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Zhang L, Sahar AM, Li C, Chaudhary A, Yousaf I, Saeedah MA, Mubarak A, Haris M, Nawaz M, Reem MA, Ramadan FA, Mostafa AAM, Feng W, Hameed Y. A detailed multi-omics analysis of GNB2 gene in human cancers. BRAZ J BIOL 2024; 84. [DOI: 10.1590/1519-6984.260169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Abstract The Guanine-nucleotide binding protein 2 (GNB2) encodes for β2 subunit (Gβ2) of the G-protein complex. Keeping in view the increased demand of reliable biomarkers in cancer, the current study was planned to extensively explored GNB2 expression variation and its roles in different cancers using online available databases and diverse methodology. In view of our results, the GNB2 was notably up-regulated relative to corresponding controls in twenty three cancer types. As well, the elevated expression of GNB2 was found to be associated with the reduced overall survival (OS) of the Liver Hepatocellular Carcinoma (LIHC) and Rectum Adenocarcinoma (READ) only out of all analyzed cancer types. This implies GNB2 plays vital role in the tumorigenesis of LIHC and READ. Several additional analysis also explored six critical pathways and few important correlations related to GNB2 expression and different other parameters such as promoter methylation, tumor purity, CD8+ T immune cells infiltration, and genetic alteration, and chemotherapeutic drugs. In conclusion, GNB2 gene has been identified in this study as a shared potential biomarker (diagnostic and prognostic) of LIHC and READ.
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Affiliation(s)
| | | | - C. Li
- Sichuan University, PR China
| | | | - I. Yousaf
- Government College University Faisalabad, Pakistan
| | | | | | - M. Haris
- Nowshera Medical College, Pakistan
| | | | | | | | | | - W. Feng
- Sichuan University, PR China
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Ferreira LM, Sáfadi T, Ferreira JL. K-mer applied in Mycobacterium tuberculosis genome cluster analysis. BRAZ J BIOL 2024; 84. [DOI: 10.1590/1519-6984.258258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Abstract According to studies carried out, approximately 10 million people developed tuberculosis in 2018. Of this total, 1.5 million people died from the disease. To study the behavior of the genome sequences of Mycobacterium tuberculosis (MTB), the bacterium responsible for the development of tuberculosis (TB), an analysis was performed using k-mers (DNA word frequency). The k values ranged from 1 to 10, because the analysis was performed on the full length of the sequences, where each sequence is composed of approximately 4 million base pairs, k values above 10, the analysis is interrupted, as consequence of the program's capacity. The aim of this work was to verify the formation of the phylogenetic tree in each k-mer analyzed. The results showed the formation of distinct groups in some k-mers analyzed, taking into account the threshold line. However, in all groups, the multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains remained together and separated from the other strains.
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Wang L, Tian R, Wang G, Zhao M, Zhang Y, Li J. Proteomic analysis of fetal skin by iTRAQ reveals molecular signals underlying Inner Mongolia Cashmere goat hair follicle initiation. All Life 2023; 16. [DOI: 10.1080/26895293.2023.2169363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Lele Wang
- Ulanqab of Medical College, Ulanqab, People’s Republic of China
| | - Rugang Tian
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, People’s Republic of China
| | - Gaofeng Wang
- Ulanqab Center for Animal Disease Control and Prevention, Ulanqab, People’s Republic of China
| | - Meng Zhao
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, People’s Republic of China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
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Creighton CJ, Zhang F, Zhang Y, Castro P, Hu R, Islam M, Ghosh S, Ittmann M, Kwabi-addo B. Comparative and integrative analysis of transcriptomic and epigenomic-wide DNA methylation changes in African American prostate cancer. Epigenetics 2023; 18. [DOI: 10.1080/15592294.2023.2180585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Affiliation(s)
- Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Flora Zhang
- Center for Women’s Studies, Colgate University, Hamilton, New York, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Patricia Castro
- Department of Pathology and Immunology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Rong Hu
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Md Islam
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Somiranjan Ghosh
- Department of Biology, Howard University, Washington, Columbia, USA
| | - Michael Ittmann
- Department of Pathology and Immunology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Bernard Kwabi-Addo
- Department of Biochemistry and Molecular Biology, Howard University, Washington, Columbia, USA
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5
