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Chen JP, Diekmann C, Wu H, Chen C, Della Chiara G, Berrino E, Georgiadis KL, Bouwman BAM, Virdi M, Harbers L, Bellomo SE, Marchiò C, Bienko M, Crosetto N. Author Correction: scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells. Nat Commun 2024; 15:3390. [PMID: 38649373 PMCID: PMC11035616 DOI: 10.1038/s41467-024-47535-7] [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] [Indexed: 04/25/2024] Open
Affiliation(s)
- Jinxin Phaedo Chen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
| | - Constantin Diekmann
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Honggui Wu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, PR China
- School of Life Sciences, Peking University, Beijing, PR China
| | - Chong Chen
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | | | - Enrico Berrino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Konstantinos L Georgiadis
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Britta A M Bouwman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Mohit Virdi
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy
| | - Luuk Harbers
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Sara Erika Bellomo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
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2
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Kosugi S, Terao C. Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data. Hum Genome Var 2024; 11:18. [PMID: 38632226 PMCID: PMC11024196 DOI: 10.1038/s41439-024-00276-x] [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: 01/18/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
Short- and long-read sequencing technologies are routinely used to detect DNA variants, including SNVs, indels, and structural variations (SVs). However, the differences in the quality and quantity of variants detected between short- and long-read data are not fully understood. In this study, we comprehensively evaluated the variant calling performance of short- and long-read-based SNV, indel, and SV detection algorithms (6 for SNVs, 12 for indels, and 13 for SVs) using a novel evaluation framework incorporating manual visual inspection. The results showed that indel-insertion calls greater than 10 bp were poorly detected by short-read-based detection algorithms compared to long-read-based algorithms; however, the recall and precision of SNV and indel-deletion detection were similar between short- and long-read data. The recall of SV detection with short-read-based algorithms was significantly lower in repetitive regions, especially for small- to intermediate-sized SVs, than that detected with long-read-based algorithms. In contrast, the recall and precision of SV detection in nonrepetitive regions were similar between short- and long-read data. These findings suggest the need for refined strategies, such as incorporating multiple variant detection algorithms, to generate a more complete set of variants using short-read data.
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Affiliation(s)
- Shunichi Kosugi
- Center for Genome Informatics, Research Organization of Information and Systems, Joint Support-Center for Data Science Research, Shizuoka, Japan.
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan.
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan.
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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3
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Lim FS, González-Cabrera J, Keilwagen J, Kleespies RG, Jehle JA, Wennmann JT. Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets. Sci Rep 2024; 14:8525. [PMID: 38609404 PMCID: PMC11014933 DOI: 10.1038/s41598-024-58768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Rapid and reliable detection of pathogens is crucial to complement the growing industry of mass-reared insects, in order to safeguard the insect colonies from outbreak of diseases, which may cause significant economic loss. Current diagnostic methods are mainly based on conventional PCR and microscopic examination, requiring prior knowledge of disease symptoms and are limited to identifying known pathogens. Here, we present a rapid nanopore-based metagenomics approach for detecting entomopathogens from the European house cricket (Acheta domesticus). In this study, the Acheta domesticus densovirus (AdDV) was detected from diseased individuals using solely Nanopore sequencing. Virus reads and genome assemblies were obtained within twenty-four hours after sequencing. Subsequently, due to the length of the Nanopore reads, it was possible to reconstruct significantly large parts or even the entire AdDV genome to conduct studies for genotype identification. Variant analysis indicated the presence of three AdDV genotypes within the same house cricket population, with association to the vital status of the diseased crickets. This contrast provided compelling evidence for the existence of non-lethal AdDV genotypes. These findings demonstrated nanopore-based metagenomics sequencing as a powerful addition to the diagnostic tool kit for routine pathogen surveillance and diagnosis in the insect rearing industry.
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Affiliation(s)
- Fang Shiang Lim
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
- Department of Genetics and Institute BIOTECMED, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - Joel González-Cabrera
- Department of Genetics and Institute BIOTECMED, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - Jens Keilwagen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for the Safety of Biotechnological Processes in Plants, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Regina G Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany.
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4
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Zhou Q, Ji F, Lin D, Liu X, Zhu Z, Ruan J. KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost. Nat Commun 2024; 15:3126. [PMID: 38605047 PMCID: PMC11009271 DOI: 10.1038/s41467-024-47562-4] [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: 06/20/2022] [Accepted: 04/04/2024] [Indexed: 04/13/2024] Open
Abstract
Long reads that cover more variants per read raise opportunities for accurate haplotype construction, whereas the genotype errors of single nucleotide polymorphisms pose great computational challenges for haplotyping tools. Here we introduce KSNP, an efficient haplotype construction tool based on the de Bruijn graph (DBG). KSNP leverages the ability of DBG in handling high-throughput erroneous reads to tackle the challenges. Compared to other notable tools in this field, KSNP achieves at least 5-fold speedup while producing comparable haplotype results. The time required for assembling human haplotypes is reduced to nearly the data-in time.
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Affiliation(s)
- Qian Zhou
- PengCheng Laboratory, Shenzhen, China
| | - Fahu Ji
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Dongxiao Lin
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Xianming Liu
- PengCheng Laboratory, Shenzhen, China
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zexuan Zhu
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China.
- National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China.
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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5
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Kumar K, Barbora L, Moholkar VS. Genomic insights into clostridia in bioenergy production: Comparison of metabolic capabilities and evolutionary relationships. Biotechnol Bioeng 2024; 121:1298-1313. [PMID: 38047471 DOI: 10.1002/bit.28610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 10/19/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023]
Abstract
Bacteria from diverse genera, including Acetivibrio, Bacillus, Cellulosilyticum, Clostridium, Desulfotomaculum, Lachnoclostridium, Moorella, Ruminiclostridium, and Thermoanaerobacterium, have attracted significant attention due to their versatile metabolic capabilities encompassing acetogenic, cellulolytic, and C1-metabolic properties, and acetone-butanol-ethanol fermentation. Despite their biotechnological significance, a comprehensive understanding of clostridial physiology and evolution has remained elusive. This study reports an extensive comparative genomic analysis of 48 fully sequenced bacterial genomes from these genera. Our investigation, encompassing pan-genomic analysis, central carbon metabolism comparison, exploration of general genome features, and in-depth scrutiny of Cluster of Orthologous Groups genes, has established a holistic whole-genome-based phylogenetic framework. We have classified these strains into acetogenic, butanol-producing, cellulolytic, CO2-fixating, chemo(litho/organo)trophic, and heterotrophic categories, often exhibiting overlaps. Key outcomes include the identification of misclassified species and the revelation of insights into metabolic features, energy conservation, substrate utilization, stress responses, and regulatory mechanisms. These findings can provide guidance for the development of efficient microbial systems for sustainable bioenergy production. Furthermore, by addressing fundamental questions regarding genetic relationships, conserved genomic features, pivotal enzymes, and essential genes, this study has also contributed to our comprehension of clostridial biology, evolution, and their shared metabolic potential.
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Affiliation(s)
- Karan Kumar
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Lepakshi Barbora
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Vijayanand S Moholkar
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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6
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Wu S, Yang P, Geng Z, Li Y, Guo Z, Lou Y, Zhang S, Xiong J, Hu H, Guo X, Pu WT, Zhang Y, Zhu D, Zhang B. Base editing effectively prevents early-onset severe cardiomyopathy in Mybpc3 mutant mice. Cell Res 2024; 34:327-330. [PMID: 38337022 PMCID: PMC10978934 DOI: 10.1038/s41422-024-00930-7] [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] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/31/2023] [Indexed: 02/12/2024] Open
Affiliation(s)
- Shuo Wu
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Yang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zilong Geng
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yige Li
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhizhao Guo
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingmei Lou
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shasha Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junhao Xiong
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huan Hu
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoling Guo
- Basic Medical Research Center, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Boston, MA, USA
| | - Yan Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Dan Zhu
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Bing Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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7
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Gleber-Netto FO, Nagarajan P, Sagiv O, Pickering CR, Gross N, Ning J, Yeshi MM, Mitku Y, Tetzlaff MT, Esmaeli B. Histologic and Genomic Analysis of Conjunctival SCC in African and American Cohorts Reveal UV Light and HPV Signatures and High Tumor Mutation Burden. Invest Ophthalmol Vis Sci 2024; 65:24. [PMID: 38597722 PMCID: PMC11008748 DOI: 10.1167/iovs.65.4.24] [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: 10/12/2023] [Accepted: 12/12/2023] [Indexed: 04/11/2024] Open
Abstract
Purpose Conjunctival squamous cell carcinoma (conjSCC) is more prevalent and aggressive in sub-Saharan African countries compared with the rest of the world. This study aims to compare the genomic, immunophenotypic, and histologic features between patients from the United States and Ethiopia, to identify etiopathogenic mechanisms and unveil potential treatment strategies. Methods We compared histologic features and mutational profiles using whole exome sequencing, high-risk human papillomavirus (HPV) status, PD-L1 expression, and tumor-infiltrating lymphocytes in conjSCC tumors of patients from Ethiopia (ETH; n = 25) and the United States (from MD Anderson [the MDA cohort]; n = 29). Genomic alterations were compared with SCCs from other anatomic sites using data from The Cancer Genome Atlas. Results Solar elastosis was seen in 78% of ETH and 10% of MDA samples. Thicker tumors had higher density of CD8+ and CD3+ cells. HPV status was similar between the cohorts (ETH = 21% and MDA = 28%). The mean tumor mutation burden (TMB) was significantly higher in conjSCC (3.01/Mb, log10) and cutaneous SCC compared other SCC subtypes. ETH samples had higher TMB compared to the MDA cohort (3.34 vs. 2.73). Mutations in genes associated with ultraviolet light (UV) signature were most frequently encountered (SBS7b = 74% and SBS7a = 72%), with higher prevalence in the ETH cohort, whereas SBS2 and SBS13 signatures were more common among MDA HPV+ conjSCCs. Conclusions Our findings suggest that UV exposure may play a major role in conjSCC, with a higher prevalence in the ETH cohort compared with the MDA cohort, where HPV also contributes.
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Affiliation(s)
- Frederico O. Gleber-Netto
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Priyadharsini Nagarajan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Oded Sagiv
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
- The Goldschleger Eye Institute, Sheba Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Curtis R. Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Neil Gross
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Jing Ning
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | | | - Yonas Mitku
- Department of Ophthalmology, Mekelle University, Mekelle, Ethiopia
| | - Michael T. Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Bita Esmaeli
- Orbital Oncology and Ophthalmic Plastic Surgery, Department of Plastic Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
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8
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Yao D, Tycko J, Oh JW, Bounds LR, Gosai SJ, Lataniotis L, Mackay-Smith A, Doughty BR, Gabdank I, Schmidt H, Guerrero-Altamirano T, Siklenka K, Guo K, White AD, Youngworth I, Andreeva K, Ren X, Barrera A, Luo Y, Yardımcı GG, Tewhey R, Kundaje A, Greenleaf WJ, Sabeti PC, Leslie C, Pritykin Y, Moore JE, Beer MA, Gersbach CA, Reddy TE, Shen Y, Engreitz JM, Bassik MC, Reilly SK. Multicenter integrated analysis of noncoding CRISPRi screens. Nat Methods 2024; 21:723-734. [PMID: 38504114 PMCID: PMC11009116 DOI: 10.1038/s41592-024-02216-7] [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: 12/02/2022] [Accepted: 02/18/2024] [Indexed: 03/21/2024]
Abstract
The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.
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Affiliation(s)
- David Yao
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| | - Jin Woo Oh
- Departments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lexi R Bounds
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Sager J Gosai
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Center for System Biology, Harvard University, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
| | - Lazaros Lataniotis
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
| | - Ava Mackay-Smith
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
| | | | - Idan Gabdank
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Henri Schmidt
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tania Guerrero-Altamirano
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
- Department of Biology, Duke University, Durham, NC, USA
| | - Keith Siklenka
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Katherine Guo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alexander D White
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | | | - Kalina Andreeva
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Xingjie Ren
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Center for System Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christina Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuri Pritykin
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael A Beer
- Departments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Timothy E Reddy
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Yin Shen
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jesse M Engreitz
- Department of Genetics, Stanford University, Stanford, CA, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Steven K Reilly
- Department of Genetics, Yale University, New Haven, CT, USA.
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9
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Tamura K, Inasaki N, Itamochi M, Saga Y, Shimada T, Yazawa S, Sasajima H, Kawashiri C, Yamazaki E, Ichikawa T, Kaya H, Yamamoto Y, Morinaga Y, Yamashiro S, Nomura S, Takeda S, Ito H, Hirota K, Horie Y, Hirano N, Sekizuka T, Kuroda M, Tani H, Oishi K. Impact of COVID-19 and Closed Transmission of SARS-CoV-2 during the First Wave in Toyama Prefecture, Japan, March 30 to May 18, 2020. Jpn J Infect Dis 2024; 77:75-82. [PMID: 37914293 DOI: 10.7883/yoken.jjid.2023.210] [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] [Indexed: 11/03/2023]
Abstract
We studied 226 patients in Toyama Prefecture who were notified of COVID-19 during the first wave between March 30 and May 18, 2020. Of the 226 patients, 22 (9.7%) died, most (95%) of whom were aged ≥65 years. A large cluster comprising 59 patients (41 residents and 18 staff members) was identified in a nursing home on April 17. No deaths occurred among staff members; however, 12 of the 41 residents (29%) died. Although the threshold cycle (Ct) values were significantly lower in the 20-64 and ≥65 years age groups than in the <20 years age group, no correlation was found between the Ct values and severity, fatal outcome, or secondary infection. The haplotype network of 145 SARS-CoV-2 isolates (64%) from 226 patients was analyzed. The viral genomes of the case groups differed by less than five nucleotide bases. These data suggest that the SARS-CoV-2 strains, which were initially introduced into Toyama Prefecture in late March and early April 2020, and their closely related strains, identified as lineage B.1.1, circulated during the first wave. The reduced inter-prefectural mobility of local residents may support the lack of strain diversity in SARS-CoV-2 during the first wave of the state of emergency.
