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Podgrajsek R, Hodzic A, Stimpfel M, Kunej T, Peterlin B. Insight into the complexity of male infertility: a multi-omics review. Syst Biol Reprod Med 2024; 70:73-90. [PMID: 38517373 DOI: 10.1080/19396368.2024.2317804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024]
Abstract
Male infertility is a reproductive disorder, accounting for 40-50% of infertility. Currently, in about 70% of infertile men, the cause remains unknown. With the introduction of novel omics and advancement in high-throughput technology, potential biomarkers are emerging. The main purpose of our work was to overview different aspects of omics approaches in association with idiopathic male infertility and highlight potential genes, transcripts, non-coding RNA, proteins, and metabolites worth further exploring. Using the Gene Ontology (GO) analysis, we aimed to compare enriched GO terms from each omics approach and determine their overlapping. A PubMed database screening for the literature published between February 2014 and June 2022 was performed using the keywords: male infertility in association with different omics approaches: genomics, epigenomics, transcriptomics, ncRNAomics, proteomics, and metabolomics. A GO enrichment analysis was performed using the Enrichr tool. We retrieved 281 global studies: 171 genomics (DNA level), 21 epigenomics (19 of methylation and two histone residue modifications), 15 transcriptomics, 31 non-coding RNA, 29 proteomics, two protein posttranslational modification, and 19 metabolomics studies. Gene ontology comparison showed that different omics approaches lead to the identification of different molecular factors and that the corresponding GO terms, obtained from different omics approaches, do not overlap to a larger extent. With the integration of novel omics levels into the research of idiopathic causes of male infertility, using multi-omic systems biology approaches, we will be closer to finding the potential biomarkers and consequently becoming aware of the entire spectrum of male infertility, their cause, prognosis, and potential treatment.
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Affiliation(s)
- Rebeka Podgrajsek
- Department of Human Reproduction, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Alenka Hodzic
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Faculty of Health Sciences, University of Novo mesto, Novo Mesto, Slovenia
| | - Martin Stimpfel
- Department of Human Reproduction, University Medical Center Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Wang T, Ma X, Zheng Q, Ma C, Zhang Z, Pan H, Guo X, Wu X, Chu M, Liang C, Yan P. A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses. Anim Biotechnol 2024; 35:2294785. [PMID: 38193799 DOI: 10.1080/10495398.2023.2294785] [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: 01/10/2024]
Abstract
Yak is an important dominant livestock species at high altitude, and the growth performance of yak has obvious differences under different feeding methods. This experiment was conducted to compare the effects of different feeding practices on growth performance and meat quality of yaks through combined transcriptomic and metabolomic analyses. In terms of yak growth performance, compared with traditional grazing, in-house feeding can significantly improve the average daily weight gain, carcass weight and net meat weight of yaks; in terms of yak meat quality, in-house feeding can effectively improve the quality of yak meat. A combined transcriptomic and metabolomic analysis revealed 31 co-enriched pathways, among which arginine metabolism, proline metabolism and glycerophospholipid metabolism may be involved in the development of the longissimus dorsi muscle of yak and the regulation of meat quality-related traits. The experimental results increased our understanding of yak meat quality and provided data materials for subsequent deep excavation of the mechanism of yak meat quality.
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Affiliation(s)
- Tong Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - Xiaoming Ma
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Qingbo Zheng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Chaofan Ma
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - Zhilong Zhang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Heping Pan
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - Xian Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoyun Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Min Chu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Chunnian Liang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
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3
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Guo X, Zhang Z, Li J, Zhang S, Sun W, Xiao X, Sun Z, Xue X, Wang Z, Zhang Y. Phenotypic and transcriptome profiling of spikes reveals the regulation of light regimens on spike growth and fertile floret number in wheat. Plant Cell Environ 2024; 47:1575-1591. [PMID: 38269615 DOI: 10.1111/pce.14832] [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] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/25/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024]
Abstract
The spike growth phase is critical for the establishment of fertile floret (grain) numbers in wheat (Triticum aestivum L.). Then, how to shorten the spike growth phase and increase grain number synergistically? Here, we showed high-resolution analyses of floret primordia (FP) number, morphology and spike transcriptomes during the spike growth phase under three light regimens. The development of all FP in a spike could be divided into four distinct stages: differentiation (Stage I), differentiation and morphology development concurrently (Stage II), morphology development (Stage III), and polarization (Stage IV). Compared to the short photoperiod, the long photoperiod shortened spike growth and stimulated early flowering by shortening Stage III; however, this reduced assimilate accumulation, resulting in fertile floret loss. Interestingly, long photoperiod supplemented with red light shortened the time required to complete Stages I-II, then raised assimilates supply in the spike and promoted anther development before polarization initiation, thereby increasing fertile FP number during Stage III, and finally maintained fertile FP development during Stage IV until they became fertile florets via a predicted dynamic gene network. Our findings proposed a light regimen, critical stages and candidate regulators that achieved a shorter spike growth phase and a higher fertile floret number in wheat.
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Affiliation(s)
- Xiaolei Guo
- Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- National Research Center of Intelligent Equipment for Agriculture, Beijing, China
- Department of Agronomy, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Zhang
- Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Junyan Li
- Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- National Research Center of Intelligent Equipment for Agriculture, Beijing, China
| | - Siqi Zhang
- Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- National Research Center of Intelligent Equipment for Agriculture, Beijing, China
| | - Wan Sun
- Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xuechen Xiao
- Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhencai Sun
- Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xuzhang Xue
- National Research Center of Intelligent Equipment for Agriculture, Beijing, China
| | - Zhimin Wang
- Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yinghua Zhang
- Department of Agronomy, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Meng Y, Toledo-Rodriguez M, Fedorenko O, Smith PA. Sex and age affect depot expression of Ca2+ channels in rat white fat adipocytes. J Mol Endocrinol 2024; 72:e230108. [PMID: 38299791 PMCID: PMC10959010 DOI: 10.1530/jme-23-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/01/2024] [Indexed: 02/02/2024]
Abstract
White adipose tissue (WAT) requires extracellular Ca2+ influx for lipolysis, differentiation, and expansion. This partly occurs via plasma membrane Ca2+ voltage-dependent channels (CaVs). However, WFA exists in different depots whose function varies with age, sex, and location. To explore whether their CaV expression profiles also differ we used RNAseq and qPCR on gonadal, mesenteric, retroperitoneal, and inguinal subcutaneous fat depots from rats of different ages and sex. CaV expression was found dependent on age, sex, and WFA location. In the gonadal depots of both sexes a significantly lower expression of CaV1.2 and CaV1.3 was seen for adults compared to pre-pubescent juveniles. A lower level of expression was also seen for CaV3.1 in adult male but not female gonadal WFA, the latter of whose expression remained unchanged with age. Relatively little expression of CaV3.2 and 3.2 was observed. In post-pubescent inguinal subcutaneous fat, where the third and fourth mammary glands are located, CaV3.1 was decreased in males but increased in females - thus suggesting that this channel is associated with mammogenesis; however, no difference in intracellular Ca2+ levels or adipocyte size were noted. For all adult depots, CaV3.1 expression was larger in females than males - a difference not seen in pre-pubescent rats. These observations are consistent with the changes of CaV3.1 expression seen in 3T3-L1 cell differentiation and the ability of selective CaV3.1 antagonists to inhibit adipogensis. Our results show that changes in CaV expression patterns occur in fat depots related to sexual dimorphism: reproductive tracts and mammogenesis.
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Affiliation(s)
- Yan Meng
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Maria Toledo-Rodriguez
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Olena Fedorenko
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Paul A Smith
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
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Bedu-Ferrari C, Biscarrat P, Pepke F, Vati S, Chaudemanche C, Castelli F, Chollet C, Rué O, Hennequet-Antier C, Langella P, Cherbuy C. In-depth characterization of a selection of gut commensal bacteria reveals their functional capacities to metabolize dietary carbohydrates with prebiotic potential. mSystems 2024; 9:e0140123. [PMID: 38441031 DOI: 10.1128/msystems.01401-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/11/2024] [Indexed: 03/06/2024] Open
Abstract
The microbial utilization of dietary carbohydrates is closely linked to the pivotal role of the gut microbiome in human health. Inherent to the modulation of complex microbial communities, a prebiotic implies the selective utilization of a specific substrate, relying on the metabolic capacities of targeted microbes. In this study, we investigated the metabolic capacities of 17 commensal bacteria of the human gut microbiome toward dietary carbohydrates with prebiotic potential. First, in vitro experiments allowed the classification of bacterial growth and fermentation profiles in response to various carbon sources, including agave inulin, corn fiber, polydextrose, and citrus pectin. The influence of phylogenetic affiliation appeared to statistically outweigh carbon sources in determining the degree of carbohydrate utilization. Second, we narrowed our focus on six commensal bacteria representative of the Bacteroidetes and Firmicutes phyla to perform an untargeted high-resolution liquid chromatography-mass spectrometry metabolomic analysis: Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Bacteroides intestinalis, Subdoligranulum variabile, Roseburia intestinalis, and Eubacterium rectale exhibited distinct metabolomic profiles in response to different carbon sources. The relative abundance of bacterial metabolites was significantly influenced by dietary carbohydrates, with these effects being strain-specific and/or carbohydrate-specific. Particularly, the findings indicated an elevation in short-chain fatty acids and other metabolites, including succinate, gamma-aminobutyric acid, and nicotinic acid. These metabolites were associated with putative health benefits. Finally, an RNA-Seq transcriptomic approach provided deeper insights into the underlying mechanisms of carbohydrate metabolization. Restricting our focus on four commensal bacteria, including B. xylanisolvens, B. thetaiotaomicron, S. variabile, and R. intestinalis, carbon sources did significantly modulate the level of bacterial genes related to the enzymatic machinery involved in the metabolization of dietary carbohydrates. This study provides a holistic view of the molecular strategies induced during the dynamic interplay between dietary carbohydrates with prebiotic potential and gut commensal bacteria. IMPORTANCE This study explores at a molecular level the interactions between commensal health-relevant bacteria and dietary carbohydrates holding prebiotic potential. We showed that prebiotic breakdown involves the specific activation of gene expression related to carbohydrate metabolism. We also identified metabolites produced by each bacteria that are potentially related to our digestive health. The characterization of the functional activities of health-relevant bacteria toward prebiotic substances can yield a better application of prebiotics in clinical interventions and personalized nutrition. Overall, this study highlights the importance of identifying the impact of prebiotics at a low resolution of the gut microbiota to characterize the activities of targeted bacteria that can play a crucial role in our health.
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Affiliation(s)
- Cassandre Bedu-Ferrari
- Micalis Institute, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- General Mills France, Boulogne Billancourt, France
| | - Paul Biscarrat
- Micalis Institute, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Frederic Pepke
- Micalis Institute, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sarah Vati
- Micalis Institute, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Florence Castelli
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments,, CEA, INRAE, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
| | - Céline Chollet
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments,, CEA, INRAE, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
| | - Olivier Rué
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France
| | - Christelle Hennequet-Antier
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Claire Cherbuy
- Micalis Institute, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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Manck LE, Coale TH, Stephens BM, Forsch KO, Aluwihare LI, Dupont CL, Allen AE, Barbeau KA. Iron limitation of heterotrophic bacteria in the California current system tracks relative availability of organic carbon and iron. ISME J 2024:wrae061. [PMID: 38624181 DOI: 10.1093/ismejo/wrae061] [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: 03/05/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Iron is an essential nutrient for all microorganisms in the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected in situ. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.
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Affiliation(s)
- Lauren E Manck
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
- Flathead Lake Biological Station, University of Montana, Polson, MT, United States
| | - Tyler H Coale
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, United States
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA, United States
| | - Brandon M Stephens
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Kiefer O Forsch
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Lihini I Aluwihare
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Christopher L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA, United States
- Department of Human Health, J. Craig Venter Institute, La Jolla, CA, United States
- Department of Synthetic Biology, J. Craig Venter Institute, La Jolla, CA, United States
| | - Andrew E Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA, United States
| | - Katherine A Barbeau
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
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Yuan X, Xue X, Liang Z, He C. Study on the potential hypoglycemic flavonoids in Abrus precatorius leaves: purification process, quality profile and activity mechanisms by transcriptomics and network pharmacology. Nat Prod Res 2024:1-8. [PMID: 38623836 DOI: 10.1080/14786419.2024.2340756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/31/2024] [Indexed: 04/17/2024]
Abstract
The aim of the study was to investigate the relationship between flavonoids in Abrus precatorius leaves (APL) and their hypoglycaemic effects, which have not been studied before. An efficient purification process, transcriptomics and network pharmacology analysis were applied for the first time. High-performance liquid chromatography (HPLC) was used to determine the content of total flavonoids. The results showed that D101 resin was most suitable for purification of flavonoids of APL, which could increase its purity from 25.2% to 85.2% and achieve a recovery rate of 86.9%. The analysis of transcriptomics and network pharmacology revealed that flavonoids of APL could play a hypoglycaemic role by regulating 31 targets through AGE-RAGE and other signal pathways. Flavonoids of APL could exert hydroglycaemic effects by inhibiting AGEs, α-glucosidase and DPPH. This study provides a solid basis for hypoglycaemic product development and in-depth research of flavonoids in APL.
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Key Words
- APL, Abrus precatorius leaves; HPLC, High-performance liquid chromatography; T2D, type 2 diabetes; AGEs, advanced glycation end products; LPS, lipopolysaccharide; DPPH, 2,2-Diphenyl-1-picrylhydrazyl; BV, bed volume; DEGs, differentially expressed genes; GO, gene ontology; KEGG, Kyoto Encyclopaedia of Genes and Genomes.
