Biophysics reports最新文献_第3页

Advancements in proteogenomics for preclinical targeted cancer therapy research. 蛋白质基因组学在临床前靶向癌症治疗研究中的进展。

Biophysics reports Pub Date : 2025-02-28 DOI: 10.52601/bpr.2024.240053

Yuying Suo, Yuanli Song, Yuqiu Wang, Qian Liu, Henry Rodriguez, Hu Zhou

{"title":"Advancements in proteogenomics for preclinical targeted cancer therapy research.","authors":"Yuying Suo, Yuanli Song, Yuqiu Wang, Qian Liu, Henry Rodriguez, Hu Zhou","doi":"10.52601/bpr.2024.240053","DOIUrl":"10.52601/bpr.2024.240053","url":null,"abstract":"Advancements in molecular characterization technologies have accelerated targeted cancer therapy research at unprecedented resolution and dimensionality. Integrating comprehensive multi-omic molecular profiling of a tumor, proteogenomics, marks a transformative milestone for preclinical cancer research. In this paper, we initially provided an overview of proteogenomics in cancer research, spanning genomics, transcriptomics, and proteomics. Subsequently, the applications were introduced and examined from different perspectives, including but not limited to genetic alterations, molecular quantifications, single-cell patterns, different post-translational modification levels, subtype signatures, and immune landscape. We also paid attention to the combined multi-omics data analysis and pan-cancer analysis. This paper highlights the crucial role of proteogenomics in preclinical targeted cancer therapy research, including but not limited to elucidating the mechanisms of tumorigenesis, discovering effective therapeutic targets and promising biomarkers, and developing subtype-specific therapies.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 1","pages":"56-76"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607548","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}

引用次数: 0

Features of the monocyte inflammatory response in patients with premature coronary artery disease. 早发冠心病患者单核细胞炎症反应的特点

Biophysics reports Pub Date : 2025-02-28 DOI: 10.52601/bpr.2024.240030

Tatiana Blokhina, Tatiana Kirichenko, Yuliya Markina, Ulyana Khovantseva, Ivan Melnikov, Olga Guseva, Sergey Bazanovich, Sergey Kozlov, Alexander Orekhov

{"title":"Features of the monocyte inflammatory response in patients with premature coronary artery disease.","authors":"Tatiana Blokhina, Tatiana Kirichenko, Yuliya Markina, Ulyana Khovantseva, Ivan Melnikov, Olga Guseva, Sergey Bazanovich, Sergey Kozlov, Alexander Orekhov","doi":"10.52601/bpr.2024.240030","DOIUrl":"10.52601/bpr.2024.240030","url":null,"abstract":"The purpose of this study was to examine the secretion of inflammatory cytokines by cultured monocytes/macrophages in patients with premature coronary artery disease (CAD). The study included 38 patients with premature CAD and 35 patients without CAD. A primary culture of CD14+ monocytes was obtained by immunomagnetic separation. The inflammatory response was induced by incubation of a cell culture with lipopolysaccharide (LPS) for 24 hours on Days 1 and 6. Basal and LPS-stimulated secretion of the cytokines, tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8) and monocyte chemotactic protein-1 (MCP-1) was assessed by enzyme immunoassay on Days 2 and 7 of cultivation. The level of basal secretion of TNF-α, IL-1β, IL-6, MCP-1 was higher in patients with CAD compared to patients in the control group. The levels of re-stimulated TNF-α secretion and the levels of LPS-stimulated and re-stimulated IL-1β secretion on the second and sixth days were also higher in patients with CAD. LPS-stimulated MCP-1 secretion on the second day did not differ in patients of both groups, but re-stimulated MCP-1 secretion was higher in patients with CAD. The results of logistic regression analysis showed that the basal secretion levels of IL-1β and IL-6 were independently associated with premature CAD, along with smoking, body mass index and serum HDL-cholesterol levels.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 1","pages":"12-17"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607554","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}

引用次数: 0

Single-molecule tracking in living microbial cells. 活微生物细胞的单分子追踪。

Biophysics reports Pub Date : 2025-02-28 DOI: 10.52601/bpr.2024.240028

Xiaomin Chen, Qianhong Guo, Jiexin Guan, Lu Zhang, Ting Jiang, Liping Xie, Jun Fan

