Phenomics (Cham, Switzerland)最新文献

{"title":"Global Quantitative Proteomics Analysis Reveals the Downstream Signaling Networks of Msx1 and Msx2 in Myoblast Differentiation.","authors":"Guoqiang Zhou,&nbsp;Shuangping Ma,&nbsp;Ming Yang,&nbsp;Yenan Yang","doi":"10.1007/s43657-022-00049-y","DOIUrl":"https://doi.org/10.1007/s43657-022-00049-y","url":null,"abstract":"<p><p>The msh homeobox 1 (Msx1) and msh homeobox 2 (Msx2) coordinate in myoblast differentiation and also contribute to muscle defects if altered during development. Deciphering the downstream signaling networks of Msx1 and Msx2 in myoblast differentiation will help us to understand the molecular events that contribute to muscle defects. Here, the proteomics characteristics in Msx1- and Msx2-mediated myoblast differentiation was evaluated  using isobaric tags for the relative and absolute quantification labeling technique (iTRAQ). The downstream regulatory proteins of Msx1- and Msx2-mediated differentiation were identified. Bioinformatics analysis revealed that these proteins were primarily associated with xenobiotic metabolism by cytochrome P450, fatty acid degradation, glycolysis/gluconeogenesis, arginine and proline metabolism, and apoptosis. In addition, our data show Acta1 was probably a core of the downstream regulatory networks of Msx1 and Msx2 in myoblast differentiation.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-022-00049-y.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"2 3","pages":"201-210"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590559/pdf/43657_2022_Article_49.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9559314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emerging Regulatory Mechanisms of N⁶-Methyladenosine Modification in Cancer Metastasis.","authors":"Jing Zhao, Hao Xu, Yinghan Su, Junjie Pan, Sunzhe Xie, Jianfeng Xu, Lunxiu Qin","doi":"10.1007/s43657-021-00043-w","DOIUrl":"10.1007/s43657-021-00043-w","url":null,"abstract":"<p><p>Cancer metastasis is the major cause of cancer-related deaths and accounts for poor therapeutic outcomes. A metastatic cascade is a series of complicated biological processes. N⁶-methyladenosine (m⁶A) is the most abundant and conserved epitranscriptomic modification in eukaryotic cells, which has great impacts on RNA production and metabolism, including RNA splicing, processing, degradation and translation. Accumulating evidence demonstrates that m⁶A plays a critical role in regulating cancer metastasis. However, there is a lack of studies that review the recent advances of m⁶A in cancer metastasis. Here, we systematically retrieved the functions and mechanisms of how the m⁶A axis regulates metastasis, and especially summarized the organ-specific liver, lung and brain metastasis mediated by m⁶A in various cancers. Moreover, we discussed the potential application of m⁶A modification in cancer diagnosis and therapy, as well as the present limitations and future perspectives of m⁶A in cancer metastasis. This review provides a comprehensive knowledge on the m⁶A-mediated regulation of gene expression, which is helpful to extensively understand the complexity of cancer metastasis from a new epitranscriptomic point of view and shed light on the developing novel strategies to anti-metastasis based on m⁶A alteration.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"3 1","pages":"83-100"},"PeriodicalIF":0.0,"publicationDate":"2022-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9883376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9186076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep Clinical Phenotyping of Parkinson's Disease: Towards a New Era of Research and Clinical Care.","authors":"Zhiheng Xu,&nbsp;Bo Shen,&nbsp;Yilin Tang,&nbsp;Jianjun Wu,&nbsp;Jian Wang","doi":"10.1007/s43657-022-00051-4","DOIUrl":"10.1007/s43657-022-00051-4","url":null,"abstract":"<p><p>Despite recent advances in technology, clinical phenotyping of Parkinson's disease (PD) has remained relatively limited as current assessments are mainly based on empirical observation and subjective categorical judgment at the clinic. A lack of comprehensive, objective, and quantifiable clinical phenotyping data has hindered our capacity to diagnose, assess patients' conditions, discover pathogenesis, identify preclinical stages and clinical subtypes, and evaluate new therapies. Therefore, deep clinical phenotyping of PD patients is a necessary step towards understanding PD pathology and improving clinical care. In this review, we present a growing community consensus and perspective on how to clinically phenotype this disease, that is, to phenotype the entire course of disease progression by integrating capacity, performance, and perception approaches with state-of-the-art technology. We also explore the most studied aspects of PD deep clinical phenotypes, namely, bradykinesia, tremor, dyskinesia and motor fluctuation, gait impairment, speech impairment, and non-motor phenotypes.