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Han FY, Wu RX, Miao BB, Niu SF, Wang QH, Liang ZB. Whole-Genome Sequencing Analyses Reveal the Whip-like Tail Formation, Innate Immune Evolution, and DNA Repair Mechanisms of Eupleurogrammus muticus. Animals (Basel) 2024; 14:434. [PMID: 38338077 PMCID: PMC10854985 DOI: 10.3390/ani14030434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Smallhead hairtail (Eupleurogrammus muticus) is an important marine economic fish distributed along the northern Indian Ocean and the northwest Pacific coast; however, little is known about the mechanism of its genetic evolution. This study generated the first genome assembly of E. muticus at the chromosomal level using a combination of PacBio SMRT, Illumina Nova-Seq, and Hi-C technologies. The final assembled genome size was 709.27 Mb, with a contig N50 of 25.07 Mb, GC content of 40.81%, heterozygosity rate of 1.18%, and repetitive sequence rate of 35.43%. E. muticus genome contained 21,949 protein-coding genes (97.92% of the genes were functionally annotated) and 24 chromosomes. There were 143 expansion gene families, 708 contraction gene families, and 4888 positively selected genes in the genome. Based on the comparative genomic analyses, we screened several candidate genes and pathways related to whip-like tail formation, innate immunity, and DNA repair in E. muticus. These findings preliminarily reveal some molecular evolutionary mechanisms of E. muticus at the genomic level and provide important reference genomic data for the genetic studies of other trichiurids.
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Affiliation(s)
- Fang-Yuan Han
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Ben-Ben Miao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China;
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Qing-Hua Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China;
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
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2
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Jadi O, Tang H, Olsen K, Vensko S, Zhu Q, Wang Y, Haiman CA, Pooler L, Sheng X, Brock G, Webb A, Pasquini MC, McCarthy PL, Spellman SR, Hahn T, Vincent B, Armistead P, Sucheston-Campbell LE. Associations of minor histocompatibility antigens with outcomes following allogeneic hematopoietic cell transplantation. Am J Hematol 2023; 98:940-950. [PMID: 37052167 PMCID: PMC10368187 DOI: 10.1002/ajh.26925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/09/2023] [Accepted: 03/23/2023] [Indexed: 04/14/2023]
Abstract
The role of minor histocompatibility antigens (mHAs) in mediating graft versus leukemia and graft versus host disease (GvHD) following allogeneic hematopoietic cell transplantation (alloHCT) is recognized but not well-characterized. By implementing improved methods for mHA prediction in two large patient cohorts, this study aimed to comprehensively explore the role of mHAs in alloHCT by analyzing whether (1) the number of predicted mHAs, or (2) individual mHAs are associated with clinical outcomes. The study population consisted of 2249 donor-recipient pairs treated for acute myeloid leukemia and myelodysplastic syndrome with alloHCT. A Cox proportional hazard model showed that patients with a class I mHA count greater than the population median had an increased hazard of GvHD mortality (hazard ratio [HR] = 1.39, 95% confidence interval [CI] = 1.01, 1.77, p = .046). Competing risk analyses identified the class I mHAs DLRCKYISL (GSTP), WEHGPTSLL (CRISPLD2), and STSPTTNVL (SERPINF2) were associated with increased GVHD mortality (HR = 2.84, 95% CI = 1.52, 5.31, p = .01), decreased leukemia-free survival (LFS) (HR = 1.94, 95% CI = 1.27, 2.95, p = .044), and increased disease-related mortality (DRM) (HR = 2.32, 95% CI = 1.5, 3.6, p = .008), respectively. One class II mHA YQEIAAIPSAGRERQ (TACC2) was associated with increased risk of treatment-related mortality (TRM) (HR = 3.05, 95% CI = 1.75, 5.31, p = .02). WEHGPTSLL and STSPTTNVL were both present within HLA haplotype B*40:01-C*03:04 and showed a positive dose-response relationship with increased all-cause mortality and DRM and decreased LFS, indicating these two mHAs contribute to the risk of mortality in an additive manner. Our study reports the first large-scale investigation of the associations of predicted mHA peptides with clinical outcomes following alloHCT.
