99901
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Xiang S, Wang J, Huang H, Wang Z, Song X, Zhou Y, Jin F, He X, Zhang ZM, Tu Z, Ding K, Zhang Z, Lu X. Switch type I to type II TRK inhibitors for combating clinical resistance induced by xDFG mutation for cancer therapy. Eur J Med Chem 2022; 245:114899. [DOI: 10.1016/j.ejmech.2022.114899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/13/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
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99902
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Wang J, Sang Y, Jin S, Wang X, Azad GK, McCormick MA, Kennedy BK, Li Q, Wang J, Zhang X, Zhang Y, Huang Y. Single-cell RNA-seq reveals early heterogeneity during aging in yeast. Aging Cell 2022; 21:e13712. [PMID: 36181361 PMCID: PMC9649600 DOI: 10.1111/acel.13712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/25/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae (S. cerevisiae) has relatively short lifespan and is genetically tractable, making it a widely used model organism in aging research. Here, we carried out a systematic and quantitative investigation of yeast aging with single-cell resolution through transcriptomic sequencing. We optimized a single-cell RNA sequencing (scRNA-seq) protocol to quantitatively study the whole transcriptome profiles of single yeast cells at different ages, finding increased cell-to-cell transcriptional variability during aging. The single-cell transcriptome analysis also highlighted key biological processes or cellular components, including oxidation-reduction process, oxidative stress response (OSR), translation, ribosome biogenesis and mitochondrion that underlie aging in yeast. We uncovered a molecular marker of FIT3, indicating the early heterogeneity during aging in yeast. We also analyzed the regulation of transcription factors and further characterized the distinctive temporal regulation of the OSR by YAP1 and proteasome activity by RPN4 during aging in yeast. Overall, our data profoundly reveal early heterogeneity during aging in yeast and shed light on the aging dynamics at the single cell level.
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Affiliation(s)
- Jincheng Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking‐Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics (ICG), School of Life SciencesPeking UniversityBeijingChina
| | - Yuchen Sang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking‐Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics (ICG), School of Life SciencesPeking UniversityBeijingChina
| | - Shengxian Jin
- Biomedical Pioneering Innovation Center (BIOPIC), Peking‐Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics (ICG), School of Life SciencesPeking UniversityBeijingChina
| | - Xuezheng Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina,Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | - Gajendra Kumar Azad
- Departments of Biochemistry, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore,Department of ZoologyPatna UniversityPatnaIndia
| | - Mark A. McCormick
- Department of Biochemistry and Molecular Biology, School of MedicineUniversity of New Mexico Health Sciences CenterAlbuquerqueNew MexicoUSA,Autophagy Inflammation and Metabolism Center of Biomedical Research ExcellenceAlbuquerqueNew MexicoUSA
| | - Brian K. Kennedy
- Departments of Biochemistry, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore,Healthy Longevity Programme, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore,Centre for Healthy LongevityNational University Health SystemSingaporeSingapore
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Jianbin Wang
- School of Life Sciences, Beijing Advanced Innovation Center for Structural BiologyTsinghua UniversityBeijingChina
| | - Xiannian Zhang
- School of Basic Medical Sciences, Beijing Advanced Innovation Center for Human Brain ProtectionCapital Medical UniversityBeijingChina
| | - Yi Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking‐Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics (ICG), School of Life SciencesPeking UniversityBeijingChina
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking‐Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics (ICG), School of Life SciencesPeking UniversityBeijingChina,Analytical Chemistry, College of ChemistryPeking UniversityBeijingChina,Institute for Cell AnalysisShenzhen Bay LaboratoryShenzhenChina
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99903
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Feng S, Xu Z, Zhang Z, Mo Y, Deng Y, Li L, Fei S, Wu J, Wang K, Zhang Q, Song J, Zhou R. RNA-Seq approach to investigate the effects of melatonin on bone marrow-derived dendritic cells from dextran sodium sulfate-induced colitis mice. Toxicology 2022; 481:153354. [DOI: 10.1016/j.tox.2022.153354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]
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99904
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ESR1 dysfunction triggers neuroinflammation as a critical upstream causative factor of the Alzheimer’s disease process. Aging (Albany NY) 2022; 14:8595-8614. [DOI: 10.18632/aging.204359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022]
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99905
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Liu Z, Huang J, Kang D, Zhou Y, Du L, Qu Q, Wang J, Wen L, Fu D, Hu Z, Miao Y. Microenvironmental Reprogramming of Human Dermal Papilla Cells for Hair Follicle Tissue Engineering. Acta Biomater 2022:S1742-7061(22)00730-9. [DOI: 10.1016/j.actbio.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/16/2022] [Accepted: 11/02/2022] [Indexed: 11/08/2022]
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99906
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Fu Q, Li Y, Zhao S, Wang H, Zhao C, Zhang P, Cao M, Yang N, Li C. Comprehensive identification and expression profiling of immune-related lncRNAs and their target genes in the intestine of turbot (Scophthalmus maximus L.) in response to Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2022; 130:233-243. [PMID: 36084890 DOI: 10.1016/j.fsi.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/22/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Long non-coding RNA (lncRNA) play vital regulatory roles in various biological processes. Intestine is one of the most sensitive organs to environmental and homeostatic disruptions for fish. However, systematic profiles of lncRNAs in the intestine of teleost in responses to pathogen infections is still limited. Turbot (Scophthalmus maximus L.), an important commercial fish species in China, has been suffering with Vibrio anguillarum infection, resulted in dramatic economic loss. Hereinto, the intestinal tissues of turbot were sampled at 0 h, 2 h, 12 h, and 48 h following V. anguillarum infection. The histopathological analysis revealed that the pathological trauma was mainly present in intestinal tunica mucosal epithelium. After high-throughput sequencing and bioinformatic analysis, a total of 9722 lncRNAs and 21,194 mRNAs were obtained, and the average length and exon number of lncRNAs were both less than those of mRNAs. Among which, a set of 158 lncRNAs and 226 mRNAs were differentially expressed (DE-lncRNAs and DEGs) in turbot intestine at three time points, related to many immune-related genes such as complement, interleukin, chemokine, lysosome, and macrophage, indicating their potential critical roles in immune responses. In addition, 2803 and 1803 GO terms were enriched for DEGs and co-expressed target genes of DE-lncRNAs, respectively. Moreover, 127 and 50 KEGG pathways including cell adhesion molecules (CAMs), phagosome, JAK-STAT signaling pathway, cytokine-cytokine receptor interaction, and intestinal immune network for IgA production, were enriched for DEGs and co-expressed target genes of DE-lncRNAs, respectively. Finally, qRT-PCR was conducted to confirm the reliability of sequencing data. The present study will set the foundation for the future exploration of lncRNA functions in teleost in response to bacterial infection.
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Affiliation(s)
- Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuqing Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shoucong Zhao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Haojie Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Chunyan Zhao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Pei Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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99907
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Ahn J, Heo S, Ahn SJ, Bang D, Lee SH. Differentially hypomethylated cell-free DNA and coronary collateral circulation. Clin Epigenetics 2022; 14:140. [PMID: 36320085 PMCID: PMC9628091 DOI: 10.1186/s13148-022-01349-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The factors affecting cardioprotective collateral circulation are still incompletely understood. Recently, characteristics, such as CpG methylation of cell-free DNA (cfDNA), have been reported as markers with clinical utility. The aim of this study was to evaluate whether cfDNA methylation patterns are associated with the grade of coronary collateral circulation (CCC). RESULT In this case-control study, clinical and angiographic data were obtained from 143 patients (mean age, 58 years, male 71%) with chronic total coronary occlusion. Enzymatic methyl-sequencing (EM-seq) libraries were prepared using the cfDNA extracted from the plasma. Data were processed to obtain the average methylation fraction (AMF) tables of genomic regions from which blacklisted regions were removed. Unsupervised analysis of the obtained AMF values showed that some of the changes in methylation were due to CCC. Through random forest preparation process, 256 differentially methylated region (DMR) candidates showing strong association with CCC were selected. A random forest classifier was then constructed, and the area under the curve of the receiver operating characteristic curve indicated an appropriate predictive function for CCC. Finally, 20 DMRs were identified to have significantly different AMF values between the good and poor CCC groups. Particularly, the good CCC group exhibited hypomethylated DMRs. Pathway analysis revealed five pathways, including TGF-beta signaling, to be associated with good CCC. CONCLUSION These data have demonstrated that differential hypomethylation was identified in dozens of cfDNA regions in patients with good CCC. Our results support the clinical utility of noninvasively obtained epigenetic signatures for predicting collateral circulation in patients with vascular diseases.
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Affiliation(s)
- Jongseong Ahn
- Department of Chemistry, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | | | - Soo-Jin Ahn
- Integrative Research Center for Cerebrovascular and Cardiovascular Diseases, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Sang-Hak Lee
- Division of Cardiology, Severance Hospital, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.,Pohang University of Science and Technology (POSTECH), Pohang, Korea
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99908
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Cobaleda C, Vicente-Dueñas C, Ramírez-Orellana M, Sanchez-Garcia I. Revisiting the concept of childhood preleukemia. Trends Cancer 2022; 8:887-889. [PMID: 35871053 DOI: 10.1016/j.trecan.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022]
Abstract
Preleukemic has been used to describe children with a propensity to develop B cell acute lymphoblastic leukemia (B-ALL). However, leukemia-predisposing mutations can also be present in differentiated cells unable to transform. We postulate that preleukemia should only be used when such mutations arise in progenitors capable of evolving to B-ALL.