- Abrus precatorius L
- hypoglycaemic activity
- network pharmacology
- purification
- total flavonoids
- transcriptomics
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Affiliation(s)
- Xujiang Yuan
- Center for Drug Research and Development/Class III Laboratory of Modern Chinese Medicine Preparation, State Administration of Traditional Chinese Medicine of the P.R.C/ Key Laboratory of modern Chinese medicine of Education Department of Guangdong Province/Guangdong Provincial Key Laboratory of Advanced Drug Delivery Systems/ Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, P R China
| | - Xianmei Xue
- Center for Drug Research and Development/Class III Laboratory of Modern Chinese Medicine Preparation, State Administration of Traditional Chinese Medicine of the P.R.C/ Key Laboratory of modern Chinese medicine of Education Department of Guangdong Province/Guangdong Provincial Key Laboratory of Advanced Drug Delivery Systems/ Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, P R China
| | - Zhike Liang
- Center for Drug Research and Development/Class III Laboratory of Modern Chinese Medicine Preparation, State Administration of Traditional Chinese Medicine of the P.R.C/ Key Laboratory of modern Chinese medicine of Education Department of Guangdong Province/Guangdong Provincial Key Laboratory of Advanced Drug Delivery Systems/ Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, P R China
| | - Cuimin He
- Center for Drug Research and Development/Class III Laboratory of Modern Chinese Medicine Preparation, State Administration of Traditional Chinese Medicine of the P.R.C/ Key Laboratory of modern Chinese medicine of Education Department of Guangdong Province/Guangdong Provincial Key Laboratory of Advanced Drug Delivery Systems/ Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, P R China
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8
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Griesser M, Savoi S, Bondada B, Forneck A, Keller M. Berry shrivel in grapevine: a review considering multiple approaches. J Exp Bot 2024; 75:2196-2213. [PMID: 38174592 PMCID: PMC11016843 DOI: 10.1093/jxb/erae001] [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] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/03/2024] [Indexed: 01/05/2024]
Abstract
Grapevine berry shrivel, a ripening disorder, causes significant economic losses in the worldwide wine and table grape industries. An early interruption in ripening leads to this disorder, resulting in shriveling and reduced sugar accumulation affecting yield and fruit quality. Loss of sink strength associated with berry mesocarp cell death is an early symptom of this disorder; however, potential internal or external triggers are yet to be explored. No pathogens have been identified that might cause the ripening syndrome. Understanding the underlying causes and mechanisms contributing to berry shrivel is crucial for developing effective mitigation strategies and finding solutions for other ripening disorders associated with climacteric and non-climacteric fruits. This review discusses alterations in the fruit ripening mechanism induced by berry shrivel disorder, focusing primarily on sugar transport and metabolism, cell wall modification and cell death, and changes in the phytohormone profile. The essential open questions are highlighted and analyzed, thus identifying the critical knowledge gaps and key challenges for future research.
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Affiliation(s)
- Michaela Griesser
- Institute of Viticulture and Pomology, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Konrad Lorenz Strasse 24, 3430 Tulln, Austria
| | - Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Italy
| | - Bhaskar Bondada
- Department of Viticulture and Enology, Washington State University Tri-Cities, Richland, WA 99354, USA
| | - Astrid Forneck
- Institute of Viticulture and Pomology, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Konrad Lorenz Strasse 24, 3430 Tulln, Austria
| | - Markus Keller
- Department of Viticulture and Enology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA
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9
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Atkinson R, Georgiou M, Yang C, Szymanska K, Lahat A, Vasconcelos EJR, Ji Y, Moya Molina M, Collin J, Queen R, Dorgau B, Watson A, Kurzawa-Akanbi M, Laws R, Saxena A, Shyan Beh C, Siachisumo C, Goertler F, Karwatka M, Davey T, Inglehearn CF, McKibbin M, Lührmann R, Steel DH, Elliott DJ, Armstrong L, Urlaub H, Ali RR, Grellscheid SN, Johnson CA, Mozaffari-Jovin S, Lako M. PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5´-splice-site selection causing tissue-specific defects. Nat Commun 2024; 15:3138. [PMID: 38605034 PMCID: PMC11009313 DOI: 10.1038/s41467-024-47253-0] [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: 09/21/2023] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
The carboxy-terminus of the spliceosomal protein PRPF8, which regulates the RNA helicase Brr2, is a hotspot for mutations causing retinitis pigmentosa-type 13, with unclear role in human splicing and tissue-specificity mechanism. We used patient induced pluripotent stem cells-derived cells, carrying the heterozygous PRPF8 c.6926 A > C (p.H2309P) mutation to demonstrate retinal-specific endophenotypes comprising photoreceptor loss, apical-basal polarity and ciliary defects. Comprehensive molecular, transcriptomic, and proteomic analyses revealed a role of the PRPF8/Brr2 regulation in 5'-splice site (5'SS) selection by spliceosomes, for which disruption impaired alternative splicing and weak/suboptimal 5'SS selection, and enhanced cryptic splicing, predominantly in ciliary and retinal-specific transcripts. Altered splicing efficiency, nuclear speckles organisation, and PRPF8 interaction with U6 snRNA, caused accumulation of active spliceosomes and poly(A)+ mRNAs in unique splicing clusters located at the nuclear periphery of photoreceptors. Collectively these elucidate the role of PRPF8/Brr2 regulatory mechanisms in splicing and the molecular basis of retinal disease, informing therapeutic approaches.
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Affiliation(s)
| | - Maria Georgiou
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Chunbo Yang
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | - Albert Lahat
- Department of Biosciences, Durham University, Durham, UK
| | | | - Yanlong Ji
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Marina Moya Molina
- Biosciences Institute, Newcastle University, Newcastle, UK
- Newcells Biotech, Newcastle, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Avril Watson
- Biosciences Institute, Newcastle University, Newcastle, UK
- Newcells Biotech, Newcastle, UK
| | | | - Ross Laws
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Abhijit Saxena
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Chia Shyan Beh
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | | | | | - Tracey Davey
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | | | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Reinhard Lührmann
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - David H Steel
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Henning Urlaub
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg August University of Göttingen, Göttingen, Germany
| | - Robin R Ali
- Centre for Cell and Gene Therapy, Kings College London, London, UK
| | - Sushma-Nagaraja Grellscheid
- Department of Biosciences, Durham University, Durham, UK
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Colin A Johnson
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
| | - Sina Mozaffari-Jovin
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Department of Medical Genetics and Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle, UK.
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10
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Sezen UU, Shue JE, Worthy SJ, Davies SJ, McMahon SM, Swenson NG. Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech. Proc Biol Sci 2024; 291:20232338. [PMID: 38593851 PMCID: PMC11003779 DOI: 10.1098/rspb.2023.2338] [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: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 04/11/2024] Open
Abstract
Transcriptomics provides a versatile tool for ecological monitoring. Here, through genome-guided profiling of transcripts mapping to 33 042 gene models, expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck due to post-Columbian deforestation, the single nucleotide polymorphism-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our expression analyses during spring-summer and summer-autumn transitions for two consecutive years involved 4197 differentially expressed protein coding genes. Using Populus orthologues we reconstructed a protein-protein interactome representing leaf physiological states of trees during the seasonal transitions. Gene set enrichment analysis revealed gene ontology terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of GO terms that could be putatively attributed to late spring phenological shifts. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture diverse ranges of responses including air quality, chronic disease, as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms maintaining the survival of long living trees such as the American beech.
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Affiliation(s)
- U. Uzay Sezen
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, USA
| | - Jessica E. Shue
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, USA
| | - Samantha J. Worthy
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Stuart J. Davies
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Gamboa, Panama
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA
| | - Sean M. McMahon
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, USA
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Nathan G. Swenson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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11
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Li X, Li B, Gu S, Pang X, Mason P, Yuan J, Jia J, Sun J, Zhao C, Henry R. Single-cell and spatial RNA sequencing reveal the spatiotemporal trajectories of fruit senescence. Nat Commun 2024; 15:3108. [PMID: 38600080 PMCID: PMC11006883 DOI: 10.1038/s41467-024-47329-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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
The senescence of fruit is a complex physiological process, with various cell types within the pericarp, making it highly challenging to elucidate their individual roles in fruit senescence. In this study, a single-cell expression atlas of the pericarp of pitaya (Hylocereus undatus) is constructed, revealing exocarp and mesocarp cells undergoing the most significant changes during the fruit senescence process. Pseudotime analysis establishes cellular differentiation and gene expression trajectories during senescence. Early-stage oxidative stress imbalance is followed by the activation of resistance in exocarp cells, subsequently senescence-associated proteins accumulate in the mesocarp cells at late-stage senescence. The central role of the early response factor HuCMB1 is unveiled in the senescence regulatory network. This study provides a spatiotemporal perspective for a deeper understanding of the dynamic senescence process in plants.
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Affiliation(s)
- Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
- Queensland Alliance for Agriculture & Food Innovation, Queensland Biosciences Precinct, The University of Queensland, St Lucia, QLD 4072, Australia
- National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang, 471023, China
| | - Bairu Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Shaobin Gu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xinyue Pang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Patrick Mason
- Queensland Alliance for Agriculture & Food Innovation, Queensland Biosciences Precinct, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Jiangfeng Yuan
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jingyu Jia
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jiaju Sun
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Chunyan Zhao
- Institute of Environment and Health, Jianghan University, Wuhan, 430056, China.
| | - Robert Henry
- Queensland Alliance for Agriculture & Food Innovation, Queensland Biosciences Precinct, The University of Queensland, St Lucia, QLD 4072, Australia.
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12
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Bentley-Abbot C, Heslop R, Pirillo C, Chandrasegaran P, McConnell G, Roberts E, Hutchinson E, MacLeod A. An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Sci Rep 2024; 14:8348. [PMID: 38594373 PMCID: PMC11004122 DOI: 10.1038/s41598-024-58641-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/01/2024] [Indexed: 04/11/2024] Open
Abstract
Single molecule fluorescence in situ hybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of programming expertise to use currently available open-source analytical software packages to extract and analyse quantitative data about transcript expression. Here, we present FISHtoFigure, a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data. FISHtoFigure facilitates the automated spatial analysis of transcripts of interest, allowing users to analyse populations of cells positive for specific combinations of mRNA targets without the need for computational image analysis expertise. As a proof of concept and to demonstrate the capabilities of this new research tool, we have validated FISHtoFigure in multiple biological systems. We used FISHtoFigure to identify an upregulation in the expression of Cd4 by T-cells in the spleens of mice infected with influenza A virus, before analysing more complex data showing crosstalk between microglia and regulatory B-cells in the brains of mice infected with Trypanosoma brucei brucei. These analyses demonstrate the ease of analysing cell expression profiles using FISHtoFigure and the value of this new tool in the field of smFISH data analysis.
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Affiliation(s)
- Calum Bentley-Abbot
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK.
- School of Biodiversity, One Health, Veterinary Medicine (SBOHVM), College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Rhiannon Heslop
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health, Veterinary Medicine (SBOHVM), College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Praveena Chandrasegaran
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health, Veterinary Medicine (SBOHVM), College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Gail McConnell
- Department of Physics, University of Strathclyde, Glasgow, UK
| | - Ed Roberts
- Beatson Institute for Cancer Research, Glasgow, UK
| | - Edward Hutchinson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Annette MacLeod
- Wellcome Centre for Integrative Parasitology (WCIP), University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health, Veterinary Medicine (SBOHVM), College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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13
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Lee H, Stead JD, Williams A, Cortés Ramírez SA, Atlas E, Mennigen JA, O’Brien JM, Yauk C. Empirical Characterization of False Discovery Rates of Differentially Expressed Genes and Transcriptomic Benchmark Concentrations in Zebrafish Embryos. Environ Sci Technol 2024; 58:6128-6137. [PMID: 38530926 PMCID: PMC11008580 DOI: 10.1021/acs.est.3c10543] [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] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
High-throughput transcriptomics (HTTr) is increasingly applied to zebrafish embryos to survey the toxicological effects of environmental chemicals. Before the adoption of this approach in regulatory testing, it is essential to characterize background noise in order to guide experimental designs. We thus empirically quantified the HTTr false discovery rate (FDR) across different embryo pool sizes, sample sizes, and concentration groups for toxicology studies. We exposed zebrafish embryos to 0.1% dimethyl sulfoxide (DMSO) for 5 days. Pools of 1, 5, 10, and 20 embryos were created (n = 24 samples for each pool size). Samples were sequenced on the TempO-Seq platform and then randomly assigned to mock treatment groups before differentially expressed gene (DEG), pathway, and benchmark concentration (BMC) analyses. Given that all samples were treated with DMSO, any significant DEGs, pathways, or BMCs are false positives. As expected, we found decreasing FDRs for DEG and pathway analyses with increasing pool and sample sizes. Similarly, FDRs for BMC analyses decreased with increasing pool size and concentration groups, with more stringent BMC premodel filtering reducing BMC FDRs. Our study provides foundational data for determining appropriate experiment designs for regulatory toxicity testing with HTTr in zebrafish embryos.
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Affiliation(s)
- Hyojin Lee
- Department
of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - John D.H. Stead
- Department
of Neuroscience, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Andrew Williams
- Environmental
Health Science and Research Bureau, Health
Canada, Ottawa, Ontario K1A 0K9, Canada
| | | | - Ella Atlas
- Environmental
Health Science and Research Bureau, Health
Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Jan A. Mennigen
- Department
of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Jason M. O’Brien
- Ecotoxicology
and Wildlife Health Division, Environment
and Climate Change Canada, Ottawa, Ontario K1A 0H3, Canada
| | - Carole Yauk
- Department
of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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14
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Poonawala H, Zhang Y, Kuchibhotla S, Green AG, Cirillo DM, Di Marco F, Spitlaeri A, Miotto P, Farhat MR. Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2024:e0118523. [PMID: 38587412 DOI: 10.1128/aac.01185-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/06/2024] [Indexed: 04/09/2024] Open
Abstract
Transcriptional responses in bacteria following antibiotic exposure offer insights into antibiotic mechanism of action, bacterial responses, and characterization of antimicrobial resistance. We aimed to define the transcriptional antibiotic response (TAR) in Mycobacterium tuberculosis (Mtb) isolates for clinically relevant drugs by pooling and analyzing Mtb microarray and RNA-seq data sets. We generated 99 antibiotic transcription profiles across 17 antibiotics, with 76% of profiles generated using 3-24 hours of antibiotic exposure and 49% within one doubling of the WHO antibiotic critical concentration. TAR genes were time-dependent, and largely specific to the antibiotic mechanism of action. TAR signatures performed well at predicting antibiotic exposure, with the area under the receiver operating curve (AUC) ranging from 0.84-1.00 (TAR <6 hours of antibiotic exposure) and 0.76-1.00 (>6 hours of antibiotic exposure) for upregulated genes and 0.57-0.90 and 0.87-1.00, respectfully, for downregulated genes. This work desmonstrates that transcriptomics allows for the assessment of antibiotic activity in Mtb within 6 hours of exposure.