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Wang Y, Shen R, Liu M, Zhou Q, Zhai Y, Fan L, Lan Y, Zhu X. Metagenomic analysis of Tongxie Yaofang therapy for rat models of ulcerative colitis with liver depression and spleen deficiency syndrome. All Life 2023; 16:1-12. [DOI: 10.1080/26895293.2022.2147221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Yan Wang
- Teaching Experiment Training Center, Ningxia Medical University, Yinchuan City, Ningxia, People’s Republic of China
| | - Rui Shen
- Department of Integrated Traditional Chinese and Western Medicine, Zhangye People's Hospital Affiliated to Hexi University, Zhangye City, Gansu, People’s Republic of China
| | - Miao Liu
- College of Basic Medicine, Ningxia Medical University, Yinchuan City, Ningxia, People’s Republic of China
| | - Qi Zhou
- College of Basic Medicine, Ningxia Medical University, Yinchuan City, Ningxia, People’s Republic of China
| | - Yan-hui Zhai
- College of Basic Medicine, Ningxia Medical University, Yinchuan City, Ningxia, People’s Republic of China
| | - Li-hui Fan
- College of Basic Medicine, Ningxia Medical University, Yinchuan City, Ningxia, People’s Republic of China
| | - Yu-ze Lan
- College of Basic Medicine, Ningxia Medical University, Yinchuan City, Ningxia, People’s Republic of China
| | - Xiang-dong Zhu
- College of Basic Medicine, Ningxia Medical University, Yinchuan City, Ningxia, People’s Republic of China
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6
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Qian H, Zhang Z, Tao Z, Xie Y, Yin Y, He W, Zhang L. Association of Circular RNAs levels in blood and Essential Hypertension with Carotid Plaque. Clin Exp Hypertens 2023; 45:2180020. [PMID: 36843004 DOI: 10.1080/10641963.2023.2180020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
BACKGROUND As one of the essential hypertension (EH)-mediated target organ damage, carotid plaque is a crucial subclinical precursor for cardiovascular events. Therefore, it is vital to identify the risk factors and pathogenesis for EH with carotid plaque. METHODS Based on our previous microarray analysis, we selected four circRNAs as the candidate circRNAs and detected their expression levels in blood of 192 subjects (64 healthy controls, 64 EH patients, and 64 EH patients with carotid plaque) by qRT-PCR analysis. The regulatory mechanism of circRNAs involved in carotid plaque was predicted by bioinformatics analysis. RESULTS The level of hsa_circ_0124782 increased significantly and the levels of hsa_circ_0131618 and hsa_circ_0127342 decreased significantly in the EH group and EH with carotid plaque group compared with the control group (P < .05). Functional enrichment analysis showed that three circRNAs might be implicated in pathogenesis for carotid plaque. CONCLUSION Our study revealed the relationship between three circRNAs and carotid plaque, suggesting that they may serve as potential biomarkers for EH with carotid plaque.
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Affiliation(s)
- Haiyan Qian
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Zebo Zhang
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Zhenbo Tao
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China.,Ningbo Municipal Centre for Disease Control and Prevention, Ningbo, China
| | - Yanqing Xie
- Institute of Geriatrics, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Yueqi Yin
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Wenming He
- Institute of Geriatrics, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Lina Zhang
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China.,Institute of Geriatrics, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
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Hu F, Zhang Y, Guo J. Effects of drought stress on photosynthetic physiological characteristics, leaf microstructure, and related gene expression of yellow horn. Plant Signal Behav 2023; 18:2215025. [PMID: 37243677 DOI: 10.1080/15592324.2023.2215025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/29/2023]
Abstract
Yellow horn grows in northern China and has a high tolerance to drought and poor soil. Improving photosynthetic efficiency and increasing plant growth and yield under drought conditions have become important research content for researchers worldwide. Our study goal is to provide comprehensive information on photosynthesis and some candidate genes breeding of yellow horn under drought stress. In this study, seedlings' stomatal conductance, chlorophyll content, and fluorescence parameters decreased under drought stress, but non-photochemical quenching increased. The leaf microstructure showed that stomata underwent a process from opening to closing, guard cells from complete to dry, and surrounding leaf cells from smooth to severe shrinkage. The chloroplast ultrastructure showed that the changes of starch granules were different under different drought stress, while plastoglobules increased and expanded continuously. In addition, we found some differentially expressed genes related to photosystem, electron transport component, oxidative phosphate ATPase, stomatal closure, and chloroplast ultrastructure. These results laid a foundation for further genetic improvement and deficit resistance breeding of yellow horn under drought stress.