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Affiliation(s)
- Kosuke Tamura
- Department of Research Planning, Toyama Institute of Health, Japan
| | - Noriko Inasaki
- Department of Virology, Toyama Institute of Health, Japan
| | - Masae Itamochi
- Department of Virology, Toyama Institute of Health, Japan
| | - Yumiko Saga
- Department of Virology, Toyama Institute of Health, Japan
| | | | | | | | | | | | | | - Hiroyasu Kaya
- Department of Infectious Disease, Toyama Prefectural Central Hospital, Japan
| | - Yoshihiro Yamamoto
- Department of Clinical Infectious Diseases, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Japan
| | - Yoshitomo Morinaga
- Department of Microbiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Japan
| | - Seiji Yamashiro
- Department of Internal Medicine, Asahi General Hospital, Japan
| | | | | | | | | | | | | | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Japan
| | - Hideki Tani
- Department of Virology, Toyama Institute of Health, Japan
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10
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Segawa T, Masuda K, Hisatsune J, Ishida-Kuroki K, Sugawara Y, Kuwabara M, Nishikawa H, Hiratsuka T, Aota T, Tao Y, Iwahashi Y, Ueda K, Mae K, Masumoto K, Kitagawa H, Komatsuzawa H, Ohge H, Sugai M. Genomic analysis of inter-hospital transmission of vancomycin-resistant Enterococcus faecium sequence type 80 isolated during an outbreak in Hiroshima, Japan. Antimicrob Agents Chemother 2024:e0171623. [PMID: 38506550 DOI: 10.1128/aac.01716-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/01/2024] [Indexed: 03/21/2024] Open
Abstract
Outbreaks caused by vancomycin-resistant enterococci that transcend jurisdictional boundaries are occurring worldwide. This study focused on a vancomycin-resistant enterococcus outbreak that occurred between 2018 and 2021 across two cities in Hiroshima, Japan. The study involved genetic and phylogenetic analyses using whole-genome sequencing of 103 isolates of vancomycin-resistant enterococci to identify the source and transmission routes of the outbreak. Phylogenetic analysis was performed using core genome multilocus sequence typing and core single-nucleotide polymorphisms; infection routes between hospitals were inferred using BadTrIP. The outbreak was caused by Enterococcus faecium sequence type (ST) 80 carrying the vanA plasmid, which was derived from strain A10290 isolated in India. Of the 103 isolates, 93 were E. faecium ST80 transmitted across hospitals. The circular vanA plasmid of the Hiroshima isolates was similar to the vanA plasmid of strain A10290 and transferred from E. faecium ST80 to other STs of E. faecium and other Enterococcus species by conjugation. The inferred transmission routes across hospitals suggest the existence of a central hospital serving as a hub, propagating vancomycin-resistant enterococci to multiple hospitals. Our study highlights the importance of early intervention at the key central hospital to prevent the spread of the infection to small medical facilities, such as nursing homes, with limited medical resources and a high number of vulnerable individuals.
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Affiliation(s)
- Takaya Segawa
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Kanako Masuda
- Hiroshima Prefectural Center for Disease Control and Prevention, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Junzo Hisatsune
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Kasumi Ishida-Kuroki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Yo Sugawara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Masao Kuwabara
- Hiroshima Prefectural Center for Disease Control and Prevention, Hiroshima, Japan
| | - Hideki Nishikawa
- Hiroshima Prefectural Center for Disease Control and Prevention, Hiroshima, Japan
| | - Takahiro Hiratsuka
- Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Hiroshima, Japan
| | - Tatsuaki Aota
- Hiroshima City Institute of Public Health, Hiroshima, Japan
| | - Yasuo Tao
- Hiroshima City Public Health Center, Hiroshima, Japan
| | | | - Kuniko Ueda
- Hiroshima City Public Health Center, Hiroshima, Japan
| | - Kaori Mae
- Hiroshima City Medical Association Clinical Laboratory, Hiroshima, Japan
| | - Ken Masumoto
- Hiroshima City Medical Association Clinical Laboratory, Hiroshima, Japan
| | - Hiroki Kitagawa
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Hitoshi Komatsuzawa
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Hiroki Ohge
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
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11
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Wang M, Sun Z, Liu Y, Yin P, Liang C, Tan L, Wei L, Wang Y, Yu H, Zhu Y, Hu X, Li N, Zhang R. Hypercompact TnpB and truncated TnpB systems enable efficient genome editing in vitro and in vivo. Cell Discov 2024; 10:31. [PMID: 38503726 PMCID: PMC10951260 DOI: 10.1038/s41421-023-00645-w] [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: 08/09/2023] [Accepted: 12/24/2023] [Indexed: 03/21/2024] Open
Affiliation(s)
- Ming Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
- SciFriend Biotechnology Co., Ltd, Beijing, China
| | - Zhaolin Sun
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, Beijing, China
| | - Yue Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Pengbin Yin
- Department of Orthopaedics, Chinese PLA General Hospital, Beijing, China
| | - Chuanyu Liang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lin Tan
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lei Wei
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuzhan Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haikuan Yu
- Department of Orthopaedics, Chinese PLA General Hospital, Beijing, China
| | - Yunfei Zhu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiaoxiang Hu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ning Li
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, Beijing, China.
| | - Ran Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China.
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China.
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12
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Zhao JH, Cheng P, Wang Y, Yan X, Xu ZM, Peng DH, Yu GH, Shao MW. Using kin discrimination to construct synthetic microbial communities of Bacillus subtilis strains impacts the growth of black soldier fly larvae. Insect Sci 2024. [PMID: 38494587 DOI: 10.1111/1744-7917.13356] [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: 10/03/2023] [Revised: 01/04/2024] [Accepted: 01/25/2024] [Indexed: 03/19/2024]
Abstract
Using synthetic microbial communities to promote host growth is an effective approach. However, the construction of such communities lacks theoretical guidance. Kin discrimination is an effective means by which strains can recognize themselves from non-self, and construct competitive microbial communities to produce more secondary metabolites. However, the construction of cooperative communities benefits from the widespread use of beneficial microorganisms. We used kin discrimination to construct synthetic communities (SCs) comprising 13 Bacillus subtilis strains from the surface and gut of black soldier fly (BSF) larvae. We assessed larval growth promotion in a pigeon manure system and found that the synthetic community comprising 4 strains (SC 4) had the most profound effect. Genomic analyses of these 4 strains revealed that their complementary functional genes underpinned the robust functionality of the cooperative synthetic community, highlighting the importance of strain diversity. After analyzing the bacterial composition of BSF larvae and the pigeon manure substrate, we observed that SC 4 altered the bacterial abundance in both the larval gut and pigeon manure. This also influenced microbial metabolic functions and co-occurrence network complexity. Kin discrimination facilitates the rapid construction of synthetic communities. The positive effects of SC 4 on larval weight gain resulted from the functional redundancy and complementarity among the strains. Furthermore, SC 4 may enhance larval growth by inducing shifts in the bacterial composition of the larval gut and pigeon manure. This elucidated how the SC promoted larval growth by regulating bacterial composition and provided theoretical guidance for the construction of SCs.
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Affiliation(s)
- Jun-Hui Zhao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Ping Cheng
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yi Wang
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xun Yan
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zhi-Min Xu
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Dong-Hai Peng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Guo-Hui Yu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ming-Wei Shao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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13
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Ikezawa K, Urabe M, Kai Y, Takada R, Akita H, Nagata S, Ohkawa K. Comprehensive review of pancreatic acinar cell carcinoma: epidemiology, diagnosis, molecular features and treatment. Jpn J Clin Oncol 2024; 54:271-281. [PMID: 38109477 PMCID: PMC10925851 DOI: 10.1093/jjco/hyad176] [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: 09/26/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023] Open
Abstract
Pancreatic acinar cell carcinoma is a rare form (0.2-4.3%) of pancreatic neoplasm with unique clinical and molecular characteristics, which largely differ from pancreatic ductal adenocarcinoma. Pancreatic acinar cell carcinoma occurs more frequently in males and can occur in children. Serum lipase is elevated in 24-58% of patients with pancreatic acinar cell carcinoma. Pancreatic acinar cell carcinomas tend to be large at diagnosis (median tumour size: ~5 cm) and are frequently located in the pancreas head. Radiologically, pancreatic acinar cell carcinoma generally exhibits a solid appearance; however, necrosis, cystic changes and intratumoral haemorrhage can occur in larger lesions. Immunostaining is essential for the definitive diagnosis of pancreatic acinar cell carcinoma. Compared with pancreatic ductal adenocarcinoma, pancreatic acinar cell carcinoma has a more favourable prognosis. Although radical surgery is recommended for patients with pancreatic acinar cell carcinoma who do not have distant metastases, the recurrence rate is high. The effectiveness of adjuvant therapy for pancreatic acinar cell carcinoma is unclear. The response to FOLFIRINOX is generally favourable, and some patients achieve a complete response. Pancreatic acinar cell carcinoma has a different genomic profile compared with pancreatic ductal adenocarcinoma. Although genomic analyses have shown that pancreatic acinar cell carcinoma rarely has KRAS, TP53 and CDKN2A mutations, it has a higher prevalence of homologous recombination-related genes, including BRCA1/2 and ATM, than pancreatic ductal adenocarcinoma, suggesting high sensitivity to platinum-containing regimens and PARP inhibitors. Targeted therapies for genomic alternations are beneficial. Therefore, genetic testing is important for patients with pancreatic acinar cell carcinoma to choose the optimal therapeutic strategy.
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Affiliation(s)
- Kenji Ikezawa
- Department of Hepatobiliary and Pancreatic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Makiko Urabe
- Department of Hepatobiliary and Pancreatic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Yugo Kai
- Department of Hepatobiliary and Pancreatic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Ryoji Takada
- Department of Hepatobiliary and Pancreatic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Hirofumi Akita
- Department of Gastroenterological Surgery, Osaka International Cancer Institute, Osaka, Japan
| | - Shigenori Nagata
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan
| | - Kazuyoshi Ohkawa
- Department of Hepatobiliary and Pancreatic Oncology, Osaka International Cancer Institute, Osaka, Japan
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14
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Holtappels D, Abelson SA, Nouth SC, Rickus GEJ, Amare SZ, Giller JP, Jian DZ, Koskella B. Genomic characterization of Pseudomonas syringae pv. syringae from Callery pear and the efficiency of associated phages in disease protection. Microbiol Spectr 2024; 12:e0283323. [PMID: 38323825 PMCID: PMC10913373 DOI: 10.1128/spectrum.02833-23] [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: 07/14/2023] [Accepted: 12/11/2023] [Indexed: 02/08/2024] Open
Abstract
The Pseudomonas syringae species complex is a heterogeneous group of plant pathogenic bacteria associated with a wide distribution of plant species. Advances in genomics are revealing the complex evolutionary history of this species complex and the wide array of genetic adaptations underpinning their diverse lifestyles. Here, we genomically characterize two P. syringae isolates collected from diseased Callery pears (Pyrus calleryana) in Berkeley, California in 2019 and 2022. We also isolated a lytic bacteriophage, which we characterized and evaluated for biocontrol efficiency. Using a multilocus sequence analysis and core genome alignment, we classified the P. syringae isolates as members of phylogroup 2, related to other strains previously isolated from Pyrus and Prunus. An analysis of effector proteins demonstrated an evolutionary conservation of effectoromes across isolates classified in PG2 and yet uncovered unique effector profiles for each, including the two newly identified isolates. Whole-genome sequencing of the associated phage uncovered a novel phage genus related to Pseudomonas syringae pv. actinidiae phage PHB09 and the Flaumdravirus genus. Finally, using in planta infection assays, we demonstrate that the phage was equally useful in symptom mitigation of immature pear fruit regardless of the Pss strain tested. Overall, this study demonstrates the diversity of P. syringae and their viruses associated with ornamental pear trees, posing spill-over risks to commercial pear trees and the possibility of using phages as biocontrol agents to reduce the impact of disease.IMPORTANCEGlobal change exacerbates the spread and impact of pathogens, especially in agricultural settings. There is a clear need to better monitor the spread and diversity of plant pathogens, including in potential spillover hosts, and for the development of novel and sustainable control strategies. In this study, we characterize the first described strains of Pseudomonas syringae pv. syringae isolated from Callery pear in Berkeley, California from diseased tissues in an urban environment. We show that these strains have divergent virulence profiles from previously described strains and that they can cause disease in commercial pears. Additionally, we describe a novel bacteriophage that is associated with these strains and explore its potential to act as a biocontrol agent. Together, the data presented here demonstrate that ornamental pear trees harbor novel P. syringae pv. syringae isolates that potentially pose a risk to local fruit production, or vice versa-but also provide us with novel associated phages, effective in disease mitigation.
