Article
Biochemical Research Methods
Vid Jazbec, Roman Jerala, Mojca Bencina
Summary: This study introduces an innovative genetically engineered protease-activated calcium channel activator named PACE. By introducing a protease cleavage site in CAD and utilizing split protease activation, sustained calcium entry can be generated. The researchers also found that NFAT signaling pathway and cytokine production can be activated using PACE in a T-cell line. This study is of significant importance for artificial regulation of cellular activity.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Jing Li, Leyi Wei, Fei Guo, Quan Zou
Summary: A new T3SEs ensemble predictor EP3 was developed to accurately distinguish T3SEs, demonstrating better performance and aiming to facilitate further investigations on pathogenic bacterial infections.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Cell Biology
Ipsita Nandi, Lior Aroeti, Rachana Pattani Ramachandran, Ephrem G. Kassa, Efrat Zlotkin-Rivkin, Benjamin Aroeti
Summary: Type III secretion system is utilized by Gram-negative bacterial pathogens to transport effectors into host cells. These effectors play a crucial role in virulence by manipulating host cell organelles, especially mitochondria. However, the mechanisms underlying the mitochondrial activity of type III secreted effectors are not yet fully understood.
CELLULAR MICROBIOLOGY
(2021)
Article
Oncology
Yaling Hu, Bo Zhang, Peihua Lu, Jingying Wang, Cheng Chen, Ying Yin, Quan Wan, Jingjing Wang, Jiantong Jiao, Xiangming Fang, Zhening Pu, Lingli Gong, Li Ji, Lingpeng Zhu, Rui Zhang, Jia Zhang, Xusheng Yang, Qing Wang, Zhaohui Huang, Jian Zou
Summary: NF-kappa B signaling plays dual roles in cancer, and understanding its function requires mutual regulation with TCF4N; TCF4N regulates p65 subunit phosphorylation and nuclear stability, playing a significant role in glioblastoma, and forming a positive feedback regulation loop with p65.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Erin Armentrout, Emma C. Kundracik, Arne Rietsch
Summary: It has been found that many Gram-negative pathogens use a type III secretion system to inject effector proteins into host cells, but the injection is feedback inhibited. The effector protein ExoS in P. aeruginosa plays a central role in this feedback inhibition. The feedback inhibition is due to the loss of the activating trigger for effector injection and potentially decreased translocon stability. Surprisingly, feedback inhibition is abrogated in phagocytic cells, which suggests its importance in controlling P. aeruginosa infections.
MOLECULAR MICROBIOLOGY
(2021)
Article
Microbiology
Lezheng Yu, Fengjuan Liu, Yizhou Li, Jiesi Luo, Runyu Jing
Summary: Researchers have developed a deep learning approach called DeepT3_4 to accurately classify type III and type IV secreted effectors, achieving over 80.0% accuracy, F-value, and recall. This method provides a promising supplementary tool for further secretome studies, by integrating recurrent neural networks and deep neural networks into a hybrid model.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Fisheries
Qing Tan, Cui-Luan Yao
Summary: In this study, the role of LcNEMO in immune activation mediated by p65 was investigated in the large yellow croaker. The results showed that LcNEMO enhanced p65-triggered immune activation and promoted the nuclear translocation of p65.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Oncology
Jingya Wang, Tao Sun, Zhaoting Meng, Liuchun Wang, Mengjie Li, Jinliang Chen, Tingting Qin, Jiangyong Yu, Miao Zhang, Zhixin Bie, Zhiqiang Dong, Xiangli Jiang, Li Lin, Cuicui Zhang, Zhujun Liu, Richeng Jiang, Guang Yang, Lin Li, Yan Zhang, Dingzhi Huang
Summary: Combining a PARP inhibitor with an XPO1 inhibitor significantly improves efficacy and tolerability in treating small cell lung cancer, restoring the balance and activity of FOXO3a. This dual inhibition provides a new therapeutic approach for SCLC, warranting further investigation in potential clinical trials.