{"title":"Single-molecule tracking in living microbial cells.","authors":"Xiaomin Chen, Qianhong Guo, Jiexin Guan, Lu Zhang, Ting Jiang, Liping Xie, Jun Fan","doi":"10.52601/bpr.2024.240028","DOIUrl":"10.52601/bpr.2024.240028","url":null,"abstract":"Some microbes are referred to as model organisms because they are easy to study in the laboratory and hold the ability to retain their characteristics during DNA replication, DNA transcription, and other fundamental processes. Studying these microbes in living cells via single-molecule imaging allows us to better understand these processes at highly improved spatiotemporal resolution. Single particle tracking photoactivated localization microscopy (sptPALM) is a robust tool for detecting the positions and motions of individual molecules with tens of nanometers of spatial and millisecond temporal resolution in vivo, providing insights into intricate intracellular environments that traditional ensemble methods cannot. With this approach, the fluorophores are photoactivated stochastically, a series of images are recorded, and the positions of fluorophores are identified in these images, and ultimately the locations are linked together to yield trajectories of individual molecules. Quantitative kinetic and spatial information, such as reaction rates, diffusion coefficients, and localization maps, can be obtained by further analysis. Here, we present a single-molecule tracking protocol that includes sample preparation, data acquisition and brief data processing. This protocol will enable researchers to directly unveil molecular and cellular mechanisms underlying the essential biological processes.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 1","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607569","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}

引用次数: 0

TRIM66-HP1γ remodels the chromatin through phase separation. TRIM66-HP1γ通过相分离重塑染色质。

Biophysics reports Pub Date : 2025-02-28 DOI: 10.52601/bpr.2024.240038

Siyuan Shen, Feng Chen, Yifan Zhang, Fudong Li, Xuebiao Yao, Dan Liu, Yunyu Shi, Liang Zhang

{"title":"TRIM66-HP1γ remodels the chromatin through phase separation.","authors":"Siyuan Shen, Feng Chen, Yifan Zhang, Fudong Li, Xuebiao Yao, Dan Liu, Yunyu Shi, Liang Zhang","doi":"10.52601/bpr.2024.240038","DOIUrl":"10.52601/bpr.2024.240038","url":null,"abstract":"Chromatin contains not only heterochromatin (HC) and euchromatins (EC) but also facultative heterochromatin (fHC), which experience the dynamic remodeling between HCs and ECs by different regulators. The regulation of fHCs involves lots of different cell functions, like genomic stability and gene transcription. Heterochromatin protein 1 (HP1) recognizes methylated H3K9 and reshapes the chromatin into the fHCs through liquid-liquid phase separation (LLPS). Among the three members of the HP1 family, HP1α can condensate by itself and HP1β forms granules with the help of TRIM28, while the HP1γ cannot phase separation alone either and the coordinator is still unclear. So, in this study, we investigated the molecular mechanism of how HP1γ interacts with TRIM66 through PxVxL motif. Based on that, we examined the key regions that controlled the TRIM66-HP1γ co-phase separation behaviors both in vitro and in vivo. Furthermore, we proved that the liquid granules of TRIM66-HP1γ and chromatin highly correlated with H3K9me3 sites, which indicated the relationship with DNA damage response. Finally, combined with our previous study, we proposed the system for how TRIM66 remodeled the chromatin into compressed fHC through the TRIM66-HP1γ-H3K9me3 axis with liquid-liquid phase separation.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 1","pages":"18-33"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607573","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}

引用次数: 0

Neuronal STING activation mediates inflammation-induced neurodegeneration via ferroptosis pathways in multiple sclerosis. 在多发性硬化症中，神经元STING激活通过铁下垂途径介导炎症诱导的神经变性。

Biophysics reports Pub Date : 2024-12-31 DOI: 10.52601/bpr.2024.240908

Weiyan Wang, Mengdi Guo, Xiao Tu, Meiling Jiang, Cun-Jin Zhang

引用次数: 0

Characterization of auditory sensation in C. elegans. 秀丽隐杆线虫听觉感觉的表征。

Biophysics reports Pub Date : 2024-12-31 DOI: 10.52601/bpr.2024.240027

Can Wang, Elizabeth A Ronan, Adam J Iliff, Rawan Al-Ebidi, Panagiota Kitsopoulos, Karl Grosh, Jianfeng Liu, X Z Shawn Xu

