of Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Sophie C Schneider
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Ethan J Schweissing
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Laura D Seligman
- Department of Psychological Science, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Roseli G Shavitt
- Departamento de Psiquiatria, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Keaton J Soileau
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - S Evelyn Stewart
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
- BC Mental Health and Substance Use Services, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Shaina B Storch
- Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Vissente Tapia Cuevas
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaiso, Valparaiso, Chile
| | - Kiara R Timpano
- Department of Psychology, University of Miami, Coral Gables, Florida, USA
| | | | - Alexie Vallejo-Silva
- Center for Mental Health-Cersame, School of Medicine and Health Sciences, Universidad del Rosario, Bogota, District of Colombia, Colombia
| | - Javier Vargas-Medrano
- Department of Psychiatry, Texas Tech University Health Sciences Center El Paso, El Paso, Texas, USA
| | - María I Vásquez
- Hospital Nacional Arzobispo Loayza, Servicio de Salud Mental, Lima, Lima, Peru
| | - Guadalupe Vidal Martinez
- Department of Psychiatry, Texas Tech University Health Sciences Center El Paso, El Paso, Texas, USA
| | - Saira A Weinzimmer
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Mauricio A Yanez
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Gwyneth Zai
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Brain Sciences, Centre for Addiction and Mental Health, Neurogenetics Section, Toronto, Ontario, Canada
| | - Lina M Zapata-Restrepo
- Departamento de Psiquiatria, Fundación Valle del Lili, Cali, Valle del Cauca, Colombia
- Facultad de Ciencias de la Salud, Universidad ICESI, Cali, Valle, Colombia
- Department of Neurology, Global Brain Health Institute-University of California San Francisco, San Francisco, California, USA
| | - Luz M Zappa
- Centro Interdisciplinario de Tourette, TOC, TDAH y Trastornos Asociados (CITA), Buenos Aires, Buenos Aires, Argentina
- Departamento de Salud Mental, Hospital de Niños Ricardo Gutierrez, Buenos Aires, Buenos Aires, Argentina
- Hospital Universitario Austral, Materno Infantil, Buenos Aires, Buenos Aires, Argentina
| | - Raquel M Zepeda-Burgos
- Centro de Investigación en Ciencias y Humanidades, Universidad Dr. José Matías Delgado, Santa Tecla, La Libertad, El Salvador
| | - Anthony W Zoghbi
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
- Department of Psychiatry, New York State Psychiatric Institute, New York, New York, USA
| | - Euripedes C Miguel
- Departamento de Psiquiatria, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Carolyn I Rodriguez
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA
- Department of Psychiatry, Temerty Faculty of Medicine, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
| | | | - Pablo R Moya
- Universidad de Valparaíso, Instituto de Fisiología Valparaiso, Valparaiso, Chile
- Centro Interdisciplinario de Neurociencia de Valparaiso (CINV), Valparaiso, Chile
| | - Tania Borda
- Instituto Realize, Buenos Aires, Buenos Aires, Argentina
- Facultad de Psicología, Universidad Catolica Argentina, Buenos Aires, Buenos Aires, Argentina
| | - María Beatriz Moyano
- Centro Interdisciplinario de Tourette, TOC, TDAH y Trastornos Asociados (CITA), Buenos Aires, Buenos Aires, Argentina
- Asociación de Psiquiatras Argentinos (APSA), Buenos Aires, Buenos Aires, Argentina
- Asociación de Psiquiatras Argentinos (APSA), Presidente del Capítulo de Investigacion en Psiquiatria, Buenos Aires, Buenos Aires, Argentina
| | - Manuel Mattheisen
- Department of Community Health and Epidemiology & Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
- LMU Munich, Institute of Psychiatric Phenomics and Genomics (IPPG), Munich, Germany
| | - Stacey Pereira
- Baylor College of Medicine, Center for Medical Ethics and Health Policy, Houston, Texas, USA
| | - Gabriel Lázaro-Muñoz
- Center for Bioethics, Harvard University School of Medicine, Boston, Massachusetts, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Michele T Pato
- Department of Psychiatry, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Humberto Nicolini
- Departamento de Psiquiatría, Ciudad de México, Grupo Médico Carracci, Ciudad de Mexico, Mexico
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Ciudad de México, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, Mexico
| | - Eric A Storch
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
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Huang H, Li N, Liang Y, Li R, Tong X, Xiao J, Tang H, Jiang D, Xie K, Fang C, Chen S, Li G, Wang B, Wang J, Luo H, Guo L, Ma H, Jiang W, Feng Y. Multi-omics analyses reveal spatial heterogeneity in primary and metastatic oesophageal squamous cell carcinoma. Clin Transl Med 2023; 13:e1493. [PMID: 38009315 PMCID: PMC10679972 DOI: 10.1002/ctm2.1493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND Biopsies obtained from primary oesophageal squamous cell carcinoma (ESCC) guide diagnosis and treatment. However, spatial intra-tumoral heterogeneity (ITH) influences biopsy-derived information and patient responsiveness to therapy. Here, we aimed to elucidate the spatial ITH of ESCC and matched lymph node metastasis (LNmet ). METHODS Primary tumour superficial (PTsup ), deep (PTdeep ) and LNmet subregions of patients with locally advanced resectable ESCC were evaluated using whole-exome sequencing (WES), whole-transcriptome sequencing and spatially resolved digital spatial profiling (DSP). To validate the findings, immunohistochemistry was conducted and a single-cell transcriptomic dataset was analysed. RESULTS WES revealed 15.72%, 5.02% and 32.00% unique mutations in PTsup , PTdeep and LNmet , respectively. Copy number alterations and phylogenetic trees showed spatial ITH among subregions both within and among patients. Driver mutations had a mixed intra-tumoral clonal status among subregions. Transcriptome data showed distinct differentially expressed genes among subregions. LNmet exhibited elevated expression of immunomodulatory genes and enriched immune cells, particularly when compared with PTsup (all P < .05). DSP revealed orthogonal support of bulk transcriptome results, with differences in protein and immune cell abundance between subregions in a spatial context. The integrative analysis of multi-omics data revealed complex heterogeneity in mRNA/protein levels and immune cell abundance within each subregion. CONCLUSIONS This study comprehensively characterised spatial ITH in ESCC, and the findings highlight the clinical significance of unbiased molecular classification based on multi-omics data and their potential to improve the understanding and management of ESCC. The current practices for tissue sampling are insufficient for guiding precision medicine for ESCC, and routine profiling of PTdeep and/or LNmet should be systematically performed to obtain a more comprehensive understanding of ESCC and better inform treatment decisions.
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Affiliation(s)
- Haitao Huang
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Na Li
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Yingkuan Liang
- Department of Thoracic SurgeryNanjing Medical University Affiliated Cancer HospitalNanjingChina
| | - Rutao Li
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Xing Tong
- Department of Pathologythe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Jinyuan Xiao
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Hongzhen Tang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Dong Jiang
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Kai Xie
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chen Fang
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Shaomu Chen
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Guangbin Li
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Bin Wang
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Jiaqian Wang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Haitao Luo
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Lingchuan Guo
- Department of Pathologythe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Haitao Ma
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Wei Jiang
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Yu Feng
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
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Anastasiadi D, Wellenreuther M. A conserved genomic code underpins animal DNA methylation patterns. Trends Ecol Evol 2023; 38:1016-1018. [PMID: 37620218 DOI: 10.1016/j.tree.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
Evidence is mounting that non-genetic inheritance impacts evolution, however, how conserved the underlying processes are remains unexplored. Klughammer et al. investigated DNA methylation across the animal kingdom, one important mechanism of non-genetic inheritance. Using a dataset encompassing 580 species, the authors identified conserved associations between sequence and DNA methylation.