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Affiliation(s)
- D. Holtappels
- Integrative Biology University of California, Berkeley, California, USA
| | - S. A. Abelson
- Integrative Biology University of California, Berkeley, California, USA
| | - S. C. Nouth
- Integrative Biology University of California, Berkeley, California, USA
| | - G. E. J. Rickus
- Integrative Biology University of California, Berkeley, California, USA
| | - S. Z. Amare
- Integrative Biology University of California, Berkeley, California, USA
| | - J. P. Giller
- Integrative Biology University of California, Berkeley, California, USA
| | - D. Z. Jian
- Integrative Biology University of California, Berkeley, California, USA
| | - B. Koskella
- Integrative Biology University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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15
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Li H, Ren X, Zhang H, Li S, He Y, Qi T, Cai Z. A Clinical Study on Video Bronchoscopy-guided Coblation for Benign Central Airway Stenosis. Ear Nose Throat J 2024:1455613241235513. [PMID: 38439622 DOI: 10.1177/01455613241235513] [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: 03/06/2024] Open
Abstract
Background: Benign central airway stenosis poses a significant challenge to respiratory and thoracic surgeons due to the high recurrence rate associated with current treatment methods, causing severe breathing difficulties and potentially life-threatening complications. This article aims to investigate the therapeutic efficacy and prospects of using coblation in the management of benign central airway stenosis in adults. Moreover, the pathogenesis of benign central airway stenosis was deeply explored to provide better guidance for future clinical treatments. Materials and Methods: This retrospective study examined patients with benign central airway stenosis who were treated at The Second Hospital of Hebei Medical University from 2017 to 2020. In addition, a comparative analysis of whole-genome sequencing was conducted between the aforementioned patient group and healthy populations to investigate the underlying etiology of this stenotic condition. Results: The present study encompassed 32 patients who underwent 43 treatments in total between 2017 and 2020. All patients exhibited alleviation of airway stenosis and an improvement in clinical symptoms following surgery, without any significant surgical or postoperative complications. Whole-genome analysis revealed significant changes in gene expression in the airway mucosa of patients with benign airway stenosis in comparison to healthy populations. A total of 91 differentially expressed genes were identified, among which 44 upregulated genes displayed characteristics of promoting inflammatory responses. Conclusion: Coblation demonstrates promise as an efficacious treatment modality for adults suffering from benign central airway stenosis, and its widespread application in clinical settings is anticipated. The direct pathogenesis of benign central airway stenosis involves airway lumen narrowing and obstruction resulting from excessive inflammation and proliferative granulation.
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Affiliation(s)
- Haitao Li
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Respiratory Critical Care, Hebei Institute of Respiratory Diseases, Shijiazhuang, Hebei, China
| | - Xuezhu Ren
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Respiratory Critical Care, Hebei Institute of Respiratory Diseases, Shijiazhuang, Hebei, China
| | - Haizhong Zhang
- Department of Otolaryngology, Head & Neck Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Shuai Li
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Respiratory Critical Care, Hebei Institute of Respiratory Diseases, Shijiazhuang, Hebei, China
| | - Yuzheng He
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Tianjie Qi
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Respiratory Critical Care, Hebei Institute of Respiratory Diseases, Shijiazhuang, Hebei, China
| | - Zhigang Cai
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Respiratory Critical Care, Hebei Institute of Respiratory Diseases, Shijiazhuang, Hebei, China
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16
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Lee M, Choi CH, Kim JW, Sim G, Lee SE, Shin H, Lee JH, Choi MM, Yi H, Chung YS. Prolonged viral shedding in an immunocompromised Korean patient infected with hMPXV, sub-lineage B.1.3, with acquired drug resistant mutations during tecovirimat treatment. J Med Virol 2024; 96:e29536. [PMID: 38488495 DOI: 10.1002/jmv.29536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/12/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
Following the worldwide surge in mpox (monkeypox) in 2022, cases have persisted in Asia, including South Korea, and sexual contact is presumed as the predominant mode of transmission, with a discernible surge in prevalence among immunocompromised patients. Drugs such as tecovirimat can result in drug-resistant mutations, presenting obstacles to treatment. This study aimed to ascertain the presence of tecovirimat-related resistant mutations through genomic analysis of the monkeypox virus isolated from a reported case involving prolonged viral shedding in South Korea. Here, tecovirimat-resistant mutations, previously identified in the B.1 clade, were observed in the B.1.3 clade, predominant in South Korea. These mutations exhibited diverse patterns across different samples from the same patient and reflected the varied distribution of viral subpopulations in different anatomical regions. The A290V and A288P mutant strains we isolated hold promise for elucidating these mechanisms, enabling a comprehensive analysis of viral pathogenesis, replication strategies, and host interactions. Our findings imply that acquired drug-resistant mutations, may present a challenge to individual patient treatment. Moreover, they have the potential to give rise to transmitted drug-resistant mutations, thereby imposing a burden on the public health system. Consequently, the meticulous genomic surveillance among immunocompromised patients, conducted in this research, assumes paramount importance.
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Affiliation(s)
- Minji Lee
- Division of High-risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Chi-Hwan Choi
- Division of High-risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Jin-Won Kim
- Division of High-risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Gyuri Sim
- Division of High-risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Sang Eun Lee
- Division of High-risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Hwachul Shin
- Division of High-risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Jeong Hyun Lee
- Division of High-risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Myung-Min Choi
- Division of High-risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Hwajung Yi
- Division of High-risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Yoon-Seok Chung
- Division of High-risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
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17
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Folkertsma R, Charbonnel N, Henttonen H, Heroldová M, Huitu O, Kotlík P, Manzo E, Paijmans JLA, Plantard O, Sándor AD, Hofreiter M, Eccard JA. Genomic signatures of climate adaptation in bank voles. Ecol Evol 2024; 14:e10886. [PMID: 38455148 PMCID: PMC10918726 DOI: 10.1002/ece3.10886] [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: 05/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate-mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis, we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.
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Affiliation(s)
- Remco Folkertsma
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Comparative Cognition Unit, Messerli Research InstituteUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | - Marta Heroldová
- Department of Forest Ecology, FFWTMendel University in BrnoBrnoCzech Republic
| | - Otso Huitu
- Natural Resources Institute FinlandHelsinkiFinland
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and GeneticsCzech Academy of SciencesLiběchovCzech Republic
| | - Emiliano Manzo
- Fondazione Ethoikos, Convento dell'OsservanzaRadicondoliItaly
| | - Johanna L. A. Paijmans
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Present address:
Evolutionary Ecology Group, Department of ZoologyUniversity of CambridgeCambridgeUK
| | | | - Attila D. Sándor
- HUN‐RENClimate Change: New Blood‐Sucking Parasites and Vector‐Borne Pathogens Research GroupBudapestHungary
- Department of Parasitology and ZoologyUniversity of Veterinary MedicineBudapestHungary
- Department of Parasitology and Parasitic DiseasesUniversity of Agricultural Sciences and Veterinary MedicineCluj‐NapocaRomania
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
| | - Jana A. Eccard
- Animal Ecology, Institute for Biochemistry and Biology, Faculty of ScienceBerlin‐Brandenburg Institute for Biodiversity ResearchUniversity of PotsdamPotsdamGermany
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18
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Weng C, Yu F, Yang D, Poeschla M, Liggett LA, Jones MG, Qiu X, Wahlster L, Caulier A, Hussmann JA, Schnell A, Yost KE, Koblan LW, Martin-Rufino JD, Min J, Hammond A, Ssozi D, Bueno R, Mallidi H, Kreso A, Escabi J, Rideout WM, Jacks T, Hormoz S, van Galen P, Weissman JS, Sankaran VG. Deciphering cell states and genealogies of human haematopoiesis. Nature 2024; 627:389-398. [PMID: 38253266 PMCID: PMC10937407 DOI: 10.1038/s41586-024-07066-z] [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: 12/01/2022] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems2-5, simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.
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Affiliation(s)
- Chen Weng
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, P.R. China
| | - Dian Yang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular Pharmacology and Therapeutics, Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michael Poeschla
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - L Alexander Liggett
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew G Jones
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Genetics and Computer Science, BASE Research Initiative, Betty Irene Moore Children's Heart Center, Stanford University, Stanford, CA, USA
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey A Hussmann
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexandra Schnell
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kathryn E Yost
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke W Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jorge D Martin-Rufino
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph Min
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alessandro Hammond
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Ssozi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Raphael Bueno
- Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Hari Mallidi
- Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Antonia Kreso
- Division of Cardiac Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Javier Escabi
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William M Rideout
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA
| | - Tyler Jacks
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA
| | - Sahand Hormoz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter van Galen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA.
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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19
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Chen JP, Diekmann C, Wu H, Chen C, Della Chiara G, Berrino E, Georgiadis KL, Bouwman BAM, Virdi M, Harbers L, Bellomo SE, Marchiò C, Bienko M, Crosetto N. scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells. Nat Commun 2024; 15:1768. [PMID: 38409079 PMCID: PMC10897160 DOI: 10.1038/s41467-024-45972-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for profiling eccDNAs and unraveling their diversity and complexity in single cells. We implement and validate scCircle-seq in normal and cancer cell lines, demonstrating that most eccDNAs vary largely between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. eccDNAs are preferentially produced from chromatin regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress conditions. Concomitant sequencing of eccDNAs and RNA from the same cell uncovers the absence of correlation between eccDNA copy number and gene expression levels, except for a few oncogenes, including MYC, contained within a large eccDNA in colorectal cancer cells. Lastly, we apply scCircle-seq to one prostate cancer and two breast cancer specimens, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, and further expands the potential of eccDNAs for cancer diagnostics.
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Affiliation(s)
- Jinxin Phaedo Chen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
| | - Constantin Diekmann
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Honggui Wu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, PR China
- School of Life Sciences, Peking University, Beijing, PR China
| | - Chong Chen
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | | | - Enrico Berrino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Konstantinos L Georgiadis
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Britta A M Bouwman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Mohit Virdi
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy
| | - Luuk Harbers
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Sara Erika Bellomo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
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20
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Chang Y, Wu S, Li J, Bao H, Wu C. Identification of Candidate Genes for Red-Eyed (Albinism) Domestic Guppies Using Genomic and Transcriptomic Analyses. Int J Mol Sci 2024; 25:2175. [PMID: 38396851 PMCID: PMC10888696 DOI: 10.3390/ijms25042175] [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: 12/15/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Guppies are small tropical fish with brightly colored bodies and variable tail shapes. There are two phenotypes of domestic guppy eye color: red and black. The wild type is black-eyed. The main object of this study was to identify candidate genes for the red-eyed phenotype in domestic guppies. We hope to provide molecular genetic information for the development of new domestic guppy strains. Additionally, the results also contribute to basic research concerning guppies. In this study, 121 domestic guppies were used for genomic analysis (GWAS), and 44 genes were identified. Furthermore, 21 domestic guppies were used for transcriptomic analysis, and 874 differentially expressed genes (DEGs) were identified, including 357 upregulated and 517 downregulated genes. Through GO and KEGG enrichment, we identified some important terms or pathways mainly related to melanin biosynthesis and ion transport. qRT-PCR was also performed to verify the differential expression levels of four important candidate genes (TYR, OCA2, SLC45A2, and SLC24A5) between red-eyed and black-eyed guppies. Based on the results of genomic and transcriptomic analyses, we propose that OCA2 is the most important candidate gene for the red-eyed phenotype in guppies.
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Affiliation(s)
| | | | | | - Haigang Bao
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.C.); (S.W.); (J.L.); (C.W.)
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21
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Schottlender G, Prieto JM, Clemente C, Schuster CD, Dumas V, Fernández Do Porto D, Martí MA. Bacterial cytochrome P450s: a bioinformatics odyssey of substrate discovery. Front Microbiol 2024; 15:1343029. [PMID: 38384262 PMCID: PMC10879549 DOI: 10.3389/fmicb.2024.1343029] [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: 11/22/2023] [Accepted: 01/23/2024] [Indexed: 02/23/2024] Open
Abstract
Bacterial P450 cytochromes (BacCYPs) are versatile heme-containing proteins responsible for oxidation reactions on a wide range of substrates, contributing to the production of valuable natural products with limitless biotechnological potential. While the sequencing of microbial genomes has provided a wealth of BacCYP sequences, functional characterization lags behind, hindering our understanding of their roles. This study employs a comprehensive approach to predict BacCYP substrate specificity, bridging the gap between sequence and function. We employed an integrated approach combining sequence and functional data analysis, genomic context exploration, 3D structural modeling with molecular docking, and phylogenetic clustering. The research begins with an in-depth analysis of BacCYP sequence diversity and structural characteristics, revealing conserved motifs and recurrent residues in the active site. Phylogenetic analysis identifies distinct groups within the BacCYP family based on sequence similarity. However, our study reveals that sequence alone does not consistently predict substrate specificity, necessitating additional perspectives. The study delves into the genetic context of BacCYPs, utilizing neighboring gene information to infer potential substrates, a method proven very effective in many cases. Molecular docking is employed to assess BacCYP-substrate interactions, confirming potential substrates and providing insights into selectivity. Finally, a comprehensive strategy is proposed for predicting BacCYP substrates, involving all the evaluated approaches. The effectiveness of this strategy is demonstrated with two case studies, highlighting its potential for substrate discovery.