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Affiliation(s)
- Fang Hu
- College of Forestry, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Yunxiang Zhang
- College of Forestry, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Jinping Guo
- College of Forestry, Shanxi Agricultural University, Jinzhong, Shanxi, China
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Haresh Liya D, Elanchezhian M, Pahari M, Mouroug Anand N, Suresh S, Balaji N, Kumar Jainarayanan A. QPromoters: sequence based prediction of promoter strength in Saccharomyces cesrevisiae. All Life 2023; 16. [DOI: 10.1080/26895293.2023.2168304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Devang Haresh Liya
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Mirudula Elanchezhian
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Mukulika Pahari
- Department of Computer Engineering, Ramrao Adik Institute of Technology, DY Patil Deemed to be University, Navi Mumbai, India
| | - Nithishwer Mouroug Anand
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Shivani Suresh
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Nivedha Balaji
- School of Biology and Environmental Sciences (SBES), University College Dublin, Dublin, Ireland
| | - Ashwin Kumar Jainarayanan
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Interdisciplinary Bioscience Doctoral Training Program and Exeter College, University of Oxford, Oxford, UK
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9
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Yaqoob H, Tariq A, Bhat BA, Bhat KA, Nehvi IB, Raza A, Djalovic I, Prasad PV, Mir RA. Integrating genomics and genome editing for orphan crop improvement: a bridge between orphan crops and modern agriculture system. GM Crops Food 2023; 14:1-20. [PMID: 36606637 DOI: 10.1080/21645698.2022.2146952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Domestication of orphan crops could be explored by editing their genomes. Genome editing has a lot of promise for enhancing agricultural output, and there is a lot of interest in furthering breeding in orphan crops, which are sometimes plagued with unwanted traits that resemble wild cousins. Consequently, applying model crop knowledge to orphan crops allows for the rapid generation of targeted allelic diversity and innovative breeding germplasm. We explain how plant breeders could employ genome editing as a novel platform to accelerate the domestication of semi-domesticated or wild plants, resulting in a more diversified base for future food and fodder supplies. This review emphasizes both the practicality of the strategy and the need to invest in research that advances our understanding of plant genomes, genes, and cellular systems. Planting more of these abandoned orphan crops could help alleviate food scarcities in the challenge of future climate crises.
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Affiliation(s)
- Huwaida Yaqoob
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Arooj Tariq
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Basharat Ahmad Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Kaisar Ahmad Bhat
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Iqra Bashir Nehvi
- Department of Clinical Biochemistry, SKIMS, Srinagar, Jammu and Kashmir, India
| | - Ali Raza
- College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China,Ali Raza College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - PV Vara Prasad
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, Kansas, USA
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Jammu and Kashmir, India,CONTACT Rakeeb Ahmad MirDepartment of Biotechnology, School of Life Sciences, Central University of Kashmir, Jammu and Kashmir, India
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10
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Huang Y, Ge MX, Li YH, Li JL, Yu Q, Xiao FH, Ao HS, Yang LQ, Li J, He Y, Kong QP. Longevity-Associated Transcription Factor ATF7 Promotes Healthspan by Suppressing Cellular Senescence and Systematic Inflammation. Aging Dis 2023. [PMID: 37163432 DOI: 10.14336/AD.2022.1217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Aging is characterized by persistent low-grade systematic inflammation, which is largely responsible for the occurrence of various age-associated diseases. We and others have previously reported that long-lived people (such as centenarians) can delay the onset of or even escape certain major age-related diseases. Here, by screening blood transcriptome and inflammatory profiles, we found that long-lived individuals had a relatively lower inflammation level (IL6, TNFα), accompanied by up-regulation of activating transcription factor 7 (ATF7). Interestingly, ATF7 expression was gradually reduced during cellular senescence. Loss of ATF7 induced cellular senescence, while overexpression delayed senescence progress and senescence-associated secretory phenotype (SASP) secretion. We showed that the anti-senescence effects of ATF7 were achieved by inhibiting nuclear factor kappa B (NF-κB) signaling and increasing histone H3K9 dimethylation (H3K9me2). In Caenorhabditis elegans, ATF7 overexpression significantly suppressed aging biomarkers and extended lifespan. Our findings suggest that ATF7 is a longevity-promoting factor that lowers cellular senescence and inflammation in long-lived individuals.