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Affiliation(s)
- Husain Poonawala
- Department of Medicine and Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Medicine and Department of Anatomic and Clinical Pathology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yu Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Anna G Green
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federico Di Marco
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Spitlaeri
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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15
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Hatje K, Kam-Thong T, Giroud N, Saviano A, Simo-Noumbissie P, Kumpesa N, Nilsson T, Habersetzer F, Baumert TF, Pelletier N, Forkel M. Single-cell RNA-sequencing of virus-specific cellular immune responses in chronic hepatitis B patients. Sci Data 2024; 11:355. [PMID: 38589415 PMCID: PMC11001867 DOI: 10.1038/s41597-024-03187-2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/25/2024] [Indexed: 04/10/2024] Open
Abstract
Chronic hepatitis B (CHB) is a major global health challenge. CHB can be controlled by antivirals but a therapeutic cure is lacking. CHB is characterized by limited HBV-specific T cell reactivity and functionality and expression of inhibitory receptors. The mechanisms driving these T cell phenotypes are only partially understood. Here, we created a single-cell RNA-sequencing dataset of HBV immune responses in patients to contribute to a better understanding of the dysregulated immunity. Blood samples of a well-defined cohort of 21 CHB and 10 healthy controls, including a subset of 5 matched liver biopsies, were collected. scRNA-seq data of total immune cells (55,825) plus sorted HBV-specific (1,963), non-naive (32,773) and PD1+ T cells (96,631) was generated using the 10X Genomics platform (186,123 cells) or the full-length Smart-seq2 protocol (1,069 cells). The shared transcript count matrices of single-cells serve as a valuable resource describing transcriptional changes underlying dysfunctional HBV-related T cell responses in blood and liver tissue and offers the opportunity to identify targets or biomarkers for HBV-related immune exhaustion.
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Affiliation(s)
- Klas Hatje
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland.
| | - Tony Kam-Thong
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Nicolas Giroud
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Antonio Saviano
- Service d'hépato-gastroentérologie, Pôle hépato-digestif, Institut Hospitalo-Universitaire de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
- Institut de Recherche sur les Maladies Virales et Hépatiques, Inserm UMR_S1110, University of Strasbourg, Strasbourg, France.
| | - Pauline Simo-Noumbissie
- Service d'hépato-gastroentérologie, Pôle hépato-digestif, Institut Hospitalo-Universitaire de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Nadine Kumpesa
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Tobias Nilsson
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - François Habersetzer
- Service d'hépato-gastroentérologie, Pôle hépato-digestif, Institut Hospitalo-Universitaire de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Thomas F Baumert
- Service d'hépato-gastroentérologie, Pôle hépato-digestif, Institut Hospitalo-Universitaire de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Institut de Recherche sur les Maladies Virales et Hépatiques, Inserm UMR_S1110, University of Strasbourg, Strasbourg, France
| | - Nadege Pelletier
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Marianne Forkel
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland.
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16
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Dos Santos GA, Magdaleno GDV, de Magalhães JP. Evidence of a pan-tissue decline in stemness during human aging. Aging (Albany NY) 2024; 16:205717. [PMID: 38604248 DOI: 10.18632/aging.205717] [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: 10/08/2023] [Accepted: 02/02/2024] [Indexed: 04/13/2024]
Abstract
Despite their biological importance, the role of stem cells in human aging remains to be elucidated. In this work, we applied a machine learning methodology to GTEx transcriptome data and assigned stemness scores to 17,382 healthy samples from 30 human tissues aged between 20 and 79 years. We found that ~60% of the studied tissues exhibit a significant negative correlation between the subject's age and stemness score. The only significant exception was the uterus, where we observed an increased stemness with age. Moreover, we observed that stemness is positively correlated with cell proliferation and negatively correlated with cellular senescence. Finally, we also observed a trend that hematopoietic stem cells derived from older individuals might have higher stemness scores. In conclusion, we assigned stemness scores to human samples and show evidence of a pan-tissue loss of stemness during human aging, which adds weight to the idea that stem cell deterioration may contribute to human aging.
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Affiliation(s)
- Gabriel Arantes Dos Santos
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo 01246 903, Brazil
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, United Kingdom
| | | | - João Pedro de Magalhães
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, United Kingdom
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17
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Crist SB, Azzag K, Kiley J, Coleman I, Magli A, Perlingeiro RCR. The adult environment promotes the transcriptional maturation of human iPSC-derived muscle grafts. NPJ Regen Med 2024; 9:16. [PMID: 38575647 PMCID: PMC10994941 DOI: 10.1038/s41536-024-00360-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Pluripotent stem cell (PSC)-based cell therapy is an attractive option for the treatment of multiple human disorders, including muscular dystrophies. While in vitro differentiating PSCs can generate large numbers of human lineage-specific tissue, multiple studies evidenced that these cell populations mostly display embryonic/fetal features. We previously demonstrated that transplantation of PSC-derived myogenic progenitors provides long-term engraftment and functional improvement in several dystrophic mouse models, but it remained unknown whether donor-derived myofibers mature to match adult tissue. Here, we transplanted iPAX7 myogenic progenitors into muscles of non-dystrophic and dystrophic mice and compared the transcriptional landscape of human grafts with respective in vitro-differentiated iPAX7 myotubes as well as human skeletal muscle biospecimens. Pairing bulk RNA sequencing with computational deconvolution of human reads, we were able to pinpoint key myogenic changes that occur during the in vitro-to-in vivo transition, confirm developmental maturity, and consequently evaluate their applicability for cell-based therapies.
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Affiliation(s)
- Sarah B Crist
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Karim Azzag
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - James Kiley
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Ilsa Coleman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alessandro Magli
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
- Sanofi, Genomic Medicine Unit, 225 2nd Ave, Waltham, MA, 02451, USA.
| | - Rita C R Perlingeiro
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
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18
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Heintz MM, Klaren WD, East AW, Haws LC, McGreal SR, Campbell RR, Thompson CM. Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and PPARα knockout mouse hepatocytes. Toxicol Sci 2024:kfae045. [PMID: 38574385 DOI: 10.1093/toxsci/kfae045] [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: 04/06/2024] Open
Abstract
Recent in vitro transcriptomic analyses for the short-chain polyfluoroalkyl substance (PFAS), HFPO-DA (ammonium, 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate), support conclusions from in vivo data that HFPO-DA-mediated liver effects in mice are part of the early key events of the peroxisome proliferator-activated receptor alpha (PPARα) activator-induced rodent hepatocarcinogenesis mode of action (MOA). Transcriptomic responses in HFPO-DA-treated rodent hepatocytes have high concordance with those treated with a PPARα agonist and lack concordance with those treated with PPARγ agonists or cytotoxic agents. To elucidate whether HFPO-DA-mediated transcriptomic responses in mouse liver are PPARα-dependent, additional transcriptomic analyses were conducted on samples from primary PPARα knockout (KO) and wild-type (WT) mouse hepatocytes exposed for 12, 24 or 72 hours with various concentrations of HFPO-DA, or well-established agonists of PPARα (GW7647) and PPARγ (rosiglitazone), or cytotoxic agents (acetaminophen or d-galactosamine). Pathway and predicted upstream regulator-level responses were highly concordant between HFPO-DA and GW7647 in WT hepatocytes. A similar pattern was observed in PPARα KO hepatocytes, albeit with a distinct temporal and concentration-dependent delay potentially mediated by compensatory responses. This delay was not observed in PPARα KO hepatocytes exposed to rosiglitazone, acetaminophen, d-galactosamine. The similarity in transcriptomic signaling between HFPO-DA and GW7647 in both the presence and absence of PPARα in vitro indicates these compounds share a common MOA.
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Heintz MM, Klaren WD, East AW, Haws LC, McGreal SR, Campbell RR, Thompson CM. Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in mouse, rat, and pooled human hepatocytes. Toxicol Sci 2024:kfae044. [PMID: 38574381 DOI: 10.1093/toxsci/kfae044] [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: 04/06/2024] Open
Abstract
Like many per- or polyfluorinated alkyl substances (PFAS), toxicity studies with HFPO-DA (ammonium, 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate), a short-chain PFAS used in the manufacture of some types of fluorinated polymers, indicate that the liver is the primary target of toxicity in rodents following oral exposure. Although the current weight of evidence supports the PPARα mode of action (MOA) for liver effects in HFPO-DA-exposed mice, alternate MOAs have also been hypothesized including PPARγ or cytotoxicity. To further evaluate the MOA for HFPO-DA in rodent liver, transcriptomic analyses were conducted on samples from primary mouse, rat and pooled human hepatocytes treated for 12, 24 or 72 hours with various concentrations of HFPO-DA, or agonists of PPARα (GW7647), PPARγ (rosiglitazone), or cytotoxic agents (ie, acetaminophen or d-galactosamine). Concordance analyses of enriched pathways across chemicals within each species demonstrated greatest concordance between HFPO-DA and PPARα agonist GW7647-treated hepatocytes compared to the other chemicals evaluated. These findings were supported by benchmark concentration modeling and predicted upstream regulator results. In addition, transcriptomic analyses across species demonstrated a greater transcriptomic response in rodent hepatocytes treated with HFPO-DA or agonists of PPARα or PPARγ, indicating rodent hepatocytes are more sensitive to HFPO-DA or PPARα/γ agonist treatment. These results are consistent with previously published transcriptomic analyses and further support that liver effects in HFPO-DA-exposed rodents are mediated through rodent-specific PPARα signaling mechanisms as part of the MOA for PPARα activator-induced rodent hepatocarcinogenesis. Thus, effects observed in mouse liver are not appropriate endpoints for toxicity value development for HFPO-DA in human health risk assessment.
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Molteni E, Baldan F, Damante G, Allegri L. Dihydrotanshinone I exhibits antitumor effects via β-catenin downregulation in papillary thyroid cancer cell lines. Sci Rep 2024; 14:7853. [PMID: 38570592 PMCID: PMC10991365 DOI: 10.1038/s41598-024-58495-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 03/29/2024] [Indexed: 04/05/2024] Open
Abstract
Thyroid cancer is the most common endocrine carcinoma and, among its different subtypes, the papillary subtype (PTC) is the most frequent. Generally, PTCs are well differentiated, but a minor percentage of PTCs are characterized by a worse prognosis and more aggressive behavior. Phytochemicals, naturally found in plant products, represent a heterogeneous group of bioactive compounds that can interfere with cell proliferation and the regulation of the cell cycle, taking part in multiple signaling pathways that are often disrupted in tumor initiation, proliferation, and progression. In this work, we focused on 15,16-dihydrotanshinone I (DHT), a tanshinone isolated from Salvia miltiorrhiza Bunge (Danshen). We first evaluated DHT biological effect on PTC cells regarding cell viability, colony formation ability, and migration capacity. All of these parameters were downregulated by DHT treatment. We then investigated gene expression changes after DHT treatment by performing RNA-seq. The analysis revealed that DHT significantly reduced the Wnt signaling pathway, which plays a role in various diseases, including cancer. Finally, we demonstrate that DHT treatment decreases protein levels of β-catenin, a final effector of canonical Wnt signaling pathway. Overall, our data suggest a possible use of this nutraceutical as an adjuvant in the treatment of aggressive papillary thyroid carcinoma.
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Affiliation(s)
| | - Federica Baldan
- Department of Medicine, University of Udine, 33100, Udine, Italy.
| | - Giuseppe Damante
- Department of Medicine, University of Udine, 33100, Udine, Italy
- Institute of Medical Genetics, Academic Hospital of Udine, Azienda Sanitaria Universitaria Friuli Centrale, 33100, Udine, Italy
| | - Lorenzo Allegri
- Department of Medicine, University of Udine, 33100, Udine, Italy
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21
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Deehan MA, Kothuis JM, Sapp E, Chase K, Ke Y, Seeley C, Iuliano M, Kim E, Kennington L, Miller R, Boudi A, Shing K, Li X, Pfister E, Anaclet C, Brodsky M, Kegel-Gleason K, Aronin N, DiFiglia M. Nacc1 Mutation in Mice Models Rare Neurodevelopmental Disorder with Underlying Synaptic Dysfunction. J Neurosci 2024; 44:e1610232024. [PMID: 38388424 PMCID: PMC10993038 DOI: 10.1523/jneurosci.1610-23.2024] [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: 08/24/2023] [Revised: 01/05/2024] [Accepted: 02/03/2024] [Indexed: 02/24/2024] Open
Abstract
A missense mutation in the transcription repressor Nucleus accumbens-associated 1 (NACC1) gene at c.892C>T (p.Arg298Trp) on chromosome 19 causes severe neurodevelopmental delay ( Schoch et al., 2017). To model this disorder, we engineered the first mouse model with the homologous mutation (Nacc1+/R284W ) and examined mice from E17.5 to 8 months. Both genders had delayed weight gain, epileptiform discharges and altered power spectral distribution in cortical electroencephalogram, behavioral seizures, and marked hindlimb clasping; females displayed thigmotaxis in an open field. In the cortex, NACC1 long isoform, which harbors the mutation, increased from 3 to 6 months, whereas the short isoform, which is not present in humans and lacks aaR284 in mice, rose steadily from postnatal day (P) 7. Nuclear NACC1 immunoreactivity increased in cortical pyramidal neurons and parvalbumin containing interneurons but not in nuclei of astrocytes or oligodendroglia. Glial fibrillary acidic protein staining in astrocytic processes was diminished. RNA-seq of P14 mutant mice cortex revealed over 1,000 differentially expressed genes (DEGs). Glial transcripts were downregulated and synaptic genes upregulated. Top gene ontology terms from upregulated DEGs relate to postsynapse and ion channel function, while downregulated DEGs enriched for terms relating to metabolic function, mitochondria, and ribosomes. Levels of synaptic proteins were changed, but number and length of synaptic contacts were unaltered at 3 months. Homozygosity worsened some phenotypes including postnatal survival, weight gain delay, and increase in nuclear NACC1. This mouse model simulates a rare form of autism and will be indispensable for assessing pathophysiology and targets for therapeutic intervention.