{"title":"Characterization of auditory sensation in C. elegans.","authors":"Can Wang, Elizabeth A Ronan, Adam J Iliff, Rawan Al-Ebidi, Panagiota Kitsopoulos, Karl Grosh, Jianfeng Liu, X Z Shawn Xu","doi":"10.52601/bpr.2024.240027","DOIUrl":"10.52601/bpr.2024.240027","url":null,"abstract":"Research using the model organism nematode C. elegans has greatly facilitated our understanding of sensory biology, including touch, olfaction, taste, vision and proprioception. While hearing had long been considered to be restricted to vertebrates and some arthropods, we recently discovered that C. elegans is capable of sensing and responding to airborne sound in a frequency and sound source-size-dependent manner. C. elegans auditory sensation occurs when airborne sound physically vibrates their external cuticle (skin) to activate the sound-sensitive mechanosensory FLP/PVD neurons via nicotinic acetylcholine receptors (nAChRs), triggering aversive phonotaxis behavior. Here, we report stepwise methods to characterize these three features of C. elegans auditory sensation, including sound-evoked skin vibration, neuronal activation, and behavior. This approach provides an accessible platform to investigate the cellular and molecular mechanisms underlying auditory sensation and mechanotransduction mechanisms in C. elegans.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 6","pages":"351-363"},"PeriodicalIF":0.0,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142933888","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}

引用次数: 0

Mechanism and application of mesenchymal stem cells and their secreting extracellular vesicles in regulating CD4⁺T cells in immune diseases. 间充质干细胞及其分泌胞外囊泡在免疫疾病中调节CD4+T细胞的机制及应用

Biophysics reports Pub Date : 2024-12-31 DOI: 10.52601/bpr.2024.240005

Zehua Lin, Weisong Cai, Yuechen Sun, Baoai Han, Yifan Hu, Zuhong He, Xiong Chen

{"title":"Mechanism and application of mesenchymal stem cells and their secreting extracellular vesicles in regulating CD4+T cells in immune diseases.","authors":"Zehua Lin, Weisong Cai, Yuechen Sun, Baoai Han, Yifan Hu, Zuhong He, Xiong Chen","doi":"10.52601/bpr.2024.240005","DOIUrl":"https://doi.org/10.52601/bpr.2024.240005","url":null,"abstract":"Mesenchymal stem cells (MSCs) show significant promise in treating immune diseases due to their ability to differentiate into various cell types and their immunomodulatory properties. However, the mechanisms by which MSCs regulate CD4+T cells, essential for immune responses, are not yet fully understood. This study aims to provide a comprehensive overview of how MSCs and their secreted extracellular vesicles (EVs) modulate CD4+T cells in immune diseases. We begin by discussing the immunomodulatory properties of MSCs and the factors contributing to their effectiveness. Following this, we explore how MSCs interact with CD4+T cells through various pathways, including the secretion of soluble factors, direct cell-cell contact, and EV-mediated communication. A key focus is on the therapeutic potential of MSC-derived EVs, which are rich in bioactive molecules such as proteins, lipids, and nucleic acids. These molecules can regulate the phenotype and function of CD4+T cells. The challenges and future perspectives in utilizing MSCs and EVs for immune-disease therapy are also addressed. Overall, this research aims to enhance our understanding of the mechanisms behind MSC-mediated regulation of CD4+T cells and provide insights into the potential use of MSCs and EVs as therapeutic tools in immune diseases. In summary, understanding how MSCs and their EVs control CD4+T cells can offer valuable perspectives for developing innovative immunotherapeutic approaches. Leveraging the immunomodulatory capacity of MSCs and EVs holds promise for managing immune-related disorders.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 6","pages":"403-415"},"PeriodicalIF":0.0,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142933943","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}

引用次数: 0

Special issue on "calcium signaling". “钙信号”特刊。

Biophysics reports Pub Date : 2024-12-31 DOI: 10.52601/bpr.2024.240061

Zong Jie Cui

引用次数: 0

Current status of FAP-directed cancer theranostics: a bibliometric analysis. fap导向癌症治疗的现状：文献计量学分析。