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Affiliation(s)
- Cesar Cobaleda
- Immune system development and function Unit, Centro de Biología Molecular Severo Ochoa (CSIC -Universidad Autónoma de Madrid), Madrid, Spain.
| | | | - Manuel Ramírez-Orellana
- Department of Pediatric Hematology and Oncology, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Isidro Sanchez-Garcia
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Salamanca, Spain.
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99909
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Guo C, Liu Q, Zong D, Zhang W, Zuo Z, Yu Q, Sha Q, Zhu L, Gao X, Fang J, Tao J, Wu Q, Li X, Qu K. Single-cell transcriptome profiling and chromatin accessibility reveal an exhausted regulatory CD4+ T cell subset in systemic lupus erythematosus. Cell Rep 2022; 41:111606. [DOI: 10.1016/j.celrep.2022.111606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/02/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
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99910
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Villagomez Fuentes LE, Algharably EAH, Toepfer S, König M, Demuth I, Bertram L, Kreutz R, Bolbrinker J. Effect of a common UMOD variant on kidney function, blood pressure, cognitive and physical function in a community-based cohort of older adults. J Hum Hypertens 2022; 36:983-988. [PMID: 34593962 PMCID: PMC9649423 DOI: 10.1038/s41371-021-00608-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/27/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022]
Abstract
In genome-wide association studies, genetic variants in the UMOD gene associate with kidney function, blood pressure (BP), and hypertension. Elevated BP is linked to kidney function and impaired cognitive as well as physical performance in later life. We investigated the association between UMOD rs4293393-A > G and kidney function, BP, cognitive and physical function in the Berlin Aging Study II (BASE-II). Data of 1556 older BASE-II participants (mean age 68.2 ± 3.7 years) were analyzed. BP was determined by standardized automated measurements, estimated glomerular filtration rate (eGFR) by CKD Epidemiology Collaboration creatinine equation. Cognitive function was assessed by Mini-Mental State Examination and Digit Symbol Substitution Test, while physical function by Handgrip Strength and Timed Up and Go-Test. Association analyses were performed by covariance and logistic regression models adjusting for sex. G-allele carriers at UMOD rs4293393 exhibited significantly higher eGFR values compared to non-carriers (AA, 76.4 ml/min/1.73 m², CI: 75.7-77.2 vs. AG, 78.4 ml/min/1.73 m², CI: 77.3-79.5 vs. GG, 78.5 ml/min/1.73 m², CI: 75.4-81.7; P = 0.010), and a lower risk of eGFR < 60 mL/min/1.73 m2 (AG, OR: 0.63, CI: 0.41-0.97, P = 0.033). However, UMOD rs4293393 genotypes were not associated with BP, diagnosis of hypertension or cognitive and physical function parameters. Our data corroborate previous findings on the association of UMOD rs4293393-G with better kidney function in older adults. However, no association between UMOD and BP or physical and cognitive parameters in these community-dwelling older adults was detected.
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Affiliation(s)
- Linda Elizabeth Villagomez Fuentes
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Clinical Pharmacology and Toxicology, Charitéplatz 1, 10117, Berlin, Germany
| | - Engi Abdel-Hady Algharably
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Clinical Pharmacology and Toxicology, Charitéplatz 1, 10117, Berlin, Germany
| | - Sarah Toepfer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolism, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Maximilian König
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolism, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Ilja Demuth
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolism, Augustenburger Platz 1, 13353, Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies BCRT, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany.,Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Reinhold Kreutz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Clinical Pharmacology and Toxicology, Charitéplatz 1, 10117, Berlin, Germany
| | - Juliane Bolbrinker
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Clinical Pharmacology and Toxicology, Charitéplatz 1, 10117, Berlin, Germany.
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99911
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Kakkar V, Assassi S, Allanore Y, Kuwana M, Denton CP, Khanna D, Del Galdo F. Type 1 interferon activation in systemic sclerosis: a biomarker, a target or the culprit. Curr Opin Rheumatol 2022; 34:357-364. [PMID: 36125916 PMCID: PMC9594133 DOI: 10.1097/bor.0000000000000907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
PURPOSE OF REVIEW Activation of the type 1 interferon (T1 IFN) pathway has been implicated in the pathogenesis of systemic sclerosis (SSc) by an increasing number of studies, most of which share key findings with similar studies in systemic lupus erythematosus (SLE). Here we will focus on the evidence for T1 IFN activation and dysregulation in SSc, and the rationale behind targeting the pathway going forward. RECENT FINDINGS An increased expression and activation of T1 IFN-regulated genes has been shown to be present in a significant proportion of SSc patients. TI IFN activation markers have been found to predict and correlate with response to immunosuppressive treatment as well as severity of organ involvement. As inhibition of the IFN-α receptor has been proven to be effective in active SLE, benefit may be seen in targeting the IFN pathway in SSc. SUMMARY The role played by T1 IFN and its regulatory genes in SSc is becoming increasingly evident and strikingly similar to the role observed in SLE. This observation, together with the benefit of type 1 IFN targeting in SLE, supports the notion of a potential therapeutic benefit in targeting T1 IFN in SSc.
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Affiliation(s)
- Vishal Kakkar
- Department of Rheumatology, Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Shervin Assassi
- Division of Rheumatology, University of Texas Health Science Center at Houston, Texas, USA
| | - Yannick Allanore
- INSERM U1016 UMR 8104, Université Paris Cité, Hôpital Cochin, Paris, France
| | - Masataka Kuwana
- Department of Allergy and Rheumatology, Nippon Medical School, Tokyo, Japan
| | | | - Dinesh Khanna
- University of Michigan Scleroderma Program, Ann Arbor, Michigan, USA
| | - Francesco Del Galdo
- Department of Rheumatology, Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
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99912
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Chamlal H, Ouaderhman T, Rebbah FE. A hybrid feature selection approach for Microarray datasets using graph theoretic-based method. Inf Sci (N Y) 2022. [DOI: 10.1016/j.ins.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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99913
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Leng X, Zhang T, Guan Y, Tang M. Genotype and phenotype analysis of epilepsy caused by ADGRV1 mutations in Chinese children. Seizure 2022; 103:108-114. [DOI: 10.1016/j.seizure.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
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99914
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Testis-expressed gene 11 inhibits cisplatin-induced DNA damage and contributes to chemoresistance in testicular germ cell tumor. Sci Rep 2022; 12:18423. [PMID: 36319719 PMCID: PMC9626550 DOI: 10.1038/s41598-022-21856-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022] Open
Abstract
Testicular germ cell tumor (TGCT) is a rare cancer but the most common tumor among adolescent and young adult males. Patients with advanced TGCT often exhibit a worse prognosis due to the acquisition of therapeutic resistance. Cisplatin-based chemotherapy is a standard treatment for advanced TGCTs initially sensitive to cisplatin, as exemplified by embryonal carcinoma. The acquisition of cisplatin resistance, however, could be a fatal obstacle for TGCT management. To identify cisplatin resistance-related genes, we performed transcriptome analysis for cisplatin-resistant TGCT cells compared to parental cells. In two types of cisplatin-resistant TGCT cell models that we established from patient-derived TGCT cells, and from the NEC8 cell line, we found that mRNA levels of the high-mobility-group nucleosome-binding gene HMGN5 and meiosis-related gene TEX11 were remarkably upregulated compared to those in the corresponding parental cells. We showed that either HMGN5 or TEX11 knockdown substantially reduced the viability of cisplatin-resistant TGCT cells in the presence of cisplatin. Notably, TEX11 silencing in cisplatin-resistant TGCT cells increased the level of cleaved PARP1 protein, and the percentage of double-strand break marker γH2AX-positive cells. We further demonstrated the therapeutic efficiency of TEX11-specific siRNA on in vivo xenograft models derived from cisplatin-resistant patient-derived TGCT cells. Taken together, the present study provides a potential insight into a mechanism of cisplatin resistance via TEX11-dependent pathways that inhibit apoptosis and DNA damage. We expect that our findings can be applied to the improvement of cisplatin-based chemotherapy for TGCT, particularly for TEX11-overexpressing tumor.
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99915
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Zhang Y, Yang X, Van de Peer Y, Chen J, Marchal K, Shi T. Evolution of isoform-level gene expression patterns across tissues during lotus species divergence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:830-846. [PMID: 36123806 PMCID: PMC7613771 DOI: 10.1111/tpj.15984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/09/2022] [Indexed: 05/03/2023]
Abstract
Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contributions of the two key mechanisms to the evolution of gene function are largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea and Nelumbo nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms of local, small-scale duplicates, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection pressure for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contributed to the diversity of gene function during the evolution of lotus.