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Affiliation(s)
- Mark A Deehan
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
| | - Josine M Kothuis
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
| | - Kathryn Chase
- Department of Medicine, UMass Chan Medical School, Worcester, Massachusetts 01655
| | - Yuting Ke
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Connor Seeley
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
| | - Maria Iuliano
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
| | - Emily Kim
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
| | - Lori Kennington
- Department of Medicine, UMass Chan Medical School, Worcester, Massachusetts 01655
| | - Rachael Miller
- Department of Medicine, UMass Chan Medical School, Worcester, Massachusetts 01655
| | - Adel Boudi
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
| | - Kai Shing
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
| | - Xueyi Li
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
| | - Edith Pfister
- Department of Medicine, UMass Chan Medical School, Worcester, Massachusetts 01655
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, Massachusetts 01655
| | - Christelle Anaclet
- Department of Neurological Surgery, University of California Davis School of Medicine, Davis, California 95817
| | - Michael Brodsky
- Department of Molecular, Cell and Cancer Biology, UMass Chan Medical School, Worcester, Massachusetts 01655
| | - Kimberly Kegel-Gleason
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
| | - Neil Aronin
- Department of Medicine, UMass Chan Medical School, Worcester, Massachusetts 01655
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129
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Bunyavanich S, Becker PM, Altman MC, Lasky-Su J, Ober C, Zengler K, Berdyshev E, Bonneau R, Chatila T, Chatterjee N, Chung KF, Cutcliffe C, Davidson W, Dong G, Fang G, Fulkerson P, Himes BE, Liang L, Mathias RA, Ogino S, Petrosino J, Price ND, Schadt E, Schofield J, Seibold MA, Steen H, Wheatley L, Zhang H, Togias A, Hasegawa K. Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop. J Allergy Clin Immunol 2024; 153:954-968. [PMID: 38295882 PMCID: PMC10999353 DOI: 10.1016/j.jaci.2024.01.014] [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: 12/13/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Studies of asthma and allergy are generating increasing volumes of omics data for analysis and interpretation. The National Institute of Allergy and Infectious Diseases (NIAID) assembled a workshop comprising investigators studying asthma and allergic diseases using omics approaches, omics investigators from outside the field, and NIAID medical and scientific officers to discuss the following areas in asthma and allergy research: genomics, epigenomics, transcriptomics, microbiomics, metabolomics, proteomics, lipidomics, integrative omics, systems biology, and causal inference. Current states of the art, present challenges, novel and emerging strategies, and priorities for progress were presented and discussed for each area. This workshop report summarizes the major points and conclusions from this NIAID workshop. As a group, the investigators underscored the imperatives for rigorous analytic frameworks, integration of different omics data types, cross-disciplinary interaction, strategies for overcoming current limitations, and the overarching goal to improve scientific understanding and care of asthma and allergic diseases.
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Affiliation(s)
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Jessica Lasky-Su
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | | | - Talal Chatila
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | - Wendy Davidson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Dong
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Fang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Patricia Fulkerson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Liming Liang
- Harvard T. H. Chan School of Public Health, Boston, Mass
| | | | - Shuji Ogino
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass; Harvard T. H. Chan School of Public Health, Boston, Mass; Broad Institute of MIT and Harvard, Boston, Mass
| | | | | | - Eric Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Max A Seibold
- National Jewish Health, Denver, Colo; University of Colorado School of Medicine, Aurora, Colo
| | - Hanno Steen
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Lisa Wheatley
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Hongmei Zhang
- School of Public Health, University of Memphis, Memphis, Tenn
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Kohei Hasegawa
- Massachusetts General Hospital and Harvard Medical School, Boston, Mass
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Grünhofer P, Heimerich I, Pohl S, Oertel M, Meng H, Zi L, Lucignano K, Bokhari SNH, Guo Y, Li R, Lin J, Fladung M, Kreszies T, Stöcker T, Schoof H, Schreiber L. Suberin deficiency and its effect on the transport physiology of young poplar roots. New Phytol 2024; 242:137-153. [PMID: 38366280 DOI: 10.1111/nph.19588] [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] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The precise functions of suberized apoplastic barriers in root water and nutrient transport physiology have not fully been elucidated. While lots of research has been performed with mutants of Arabidopsis, little to no data are available for mutants of agricultural crop or tree species. By employing a combined set of physiological, histochemical, analytical, and transport physiological methods as well as RNA-sequencing, this study investigated the implications of remarkable CRISPR/Cas9-induced suberization defects in young roots of the economically important gray poplar. While barely affecting overall plant development, contrary to literature-based expectations significant root suberin reductions of up to 80-95% in four independent mutants were shown to not evidently affect the root hydraulic conductivity during non-stress conditions. In addition, subliminal iron deficiency symptoms and increased translocation of a photosynthesis inhibitor as well as NaCl highlight the involvement of suberin in nutrient transport physiology. The multifaceted nature of the root hydraulic conductivity does not allow drawing simplified conclusions such as that the suberin amount must always be correlated with the water transport properties of roots. However, the decreased masking of plasma membrane surface area could facilitate the uptake but also leakage of beneficial and harmful solutes.
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Affiliation(s)
- Paul Grünhofer
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Ines Heimerich
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Svenja Pohl
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Marlene Oertel
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Hongjun Meng
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Lin Zi
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Kevin Lucignano
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Syed Nadeem Hussain Bokhari
- Department Plant Biophysics and Biochemistry, Institute of Plant Molecular Biology, Czech Academy of Sciences, Biology Centre, Branišovská 31/1160, CZ-37005, České Budějovice, Czech Republic
| | - Yayu Guo
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ruili Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jinxing Lin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, Sieker Landstraße 2, 22927, Grosshansdorf, Germany
| | - Tino Kreszies
- Department of Crop Sciences, Plant Nutrition and Crop Physiology, University of Göttingen, Carl-Sprengel-Weg 1, 37075, Göttingen, Germany
| | - Tyll Stöcker
- Department of Crop Bioinformatics, Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 2, 53115, Bonn, Germany
| | - Heiko Schoof
- Department of Crop Bioinformatics, Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 2, 53115, Bonn, Germany
| | - Lukas Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
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24
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Wipperman MF, Gayvert KM, Atanasio A, Wang CQ, Corren J, Covarrubias A, Setliff I, Chio E, Laws E, Wolfe K, Harel S, Maloney J, Herman G, Orengo JM, Lim WK, Hamon SC, Hamilton JD, O'Brien MP. Differential modulation of allergic rhinitis nasal transcriptome by dupilumab and allergy immunotherapy. Allergy 2024; 79:894-907. [PMID: 38279910 DOI: 10.1111/all.16001] [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: 09/20/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 01/29/2024]
Abstract
BACKGROUND Nasal epithelial cells are important regulators of barrier function and immune signaling; however, in allergic rhinitis (AR) these functions can be disrupted by inflammatory mediators. We aimed to better discern AR disease mechanisms using transcriptome data from nasal brushing samples from individuals with and without AR. METHODS Data were drawn from a feasibility study of individuals with and without AR to Timothy grass and from a clinical trial evaluating 16 weeks of treatment with the following: dupilumab, a monoclonal antibody that binds interleukin (IL)-4Rα and inhibits type 2 inflammation by blocking signaling of both IL-4/IL-13; subcutaneous immunotherapy with Timothy grass (SCIT), which inhibits allergic responses through pleiotropic effects; SCIT + dupilumab; or placebo. Using nasal brushing samples from these studies, we defined distinct gene signatures in nasal tissue of AR disease and after nasal allergen challenge (NAC) and assessed how these signatures were modulated by study drug(s). RESULTS Treatment with dupilumab (normalized enrichment score [NES] = -1.73, p = .002) or SCIT + dupilumab (NES = -2.55, p < .001), but not SCIT alone (NES = +1.16, p = .107), significantly repressed the AR disease signature. Dupilumab (NES = -2.55, p < .001), SCIT (NES = -2.99, p < .001), and SCIT + dupilumab (NES = -3.15, p < .001) all repressed the NAC gene signature. CONCLUSION These results demonstrate type 2 inflammation is an important contributor to the pathophysiology of AR disease and that inhibition of the type 2 pathway with dupilumab may normalize nasal tissue gene expression.
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Affiliation(s)
| | | | | | - Claire Q Wang
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | - Jonathan Corren
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Angelica Covarrubias
- Clinical Research Division, Jonathan Corren, MD. Inc., Los Angeles, California, USA
| | - Ian Setliff
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | - Erica Chio
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | | | | | - Sivan Harel
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | | | - Gary Herman
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | - Jamie M Orengo
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | - Wei Keat Lim
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | - Sara C Hamon
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
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25
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Neyton LPA, Sinha P, Sarma A, Mick E, Kalantar K, Chen S, Wu N, Delucchi K, Zhuo H, Bos LDJ, Jauregui A, Gomez A, Hendrickson CM, Kangelaris KN, Leligdowicz A, Liu KD, Matthay MA, Langelier CR, Calfee CS. Host and Microbe Blood Metagenomics Reveals Key Pathways Characterizing Critical Illness Phenotypes. Am J Respir Crit Care Med 2024; 209:805-815. [PMID: 38190719 PMCID: PMC10995577 DOI: 10.1164/rccm.202308-1328oc] [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: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 01/10/2024] Open
Abstract
Rationale: Two molecular phenotypes of sepsis and acute respiratory distress syndrome, termed hyperinflammatory and hypoinflammatory, have been consistently identified by latent class analysis in numerous cohorts, with widely divergent clinical outcomes and differential responses to some treatments; however, the key biological differences between these phenotypes remain poorly understood.Objectives: We used host and microbe metagenomic sequencing data from blood to deepen our understanding of biological differences between latent class analysis-derived phenotypes and to assess concordance between the latent class analysis-derived phenotypes and phenotypes reported by other investigative groups (e.g., Sepsis Response Signature [SRS1-2], molecular diagnosis and risk stratification of sepsis [MARS1-4], reactive and uninflamed).Methods: We analyzed data from 113 patients with hypoinflammatory sepsis and 76 patients with hyperinflammatory sepsis enrolled in a two-hospital prospective cohort study. Molecular phenotypes had been previously assigned using latent class analysis.Measurements and Main Results: The hyperinflammatory and hypoinflammatory phenotypes of sepsis had distinct gene expression signatures, with 5,755 genes (31%) differentially expressed. The hyperinflammatory phenotype was associated with elevated expression of innate immune response genes, whereas the hypoinflammatory phenotype was associated with elevated expression of adaptive immune response genes and, notably, T cell response genes. Plasma metagenomic analysis identified differences in prevalence of bacteremia, bacterial DNA abundance, and composition between the phenotypes, with an increased presence and abundance of Enterobacteriaceae in the hyperinflammatory phenotype. Significant overlap was observed between these phenotypes and previously identified transcriptional subtypes of acute respiratory distress syndrome (reactive and uninflamed) and sepsis (SRS1-2). Analysis of data from the VANISH trial indicated that corticosteroids might have a detrimental effect in patients with the hypoinflammatory phenotype.Conclusions: The hyperinflammatory and hypoinflammatory phenotypes have distinct transcriptional and metagenomic features that could be leveraged for precision treatment strategies.
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Affiliation(s)
| | - Pratik Sinha
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri
| | - Aartik Sarma
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine
| | - Eran Mick
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine
- Division of Infectious Diseases
- Chan Zuckerberg Biohub, San Francisco, California
| | | | | | - Nelson Wu
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine
| | | | | | - Lieuwe D J Bos
- Department of Intensive Care and Laboratory of Experimental Intensive Care and Anesthesiology, Academic Medical Center, Amsterdam, the Netherlands
| | | | - Antonio Gomez
- Department of Medicine
- Department of Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, California; and
| | - Carolyn M Hendrickson
- Department of Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, California; and
| | | | | | | | - Michael A Matthay
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California
| | - Charles R Langelier
- Division of Infectious Diseases
- Chan Zuckerberg Biohub, San Francisco, California
| | - Carolyn S Calfee
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine
- Department of Anesthesiology, and
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California
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26
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Iwanaszko M, Waldeck N, Anafi R, Paller AS, Zee P, Fishbein A. Circadian Rhythms in Skin Barrier Function in Atopic Dermatitis: A Pilot Study. J Biol Rhythms 2024; 39:208-214. [PMID: 38305093 PMCID: PMC10994754 DOI: 10.1177/07487304231220695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Atopic dermatitis (AD) is symptomatically worse in the evening, but the mechanism driving nocturnal eczema remains elusive. Our objective was to determine the circadian rhythm of skin barrier function measured by transepidermal water loss (TEWL) in AD patients and explore the molecular underpinnings. A pilot study was performed on a diverse group of AD (n = 4) and control (n = 2) young patients. We used an inpatient tightly controlled, modified, constant routine protocol. TEWL was measured at least every 90 min in the antecubital fossa (lesional) and forearm, while whole blood samples were collected every 4 h. Results show a significant difference in the antecubital fossa TEWL in the AD group versus controls. TEWL in control skin decreases starting a few hours prior to bedtime, both in the antecubital fossa and in the forearm, while in the AD forearm skin, pre-bedtime TEWL increases. We identified 1576 differentially expressed genes using a time-dependent model. The top 20 upregulated gene ontology pathways included neuronal pathways, while the downregulated functional terms included innate immune signaling and viral response. Similar pathways positively correlated with forearm TEWL in controls and inversely with the AD group. Upregulation in sensory perception pathways correlated with increases in lesional (antecubital fossa) TEWL in the evening. Results show skin barrier function worsens in the evening in the AD group, at a time when barrier is normally rejuvenating in healthy skin. This timing and the detection of transcriptomic signatures of sensory perception and diminished viral response might correspond to the nocturnal itch. Larger studies are needed to evaluate these associations in the skin.