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Affiliation(s)
- Gustavo Schottlender
- Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan Manuel Prieto
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Buenos Aires, Argentina
| | - Camila Clemente
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Buenos Aires, Argentina
| | - Claudio David Schuster
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Buenos Aires, Argentina
| | - Victoria Dumas
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina
| | - Darío Fernández Do Porto
- Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina
| | - Marcelo Adrian Martí
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina
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22
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Zhao P, Zhao W, Zhai X, He Y, Shu W, Qiao G. Biological characterization and genomic analysis of a novel methicillin-resistant Staphylococcus aureus phage, SauPS-28. Microbiol Spectr 2024; 12:e0029523. [PMID: 38193720 PMCID: PMC10846126 DOI: 10.1128/spectrum.00295-23] [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: 06/15/2023] [Accepted: 11/23/2023] [Indexed: 01/10/2024] Open
Abstract
Staphylococcus aureus, a representative gram-positive bacterium, is a common infectious pathogen widely present in the natural environment. The increasing application of antibiotics is witnessing an increment in the number of clinically resistant strains (such as methicillin-resistant S. aureus [MRSA]), which has posed a great challenge to antimicrobial therapy. In this study, a novel MRSA phage, SauPS-28, was isolated from the lake water of the Guangxi Zhuang Autonomous Region. This phage has an incubation period of approximately 30 min, a lysis period of approximately 40 min, and a burst size of approximately 25 PFU/cell. The isolated phage exhibited good biological stability at a pH range of 6.0-9.0 and temperature range of 4°C-37°C. In addition, the identification of an elongated tail using transmission electron microscopy confirmed that SauPS-28 belongs to the long-tailed phage family. Whole-genome sequencing analysis revealed that SauPS-28 has a 43,286-bp-long genome with 31.03% G + C content. Moreover, SauPS-28 exhibited 95.69% sequence identity with ECel-2020k, while the query coverage was only 66%, which is a newly discovered phage. Whole-genome functional annotation results revealed that SauPS-28 had 68 open reading frames (ORFs). Of these, 30 ORFs are unknown proteins. The results suggest that SauPS-28 could be a lysogenic phage strain. This study thus provides preliminary data to conduct further in-depth analysis of the mechanism of phage-host interaction and provides a reference value for phage therapy.IMPORTANCEIn recent years, drug-resistant bacterial infections have become increasingly serious. As a kind of virus with the ability to infect and lyse drug-resistant bacteria, phage is expected to be a new therapeutic method. In this study, we isolated and purified a new methicillin-resistant Staphylococcus aureus bacteriophage SauPS-28, studied a series of biological characteristics of the bacteriophage, analyzed the genome and structural proteome data of the bacteriophage, and provided reference data for further study of the interaction mechanism between bacteriophage and host bacteria and promoted new antibacterial strategies.
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Affiliation(s)
- Peisong Zhao
- Department of Microbiology, School of Basic Medicine, Guilin Medical University, Guilin, Guangxi, China
- Key Laboratory of Pathogenic Biology, Guilin Medical University, Guilin, Guangxi, China
- Department of Medical Laboratory, Handan Central Hospital, Handan, Hebei, China
| | - Wenli Zhao
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xin Zhai
- Office of Health Insurance, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yulin He
- Department of Microbiology, School of Basic Medicine, Guilin Medical University, Guilin, Guangxi, China
- Key Laboratory of Pathogenic Biology, Guilin Medical University, Guilin, Guangxi, China
| | - Wei Shu
- College of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin, Guangxi, China
- Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guilin Medical University, Guilin, Guangxi, China
| | - Guanhua Qiao
- Department of Microbiology, School of Basic Medicine, Guilin Medical University, Guilin, Guangxi, China
- Key Laboratory of Pathogenic Biology, Guilin Medical University, Guilin, Guangxi, China
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23
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Giancotti R, Lomoio U, Puccio B, Tradigo G, Vizza P, Torti C, Veltri P, Guzzi PH. The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics. Biology (Basel) 2024; 13:90. [PMID: 38392308 PMCID: PMC10886209 DOI: 10.3390/biology13020090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
The SARS-CoV-2 virus, which is a major threat to human health, has undergone many mutations during the replication process due to errors in the replication steps and modifications in the structure of viral proteins. The XBB variant was identified for the first time in Singapore in the fall of 2022. It was then detected in other countries, including the United States, Canada, and the United Kingdom. We study the impact of sequence changes on spike protein structure on the subvariants of XBB, with particular attention to the velocity of variant diffusion and virus activity with respect to its diffusion. We examine the structural and functional distinctions of the variants in three different conformations: (i) spike glycoprotein in complex with ACE2 (1-up state), (ii) spike glycoprotein (closed-1 state), and (iii) S protein (open-1 state). We also estimate the affinity binding between the spike protein and ACE2. The market binding affinity observed in specific variants raises questions about the efficacy of current vaccines in preparing the immune system for virus variant recognition. This work may be useful in devising strategies to manage the ongoing COVID-19 pandemic. To stay ahead of the virus evolution, further research and surveillance should be carried out to adjust public health measures accordingly.
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Affiliation(s)
- Raffaele Giancotti
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Ugo Lomoio
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Barbara Puccio
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | | | - Patrizia Vizza
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Carlo Torti
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Pierangelo Veltri
- Department of Computer Engineering, Modelling, Electronics and System, University of Calabria, 87036 Rende, Italy
| | - Pietro Hiram Guzzi
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
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24
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Kan M, Kouchi Y, Ohyama H, Usui G, Fukuyo M, Takano S, Kishimoto T, Kaneda A, Ohtsuka M, Kato N. Genomic Analysis of Undifferentiated Carcinoma of the Pancreas with Squamous Differentiation: A Case Report. Cureus 2024; 16:e55175. [PMID: 38558649 PMCID: PMC10980578 DOI: 10.7759/cureus.55175] [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] [Accepted: 02/25/2024] [Indexed: 04/04/2024] Open
Abstract
Pancreatic cancer is an intractable malignancy associated with a dismal prognosis. Undifferentiated carcinoma, a rare subtype, poses a clinical challenge owing to a limited understanding of its molecular characteristics. In this study, we conducted genomic analysis specifically on a case of undifferentiated carcinoma of the pancreas exhibiting squamous differentiation. An 80-year-old male, previously treated for colorectal cancer, presented with a mass with central cystic degeneration in the pancreatic tail. The mass was diagnosed pathologically as undifferentiated carcinoma of the pancreas with squamous differentiation. Despite surgical resection and chemotherapy, the patient faced early postoperative recurrence, emphasizing the aggressive nature of this malignancy. Genomic analysis of distinct histologic components revealed some common mutations between undifferentiated and squamous components, including Kirsten rat sarcoma virus (KRAS) and TP53. Notably, the squamous component harbored some specific mutations in SMARCA4 and SMARCB1 genes that code for members of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex. The common mutations in the undifferentiated and squamous cell carcinoma components from this analysis suggest that they originate from a common origin. The discussion also underscores the scarcity of genomic analyses on undifferentiated carcinoma of the pancreas, with existing literature pointing to SWI/SNF complex-related gene mutations. However, our case introduces chromatin remodeling factor mutations as relevant in squamous differentiation. In conclusion, this study provides valuable insights into the genomic landscape of undifferentiated pancreatic carcinoma with squamous differentiation. These findings suggest the importance of further research and targeted therapies to improve the management of undifferentiated carcinoma of the pancreas and enhance patient outcomes.
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Affiliation(s)
| | | | | | - Genki Usui
- Molecular Oncology, Chiba University, Chiba, JPN
| | | | | | | | | | | | - Naoya Kato
- Gastroenterology, Chiba University, Chiba, JPN
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25
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Medina-Munoz HC, Kofman E, Jagannatha P, Boyle EA, Yu T, Jones KL, Mueller JR, Lykins GD, Doudna AT, Park SS, Blue SM, Ranzau BL, Kohli RM, Komor AC, Yeo GW. Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. Nat Commun 2024; 15:875. [PMID: 38287010 PMCID: PMC10825223 DOI: 10.1038/s41467-024-45009-4] [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: 10/03/2023] [Accepted: 01/03/2024] [Indexed: 01/31/2024] Open
Abstract
RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.
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Affiliation(s)
- Hugo C Medina-Munoz
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eric Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Pratibha Jagannatha
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Evan A Boyle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tao Yu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Krysten L Jones
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jasmine R Mueller
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Grace D Lykins
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrew T Doudna
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Samuel S Park
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
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26
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Liu J, Huang H, Han Y, Hua Y, Li B, Liu H, Chen J. Genomic analysis of hypoxia and mitophagy related genes with prognosis and characterization of the immune microenvironment in LUAD. J Cancer 2024; 15:1342-1354. [PMID: 38356715 PMCID: PMC10861832 DOI: 10.7150/jca.91762] [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: 11/01/2023] [Accepted: 12/22/2023] [Indexed: 02/16/2024] Open
Abstract
Background: Lung adenocarcinoma (LUAD) stands as a prominent subtype within the realm of non-small cell lung cancer and constitutes a primary contributor to cancer-related mortality on a global scale. Notably, hypoxia, a prevalent attribute within solid tumor environments, and mitophagy, a selective manifestation of autophagy dedicated to the removal of damaged mitochondria, have risen to prominence as pivotal factors influencing the initiation and advancement of tumorigenesis. Methods: This investigation harnessed publicly accessible genomic datasets encompassing LUAD patients to delineate genes linked to hypoxia and mitophagy, termed hereafter as hypoxia and mitophagy-related genes (HMRGs). Large-scale repositories furnished both gene expression profiles and clinical particulars. The expression profiles of HMRGs were meticulously scrutinized across 1,093 LUAD specimens, leveraging resources such as The Cancer Genome Atlas and Gene Expression Omnibus datasets. A methodical exploration of HMRG patterns within LUAD led to the discernment of two distinct molecular subtypes. Moreover, a discernible correlation emerged between the subtypes and their respective clinical attributes. A risk scoring system was formulated to prognosticate overall survival (OS) and therapeutic responsiveness in LUAD patients. Subsequently, the reliability of this scoring system was authenticated, and a nomogram was adopted to refine the clinical utility range of the risk score. The proliferation and migration impacts of KRT8 on LUAD cells were evaluated through cck8 assays, edu assays, and transwell assays, the results were further validated in vivo. Results: Elevated risk scores were indicative of unfavorable OS probabilities. Furthermore, these risk scores exhibited associations with immune checkpoints and chemotherapeutic drug sensitivity. Collectively, our exhaustive analysis of HMRGs in LUAD patients unveiled their conceivable participation in configuring the multifaceted tumor microenvironment, encompassing clinicopathological attributes and prognosis. A sequence of experiments illuminated the pro-proliferative and pro-migratory attributes of KRT8 in vitro and vivo, thus underscoring its carcinogenic potential. Conclusions: In this study, we have unearthed innovative gene signatures tethered to HMRGs, which harbor prognostic implications concerning patient outcomes. These insights hold potential for steering the development of targeted therapeutic modalities tailored for LUAD.
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Affiliation(s)
- Jinghao Liu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Hua Huang
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yueting Han
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Yu Hua
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Boshi Li
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongyu Liu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Jun Chen
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
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27
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Taheri Bajgan E, Zahedmehr A, Shakerian F, Maleki M, Bakhshandeh H, Mowla SJ, Malakootian M. Associations between low serum levels of ANRIL and some common gene SNPs in Iranian patients with premature coronary artery disease. Sci Rep 2024; 14:1244. [PMID: 38218954 PMCID: PMC10787829 DOI: 10.1038/s41598-024-51715-2] [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: 03/02/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024] Open
Abstract
Coronary artery disease (CAD) is the major cause of mortality in the world. Premature development of CAD can be attributed to women under 55 and men under 45. Many genetic factors play a part in premature CAD. Among them, ANRIL, a long noncoding RNA is located at the 9p21 risk locus, and its expression seems to be correlated with CAD. In the current study, premature CAD and control blood samples, with and without Type 2 Diabetes (T2D), were genotyped for six SNPs at the 9p21 locus. Additionally, ANRIL serum expression was assessed in both groups using real-time PCR. It was performed using different primers targeting exons 1, 5-6, and 19. The χ2 test for association, along with t-tests and ANOVA, was employed for statistical analysis. In this study, we did not find any significant correlation between premature coronary artery disease and rs10757274, rs2383206, rs2383207, rs496892, rs10757278 and rs10738605. However, a lower ANRIL expression was correlated with each SNP risk genotype. Despite the correlation between lower ANRIL expression and CAD, Type 2 diabetes was associated with higher ANRIL expression. Altogether, the correlation between ANRIL expression and the genotypes of the studied SNPs indicated that genetic variants, even those in intronic regions, affect long noncoding RNA expression levels. In conclusion, we recommend combining genetic variants with expression analysis when developing screening strategies for families with premature CAD. To prevent the devastating outcomes of CAD in young adults, it is crucial to discover noninvasive genetic-based screening tests.