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Affiliation(s)
- Yue Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan 430081, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, and VIB Center for Plant Systems Biology, Ghent 9052, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Corresponding author details: Jinming Chen: ; Kathleen Marchal: ; Tao Shi:
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, and VIB Center for Plant Systems Biology, Ghent 9052, Belgium
- Department of Information Technology, IDLab, IMEC, Ghent University, Ghent 9052, Belgium
- Corresponding author details: Jinming Chen: ; Kathleen Marchal: ; Tao Shi:
| | - Tao Shi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Corresponding author details: Jinming Chen: ; Kathleen Marchal: ; Tao Shi:
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99916
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Shen Y, Ma K, Zhu Q, Xu X, Li J. Transcriptomic analysis reveals growth-related genes in juvenile grass carp, Ctenopharyngodon idella. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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99917
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Novel germline SMARCA4 mutation in Small Cell Carcinoma of the Ovary, Hypercalcemic Type. CURRENT PROBLEMS IN CANCER: CASE REPORTS 2022. [DOI: 10.1016/j.cpccr.2022.100205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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99918
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Clonal evolution in adult TCF3::HLF-positive acute lymphoblastic leukemia undergoing stem cell transplantation. Ann Hematol 2022; 101:2553-2554. [PMID: 35907039 DOI: 10.1007/s00277-022-04941-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 07/23/2022] [Indexed: 01/26/2023]
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99919
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Kotmayer L, Romero‐Moya D, Marin‐Bejar O, Kozyra E, Català A, Bigas A, Wlodarski MW, Bödör C, Giorgetti A. GATA2 deficiency and MDS/AML: Experimental strategies for disease modelling and future therapeutic prospects. Br J Haematol 2022; 199:482-495. [PMID: 35753998 PMCID: PMC9796058 DOI: 10.1111/bjh.18330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 12/30/2022]
Abstract
The importance of predisposition to leukaemia in clinical practice is being increasingly recognized. This is emphasized by the establishment of a novel WHO disease category in 2016 called "myeloid neoplasms with germline predisposition". A major syndrome within this group is GATA2 deficiency, a heterogeneous immunodeficiency syndrome with a very high lifetime risk to develop myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). GATA2 deficiency has been identified as the most common hereditary cause of MDS in adolescents with monosomy 7. Allogenic haematopoietic stem cell transplantation is the only curative option; however, chances of survival decrease with progression of immunodeficiency and MDS evolution. Penetrance and expressivity within families carrying GATA2 mutations is often variable, suggesting that co-operating extrinsic events are required to trigger the disease. Predictive tools are lacking, and intrafamilial heterogeneity is poorly understood; hence there is a clear unmet medical need. On behalf of the ERAPerMed GATA2 HuMo consortium, in this review we describe the genetic, clinical, and biological aspects of familial GATA2-related MDS, highlighting the importance of developing robust disease preclinical models to improve early detection and clinical decision-making of GATA2 carriers.
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Affiliation(s)
- Lili Kotmayer
- HCEMM‐SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Damia Romero‐Moya
- Regenerative Medicine ProgramInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL)BarcelonaSpain
| | - Oskar Marin‐Bejar
- Regenerative Medicine ProgramInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL)BarcelonaSpain
| | - Emilia Kozyra
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of MedicineUniversity of FreiburgFreiburgGermany,Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Albert Català
- Department of Hematology and OncologyInstitut de Recerca Sant Joan de DéuHospital Sant Joan de DeuBarcelonaSpain,Biomedical Network Research Centre on Rare DiseasesInstituto de Salud Carlos IIIMadridSpain
| | - Anna Bigas
- Cancer Research ProgramInstitut Hospital del Mar d'Investigacions Mèdiques, CIBERONC, Hospital del MarBarcelonaSpain,Josep Carreras Research Institute (IJC), BadalonaBarcelonaSpain
| | - Marcin W. Wlodarski
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of MedicineUniversity of FreiburgFreiburgGermany,Department of HematologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - Csaba Bödör
- HCEMM‐SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Alessandra Giorgetti
- Regenerative Medicine ProgramInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL)BarcelonaSpain,Fondazione Pisana Per la Scienza ONLUS (FPS)San Giuliano TermeItaly,Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health SciencesBarcelona UniversityBarcelonaSpain
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99920
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Kanta Acharya T, Kumar A, Kumar Majhi R, Kumar S, Chakraborty R, Tiwari A, Smalla KH, Liu X, Chang YT, Gundelfinger ED, Goswami C. TRPV4 acts as a mitochondrial Ca 2+-importer and regulates mitochondrial temperature and metabolism. Mitochondrion 2022; 67:38-58. [PMID: 36261119 DOI: 10.1016/j.mito.2022.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 08/28/2022] [Accepted: 10/09/2022] [Indexed: 12/24/2022]
Abstract
TRPV4 is associated with the development of neuropathic pain, sensory defects, muscular dystrophies, neurodegenerative disorders, Charcot Marie Tooth and skeletal dysplasia. In all these cases, mitochondrial abnormalities are prominent. Here, we demonstrate that TRPV4, localizes to a subpopulation of mitochondria in various cell lines. Improper expression and/or function of TRPV4 induces several mitochondrial abnormalities. TRPV4 is also involved in the regulation of mitochondrial numbers, Ca2+-levels and mitochondrial temperature. Accordingly, several naturally occurring TRPV4 mutations affect mitochondrial morphology and distribution. These findings may help in understanding the significance of mitochondria in TRPV4-mediated channelopathies possibly classifying them as mitochondrial diseases.
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Affiliation(s)
- Tusar Kanta Acharya
- National Institute of Science Education and Research Bhubaneswar, School of Biological Sciences, P.O. Jatni, Khurda 752050, Odisha, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Ashutosh Kumar
- National Institute of Science Education and Research Bhubaneswar, School of Biological Sciences, P.O. Jatni, Khurda 752050, Odisha, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Rakesh Kumar Majhi
- National Institute of Science Education and Research Bhubaneswar, School of Biological Sciences, P.O. Jatni, Khurda 752050, Odisha, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Shamit Kumar
- National Institute of Science Education and Research Bhubaneswar, School of Biological Sciences, P.O. Jatni, Khurda 752050, Odisha, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Ranabir Chakraborty
- National Institute of Science Education and Research Bhubaneswar, School of Biological Sciences, P.O. Jatni, Khurda 752050, Odisha, India
| | - Ankit Tiwari
- National Institute of Science Education and Research Bhubaneswar, School of Biological Sciences, P.O. Jatni, Khurda 752050, Odisha, India
| | - Karl-Heinz Smalla
- Leibniz Institute for Neurobiology, RG Neuroplasticity, Brenneckestr 6, 39118 Magdeburg, Germany; Center for Behavioral Brain Sciences (CBBS) and Institute of Pharmacology and Toxicology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Xiao Liu
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea; Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Young-Tae Chang
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea; Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Eckart D Gundelfinger
- Leibniz Institute for Neurobiology, RG Neuroplasticity, Brenneckestr 6, 39118 Magdeburg, Germany; Center for Behavioral Brain Sciences (CBBS) and Institute of Pharmacology and Toxicology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Chandan Goswami
- National Institute of Science Education and Research Bhubaneswar, School of Biological Sciences, P.O. Jatni, Khurda 752050, Odisha, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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99921
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Metwalley KA, Farghaly HS. Overview of endocrine hypertension in children. PROGRESS IN PEDIATRIC CARDIOLOGY 2022. [DOI: 10.1016/j.ppedcard.2022.101581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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99922
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Abstract
The aim of the current study was to compare the longitudinal clinical course of patients with a history of melancholic and nonmelancholic bipolar depression. Seventy-seven euthymic outpatients with bipolar disorder were categorized as melancholic or nonmelancholic through the clinician-rated Sydney Melancholia Prototype Index. Clinical course was assessed for a period longer than 48 months by time spent ill, density of affective episodes, severity and duration of depressive episodes, and time to depressive recurrence. The mean follow-up time was 69.05 months. Patients with melancholic depressions had more severe and longer depressive episodes during follow-up, whereas patients with nonmelancholic depressions had a shorter time to depressive recurrence and more subsyndromal depressive symptoms and affective instability. These findings highlight the heterogeneity inherent to the current construct of bipolar depression and position melancholia as an interesting target for comparison with nonmelancholic depressions in other external validators in the field of bipolar disorder.
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99923
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Nakamura JL. Considerations for carcinogenesis countermeasure development using mouse models. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:158-162. [PMID: 36336361 DOI: 10.1016/j.lssr.2022.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/02/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
Activities in space will expose humans to profoundly new environments, challenging human performance and will require innovative supportive technologies. Among these environmental variables, exposure to ionizing radiation is a major concern for astronauts, as the long-term effects of exposure on diverse tissues are poorly understood. This need however creates opportunities for novel approaches, particularly in the development of countermeasures against the effects of ionizing radiation exposure. Carcinogenesis presents a unique challenge as a disease process, due to the inherent complexities of the process and the challenges of obtaining a large volume of clinical evidence. Thus, developing the countermeasures to address potential effects of ionizing radiation exposure will require understanding biological underpinnings to design countermeasures effectively in conjunction with highly robust modeling approaches to test and examine in vivo. This review will highlight specific considerations for accelerated development of space radiation countermeasures against carcinogenesis.
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Affiliation(s)
- Jean L Nakamura
- University of California, San Francisco, Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, United States.