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Affiliation(s)
- Marta Iwanaszko
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611
| | - Nathan Waldeck
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 606112
| | - Ron Anafi
- Department of Medicine, Penn Institute for Bioinformatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104
| | - Amy S. Paller
- Departments of Dermatology and Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611
| | - Phyllis Zee
- Department of Neurology and Center for Circadian and Sleep Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611
| | - Anna Fishbein
- Department of Pediatrics, Division of Allergy-Immunology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611
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Ekvall M, Bergenstråhle L, Andersson A, Czarnewski P, Olegård J, Käll L, Lundeberg J. Spatial landmark detection and tissue registration with deep learning. Nat Methods 2024; 21:673-679. [PMID: 38438615 PMCID: PMC11009106 DOI: 10.1038/s41592-024-02199-5] [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: 07/10/2023] [Accepted: 01/30/2024] [Indexed: 03/06/2024]
Abstract
Spatial landmarks are crucial in describing histological features between samples or sites, tracking regions of interest in microscopy, and registering tissue samples within a common coordinate framework. Although other studies have explored unsupervised landmark detection, existing methods are not well-suited for histological image data as they often require a large number of images to converge, are unable to handle nonlinear deformations between tissue sections and are ineffective for z-stack alignment, other modalities beyond image data or multimodal data. We address these challenges by introducing effortless landmark detection, a new unsupervised landmark detection and registration method using neural-network-guided thin-plate splines. Our proposed method is evaluated on a diverse range of datasets including histology and spatially resolved transcriptomics, demonstrating superior performance in both accuracy and stability compared to existing approaches.
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Affiliation(s)
- Markus Ekvall
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden.
| | - Ludvig Bergenstråhle
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden
| | - Alma Andersson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden
| | - Paulo Czarnewski
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden
| | - Johannes Olegård
- Department of Computer and Systems Sciences, Stockholm University, Kista, Sweden
| | - Lukas Käll
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology - KTH, Solna, Sweden.
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Cristoferi I, Varol H, van Baardwijk M, Rahiem L, Lila KA, van den Bosch TPP, Baan CC, Hesselink DA, Kramann R, Minnee RC, Mustafa DAM, Reinders MEJ, Roelen DL, Shahzad-Arshad SP, Smith RN, Stubbs AP, Colvin RB, Rosales IA, Clahsen-van Groningen MC. Multiomic profiling of transplant glomerulopathy reveals a novel T-cell dominant subclass. Kidney Int 2024; 105:812-823. [PMID: 38128610 DOI: 10.1016/j.kint.2023.11.026] [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: 06/13/2023] [Revised: 09/04/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Kidney transplant (KTx) biopsies showing transplant glomerulopathy (TG) (glomerular basement membrane double contours (cg) > 0) and microvascular inflammation (MVI) in the absence of C4d staining and donor-specific antibodies (DSAs) do not fulfill the criteria for chronic active antibody-mediated rejection (CA-AMR) diagnosis and do not fit into any other Banff category. To investigate this, we initiated a multicenter intercontinental study encompassing 36 cases, comparing the immunomic and transcriptomic profiles of 14 KTx biopsies classified as cg+MVI DSA-/C4d- with 22 classified as CA-AMR DSA+/C4d+ through novel transcriptomic analysis using the NanoString Banff-Human Organ Transplant (B-HOT) panel and subsequent orthogonal subset analysis using two innovative 5-marker multiplex immunofluorescent panels. Nineteen genes were differentially expressed between the two study groups. Samples diagnosed with CA-AMR DSA+/C4d+ showed a higher glomerular abundance of natural killer cells and higher transcriptomic cell type scores for macrophages in an environment characterized by increased expression of complement-related genes (i.e., C5AR1) and higher activity of angiogenesis, interstitial fibrosis tubular atrophy, CA-AMR, and DSA-related pathways when compared to samples diagnosed with cg+MVI DSA-/C4d-. Samples diagnosed with cg+MVI DSA-/C4d- displayed a higher glomerular abundance and activity of T cells (CD3+, CD3+CD8+, and CD3+CD8-). Thus, we show that using novel multiomic techniques, KTx biopsies with cg+MVI DSA-/C4d- have a prominent T-cell presence and activity, putting forward the possibility that these represent a more T-cell dominant phenotype.
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Affiliation(s)
- Iacopo Cristoferi
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Transplant Institute, Rotterdam, the Netherlands; Department of Surgery, Division of HPB & Transplant Surgery, Erasmus MC Transplant Institute, Rotterdam, the Netherlands.
| | - Hilal Varol
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Myrthe van Baardwijk
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Transplant Institute, Rotterdam, the Netherlands; Department of Surgery, Division of HPB & Transplant Surgery, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Layla Rahiem
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Karishma A Lila
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Thierry P P van den Bosch
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Carla C Baan
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Dennis A Hesselink
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Rafael Kramann
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC Transplant Institute, Rotterdam, the Netherlands; Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany; Department of Nephrology and Clinical Immunology, University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Robert C Minnee
- Department of Surgery, Division of HPB & Transplant Surgery, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Dana A M Mustafa
- Department of Pathology and Clinical Bioinformatics, the Tumor Immuno-Pathology Laboratory, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Marlies E J Reinders
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Dave L Roelen
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Shazia P Shahzad-Arshad
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Rex N Smith
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew P Stubbs
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Transplant Institute, Rotterdam, the Netherlands
| | - Robert B Colvin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ivy A Rosales
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marian C Clahsen-van Groningen
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Transplant Institute, Rotterdam, the Netherlands; Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany.
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Gai Q, Chu T, Li Q, Guo Y, Ma H, Shi Y, Che K, Zhao F, Dong F, Li Y, Xie H, Mao N. Altered intersubject functional variability of brain white-matter in major depressive disorder and its association with gene expression profiles. Hum Brain Mapp 2024; 45:e26670. [PMID: 38553866 PMCID: PMC10980843 DOI: 10.1002/hbm.26670] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/02/2024] [Accepted: 03/13/2024] [Indexed: 04/02/2024] Open
Abstract
Major depressive disorder (MDD) is a clinically heterogeneous disorder. Its mechanism is still unknown. Although the altered intersubject variability in functional connectivity (IVFC) within gray-matter has been reported in MDD, the alterations to IVFC within white-matter (WM-IVFC) remain unknown. Based on the resting-state functional MRI data of discovery (145 MDD patients and 119 healthy controls [HCs]) and validation cohorts (54 MDD patients, and 78 HCs), we compared the WM-IVFC between the two groups. We further assessed the meta-analytic cognitive functions related to the alterations. The discriminant WM-IVFC values were used to classify MDD patients and predict clinical symptoms in patients. In combination with the Allen Human Brain Atlas, transcriptome-neuroimaging association analyses were further conducted to investigate gene expression profiles associated with WM-IVFC alterations in MDD, followed by a set of gene functional characteristic analyses. We found extensive WM-IVFC alterations in MDD compared to HCs, which were associated with multiple behavioral domains, including sensorimotor processes and higher-order functions. The discriminant WM-IVFC could not only effectively distinguish MDD patients from HCs with an area under curve ranging from 0.889 to 0.901 across three classifiers, but significantly predict depression severity (r = 0.575, p = 0.002) and suicide risk (r = 0.384, p = 0.040) in patients. Furthermore, the variability-related genes were enriched for synapse, neuronal system, and ion channel, and predominantly expressed in excitatory and inhibitory neurons. Our results obtained good reproducibility in the validation cohort. These findings revealed intersubject functional variability changes of brain WM in MDD and its linkage with gene expression profiles, providing potential implications for understanding the high clinical heterogeneity of MDD.
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Affiliation(s)
- Qun Gai
- Department of Radiology, Yantai Yuhuangding HospitalQingdao UniversityYantaiShandongChina
- Big Data & Artificial Intelligence LaboratoryYantai Yuhuangding HospitalYantaiShandongChina
- Shandong Provincial Key Medical and Health Laboratory of Intelligent Diagnosis and Treatment for Women's DiseasesYantai Yuhuangding HospitalYantaiShandongChina
| | - Tongpeng Chu
- Department of Radiology, Yantai Yuhuangding HospitalQingdao UniversityYantaiShandongChina
- Big Data & Artificial Intelligence LaboratoryYantai Yuhuangding HospitalYantaiShandongChina
- Shandong Provincial Key Medical and Health Laboratory of Intelligent Diagnosis and Treatment for Women's DiseasesYantai Yuhuangding HospitalYantaiShandongChina
| | - Qinghe Li
- School of Medical ImagingBinzhou Medical UniversityYantaiShandongChina
| | - Yuting Guo
- School of Medical ImagingBinzhou Medical UniversityYantaiShandongChina
| | - Heng Ma
- Department of Radiology, Yantai Yuhuangding HospitalQingdao UniversityYantaiShandongChina
| | - Yinghong Shi
- Department of Radiology, Yantai Yuhuangding HospitalQingdao UniversityYantaiShandongChina
| | - Kaili Che
- Department of Radiology, Yantai Yuhuangding HospitalQingdao UniversityYantaiShandongChina
| | - Feng Zhao
- School of Computer Science and TechnologyShandong Technology and Business UniversityYantaiShandongChina
| | - Fanghui Dong
- School of Medical ImagingBinzhou Medical UniversityYantaiShandongChina
| | - Yuna Li
- Department of Radiology, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Haizhu Xie
- Department of Radiology, Yantai Yuhuangding HospitalQingdao UniversityYantaiShandongChina
| | - Ning Mao
- Department of Radiology, Yantai Yuhuangding HospitalQingdao UniversityYantaiShandongChina
- Big Data & Artificial Intelligence LaboratoryYantai Yuhuangding HospitalYantaiShandongChina
- Shandong Provincial Key Medical and Health Laboratory of Intelligent Diagnosis and Treatment for Women's DiseasesYantai Yuhuangding HospitalYantaiShandongChina
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30
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Ge Y, Shi Y, Wei C, Uthamapriya RA, Wu Y, Cao L. The effects of quinoa bran dietary fiber on glucose and lipid metabolism and hepatic transcriptome in obese rats. J Sci Food Agric 2024; 104:2692-2703. [PMID: 37994153 DOI: 10.1002/jsfa.13154] [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] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/25/2023] [Accepted: 11/23/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND As a complex chronic metabolic disease, obesity not only affects the quality of human life but also increases the risk of various other diseases. Therefore, it is important to investigate the molecular mechanisms and therapeutic effects of dietary interventions that counteract obesity. RESULTS In this study, we extracted soluble (SDF) and insoluble dietary fiber (IDF) from quinoa bran using an enzymatic method and further investigated their effects on lipid metabolism and blood lipid levels in obese rats. Quinoa bran dietary fiber showed significantly reduced body weight, blood glucose level, total cholesterol, triglyceride, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol levels compared to those in the model group of obese rats. Aspartate aminotransferase and alanine aminotransferase levels were significantly lower in the IDF group, demonstrating that IDF improved liver injury more significantly than SDF, which was consistent with the analysis of liver tissue sections. IDF supplementation significantly improved the oxidation resistance of obese rats by decreasing malondialdehyde and increasing superoxide dismutase and glutathione peroxidase levels compared to the high-fat diet group levels. Transcriptome analysis showed that IDF caused hepatic changes in genes (Ehhadh, PPARα, FADS, CPT1, CPT2, SCD-1, Acadm, and CYP7A1) related to fatty acid degradation, and this result coincided with that of the gene expression validation result. CONCLUSION Overall, our research offers crucial data for the logical development of dietary fiber from quinoa bran with nutritional purposes. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yunfei Ge
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
- Department of Marine Food Science and Technology, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Yu Shi
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chunhong Wei
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Rajavel Arumugam Uthamapriya
- Department of Marine Food Science and Technology, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Yunjiao Wu
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
| | - LongKui Cao
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
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31
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Rowley SD, Gunning TS, Pelliccia M, Della Pia A, Lee A, Behrmann J, Bangolo A, Jandir P, Zhang H, Kaur S, Suh HC, Donato M, Albitar M, Ip A. Using Targeted Transcriptome and Machine Learning of Pre- and Post-Transplant Bone Marrow Samples to Predict Acute Graft-versus-Host Disease and Overall Survival after Allogeneic Stem Cell Transplantation. Cancers (Basel) 2024; 16:1357. [PMID: 38611035 PMCID: PMC11011125 DOI: 10.3390/cancers16071357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Acute graft-versus-host disease (aGvHD) remains a major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (HSCT). We performed RNA analysis of 1408 candidate genes in bone marrow samples obtained from 167 patients undergoing HSCT. RNA expression data were used in a machine learning algorithm to predict the presence or absence of aGvHD using either random forest or extreme gradient boosting algorithms. Patients were randomly divided into training (2/3 of patients) and validation (1/3 of patients) sets. Using post-HSCT RNA data, the machine learning algorithm selected 92 genes for predicting aGvHD that appear to play a role in PI3/AKT, MAPK, and FOXO signaling, as well as microRNA. The algorithm selected 20 genes for predicting survival included genes involved in MAPK and chemokine signaling. Using pre-HSCT RNA data, the machine learning algorithm selected 400 genes and 700 genes predicting aGvHD and overall survival, but candidate signaling pathways could not be specified in this analysis. These data show that NGS analyses of RNA expression using machine learning algorithms may be useful biomarkers of aGvHD and overall survival for patients undergoing HSCT, allowing for the identification of major signaling pathways associated with HSCT outcomes and helping to dissect the complex steps involved in the development of aGvHD. The analysis of pre-HSCT bone marrow samples may lead to pre-HSCT interventions including choice of remission induction regimens and modifications in patient health before HSCT.
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Affiliation(s)
- Scott D. Rowley
- Georgetown University School of Medicine, Washington, DC 20007, USA
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
| | - Thomas S. Gunning
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Michael Pelliccia
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Alexandra Della Pia
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
| | - Albert Lee
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - James Behrmann
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Ayrton Bangolo
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Parul Jandir
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Hong Zhang
- Genomic Testing Cooperative, Irvine, CA 92618, USA; (H.Z.); (M.A.)
| | - Sukhdeep Kaur
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Hyung C. Suh
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Michele Donato
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Maher Albitar
- Genomic Testing Cooperative, Irvine, CA 92618, USA; (H.Z.); (M.A.)
| | - Andrew Ip
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
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Czubala MA, Jenkins RH, Gurney M, Wallace L, Cossins B, Dennis J, Rosas M, Andrews R, Fraser D, Taylor PR. Tissue-specific transcriptional programming of macrophages controls the microRNA transcriptome targeting multiple functional pathways. J Biol Chem 2024:107244. [PMID: 38556087 DOI: 10.1016/j.jbc.2024.107244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
Recent interest in the biology and function of peritoneal tissue resident macrophages (pMΦ) has led to a better understanding of their cellular origin, programming and renewal. The programming of pMΦ is dependent on microenvironmental cues and tissue specific transcription factors, including GATA6. However, the contribution of microRNAs remains poorly defined. We conducted a detailed analysis of the impact of GATA6-deficiency on microRNA expression in mouse pMΦ. Our data suggest that for many of the pMΦ, microRNA composition may be established during tissue specialization, and that the effect of GATA6 knockout is largely unable to be rescued in the adult by exogenous GATA6. The data are consistent with GATA6 modulating the expression pattern of specific microRNAs, directly or indirectly, and including miR-146a, -223, and -203 established by the lineage-determining transcription factor PU.1, to achieve a differentiated pMΦ phenotype. Lastly, we showed a significant dysregulation of miR-708 in pMΦ in the absence of GATA6 during homeostasis and in response to LPS/IFN-γ stimulation. Overexpression of miR-708 in mouse pMΦ in vivo altered 167 mRNA species demonstrating functional downregulation of predicted targets, including cell immune responses and cell cycle regulation. In conclusion, we demonstrate dependence of the microRNA transcriptome on tissue-specific programming of tissue macrophages as exemplified by the role of GATA6 in pMΦ specialization.