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Affiliation(s)
- Othmane Jadi
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC
| | - Hancong Tang
- College of Pharmacy, The Ohio State University, Columbus, OH
| | - Kelly Olsen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Yiwen Wang
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Christopher A Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Loreall Pooler
- The Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA
| | - Xin Sheng
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Guy Brock
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Marcelo C. Pasquini
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Philip L McCarthy
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Stephen R. Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Theresa Hahn
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Benjamin Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC
- Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC
| | - Paul Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC
- Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC
| | - Lara E. Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, OH
- College of Veterinary Medicine, The Ohio State University, Columbus, OH
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3
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Stikker BS, Hendriks RW, Stadhouders R. Decoding the genetic and epigenetic basis of asthma. Allergy 2023; 78:940-956. [PMID: 36727912 DOI: 10.1111/all.15666] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 02/03/2023]
Abstract
Asthma is a complex and heterogeneous chronic inflammatory disease of the airways. Alongside environmental factors, asthma susceptibility is strongly influenced by genetics. Given its high prevalence and our incomplete understanding of the mechanisms underlying disease susceptibility, asthma is frequently studied in genome-wide association studies (GWAS), which have identified thousands of genetic variants associated with asthma development. Virtually all these genetic variants reside in non-coding genomic regions, which has obscured the functional impact of asthma-associated variants and their translation into disease-relevant mechanisms. Recent advances in genomics technology and epigenetics now offer methods to link genetic variants to gene regulatory elements embedded within non-coding regions, which have started to unravel the molecular mechanisms underlying the complex (epi)genetics of asthma. Here, we provide an integrated overview of (epi)genetic variants associated with asthma, focusing on efforts to link these disease associations to biological insight into asthma pathophysiology using state-of-the-art genomics methodology. Finally, we provide a perspective as to how decoding the genetic and epigenetic basis of asthma has the potential to transform clinical management of asthma and to predict the risk of asthma development.
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Affiliation(s)
- Bernard S Stikker
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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Paczesny S. Post-haematopoietic cell transplantation outcomes: why ST2 became a 'golden nugget' biomarker. Br J Haematol 2021; 192:951-967. [PMID: 32039480 PMCID: PMC7415515 DOI: 10.1111/bjh.16497] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Immunotherapies have emerged as highly promising approaches to treat cancer patients. Allogeneic haematopoietic cell transplantation (HCT) is the most validated tumour immunotherapy available to date but its clinical efficacy is limited by toxicities, such as graft-versus-host disease (GVHD) and treatment resistance leading to relapse. The problems with new cellular therapies and checkpoint inhibitors are similar. However, development of biomarkers post-HCT, particularly for toxicities, has taken off in the last decade and has expanded greatly. Thanks to the advances in genomics, transcriptomics, proteomics and cytomics technologies, blood biomarkers have been identified and validated in promising diagnostic tests, prognostic tests stratifying for future occurrence of GVHD, and predictive tests for responsiveness to GVHD therapy and non-relapse mortality. These biomarkers may facilitate timely and selective therapeutic intervention. This review outlines a path from biomarker discovery to first clinical correlation, focusing on soluble STimulation-2 (sST2) - the interleukin (IL)-33-decoy receptor - which is the most validated biomarker.
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Affiliation(s)
- Sophie Paczesny
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
- Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
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5
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Giaccone L, Faraci DG, Butera S, Lia G, Di Vito C, Gabrielli G, Cerrano M, Mariotti J, Dellacasa C, Felicetti F, Brignardello E, Mavilio D, Bruno B. Biomarkers for acute and chronic graft versus host disease: state of the art. Expert Rev Hematol 2020; 14:79-96. [PMID: 33297779 DOI: 10.1080/17474086.2021.1860001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Despite significant advances in treatment and prevention, graft-versus-host disease (GVHD) still represents the main cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Thus, considerable research efforts have been made to find and validate reliable biomarkers for diagnosis, prognosis, and risk stratification of GVHD. AREAS COVERED In this review the most recent evidences on different types of biomarkers studied for GVHD, such as genetic, plasmatic, cellular markers, and those associated with microbiome, were summarized. A comprehensive search of peer-review literature was performed in PubMed including meta-analysis, preclinical and clinical trials, using the terms: cellular and plasma biomarkers, graft-versus-host disease, cytokines, and allogeneic hematopoietic stem cell transplantation. EXPERT OPINION In the near future, several validated biomarkers will be available to help clinicians in the diagnosis of GVHD, the identification of patients at high risk of GVHD development and in patients' stratification according to its severity. Then, immunosuppressive treatment could be tailored to each patient's real needs. However, more efforts are needed to achieve this goal. Although most of the proposed biomarkers currently lack validation with large-scale clinical data, their study led to improved knowledge of the biological basis of GVHD, and ultimately to implementation of GHVD treatment.