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99924
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Transcription factor Sp1 and oncoprotein PPP1R13L regulate nicotine-induced epithelial-mesenchymal transition in lung adenocarcinoma via a feedback loop. Biochem Pharmacol 2022; 206:115344. [DOI: 10.1016/j.bcp.2022.115344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/24/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
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99925
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Hughes E, Wagner S, Pruss D, Bernhisel R, Probst B, Abkevich V, Simmons T, Hullinger B, Judkins T, Rosenthal E, Roa B, Domchek SM, Eng C, Garber J, Gary M, Klemp J, Mukherjee S, Offit K, Olopade OI, Vijai J, Weitzel JN, Whitworth P, Yehia L, Gordon O, Pederson H, Kurian A, Slavin TP, Gutin A, Lanchbury JS. Development and Validation of a Breast Cancer Polygenic Risk Score on the Basis of Genetic Ancestry Composition. JCO Precis Oncol 2022; 6:e2200084. [PMID: 36331239 PMCID: PMC9666117 DOI: 10.1200/po.22.00084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/11/2022] [Accepted: 09/08/2022] [Indexed: 08/12/2023] Open
Abstract
PURPOSE Polygenic risk scores (PRSs) for breast cancer (BC) risk stratification have been developed primarily in women of European ancestry. Their application to women of non-European ancestry has lagged because of the lack of a formal approach to incorporate genetic ancestry and ancestry-dependent variant frequencies and effect sizes. Here, we propose a multiple-ancestry PRS (MA-PRS) that addresses these issues and may be useful in the development of equitable PRSs across other cancers and common diseases. MATERIALS AND METHODS Women referred for hereditary cancer testing were divided into consecutive cohorts for development (n = 189,230) and for independent validation (n = 89,126). Individual genetic composition as fractions of three reference ancestries (African, East Asian, and European) was determined from ancestry-informative single-nucleotide polymorphisms. The MA-PRS is a combination of three ancestry-specific PRSs on the basis of genetic ancestral composition. Stratification of risk was evaluated by multivariable logistic regression models controlling for family cancer history. Goodness-of-fit analysis compared expected with observed relative risks by quantiles of the MA-PRS distribution. RESULTS In independent validation, the MA-PRS was significantly associated with BC risk in the full cohort (odds ratio, 1.43; 95% CI, 1.40 to 1.46; P = 8.6 × 10-308) and within each major ancestry. The top decile of the MA-PRS consistently identified patients with two-fold increased risk of developing BC. Goodness-of-fit tests showed that the MA-PRS was well calibrated and predicted BC risk accurately in the tails of the distribution for both European and non-European women. CONCLUSION The MA-PRS uses genetic ancestral composition to expand the utility of polygenic risk prediction to non-European women. Inclusion of genetic ancestry in polygenic risk prediction presents an opportunity for more personalized treatment decisions for women of varying and mixed ancestries.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Susan M. Domchek
- Basser Center for BRCA, University of Pennsylvania, Philadelphia, PA
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH
| | | | | | - Jennifer Klemp
- The University of Kansas Cancer Center, The University of Kansas Medical Center, Kansas City, KS
| | | | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Joseph Vijai
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Lamis Yehia
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Ora Gordon
- Providence Health and Services, Renton, WA
| | - Holly Pederson
- Medical Breast Services, Cleveland Clinic, Cleveland, OH
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99926
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Jing Zhang F, Zhang SW, Zhang S. Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3614-3623. [PMID: 34752400 DOI: 10.1109/tcbb.2021.3126623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Identification of transcription factor binding sites (TFBSs) is essential for revealing the rules of protein-DNA binding. Although some computational methods have been presented to predict TFBSs using epigenomic and sequence features, most of them ignore the common features among cross-cell types. It is still unclear to what extent the common features could help for this task. To this end, we proposed a new method (named Attention-augmented Convolutional Neural Network, or ACNN) to predict TFBSs. ACNN uses attention-augmented convolutional layers to capture global and local contexts in DNA sequences and employs the convolutional layers to capture features of histone modification markers. In addition, ACNN adopts the private and shared convolutional neural network (CNN) modules to learn specific and common features, respectively. To encourage the shared CNN module to learn the common features, adversarial training is applied in ACNN. The results on 253 ChIP-seq datasets show that ACNN outperforms other existing methods. The attention-augmented convolutional layers and adversarial training mechanism in ACNN can effectively improve the prediction performance. Moreover, in the case of limited labeled data, ACNN also performs better than a baseline method. We further visualize the convolution kernels as motifs to explain the interpretability of ACNN.
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99927
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Patankar A, Sudhakar DVS, Gajbhiye R, Surve S, Thangaraj K, Parte P. Proteomic and genetic dissection of testis-specific histone 2B in infertile men reveals its contribution to meiosis and sperm motility. F&S SCIENCE 2022; 3:322-330. [PMID: 35840050 DOI: 10.1016/j.xfss.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To investigate testis-specific histone 2B (TSH2B) and its gene anomalies in infertile men. DESIGN Case-control study. SETTING Basic science laboratory. PATIENT(S) Fertile and infertile men. INTERVENTION(S) Not applicable. MAIN OUTCOME MEASURE(S) The histone and protamine status of sperm was studied by aniline blue and chromomycin A3 staining, respectively. Testis-specific histone 2B, total H2B, and phosphorylated TSH2B (pTSH2B) were estimated by Western blot analysis. The frequency of genetic polymorphisms and rare variants in H2BC1 was studied by Sanger sequencing. Phosphosites on TSH2B in sperm were identified by reverse-phase high-performance liquid chromatography purification of TSH2B followed by mass spectrometric analysis. RESULT(S) Aniline blue and chromomycin A3 staining revealed significantly higher histone retention and low protamine in sperm of infertile men. Sperm TSH2B and total H2B levels were significantly lower in oligozoospermic and oligoasthenozoospermic men (in both groups). The TSH2B levels were comparable in asthenozoospermic men; however, the pTSH2B level was significantly low. The H2BC1 gene sequencing identified 6 variants, of which 2 are rare variants (rs368672899 and rs544942090) and 4 (rs4711096, rs4712959, rs4712960 and rs4712961) are single nucleotide polymorphisms. Minor allele frequency of 5'-untranslated region variant rs4711096 was significantly lower in infertile men (OR = 0.65). The rare nonsynonymous variant, rs368672899, p.Ser5Pro was seen in 1 oligoasthenoteratozoospermic individual. Interestingly, mass spectrometric analysis identified a site on TSH2B to bear a phosphate group in the sperm of fertile men. CONCLUSION(S) Our study reveals a defect in the replacement of somatic histones with testis-specific variants in infertile men. Chromatin compaction positively correlates with sperm motility, which is suggestive of its utility in diagnostic semen analysis of infertile individuals. Our observations with TSH2B and its cognate gene in sperm of infertile men indicate an essential role for TSH2B in meiosis and its phosphorylation in sperm motility, respectively.
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Affiliation(s)
- Aniket Patankar
- Department of Gamete Immunobiology, Indian Council of Medical Research (ICMR)-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Digumarthi V S Sudhakar
- Department of Gamete Immunobiology, Indian Council of Medical Research (ICMR)-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Rahul Gajbhiye
- Clinical Research Laboratory & Andrology Clinic, Indian Council of Medical Research (ICMR)-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Suchitra Surve
- Clinical Research Laboratory & Andrology Clinic, Indian Council of Medical Research (ICMR)-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Kumarasamy Thangaraj
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology, Hyderabad, India; Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Priyanka Parte
- Department of Gamete Immunobiology, Indian Council of Medical Research (ICMR)-National Institute for Research in Reproductive and Child Health, Mumbai, India.
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99928
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Abbas M, Abid MA, Meng Z, Abbas M, Wang P, Lu C, Askari M, Akram U, Ye Y, Wei Y, Wang Y, Guo S, Liang C, Zhang R. Integrating advancements in root phenotyping and genome-wide association studies to open the root genetics gateway. PHYSIOLOGIA PLANTARUM 2022; 174:e13787. [PMID: 36169590 DOI: 10.1111/ppl.13787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Plant adaptation to challenging environmental conditions around the world has made root growth and development an important research area for plant breeders and scientists. Targeted manipulation of root system architecture (RSA) to increase water and nutrient use efficiency can minimize the adverse effects of climate change on crop production. However, phenotyping of RSA is a major bottleneck since the roots are hidden in the soil. Recently the development of 2- and 3D root imaging techniques combined with the genome-wide association studies (GWASs) have opened up new research tools to identify the genetic basis of RSA. These approaches provide a comprehensive understanding of the RSA, by accelerating the identification and characterization of genes involved in root growth and development. This review summarizes the latest developments in phenotyping techniques and GWAS for RSA, which are used to map important genes regulating various aspects of RSA under varying environmental conditions. Furthermore, we discussed about the state-of-the-art image analysis tools integrated with various phenotyping platforms for investigating and quantifying root traits with the highest phenotypic plasticity in both artificial and natural environments which were used for large scale association mapping studies, leading to the identification of RSA phenotypes and their underlying genetics with the greatest potential for RSA improvement. In addition, challenges in root phenotyping and GWAS are also highlighted, along with future research directions employing machine learning and pan-genomics approaches.