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Affiliation(s)
- Dafni Anastasiadi
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, 293 Akersten St, Nelson 7010, New Zealand.
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, 293 Akersten St, Nelson 7010, New Zealand; School of Biological Sciences, The University of Auckland, 3A Symonds St, Auckland 1010, New Zealand.
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24
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Yang Y, Wan Z, Zhang E, Piao Y. Genomic profiling and immune landscape of olfactory neuroblastoma in China. Front Oncol 2023; 13:1226494. [PMID: 38023213 PMCID: PMC10646513 DOI: 10.3389/fonc.2023.1226494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
Background Olfactory neuroblastoma (ONB) is a rare malignant neoplasm of the olfactory mucosa. The paucity of genomic data has prevented the development of individualized ONB treatments. Here, we investigated the genomic and immune landscape of ONB in Chinese patients. Methods Whole exome sequencing (WES) and multiplex immunofluorescence (MIF) analysis were performed on tissue samples from 19 Chinese ONB patients. Patients were divided into low- and high-grade groups. Results Overall, 929 nonsynonymous alterations were identified in 18 (94.74%) ONB cases. The most prevalent altered cancer-related genes were CTNNB1 (16%) and ZNRF3 (16%). The most mutated oncogenic pathways were the WNT and RAS pathways. The median tumor mutation burden (TMB) was 0.45, ranging from 0 to 3.25. Only one case expressed PD-L1 (> 1%) in the tumor region. The percentage of CD8+ tumor-infiltrating lymphocytes (TILs) in the tumor region ranged from 0.03% to 84.9%, with a median of 1.08%. No significant differences were observed between the low- and high-grade groups for clinicopathological features, mutant genes, mutant pathways, TMB, tumor neoantigen burden (TNB), mutant-allele tumor heterogeneity (MATH), PD-L1 expression levels, or CD8+ TIL percentage. However, the low-grade group showed significantly more CD68+ macrophages in both the tumor and total region than the high-grade group. Notably, CD68+CD163- macrophages accounted for an average of 80.5% of CD68+ macrophages. Conclusion This study presents data on the genomic and immune landscape of ONB cases in China. CTNNB1 and ZNRF3 were the most prevalent altered cancer-related genes. The results of TMB, PD-L1, and CD8+ Tils suggest that ONB may be insensitive to immunotherapy. M1 macrophages may be positively associated with the prognosis of ONB. Implications for Practice In this study, the most prevalent altered cancer-related genes were CTNNB1 (16%) and ZNRF3 (16%). The most mutated oncogenic pathways were the WNT and RAS pathways. The median tumor mutation burden (TMB) was 0.45, ranging from 0 to 3.25. Only one (1/15) case expressed PD-L1 (> 1%) in the tumor region. However, the low-grade group showed significantly more CD68+ macrophages in both the tumor and total region than the high-grade group. The higher level of CD68-related macrophages indicates that M1 macrophages potentially play an important role in ONB development that is possibly associated with prognosis.
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Affiliation(s)
- Yunyun Yang
- Department of Pathology, Beijing Tongren Hospital Affiliated to Capital Medical University, Beijing, China
- Department of Medicine, Beijing Key Laboratory of Head and Neck Molecular Diagnostic Pathology, Beijing, China
| | - Zhiyi Wan
- Department of Medicine, Genecast Biotechnology Co., Ltd., Wuxi, China
| | - Enli Zhang
- Department of Medicine, Genecast Biotechnology Co., Ltd., Wuxi, China
| | - Yingshi Piao
- Department of Pathology, Beijing Tongren Hospital Affiliated to Capital Medical University, Beijing, China
- Department of Medicine, Beijing Key Laboratory of Head and Neck Molecular Diagnostic Pathology, Beijing, China
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25
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Krishnamurthy G, Nguyen PT, Tran BN, Phan HT, Brennecke SP, Moses EK, Melton PE. Genomic variation associated with cardiovascular disease progression following preeclampsia: a systematic review. Front Epidemiol 2023; 3:1221222. [PMID: 38455895 PMCID: PMC10911037 DOI: 10.3389/fepid.2023.1221222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/14/2023] [Indexed: 03/09/2024]
Abstract
Background Women with a history of preeclampsia (PE) have been shown to have up to five times the risk of developing later-life cardiovascular disease (CVD). While PE and CVD are known to share clinical and molecular characteristics, there are limited studies investigating their shared genomics (genetics, epigenetics or transcriptomics) variation over time. Therefore, we sought to systematically review the literature to identify longitudinal studies focused on the genomic progression to CVD following PE. Methods A literature search of primary sources through PubMed, Scopus, Web of Science and Embase via OVID was performed. Studies published from January 1, 1980, to July 28, 2023, that investigated genomics in PE and CVD were eligible for inclusion. Included studies were screened based on Cochrane systematic review guidelines in conjunction with the PRISMA 2020 checklist. Eligible articles were further assessed for quality using the Newcastle-Ottawa scale. Results A total of 9,231 articles were screened, with 14 studies subjected to quality assessment. Following further evaluation, six studies were included for the final review. All six of these studies were heterogeneous in regard to CVD/risk factor as outcome, gene mapping approach, and in different targeted genes. The associated genes were RGS2, LPA, and AQP3, alongside microRNAs miR-122-5p, miR-126-3p, miR-146a-5p, and miR-206. Additionally, 12 differentially methylated regions potentially linked to later-life CVD following PE were identified. The only common variable across all six studies was the use of a case-control study design. Conclusions Our results provide critical insight into the heterogeneous nature of genomic studies investigating CVD following PE and highlight the urgent need for longitudinal studies to further investigate the genetic variation underlying the progression to CVD following PE.
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Affiliation(s)
- Gayathry Krishnamurthy
- Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, TAS, Australia
| | - Phuong Tram Nguyen
- Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, TAS, Australia
| | - Bao Ngoc Tran
- Wicking Dementia Research and Education Center, College of Health and Medicine, The University of Tasmania, Hobart, TAS, Australia
| | - Hoang T. Phan
- Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, TAS, Australia
| | - Shaun P. Brennecke
- Pregnancy Research Centre, Department of Maternal-Fetal Medicine, The Royal Women’s Hospital, Melbourne, VIC, Australia
- Department of Obstetrics and Gynaecology, The Royal Women’s Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Eric K. Moses
- Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, TAS, Australia
| | - Phillip E. Melton
- Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, TAS, Australia
- School of Global and Population Health, The University of Western Australia, Crawley, WA, Australia
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26
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Zhang X, Zhang P, Cong A, Feng Y, Chi H, Xia Z, Tang H. Unraveling molecular networks in thymic epithelial tumors: deciphering the unique signatures. Front Immunol 2023; 14:1264325. [PMID: 37849766 PMCID: PMC10577431 DOI: 10.3389/fimmu.2023.1264325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 10/19/2023] Open
Abstract
Thymic epithelial tumors (TETs) are a rare and diverse group of neoplasms characterized by distinct molecular signatures. This review delves into the complex molecular networks of TETs, highlighting key aspects such as chromosomal abnormalities, molecular subtypes, aberrant gene mutations and expressions, structural gene rearrangements, and epigenetic changes. Additionally, the influence of the dynamic tumor microenvironment on TET behavior and therapeutic responses is examined. A thorough understanding of these facets elucidates TET pathogenesis, offering avenues for enhancing diagnostic accuracy, refining prognostic assessments, and tailoring targeted therapeutic strategies. Our review underscores the importance of deciphering TETs' unique molecular signatures to advance personalized treatment paradigms and improve patient outcomes. We also discuss future research directions and anticipated challenges in this intriguing field.