Biophysics reports Pub Date : 2024-12-31 DOI: 10.52601/bpr.2024.240022

Dan Ruan, Simin Wu, Xuehua Lin, Liang Zhao, Jiayu Cai, Weizhi Xu, Yizhen Pang, Qiang Xie, Xiaobo Qu, Haojun Chen

{"title":"Current status of FAP-directed cancer theranostics: a bibliometric analysis.","authors":"Dan Ruan, Simin Wu, Xuehua Lin, Liang Zhao, Jiayu Cai, Weizhi Xu, Yizhen Pang, Qiang Xie, Xiaobo Qu, Haojun Chen","doi":"10.52601/bpr.2024.240022","DOIUrl":"https://doi.org/10.52601/bpr.2024.240022","url":null,"abstract":"Fibroblast activation protein (FAP) is a key molecule in the field of oncology, with significant impacts on tumor diagnosis and treatment. Importantly, it has paved the way for the development of radiotracers for quinoline-based FAP inhibitors (FAPIs), which are currently among the most promising radiotracers for PET imaging in cancer. We performed a bibliometric analysis of scientific publications related to FAP and FAPI-based radiotracers, which included the quantification and visualization of current research trends and prospects based on various bibliometric indicators. In our survey of FAP-related studies in the Web of Science Core Collection databases, R and VOSviewer were used for visualization and bibliometric analyses based on country, institute, author, journal, and keywords. We also examined the methodology, radionuclide type, imaging instruments, and major diseases associated with studies on FAPI-based radiotracers. The results revealed 2,664 FAP-related publications from 1992 to the present. Germany, the USA, and China dominated paper publications, multinational collaborations, and societal impacts on FAP research. Southwest Medical University was the most productive institute, while Haberkorn Uwe authored the most cited papers and the highest H-index. The European Journal of Nuclear Medicine and Molecular Imaging and the Journal of Nuclear Medicine were the most influential periodicals. Keywords \"FAP\", \"68Ga-FAPI\", and \"PET/CT\" emerged as the most significant in this field. This study may help elucidate current research trends, hotspots, and directions for future research.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 6","pages":"388-402"},"PeriodicalIF":0.0,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142933941","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}

引用次数: 0

A prognostic model for acute myeloid leukemia based on ferroptosis-related lncRNA and immune infiltration analysis. 基于凋亡相关lncRNA和免疫浸润分析的急性髓系白血病预后模型

Biophysics reports Pub Date : 2024-12-31 DOI: 10.52601/bpr.2024.240029

Shuhan Liu, Yingli Chen, Qianzhong Li, Zhiyu Fan, Menglan Li, Pengyu Du

{"title":"A prognostic model for acute myeloid leukemia based on ferroptosis-related lncRNA and immune infiltration analysis.","authors":"Shuhan Liu, Yingli Chen, Qianzhong Li, Zhiyu Fan, Menglan Li, Pengyu Du","doi":"10.52601/bpr.2024.240029","DOIUrl":"https://doi.org/10.52601/bpr.2024.240029","url":null,"abstract":"Acute myeloid leukemia (AML) is a rare tumor that invades the blood and bone marrow, it is rapidly progressive, highly aggressive, and difficult to cure. Studies have shown that long non-coding RNA (lncRNA) and ferroptosis play important roles in AML. However, few studies have been done on ferroptosis-related lncRNA for AML. To investigate the role of ferroptosis-related lncRNA in AML prognosis, we screened the differentially expressed genes related to ferroptosis and lncRNA. Ferroptosis-related lncRNA associated with AML prognosis was obtained by Pearson correlation analysis. By using univariate Cox analysis, least absolute shrinkage and selection operator (LASSO) analysis, and multivariate Cox analysis, the ten prognostic genes were used for constructing the prognostic model. The model was then validated using a Kaplan-Meier analysis and Cox regression analysis. The ROC results have shown that the model could better predict AML survival. We identified some mutated genes that may affect the poor prognosis based on the somatic mutation analysis. The enrichment pathway analysis of prognostic genes revealed that these genes were mainly enriched in some immune pathways and cancer pathways. By immune infiltration analysis, we found that high-risk patients may respond better to immunotherapy.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 6","pages":"377-387"},"PeriodicalIF":0.0,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142933832","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}

引用次数: 0