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Affiliation(s)
- Elham Taheri Bajgan
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Zahedmehr
- Cardiovascular Intervention Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Farshad Shakerian
- Cardiovascular Intervention Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hooman Bakhshandeh
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Javad Mowla
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Mahshid Malakootian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
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28
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Mandiracioglu B, Ozden F, Kaynar G, Yilmaz MA, Alkan C, Cicek AE. ECOLE: Learning to call copy number variants on whole exome sequencing data. Nat Commun 2024; 15:132. [PMID: 38167256 PMCID: PMC10762021 DOI: 10.1038/s41467-023-44116-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Copy number variants (CNV) are shown to contribute to the etiology of several genetic disorders. Accurate detection of CNVs on whole exome sequencing (WES) data has been a long sought-after goal for use in clinics. This was not possible despite recent improvements in performance because algorithms mostly suffer from low precision and even lower recall on expert-curated gold standard call sets. Here, we present a deep learning-based somatic and germline CNV caller for WES data, named ECOLE. Based on a variant of the transformer architecture, the model learns to call CNVs per exon, using high-confidence calls made on matched WGS samples. We further train and fine-tune the model with a small set of expert calls via transfer learning. We show that ECOLE achieves high performance on human expert labelled data for the first time with 68.7% precision and 49.6% recall. This corresponds to precision and recall improvements of 18.7% and 30.8% over the next best-performing methods, respectively. We also show that the same fine-tuning strategy using tumor samples enables ECOLE to detect RT-qPCR-validated variations in bladder cancer samples without the need for a control sample. ECOLE is available at https://github.com/ciceklab/ECOLE .
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Affiliation(s)
- Berk Mandiracioglu
- Department of Computer and Communication Sciences, EPFL, Lausanne, Switzerland
| | - Furkan Ozden
- Department of Computer Science, Oxford University, Oxford, UK
| | - Gun Kaynar
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | | | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - A Ercument Cicek
- Department of Computer Engineering, Bilkent University, Ankara, Turkey.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, US.
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29
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Gupta S, Sholl LM, Yang Y, Osunkoya AO, Gordetsky JB, Cornejo KM, Michalova K, Maclean F, Dvindenko E, Snuderl M, Hirsch MS, Anderson WJ, Rowsey RA, Jimenez RE, Cheville JC, Sadow PM, Colecchia M, Ricci C, Ulbright TM, Berney DM, Acosta AM. Genomic analysis of spermatocytic tumors demonstrates recurrent molecular alterations in cases with malignant clinical behavior. J Pathol 2024; 262:50-60. [PMID: 37792634 DOI: 10.1002/path.6210] [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: 06/12/2023] [Revised: 08/03/2023] [Accepted: 08/24/2023] [Indexed: 10/06/2023]
Abstract
Spermatocytic tumor (ST) is a rare type of germ cell tumor that occurs exclusively in the postpubertal testis and typically affects elderly men. Most STs are benign, but rare cases exhibit aggressive clinical behavior, often in association with transition to sarcomatoid histology. Limited molecular analyses have been performed on STs; therefore, their genomic and epigenomic features remain incompletely described. Twenty-seven samples from 25 individual patients were analyzed with a combination of DNA sequencing panels, genomic methylation profiling, SNP array, isochromosome (12p) [i(12p)] FISH, and immunohistochemistry. The series included five metastasizing tumors (three with sarcomatoid transformation, one anaplastic, and one conventional) and 20 non-metastasizing tumors (14 anaplastic and six conventional). Anaplastic tumors comprised a monomorphic population of intermediate-sized neoplastic cells, as previously described. Multiomic analyses demonstrated that there were two genomic subgroups of STs: one with diploid genomes and hotspot RAS/RAF variants and the other with global ploidy shift and absence of recurrent mutations. Relative gain of chromosome 9 was a consistent finding in both subgroups. A comparison of metastasizing and non-metastasizing cases demonstrated that aggressive behavior was associated with the acquisition of pathogenic TP53 mutations and/or relative gains of 12p/i(12p). In cases with sarcomatoid transformation, TP53 mutations seem to underlie the transition to sarcomatoid histology. Genomic methylation analysis demonstrated that aggressive cases with gains of 12p cluster closer to pure seminomas than to STs without gains of 12p. In conclusion, STs include two genomic subgroups, characterized by global ploidy shifts without recurrent mutations and diploid genomes with RAS/RAF hotspot mutations, respectively. Biologic progression was associated with relative gains of 12p and TP53 mutations. The findings in STs with relative gains of 12p suggest that they may exhibit biologic characteristics akin to those seen in germ cell neoplasia in situ-related germ cell tumors rather than non-germ cell neoplasia in situ-derived STs. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sounak Gupta
- Department of Pathology, Mayo Clinic, Rochester, MN, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yiying Yang
- Department of Pathology, New York University, New York, NY, USA
| | - Adeboye O Osunkoya
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Kristine M Cornejo
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Fiona Maclean
- Department of Pathology, Douglass Hanly Moir Pathology, Macquarie University, Sydney, NSW, Australia
| | - Eugénia Dvindenko
- Department of Pathology, Instituto Português de Oncologia, Lisbon, Portugal
| | - Matija Snuderl
- Department of Pathology, New York University, New York, NY, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William J Anderson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ross A Rowsey
- Department of Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Peter M Sadow
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Maurizio Colecchia
- Department of Pathology, Universita Vita Salute San Raffaele, Milan, Italy
| | - Costantino Ricci
- Pathology Unit, Maggiore Hospital-AUSL Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | | | - Daniel M Berney
- Centre for Cancer Biomarkers & Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Andres Martin Acosta
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Indiana University, Indianapolis, IN, USA
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30
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Masood SH, Khan TA, Baloch AA, Hasan SM, Naqvi AM, Iqbal MUN. Association of Visfatin gene polymorphism with obesity related metabolic disorders among Pakistani population: a case control study. Sci Rep 2023; 13:23002. [PMID: 38155161 PMCID: PMC10754880 DOI: 10.1038/s41598-023-48402-z] [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: 04/04/2023] [Accepted: 11/26/2023] [Indexed: 12/30/2023] Open
Abstract
In recent years, the global prevalence of obesity and its associated metabolic disorders has reached alarming levels, presenting a significant challenge to public health worldwide. Visfatin, also known as pre-B cell colony-enhancing factor (PBEF) or nicotinamide phosphoribosyltransferase (NAMPT), is an adipokine that has been implicated in various physiological processes, including glucose homeostasis, lipid metabolism, and inflammation. The main objective of this proposed study is to find out the association between visfatin genetic variants and metabolic syndrome. The sample size of the study consisted of 300 blood samples (150 control and 150 cases). This study found that the genotypic frequency of visfatin SNPs, including rs2302559 (OD: 18.222; 95% CI 10.228-32.466; p-value < 0.001) and rs1215113036 (OD: 129.40; 95% CI 44.576-375.693; p-value < 0.001) were significantly associated with metabolic syndrome. Moreover, the frequency of the mutant alleles of both visfatin SNPs was found to be higher in patients with metabolic syndrome as compared to controls. Results of the current study indicate that people with any genetic variation of Visfatin, such as rs2302559 and rs1215113036, are more likely to develop metabolic syndrome. Visfatin genetic variants are linked to an increased risk of metabolic syndrome, implying it's role in disease pathophysiology.
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Affiliation(s)
- Sayyada Humaira Masood
- Department of Physiology, University of Karachi, Karachi, Pakistan.
- Al-Tibri Medical College and Hospital, Isra University Karachi Campus, Karachi, Pakistan.
| | | | - Akhter Ali Baloch
- National Institute of Diabetes and Endocrinology (NIDE), Dow University of Health Sciences (DUHS), Ojha Campus, Karachi, Pakistan
| | - Syed Muhammad Hasan
- National Institute of Diabetes and Endocrinology (NIDE), Dow University of Health Sciences (DUHS), Ojha Campus, Karachi, Pakistan
| | - Ali Muntazir Naqvi
- Al-Tibri Medical College and Hospital, Isra University Karachi Campus, Karachi, Pakistan
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31
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Ngom SI, Maski S, Rached B, Chouati T, Oliveira Correia L, Juste C, Meylheuc T, Henrissat B, El Fahime E, Amar M, Béra-Maillet C. Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes. Sci Rep 2023; 13:22785. [PMID: 38129471 PMCID: PMC10740013 DOI: 10.1038/s41598-023-49724-8] [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: 01/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Bacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius, re-identified as Bacillus paralicheniformis and Bacillus licheniformis, using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis. Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.
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Affiliation(s)
- Serigne Inssa Ngom
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Soufiane Maski
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Département de Biologie, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Bahia Rached
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Laboratoire de Chimie-Physique et Biotechnologies des Biomolécules et Matériaux/Equipe Microbiologie Biomolécules et Biotechnologies, Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Taha Chouati
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Lydie Oliveira Correia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, PAPPSO, 78350, Jouy-en-Josas, France
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Thierry Meylheuc
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, MIMA2, 78350, Jouy en Josas, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Elmostafa El Fahime
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Mohamed Amar
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
| | - Christel Béra-Maillet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco.
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Belkacem N, Deghmane AE, Taha MK. Biofilm formation by non-typeable Haemophilus influenzae confers resistance to complement-mediated clearance. J Infect Dis 2023:jiad584. [PMID: 38114092 DOI: 10.1093/infdis/jiad584] [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: 10/05/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
Biofilm formation is suggested to be associated with phenotype changes compared to planktonic form. We screened 1092 Haemophilus influenzae isolates for their genetic relationships and then selected 29 isolates from different genotypes and phenotypes and tested their ability to form biofilm. Our data showed a higher capacity of non-typeable isolates and particularly isolates from respiratory and genital infections to form biofilm compared to typeable isolates. This ability to form biofilm was also correlated with reduced deposition of the complement component C3b on biofilm-involved bacteria. These data suggest that the biofilm formation contributes to the virulence of non-typeable H. influenzae.
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Affiliation(s)
- Nouria Belkacem
- Institut Pasteur, Université Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
| | - Ala-Eddine Deghmane
- Institut Pasteur, Université Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
| | - Muhamed-Kheir Taha
- Institut Pasteur, Université Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
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Scholz SW, Moroz BE, Saez-Atienzar S, Chia R, Cahoon EK, Dalgard CL, Freedman DM, Pfeiffer RM. Association of cardiovascular disease management drugs with Lewy body dementia: a case-control study. Brain Commun 2023; 6:fcad346. [PMID: 38162907 PMCID: PMC10754316 DOI: 10.1093/braincomms/fcad346] [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: 10/19/2023] [Revised: 11/04/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Lewy body dementia is the second most common neurodegenerative dementia after Alzheimer's disease. Disease-modifying therapies for this disabling neuropsychiatric condition are critically needed. To identify drugs associated with the risk of developing Lewy body dementia, we performed a population-based case-control study of 148 170 US Medicare participants diagnosed with Lewy body dementia between 1 January 2008 and 31 December 2014 and of 1 253 043 frequency-matched controls. We estimated odds ratios and 95% confidence intervals for the association of Lewy body dementia risk with 1017 prescription drugs overall and separately for the three major racial groups (Black, Hispanic and White Americans). We identified significantly reduced Lewy body dementia risk associated with drugs used to treat cardiovascular diseases (anti-hypertensives: odds ratio = 0.72, 95% confidence interval = 0.70-0.74, P-value = 0; cholesterol-lowering agents: odds ratio = 0.85, 95% confidence interval = 0.83-0.87, P-value = 0; anti-diabetics: odds ratio = 0.83, 95% confidence interval = 0.62-0.72, P-value = 0). Notably, anti-diabetic medications were associated with a larger risk reduction among Black Lewy body dementia patients compared with other racial groups (Black: odds ratio = 0.67, 95% confidence interval = 0.62-0.72, P-value = 0; Hispanic: odds ratio = 0.86, 95% = 0.80-0.92, P-value = 5.16 × 10-5; White: odds ratio = 0.85, 95% confidence interval = 0.82-0.88, P-value = 0). To independently confirm the epidemiological findings, we looked for evidence of genetic overlap between Lewy body dementia and cardiovascular traits using whole-genome sequence data generated for 2591 Lewy body dementia patients and 4027 controls. Bivariate mixed modelling identified shared genetic risk between Lewy body dementia and low-density lipoprotein cholesterol levels, Type 2 diabetes and hypertension. By combining epidemiological and genomic data, we demonstrated that drugs treating cardiovascular diseases are associated with reduced Lewy body dementia risk, and these associations varied across racial groups. Future randomized clinical trials need to confirm our findings, but our data suggest that assiduous management of cardiovascular diseases may be beneficial in this understudied form of dementia.