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Affiliation(s)
- Yaqun Huang
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Ming-Xia Ge
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Hong Li
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jing-Lin Li
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Qin Yu
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hong-Shun Ao
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ji Li
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Yonghan He
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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11
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Morrison LJ, Steketee PC, Tettey MD, Matthews KR. Pathogenicity and virulence of African trypanosomes: From laboratory models to clinically relevant hosts. Virulence 2023; 14:2150445. [PMID: 36419235 DOI: 10.1080/21505594.2022.2150445] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
African trypanosomes are vector-borne protozoa, which cause significant human and animal disease across sub-Saharan Africa, and animal disease across Asia and South America. In humans, infection is caused by variants of Trypanosoma brucei, and is characterized by varying rate of progression to neurological disease, caused by parasites exiting the vasculature and entering the brain. Animal disease is caused by multiple species of trypanosome, primarily T. congolense, T. vivax, and T. brucei. These trypanosomes also infect multiple species of mammalian host, and this complexity of trypanosome and host diversity is reflected in the spectrum of severity of disease in animal trypanosomiasis, ranging from hyperacute infections associated with mortality to long-term chronic infections, and is also a main reason why designing interventions for animal trypanosomiasis is so challenging. In this review, we will provide an overview of the current understanding of trypanosome determinants of infection progression and severity, covering laboratory models of disease, as well as human and livestock disease. We will also highlight gaps in knowledge and capabilities, which represent opportunities to both further our fundamental understanding of how trypanosomes cause disease, as well as facilitating the development of the novel interventions that are so badly needed to reduce the burden of disease caused by these important pathogens.
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Affiliation(s)
- Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Pieter C Steketee
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Mabel D Tettey
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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12
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Capra E, Lazzari B, Milanesi M, Nogueira GP, Garcia JF, Utsunomiya YT, Ajmone-Marsan P, Stella A. Comparison between indicine and taurine cattle DNA methylation reveals epigenetic variation associated to differences in morphological adaptive traits. Epigenetics 2023; 18:2163363. [PMID: 36600398 DOI: 10.1080/15592294.2022.2163363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Indicine and taurine subspecies present distinct morphological traits as a consequence of environmental adaptation and artificial selection. Although the two subspecies have been characterized and compared at genome-wide level and at specific loci, their epigenetic diversity has not yet been explored. In this work, Reduced Representation Bisulphite Sequencing (RRBS) profiling of the taurine Angus (A) and indicine Nellore (N) cattle breeds was applied to identify methylation differences between the two subspecies. Genotyping by sequencing (GBS) of the same animals was performed to detect single nucleotide polymorphisms (SNPs) at cytosines in CpG dinucleotides and remove them from the differential methylation analysis. A total of 660,845 methylated cytosines were identified within the CpG context (CpGs) across the 10 animals sequenced (5 N and 5 A). A total of 25,765 of these were differentially methylated (DMCs). Most DMCs clustered in CpG stretches nearby genes involved in cellular and anatomical structure morphogenesis. Also, sequences flanking DMC were enriched in SNPs compared to all other CpGs, either methylated or unmethylated in the two subspecies. Our data suggest a contribution of epigenetics to the regulation and divergence of anatomical morphogenesis in the two subspecies relevant for cattle evolution and sub-species differentiation and adaptation.