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Affiliation(s)
- Xiao Zhang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengpeng Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Ansheng Cong
- Division of Nephrology, Nanfang Hospital, Southern Medical University, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, China
| | - Yanlong Feng
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Chi
- School of Clinical Medical Sciences, Southwest Medical University, Luzhou, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians University Munich, Munich, Germany
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China
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Giovannini S, Strillacci MG, Bagnato A, Albertini E, Sarti FM. Genetic and Phenotypic Characteristics of Belted Pig Breeds: A Review. Animals (Basel) 2023; 13:3072. [PMID: 37835678 PMCID: PMC10571877 DOI: 10.3390/ani13193072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Belted pig breeds have unique, distinguishing phenotypic characteristics. This review summarises the current knowledge on pig breeds displaying a belted coat pattern. Belts of different widths and positions around the animal's trunk characterise specific pig breeds from all around the world. All the breeds included in the present paper have been searched through the FAO domestic animal diversity information system (DAD-IS), Every country was checked to identify all breeds described as having black or red piebald coat pattern variations. Advances in genomic technologies have made it possible to identify the specific genes and genetic markers associated with the belted phenotype and explore the genetic relationships between different local breeds. Thus, the origin, history, and production traits of these breeds, together with all the genomic information related to the mechanism of skin pigmentation, are discussed. By increasing our understanding of these breeds, we can appreciate the richness of our biological and cultural heritage and work to preserve the biodiversity of the world's animals.
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Affiliation(s)
- Samira Giovannini
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (E.A.); (F.M.S.)
| | - Maria Giuseppina Strillacci
- Department of Veterinary and Animal Science, Università degli Studi di Milano, Via Dell’Università 6, 26900 Lodi, Italy; (M.G.S.); (A.B.)
| | - Alessandro Bagnato
- Department of Veterinary and Animal Science, Università degli Studi di Milano, Via Dell’Università 6, 26900 Lodi, Italy; (M.G.S.); (A.B.)
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (E.A.); (F.M.S.)
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (E.A.); (F.M.S.)
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Han X, Han B, Luo H, Ling H, Hu X. Integrated Multi-Omics Profiling of Young Breast Cancer Patients Reveals a Correlation between Galactose Metabolism Pathway and Poor Disease-Free Survival. Cancers (Basel) 2023; 15:4637. [PMID: 37760606 PMCID: PMC10526161 DOI: 10.3390/cancers15184637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
In recent years, there has been a notable rise in the incidence of breast cancer among young patients, who exhibit worse survival outcomes and distinct characteristics compared to intermediate and elderly patients. Therefore, it is imperative to identify the specific features unique to young patients, which could offer insights into potential therapeutic strategies and improving survival outcomes. In our study, we performed an integrative analysis of bulk transcriptional and genomic data from extensive clinical cohorts to identify the prognostic factotrs. Additionally, we analyzed the single-cell transcriptional data and conducted in vitro experiments. Our work confirmed that young patients exhibited higher grading, worse disease-free survival (DFS), a higher frequency of mutations in TP53 and BRCA1, a lower frequency of mutations in PIK3CA, and upregulation of eight metabolic pathways. Notably, the galactose metabolism pathway showed upregulation in young patients and was associated with worse DFS. Further analysis and experiments indicated that the galactose metabolism pathway may regulate the stemness of cancer cells and ultimately contribute to worse survival outcomes. In summary, our finding identified distinct clinicopathological, transcriptional, and genomics features and revealed a correlation between the galactose metabolism pathway, stemness, and poor disease-free survival of breast cancer in young patients.
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Affiliation(s)
- Xiangchen Han
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (X.H.); (B.H.)
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai 200032, China;
| | - Boyue Han
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (X.H.); (B.H.)
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai 200032, China;
| | - Hong Luo
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai 200032, China;
| | - Hong Ling
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (X.H.); (B.H.)
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xin Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai 200032, China;
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29
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Averina OV, Kovtun AS, Mavletova DA, Ziganshin RH, Danilenko VN, Mihaylova D, Blazheva D, Slavchev A, Brazkova M, Ibrahim SA, Krastanov A. Oxidative Stress Response of Probiotic Strain Bifidobacterium longum subsp. longum GT15. Foods 2023; 12:3356. [PMID: 37761064 PMCID: PMC10530004 DOI: 10.3390/foods12183356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Bifidobacterium is a predominant and important genus in the bacterial population of the human gut microbiota. Despite the increasing number of studies on the beneficial functionality of bifidobacteria for human health, knowledge about their antioxidant potential is still insufficient. Several in vivo and in vitro studies of Bifidobacterium strains and their cellular components have shown good antioxidant capacity that provided a certain protection of their own and the host's cells. Our work presents the data of transcriptomic, proteomic, and metabolomic analyses of the growing and stationary culture of the probiotic strain B. longum subsp. longum GT15 after exposure to hydrogen peroxide for 2 h and oxygen for 2 and 4 h. The results of the analysis of the sequenced genome of B. longum GT15 showed the presence of 16 gene-encoding proteins with known antioxidant functions. The results of the full transcriptomic analysis demonstrated a more than two-fold increase of levels of transcripts for eleven genes, encoding proteins with antioxidant functions. Proteomic data analysis showed an increased level of more than two times for glutaredoxin and thioredoxin after the exposure to oxygen, which indicates that the thioredoxin-dependent antioxidant system may be the major redox homeostasis system in B. longum bacteria. We also found that the levels of proteins presumably involved in global stress, amino acid metabolism, nucleotide and carbohydrate metabolism, and transport had significantly increased in response to oxidative stress. The metabolic fingerprint analysis also showed good discrimination between cells responding to oxidative stress and the untreated controls. Our results provide a greater understanding of the mechanism of oxidative stress response in B. longum and the factors that contribute to its survival in functional food products.
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Affiliation(s)
- Olga V. Averina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Aleksey S. Kovtun
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Dilara A. Mavletova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia;
| | - Valery N. Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.K.); (D.A.M.); (V.N.D.)
| | - Dasha Mihaylova
- Department of Biotechnology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.M.); (A.K.)
| | - Denica Blazheva
- Department of Microbiology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.B.); (A.S.)
| | - Aleksandar Slavchev
- Department of Microbiology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.B.); (A.S.)
| | - Mariya Brazkova
- Department of Biotechnology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.M.); (A.K.)
| | - Salam A. Ibrahim
- Food Microbiology and Biotechnology Laboratory, Food and Nutritional Science Program, North Carolina A&T State University, Greensboro, NC 27411-1064, USA;
| | - Albert Krastanov
- Department of Biotechnology, University of Food Technologies, 4002 Plovdiv, Bulgaria; (D.M.); (A.K.)
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Erratum: IRIDA-ARIES Genomics, a key player in the One Health surveillance of diseases caused by infectious agents in Italy. Front Public Health 2023; 11:1276201. [PMID: 37736081 PMCID: PMC10509462 DOI: 10.3389/fpubh.2023.1276201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 09/23/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fpubh.2023.1151568.].