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Affiliation(s)
- Magdalena A Czubala
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, CF14 0NN, UK
| | - Robert H Jenkins
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, CF14 0NN, UK
| | - Mark Gurney
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, CF14 0NN, UK
| | - Leah Wallace
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, CF14 0NN, UK
| | - Benjamin Cossins
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, CF14 0NN, UK
| | - James Dennis
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, CF14 0NN, UK
| | - Marcela Rosas
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, CF14 0NN, UK
| | - Robert Andrews
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, CF14 0NN, UK
| | - Donald Fraser
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, CF14 0NN, UK; Wales Kidney Research Unit, Cardiff University, CF14 0NN, UK
| | - Philip R Taylor
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, CF14 0NN, UK; UK Dementia Research Institute at Cardiff, Cardiff University, CF24 4HQ, UK
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Fayazzadeh S, Ghorbaninejad M, Rabbani A, Zahiri J, Meyfour A. Predictive three-biomarker panel in peripheral blood mononuclear cells for detecting hepatocellular carcinoma. Sci Rep 2024; 14:7527. [PMID: 38553531 PMCID: PMC10980807 DOI: 10.1038/s41598-024-58158-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024] Open
Abstract
Hepatocellular carcinoma (HCC) ranks among the most prevalent cancers and accounts for a significant proportion of cancer-associated deaths worldwide. This disease, marked by multifaceted etiology, often poses diagnostic challenges. Finding a reliable and non-invasive diagnostic method seems to be necessary. In this study, we analyzed the gene expression profiles of 20 HCC patients, 12 individuals with chronic hepatitis, and 15 healthy controls. Enrichment analysis revealed that platelet aggregation, secretory granule lumen, and G-protein-coupled purinergic nucleotide receptor activity were common biological processes, cellular components, and molecular function in HCC and chronic hepatitis B (CHB) compared to healthy controls, respectively. Furthermore, pathway analysis demonstrated that "estrogen response" was involved in the pathogenesis of HCC and CHB conditions, while, "apoptosis" and "coagulation" pathways were specific for HCC. Employing computational feature selection and logistic regression classification, we identified candidate genes pivotal for diagnostic panel development and evaluated the performance of these panels. Subsequent machine learning evaluations assessed these panels' performance in an independent cohort. Remarkably, a 3-marker panel, comprising RANSE2, TNF-α, and MAP3K7, demonstrated the best performance in qRT-PCR-validated experimental data, achieving 98.4% accuracy and an area under the curve of 1. Our findings highlight this panel's promising potential as a non-invasive approach not only for detecting HCC but also for distinguishing HCC from CHB patients.
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Affiliation(s)
- Sara Fayazzadeh
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahsa Ghorbaninejad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirhassan Rabbani
- Department of Transplant and Hepatobiliary Surgery, Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Kumwenda B, Canals R, Predeus AV, Zhu X, Kröger C, Pulford C, Wenner N, Lora LL, Li Y, Owen SV, Everett D, Hokamp K, Heyderman RS, Ashton PM, Gordon MA, Msefula CL, Hinton JCD. Salmonella enterica serovar Typhimurium ST313 sublineage 2.2 has emerged in Malawi with a characteristic gene expression signature and a fitness advantage. Microlife 2024; 5:uqae005. [PMID: 38623411 PMCID: PMC11018118 DOI: 10.1093/femsml/uqae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024]
Abstract
Invasive non-typhoidal Salmonella (iNTS) disease is a serious bloodstream infection that targets immune-compromised individuals, and causes significant mortality in sub-Saharan Africa. Salmonella enterica serovar Typhimurium ST313 causes the majority of iNTS in Malawi. We performed an intensive comparative genomic analysis of 608 S. Typhimurium ST313 isolates dating between 1996 and 2018 from Blantyre, Malawi. We discovered that following the arrival of the well-characterized S. Typhimurium ST313 lineage 2 in 1999, two multidrug-resistant variants emerged in Malawi in 2006 and 2008, designated sublineages 2.2 and 2.3, respectively. The majority of S. Typhimurium isolates from human bloodstream infections in Malawi now belong to sublineages 2.2 or 2.3. To understand the emergence of the prevalent ST313 sublineage 2.2, we studied two representative strains, D23580 (lineage 2) and D37712 (sublineage 2.2). The chromosome of ST313 lineage 2 and sublineage 2.2 only differed by 29 SNPs/small indels and a 3 kb deletion of a Gifsy-2 prophage region including the sseI pseudogene. Lineage 2 and sublineage 2.2 had distinctive plasmid profiles. The transcriptome was investigated in 15 infection-relevant in vitro conditions and within macrophages. During growth in physiological conditions that do not usually trigger S. Typhimurium SPI2 gene expression, the SPI2 genes of D37712 were transcriptionally active. We identified down-regulation of flagellar genes in D37712 compared with D23580. Following phenotypic confirmation of transcriptomic differences, we discovered that sublineage 2.2 had increased fitness compared with lineage 2 during mixed growth in minimal media. We speculate that this competitive advantage is contributing to the emergence of sublineage 2.2 in Malawi.
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Affiliation(s)
- Benjamin Kumwenda
- School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences Blantyre, Blantyre, 265, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
| | - Rocío Canals
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Alexander V Predeus
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Xiaojun Zhu
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Carsten Kröger
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Caisey Pulford
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Nicolas Wenner
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Lizeth Lacharme Lora
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Yan Li
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Siân V Owen
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Dean Everett
- Department of Public Health and Epidemiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, P.O. Box 127788, United Arab Emirates
| | - Karsten Hokamp
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Robert S Heyderman
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
- Research Department of Infection, Division of Infection & Immunity, University College London, London, WC1E 6BT, United Kingdom
| | | | - Melita A Gordon
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
| | - Chisomo L Msefula
- School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences Blantyre, Blantyre, 265, Malawi
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
| | - Jay C D Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
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Rahimzadeh N, Srinivasan SS, Zhang J, Swarup V. Gene networks and systems biology in Alzheimer's disease: Insights from multi-omics approaches. Alzheimers Dement 2024. [PMID: 38534018 DOI: 10.1002/alz.13790] [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: 10/20/2023] [Revised: 01/25/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
Despite numerous studies in the field of dementia and Alzheimer's disease (AD), a comprehensive understanding of this devastating disease remains elusive. Bulk transcriptomics have provided insights into the underlying genetic factors at a high level. Subsequent technological advancements have focused on single-cell omics, encompassing techniques such as single-cell RNA sequencing and epigenomics, enabling the capture of RNA transcripts and chromatin states at a single cell or nucleus resolution. Furthermore, the emergence of spatial omics has allowed the study of gene responses in the vicinity of amyloid beta plaques or across various brain regions. With the vast amount of data generated, utilizing gene regulatory networks to comprehensively study this disease has become essential. This review delves into some techniques employed in the field of AD, explores the discoveries made using these techniques, and provides insights into the future of the field.
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Affiliation(s)
- Negin Rahimzadeh
- Mathematical, Computational, and Systems Biology (MCSB) Program, University of California Irvine, Irvine, California, USA
| | - Shushrruth Sai Srinivasan
- Mathematical, Computational, and Systems Biology (MCSB) Program, University of California Irvine, Irvine, California, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, California, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, California, USA
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Gu Y, Liu Y, Mao W, Peng Y, Han X, Jin H, Xu J, Chang L, Hou Y, Shen X, Liu X, Yang Y. Functional versatility of Zur in metal homeostasis, motility, biofilm formation, and stress resistance in Yersinia pseudotuberculosis. Microbiol Spectr 2024:e0375623. [PMID: 38534119 DOI: 10.1128/spectrum.03756-23] [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: 10/23/2023] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
Zur (zinc uptake regulator) is a significant member of the Fur (ferric uptake regulator) superfamily, which is widely distributed in bacteria. Zur plays crucial roles in zinc homeostasis and influences cell development and environmental adaptation in various species. Yersinia pseudotuberculosis is a Gram-negative enteric that pathogen usually serves as a model organism in pathogenicity studies. The regulatory effects of Zur on the zinc transporter ZnuABC and the protein secretion system T6SS have been documented in Y. pseudotuberculosis. In this study, a comparative transcriptomics analysis between a ∆zur mutant and the wild-type (WT) strain of Y. pseudotuberculosis was conducted using RNA-seq. This analysis revealed global regulation by Zur across multiple functional categories, including membrane transport, cell motility, and molecular and energy metabolism. Additionally, Zur mediates the homeostasis not only of zinc but also ferric and magnesium in vivo. There was a notable decrease in 35 flagellar biosynthesis and assembly-related genes, leading to reduced swimming motility in the ∆zur mutant strain. Furthermore, Zur upregulated multiple simple sugar and oligopeptide transport system genes by directly binding to their promoters. The absence of Zur inhibited biofilm formation as well as reduced resistance to chloramphenicol and acidic stress. This study illustrates the comprehensive regulatory functions of Zur, emphasizing its importance in stress resistance and pathogenicity in Y. pseudotuberculosis. IMPORTANCE Bacteria encounter diverse stresses in the environment and possess essential regulators to modulate the expression of genes in responding to the stresses for better fitness and survival. Zur (zinc uptake regulator) plays a vital role in zinc homeostasis. Studies of Zur from multiple species reviewed that it influences cell development, stress resistance, and virulence of bacteria. Y. pseudotuberculosis is an enteric pathogen that serves a model organism in the study of pathogenicity, virulence factors, and mechanism of environmental adaptation. In this study, transcriptomics analysis of Zur's regulons was conducted in Y. pseudotuberculosis. The functions of Zur as a global regulator in metal homeostasis, motility, nutrient acquisition, glycan metabolism, and nucleotide metabolism, in turn, increasing the biofilm formation, stress resistance, and virulence were reviewed. The importance of Zur in environmental adaptation and pathogenicity of Y. pseudotuberculosis was emphasized.
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Affiliation(s)
- Yanchao Gu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yongde Liu
- Qingyang Longfeng Sponge City Construction Management and Operation Co., Ltd, Qingyang, China
| | - Wei Mao
- Qingyang Longfeng Sponge City Construction Management and Operation Co., Ltd, Qingyang, China
| | - Ying Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiaoru Han
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Han Jin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Jingling Xu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Liyang Chang
- College of Enology, Northwest A&F University, Yangling, China
| | - Yixin Hou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xingyu Liu
- General Research Institute for Nonferrous Metals, Beijing, China
| | - Yantao Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
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Machado JPD, de Almeida V, Zuardi AW, Hallak JEC, Crippa JA, Vieira AS. Cannabidiol modulates hippocampal genes involved in mitochondrial function, ribosome biogenesis, synapse organization, and chromatin modifications. Acta Neuropsychiatr 2024:1-20. [PMID: 38528655 DOI: 10.1017/neu.2024.13] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
BACKGROUND Cannabidiol (CBD) is one of the main cannabinoids present in Cannabis sativa female flowers. Previous investigation has already provided insights into the CBD molecular mechanism, however, there is no transcriptome data for CBD effects on hippocampal subfields. Here, we investigate transcriptomic changes in dorsal and ventral CA1 of adult mice hippocampus after 100 mg/kg of CBD administration (i.p.) for one or seven consecutive days. METHODS C57BL/6JUnib mice were treated with either vehicle or CBD for 1 or 7 days. The collected brains were sectioned and the hippocampal subregions were laser microdissected for RNA-Seq analysis. RESULTS The transcriptome analysis following 7 days of CBD administration indicates the differential expression of 1559 genes in dCA1 and 2924 genes in vCA1. Furthermore, GO/KEGG analysis identified 88 significantly enriched Biological Process (BPs) and 26 significantly enriched pathways for dCBD7, whereas vCBD7 revealed 128 enriched BPs and 24 pathways. CONCLUSION This dataset indicates a widespread decrease of electron transport chain and ribosome biogenesis transcripts in CA1, while chromatin modifications and synapse organization transcripts were increased following CBD administration for 7 days.
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Affiliation(s)
- João P D Machado
- Laboratory of Electrophysiology, Neurobiology and Behaviour, Dept. Functional and Structural Biology, Institute of Biology, University of Campinas
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - Valéria de Almeida
- Laboratory of Neuroproteomics, Dept. Biochemistry and Tissue Biology, Institute of Biology, University of Campinas
| | - Antonio W Zuardi
- Department of Neuroscience and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National Institute for Science and Technology - Translational Medicine, Brazil
| | - Jaime E C Hallak
- Department of Neuroscience and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National Institute for Science and Technology - Translational Medicine, Brazil
| | - José A Crippa
- Department of Neuroscience and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National Institute for Science and Technology - Translational Medicine, Brazil
| | - André S Vieira
- Laboratory of Electrophysiology, Neurobiology and Behaviour, Dept. Functional and Structural Biology, Institute of Biology, University of Campinas
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
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Bergum OET, Singleton AH, Røst LM, Bodein A, Scott-Boyer MP, Rye MB, Droit A, Bruheim P, Otterlei M. SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated. Front Microbiol 2024; 15:1373344. [PMID: 38596376 PMCID: PMC11002266 DOI: 10.3389/fmicb.2024.1373344] [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: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
The DNA damage inducible SOS response in bacteria serves to increase survival of the species at the cost of mutagenesis. The SOS response first initiates error-free repair followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions, and a low dose of the antibiotic ciprofloxacin was used to activate the SOS response while avoiding extensive cell death. Our results show that expression of genes involved in error-free and error-prone repair were both induced shortly after DNA damage, thus, challenging the established perception that the expression of error-prone repair genes is delayed. By combining transcriptomics and a sub-proteomics approach termed signalomics, we found that the temporal segregation of error-free and error-prone repair is primarily regulated after transcription, supporting the current literature. Furthermore, the heterology index (i.e., the binding affinity of LexA to the SOS box) was correlated to the maximum increase in gene expression and not to the time of induction of SOS genes. Finally, quantification of metabolites revealed increasing pyrimidine pools as a late feature of the SOS response. Our results elucidate how the SOS response is coordinated, showing a rapid transcriptional response and temporal regulation of mutagenesis on the protein and metabolite levels.