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"2 5","pages":"349-361"},"PeriodicalIF":0.0,"publicationDate":"2022-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590510/pdf/43657_2022_Article_51.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9145059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Hashing-Based Framework for Enhancing Cluster Delineation of High-Dimensional Single-Cell Profiles.","authors":"Xiao Liu,&nbsp;Ting Zhang,&nbsp;Ziyang Tan,&nbsp;Antony R Warden,&nbsp;Shanhe Li,&nbsp;Edwin Cheung,&nbsp;Xianting Ding","doi":"10.1007/s43657-022-00056-z","DOIUrl":"10.1007/s43657-022-00056-z","url":null,"abstract":"<p><p>Although many methods have been developed to explore the function of cells by clustering high-dimensional (HD) single-cell omics data, the inconspicuously differential expressions of biomarkers of proteins or genes across all cells disturb the cell cluster delineation and downstream analysis. Here, we introduce a hashing-based framework to improve the delineation of cell clusters, which is based on the hypothesis that one variable with no significant differences can be decomposed into more diversely latent variables to distinguish cells. By projecting the original data into a sparse HD space, fly and densefly hashing preprocessing retain the local structure of data, and improve the cluster delineation of existing clustering methods, such as PhenoGraph. Moreover, the analyses on mass cytometry dataset show that our hashing-based framework manages to unveil new hidden heterogeneities in cell clusters. The proposed framework promotes the utilization of cell biomarkers and enriches the biological findings by introducing more latent variables.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-022-00056-z.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"2 5","pages":"323-335"},"PeriodicalIF":0.0,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590516/pdf/43657_2022_Article_56.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9145056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Comprehensive Review of High Throughput Phenotyping and Machine Learning for Plant Stress Phenotyping.","authors":"Taqdeer Gill, Simranveer K Gill, Dinesh K Saini, Yuvraj Chopra, Jason P de Koff, Karansher S Sandhu","doi":"10.1007/s43657-022-00048-z","DOIUrl":"10.1007/s43657-022-00048-z","url":null,"abstract":"<p><p>During the last decade, there has been rapid adoption of ground and aerial platforms with multiple sensors for phenotyping various biotic and abiotic stresses throughout the developmental stages of the crop plant. High throughput phenotyping (HTP) involves the application of these tools to phenotype the plants and can vary from ground-based imaging to aerial phenotyping to remote sensing. Adoption of these HTP tools has tried to reduce the phenotyping bottleneck in breeding programs and help to increase the pace of genetic gain. More specifically, several root phenotyping tools are discussed to study the plant's hidden half and an area long neglected. However, the use of these HTP technologies produces big data sets that impede the inference from those datasets. Machine learning and deep learning provide an alternative opportunity for the extraction of useful information for making conclusions. These are interdisciplinary approaches for data analysis using probability, statistics, classification, regression, decision theory, data visualization, and neural networks to relate information extracted with the phenotypes obtained. These techniques use feature extraction, identification, classification, and prediction criteria to identify pertinent data for use in plant breeding and pathology activities. This review focuses on the recent findings where machine learning and deep learning approaches have been used for plant stress phenotyping with data being collected using various HTP platforms. We have provided a comprehensive overview of different machine learning and deep learning tools available with their potential advantages and pitfalls. Overall, this review provides an avenue for studying various HTP platforms with particular emphasis on using the machine learning and deep learning tools for drawing legitimate conclusions. Finally, we propose the conceptual challenges being faced and provide insights on future perspectives for managing those issues.