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Affiliation(s)
- Sonja W Scholz
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian E Moroz
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sara Saez-Atienzar
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Elizabeth K Cahoon
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Daryl Michal Freedman
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruth M Pfeiffer
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Yang R, Ahmad S, Liu H, Xu Q, Yin C, Liu Y, Zhang H, Yan H. Biodegradation of Cholesterol by Enterococcus faecium YY01. Microorganisms 2023; 11:2979. [PMID: 38138122 PMCID: PMC10745435 DOI: 10.3390/microorganisms11122979] [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: 10/27/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Cholesterol (CHOL) is one of the risk factors causing the blockage of the arterial wall, atherosclerosis, coronary heart disease, and other serious cardiovascular diseases. Here, a promising bacterial strain for biodegrading CHOL was successfully isolated from the gut of healthy individuals and identified as Enterococcus faecium YY01 with an analysis of the 16S rDNA sequence. An initial CHOL of 1.0 g/L was reduced to 0.5 g/L in 5 days, and glucose and beef extract were found to be optimal carbon and nitrogen sources for the rapid growth of YY01, respectively. To gain further insight into the mechanisms underlying CHOL biodegradation, the draft genome of YY01 was sequenced using Illumina HiSeq. Choloylglycine hydrolase, acyltransferase, and alkyl sulfatase was encoded by gene0586, gene1890, and gene2442, which play crucial roles in converting 3α, 7α, 12α-trihydroxy-5β-choranic acid to choline-CoA and then choline-CoA to bile acid. Notably, choloylglycine hydrolase was closely related to the biosynthesis of both primary and secondary bile acid. The findings of this study provide valuable insights into the metabolism pathway of CHOL biodegradation by YY01 and offer a potential avenue for the development of bacterioactive drugs against hypercholesterolemia.
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Affiliation(s)
| | | | | | | | | | | | | | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (R.Y.); (S.A.); (H.L.); (Q.X.); (C.Y.); (Y.L.); (H.Z.)
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Nyamgerel N, Baasanmunkh S, Oyuntsetseg B, Bayarmaa GA, Erst A, Park I, Choi HJ. Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe. Sci Rep 2023; 13:22014. [PMID: 38086985 PMCID: PMC10716127 DOI: 10.1038/s41598-023-49381-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
Adonis mongolica is a threatened species that is endemic to Mongolia. It is a medicinal plant from the Adonis genus and has been used to treat heart diseases. However, the genomics and evolution of this species have not been thoroughly studied. We sequenced the first complete plastome of A. mongolica and compared it with ten Adonideae species to describe the plastome structure and infer phylogenetic relationships. The complete plastome of A. mongolica was 157,521 bp long and had a typical quadripartite structure with numerous divergent regions. The plastomes of Adonideae had relatively constant genome structures and sizes, except for those of Adonis. The plastome structure was consistent across Adonis. We identified a 44.8 kb large-scale inversion within the large single-copy region and rpl32 gene loss in the Adonis plastomes compared to other members of the Adonideae tribe. Additionally, Adonis had a smaller plastome size (156,917-157,603 bp) than the other genera within the tribe (159,666-160,940 bp), which was attributed to deletions of intergenic regions and partial and complete gene losses. These results suggested that an intramolecular mutation occurred in the ancestor of the Adonis genus. Based on the phylogenetic results, Adonis separated earlier than the other genera within the Adonideae tribe. The genome structures and divergences of specific regions in the Adonis genus were unique to the Adonideae tribe. This study provides fundamental knowledge for further genomic research in Mongolia and a better understanding of the evolutionary history of endemic plants.
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Affiliation(s)
- Nudkhuu Nyamgerel
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea
| | - Shukherdorj Baasanmunkh
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea
| | - Batlai Oyuntsetseg
- Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, 14201, Mongolia
| | - Gun-Aajav Bayarmaa
- Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, 14201, Mongolia
| | - Andrey Erst
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Science, Novosibirsk, 630090, Russia
| | - Inkyu Park
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea.
| | - Hyeok Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea.
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Liu Y, Li H, Ouyang Y, Zhang Y, Pan P. Exploration of the role of oxidative stress-related genes in LPS-induced acute lung injury via bioinformatics and experimental studies. Sci Rep 2023; 13:21804. [PMID: 38071255 PMCID: PMC10710410 DOI: 10.1038/s41598-023-49165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
During the progression of acute lung injury (ALI), oxidative stress and inflammatory responses always promote each other. The datasets analyzed in this research were acquired from the Gene Expression Omnibus (GEO) database. The Weighted Gene Co-expression Network Analysis (WGCNA) and limma package were used to obtain the ALI-related genes (ALIRGs) and differentially expressed genes (DEGs), respectively. In total, two biological markers (Gch1 and Tnfaip3) related to oxidative stress were identified by machine learning algorithms, Receiver Operator Characteristic (ROC), and differential expression analyses. The area under the curve (AUC) value of biological markers was greater than 0.9, indicating an excellent power to distinguish between ALI and control groups. Moreover, 15 differential immune cells were selected between the ALI and control samples, and they were correlated to biological markers. The transcription factor (TF)-microRNA (miRNA)-Target network was constructed to explore the potential regulatory mechanisms. Finally, based on the quantitative reverse transcription polymerase chain reaction (qRT-PCR), the expression of Gch1 and Tnfaip3 was significantly higher in ALI lung tissue than in healthy controls. In conclusion, the differences in expression profiles between ALI and normal controls were found, and two biological markers were identified, providing a research basis for further understanding the pathogenesis of ALI.
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Affiliation(s)
- Yuanshui Liu
- Department of Emergency Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, 570311, People's Republic of China.
- Department of Respiratory Medicine, Key Cite of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.
| | - Huamei Li
- Department of Ultrasound, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, 570311, People's Republic of China.
| | - Yanhong Ouyang
- Department of Emergency Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, 570311, People's Republic of China
| | - Yan Zhang
- Department of Respiratory Medicine, Key Cite of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.
| | - Pinhua Pan
- Department of Respiratory Medicine, Key Cite of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.
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Atrian-Afiani F, Berger B, Draxl C, Sölkner J, Mészáros G. Selective Sweeps in the Austrian Turopolje and Other Commercial Pig Populations. Animals (Basel) 2023; 13:3749. [PMID: 38136787 PMCID: PMC10741191 DOI: 10.3390/ani13243749] [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: 10/16/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
The goal of our study was to identify signatures of selection in the Turopolje pigs and other commercial pig breeds. We conducted a comprehensive analysis of five datasets, including one local pig breed (Turopolje) and four commercial pig breeds (Large White, Landrace, Pietrain, and Duroc), using strict quality control measures. Our final dataset consisted of 485 individuals and 54,075 single nucleotide polymorphisms (SNPs). To detect selection signatures within these pig breeds, we utilized the XP-EHH and XP-nSL methodologies, which allowed us to identify candidate genes that have been subject to positive selection. Our analysis consistently highlighted the PTBP2 and DPYD genes as commonly targeted by selection in the Turopolje breed. DPYD is associated with muscular development in pigs and other species and PTBP2 emerges as one of the potential genes linked to seminal characteristics. Furthermore, in the Large White breed, a number of genes were detected with the two methods, such as ATP1A1, CASQ2, CD2, IGSF3, MAB21L3, NHLH2, SLC22A15, VANGL1. In the Duroc breed, a different set of genes was detected, such as ARSB, BHMT, BHMT2, DMGDH, JMY. The function of these genes was related to body weight, production efficiency and meat quality, average daily gain, and other similar traits. Overall, our results have identified a number of genomic regions that are under selective pressure between local and commercial pig breeds. This information can help to improve our understanding of the mechanisms underlying pig breeding, and ultimately contribute to the development of more efficient and sustainable pig production practices. Our study highlights the power of using multiple genomic methodologies to detect genetic signatures of selection, and provides important insights into the genetic diversity of pig breeds.
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Affiliation(s)
- Farzad Atrian-Afiani
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Vienna, 1180 Vienna, Austria; (F.A.-A.); (J.S.)
| | - Beate Berger
- Institut für Biologische Landwirtschaft und Biodiversität der Nutztiere, HBLFA Raumberg-Gumpenstein 2, 4600 Thalheim bei Wels, Austria;
| | - Christian Draxl
- Österreichische Schweineprüfanstalt GmbH, 2004 Streitdorf, Austria;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Vienna, 1180 Vienna, Austria; (F.A.-A.); (J.S.)
| | - Gábor Mészáros
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Vienna, 1180 Vienna, Austria; (F.A.-A.); (J.S.)
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Kim J, Moon JW, Kim GR, Kim W, Hu HJ, Jo WJ, Baek SK, Sung GH, Park JH, Park JH. Safety tests and clinical research on buccal and nasal microneedle swabs for genomic analysis. Front Bioeng Biotechnol 2023; 11:1296832. [PMID: 38116201 PMCID: PMC10729317 DOI: 10.3389/fbioe.2023.1296832] [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: 09/19/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023] Open
Abstract
Conventional swabs have been used as a non-invasive method to obtain samples for DNA analysis from the buccal and the nasal mucosa. However, swabs may not always collect pure enough genetic material. In this study, buccal and nasal microneedle swab is developed to improve the accuracy and reliability of genomic analysis. A cytotoxicity test, a skin sensitivity test, and a skin irritation test are conducted with microneedle swabs. Polymer microneedle swabs meet the safety requirements for clinical research and commercial use. When buccal and nasal microneedle swabs are used, the amount of genetic material obtained is greater than that from commercially available swabs, and DNA purity is also high. The comparatively short microneedle swab (250 μm long) cause almost no pain to all 25 participants. All participants also report that the microneedle swabs are very easy to use. When genotypes are compared at five SNP loci from blood of a participant and from that person's buccal or nasal microneedle swab, the buccal and nasal microneedle swabs show 100% concordance for all five SNP genotypes. Microneedle swabs can be effectively used for genomic analysis and prevention through genomic analysis, so the utilization of microneedle swabs is expected to be high.
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Affiliation(s)
- JeongHyeon Kim
- Department of Bionano Technology and Gachon BioNano Research Institute, Gachon University, Seongnam, Republic of Korea
| | | | | | - Wonsub Kim
- Endomics Inc, Seongnam, Republic of Korea
| | - Hae-Jin Hu
- Endomics Inc, Seongnam, Republic of Korea
| | - Won-Jun Jo
- QuadMedicine R&D Centre, QuadMedicine Co. Ltd., Seongnam, Republic of Korea
| | - Seung-Ki Baek
- QuadMedicine R&D Centre, QuadMedicine Co. Ltd., Seongnam, Republic of Korea
| | - Gil-Hwan Sung
- QuadMedicine R&D Centre, QuadMedicine Co. Ltd., Seongnam, Republic of Korea
| | - Jung Ho Park
- Department of Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jung-Hwan Park
- Department of Bionano Technology and Gachon BioNano Research Institute, Gachon University, Seongnam, Republic of Korea
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Zhou W, Jin Y, Teng G, Chen W, Chen Y, Luo Q, Xiao Y. Comparative analysis of genomic characteristics, virulence and fitness of community-associated Staphylococcus aureus ST121 clone causing fatal diseases in China and other CA-MRSA clones. Virulence 2023; 14:2242547. [PMID: 37534993 PMCID: PMC10402838 DOI: 10.1080/21505594.2023.2242547] [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] [Indexed: 08/04/2023] Open
Abstract
The increasing rate of community-associated Staphylococcus aureus (CA-SA) worldwide has aroused global public concern for decades. Although ST121 clone is one of the prevalent CA-SA in China, there is still limited knowledge about it. In this study, we conducted a genomic analysis of 28 CA-SA ST121 isolates from severe bloodstream infection cases and 175 ST121 isolates from the public database. Phylogenetic analysis revealed the consistency and the complexity of global ST121 lineages, and suggested potential cross-country even cross-continental transmission of ST121 isolates. By investigating the virulence and fitness between ST121-CA-methicillin-resistant SA (CA-MRSA) and other CA-MRSA clones, we found that ST121-MRSA exhibits virulence comparable to the highly virulent USA300 clone, exceeding that of the predominant CA-MRSA lineage ST59 in China and the other American CA-MRSA clone MW2. Notably, based on analyses of virulence genes, eta, etb, edin-C and egc were only found in ST121, suggesting that the high virulence of ST121 may be attributed to the combination of these virulence factors encoded by mobile genetic elements. However, results of experiments in mice nasal and human alveolar epithelial cells showed that the colonization capacity of ST121 is much lower than that of other clones. Moreover, ST121-MRSA displayed much lower acid tolerance, suggesting that ST121-MRSA may not have such capacity to achieve the epidemiological success of other CA-MRSA clones and become the dominant lineage. Our findings expand current understanding of the epidemiology and pathogenicity of the hypervirulent ST121 clone, and highlight the importance of colonization capacity and environmental adaption in MRSA epidemiological success.