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Affiliation(s)
- Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ali Abid
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Askari
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Umar Akram
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yulu Ye
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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99929
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Migraine research comes of age in the 21st century. Lancet Neurol 2022; 21:955-958. [DOI: 10.1016/s1474-4422(22)00398-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022]
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99930
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Lednovich KR, Gough S, Brenner M, Qadri T, Layden BT. G
Protein‐Coupled Receptors in Metabolic Disease. GPCRS AS THERAPEUTIC TARGETS 2022:521-552. [DOI: 10.1002/9781119564782.ch15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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99931
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Huang JJ, Geduldig JE, Jacobs EB, Tai TYT, Ahmad S, Chadha N, Buxton DF, Vinod K, Wirostko BM, Kang JH, Wiggs JL, Ritch R, Pasquale LR. Head and Neck Region Dermatological Ultraviolet-Related Cancers are Associated with Exfoliation Syndrome in a Clinic-Based Population. Ophthalmol Glaucoma 2022; 5:663-671. [PMID: 35470101 PMCID: PMC9587131 DOI: 10.1016/j.ogla.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/12/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVE We assessed the relationship between ultraviolet (UV)-associated dermatological carcinomas (basal cell carcinoma [BCC] and squamous cell carcinoma [SCC]) and exfoliation syndrome (XFS) or exfoliation glaucoma (XFG). DESIGN Case-control study. PARTICIPANTS Between 2019 and 2021, 321 participants and control subjects (XFS or XFG = 98; primary open-angle glaucoma [POAG] = 117; controls = 106; ages 50-90 years) were recruited. METHODS A cross-sectional survey assessing medical history, maximum known intraocular pressure, cup-to-disc ratio, Humphrey visual field 24-2, the propensity to tan or burn in early life, history of BCC or SCC, and XFS or XFG diagnosis. The multivariable models adjusted for age, sex, medical history, eye color, hair color, and likeliness of tanning versus burning at a young age. MAIN OUTCOME MEASURES History of diagnosed XFS or XFG. RESULTS Any history of BCC or SCC in the head and neck region was associated with a 2-fold higher risk of having XFS or XFG versus having POAG or being a control subject (odds ratio [OR], 2.01; 95% confidence interval [CI], 1.04-3.89) in a multivariable-adjusted analysis. We observed a dose-response association in which the chance of having XFS or XFG increased by 67% per head and neck BCC or SCC occurrence (OR, 1.67; 95% CI, 1.09-2.56). When we excluded POAG participants, head and neck BCC or SCC was associated with a 2.8-fold higher risk of XFS or XFG (OR, 2.80; 95% CI, 1.12-7.02), and each additional occurrence had a 2-fold higher risk of XFS or XFG (OR, 1.97; 95% CI, 1.09-3.58). The association between head and neck region BCC or SCC and POAG compared with the control subjects was null (OR, 1.42; 95% CI, 0.58-3.48). With BCC or SCC located anywhere on the body, there was a nonsignificantly higher risk of having XFS or XFG compared with having POAG or being a control subject (OR, 1.65; 95% CI, 0.88-3.09). CONCLUSIONS Head and neck region BCCs or SCCs are associated with a higher risk of having XFS or XFG. These findings support prior evidence that head and neck UV exposure may be a risk factor for XFS.
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Affiliation(s)
- Jeff J Huang
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Jack E Geduldig
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Erica B Jacobs
- New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - Tak Yee T Tai
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York; New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - Sumayya Ahmad
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York; New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - Nisha Chadha
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York; New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - Douglas F Buxton
- New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - Kateki Vinod
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York; New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | | | - Jae H Kang
- Channing Division of Network of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Robert Ritch
- New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York; New York Eye and Ear Infirmary of Mount Sinai, New York, New York
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99932
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Gao R, Luo Y, Pan X, Wang C, Liao W. Genome-wide identification of SHMT family genes in cucumber ( Cucumis sativus L.) and functional analyses of CsSHMTs in response to hormones and abiotic stresses. 3 Biotech 2022; 12:305. [PMID: 36276449 PMCID: PMC9526767 DOI: 10.1007/s13205-022-03378-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/22/2022] [Indexed: 11/01/2022] Open
Abstract
Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate-dependent enzyme that plays crucial roles in the photorespiration and one-carbon metabolism of plants. In the present research, we conducted a systematic analysis of the SHMT gene family in cucumber (Cucumis sativus L). Results show that a total of 6 SHMT members were identified from the cucumber genome database. CsSHMT1 and CsSHMT2 participate in a fragment duplication event, indicating that CsSHMTs may complete the expansion of family members through fragment duplication. Gene structure analysis found that the number of exons of CsSHMTs ranges from 4 to 15. Members with the same number of exons are classified into the same class in the phylogenetic analysis. Each class reflects its subcellular distribution. Expression and function analysis reveals that CsSHMTs express in a variety of plant tissues, indicating that SHMT gene expression pattern is not organ-specific. qRT-PCR analysis found that CsSHMT3 and CsSHMT5 positively respond to abscisic acid (ABA), and CsSHMT2-6 are induced by indole-3-acetic acid (IAA) and methyl jasmonate (MeJA). Abiotic stress analysis shows that CsSHMT3 is significantly induced by drought and salt stress. These results may provide useful information for further function and evolution analysis of cucumber SHMT genes. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03378-x.
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Affiliation(s)
- Rong Gao
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070 People’s Republic of China
| | - Yanyan Luo
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070 People’s Republic of China
| | - Xuejuan Pan
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070 People’s Republic of China
| | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070 People’s Republic of China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070 People’s Republic of China
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99933
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Seifar F, Dinasarapu AR, Jinnah HA. Uric Acid in Parkinson's Disease: What Is the Connection? Mov Disord 2022; 37:2173-2183. [PMID: 36056888 PMCID: PMC9669180 DOI: 10.1002/mds.29209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
Numerous studies have linked Parkinson's disease (PD) with low levels of uric acid (UA). Low UA has been associated with the risk of developing PD, and its progression and severity. The biological mechanisms underlying these relationships have never been firmly established. The most frequently proposed mechanism is that UA is an antioxidant. Low UA is thought to predispose to oxidative stress, which contributes to dopamine neuron degeneration, and leads to initial appearance of symptoms of PD and its worsening over time. Several recent studies have questioned this explanation. In this review, we describe the biology of UA, its many links with PD, evidence regarding UA as an antioxidant, and we question whether UA causes PD or contributes to its progression. We also address the possibility that something about PD causes low UA (reverse causation) or that low UA is a biomarker of some other more relevant mechanism in PD. We hope the evidence provided here will stimulate additional studies to better understand the links between UA and PD. Elucidating these mechanisms remains important, because they may provide new insights into the pathogenesis of PD or novel approaches to treatments. © 2022 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Fatemeh Seifar
- Neurosciences Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta GA, USA
- Department of Neurology, Emory University, Atlanta GA, USA
| | | | - H. A. Jinnah
- Department of Neurology, Emory University, Atlanta GA, USA
- Department of Human Genetics, Emory University, Atlanta GA, USA
- Department of Pediatrics, Emory University, Atlanta GA, USA
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99934
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Weinreb JT, Bowman TV. Clinical and mechanistic insights into the roles of DDX41 in haematological malignancies. FEBS Lett 2022; 596:2736-2745. [PMID: 36036093 PMCID: PMC9669125 DOI: 10.1002/1873-3468.14487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022]
Abstract
DEAD-box Helicase 41 (DDX41) is a member of the DExD/H-box helicase family that has a variety of cellular functions. Of note, germline and somatic mutations in the DDX41 gene are prevalently found in myeloid malignancies. Here, we present a comprehensive and analytic review covering relevant clinical, translational and basic science findings on DDX41. We first describe the initial characterisation of DDX41 mutations in patients affected by myelodysplastic syndromes, their associated clinical characteristics, and current treatment modalities. We then cover the known cellular functions of DDX41, spanning from its discovery in Drosophila as a neuroregulator through its more recently described roles in inflammatory signalling, R-loop metabolism and snoRNA processing. We end with a summary of the identified basic functions of DDX41 that when perturbed may contribute to the underlying pathology of haematologic neoplasms.
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Affiliation(s)
- Joshua T. Weinreb
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA
- Albert Einstein College of Medicine, Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Teresa V. Bowman
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA
- Albert Einstein College of Medicine, Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
- Albert Einstein College of Medicine and the Montefiore Medical Center, Department of Oncology, Bronx, NY, USA
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99935
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Samad MA, Mahboob E, Shafiq A, Ur Rehman MH, Sheikh A, Tharwani ZH. Types of T-cell lymphoma-a cytogenetic perspective. Ann Med Surg (Lond) 2022; 84:104844. [DOI: 10.1016/j.amsu.2022.104844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/25/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022] Open
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99936
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Obesity-associated mesenteric lymph leakage impairs the trafficking of lipids, lipophilic drugs and antigens from the intestine to mesenteric lymph nodes. Eur J Pharm Biopharm 2022; 180:319-331. [DOI: 10.1016/j.ejpb.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 11/23/2022]
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99937
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Kumar N, Vyas A, Agnihotri SK, Chattopadhyay N, Sachdev M. Small secretory proteins of immune cells can modulate gynecological cancers. Semin Cancer Biol 2022; 86:513-531. [PMID: 35150864 DOI: 10.1016/j.semcancer.2022.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 01/27/2023]
Abstract
Small secretory proteins of immune cells are mostly Cytokines, which include chemokines, interleukins, interferons, lymphokines and tumor necrosis factors but not hormones or growth factors. These secretory proteins are the molecular messengers and primarily involved in autocrine, paracrine and endocrine signaling as immunomodulating agents. Hence, these proteins actually regulate the cells of immune system to communicate with one another to produce a synchronized, robust, still self-regulated response to a specific antigen. Chemokines are smaller secreted proteins that control overall immune cell movement and location; these chemokines are divided into 4 subgroups, namely, CXC, CC, CX3C and C according to the position of 4 conserved cysteine residues. Complete characterization of cytokines and chemokines can exploit their vast signaling networks to develop cancer treatments. These secretory proteins like IL-6, IL-10, IL-12, TNFα, CCL2, CXCL4 & CXCL8 are predominantly expressed in most of the gynecological cancers, which directly stimulate immune effector cells and stromal cells at the tumor site and augment tumor cell recognition by cytotoxic T-cells. Hence; these secretory proteins are the major regulators, which can actually modulate all kinds of gynecological cancers. Furthermore, advancements in adoptive T-cell treatment have relied on the use of multiple cytokines/chemokines to establish a highly regulated environment for anti-tumor T cell growth. A number of in vitro studies as well as animal models and clinical subjects have also shown that cytokines/chemokines have broad antitumor activity, which has been translated into a number of cancer therapy approaches. This review will focus on the foremost cytokines & chemokines involved in the majority of the gynecological malignancies and discuss their basic biology as well as clinical applications.