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31
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Bonilla CE, Montenegro P, O’Connor JM, Hernando-Requejo O, Aranda E, Pinto Llerena J, Llontop A, Gallardo Escobar J, Díaz Romero MDC, Bautista Hernández Y, Graña Suárez B, Batagelj EJ, Wali Mushtaq A, García-Foncillas J. Ibero-American Consensus Review and Incorporation of New Biomarkers for Clinical Practice in Colorectal Cancer. Cancers (Basel) 2023; 15:4373. [PMID: 37686649 PMCID: PMC10487247 DOI: 10.3390/cancers15174373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Advances in genomic technologies have significantly improved the management of colorectal cancer (CRC). Several biomarkers have been identified in CRC that enable personalization in the use of biologic agents that have shown to enhance the clinical outcomes of patients. However, technologies used for their determination generate massive amounts of information that can be difficult for the clinician to interpret and use adequately. Through several discussion meetings, a group of oncology experts from Spain and several Latin American countries reviewed the latest literature to provide practical recommendations on the determination of biomarkers in CRC based on their clinical experience. The article also describes the importance of looking for additional prognostic biomarkers and the use of histopathology to establish an adequate molecular classification. Present and future of immunotherapy biomarkers in CRC patients are also discussed, together with several techniques for marker determination, including liquid biopsy, next-generation sequencing (NGS), polymerase chain reaction (PCR), and fecal immunohistochemical tests. Finally, the role of Molecular Tumor Boards in the diagnosis and treatment of CRC is described. All of this information will allow us to highlight the importance of biomarker determination in CRC.
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Affiliation(s)
- Carlos Eduardo Bonilla
- Fundación CTIC—Centro de Tratamiento e Investigación sobre Cáncer, Bogotá 1681442, Colombia
| | - Paola Montenegro
- Institución AUNA OncoSalud e Instituto Nacional de Enfermedades Neoplásicas, Lima 15023, Peru
| | | | | | - Enrique Aranda
- Departamento de Oncología Médica, Hospital Reina Sofía, IMIBIC, UCO, CIBERONC, 14004 Cordoba, Spain;
| | | | - Alejandra Llontop
- Instituto de Oncología Ángel H. Roffo, Ciudad Autónoma de Buenos Aires C1437FBG, Argentina
| | | | | | | | - Begoña Graña Suárez
- Servicio de Oncología Médica, Hospital Universitario de A Coruña, Servicio Galego de Saúde (SERGAS), 15006 A Coruña, Spain;
| | | | | | - Jesús García-Foncillas
- Hospital Universitario Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain
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Logotheti S, Papadaki E, Zolota V, Logothetis C, Vrahatis AG, Soundararajan R, Tzelepi V. Lineage Plasticity and Stemness Phenotypes in Prostate Cancer: Harnessing the Power of Integrated "Omics" Approaches to Explore Measurable Metrics. Cancers (Basel) 2023; 15:4357. [PMID: 37686633 PMCID: PMC10486655 DOI: 10.3390/cancers15174357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Prostate cancer (PCa), the most frequent and second most lethal cancer type in men in developed countries, is a highly heterogeneous disease. PCa heterogeneity, therapy resistance, stemness, and lethal progression have been attributed to lineage plasticity, which refers to the ability of neoplastic cells to undergo phenotypic changes under microenvironmental pressures by switching between developmental cell states. What remains to be elucidated is how to identify measurements of lineage plasticity, how to implement them to inform preclinical and clinical research, and, further, how to classify patients and inform therapeutic strategies in the clinic. Recent research has highlighted the crucial role of next-generation sequencing technologies in identifying potential biomarkers associated with lineage plasticity. Here, we review the genomic, transcriptomic, and epigenetic events that have been described in PCa and highlight those with significance for lineage plasticity. We further focus on their relevance in PCa research and their benefits in PCa patient classification. Finally, we explore ways in which bioinformatic analyses can be used to determine lineage plasticity based on large omics analyses and algorithms that can shed light on upstream and downstream events. Most importantly, an integrated multiomics approach may soon allow for the identification of a lineage plasticity signature, which would revolutionize the molecular classification of PCa patients.
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Affiliation(s)
- Souzana Logotheti
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
| | - Eugenia Papadaki
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
- Department of Informatics, Ionian University, 49100 Corfu, Greece;
| | - Vasiliki Zolota
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | | | - Rama Soundararajan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vasiliki Tzelepi
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
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Dean LL, Magalhaes IS, D’Agostino D, Hohenlohe P, MacColl ADC. On the Origins of Phenotypic Parallelism in Benthic and Limnetic Stickleback. Mol Biol Evol 2023; 40:msad191. [PMID: 37652053 PMCID: PMC10490448 DOI: 10.1093/molbev/msad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Rapid evolution of similar phenotypes in similar environments, giving rise to in situ parallel adaptation, is an important hallmark of ecological speciation. However, what appears to be in situ adaptation can also arise by dispersal of divergent lineages from elsewhere. We test whether two contrasting phenotypes repeatedly evolved in parallel, or have a single origin, in an archetypal example of ecological adaptive radiation: benthic-limnetic three-spined stickleback (Gasterosteus aculeatus) across species pair and solitary lakes in British Columbia. We identify two genomic clusters across freshwater populations, which differ in benthic-limnetic divergent phenotypic traits and separate benthic from limnetic individuals in species pair lakes. Phylogenetic reconstruction and niche evolution modeling both suggest a single evolutionary origin for each of these clusters. We detected strong phylogenetic signal in benthic-limnetic divergent traits, suggesting that they are ancestrally retained. Accounting for ancestral state retention, we identify local adaptation of body armor due to the presence of an intraguild predator, the sculpin (Cottus asper), and environmental effects of lake depth and pH on body size. Taken together, our results imply a predominant role for retention of ancestral characteristics in driving trait distribution, with further selection imposed on some traits by environmental factors.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Isabel Santos Magalhaes
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- Department of Life Sciences, School of Health and Life Sciences, Whitelands College, University of Roehampton, London, UK
| | - Daniele D’Agostino
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- Water Research Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Paul Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Andrew D C MacColl
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
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Salloum-Asfar S. Editorial: Molecular advances and applications of machine learning in understanding autism and comorbid psychiatric disorders. Front Mol Neurosci 2023; 16:1277814. [PMID: 37720553 PMCID: PMC10501772 DOI: 10.3389/fnmol.2023.1277814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/19/2023] Open
Affiliation(s)
- Salam Salloum-Asfar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
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Bagal UR, Gade L, Benedict K, Howell V, Christophe N, Gibbons-Burgener S, Hallyburton S, Ireland M, McCracken S, Metobo AK, Signs K, Warren KA, Litvintseva AP, Chow NA. A Phylogeographic Description of Histoplasma capsulatum in the United States. J Fungi (Basel) 2023; 9:884. [PMID: 37754992 PMCID: PMC10532573 DOI: 10.3390/jof9090884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
Histoplasmosis is one of the most under-diagnosed and under-reported endemic mycoses in the United States. Histoplasma capsulatum is the causative agent of this disease. To date, molecular epidemiologic studies detailing the phylogeographic structure of H. capsulatum in the United States have been limited. We conducted genomic sequencing using isolates from histoplasmosis cases reported in the United States. We identified North American Clade 2 (NAm2) as the most prevalent clade in the country. Despite high intra-clade diversity, isolates from Minnesota and Michigan cases were predominately clustered by state. Future work incorporating environmental sampling and veterinary surveillance may further elucidate the molecular epidemiology of H. capsulatum in the United States and how genomic sequencing can be applied to the surveillance and outbreak investigation of histoplasmosis.