Article
Biochemistry & Molecular Biology
Moumita Kundu, Subhayan Das, Suvendu Nandi, Dibakar Dhara, Mahitosh Mandal
Summary: The study found that magnolol (MGN) enhances the therapeutic effect of temozolomide (TMZ) on glioma. MGN promotes glioma cell apoptosis induced by TMZ by inhibiting NF-xB pathway-mediated MGMT activation.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2023)
Article
Plant Sciences
Chao-Sheng Lu, Chen-Yu Wu, Yi-Hong Wang, Qing-Qing Hu, Rong-Yue Sun, Min-Jie Pan, Xin-Yu Lu, Ting Zhu, Shuang Luo, Hong-Jing Yang, Dan Wang, Hong-Wei Wang
Summary: This study demonstrates the potential of icariin in alleviating testicular dysfunction induced by T1D, with the involvement of AMPK-mediated Nrf2 activation and NF-kappa B p65 inhibition.
Article
Immunology
Chuntian Li, Mudan Zhang, Xinmeng Guan, Huimin Hu, Ming Fu, Yalan Liu, Qinxue Hu
Summary: NF-kappa B is crucial in cell regulation, with HSV-2 gD interacting with p65 to affect subcellular localization and gene expression, which may contribute to HSV-2 immune evasion and pathogenesis.
JOURNAL OF IMMUNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Jurre A. Steens, Carl Raymund P. Salazar, Raymond H. J. Staals
Summary: Type III CRISPR-Cas systems utilize a multi-subunit effector complex to target foreign mRNA transcripts. This triggers cleavage of the target RNA and activates a variety of catalytic activities, leading to the production of cOA messenger molecules. These molecules activate ancillary effector proteins, including CARF and SAVED proteins, which protect the host through diverse defense mechanisms.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Review
Oncology
Rui Han, Changquan Ling, Yuqian Wang, Lingeng Lu
Summary: Hepatocellular carcinoma (HCC) is a malignancy with limited treatment options. The combination of immune checkpoint inhibitors (ICIs) has shown promise, but there is still a need for effective therapies. Recent evidence suggests that histone deacetylase 2 inhibitors can enhance the efficacy of ICIs by regulating PD-L1 acetylation, and a novel HDAC2 inhibitor, valetric acid (VA), has shown potential as a monotherapy in HCC treatment. This perspective highlights the development value of combining HDAC2 inhibitors with ICIs for HCC.
CANCER CELL INTERNATIONAL
(2023)
Article
Medicine, Research & Experimental
Qian Xia, Meng Mao, Zhen Zeng, Zhenzhao Luo, Yin Zhao, Jing Shi, Xing Li
Summary: This study identified SENP6 as a negative regulator of ANXA1 SUMOylation, which induced ANXA1 nuclear translocation and triggered neuronal apoptosis during cerebral ischemic injury. Blocking SENP6-mediated deSUMOylation of ANXA1 inhibited neuronal apoptosis and improved neurological function in a mouse model of ischemic stroke.
Article
Microbiology
Natalie Sirisaengtaksin, Eloise J. O'Donoghue, Sara Jabbari, Andrew J. Roe, Anne Marie Krachler
Summary: This study demonstrates that outer membrane vesicles (OMVs) can serve as an alternative pathway for the delivery of type III secretion system (T3SS) cargo in enterohemorrhagic Escherichia coli (EHEC). The OMV-delivered effector proteins can enter host cells and retain their biological activity.
Review
Biochemistry & Molecular Biology
Qian Liu, Pingzhao Hu
Summary: Radiogenomics is a field that combines medical images and genomic analysis to address important clinical questions. This review provides an overview of the current state, limitations, and potential future directions of deep learning in pan-cancer radiogenomic research, while also briefly discussing traditional machine learning methods and research resources. The extendibility and explainability of deep learning in pan-cancer radiogenomics are emphasized.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Medicine, Research & Experimental
Yao Li, Charles N. Bernstein, Wei Xu, Pingzhao Hu
Summary: This study evaluated the contribution of genetic variants to psychiatric comorbidities among persons with inflammatory bowel disease (IBD) and found that the expression level of the RBPMS gene acts as a mediator. The polygenic risk score (PRS) could be potentially used for PC risk screening in IBD patients.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Biochemical Research Methods
Jasper Zhongyuan Zhang, Wei Xu, Pingzhao Hu
Summary: This study aims to develop a new deep learning-based algorithm that integrates multiple high-dimensional omics data to improve cancer survival outcome prediction. The algorithm was applied to breast cancer and colon and rectal cancer data, and demonstrated better performance in survival prediction compared to other omics-based and genomic-based algorithms, as well as conventional data integration methods.