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"2 3","pages":"156-183"},"PeriodicalIF":3.7,"publicationDate":"2022-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590503/pdf/43657_2022_Article_48.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9559320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beyond Mendelian Inheritance: Genetic Buffering and Phenotype Variability.","authors":"Andrea Rossi,&nbsp;Zacharias Kontarakis","doi":"10.1007/s43657-021-00030-1","DOIUrl":"https://doi.org/10.1007/s43657-021-00030-1","url":null,"abstract":"<p><p>Understanding the way genes work amongst individuals and across generations to shape form and function is a common theme for many genetic studies. The recent advances in genetics, genome engineering and DNA sequencing reinforced the notion that genes are not the only players that determine a phenotype. Due to physiological or pathological fluctuations in gene expression, even genetically identical cells can behave and manifest different phenotypes under the same conditions. Here, we discuss mechanisms that can influence or even disrupt the axis between genotype and phenotype; the role of modifier genes, the general concept of genetic redundancy, genetic compensation, the recently described transcriptional adaptation, environmental stressors, and phenotypic plasticity. We furthermore highlight the usage of induced pluripotent stem cells (iPSCs), the generation of isogenic lines through genome engineering, and sequencing technologies can help extract new genetic and epigenetic mechanisms from what is hitherto considered 'noise'.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"2 2","pages":"79-87"},"PeriodicalIF":0.0,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9500441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optical Imaging of Epigenetic Modifications in Cancer: A Systematic Review.","authors":"Yang Du,&nbsp;Pei Zhang,&nbsp;Wei Liu,&nbsp;Jie Tian","doi":"10.1007/s43657-021-00041-y","DOIUrl":"https://doi.org/10.1007/s43657-021-00041-y","url":null,"abstract":"<p><p>Increasing evidence has demonstrated that abnormal epigenetic modifications are strongly related to cancer initiation. Thus, sensitive and specific detection of epigenetic modifications could markedly improve biological investigations and cancer precision medicine. A rapid development of molecular imaging approaches for the diagnosis and prognosis of cancer has been observed during the past few years. Various biomarkers unique to epigenetic modifications and targeted imaging probes have been characterized and used to discriminate cancer from healthy tissues, as well as evaluate therapeutic responses. In this study, we summarize the latest studies associated with optical molecular imaging of epigenetic modification targets, such as those involving DNA methylation, histone modification, noncoding RNA regulation, and chromosome remodeling, and further review their clinical application on cancer diagnosis and treatment. Lastly, we further propose the future directions for precision imaging of epigenetic modification in cancer. Supported by promising clinical and preclinical studies associated with optical molecular imaging technology and epigenetic drugs, the central role of epigenetics in cancer should be increasingly recognized and accepted.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"2 2","pages":"88-101"},"PeriodicalIF":0.0,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590553/pdf/43657_2021_Article_41.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9582364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preoperative Characteristics of Ocular Biometry in Children with Unilateral Congenital Cataracts.","authors":"Jiahui Chen,&nbsp;Yating Tang,&nbsp;Yongxiang Jiang,&nbsp;Yi Lu","doi":"10.1007/s43657-021-00040-z","DOIUrl":"https://doi.org/10.1007/s43657-021-00040-z","url":null,"abstract":"<p><p>The ocular biometry characteristics are clinically significant for children with unilateral congenital cataracts, but there is a lack of data analysis concerning the preoperative measurements. The axial length (AL), mean keratometry (Km), corneal astigmatism (CA), and the anterior chamber depth (ACD) from both eyes before cataract surgery were obtained from 205 patients (410 eyes, 3-15 years of age) with unilateral congenital cataracts. In the congenital cataract eyes, shorter AL (22.44 ± 1.52 mm vs. 22.57 ± 1.04 mm, <i>p</i> = 0.036) and higher CA (- 1.89 ± 0.91 D vs. - 1.24 ± 0.67 D, <i>p</i> < 0.001) were found, and no significant difference was found in the Km and the ACD measurements compared to the contralateral normal eyes. Females had shorter AL and shallower ACD compared to males. However, the Km and CA in the females were significantly larger than that in males. Shorter AL, larger Km, higher CA, and shallower ACD were also found in females who had a binocular axial difference (the value obtained by subtraction of the contralateral normal eye from the congenital cataract eye) that less than zero. The preoperative ocular biometry of shorter AL, larger Km, higher CA, and shallower ACD should be considered in females with unilateral congenital cataracts. The age and the binocular axial differences had a statistically significant correlation (<i>r</i> = -0.192, <i>p</i> = 0.006). Therefore, changes in the binocular axial differences associated with aging may enhance the guidelines for intraocular lens selection and the management of congenital cataracts.