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Affiliation(s)
- Ujwal R. Bagal
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
- ASRT Inc., Atlanta, GA 30080, USA
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kaitlin Benedict
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Victoria Howell
- Kentucky Department for Public Health, Frankfort, KY 40601, USA
| | | | | | | | - Malia Ireland
- Minnesota Department of Health, St. Paul, MN 55101, USA
| | | | | | - Kimberly Signs
- Michigan Department of Health and Human Services, Lansing, MI 48933, USA
| | | | | | - Nancy A. Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Austin BK, Firooz A, Valafar H, Blenda AV. An Updated Overview of Existing Cancer Databases and Identified Needs. Biology (Basel) 2023; 12:1152. [PMID: 37627037 PMCID: PMC10452211 DOI: 10.3390/biology12081152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Our search of existing cancer databases aimed to assess the current landscape and identify key needs. We analyzed 71 databases, focusing on genomics, proteomics, lipidomics, and glycomics. We found a lack of cancer-related lipidomic and glycomic databases, indicating a need for further development in these areas. Proteomic databases dedicated to cancer research were also limited. To assess overall progress, we included human non-cancer databases in proteomics, lipidomics, and glycomics for comparison. This provided insights into advancements in these fields over the past eight years. We also analyzed other types of cancer databases, such as clinical trial databases and web servers. Evaluating user-friendliness, we used the FAIRness principle to assess findability, accessibility, interoperability, and reusability. This ensured databases were easily accessible and usable. Our search summary highlights significant growth in cancer databases while identifying gaps and needs. These insights are valuable for researchers, clinicians, and database developers, guiding efforts to enhance accessibility, integration, and usability. Addressing these needs will support advancements in cancer research and benefit the wider cancer community.
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Affiliation(s)
- Brittany K. Austin
- Department of Biomedical Sciences, School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA;
| | - Ali Firooz
- Department of Computer Science and Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA;
| | - Homayoun Valafar
- Department of Computer Science and Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA;
| | - Anna V. Blenda
- Department of Biomedical Sciences, School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA;
- Prisma Health Cancer Institute, Prisma Health, Greenville, SC 29605, USA
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Yin C, Wang Y, Zhou P, Shi H, Ma X, Yin Z, Liu Y. Genomic Scan for Runs of Homozygosity and Selective Signature Analysis to Identify Candidate Genes in Large White Pigs. Int J Mol Sci 2023; 24:12914. [PMID: 37629094 PMCID: PMC10454931 DOI: 10.3390/ijms241612914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Large White pigs are extensively utilized in China for their remarkable characteristics of rapid growth and the high proportion of lean meat. The economic traits of pigs, comprising reproductive and meat quality traits, play a vital role in swine production. In this study, 2295 individuals, representing three different genetic backgrounds Large White pig populations were used: 500 from the Canadian line, 295 from the Danish line, and 1500 from the American line. The GeneSeek 50K GGP porcine HD array was employed to genotype the three pig populations. Firstly, genomic selective signature regions were identified using the pairwise fixation index (FST) and locus-specific branch length (LSBL). By applying a top 1% threshold for both parameters, a total of 888 candidate selective windows were identified, harbouring 1571 genes. Secondly, the investigation of regions of homozygosity (ROH) was performed utilizing the PLINK software. In total, 25 genomic regions exhibiting a high frequency of ROHs were detected, leading to the identification of 1216 genes. Finally, the identified potential functional genes from candidate genomic regions were annotated, and several important candidate genes associated with reproductive traits (ADCYAP1, U2, U6, CETN1, Thoc1, Usp14, GREB1L, FGF12) and meat quality traits (MiR-133, PLEKHO1, LPIN2, SHANK2, FLVCR1, MYL4, SFRP1, miR-486, MYH3, STYX) were identified. The findings of this study provide valuable insights into the genetic basis of economic traits in Large White pigs and may have potential use in future pig breeding programs.
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Affiliation(s)
- Chang Yin
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Yuwei Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Peng Zhou
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Haoran Shi
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Xinyu Ma
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Yang Liu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
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Wang Y, Sarfraz I, Pervaiz N, Hong R, Koga Y, Akavoor V, Cao X, Alabdullatif S, Zaib SA, Wang Z, Jansen F, Yajima M, Johnson WE, Campbell JD. Interactive analysis of single-cell data using flexible workflows with SCTK2. Patterns (N Y) 2023; 4:100814. [PMID: 37602214 PMCID: PMC10436054 DOI: 10.1016/j.patter.2023.100814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/27/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Analysis of single-cell RNA sequencing (scRNA-seq) data can reveal novel insights into the heterogeneity of complex biological systems. Many tools and workflows have been developed to perform different types of analyses. However, these tools are spread across different packages or programming environments, rely on different underlying data structures, and can only be utilized by people with knowledge of programming languages. In the Single-Cell Toolkit 2 (SCTK2), we have integrated a variety of popular tools and workflows to perform various aspects of scRNA-seq analysis. All tools and workflows can be run in the R console or using an intuitive graphical user interface built with R/Shiny. HTML reports generated with Rmarkdown can be used to document and recapitulate individual steps or entire analysis workflows. We show that the toolkit offers more features when compared with existing tools and allows for a seamless analysis of scRNA-seq data for non-computational users.
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Affiliation(s)
- Yichen Wang
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Irzam Sarfraz
- Bioinformatics Program, Boston University, Boston, MA, USA
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Nida Pervaiz
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Rui Hong
- Bioinformatics Program, Boston University, Boston, MA, USA
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Yusuke Koga
- Bioinformatics Program, Boston University, Boston, MA, USA
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Vidya Akavoor
- Software & Application Innovation Lab, Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston, MA, USA
| | - Xinyun Cao
- Software & Application Innovation Lab, Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston, MA, USA
| | - Salam Alabdullatif
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Syed Ali Zaib
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Zhe Wang
- Bioinformatics Program, Boston University, Boston, MA, USA
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Frederick Jansen
- Software & Application Innovation Lab, Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston, MA, USA
| | - Masanao Yajima
- Department of Mathematics and Statistics, Boston University, Boston, MA, USA
| | - W. Evan Johnson
- Bioinformatics Program, Boston University, Boston, MA, USA
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Joshua D. Campbell
- Bioinformatics Program, Boston University, Boston, MA, USA
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
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Krauze AV, Sierk M, Nguyen T, Chen Q, Yan C, Hu Y, Jiang W, Tasci E, Zgela TC, Sproull M, Mackey M, Shankavaram U, Meerzaman D, Camphausen K. Glioblastoma survival is associated with distinct proteomic alteration signatures post chemoirradiation in a large-scale proteomic panel. Front Oncol 2023; 13:1127645. [PMID: 37637066 PMCID: PMC10448824 DOI: 10.3389/fonc.2023.1127645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/20/2023] [Indexed: 08/29/2023] Open
Abstract
Background Glioblastomas (GBM) are rapidly progressive, nearly uniformly fatal brain tumors. Proteomic analysis represents an opportunity for noninvasive GBM classification and biological understanding of treatment response. Purpose We analyzed differential proteomic expression pre vs. post completion of concurrent chemoirradiation (CRT) in patient serum samples to explore proteomic alterations and classify GBM by integrating clinical and proteomic parameters. Materials and methods 82 patients with GBM were clinically annotated and serum samples obtained pre- and post-CRT. Serum samples were then screened using the aptamer-based SOMAScan® proteomic assay. Significant traits from uni- and multivariate Cox models for overall survival (OS) were designated independent prognostic factors and principal component analysis (PCA) was carried out. Differential expression of protein signals was calculated using paired t-tests, with KOBAS used to identify associated KEGG pathways. GSEA pre-ranked analysis was employed on the overall list of differentially expressed proteins (DEPs) against the MSigDB Hallmark, GO Biological Process, and Reactome databases with weighted gene correlation network analysis (WGCNA) and Enrichr used to validate pathway hits internally. Results 3 clinical clusters of patients with differential survival were identified. 389 significantly DEPs pre vs. post-treatment were identified, including 284 upregulated and 105 downregulated, representing several pathways relevant to cancer metabolism and progression. The lowest survival group (median OS 13.2 months) was associated with DEPs affiliated with proliferative pathways and exhibiting distinct oppositional response including with respect to radiation therapy related pathways, as compared to better-performing groups (intermediate, median OS 22.4 months; highest, median OS 28.7 months). Opposite signaling patterns across multiple analyses in several pathways (notably fatty acid metabolism, NOTCH, TNFα via NF-κB, Myc target V1 signaling, UV response, unfolded protein response, peroxisome, and interferon response) were distinct between clinical survival groups and supported by WGCNA. 23 proteins were statistically signficant for OS with 5 (NETO2, CST7, SEMA6D, CBLN4, NPS) supported by KM. Conclusion Distinct proteomic alterations with hallmarks of cancer, including progression, resistance, stemness, and invasion, were identified in serum samples obtained from GBM patients pre vs. post CRT and corresponded with clinical survival. The proteome can potentially be employed for glioma classification and biological interrogation of cancer pathways.