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Affiliation(s)
- E Capra
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
| | - B Lazzari
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
| | - M Milanesi
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil.,Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - G P Nogueira
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil
| | - J F Garcia
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Y T Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil
| | - P Ajmone-Marsan
- Department of Animal Science, Food and Nutrition - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - A Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
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13
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Zhang H, Qin W, Romero H, Leonhardt H, Cardoso MC. Heterochromatin organization and phase separation. Nucleus 2023; 14:2159142. [PMID: 36710442 DOI: 10.1080/19491034.2022.2159142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The eukaryotic nucleus displays a variety of membraneless compartments with distinct biomolecular composition and specific cellular activities. Emerging evidence indicates that protein-based liquid-liquid phase separation (LLPS) plays an essential role in the formation and dynamic regulation of heterochromatin compartmentalization. This feature is especially conspicuous at the pericentric heterochromatin domains. In this review, we will describe our understanding of heterochromatin organization and LLPS. In addition, we will highlight the increasing importance of multivalent weak homo- and heteromolecular interactions in LLPS-mediated heterochromatin compartmentalization in the complex environment inside living cells.
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Affiliation(s)
- Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Hector Romero
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany,CONTACT M. Cristina Cardoso Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287Darmstadt, Germany
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Tang Y. Plant nuclear envelope as a hub connecting genome organization with regulation of gene expression. Nucleus 2023; 14:2178201. [PMID: 36794966 DOI: 10.1080/19491034.2023.2178201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Eukaryotic cells organize their genome within the nucleus with a double-layered membrane structure termed the nuclear envelope (NE) as the physical barrier. The NE not only shields the nuclear genome but also spatially separates transcription from translation. Proteins of the NE including nucleoskeleton proteins, inner nuclear membrane proteins, and nuclear pore complexes have been implicated in interacting with underlying genome and chromatin regulators to establish a higher-order chromatin architecture. Here, I summarize recent advances in the knowledge of NE proteins that are involved in chromatin organization, gene regulation, and coordination of transcription and mRNA export. These studies support an emerging view of plant NE as a central hub that contributes to chromatin organization and gene expression in response to various cellular and environmental cues.
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Affiliation(s)
- Yu Tang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China,CONTACT Yu Tang Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
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15
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Barral A, Déjardin J. The chromatin signatures of enhancers and their dynamic regulation. Nucleus 2023; 14:2160551. [PMID: 36602897 DOI: 10.1080/19491034.2022.2160551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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16
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Schmøkel SS, Nordentoft I, Lindskrog SV, Lamy P, Knudsen M, Jensen JB, Dyrskjøt L. Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies. Nucleus 2023; 14:2186686. [PMID: 36878883 DOI: 10.1080/19491034.2023.2186686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
This paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times in combination with different approaches for tissue and cell dissection: sectioning, semi-automated dissociation, manual dissociation with pestles, and semi-automated dissociation combined with manual dissociation with pestles. Our results showed that a combination of IgePal lysis buffer, tissue dissection by sectioning, and short incubation time was the best conditions for gentle nuclei isolation applicable for snRNA-seq, and we found limited confounding transcriptomic changes based on the isolation procedure. This protocol makes it possible to analyze biobanked material from patients with well-described clinical and histopathological information and known clinical outcomes with snRNA-seq.