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Affiliation(s)
| | - Amanda Holstad Singleton
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Antoine Bodein
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Arnaud Droit
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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Koch B, Shehata M, Müller-Ruttloff C, Gouda SA, Wetzstein N, Patyna S, Scholz A, Schmid T, Dietrich U, Münch C, Ziebuhr J, Geiger H, Martinez-Sobrido L, Baer PC, Mostafa A, Pleschka S. Influenza A virus replicates productively in primary human kidney cells and induces factors and mechanisms related to regulated cell death and renal pathology observed in virus-infected patients. Front Cell Infect Microbiol 2024; 14:1363407. [PMID: 38590437 PMCID: PMC10999593 DOI: 10.3389/fcimb.2024.1363407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/29/2024] [Indexed: 04/10/2024] Open
Abstract
Introduction Influenza A virus (IAV) infection can cause the often-lethal acute respiratory distress syndrome (ARDS) of the lung. Concomitantly, acute kidney injury (AKI) is frequently noticed during IAV infection, correlating with an increased mortality. The aim of this study was to elucidate the interaction of IAV with human kidney cells and, thereby, to assess the mechanisms underlying IAV-mediated AKI. Methods To investigate IAV effects on nephron cells we performed infectivity assays with human IAV, as well as with human isolates of either low or highly pathogenic avian IAV. Also, transcriptome and proteome analysis of IAV-infected primary human distal tubular kidney cells (DTC) was performed. Furthermore, the DTC transcriptome was compared to existing transcriptomic data from IAV-infected lung and trachea cells. Results We demonstrate productive replication of all tested IAV strains on primary and immortalized nephron cells. Comparison of our transcriptome and proteome analysis of H1N1-type IAV-infected human primary distal tubular cells (DTC) with existing data from H1N1-type IAV-infected lung and primary trachea cells revealed enrichment of specific factors responsible for regulated cell death in primary DTC, which could be targeted by specific inhibitors. Discussion IAV not only infects, but also productively replicates on different human nephron cells. Importantly, multi-omics analysis revealed regulated cell death as potential contributing factor for the clinically observed kidney pathology in influenza.
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Affiliation(s)
- Benjamin Koch
- Department of Internal Medicine 4, Nephrology, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mahmoud Shehata
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Christin Müller-Ruttloff
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen, Giessen, Germany
| | - Shady A. Gouda
- Institute for Biochemistry II, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nils Wetzstein
- Department of Internal Medicine 2, Infectious Diseases, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sammy Patyna
- Department of Internal Medicine 4, Nephrology, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anica Scholz
- Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ursula Dietrich
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Christian Münch
- Institute for Biochemistry II, Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Frankfurt am Main, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen, Giessen, Germany
| | - Helmut Geiger
- Department of Internal Medicine 4, Nephrology, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Luis Martinez-Sobrido
- Texas Biomedical Research Institute, Disease Intervention & Prevention (DIP) and Host Pathogen Interactions (HPI) Programs, San Antonio, TX, United States
| | - Patrick C. Baer
- Department of Internal Medicine 4, Nephrology, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Texas Biomedical Research Institute, Disease Intervention & Prevention (DIP) and Host Pathogen Interactions (HPI) Programs, San Antonio, TX, United States
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen, Giessen, Germany
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Bonzi LC, Donelson JM, Spinks RK, Munday PL, Ravasi T, Schunter C. Matching maternal and paternal experiences underpin molecular thermal acclimation. Mol Ecol 2024:e17328. [PMID: 38520127 DOI: 10.1111/mec.17328] [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: 10/04/2023] [Revised: 01/25/2024] [Accepted: 03/04/2024] [Indexed: 03/25/2024]
Abstract
The environment experienced by one generation has the potential to affect the subsequent one through non-genetic inheritance of parental effects. Since both mothers and fathers can influence their offspring, questions arise regarding how the maternal, paternal and offspring experiences integrate into the resulting phenotype. We aimed to disentangle the maternal and paternal contributions to transgenerational thermal acclimation in a reef fish, Acanthochromis polyacanthus, by exposing two generations to elevated temperature (+1.5°C) in a fully factorial design and analysing the F2 hepatic gene expression. Paternal and maternal effects showed not only common but also parent-specific components, with the father having the largest influence in shaping the offspring's transcriptomic profile. Fathers contributed to transcriptional transgenerational response to warming through transfer of epigenetically controlled stress-response mechanisms while mothers influenced increased gene expression associated with lipid metabolism regulation. However, the key to acclimation potential was matching thermal experiences of the parents. When both parents were exposed to the same condition, offspring showed increased expression of genes related to structural RNA production and transcriptional regulation, whereas environmental mismatch in parents resulted in maladaptive parental condition transfer, revealed by translation suppression and endoplasmic reticulum stress. Interestingly, the offspring's own environmental experience had the smallest influence on their hepatic transcription profiles. Taken together, our results show the complex nature of the interplay among paternal, maternal and offspring cue integration, and reveal that acclimation potential to ocean warming might depend not only on maternal and paternal contributions but importantly on congruent parental thermal experiences.
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Affiliation(s)
- L C Bonzi
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - J M Donelson
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - R K Spinks
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Blue Carbon Section, Australian Government Department of Climate Change, Energy, the Environment and Water, Canberra, Australian Capital Territory, Australia
| | - P L Munday
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - T Ravasi
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - C Schunter
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong, Hong Kong SAR
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van Gurp L, Fodoulian L, Oropeza D, Furuyama K, Bru-Tari E, Vu AN, Kaddis JS, Rodríguez I, Thorel F, Herrera PL. Author Correction: Generation of human islet cell type-specific identity genesets. Nat Commun 2024; 15:2574. [PMID: 38519459 PMCID: PMC10960003 DOI: 10.1038/s41467-024-46525-z] [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: 03/25/2024] Open
Affiliation(s)
- Léon van Gurp
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Leon Fodoulian
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
| | - Daniel Oropeza
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Kenichiro Furuyama
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara, Sakyo, 606-8507, Kyoto, Japan
| | - Eva Bru-Tari
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Anh Nguyet Vu
- Department of Diabetes & Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E Duarte Rd, Duarte, CA, 91010, USA
| | - John S Kaddis
- Department of Diabetes & Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E Duarte Rd, Duarte, CA, 91010, USA
| | - Iván Rodríguez
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
| | - Fabrizio Thorel
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Pedro L Herrera
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland.
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Bolton PE, Ryder TB, Dakin R, Houtz JL, Moore IT, Balakrishnan CN, Horton BM. Neurogenomic landscape associated with status-dependent cooperative behaviour. Mol Ecol 2024:e17327. [PMID: 38511765 DOI: 10.1111/mec.17327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/04/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
The neurogenomic mechanisms mediating male-male reproductive cooperative behaviours remain unknown. We leveraged extensive transcriptomic and behavioural data on a neotropical bird species (Pipra filicauda) that performs cooperative courtship displays to understand these mechanisms. In this species, the cooperative display is modulated by testosterone, which promotes cooperation in non-territorial birds, but suppresses cooperation in territory holders. We sought to understand the neurogenomic underpinnings of three related traits: social status, cooperative display behaviour and testosterone phenotype. To do this, we profiled gene expression in 10 brain nuclei spanning the social decision-making network (SDMN), and two key endocrine tissues that regulate social behaviour. We associated gene expression with each bird's behavioural and endocrine profile derived from 3 years of repeated measures taken from free-living birds in the Ecuadorian Amazon. We found distinct landscapes of constitutive gene expression were associated with social status, testosterone phenotype and cooperation, reflecting the modular organization and engagement of neuroendocrine tissues. Sex-steroid and neuropeptide signalling appeared to be important in mediating status-specific relationships between testosterone and cooperation, suggesting shared regulatory mechanisms with male aggressive and sexual behaviours. We also identified differentially regulated genes involved in cellular activity and synaptic potentiation, suggesting multiple mechanisms underpin these genomic states. Finally, we identified SDMN-wide gene expression differences between territorial and floater males that could form the basis of 'status-specific' neurophysiological phenotypes, potentially mediated by testosterone and growth hormone. Overall, our findings provide new, systems-level insights into the mechanisms of cooperative behaviour and suggest that differences in neurogenomic state are the basis for individual differences in social behaviour.
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Affiliation(s)
- Peri E Bolton
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - T Brandt Ryder
- Migratory Bird Center, Smithsonian National Zoological Park, Washington, District of Columbia, USA
- Bird Conservancy of the Rockies, Fort Collins, Colorado, USA
| | - Roslyn Dakin
- Migratory Bird Center, Smithsonian National Zoological Park, Washington, District of Columbia, USA
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Jennifer L Houtz
- Department of Biology, Millersville University, Millersville, Pennsylvania, USA
- Department of Biology, Allegheny College, Meadville, Pennsylvania, USA
| | - Ignacio T Moore
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Brent M Horton
- Department of Biology, Millersville University, Millersville, Pennsylvania, USA
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González-Peñas J, Alloza C, Brouwer R, Díaz-Caneja CM, Costas J, González-Lois N, Gallego AG, de Hoyos L, Gurriarán X, Andreu-Bernabeu Á, Romero-García R, Fañanas L, Bobes J, Pinto AG, Crespo-Facorro B, Martorell L, Arrojo M, Vilella E, Guitiérrez-Zotes A, Perez-Rando M, Moltó MD, Buimer E, van Haren N, Cahn W, O'Donovan M, Kahn RS, Arango C, Pol HH, Janssen J, Schnack H. Accelerated Cortical Thinning in Schizophrenia is Associated With Rare and Common Predisposing Variation to Schizophrenia and Neurodevelopmental Disorders. Biol Psychiatry 2024:S0006-3223(24)01170-3. [PMID: 38521159 DOI: 10.1016/j.biopsych.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Schizophrenia is a highly heritable disorder characterized by increased cortical thinning throughout the lifespan. Studies have reported a shared genetic basis between schizophrenia and cortical thickness. However, no genes whose expression is related to abnormal cortical thinning in schizophrenia have been identified. METHODS We conducted linear mixed models to estimate the rates of accelerated cortical thinning across 68 regions from the Desikan-Killiany atlas in individuals with schizophrenia compared to healthy controls from a large longitudinal sample (NCases = 169 and NControls = 298, aged 16-70 years). We studied the correlation between gene expression data from the Allen Human Brain Atlas and accelerated thinning estimates across cortical regions. We finally explored the functional and genetic underpinnings of the genes most contributing to accelerated thinning. RESULTS We described a global pattern of accelerated cortical thinning in individuals with schizophrenia compared to healthy controls. Genes underexpressed in cortical regions exhibiting this accelerated thinning were downregulated in several psychiatric disorders and were enriched for both common and rare disrupting variation for schizophrenia and neurodevelopmental disorders. In contrast, none of these enrichments were observed for baseline cross-sectional cortical thickness differences. CONCLUSIONS Our findings suggest that accelerated cortical thinning, rather than cortical thickness alone, serves as an informative phenotype for neurodevelopmental disruptions in schizophrenia. We highlight the genetic and transcriptomic correlates of this accelerated cortical thinning, emphasizing the need for future longitudinal studies to elucidate the role of genetic variation and the temporal-spatial dynamics of gene expression in brain development and aging in schizophrenia.
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Affiliation(s)
- Javier González-Peñas
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain.
| | - Clara Alloza
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain
| | - Rachel Brouwer
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus. Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Covadonga M Díaz-Caneja
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; School of Medicine, Universidad Complutense, Madrid, Spain
| | - Javier Costas
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Galicia, Spain
| | - Noemí González-Lois
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Ana Guil Gallego
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Lucía de Hoyos
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Xaquín Gurriarán
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain
| | - Álvaro Andreu-Bernabeu
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain
| | - Rafael Romero-García
- Department of Psychiatry, University of Cambridge UK; Department of Medical Physiology and Biophysics, Instituto de Biomedicina de Sevilla (IBiS), HUVR/CSIC/Universidad de Sevilla/CIBERSAM, ISCIII, Sevilla, Spain
| | - Lourdes Fañanas
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Julio Bobes
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; Faculty of Medicine and Health Sciences - Psychiatry, Universidad de Oviedo, ISPA, INEUROPA. Oviedo, Spain
| | - Ana González Pinto
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; BIOARABA Health Research Institute, OSI Araba, University Hospital, University of the Basque Country, Vitoria, Spain
| | - Benedicto Crespo-Facorro
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; Hospital Universitario Virgen del Rocío, Department of Psychiatry, Universidad de Sevilla, Sevilla, Spain
| | - Lourdes Martorell
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; Hospital Universitari Institut Pere Mata, Institut d'Investigació Sanitària Pere Virgili-CERCA, Universitat Rovira i Virgili, Reus, Spain
| | - Manuel Arrojo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Galicia, Spain
| | - Elisabet Vilella
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; Hospital Universitari Institut Pere Mata, Institut d'Investigació Sanitària Pere Virgili-CERCA, Universitat Rovira i Virgili, Reus, Spain
| | - Alfonso Guitiérrez-Zotes
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; Hospital Universitari Institut Pere Mata, Institut d'Investigació Sanitària Pere Virgili-CERCA, Universitat Rovira i Virgili, Reus, Spain
| | - Marta Perez-Rando
- Fundación Investigación Hospital Clínico de Valencia, INCLIVA, Valencia, Spain; Unidad de Neurobiología, Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València,Valencia, Spain
| | - María Dolores Moltó
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; Unidad de Neurobiología, Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València,Valencia, Spain; Department of Genetics, Universitat de València, Campus of Burjassot, Valencia, Spain
| | - Elizabeth Buimer
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Neeltje van Haren
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Wiepke Cahn
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands; Altrecht Mental Health Institute, Altrecht Science, Utrecht, The Netherlands
| | - Michael O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics and Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - René S Kahn
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; School of Medicine, Universidad Complutense, Madrid, Spain
| | - Hilleke Hulshoff Pol
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Joost Janssen
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain; Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hugo Schnack
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
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Blomberg J, Tasselius V, Vergara A, Karamat F, Imran QM, Strand Å, Rosvall M, Björklund S. Pseudomonas syringae infectivity correlates to altered transcript and metabolite levels of Arabidopsis mediator mutants. Sci Rep 2024; 14:6771. [PMID: 38514763 PMCID: PMC10958028 DOI: 10.1038/s41598-024-57192-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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants, med16, med18, med25 and cdk8, we studied how differences in regulation of their transcript and metabolite levels correlate to their responses to Pseudomonas syringae infection. We found that med16 and cdk8 were susceptible, while med25 showed increased resistance. Glucosinolate, phytoalexin and carbohydrate levels were reduced already before infection in med16 and cdk8, but increased in med25, which also displayed increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzenoids, oxylipins and the phytoalexin camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlated to their infection response phenotypes. Our results reveal that MED16, MED25 and CDK8 are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses to Pseudomonas syringae infections.