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Affiliation(s)
- Andra Valentina Krauze
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Michael Sierk
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - Trinh Nguyen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - Qingrong Chen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - Chunhua Yan
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - Ying Hu
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - William Jiang
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Erdal Tasci
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Theresa Cooley Zgela
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Mary Sproull
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Megan Mackey
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Uma Shankavaram
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - Kevin Camphausen
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
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Zhang L, Wang Y, Kong D, Ma Q, Li Y, Xing Z, Ruan Z. Chryseobacterium herbae Isolated from the Rhizospheric Soil of Pyrola calliantha H. Andres in Segrila Mountain on the Tibetan Plateau. Microorganisms 2023; 11:2017. [PMID: 37630577 PMCID: PMC10459008 DOI: 10.3390/microorganisms11082017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/22/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
A non-motile, Gram-staining-negative, orange-pigmented bacterium called herbae pc1-10T was discovered in Tibet in the soil around Pyrola calliantha H. Andres' roots. The isolate thrived in the temperature range of 10-30 °C (optimal, 25 °C), pH range of 5.0-9.0 (optimum, pH = 6.0), and the NaCl concentration range of 0-1.8% (optimal, 0%). The DNA G+C content of the novel strain was 37.94 mol%. It showed the function of dissolving organophosphorus, acquiring iron from the environment by siderophore and producing indole acetic acid. Moreover, the genome of strain herbae pc1-10T harbors two antibiotic resistance genes (IND-4 and AdeF) encoding a β-lactamase, and the membrane fusion protein of the multidrug efflux complex AdeFGH; antibiotic-resistance-related proteins were detected using the Shotgun proteomics technology. The OrthoANIu values between strains Chryseobacterium herbae pc1-10T; Chryseobacterium oleae CT348T; Chryseobacterium kwangjuense KJ1R5T; and Chryseobacterium vrystaatense R-23566T were 90.94%, 82.96%, and 85.19%, respectively. The in silico DDH values between strains herbae pc1-10T; C. oleae CT348T; C. kwangjuense KJ1R5T; and C. vrystaatense R-23566T were 41.7%, 26.6%, and 29.7%, respectively. Chryseobacterium oleae, Chryseobacterium vrystaatense, and Chryseobacterium kwangjuense, which had 16S rRNA gene sequence similarity scores of 97.80%, 97.52%, and 96.75%, respectively, were its closest phylogenetic relatives. Chryseobacterium herbae sp. nov. is proposed as the designation for the strain herbae pc1-10T (=GDMCC 1.3255 = JCM 35711), which represented a type species based on genotypic and morphological characteristics. This study provides deep knowledge of a Chryseobacterium herbae characteristic description and urges the need for further genomic studies on microorganisms living in alpine ecosystems, especially around medicinal plants.
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Affiliation(s)
- Li Zhang
- College of Life Sciences, Yantai University, Yantai 264005, China;
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (D.K.); (Q.M.)
| | - Yan Wang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (D.K.); (Q.M.)
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China;
| | - Delong Kong
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (D.K.); (Q.M.)
| | - Qingyun Ma
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (D.K.); (Q.M.)
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Li
- College of Life Sciences, Yantai University, Yantai 264005, China;
| | - Zhen Xing
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China;
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (D.K.); (Q.M.)
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Berrios C, Neal S, Zion T, Pastinen T. Comparing Attitudes About Genomic Privacy and Data Sharing in Adolescents and Parents of Children Enrolled in a Genomic Research Repository. AJOB Empir Bioeth 2023; 15:33-40. [PMID: 37487180 PMCID: PMC10805964 DOI: 10.1080/23294515.2023.2232780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
BACKGROUND Sharing of genomic data aims to make efficient use of limited resources, which may be particularly valuable in rare disease research. Adult research participants and parents of pediatric research participants have shown support for data sharing with protections, but little is known about adolescent attitudes on genomic privacy and data sharing. METHODS In-depth interviews were conducted with 10 adolescents and 18 parents of children enrolled in a pediatric genomic research repository. Interview transcripts were analyzed for themes on attitudes toward genomic privacy, restricted-access data sharing, and open-access data sharing. Findings in adolescent and parent participants were compared and contrasted. RESULTS No adolescents endorsed privacy concerns for restricted-access data sharing. Both adolescents and parents saw value in data sharing for reaching the goals of research and discussed trust in institutions and researchers to protect their data and use it as intended. Adolescents were more likely than parents to accept open-access data sharing, including after risks were discussed. CONCLUSIONS In this exploratory study, adolescents and parents enrolled in a genomic research repository shared many attitudes about genomic data sharing, but adolescents were less concerned about privacy and more agreeable toward open-access data sharing. Future research is needed to investigate this hypothesis in expanded populations and settings, and to clarify whether adolescent attitudes change with age and experiences.