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Affiliation(s)
- Sofie S Schmøkel
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Sia V Lindskrog
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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17
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Okumura T, Horiba K, Tetsuka N, Sato Y, Sugiyama Y, Haruta K, Yamaguchi M, Suzuki T, Torii Y, Kawada JI, Ogi T, Hayakawa M, Ito Y. Next-generation sequencing-based detection of Ureaplasma in the gastric fluid of neonates with respiratory distress and chorioamnionitis. J Matern Fetal Neonatal Med 2023; 36:2207113. [PMID: 37150592 DOI: 10.1080/14767058.2023.2207113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND Respiratory distress is common in neonates admitted to neonatal intensive care units. Additionally, infectious diseases such as intrauterine infections or vertical transmission are important underlying causes of respiratory failure. However, pathogens often cannot be identified in neonates, and there are many cases in which antibacterial drugs are empirically administered. Next-generation sequencing (NGS) is advantageous in that it can detect trace amounts of bacteria that cannot be detected by culturing or bacteria that are difficult to cultivate. However, there are few reports on the diagnosis of infectious diseases using NGS in the neonatal field, especially those targeting respiratory distress. OBJECTIVE The purpose of our study was to investigate the microorganisms associated with neonatal respiratory distress and to determine whether less invasive collection specimens such as plasma and gastric fluid are useful. METHODS Neonates were prospectively recruited between January and August 2020 from Nagoya University Hospital. The inclusion criteria were as follows: 1) admission to the neonatal intensive care unit; 2) respiratory distress presentation within 48 h of birth; and 3) suspected infection, collection of blood culture, and administration of antibiotics. Plasma samples and blood cultures were simultaneously collected. Gastric fluid samples were also collected if the patient was not started on enteral nutrition. Information on the patients and their mothers were collected from the medical records. DNA was extracted from 140 µL of plasma and gastric fluid samples. DNA sequencing libraries were prepared, and their quality was analyzed. DNA libraries were sequenced using high-throughput NGS. The NGS data of plasma and gastric fluid samples were analyzed using the metagenomic pipeline PATHDET, which calculated the number of reads assigned to microorganisms and their relative abundance. Putative pathogens were listed. RESULTS Overall, 30 plasma samples and 25 gastric fluid samples from 30 neonates were analyzed. Microorganism-derived reads of gastric fluid samples were significantly higher than those of plasma samples. Transient tachypnea of the newborn was the most common cause of respiratory distress with 13 cases (43%), followed by respiratory distress syndrome with 7 cases (23%). There were 8 cases (29%) of chorioamnionitis and 7 cases (25%) of funisitis pathologically diagnosed. All blood cultures were negative, and only two gastric fluid cultures were positive for group B Streptococcus (Patient 15) and Candida albicans (Patient 24). Putative pathogens that met the positive criteria for PATHET were detected in four gastric fluid samples, one of which was group B Streptococcus from Patient 15. In the gastric fluid sample of Patient 24, Candida albicans were detected by NGS but did not meet the positive criteria for PATHDET. Cluster analysis of the plasma samples divided them into two study groups, and the indicator genera of each cluster (Phormidium or Toxoplasma) are shown in Figure 1. Clinical findings did not show any significant differences between the two groups. Cluster analysis of the gastric fluid samples divided them into three study groups, and the indicator genera of each cluster (Ureaplasma, Nostoc, and Streptococcus) are shown in Figure 2. The incidence rate of chorioamnionitis was significantly higher in Ureaplasma group than in the other two groups. CONCLUSION Gastric fluid may be useful for assessing neonatal patients with respiratory distress. To the best of our knowledge, this was the first study to reveal that the presence of Ureaplasma in the gastric fluid of neonates with respiratory distress was associated with chorioamnionitis. The early diagnosis of intra-amniotic infections using gastric fluid and its treatment may change the treatment strategy for neonatal respiratory distress. Screening for Ureaplasma in neonates with respiratory distress may reduce the need for empirical antibiotic administration. Further research is required to confirm these findings.
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Affiliation(s)
- Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuyuki Tetsuka
- Department of Infection Control, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoshiaki Sato
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, Nagoya, Japan
| | - Yuichiro Sugiyama
- Department of Pediatrics, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Hayakawa
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
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Mann R, Notani D. Transcription factor condensates and signaling driven transcription. Nucleus 2023; 14:2205758. [PMID: 37129580 DOI: 10.1080/19491034.2023.2205758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Transcription Factor (TF) condensates are a heterogenous mix of RNA, DNA, and multiple co-factor proteins capable of modulating the transcriptional response of the cell. The dynamic nature and the spatial location of TF-condensates in the 3D nuclear space is believed to provide a fast response, which is on the same pace as the signaling cascade and yet ever-so-specific in the crowded environment of the nucleus. However, the current understanding of how TF-condensates can achieve these feet so quickly and efficiently is still unclear. In this review, we draw parallels with other protein condensates and share our speculations on how the nucleus uses these TF-condensates to achieve high transcriptional specificity and fidelity. We discuss the various constituents of TF-condensates, their properties, and the known and unknown functions of TF-condensates with a particular focus on steroid signaling-induced transcriptional programs.