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Affiliation(s)
- Luisa Giaccone
- Department of Oncology/Hematology, Stem Cell Transplant Program, A.O.U. Città Della Salute E Della Scienza Di Torino, Presidio Molinette , Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino , Torino, Italy
| | - Danilo Giuseppe Faraci
- Department of Oncology/Hematology, Stem Cell Transplant Program, A.O.U. Città Della Salute E Della Scienza Di Torino, Presidio Molinette , Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino , Torino, Italy
| | - Sara Butera
- Department of Oncology/Hematology, Stem Cell Transplant Program, A.O.U. Città Della Salute E Della Scienza Di Torino, Presidio Molinette , Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino , Torino, Italy
| | - Giuseppe Lia
- Department of Oncology/Hematology, Stem Cell Transplant Program, A.O.U. Città Della Salute E Della Scienza Di Torino, Presidio Molinette , Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino , Torino, Italy
| | - Clara Di Vito
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center , Milan, Italy.,Department of Medical Biotechnologies and Translational Medicine (Biometra), University of Milan , Milan, Italy
| | - Giulia Gabrielli
- Department of Oncology/Hematology, Stem Cell Transplant Program, A.O.U. Città Della Salute E Della Scienza Di Torino, Presidio Molinette , Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino , Torino, Italy
| | - Marco Cerrano
- Department of Oncology/Hematology, Stem Cell Transplant Program, A.O.U. Città Della Salute E Della Scienza Di Torino, Presidio Molinette , Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino , Torino, Italy
| | - Jacopo Mariotti
- Bone Marrow Transplant Unit, Humanitas Clinical and Research Center, IRCCS , Rozzano, Italy
| | - Chiara Dellacasa
- Department of Oncology/Hematology, Stem Cell Transplant Program, A.O.U. Città Della Salute E Della Scienza Di Torino, Presidio Molinette , Torino, Italy
| | - Francesco Felicetti
- Transition Unit for Childhood Cancer Survivors, A.O.U. Città Della Salute E Della Scienza Di Torino , University of Torino , Torino, Italy
| | - Enrico Brignardello
- Transition Unit for Childhood Cancer Survivors, A.O.U. Città Della Salute E Della Scienza Di Torino , University of Torino , Torino, Italy
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center , Milan, Italy.,Department of Medical Biotechnologies and Translational Medicine (Biometra), University of Milan , Milan, Italy
| | - Benedetto Bruno
- Department of Oncology/Hematology, Stem Cell Transplant Program, A.O.U. Città Della Salute E Della Scienza Di Torino, Presidio Molinette , Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino , Torino, Italy
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Adom D, Rowan C, Adeniyan T, Yang J, Paczesny S. Biomarkers for Allogeneic HCT Outcomes. Front Immunol 2020; 11:673. [PMID: 32373125 PMCID: PMC7186420 DOI: 10.3389/fimmu.2020.00673] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 03/25/2020] [Indexed: 12/23/2022] Open
Abstract
Allogeneic hematopoietic cell transplantation (HCT) remains the only curative therapy for many hematological malignant and non-malignant disorders. However, key obstacles to the success of HCT include graft-versus-host disease (GVHD) and disease relapse due to absence of graft-versus-tumor (GVT) effect. Over the last decade, advances in "omics" technologies and systems biology analysis, have allowed for the discovery and validation of blood biomarkers that can be used as diagnostic test and prognostic test (that risk-stratify patients before disease occurrence) for acute and chronic GVHD and recently GVT. There are also predictive biomarkers that categorize patients based on their likely to respond to therapy. Newer mathematical analysis such as machine learning is able to identify different predictors of GVHD using clinical characteristics pre-transplant and possibly in the future combined with other biomarkers. Biomarkers are not only useful to identify patients with higher risk of disease progression, but also help guide treatment decisions and/or provide a basis for specific therapeutic interventions. This review summarizes biomarkers definition, omics technologies, acute, chronic GVHD and GVT biomarkers currently used in clinic or with potential as targets for existing or new drugs focusing on novel published work.
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Affiliation(s)
- Djamilatou Adom
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States.,Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Courtney Rowan
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States.,Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Titilayo Adeniyan
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States.,Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jinfeng Yang
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States.,Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Sophie Paczesny
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States.,Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
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