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Affiliation(s)
- Courtney Berrios
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO 64108
- School of Medicine, University of Missouri Kansas City, Kansas City, MO 64110
| | - Shelby Neal
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO 64108
- School of Medicine, University of Missouri Kansas City, Kansas City, MO 64110
| | - Tricia Zion
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO 64108
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO 64108
- School of Medicine, University of Missouri Kansas City, Kansas City, MO 64110
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Khetran SR, Mustafa R. Mutations of SARS-CoV-2 Structural Proteins in the Alpha, Beta, Gamma, and Delta Variants: Bioinformatics Analysis. JMIR Bioinform Biotech 2023; 4:e43906. [PMID: 37485046 PMCID: PMC10353769 DOI: 10.2196/43906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/02/2023] [Accepted: 06/08/2023] [Indexed: 07/25/2023]
Abstract
Background COVID-19 and Middle East Respiratory Syndrome are two pandemic respiratory diseases caused by coronavirus species. The novel disease COVID-19 caused by SARS-CoV-2 was first reported in Wuhan, Hubei Province, China, in December 2019, and became a pandemic within 2-3 months, affecting social and economic platforms worldwide. Despite the rapid development of vaccines, there have been obstacles to their distribution, including a lack of fundamental resources, poor immunization, and manual vaccine replication. Several variants of the original Wuhan strain have emerged in the last 3 years, which can pose a further challenge for control and vaccine development. Objective The aim of this study was to comprehensively analyze mutations in SARS-CoV-2 variants of concern (VoCs) using a bioinformatics approach toward identifying novel mutations that may be helpful in developing new vaccines by targeting these sites. Methods Reference sequences of the SARS-CoV-2 spike (YP_009724390) and nucleocapsid (YP_009724397) proteins were compared to retrieved sequences of isolates of four VoCs from 14 countries for mutational and evolutionary analyses. Multiple sequence alignment was performed and phylogenetic trees were constructed by the neighbor-joining method with 1000 bootstrap replicates using MEGA (version 6). Mutations in amino acid sequences were analyzed using the MultAlin online tool (version 5.4.1). Results Among the four VoCs, a total of 143 nonsynonymous mutations and 8 deletions were identified in the spike and nucleocapsid proteins. Multiple sequence alignment and amino acid substitution analysis revealed new mutations, including G72W, M2101I, L139F, 209-211 deletion, G212S, P199L, P67S, I292T, and substitutions with unknown amino acid replacement, reported in Egypt (MW533289), the United Kingdom (MT906649), and other regions. The variants B.1.1.7 (Alpha variant) and B.1.617.2 (Delta variant), characterized by higher transmissibility and lethality, harbored the amino acid substitutions D614G, R203K, and G204R with higher prevalence rates in most sequences. Phylogenetic analysis among the novel SARS-CoV-2 variant proteins and some previously reported β-coronavirus proteins indicated that either the evolutionary clade was weakly supported or not supported at all by the β-coronavirus species. Conclusions This study could contribute toward gaining a better understanding of the basic nature of SARS-CoV-2 and its four major variants. The numerous novel mutations detected could also provide a better understanding of VoCs and help in identifying suitable mutations for vaccine targets. Moreover, these data offer evidence for new types of mutations in VoCs, which will provide insight into the epidemiology of SARS-CoV-2.
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Affiliation(s)
- Saima Rehman Khetran
- Department of Life Sciences Sardar Bahadur Khan Women's University Quetta Pakistan
| | - Roma Mustafa
- Department of Life Sciences Sardar Bahadur Khan Women's University Quetta Pakistan
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Zhong JX, Zheng HR, Wang YY, Bai LL, Du XL, Wu Y, Lu JX. Molecular characteristics and phylogenetic analysis of Clostridium perfringens from different regions in China, from 2013 to 2021. Front Microbiol 2023; 14:1195083. [PMID: 37485514 PMCID: PMC10359303 DOI: 10.3389/fmicb.2023.1195083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/19/2023] [Indexed: 07/25/2023] Open
Abstract
Clostridium perfringens (C. perfringens) is a significant foodborne pathogen and a common cause of intestinal diseases in both animals and humans. Our study investigated MLST, phenotypic antimicrobial resistance profiles, and resistance genes among isolates from human, animal and food. 186 C. perfringens isolates were obtained from nine provinces in China between 2013 and 2021. Additionally, some specific ST complexes were analyzed by cgMLST and cgSNP to investigate genetic relatedness. MLST indicated the most prevalent STs of C. perfringens of human and animal origin were as follows: ST221 (5/147), ST62 (4/147), ST408 (4/147), and ST493 (4/147) were predominant in humans, while ST479 (5/25) was the major type in animals. Within the same ST complex, genetically unrelated relationships or potential clustering/transmission events were further recognized by cgMLST and cgSNP, illustrating that these two methods are valuable in defining outbreaks and transmission events. All tested isolates were susceptible to vancomycin and meropenem. The rates of resistance to metronidazole, penicillin, cefoxitin, moxifloxacin, and chloramphenicol were low (metronidazole: 1.08%; penicillin: 9.68%; cefoxitin: 0.54%; moxifloxacin: 6.45%; and chloramphenicol: 3.76%). Interestingly, 49.66% of human origin were clindamycin-resistant, and 18.2% were penicillin-insensitive. Importantly, the portion of MDR isolates was significantly lower than in previous reports. The study provides an overview of the epidemiological characteristics of C. perfringens with different origins and hosts in China. C. perfringens demonstrated remarkable genetic diversity and distinct molecular features compared to antibiotic-resistance profiles from other studies.
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Affiliation(s)
- Jia xin Zhong
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Hao ran Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Yuan yuan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Lu lu Bai
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xiao li Du
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jin xing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Tsiftsoglou SA. Heme Interactions as Regulators of the Alternative Pathway Complement Responses and Implications for Heme-Associated Pathologies. Curr Issues Mol Biol 2023; 45:5198-5214. [PMID: 37367079 DOI: 10.3390/cimb45060330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Heme (Fe2+-protoporphyrin IX) is a pigment of life, and as a prosthetic group in several hemoproteins, it contributes to diverse critical cellular processes. While its intracellular levels are tightly regulated by networks of heme-binding proteins (HeBPs), labile heme can be hazardous through oxidative processes. In blood plasma, heme is scavenged by hemopexin (HPX), albumin and several other proteins, while it also interacts directly with complement components C1q, C3 and factor I. These direct interactions block the classical pathway (CP) and distort the alternative pathway (AP). Errors or flaws in heme metabolism, causing uncontrolled intracellular oxidative stress, can lead to several severe hematological disorders. Direct interactions of extracellular heme with alternative pathway complement components (APCCs) may be implicated molecularly in diverse conditions at sites of abnormal cell damage and vascular injury. In such disorders, a deregulated AP could be associated with the heme-mediated disruption of the physiological heparan sulphate-CFH coat of stressed cells and the induction of local hemostatic responses. Within this conceptual frame, a computational evaluation of HBMs (heme-binding motifs) aimed to determine how heme interacts with APCCs and whether these interactions are affected by genetic variation within putative HBMs. Combined computational analysis and database mining identified putative HBMs in all of the 16 APCCs examined, with 10 exhibiting disease-associated genetic (SNPs) and/or epigenetic variation (PTMs). Overall, this article indicates that among the pleiotropic roles of heme reviewed, the interactions of heme with APCCs could induce differential AP-mediated hemostasis-driven pathologies in certain individuals.
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Affiliation(s)
- Stefanos A Tsiftsoglou
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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45
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Wiggenhorn AL, Abuzaid HZ, Coassolo L, Li VL, Tanzo JT, Wei W, Lyu X, Svensson KJ, Long JZ. A class of secreted mammalian peptides with potential to expand cell-cell communication. bioRxiv 2023:2023.06.02.543503. [PMID: 37333131 PMCID: PMC10274650 DOI: 10.1101/2023.06.02.543503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Peptide hormones and neuropeptides are fundamental signaling molecules that control diverse aspects of mammalian homeostasis and physiology. Here we demonstrate the endogenous presence of a sequence diverse class of orphan, blood-borne peptides that we call "capped peptides." Capped peptides are fragments of secreted proteins and defined by the presence of two post-translational modifications - N-terminal pyroglutamylation and C-terminal amidation - which function as chemical "caps" of the intervening sequence. Capped peptides share many regulatory characteristics in common with that of other signaling peptides, including dynamic regulation in blood plasma by diverse environmental and physiologic stimuli. One capped peptide, CAP-TAC1, is a tachykinin neuropeptide-like molecule and a nanomolar agonist of multiple mammalian tachykinin receptors. A second capped peptide, CAP-GDF15, is a 12-mer peptide that reduces food intake and body weight. Capped peptides therefore define a largely unexplored class of circulating molecules with potential to regulate cell-cell communication in mammalian physiology.