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Affiliation(s)
- Niranjan Kumar
- Division of Endocrinology, CSIR- Central Drug Research Institute, Lucknow, 226 031, India; Academy of Scientific and Innovative Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, 201 002, India
| | - Akanksha Vyas
- Division of Endocrinology, CSIR- Central Drug Research Institute, Lucknow, 226 031, India; Academy of Scientific and Innovative Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, 201 002, India
| | | | - Naibedya Chattopadhyay
- Division of Endocrinology, CSIR- Central Drug Research Institute, Lucknow, 226 031, India; Academy of Scientific and Innovative Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, 201 002, India.
| | - Monika Sachdev
- Division of Endocrinology, CSIR- Central Drug Research Institute, Lucknow, 226 031, India; Academy of Scientific and Innovative Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, 201 002, India.
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99938
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Phosphoproteomics reveals the BRAF-ERK1/2 axis as an important pathogenic signaling node in cartilage degeneration. Osteoarthritis Cartilage 2022; 30:1443-1454. [PMID: 36100125 DOI: 10.1016/j.joca.2022.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Osteoarthritis (OA) causes gradual cellular alterations, structural anomalies and joint dysfunction. Progressive decline of chondrocyte function plays a vital role on OA pathogenesis. Although protein phosphorylation controls cartilage metabolism, its regulation mechanism in OA remains unclear. Thus, proteomic methods were used to investigate phosphorylation changes in preserved and OA articular cartilage samples, and to explore the intervention targets of phosphorylated kinase. METHODS Preserved (control) and lesioned (OA) cartilage samples from OA cases were assessed by phosphoproteomics. Immobilized metal affinity chromatography was performed for phosphopeptide enrichment. Quantitated phosphosites were comparatively assessed in the cartilage sample pair. Kinase-substrate enrichment analyses were carried out for identifying OA-related kinases. BRAF expression in cartilage tissues was assessed by immunohistochemical staining. The effects of BRAF inhibitor on cartilage degeneration were examined in mouse chondrocytes and OA mouse model. RESULTS High-sensitivity mass spectrometry-based proteomics revealed 7,471 peptides and 4,375 phosphorylated peptides differing between preserved and lesioned cartilage samples, which represented the significant alteration of kinase hubs and transduction pathways. Phosphoproteomics identified BRAF may be involved in developing OA. BRAF regulated the downstream ERK signaling pathway. In addition, BRAF was upregulated in human OA cartilage as shown by immunohistochemistry. Remarkably, BRAF inhibition alleviated cartilage degradation in a mouse model of OA through its downstream of ERK pathway activation. CONCLUSIONS Jointly, these findings provide an overview of phosphoproteomic alterations occurring during cartilage degeneration, identifying the BRAF-ERK1/2 Axis signaling as a potential signaling pathway involved in OA.
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99939
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Chesnel F, Jullion E, Delalande O, Couturier A, Alusse A, Le Goff X, Lenglet M, Gardie B, Abadie C, Arlot-Bonnemains Y. Mutation of the proline P81 into a serine modifies the tumour suppressor function of the von Hippel-Lindau gene in the ccRCC. Br J Cancer 2022; 127:1954-1962. [PMID: 36175619 PMCID: PMC9681884 DOI: 10.1038/s41416-022-01985-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The von Hippel-Lindau disease is an autosomal dominant syndrome associated with tumour formation in various tissues, such as retina, central nervous system, kidney, and adrenal glands. VHL gene deletion or mutations support the development of various cancers. Unclassified VHL variants also referred as "of unknown significance" result from gene mutations that have an unknown or unclear effect on protein functions. The P81S mutation has been linked to low penetrance Type 1 disease but its pathogenic function was not clearly determined. METHODS We established a stable cell line expressing the pVHL213 (c.241C>T, P81S) mutant. Using biochemical and physiological approaches, we herein analysed pVHL folding, stability and function in the context of this VHL single missense mutation. RESULTS The P81S mutation mostly affects the non-canonical function of the pVHL protein. The cells expressing the pVHL213P81S acquire invasive properties in relation with modified architecture network. CONCLUSION We demonstrated the pathogenic role of this mutation in tumour development in vhl patients and confirm a medical follow up of family carrying the c.241C>T, P81S.
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Affiliation(s)
- Franck Chesnel
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Emmanuelle Jullion
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Olivier Delalande
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Anne Couturier
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Adrien Alusse
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Xavier Le Goff
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Marion Lenglet
- Ecole Pratique des Hautes Etudes, EPHE, Université Paris Sciences et Lettres, Paris, France
- Nantes Université, CNRS, INSERM, l'Institut du Thorax, F-44000, Nantes, France
| | - Betty Gardie
- Ecole Pratique des Hautes Etudes, EPHE, Université Paris Sciences et Lettres, Paris, France
- Nantes Université, CNRS, INSERM, l'Institut du Thorax, F-44000, Nantes, France
| | - Caroline Abadie
- Institut de Cancérologie, Boulevard Jacques Monod, 44805, Saint-Herblain, France
| | - Yannick Arlot-Bonnemains
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France.
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99940
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Abstract
It is well established from clinical trials that behavioural interventions can halve the risk of progression from prediabetes to type 2 diabetes but translating this evidence of efficacy into effective real-world interventions at scale is an ongoing challenge. A common suggestion is that future preventive interventions need to be more personalised in order to enhance effectiveness. This review evaluates the degree to which existing interventions are already personalised and outlines how greater personalisation could be achieved through better identification of those at high risk, division of type 2 diabetes into specific subgroups and, above all, more individualisation of the behavioural targets for preventive action. Approaches using more dynamic real-time data are in their scientific infancy. Although these approaches are promising they need longer-term evaluation against clinical outcomes. Whatever personalised preventive approaches for type 2 diabetes are developed in the future, they will need to be complementary to existing individual-level interventions that are being rolled out and that are demonstrably effective. They will also need to ideally synergise with, and at the very least not detract attention from, efforts to develop and implement strategies that impact on type 2 diabetes risk at the societal level.
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Affiliation(s)
- Nicholas J Wareham
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, University of Cambridge Clinical School, Cambridge, UK.
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99941
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Brennan CM, Hill AS, St. Andre M, Li X, Madeti V, Breitkopf S, Garren S, Xue L, Gilbert T, Hadjipanayis A, Monetti M, Emerson CP, Moccia R, Owens J, Christoforou N. DUX4 expression activates JNK and p38 MAP kinases in myoblasts. Dis Model Mech 2022; 15:dmm049516. [PMID: 36196640 PMCID: PMC10655719 DOI: 10.1242/dmm.049516] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 09/28/2022] [Indexed: 11/20/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by misexpression of the DUX4 transcription factor in skeletal muscle that results in transcriptional alterations, abnormal phenotypes and cell death. To gain insight into the kinetics of DUX4-induced stresses, we activated DUX4 expression in myoblasts and performed longitudinal RNA sequencing paired with proteomics and phosphoproteomics. This analysis revealed changes in cellular physiology upon DUX4 activation, including DNA damage and altered mRNA splicing. Phosphoproteomic analysis uncovered rapid widespread changes in protein phosphorylation following DUX4 induction, indicating that alterations in kinase signaling might play a role in DUX4-mediated stress and cell death. Indeed, we demonstrate that two stress-responsive MAP kinase pathways, JNK and p38, are activated in response to DUX4 expression. Inhibition of each of these pathways ameliorated DUX4-mediated cell death in myoblasts. These findings uncover that the JNK pathway is involved in DUX4-mediated cell death and provide additional insights into the role of the p38 pathway, a clinical target for the treatment of FSHD.