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Affiliation(s)
- Rajat Mann
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Dimple Notani
- National Centre for Biological Sciences, TIFR, Bangalore, India
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Zhong L, Bather JR, Daly BM, Kohlmann WK, Goodman MS, Rothwell E, Kaphingst KA. Investigation of interest in and timing preference for cancer predisposition testing and expanded carrier screening among women of reproductive age. PEC Innov 2023; 2:100128. [PMID: 37214524 DOI: 10.1016/j.pecinn.2023.100128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 05/24/2023]
Abstract
Objective To examine cognitive, relational, and social predictors of interest in and timing preference for cancer predisposition testing (CPT) and expanded carrier screening (ECS) offered in routine gynecologic care for women of reproductive age. Methods Women between 20 and 35 years old who were currently pregnant or had a prior pregnancy (N = 351) completed an online survey. Bivariate and multivariable analyses were used to identify significant predictors of women's interest in and timing preference for CPT and ECS. Results Most respondents reported high interest in CPT and ECS and preferred to have them when planning for a pregnancy. Perceived importance of genetic information and negative attitude towards uncertainty predicted interest in CPT and ECS in multivariable models. Genetic knowledge predicted preference for CPT or ECS when planning for a pregnancy. Conclusion Educational and decision support tools should be developed to enhance women's knowledge and awareness of CPT and ECS and to provide them with strategies to manage uncertainty. Innovation We examined women's timing preference for CPT and ECS and the impact of partner support and trust with gynecologist. A context-specific attitudes toward uncertainty scale was used to investigate women's particular perceptions of uncertainty in genetic testing.
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Affiliation(s)
- Lingzi Zhong
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
- Department of Communication, University of Utah, Salt Lake City, UT, United States
| | - Jemar R. Bather
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Brianne M. Daly
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Wendy K. Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Melody S. Goodman
- Department of Biostatistics, New York University School of Global Public Health, New York City, NY, United States
| | - Erin Rothwell
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, UT, USA
| | - Kimberly A. Kaphingst
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
- Department of Communication, University of Utah, Salt Lake City, UT, United States
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Baker MR, Lee AS, Rajadhyaksha AM. L-type calcium channels and neuropsychiatric diseases: Insights into genetic risk variant-associated genomic regulation and impact on brain development. Channels (Austin) 2023; 17:2176984. [PMID: 36803254 DOI: 10.1080/19336950.2023.2176984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
Recent human genetic studies have linked a variety of genetic variants in the CACNA1C and CACNA1D genes to neuropsychiatric and neurodevelopmental disorders. This is not surprising given the work from multiple laboratories using cell and animal models that have established that Cav1.2 and Cav1.3 L-type calcium channels (LTCCs), encoded by CACNA1C and CACNA1D, respectively, play a key role in various neuronal processes that are essential for normal brain development, connectivity, and experience-dependent plasticity. Of the multiple genetic aberrations reported, genome-wide association studies (GWASs) have identified multiple single nucleotide polymorphisms (SNPs) in CACNA1C and CACNA1D that are present within introns, in accordance with the growing body of literature establishing that large numbers of SNPs associated with complex diseases, including neuropsychiatric disorders, are present within non-coding regions. How these intronic SNPs affect gene expression has remained a question. Here, we review recent studies that are beginning to shed light on how neuropsychiatric-linked non-coding genetic variants can impact gene expression via regulation at the genomic and chromatin levels. We additionally review recent studies that are uncovering how altered calcium signaling through LTCCs impact some of the neuronal developmental processes, such as neurogenesis, neuron migration, and neuron differentiation. Together, the described changes in genomic regulation and disruptions in neurodevelopment provide possible mechanisms by which genetic variants of LTCC genes contribute to neuropsychiatric and neurodevelopmental disorders.