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Affiliation(s)
- Wangxiao Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Ye Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Gaoqin Teng
- Department of General Intensive Care Unit, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Weiwei Chen
- Department of Laboratory Medicine, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, People's Republic of China
- Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, China
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Zhong L, Zhang M, Sun L, Yang Y, Wang B, Yang H, Shen Q, Xia Y, Cui J, Hang H, Ren Y, Pang B, Deng X, Zhan Y, Li H, Zhou Z. Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century. Nat Commun 2023; 14:7706. [PMID: 38001084 PMCID: PMC10673917 DOI: 10.1038/s41467-023-43528-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Core genome multilocus sequence typing (cgMLST) is commonly used to classify bacterial strains into different types, for taxonomical and epidemiological applications. However, cgMLST schemes require central databases for the nomenclature of new alleles and sequence types, which must be synchronized worldwide and involve increasingly intensive calculation and storage demands. Here, we describe a distributed cgMLST (dcgMLST) scheme that does not require a central database of allelic sequences and apply it to study evolutionary patterns of epidemic and endemic strains of the genus Neisseria. We classify 69,994 worldwide Neisseria strains into multi-level clusters that assign species, lineages, and local disease outbreaks. We divide Neisseria meningitidis into 168 endemic lineages and three epidemic lineages responsible for at least 9 epidemics in the past century. According to our analyses, the epidemic and endemic lineages experienced very different population dynamics in the past 100 years. Epidemic lineages repetitively emerged from endemic lineages, disseminated worldwide, and apparently disappeared rapidly afterward. We propose a stepwise model for the evolutionary trajectory of epidemic lineages in Neisseria, and expect that the development of similar dcgMLST schemes will facilitate epidemiological studies of other bacterial pathogens.
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Affiliation(s)
- Ling Zhong
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, 215123, China
- Key Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, Soochow University, Suzhou, 215123, China
| | - Menghan Zhang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Libing Sun
- Department of Pathology, East District of Suzhou Municipal Hospital, Suzhou, 215000, China
| | - Yu Yang
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, 215123, China
| | - Bo Wang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Haibing Yang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Qiang Shen
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Yu Xia
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Jiarui Cui
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Hui Hang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Yi Ren
- Iotabiome Biotechnology Inc, Suzhou, 215000, China
| | - Bo Pang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiangyu Deng
- Center for Food Safety, University of Georgia, Griffin, GA, USA
| | - Yahui Zhan
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China.
| | - Heng Li
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, 215123, China.
- Key Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, Soochow University, Suzhou, 215123, China.
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Soochow University, Suzhou, 215123, China.
| | - Zhemin Zhou
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, 215123, China.
- Key Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, Soochow University, Suzhou, 215123, China.
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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Ramos-Mandujano G, Grünberg R, Zhang Y, Bi C, Guzmán-Vega FJ, Shuaib M, Gorchakov RV, Xu J, Tehseen M, Takahashi M, Takahashi E, Dada A, Ahmad AN, Hamdan SM, Pain A, Arold ST, Li M. An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing. Sci Rep 2023; 13:20349. [PMID: 37990068 PMCID: PMC10663496 DOI: 10.1038/s41598-023-47190-w] [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: 05/09/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extraction and pathogen diagnosis, which uses reagents almost entirely produced in-house. This platform integrates our methods for self-manufacturing magnetic nanoparticles and qRT-PCR reagents-both of which have received regulatory approval for clinical use-with an in-house, open-source robotic extraction protocol. It also incorporates our "Nanopore Sequencing of Isothermal Rapid Viral Amplification for Near Real-time Analysis" (NIRVANA) technology, designed for tracking SARS-CoV-2 mutations and variants. The platform exhibits high reproducibility and consistency without cross-contamination, and its limit of detection, sensitivity, and specificity are comparable to commercial assays. Automated NIRVANA effectively identifies circulating SARS-CoV-2 variants. Our in-house, cost-effective reagents, automated diagnostic workflows, and portable genomic surveillance strategies provide a scalable and rapid solution for COVID-19 diagnosis and variant tracking, essential for current and future pandemic responses.
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Affiliation(s)
- Gerardo Ramos-Mandujano
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Raik Grünberg
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Yingzi Zhang
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Chongwei Bi
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Francisco J Guzmán-Vega
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Muhammad Shuaib
- Pathogen Genomics Laboratory, Bioscience Program, Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Rodion V Gorchakov
- Health, Safety and Environment Department, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Jinna Xu
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Masateru Takahashi
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Etsuko Takahashi
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Ashraf Dada
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
- College of Medicine, Al Faisal University, Riyadh, Kingdom of Saudi Arabia
| | - Adeel Nazir Ahmad
- KAUST Health, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Arnab Pain
- Pathogen Genomics Laboratory, Bioscience Program, Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Stefan T Arold
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
| | - Mo Li
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
- Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
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Lu Y, Lee J, Li J, Allu SR, Wang J, Kim H, Bullaughey KL, Fisher SA, Nordgren CE, Rosario JG, Anderson SA, Ulyanova AV, Brem S, Chen HI, Wolf JA, Grady MS, Vinogradov SA, Kim J, Eberwine J. CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential. Nat Commun 2023; 14:7346. [PMID: 37963886 PMCID: PMC10645931 DOI: 10.1038/s41467-023-43158-6] [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: 05/30/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023] Open
Abstract
Genomic DNA (gDNA) undergoes structural interconversion between single- and double-stranded states during transcription, DNA repair and replication, which is critical for cellular homeostasis. We describe "CHEX-seq" which identifies the single-stranded DNA (ssDNA) in situ in individual cells. CHEX-seq uses 3'-terminal blocked, light-activatable probes to prime the copying of ssDNA into complementary DNA that is sequenced, thereby reporting the genome-wide single-stranded chromatin landscape. CHEX-seq is benchmarked in human K562 cells, and its utilities are demonstrated in cultures of mouse and human brain cells as well as immunostained spatially localized neurons in brain sections. The amount of ssDNA is dynamically regulated in response to perturbation. CHEX-seq also identifies single-stranded regions of mitochondrial DNA in single cells. Surprisingly, CHEX-seq identifies single-stranded loci in mouse and human gDNA that catalyze porphyrin metalation in vitro, suggesting a catalytic activity for genomic ssDNA. We posit that endogenous DNA enzymatic activity is a function of genomic ssDNA.
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Affiliation(s)
- Youtao Lu
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jaehee Lee
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jifen Li
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Srinivasa Rao Allu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jinhui Wang
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - HyunBum Kim
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kevin L Bullaughey
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephen A Fisher
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - C Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jean G Rosario
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stewart A Anderson
- Department of Psychiatry, Children's Hospital of Philadelphia, ARC 517, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Alexandra V Ulyanova
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - H Isaac Chen
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John A Wolf
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - M Sean Grady
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sergei A Vinogradov
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Simmons BC, Rhodes J, Rogers TR, Verweij PE, Abdolrasouli A, Schelenz S, Hemmings SJ, Talento AF, Griffin A, Mansfield M, Sheehan D, Bosch T, Fisher MC. Genomic Epidemiology Identifies Azole Resistance Due to TR 34/L98H in European Aspergillus fumigatus Causing COVID-19-Associated Pulmonary Aspergillosis. J Fungi (Basel) 2023; 9:1104. [PMID: 37998909 PMCID: PMC10672581 DOI: 10.3390/jof9111104] [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: 09/30/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/25/2023] Open
Abstract
Aspergillus fumigatus has been found to coinfect patients with severe SARS-CoV-2 virus infection, leading to COVID-19-associated pulmonary aspergillosis (CAPA). The CAPA all-cause mortality rate is approximately 50% and may be complicated by azole resistance. Genomic epidemiology can help shed light on the genetics of A. fumigatus causing CAPA, including the prevalence of resistance-associated alleles. We present a population genomic analysis of 21 CAPA isolates from four European countries with these isolates compared against 240 non-CAPA A. fumigatus isolates from a wider population. Bioinformatic analysis and antifungal susceptibility testing were performed to quantify resistance and identify possible genetically encoded azole-resistant mechanisms. The phylogenetic analysis of the 21 CAPA isolates showed that they were representative of the wider A. fumigatus population with no obvious clustering. The prevalence of phenotypic azole resistance in CAPA was 14.3% (n = 3/21); all three CAPA isolates contained a known resistance-associated cyp51A polymorphism. The relatively high prevalence of azole resistance alleles that we document poses a probable threat to treatment success rates, warranting the enhanced surveillance of A. fumigatus genotypes in these patients. Furthermore, potential changes to antifungal first-line treatment guidelines may be needed to improve patient outcomes when CAPA is suspected.
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Affiliation(s)
- Benjamin C. Simmons
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK; (J.R.); (S.J.H.); (M.C.F.)
- UK Health Security Agency, London EP14 4PU, UK
| | - Johanna Rhodes
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK; (J.R.); (S.J.H.); (M.C.F.)
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands;
| | - Thomas R. Rogers
- Department of Clinical Microbiology, St. James’ Hospital Campus, Trinity College Dublin, D08 NHY1 Dublin, Ireland; (T.R.R.); (A.F.T.); (M.M.); (D.S.)
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands;
- Radboudumc-CWZ Center of Expertise for Mycology, Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
- Center for Infectious Disease Research, Diagnostics and Laboratory Surveillance, National for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, The Netherlands;
| | - Alireza Abdolrasouli
- Department of Infectious Diseases, Imperial College London, London W2 1NY, UK;
- Department of Infectious Diseases, King’s College Hospital, London SE5 9RS, UK
| | - Silke Schelenz
- Infection Sciences, King’s College Hospital, London SE5 9RS, UK;
- School of Immunology & Microbial Sciences, King’s College London, London WC2R 2LS, UK
| | - Samuel J. Hemmings
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK; (J.R.); (S.J.H.); (M.C.F.)
| | - Alida Fe Talento
- Department of Clinical Microbiology, St. James’ Hospital Campus, Trinity College Dublin, D08 NHY1 Dublin, Ireland; (T.R.R.); (A.F.T.); (M.M.); (D.S.)
- Department of Microbiology, Our Lady of Lourdes Hospital, A92 VW28 Drogheda, Ireland
- Department of Microbiology, Royal College of Surgeons, D02 YN77 Dublin, Ireland
| | - Auveen Griffin
- Department of Microbiology, St. James’ Hospital, D08 NHY1 Dublin, Ireland;
| | - Mary Mansfield
- Department of Clinical Microbiology, St. James’ Hospital Campus, Trinity College Dublin, D08 NHY1 Dublin, Ireland; (T.R.R.); (A.F.T.); (M.M.); (D.S.)
| | - David Sheehan
- Department of Clinical Microbiology, St. James’ Hospital Campus, Trinity College Dublin, D08 NHY1 Dublin, Ireland; (T.R.R.); (A.F.T.); (M.M.); (D.S.)
| | - Thijs Bosch
- Center for Infectious Disease Research, Diagnostics and Laboratory Surveillance, National for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, The Netherlands;
| | - Matthew C. Fisher
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK; (J.R.); (S.J.H.); (M.C.F.)
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Li Y, Yun H, Chen R, Jiao N, Zheng Q, Yang Y, Zhang R. Characterization of a Vibriophage Infecting Pathogenic Vibrio harveyi. Int J Mol Sci 2023; 24:16202. [PMID: 38003392 PMCID: PMC10671443 DOI: 10.3390/ijms242216202] [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: 10/14/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Bacterial diseases caused by Vibrio spp. are prevalent in aquaculture and can lead to high mortality rates among aquatic species and significant economic losses. With the increasing emergence of multidrug-resistant Vibrio strains, phage therapy is being explored as a potential alternative to antibiotics for biocontrol of infectious diseases. Here, a new lytic phage named vB_VhaS_R21Y (R21Y) was isolated against Vibrio harveyi BVH1 obtained from seawater from a scallop-farming area in Rongcheng, China. Its morphology, infection cycle, lytic profile, phage stability, and genetic features were characterized. Transmission electronic microscopy indicated that R21Y is siphovirus-like, comprising an icosahedral head (diameter 73.31 ± 2.09 nm) and long noncontractile tail (205.55 ± 0.75 nm). In a one-step growth experiment, R21Y had a 40-min latent period and a burst size of 35 phage particles per infected cell. R21Y was highly species-specific in the host range test and was relatively stable at pH 4-10 and 4-55 °C. Genomic analysis showed that R21Y is a double-stranded DNA virus with a genome size of 82,795 bp and GC content of 47.48%. Its high tolerance and lytic activity indicated that R21Y may be a candidate for phage therapy in controlling vibriosis in aquacultural systems.
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Affiliation(s)
- Yingying Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.L.); (H.Y.); (R.C.); (N.J.); (Q.Z.)
- Institute for Advanced Study, Shenzhen University, Shenzhen 518061, China
| | - Huayi Yun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.L.); (H.Y.); (R.C.); (N.J.); (Q.Z.)
| | - Ruo Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.L.); (H.Y.); (R.C.); (N.J.); (Q.Z.)
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.L.); (H.Y.); (R.C.); (N.J.); (Q.Z.)