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Affiliation(s)
- Christopher M. Brennan
- Rare Disease Research Unit, Pfizer Inc., Cambridge, MA 02139, USA
- WRDM Postdoctoral Program, Pfizer Inc., Cambridge, MA 02139, USA
| | - Abby S. Hill
- Rare Disease Research Unit, Pfizer Inc., Cambridge, MA 02139, USA
| | | | - Xianfeng Li
- Rare Disease Research Unit, Pfizer Inc., Cambridge, MA 02139, USA
| | - Vijaya Madeti
- NGS Technology Center, Inflammation and Immunology Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Susanne Breitkopf
- Proteomics Technology Center, Internal Medicine Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Seth Garren
- NGS Technology Center, Inflammation and Immunology Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Liang Xue
- Machine Learning and Computational Science, Pfizer Inc., Cambridge, MA 02139, USA
| | - Tamara Gilbert
- High Content Imaging Technology Center, Internal Medicine Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Angela Hadjipanayis
- NGS Technology Center, Inflammation and Immunology Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Mara Monetti
- Proteomics Technology Center, Internal Medicine Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Charles P. Emerson
- Rare Disease Research Unit, Pfizer Inc., Cambridge, MA 02139, USA
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Robert Moccia
- Rare Disease Research Unit, Pfizer Inc., Cambridge, MA 02139, USA
| | - Jane Owens
- Rare Disease Research Unit, Pfizer Inc., Cambridge, MA 02139, USA
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99942
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Kim KH, Oh J, Yang G, Lee J, Kim J, Gwak SY, Cho I, Lee SH, Byun HK, Choi HK, Kim J, Chang JS, Kang SM, Yoon HI. Association of Sinoatrial Node Radiation Dose With Atrial Fibrillation and Mortality in Patients With Lung Cancer. JAMA Oncol 2022; 8:1624-1634. [PMID: 36136325 PMCID: PMC9501754 DOI: 10.1001/jamaoncol.2022.4202] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/19/2022] [Indexed: 11/14/2022]
Abstract
Importance Atrial fibrillation (AF) can develop following thoracic irradiation. However, the critical cardiac substructure responsible for AF has not been properly studied. Objective To describe the incidence of AF in patients with lung cancer and determine predictive cardiac dosimetric parameters. Design, Setting, and Participants This retrospective cohort study was performed at a single referral center and included 239 patients diagnosed with limited-stage small cell lung cancer (SCLC) and 321 patients diagnosed with locally advanced non-small cell lung cancer (NSCLC) between August 2008 and December 2019 who were treated with definitive chemoradiotherapy. Exposures Radiation dose exposure to cardiac substructures, including the chambers, coronary arteries, and cardiac conduction nodes, were calculated for each patient. Main Outcomes and Measures Main outcomes were AF and overall survival. Results Of the 239 and 321 patients with SCLC and NSCLC, the median (IQR) age was 68 (60-73) years and 67 (61-75) years, and 207 (86.6%) and 261 (81.3%) were men, respectively. At a median (IQR) follow-up time of 32.7 (22.1-56.6) months, 9 and 17 patients experienced new-onset AF in the SCLC and NSCLC cohorts, respectively. The maximum dose delivered to the sinoatrial node (SAN Dmax) exhibited the highest predictive value for prediction of AF. A higher SAN Dmax significantly predicted an increased risk of AF in patients with SCLC (adjusted hazard ratio [aHR], 14.91; 95% CI, 4.00-55.56; P < .001) and NSCLC (aHR, 15.67; 95% CI, 2.08-118.20; P = .008). However, SAN Dmax was not associated with non-AF cardiac events. Increased SAN Dmax was significantly associated with poor overall survival in patients with SCLC (aHR, 2.68; 95% CI, 1.53-4.71; P < .001) and NSCLC (aHR, 1.97; 95% CI, 1.45-2.68; P < .001). Conclusions and Relevance In this cohort study, results suggest that incidental irradiation of the SAN during chemoradiotherapy may be associated with the development of AF and increased mortality. This supports the need to minimize radiation dose exposure to the SAN during radiotherapy planning and to consider close follow-up for the early detection of AF in patients receiving thoracic irradiation.
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Affiliation(s)
- Kyung Hwan Kim
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jaewon Oh
- Division of Cardiology, Department of Internal Medicine, Severance Cardiovascular Hospital, Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Gowoon Yang
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joongyo Lee
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jihun Kim
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seo-yeon Gwak
- Division of Cardiology, Department of Internal Medicine, Severance Cardiovascular Hospital, Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Iksung Cho
- Division of Cardiology, Department of Internal Medicine, Severance Cardiovascular Hospital, Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung Hyun Lee
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hwa Kyung Byun
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyo-Kyoung Choi
- Research Group of Healthcare, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Jinsung Kim
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jee Suk Chang
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seok-Min Kang
- Division of Cardiology, Department of Internal Medicine, Severance Cardiovascular Hospital, Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hong In Yoon
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
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99943
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von Takach B, Ranjard L, Burridge CP, Cameron SF, Cremona T, Eldridge MDB, Fisher DO, Frankenberg S, Hill BM, Hohnen R, Jolly CJ, Kelly E, MacDonald AJ, Moussalli A, Ottewell K, Phillips BL, Radford IJ, Spencer PBS, Trewella GJ, Umbrello LS, Banks SC. Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads. Mol Ecol 2022; 31:5468-5486. [PMID: 36056907 PMCID: PMC9826391 DOI: 10.1111/mec.16680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 01/11/2023]
Abstract
Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.
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Affiliation(s)
- Brenton von Takach
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia,School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Louis Ranjard
- The Research School of Biology, Faculty of ScienceThe Australian National UniversityActonAustralian Capital TerritoryAustralia,PlantTech Research InstituteTaurangaNew Zealand
| | | | - Skye F. Cameron
- Australian Wildlife ConservancyKimberleyWestern AustraliaAustralia,School of Biological SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Teigan Cremona
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | | | - Diana O. Fisher
- School of Biological SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
| | | | - Brydie M. Hill
- Flora and Fauna Division, Department of Environment, Parks and Water SecurityNorthern Territory GovernmentNorthern TerritoryAustralia
| | - Rosemary Hohnen
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Chris J. Jolly
- Institute of Land, Water and Society, School of Environmental ScienceCharles Sturt UniversityAlburyNew South WalesAustralia,School of Natural SciencesMacquarie UniversityMacquarie ParkNew South WalesAustralia
| | - Ella Kelly
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia
| | - Anna J. MacDonald
- The Research School of Biology, Faculty of ScienceThe Australian National UniversityActonAustralian Capital TerritoryAustralia,Australian Antarctic Division, Department of AgricultureWater and the EnvironmentKingstonTasmaniaAustralia
| | - Adnan Moussalli
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia,Department of ScienceMuseums VictoriaMelbourneVictoriaAustralia
| | - Kym Ottewell
- Department of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Ben L. Phillips
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia
| | - Ian J. Radford
- Department of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Peter B. S. Spencer
- Environmental and Conservation Sciences, Murdoch UniversityPerthWestern AustraliaAustralia
| | - Gavin J. Trewella
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Linette S. Umbrello
- Department of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia,Collections and Research CentreWestern Australian MuseumWelshpoolWestern AustraliaAustralia
| | - Sam C. Banks
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
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99944
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Bracher-Smith M, Leonenko G, Baker E, Crawford K, Graham AC, Salih DA, Howell BW, Hardy J, Escott-Price V. Whole genome analysis in APOE4 homozygotes identifies the DAB1-RELN pathway in Alzheimer's disease pathogenesis. Neurobiol Aging 2022; 119:67-76. [PMID: 35977442 PMCID: PMC9548409 DOI: 10.1016/j.neurobiolaging.2022.07.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/04/2022] [Accepted: 07/23/2022] [Indexed: 11/20/2022]
Abstract
The APOE-ε4 allele is known to predispose to amyloid deposition and consequently is strongly associated with Alzheimer's disease (AD) risk. There is debate as to whether the APOE gene accounts for all genetic variation of the APOE locus. Another question which remains is whether APOE-ε4 carriers have other genetic factors influencing the progression of amyloid positive individuals to AD. We conducted a genome-wide association study in a sample of 5,390 APOE-ε4 homozygous (ε4ε4) individuals (288 cases and 5102 controls) aged 65 or over in the UK Biobank. We found no significant associations of SNPs in the APOE locus with AD in the sample of ε4ε4 individuals. However, we identified a novel genome-wide significant locus associated to AD, mapping to DAB1 (rs112437613, OR = 2.28, CI = 1.73-3.01, p = 5.4 × 10-9). This identification of DAB1 led us to investigate other components of the DAB1-RELN pathway for association. Analysis of the DAB1-RELN pathway indicated that the pathway itself was associated with AD, therefore suggesting an epistatic interaction between the APOE locus and the DAB1-RELN pathway.
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Affiliation(s)
- Matthew Bracher-Smith
- Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Cardiff, UK; Dementia Research Institute, Cardiff University, Cardiff, UK
| | - Ganna Leonenko
- Dementia Research Institute, Cardiff University, Cardiff, UK
| | - Emily Baker
- Dementia Research Institute, Cardiff University, Cardiff, UK
| | - Karen Crawford
- Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Cardiff, UK
| | | | - Dervis A Salih
- Dementia Research Institute, University College London, UK
| | - Brian W Howell
- Neuroscience and Physiology, State University of New York, Albany, NY, USA
| | - John Hardy
- Dementia Research Institute, University College London, UK.
| | - Valentina Escott-Price
- Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Cardiff, UK.
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99945
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Maguire JA, Gadue P, French DL. Highly Efficient CRISPR/Cas9-Mediated Genome Editing in Human Pluripotent Stem Cells. Curr Protoc 2022; 2:e590. [PMID: 36426905 PMCID: PMC9708095 DOI: 10.1002/cpz1.590] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Human pluripotent stem cells hold tremendous potential for both basic biology and cell-based therapies for a wide variety of diseases. The ability to manipulate the genome of these cells using the CRISPR/Cas9 technology has expanded this potential by providing a valuable tool to engineer or correct disease-associated mutations. Because of the high efficiency with which CRISPR/Cas9 creates targeted double-strand breaks, a major challenge has been the introduction of precise genetic modifications on one allele without indel formation on the non-targeted allele. To overcome this obstacle, we describe use of two oligonucleotide repair templates: one expressing the sequence change and the other maintaining the normal sequence. In addition, we have streamlined both the transfection and screening methodologies to make the protocols efficient, with small numbers of cells and a limited amount of labor-intensive clone passaging. This article provides a technically simple approach for generating valuable tools to model human disease in stem cells. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Application and optimization of CRISPR-based genome editing in human pluripotent stem cells Basic Protocol 2: Genetic modification of human pluripotent stem cells using a double-oligonucleotide CRISPR/Cas9 recombination system.