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Affiliation(s)
- Madelyn R. Baker
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, USA
| | - Andrew S. Lee
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Developmental Biology Program, Sloan Kettering Institute, New York, USA
| | - Anjali M. Rajadhyaksha
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Pediatric Neurology, Department of Pediatrics, Weill Cornell Medicine, New York, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, USA
- Weill Cornell Autism Research Program, Weill Cornell Medicine, New York, USA
- CONTACT Anjali M. Rajadhyaksha Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
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García-Morales A, Balleza D. Non-canonical helical transitions and conformational switching are associated with characteristic flexibility and disorder indices in TRP and Kv channels. Channels (Austin) 2023; 17:2212349. [PMID: 37196183 DOI: 10.1080/19336950.2023.2212349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/19/2023] Open
Abstract
Structural evidence and much experimental data have demonstrated the presence of non-canonical helical substructures (π and 310) in regions of great functional relevance both in TRP as in Kv channels. Through an exhaustive compositional analysis of the sequences underlying these substructures, we find that each of them is associated with characteristic local flexibility profiles, which in turn are implicated in significant conformational rearrangements and interactions with specific ligands. We found that α-to-π helical transitions are associated with patterns of local rigidity whereas α-to-310 transitions are mainly leagued with high local flexibility profiles. We also study the relationship between flexibility and protein disorder in the transmembrane domain of these proteins. By contrasting these two parameters, we located regions showing a sort of structural discrepancy between these similar but not identical protein attributes. Notably, these regions are presumably implicated in important conformational rearrangements during the gating in those channels. In that sense, finding these regions where flexibility and disorder are not proportional allows us to detect regions with potential functional dynamism. From this point of view, we highlighted some conformational rearrangements that occur during ligand binding events, the compaction, and refolding of the outer pore loops in several TRP channels, as well as the well-known S4 motion in Kv channels.
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Affiliation(s)
| | - Daniel Balleza
- Unidad de Investigación y desarrollo en Alimentos, Instituto Tecnológico de Veracruz. Tecnológico Nacional de México, Veracruz, MEXICO
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Stuckel AJ, Zeng S, Lyu Z, Zhang W, Zhang X, Dougherty U, Mustafi R, Khare T, Zhang Q, Joshi T, Bissonnette M, Khare S. Sprouty4 is epigenetically upregulated in human colorectal cancer. Epigenetics 2023; 18:2145068. [PMID: 36384366 DOI: 10.1080/15592294.2022.2145068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sprouty4 (SPRY4) has been frequently reported as a tumor suppressor and is therefore downregulated in various cancers. For the first time, we report that SPRY4 is epigenetically upregulated in colorectal cancer (CRC). In this study, we explored DNA methylation and hydroxymethylation levels of SPRY4 in CRC cells and patient samples and correlated these findings with mRNA and protein expression levels. Three loci within the promoter region of SPRY4 were evaluated for 5mC levels in CRC using the combined bisulfite restriction analysis. In addition, hydroxymethylation levels within SPRY4 were measured in CRC patients. Lastly, DNA methylation and mRNA expression data were extracted from CRC patients in multiple high-throughput data repositories like Gene Expression Omnibus and The Cancer Genome Atlas. Combined in vitro and in silico analysis of promoter methylation levels of SPRY4 clearly demonstrates that the distal promoter region undergoes hypomethylation in CRC patients and is associated with increased expression. Moreover, a decrease in gene body hydroxymethylation and an increase in gene body methylation within the coding region of SPRY4 were found in CRC patients and correlated with increased expression. SPRY4 is epigenetically upregulated in CRC by promoter hypomethylation and hypermethylation within the gene body that warrants future investigation of atypical roles of this established tumor suppressor.
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Affiliation(s)
- Alexei J. Stuckel
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
| | - Shuai Zeng
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65201, USA,Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, 65201, USA
| | - Zhen Lyu
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65201, USA,Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, 65201, USA
| | - Wei Zhang
- Department of Preventive Medicine and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA
| | - Xu Zhang
- Department of Medicine, University of Illinois, Chicago, Illinois, 60607, USA
| | - Urszula Dougherty
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition; the University of Chicago, Chicago, Illinois, 60637, USA
| | - Reba Mustafi
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition; the University of Chicago, Chicago, Illinois, 60637, USA
| | - Tripti Khare
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
| | - Qiong Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
| | - Trupti Joshi
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65201, USA,Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, 65211, USA,Department of Health Management and Informatics; School of Medicine, University of Missouri, Columbia, Missouri, 65212, USA
| | - Marc Bissonnette
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition; the University of Chicago, Chicago, Illinois, 60637, USA
| | - Sharad Khare
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri
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