Article
Biochemical Research Methods
Hamid Hadipour, Chengyou Liu, Rebecca Davis, Silvia T. Cardona, Pingzhao Hu
Summary: This study developed a novel analytical framework that combines feature engineering for molecule-specific atomic and bonding features with a deep learning-based embedding strategy for different molecular features. By applying these embeddings, successful clustering of a large molecule dataset was achieved, showing the potential for optimizing drug discovery.
BMC BIOINFORMATICS
(2022)
Article
Computer Science, Interdisciplinary Applications
Yongye Su, Qian Liu, Wentao Xie, Pingzhao Hu
Summary: This study proposes a deep learning model for breast cancer mass detection and segmentation using mammography. The model performs significantly better than previous works, achieving high accuracy in mass detection and segmentation. It has the potential to assist doctors in early breast cancer detection and treatment, reducing mortality.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Chengyou Liu, Andrew M. Hogan, Hunter Sturm, Mohd Wasif Khan, Md. Mohaiminul Islam, A. S. M. Zisanur Rahman, Rebecca Davis, Silvia T. Cardona, Pingzhao Hu
Summary: This study proposes a comprehensive framework based on graph-based deep learning models for predicting chemical-genetic interaction profiles (CGIPs) and generating hypotheses about the mechanism of action of new drugs. By matching genes and using neural network models for prediction, we successfully created gene clusters in Mycobacterium tuberculosis and accurately predicted activity against essential targets for this disease.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Biochemical Research Methods
Judah Zammit, Daryl L. X. Fung, Qian Liu, Carson Kai-Sang Leung, Pingzhao Hu
Summary: This study proposes a novel model that combines the image segmentation abilities of deep convolution networks and the semi-supervised learning abilities of generative models for chest CT images of COVID-19 patients. Comparing it to other segmentation models, the results show that the proposed model has comparable performance and appealing advantages.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Ram Prasad, Michael John Patton, Jason Levi. Floyd, Seth Fortmann, Mariana DuPont, Angela Harbour, Justin Wright, Regina Lamendella, Bruce R. Stevens, Gavin Y. Oudit, Maria B. Grant
Summary: This study aimed to investigate whether plasma analysis could provide insight into gut barrier dysfunction in patients with COVID-19 infection. The findings showed significant dysbiosis of the plasma microbiome in COVID-19 patients, along with increased abundance of Actinobacteria species and decreased abundance of Bacteroides species. Moreover, the concentration of gut permeability markers was significantly elevated in COVID-19 patients compared to healthy individuals. These findings suggest that the gut may contribute to worsening COVID-19 outcomes and targeting the gut could be a potential strategy for improving patient outcomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
A. S. M. Zisanur Rahman, Chengyou Liu, Hunter Sturm, Andrew M. Hogan, Rebecca Davis, Pingzhao Hu, Silvia T. Cardona
Summary: Machine learning was used to predict the antibacterial activity of compounds, resulting in the discovery of potential antibacterial compounds through virtual screening. The hit rate of the predicted compounds was significantly improved, indicating the effectiveness of this approach in increasing the hit rate of drug discovery.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Vivianne Cruz de Jesus, Betty-Anne Mittermuller, Pingzhao Hu, Robert J. Schroth, Prashen Chelikani
Summary: This study aimed to evaluate associations between severe early childhood caries (S-ECC), the oral microbiome, and variants in genes involved in taste sensation. Results showed significant associations between three loci in the PLCB2 gene and S-ECC, as well as associations between variants in other genes and dental biofilm composition. These findings contribute to our understanding of the role of genetics in S-ECC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Shujun Huang, Pingzhao Hu, Ted M. Lakowski
Summary: In this study, we identified small molecule compounds that could modulate the PPARA and FOXM1 pathways in breast cancer. Through two different methods, we found 19 compounds that could decrease the activity of the FOXM1 pathway and 13 compounds that could increase the activity of the PPARA pathway. Further experimental validation of these compounds may provide insights into their effects on triple negative breast cancer.