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Affiliation(s)
- Amanda L. Wiggenhorn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Hind Z. Abuzaid
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Laetitia Coassolo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Veronica L. Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Julia T. Tanzo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Xuchao Lyu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Katrin J. Svensson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Jonathan Z. Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
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Zhuang W, Varshney RK. Editorial: Peanut genomics and biotechnology in breeding applications. Front Plant Sci 2023; 14:1226637. [PMID: 37351209 PMCID: PMC10282998 DOI: 10.3389/fpls.2023.1226637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/24/2023]
Affiliation(s)
- Weijian Zhuang
- Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Rajeev K. Varshney
- Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- WA State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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Smith AM, Erasmus LK, Tau NP, Smouse SL, Ngomane HM, Disenyeng B, Whitelaw A, Lawrence CA, Sekwadi P, Thomas J. Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi. Microb Genom 2023; 9. [PMID: 37339282 DOI: 10.1099/mgen.0.001044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
The National Institute for Communicable Diseases in South Africa participates in national laboratory-based surveillance for human isolates of Salmonella species. Laboratory analysis includes whole-genome sequencing (WGS) of isolates. We report on WGS-based surveillance of Salmonella enterica serovar Typhi (Salmonella Typhi) in South Africa from 2020 through 2021. We describe how WGS analysis identified clusters of enteric fever in the Western Cape Province of South Africa and describe the epidemiological investigations associated with these clusters. A total of 206 Salmonella Typhi isolates were received for analysis. Genomic DNA was isolated from bacteria and WGS was performed using Illumina NextSeq technology. WGS data were investigated using multiple bioinformatics tools, including those available at the Centre for Genomic Epidemiology, EnteroBase and Pathogenwatch. Core-genome multilocus sequence typing was used to investigate the phylogeny of isolates and identify clusters. Three major clusters of enteric fever were identified in the Western Cape Province; cluster one (n=11 isolates), cluster two (n=13 isolates), and cluster three (n=14 isolates). To date, no likely source has been identified for any of the clusters. All isolates associated with the clusters, showed the same genotype (4.3.1.1.EA1) and resistome (antimicrobial resistance genes: bla TEM-1B, catA1, sul1, sul2, dfrA7). The implementation of genomic surveillance of Salmonella Typhi in South Africa has enabled rapid detection of clusters indicative of possible outbreaks. Cluster identification allows for targeted epidemiological investigations and a timely, coordinated public health response.
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Affiliation(s)
- Anthony Marius Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Linda Kathleen Erasmus
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nomsa Pauline Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shannon Lucrecia Smouse
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Hlengiwe Mimmy Ngomane
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Bolele Disenyeng
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Andrew Whitelaw
- Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Charlene Ann Lawrence
- Communicable Disease Control, Service Priorities Coordination, Department of Health, Cape Town, South Africa
| | - Phuti Sekwadi
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
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Deb SK, Edger PP, Pires JC, McKain MR. Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective. New Phytol 2023; 238:2284-2304. [PMID: 37010081 DOI: 10.1111/nph.18927] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes with common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic and complex. Homoeologous exchanges (HEs) may lead to the formation of unbalanced gametes, reduced fertility, and selective disadvantage. By contrast, HEs could act as sources of novel evolutionary substrates, shifting the relative dosage of parental gene copies, generating novel phenotypic diversity, and helping the establishment of neo-allopolyploids. However, HE patterns vary among lineages, across generations, and even within individual genomes and chromosomes. The causes and consequences of this variation are not fully understood, though interest in this evolutionary phenomenon has increased in the last decade. Recent technological advances show promise in uncovering the mechanistic basis of HEs. Here, we describe recent observations of the common patterns among allopolyploid angiosperm lineages, underlying genomic and epigenomic features, and consequences of HEs. We identify critical research gaps and discuss future directions with far-reaching implications in understanding allopolyploid evolution and applying them to the development of important phenotypic traits of polyploid crops.
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Affiliation(s)
- Sontosh K Deb
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
- Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48823, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
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Khalil M, Abbass MA. Neoadjuvant immunotherapy in microsatellite unstable colorectal cancer: Are we in the era of nonoperative management? J Surg Oncol 2023; 127:1296-1299. [PMID: 37222694 DOI: 10.1002/jso.27321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023]
Abstract
Microsatellite unstable (MSI-H) colorectal cancers (CRC) are the hallmark of Lynch Syndrome. Advances in immunotherapy have yielded a change in the treatment of those cancers. Recent publications about neoadjuvant immunotherapy in CRC are triggering a high interest to use under the umbrella of achieving a complete clinical response. Although we do not know the extent of this response over time, avoiding surgical morbidity seems to be on the horizon for this subset of CRC.
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Affiliation(s)
| | - Mohammad Ali Abbass
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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50
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Ma’ruf M, Fadli JC, Mahendra MR, Irham LM, Sulistyani N, Adikusuma W, Chong R, Septama AW. A bioinformatic approach to identify pathogenic variants for Stevens-Johnson syndrome. Genomics Inform 2023; 21:e26. [PMID: 37704211 PMCID: PMC10326529 DOI: 10.5808/gi.23010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/09/2023] [Accepted: 04/12/2023] [Indexed: 07/08/2023] Open
Abstract
Stevens-Johnson syndrome (SJS) produces a severe hypersensitivity reaction caused by Herpes simplex virus or mycoplasma infection, vaccination, systemic disease, or other agents. Several studies have investigated the genetic susceptibility involved in SJS. To provide further genetic insights into the pathogenesis of SJS, this study prioritized high-impact, SJS-associated pathogenic variants through integrating bioinformatic and population genetic data. First, we identified SJS-associated single nucleotide polymorphisms from the genome-wide association studies catalog, followed by genome annotation with HaploReg and variant validation with Ensembl. Subsequently, expression quantitative trait locus (eQTL) from GTEx identified human genetic variants with differential gene expression across human tissues. Our results indicate that two variants, namely rs2074494 and rs5010528, which are encoded by the HLA-C (human leukocyte antigen C) gene, were found to be differentially expressed in skin. The allele frequencies for rs2074494 and rs5010528 also appear to significantly differ across continents. We highlight the utility of these population-specific HLA-C genetic variants for genetic association studies, and aid in early prognosis and disease treatment of SJS.
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Affiliation(s)
- Muhammad Ma’ruf
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
| | | | | | - Lalu Muhammad Irham
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
- Center for Vaccine and Drugs, Research Organization for Health, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia
| | - Nanik Sulistyani
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
| | - Wirawan Adikusuma
- Departement of Pharmacy, University of Muhammadiyah Mataram, Mataram 83127, Indonesia
- Center for Vaccine and Drugs, Research Organization for Health, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia
| | - Rockie Chong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, CA, USA
| | - Abdi Wira Septama
- Departement of Pharmacy, University of Muhammadiyah Mataram, Mataram 83127, Indonesia
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