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Affiliation(s)
- Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia
| | - Paul Gadue
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania
| | - Deborah L. French
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania
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99946
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Ashhurst JF, Tu S, Timmins HC, Kiernan MC. Progress, development, and challenges in amyotrophic lateral sclerosis clinical trials. Expert Rev Neurother 2022; 22:905-913. [PMID: 36543326 DOI: 10.1080/14737175.2022.2161893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Amyotrophic Lateral Sclerosis (ALS) brings unique challenges to a clinical trial setting, due in part to relatively low disease prevalence coupled with a poor prognosis, in addition to the complexities linked to disease heterogeneity. As critical understanding of the disease develops, particularly in relation to clinical phenotype and the mechanisms of disease progression, so too new concepts evolve in relation to clinical trials, including the advent of precision therapy, targeted to subgroups of ALS patients. AREAS COVERED Individualized, or precision medicine in ALS recognizes the heterogeneous nature of the disease and utilizes information such as the clinical phenotype of the disease, clinical biomarkers, and genotyping to promote a tailored approach to treatment. Separate to these considerations, the present review will discuss clinical trial design and how this can be improved to better match patient and investigator needs in ALS clinical trials. EXPERT OPINION Precision therapy will promote a more focused treatment approach, with the goal of improving clinical outcomes for ALS patients. An increased community awareness of ALS, coupled with significant industry and philanthropic funding for ALS research, is accelerating this process.
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Affiliation(s)
| | - Sicong Tu
- Brain and Mind Centre, University of Sydney, Camperdown, Australia
| | - Hannah C Timmins
- Brain and Mind Centre, University of Sydney, Camperdown, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, University of Sydney, Camperdown, Australia.,Department of Neurology, Royal Prince Alfred Hospital, Sydney, Australia
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99947
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Haferlach C, Heuser M. [Diagnostics in unclear cytopenia-How and when do we screen for clonal hematopoiesis?]. INNERE MEDIZIN (HEIDELBERG, GERMANY) 2022; 63:1141-1147. [PMID: 36121473 DOI: 10.1007/s00108-022-01402-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Many studies have analyzed the clinical significance of clonal hematopoiesis. The collected data lead to the conclusion that in defined clinical constellations a targeted diagnostic search for clonal hematopoiesis seems reasonable. OBJECTIVE A diagnostic algorithm and the selection of the right methods are required for use in everyday clinical practice. METHODS A search was carried out in PubMed for relevant literature using the terms clonal hematopoiesis, CHIP, and CCUS, which was evaluated and augmented with expert knowledge. RESULTS Clonal hematopoiesis is defined as the presence of clonality in hematopoietic cells and is detectable in 5-95% of the aged population depending on the method used. Clinical relevance was demonstrated for larger clones with mutations in specific genes and subsequently the terms clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS) were introduced. For both constellations the relevant gene spectrum as well as the relevant clone size were clearly defined. In CHIP a normal blood count and differential blood count are present by definition. CHIP is therefore currently an incidental finding. In CCUS, on the other hand, cytopenia is present. The clinical risks of the two constellations differ. CHIP is associated with a very low risk of progression to a hematologic neoplasm, whereas in CCUS the risk is significantly increased depending on clone size, number and spectrum of mutated genes. CONCLUSION Screening for CHIP is currently not useful. In the presence of persistent cytopenia of unclear cause targeted diagnostic tests including bone marrow evaluation and genetic analyses should be performed.
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Affiliation(s)
- Claudia Haferlach
- MLL - Münchner Leukämielabor, Max-Lebsche-Platz 31, 81377, München, Deutschland.
| | - Michael Heuser
- Klinik für Hämatologie, Hämostaseologie, Onkologie und Stammzelltransplantation, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland.
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99948
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Apport de l'immunothérapie dans le traitement des cancers des voies biliaires avancés. Bull Cancer 2022; 109:11S11-11S20. [DOI: 10.1016/s0007-4551(22)00464-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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99949
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Egan D, Moran B, Wilkinson M, Pinyol M, Guerra E, Gatius S, Matias-Guiu X, Kolch W, le Roux CW, Brennan DJ. CRABP2 - A novel biomarker for high-risk endometrial cancer. Gynecol Oncol 2022; 167:314-322. [PMID: 36163055 DOI: 10.1016/j.ygyno.2022.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/12/2022] [Accepted: 09/17/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVE Investigate the clinical and functional implications of elevated CRABP2 expression in endometrial cancer (EC) patients. METHODS Patients were stratified into high and low CRABP2 expression groups using a decision tree classifier. Univariate and multivariate statistical analyses determined the prognostic and clinicopathological consequences of increased CRABP2 expression. A CRABP2 gene signature was generated using differential expression analysis, and analyzed using network-based approaches. The findings were validated in The Clinical Proteomic Tumor Analysis Consortium (CPTAC), a newly generated cohort of 120 endometrial tissues, and The Cancer Dependency Map (DepMap). RESULTS 60 (11%) patients in TCGA had high CRABP2 expression, whilst 468 (89%) had low expression. High expression was associated with serous EC, reduced overall survival, advanced stage and grade. Downstream retinoic acid receptors (RARG and RARA) were correlated with CRABP2 expression and were associated with worse prognosis in serous EC. The CRABP2 gene signature was enriched for Polycomb target gene sets, and was regulated by ELP3 and BMP7. BMP7 expression was increased in the CRABP2-high group, was associated with worse prognosis, and CRISPR-Cas9 screens revealed correlations in its cell-fitness score with CRABP2 following gene knockout. The opposite was true for ELP3, suggesting opposing effects from both master regulators. CONCLUSIONS CRABP2 expression is associated with poor prognosis and advanced EC. The expression of RARA and RARG correlates with CRABP2 and are associated with worse prognosis in advanced histological subtypes. Polycomb target gene sets and two master regulators, ELP3 and BMP7, were identified as functionally relevant mechanisms driving aberrant CRABP2 expression.
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Affiliation(s)
- Donagh Egan
- Systems Biology Ireland, UCD School of Medicine, Belfield, Dublin 4, Ireland.
| | - Bruce Moran
- Department of Pathology, St. Vincent's University Hospital, Dublin, Ireland
| | - Michael Wilkinson
- Diabetes Complications Research Centre, Conway Institute, University College Dublin, Dublin, Ireland
| | - Miquel Pinyol
- Department of Pathology, Hospital Universitari Arnau de Vilanova, University of Lleida, IRBLLEIDA, CIBERONC, Spain
| | - Esther Guerra
- Department of Pathology, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Spain
| | - Sonia Gatius
- Department of Pathology, Hospital Universitari Arnau de Vilanova, University of Lleida, IRBLLEIDA, CIBERONC, Spain
| | - Xavier Matias-Guiu
- Department of Pathology, Hospital Universitari Arnau de Vilanova, University of Lleida, IRBLLEIDA, CIBERONC, Spain; Department of Pathology, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Spain
| | - Walter Kolch
- Systems Biology Ireland, UCD School of Medicine, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Carel W le Roux
- Diabetes Complications Research Centre, Conway Institute, University College Dublin, Dublin, Ireland
| | - Donal J Brennan
- Systems Biology Ireland, UCD School of Medicine, Belfield, Dublin 4, Ireland
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99950
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NAFLD: genetics and its clinical implications. Clin Res Hepatol Gastroenterol 2022; 46:102003. [PMID: 35963605 DOI: 10.1016/j.clinre.2022.102003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023]
Abstract
Worldwide non-alcoholic fatty liver disease (NAFLD) is recognized as the most common type of liver disease and its burden increasing at an alarming rate. NAFLD entails steatosis, fibrosis, cirrhosis, and, finally, hepatocellular carcinoma (HCC). The substantial inter-patient variation during disease progression is the hallmark of individuals with NAFLD. The variability of NAFLD development and related complications among individuals is determined by genetic and environmental factors. Genome-wide association studies (GWAS) have discovered reproducible and robust associations between gene variants such as PNPLA3, TM6SF2, HSD17B13, MBOAT7, GCKR and NAFLD. Evidences have provided the new insights into the NAFLD biology and underlined potential pharmaceutical targets. Ideally, the candidate genes associated with the hereditability of NAFLD are mainly involved in assembly of lipid droplets, lipid remodeling, lipoprotein packing and secretion, redox status mitochondria, and de novo lipogenesis. In recent years, the ability to translate genetics into a clinical context has emerged substantially by combining genetic variants primarily associated with NAFLD into polygenic risk scores (PRS). These score in combination with metabolic factors could be utilized to identify the severe liver diseases in patients with the gene regulatory networks (GRNs). Hereby, we even have highlighted the current understanding related to the schedule therapeutic approach of an individual based on microbial colonization and dysbiosis reversal as a therapy for NAFLD. The premise of this review is to concentrate on the potential of genetic factors and their translation into the design of novel therapeutics, as well as their implications for future research into personalized medications using microbiota.
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