PHARMACOGENOMICS JOURNAL
(2023)
Article
Hematology
Seth D. Fortmann, Michael J. Patton, Blake F. Frey, Jennifer L. Tipper, Sivani B. Reddy, Cristiano P. Vieira, Vidya Sagar Hanumanthu, Sarah Sterrett, Jason L. Floyd, Ram Prasad, Jeremy D. Zucker, Andrew B. Crouse, Forest Huls, Rati Chkheidze, Peng Li, Nathaniel B. Erdmann, Kevin S. Harrod, Amit Gaggar, Paul A. Goepfert, Maria B. Grant, Matthew Might
Summary: Multiple lines of evidence suggest that the dysfunction of megakaryocytes is present in severe cases of COVID-19. This study characterized the peripheral circulating megakaryocytes in a large cohort of COVID-19 inpatients and found that megakaryocytes were increased in the bloodstream of COVID-19 patients. The presence of S100A8/A9 was identified as a marker for megakaryocyte dysfunction. It was also discovered that there was a subpopulation of S100A8/A9+ megakaryocytes containing SARS-CoV-2 proteins and RNA. These findings suggest the role of megakaryocytes in the pathogenesis of severe COVID-19 and their potential as a risk factor for mortality and organ injury.
Article
Biochemistry & Molecular Biology
Qian Liu, Shujun Huang, Danielle Desautels, Kirk J. McManus, Leigh Murphy, Pingzhao Hu
Summary: This study identified two distinct subgroups within HER2+/ER+ breast cancer using gene expression data. These subgroups showed differences in survival outcomes, drug response, and other characteristics. A classification model using a 15-gene signature achieved strong predictive performance. These findings provide insights into the molecular diversity of HER2+/ER+ breast cancer and may guide the development of precision therapies.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Critical Care Medicine
Michael John Patton, Carlos J. Orihuela, Kevin S. Harrod, Mohammad A. N. Bhuiyan, Paari Dominic, Christopher G. Kevil, Daniel Fort, Vincent X. X. Liu, Maha Farhat, Jonathan L. Koff, Charitharth V. Lal, Anuj Gaggar, Robert P. Richter, Nathaniel Erdmann, Matthew Might, Amit Gaggar
Summary: A large retrospective study found that community-acquired bacterial co-infection related to COVID-19 is a significant factor contributing to mortality, with a higher mortality rate compared to community-acquired bacteremia. An elevated neutrophil-to-lymphocyte ratio above 15 is a prognostic indicator of COVID-19 bacterial co-infection.
Article
Computer Science, Artificial Intelligence
Aleksandra Foksinska, Camerron M. Crowder, Andrew B. Crouse, Jeff Henrikson, William E. Byrd, Gregory Rosenblatt, Michael J. Patton, Kaiwen He, Thi K. Tran-Nguyen, Marissa Zheng, Stephen A. Ramsey, Nada Amin, John Osborne, Matthew Might
Summary: There are over 6,000 different rare diseases estimated to impact 300 million people worldwide. Identifying treatments for these disorders is challenging due to a limited understanding of disease mechanisms, interindividual symptom variability, and little commercial incentive to develop new treatments. To address these challenges, The Hugh Kaul Precision Medicine Institute developed an artificial intelligence tool, mediKanren, that leverages the mechanistic insight of genetic disorders to identify therapeutic options.
FRONTIERS IN ARTIFICIAL INTELLIGENCE
(2022)