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (Y.L.); (H.Y.); (R.C.); (N.J.); (Q.Z.)
| | - Yunlan Yang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518061, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518061, China
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Furlan JPR, Stehling EG. Genomic Insights into Pluralibacter gergoviae Sheds Light on Emergence of a Multidrug-Resistant Species Circulating between Clinical and Environmental Settings. Pathogens 2023; 12:1335. [PMID: 38003800 PMCID: PMC10675545 DOI: 10.3390/pathogens12111335] [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: 09/15/2023] [Revised: 10/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Pluralibacter gergoviae is a member of the Enterobacteriaceae family that has been reported sporadically. Although P. gergoviae strains exhibiting multidrug-resistant profiles have been identified an in-depth genomic analysis focusing on antimicrobial resistance (AMR) has been lacking, and was therefore performed in this study. Forty-eight P. gergoviae strains, isolated from humans, animals, foods, and the environment during 1970-2023, were analyzed. A large number of single-nucleotide polymorphisms were found, indicating a highly diverse population. Whilst P. gergoviae strains were found to be circulating at the One Health interface, only human and environmental strains exhibited multidrug resistance genotypes. Sixty-one different antimicrobial resistance genes (ARGs) were identified, highlighting genes encoding mobile colistin resistance, carbapenemases, and extended-spectrum β-lactamases. Worryingly, the co-occurrence of mcr-9.1, blaKPC-2, blaCTX-M-9, and blaSHV-12, as well as mcr-10.1, blaNDM-5, and blaSHV-7, was detected. Plasmid sequences were identified as carrying clinically important ARGs, evidencing IncX3 plasmids harboring blaKPC-2, blaNDM-5, or blaSHV-12 genes. Virulence genotyping underlined P. gergoviae as being a low-virulence species. In this regard, P. gergoviae is emerging as a new multidrug-resistant species belonging to the Enterobacteriaceae family. Therefore, continuous epidemiological genomic surveillance of P. gergoviae is required.
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Affiliation(s)
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil;
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Benabdallah NS, Dalal V, Scott RW, Marcous F, Sotiriou A, Kommoss FKF, Pejkovska A, Gaspar L, Wagner L, Sánchez-Rivera FJ, Ta M, Thornton S, Nielsen TO, Underhill TM, Banito A. Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stability. Nat Struct Mol Biol 2023; 30:1640-1652. [PMID: 37735617 PMCID: PMC10643139 DOI: 10.1038/s41594-023-01096-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
Abstract
The SS18-SSX fusion drives oncogenic transformation in synovial sarcoma by bridging SS18, a member of the mSWI/SNF (BAF) complex, to Polycomb repressive complex 1 (PRC1) target genes. Here we show that the ability of SS18-SSX to occupy H2AK119ub1-rich regions is an intrinsic property of its SSX C terminus, which can be exploited by fusion to transcriptional regulators beyond SS18. Accordingly, SS18-SSX recruitment occurs in a manner that is independent of the core components and catalytic activity of BAF. Alternative SSX fusions are also recruited to H2AK119ub1-rich chromatin and reproduce the expression signatures of SS18-SSX by engaging with transcriptional activators. Variant Polycomb repressive complex 1.1 (PRC1.1) acts as the main depositor of H2AK119ub1 and is therefore required for SS18-SSX occupancy. Importantly, the SSX C terminus not only depends on H2AK119ub1 for localization, but also further increases it by promoting PRC1.1 complex stability. Consequently, high H2AK119ub1 levels are a feature of murine and human synovial sarcomas. These results uncover a critical role for SSX-C in mediating gene deregulation in synovial sarcoma by providing specificity to chromatin and further enabling oncofusion binding by enhancing PRC1.1 stability and H2AK119ub1 deposition.
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Affiliation(s)
- Nezha S Benabdallah
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vineet Dalal
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - R Wilder Scott
- Department of Cellular and Physiological Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Fady Marcous
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Afroditi Sotiriou
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix K F Kommoss
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Anastasija Pejkovska
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ludmila Gaspar
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lena Wagner
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Francisco J Sánchez-Rivera
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY, USA
| | - Monica Ta
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Research Institute and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Shelby Thornton
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Research Institute and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Torsten O Nielsen
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Research Institute and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - T Michael Underhill
- Department of Cellular and Physiological Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ana Banito
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Balta KY, Welch S, Vincent M, Breadner D. Near 5-year survival in metastatic pancreatic cancer patient with ROS1 rearrangement, HER2 amplification, and KRAS G12C mutation-a case report. J Gastrointest Oncol 2023; 14:2273-2278. [PMID: 37969830 PMCID: PMC10643575 DOI: 10.21037/jgo-23-190] [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: 05/10/2023] [Accepted: 08/31/2023] [Indexed: 11/17/2023] Open
Abstract
Background Pancreatic cancer is a significant cause of cancer-related deaths in Canada. Although it is less common than other cancers, the mortality rate has remained high and stable since 1984, with a five-year net survival rate being the lowest of 23 reported cancers. The limited options for detection and treatment contribute to the high mortality rate. A developing area of treatment is tumour site agnostic targeted therapy, where patients' cancer is treated based on genomic alterations that are amenable to targeted agents, regardless of where the tumour originated. Case Description A 52-year-old man with no prior medical history presented with anemia, intermittent fatigue, post-prandial indigestion, and bloating, and 8-10 lbs of unintentional weight loss over a 1-year period. A computed tomography scan of the abdomen revealed pancreatic ductal adenocarcinoma and diffuse liver metastasis. He received multiple local and non-targeted systemic therapies. Serial genomic analyses sequentially revealed c-ros oncogene 1 (ROS1) receptor tyrosine kinase rearrangement, human epidermal growth factor receptor 2 (HER2) amplification, and Kirsten rat sarcoma virus (KRAS) G12C mutation throughout his journey, none of which were present at diagnosis. Each new genomic alteration prompted treatment change. Concurrent with systemic therapy, the patient also received numerous local treatments, including hepatic transarterial chemoembolization, Yttrium 90, Whipple procedure, stereotactic body radiation therapy, and CyberKnife. Over the course of the disease, metastases were found in the lungs, brain, and kidneys. Despite this, the patient had periods of remarkable response and quality of life evidenced by his cycling tour of France. However, nearly five years from diagnosis, the patient elected to pursue supportive care and died from his cancer. Conclusions This case report demonstrates the importance of repeat genomic analyses in the treatment of advanced cancer and timely access to targeted therapy. The clinical impact of utilizing a tumor-agnostic treatment approach based on these genomic alterations has the potential to yield a strong response both in survival and quality of life.
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Affiliation(s)
- Kaan Y. Balta
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - Mark Vincent
- London Regional Cancer Program, London, ON, Canada
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Recipon M, Agniel R, Leroy-Dudal J, Fritz T, Carreiras F, Hermitte F, Hubac S, Gallet O, Kellouche S. Targeting cell-derived markers to improve the detection of invisible biological traces for the purpose of genetic-based criminal identification. Sci Rep 2023; 13:18105. [PMID: 37872292 PMCID: PMC10593828 DOI: 10.1038/s41598-023-45366-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/18/2023] [Indexed: 10/25/2023] Open
Abstract
At a crime scene, investigators are faced with a multitude of traces. Among them, biological traces are of primary interest for the rapid genetic-based identification of individuals. "Touch DNA" consists of invisible biological traces left by the simple contact of a person's skin with objects. To date, these traces remain undetectable with the current methods available in the field. This study proposes a proof-of-concept for the original detection of touch DNA by targeting cell-derived fragments in addition to DNA. More specifically, adhesive-structure proteins (laminin, keratin) as well as carbohydrate patterns (mannose, galactose) have been detected with keratinocyte cells derived from a skin and fingermark touch-DNA model over two months in outdoor conditions. Better still, this combinatory detection strategy is compatible with DNA profiling. This proof-of-concept work paves the way for the optimization of tools that can detect touch DNA, which remains a real challenge in helping investigators and the delivery of justice.
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Affiliation(s)
- Mathilde Recipon
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe, (EA1391), Groupe Matrice Extracellulaire et Physiopathologie (MECuP), Institut des Matériaux, I-MAT (FD4122), CY Cergy Paris Université, Neuville sur Oise, France.
- Institut de Recherche Criminelle de la Gendarmerie Nationale, Cergy-Pontoise, France.
| | - Rémy Agniel
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe, (EA1391), Groupe Matrice Extracellulaire et Physiopathologie (MECuP), Institut des Matériaux, I-MAT (FD4122), CY Cergy Paris Université, Neuville sur Oise, France
| | - Johanne Leroy-Dudal
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe, (EA1391), Groupe Matrice Extracellulaire et Physiopathologie (MECuP), Institut des Matériaux, I-MAT (FD4122), CY Cergy Paris Université, Neuville sur Oise, France
| | - Thibaud Fritz
- Institut de Recherche Criminelle de la Gendarmerie Nationale, Cergy-Pontoise, France
| | - Franck Carreiras
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe, (EA1391), Groupe Matrice Extracellulaire et Physiopathologie (MECuP), Institut des Matériaux, I-MAT (FD4122), CY Cergy Paris Université, Neuville sur Oise, France
| | - Francis Hermitte
- Institut de Recherche Criminelle de la Gendarmerie Nationale, Cergy-Pontoise, France
| | - Sylvain Hubac
- Institut de Recherche Criminelle de la Gendarmerie Nationale, Cergy-Pontoise, France
| | - Olivier Gallet
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe, (EA1391), Groupe Matrice Extracellulaire et Physiopathologie (MECuP), Institut des Matériaux, I-MAT (FD4122), CY Cergy Paris Université, Neuville sur Oise, France
| | - Sabrina Kellouche
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe, (EA1391), Groupe Matrice Extracellulaire et Physiopathologie (MECuP), Institut des Matériaux, I-MAT (FD4122), CY Cergy Paris Université, Neuville sur Oise, France
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Mehmetoğlu E, Kaymaz Y, Ateş D, Kahraman A, Tanyolaç MB. The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species. Sci Rep 2023; 13:17871. [PMID: 37857674 PMCID: PMC10587350 DOI: 10.1038/s41598-023-44599-1] [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: 02/28/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
The chloroplast (cp) genome is an adequate genomic resource to investigate evolutionary relationships among plant species and it carries marker genes available for species identification. The Cicer reticulatum is one of perennial species as the progenitor of cultivated chickpeas. Although a large part of the land plants has a quadruple chloroplast genome organization, the cp genome of C. reticulatum consists of one LSC (Large Single Copy Region), one SSC (Small Single Copy Region), and one IR (Inverted Repeat) region, which indicates that it has an untypical and unique structure. This type of chloroplast genome belongs to the IR-lacking clade. Chloroplast DNA (cpDNA) was extracted from fresh leaves using a high salt-based protocol and sequencing was performed using DNA Nanoball Sequencing technology. The comparative analysis employed between the species to examine genomic differences and gene homology. The study also included codon usage frequency analysis, hotspot divergence analysis, and phylogenetic analysis using various bioinformatics tools. The cp genome of C. reticulatum was found 125,794 bp in length, with an overall GC content of 33.9%. With a total of 79 protein-coding genes, 34 tRNA genes, and 4 rRNA genes. Comparative genomic analysis revealed 99.93% similarity between C. reticulatum and C. arietinum. Phylogenetic analysis further indicated that the closest evolutionary relative to C. arietinum was C. reticulatum, whereas the previously sequenced wild Cicer species displayed slight distinctions across their entire coding regions. Several genomic regions, such as clpP and ycf1, were found to exhibit high nucleotide diversity, suggesting their potential utility as markers for investigating the evolutionary relationships within the Cicer genus. The first complete cp genome sequence of C. reticulatum will provide novel insights for future genetic research on Cicer crops.
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Affiliation(s)
- Ezgi Mehmetoğlu
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Yasin Kaymaz
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Duygu Ateş
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Abdullah Kahraman
- Faculty of Agriculture, Department of Field Crops, Harran University, S. Urfa, 64000, Şanlıurfa, Turkey
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Wen Y, Dong Y, Yi L, Yang G, Xiao M, Li Q, Zhao C, Ye D, Yao Y. Anlotinib combined with pembrolizumab as first-line treatment for advanced pulmonary sarcomatoid carcinoma: a case report and literature review. Front Oncol 2023; 13:1241475. [PMID: 37920159 PMCID: PMC10618617 DOI: 10.3389/fonc.2023.1241475] [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: 06/16/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023] Open
Abstract
Pulmonary sarcomatoid carcinoma (PSC) is an uncommon variant of non-small cell lung cancer (NSCLC), known for its unfavorable prognosis. Previous studies have elucidated that PSC generally exhibits a significant expression of programmed death-ligand 1 (PD-L1), an elevated tumor mutation burden, and marked vascular invasion. These factors imply the possible effectiveness of treatments like immunotherapy and anti-angiogenic therapy. The subject of this case was a 65-year-old male diagnosed with advanced PSC, characterized by high PD-L1 expression and devoid of known driver gene mutations. Owing to the restrictions imposed by the COVID-19 pandemic, the patient initially underwent home-based treatment with anlotinib, which led to symptomatic improvement after a single treatment cycle. Subsequent hospitalization allowed for the administration of anlotinib plus Pembrolizumab, resulting in a partial response. Radiotherapy was necessitated due to local disease progression. But after 15 cycles of treatment with Pembrolizumab, hyperprogression was observed. The patient's overall survival spanned 14 months, with no evident adverse reactions to the medications. Genomic analysis revealed potential associations between treatment efficacy and mutations in the TP53, NF1, and MET genes. This case underscores the effectiveness and safety of a first-line treatment regimen combining pan-target anti-angiogenic therapy (anlotinib) with anti-tumor immunotherapy.
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Affiliation(s)
- Yingmei Wen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yi Dong
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lina Yi
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Guifang Yang
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mengxia Xiao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Oncology, Yichun People's Hospital, Yichun, China
| | - Qingqing Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chen Zhao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Dafu Ye
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yi Yao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Provincial Research Center for Precision Medicine of Cancer, Wuhan, China
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