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"2 2","pages":"136-144"},"PeriodicalIF":0.0,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590497/pdf/43657_2021_Article_40.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9582365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Positron Emission Tomography Molecular Imaging for Phenotyping and Management of Lymphoma.","authors":"Xiaohui Zhang,&nbsp;Han Jiang,&nbsp;Shuang Wu,&nbsp;Jing Wang,&nbsp;Rui Zhou,&nbsp;Xuexin He,&nbsp;Shufang Qian,&nbsp;Shuilin Zhao,&nbsp;Hong Zhang,&nbsp;Ali Cahid Civelek,&nbsp;Mei Tian","doi":"10.1007/s43657-021-00042-x","DOIUrl":"https://doi.org/10.1007/s43657-021-00042-x","url":null,"abstract":"<p><p>Positron emission tomography (PET) represents molecular imaging for non-invasive phenotyping of physiological and biochemical processes in various oncological diseases. PET imaging with ¹⁸F-fluorodeoxyglucose (¹⁸F-FDG) for glucose metabolism evaluation is the standard imaging modality for the clinical management of lymphoma. One of the ¹⁸F-FDG PET applications is the detection and pre-treatment staging of lymphoma, which is highly sensitive. ¹⁸F-FDG PET is also applied during treatment to evaluate the individual chemo-sensitivity and accordingly guide the response-adapted therapy. At the end of the therapy regiment, a negative PET scan is indicative of a good prognosis in patients with advanced Hodgkin's lymphoma and diffuse large B-cell lymphoma. Thus, adjuvant radiotherapy may be alleviated. Future PET studies using non-¹⁸F-FDG radiotracers, such as ⁶⁸Ga-labeled pentixafor (a cyclic pentapeptide that enables sensitive and high-contrast imaging of C-X-C motif chemokine receptor 4), ⁶⁸Ga-labeled fibroblast activation protein inhibitor (FAPI) that reflects the tumor microenvironment, and ⁸⁹Zr-labeled atezolizumab that targets the programmed cell death-ligand 1 (PD-L1), may complement ¹⁸F-FDG and offer essential tools to decode lymphoma phenotypes further and identify the mechanisms of lymphoma therapy.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"2 2","pages":"102-118"},"PeriodicalIF":0.0,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590515/pdf/43657_2021_Article_42.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9582366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Preliminary Study on the Evaluation of Human Sperm Head Morphology with a Domestic Digital Holographic Image System.","authors":"Hong Zhu,&nbsp;Yong Zhu,&nbsp;Can Sun,&nbsp;Feng Jiang","doi":"10.1007/s43657-022-00046-1","DOIUrl":"https://doi.org/10.1007/s43657-022-00046-1","url":null,"abstract":"<p><p>The head of sperm was imaged with domestic digital holographic microscopy (DHM), and then the quantitative three-dimensional size information of normal sperm and teratozoospermic sperm was compared and analyzed. DHM sperm imaging and repeated quantitative evaluation were used to determine the morphology of the sperm head in two patients with teratozoospermia and four volunteers with normal semen parameters. Sixty and 139 sperm of teratozoospermia patients and normal people were photographed by digital hologram, respectively. The differences in head height and width were compared and statistically analyzed. The sperm head height of the teratozoospermia group was 3.06 ± 1.66 μm, which was significantly lower than that of the normal sperm group (4.54 ± 1.60 μm, <i>p</i> < 0.01), but there was no significant difference in the head width between the two groups. Compared with the traditional two-dimensional optical microscope observation method, the DHM system can provide three-dimensional quantitative information for the sperm head and thus may help in the comprehensive clinical evaluation of the sperm head structure.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"2 2","pages":"130-135"},"PeriodicalIF":0.0,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590537/pdf/43657_2022_Article_46.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9582363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}