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Affiliation(s)
- Jeanette Blomberg
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Viktor Tasselius
- Department of Physics, Umeå University, 901 87, Umeå, Sweden
- Biostatistics, School of Public Health and Community Medicine, Gothenburg University, P.O. Box 463, 405 30, Gothenburg, Sweden
| | | | - Fazeelat Karamat
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Qari Muhammad Imran
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Åsa Strand
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87, Umeå, Sweden
| | - Martin Rosvall
- Department of Physics, Umeå University, 901 87, Umeå, Sweden
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden.
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Wiśniewska K, Gaffke L, Żabińska M, Węgrzyn G, Pierzynowska K. Cellular Organelle-Related Transcriptomic Profile Abnormalities in Neuronopathic Types of Mucopolysaccharidosis: A Comparison with Other Neurodegenerative Diseases. Curr Issues Mol Biol 2024; 46:2678-2700. [PMID: 38534785 DOI: 10.3390/cimb46030169] [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: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Mucopolysaccharidoses (MPS) are a group of diseases caused by mutations in genes encoding lysosomal enzymes that catalyze reactions of glycosaminoglycan (GAG) degradation. As a result, GAGs accumulate in lysosomes, impairing the proper functioning of entire cells and tissues. There are 14 types/subtypes of MPS, which are differentiated by the kind(s) of accumulated GAG(s) and the type of a non-functional lysosomal enzyme. Some of these types (severe forms of MPS types I and II, MPS III, and MPS VII) are characterized by extensive central nervous system disorders. The aim of this work was to identify, using transcriptomic methods, organelle-related genes whose expression levels are changed in neuronopathic types of MPS compared to healthy cells while remaining unchanged in non-neuronopathic types of MPS. The study was conducted with fibroblast lines derived from patients with neuronopathic and non-neuronopathic types of MPS and control (healthy) fibroblasts. Transcriptomic analysis has identified genes related to cellular organelles whose expression is altered. Then, using fluorescence and electron microscopy, we assessed the morphology of selected structures. Our analyses indicated that the genes whose expression is affected in neuronopathic MPS are often associated with the structures or functions of the cell nucleus, endoplasmic reticulum, or Golgi apparatus. Electron microscopic studies confirmed disruptions in the structures of these organelles. Special attention was paid to up-regulated genes, such as PDIA3 and MFGE8, and down-regulated genes, such as ARL6IP6, ABHD5, PDE4DIP, YIPF5, and CLDN11. Of particular interest is also the GM130 (GOLGA2) gene, which encodes golgin A2, which revealed an increased expression in neuronopathic MPS types. We propose to consider the levels of mRNAs of these genes as candidates for biomarkers of neurodegeneration in MPS. These genes may also become potential targets for therapies under development for neurological disorders associated with MPS and candidates for markers of the effectiveness of these therapies. Although fibroblasts rather than nerve cells were used in this study, it is worth noting that potential genetic markers characteristic solely of neurons would be impractical in testing patients, contrary to somatic cells that can be relatively easily obtained from assessed persons.
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Affiliation(s)
- Karolina Wiśniewska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Magdalena Żabińska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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da Silva RH, Silva MDD, Ferreira-Neto JRC, Souza BDB, de Araújo FN, Oliveira EJDS, Benko-Iseppon AM, da Costa AF, Kido ÉA. DEAD-Box RNA Helicase Family in Physic Nut ( Jatropha curcas L.): Structural Characterization and Response to Salinity. Plants (Basel) 2024; 13:905. [PMID: 38592921 PMCID: PMC10974417 DOI: 10.3390/plants13060905] [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: 01/19/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Helicases, motor proteins present in both prokaryotes and eukaryotes, play a direct role in various steps of RNA metabolism. Specifically, SF2 RNA helicases, a subset of the DEAD-box family, are essential players in plant developmental processes and responses to biotic and abiotic stresses. Despite this, information on this family in the physic nut (Jatropha curcas L.) remains limited, spanning from structural patterns to stress responses. We identified 79 genes encoding DEAD-box RNA helicases (JcDHX) in the J. curcas genome. These genes were further categorized into three subfamilies: DEAD (42 genes), DEAH (30 genes), and DExH/D (seven genes). Characterization of the encoded proteins revealed a remarkable diversity, with observed patterns in domains, motifs, and exon-intron structures suggesting that the DEAH and DExH/D subfamilies in J. curcas likely contribute to the overall versatility of the family. Three-dimensional modeling of the candidates showed characteristic hallmarks, highlighting the expected functional performance of these enzymes. The promoter regions of the JcDHX genes revealed potential cis-elements such as Dof-type, BBR-BPC, and AP2-ERF, indicating their potential involvement in the response to abiotic stresses. Analysis of RNA-Seq data from the roots of physic nut accessions exposed to 150 mM of NaCl for 3 h showed most of the JcDHX candidates repressed. The protein-protein interaction network indicated that JcDHX proteins occupy central positions, connecting events associated with RNA metabolism. Quantitative PCR analysis validated the expression of nine DEAD-box RNA helicase transcripts, showing significant associations with key components of the stress response, including RNA turnover, ribosome biogenesis, DNA repair, clathrin-mediated vesicular transport, phosphatidyl 3,5-inositol synthesis, and mitochondrial translation. Furthermore, the induced expression of one transcript (JcDHX44) was confirmed, suggesting that it is a potential candidate for future functional analyses to better understand its role in salinity stress tolerance. This study represents the first global report on the DEAD-box family of RNA helicases in physic nuts and displays structural characteristics compatible with their functions, likely serving as a critical component of the plant's response pathways.
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Affiliation(s)
- Rahisa Helena da Silva
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - Manassés Daniel da Silva
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - José Ribamar Costa Ferreira-Neto
- Plant Genetics and Biotechnology Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - Bruna de Brito Souza
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - Francielly Negreiros de Araújo
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - Elvia Jéssica da Silva Oliveira
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - Ana Maria Benko-Iseppon
- Plant Genetics and Biotechnology Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | | | - Éderson Akio Kido
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
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Ren L, Wang J, Li W, Guo M, Yu G. Single-cell RNA-seq data clustering by deep information fusion. Brief Funct Genomics 2024; 23:128-137. [PMID: 37208992 DOI: 10.1093/bfgp/elad017] [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: 08/26/2022] [Revised: 02/13/2023] [Indexed: 05/21/2023] Open
Abstract
Determining cell types by single-cell transcriptomics data is fundamental for downstream analysis. However, cell clustering and data imputation still face the computation challenges, due to the high dropout rate, sparsity and dimensionality of single-cell data. Although some deep learning based solutions have been proposed to handle these challenges, they still can not leverage gene attribute information and cell topology in a sensible way to explore the consistent clustering. In this paper, we present scDeepFC, a deep information fusion-based single-cell data clustering method for cell clustering and data imputation. Specifically, scDeepFC uses a deep auto-encoder (DAE) network and a deep graph convolution network to embed high-dimensional gene attribute information and high-order cell-cell topological information into different low-dimensional representations, and then fuses them to generate a more comprehensive and accurate consensus representation via a deep information fusion network. In addition, scDeepFC integrates the zero-inflated negative binomial (ZINB) into DAE to model the dropout events. By jointly optimizing the ZINB loss and cell graph reconstruction loss, scDeepFC generates a salient embedding representation for clustering cells and imputing missing data. Extensive experiments on real single-cell datasets prove that scDeepFC outperforms other popular single-cell analysis methods. Both the gene attribute and cell topology information can improve the cell clustering.
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Affiliation(s)
- Liangrui Ren
- School of Software, Shandong University, 250101 Ji'nan, China
| | - Jun Wang
- Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University, 250101 Ji'nan, China
| | - Wei Li
- School of Control Science and Engineering, Shandong University, 250061 Ji'nan, China
| | - Maozu Guo
- College of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, 100044,Bei'jing, China
| | - Guoxian Yu
- School of Software, Shandong University, 250101 Ji'nan, China
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Gunter HM, Youlten SE, Reis ALM, McCubbin T, Madala BS, Wong T, Stevanovski I, Cipponi A, Deveson IW, Santini NS, Kummerfeld S, Croucher PI, Marcellin E, Mercer TR. A universal molecular control for DNA, mRNA and protein expression. Nat Commun 2024; 15:2480. [PMID: 38509097 PMCID: PMC10954659 DOI: 10.1038/s41467-024-46456-9] [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: 09/12/2022] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.
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Affiliation(s)
- Helen M Gunter
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- BASE mRNA Facility, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Scott E Youlten
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Andre L M Reis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
- School of Electrical and Information Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Tim McCubbin
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Bindu Swapna Madala
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
| | - Ted Wong
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
| | - Arcadi Cipponi
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
- School of Electrical and Information Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Nadia S Santini
- Centro Nacional de Investigación Disciplinaria en Conservación y Mejoramiento de Ecosistemas Forestales, INIFAP, Ciudad de México, 04010, Mexico
| | - Sarah Kummerfeld
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter I Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Esteban Marcellin
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Tim R Mercer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.
- BASE mRNA Facility, The University of Queensland, Brisbane, Queensland, Australia.
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia.
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
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49
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Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer CR, Yuan Y, Zhang Y, Li X, Song J, Knoten A, Lake BB, Gaut JP, Keene CD, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K. Mapping human tissues with highly multiplexed RNA in situ hybridization. Nat Commun 2024; 15:2511. [PMID: 38509069 PMCID: PMC10954689 DOI: 10.1038/s41467-024-46437-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: 08/16/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high autofluorescence. Here we report DART-FISH, a padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections. We introduce an omni-cell type cytoplasmic stain that substantially improves the segmentation of cell bodies. Our enzyme-free isothermal decoding procedure allows us to image 121 genes in large sections from the human neocortex in <10 h. We successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.
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Affiliation(s)
- Kian Kalhor
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Chien-Ju Chen
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
| | - Ho Suk Lee
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Electrical Engineering, University of California San Diego, La Jolla, CA, USA
| | - Matthew Cai
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Mahsa Nafisi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Richard Que
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Carter R Palmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Program in Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yixu Yuan
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Yida Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Jinghui Song
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Amanda Knoten
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Blue B Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University School of Medicine, St.Louis, MO, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, 98103, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Altos Labs, San Diego, CA, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St.Louis, MO, USA
| | | | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Altos Labs, San Diego, CA, USA.
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50
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Harlé O, Niay J, Parayre S, Nicolas A, Henry G, Maillard MB, Valence F, Thierry A, Guédon É, Falentin H, Deutsch SM. Deciphering the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice fermentation using phenotypic and transcriptional analysis. Appl Environ Microbiol 2024; 90:e0193623. [PMID: 38376234 PMCID: PMC10952386 DOI: 10.1128/aem.01936-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024] Open
Abstract
In the context of sustainable diet, the development of soy-based yogurt fermented with lactic acid bacteria is an attractive alternative to dairy yogurts. To decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice (SJ) fermentation, the whole genome of the strain CIRM-BIA865 (Ld865) was sequenced and annotated. Then Ld865 was used to ferment SJ. Samples were analyzed throughout fermentation for their cell number, carbohydrate, organic acid, free amino acid, and volatile compound contents. Despite acidification, the number of Ld865 cells did not rise, and microscopic observations revealed the elongation of cells from 3.6 µm (inoculation) to 36.9 µm (end of fermentation). This elongation was observed in SJ but not in laboratory-rich medium MRS. Using transcriptomic analysis, we showed that the biosynthesis genes of peptidoglycan and membrane lipids were stably expressed, in line with the cell elongation observed, whereas no genes implicated in cell division were upregulated. Among the main sugars available in SJ (sucrose, raffinose, and stachyose), Ld865 only used sucrose. The transcriptomic analysis showed that Ld865 implemented the two transport systems that it contains to import sucrose: a PTS system and an ABC transporter. To fulfill its nitrogen needs, Ld865 probably first consumed the free amino acids of the SJ and then implemented different oligopeptide transporters and proteolytic/peptidase enzymes. In conclusion, this study showed that Ld865 enables fast acidification of SJ, despite the absence of cell division, leads to a product rich in free amino acids, and also leads to the production of aromatic compounds of interest. IMPORTANCE To reduce the environmental and health concerns related to food, an alternative diet is recommended, containing 50% of plant-based proteins. Soy juice, which is protein rich, is a relevant alternative to animal milk, for the production of yogurt-like products. However, soy "beany" and "green" off-flavors limit the consumption of such products. The lactic acid bacteria (LAB) used for fermentation can help to improve the organoleptic properties of soy products. But metabolic data concerning LAB adapted to soy juice are lacking. The aim of this study was, thus, to decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during fermentation of a soy juice, based on a multidisciplinary approach. This result will contribute to give tracks for a relevant selection of starter. Indeed, the improvement of the organoleptic properties of these types of products could help to promote plant-based proteins in our diet.
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Affiliation(s)
- Olivier Harlé
- INRAE, Institut Agro, STLO, Rennes, France
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
| | - Jérôme Niay
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
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