Article
Biochemistry & Molecular Biology
Minho Won, Kyeong Ah Park, Sup Kim, Eunjin Ju, Youngbok Ko, Heonjong Yoo, Hyunju Ro, Jaeseob Lee, Junseo Oh, Eun Gyo Lee, Sang Yean Kim, Suk Woo Nam, Han-Ming Shen, Min-Kyung Yeo, Jin Man Kim, Gang Min Hur
Summary: The study shows that ANKRD13a is a novel component in TNF signaling, influencing the threshold of cell death signals and reducing the risk of cell death. Lack of ANKRD13a promotes the formation of complex-II, shifting cell response from survival to death without affecting NF-κB activation.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Multidisciplinary Sciences
Chun Gao, Jianhua Deng, Hanchenxi Zhang, Xinran Li, Shuchen Gu, Mingjie Zheng, Mei Tang, Yezhang Zhu, Xin Lin, Jianping Jin, Long Zhang, Jun Huang, Jian Zou, Zong-Ping Xia, Ping-Long Xu, Li Shen, Bin Zhao, Xin-Hua Feng
Summary: The study identified HSPA13 as a transcription-independent checkpoint to modulate the role of RIP1 in TNF alpha signaling, enhancing RIP1 recruitment to TNFR1 and promoting NF-kappa B transcriptional responses, while attenuating RIP1 participation in cytosolic complex II to prevent programmed cell death. Loss of HSPA13 shifts RIP1 from complex I to complex II, increasing apoptosis and necroptosis levels. The research provides compelling evidence for the cellular protective function of HSPA13 in fine-tuning TNF alpha responses.
Article
Immunology
Jianxin Qiu, Xiaohang Zheng, Guoping Cai, Jiajing Ye, Ting Jiang, Lihua Chen, Ze Li, Yuhang Gong, Zhenghua Hong, Haixiao Chen
Summary: This study provides evidence supporting the potential role of AZD8330 in the management of osteoarthritis by attenuating inflammation and regulating the NF-kappa B/P65 signaling pathway to alleviate chondrocyte degradation. The findings from animal experiments and in vitro cell experiments support this conclusion.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lingxia Wang, Xixi Zhang, Haiwei Zhang, Kaili Lu, Ming Li, Xiaoming Li, Yangjing Ou, Xiaoming Zhao, Xiaoxia Wu, Xuanhui Wu, Jianling Liu, Mingyan Xing, Han Liu, Yue Zhang, Yongchang Tan, Fang Li, Xiaoxue Deng, Jiangshan Deng, Xiaojie Zhang, Jinbao Li, Yuwu Zhao, Qiurong Ding, Haikun Wang, Xiuzhe Wang, Yan Luo, Ben Zhou, Haibing Zhang
Summary: This study found that T-cell-specific Rip1 KO mice show age-related T cell changes and accelerated aging-like phenotypes. Rip1-deficient T cells undergo excessive apoptosis and promote chronic inflammation. Blocking apoptosis rescues T cell imbalance and aging-like phenotypes, prolonging lifespan.
Article
Neurosciences
Wei Li, Dengping Liu, Jiaqi Xu, Jun Zha, Chen Wang, Jianzhong An, Zhanli Xie, Shigang Qiao
Summary: This study found that activated astrocytes secrete TNF-alpha, which induces platelet invasion and accumulation in the cerebral cortex during cerebral ischemia/reperfusion (I/R) injury. TNF-alpha expression enhances platelet reactivity through the RIP1/RIP3/AKT pathway. Additionally, the administration of anti-TNF-alpha antibodies alleviates ischemic damage. These findings provide novel insights into the pathological role of platelets activated by astrocyte-derived TNF-alpha in cerebral I/R injury.
MOLECULAR NEUROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yuguo Yi, Weigao Zhang, Liang Tao, Qianchao Shao, Qian Xu, Yuxin Chen, Haibing Zhang, Jianfa Zhang, Dan Weng
Summary: This study investigated the role of RIP1 kinase in APAP-induced acute liver injury through genetic or pharmacological inhibition, providing evidence that RIP1 kinase activity plays an important role in the pathogenesis of APAP-induced liver injury. The results demonstrated that RIP1 kinase inactivation significantly attenuated APAP-induced liver injury and mortality, and that Nec-1, a RIP1 kinase inhibitor formulated with PEG400, could efficiently alleviate hepatotoxicity induced by APAP.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Article
Cell Biology
Xin Chen, Rongfeng Zhu, Jinjin Zhong, Yongfa Ying, Wenxin Wang, Yating Cao, Hanyi Cai, Xiang Li, Jianwei Shuai, Jiahuai Han
Summary: Researchers used super-resolution microscopy to study the nanoscale structure of cellular necrosomes and discovered rod-shaped mosaic structures formed by RIP1 and RIP3 oligomers. They also revealed the roles and regulatory mechanisms of RIP1 and RIP3 in cell death.
NATURE CELL BIOLOGY
(2022)
Article
Immunology
Qunbo Meng, Kaiwen Liu, Zhenchuan Liu, Jinbo Liu, Ziyu Tian, Shanshan Qin, Jianlu Wei, Lei Cheng
Summary: The study demonstrated that digoxin could protect against intervertebral disc degeneration in rat models through anti-inflammatory, ECM protection, and ECM synthesis promotion pathways. LRP4 was identified as the downstream molecule of digoxin in NP cells for anti-inflammation and ECM metabolism regulation.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Irina Lousa, Flavio Reis, Alice Santos-Silva, Luis Belo
Summary: Chronic kidney disease is a global public health problem with high morbidity and mortality. Inflammation and inflammatory mediators, such as tumor necrosis factor-related biomarkers, play a role in the development and progression of CKD. Tumor necrosis factor receptors 1 and 2 have been associated with changes in kidney function and injury, and could potentially serve as biomarkers for CKD prognosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Rosalind L. Ang, Mark Chan, Diana Legarda, John P. Sundberg, Shao-Cong Sun, Virginia L. Gillespie, Nicholas Chun, Peter S. Heeger, Huabao Xiong, Sergio A. Lira, Adrian T. Ting
Summary: The study found that the phenotype of Sharpin(cpdm/cpdm) mice is dependent on CYLD, which suppresses TNF- and RIPK1-dependent cell death. Regulation of CYLD can ameliorate inflammatory symptoms such as dermatitis in mice.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Kaiwen Liu, Jianlu Wei, Guohua Li, Ronghan Liu, Dawang Zhao, Yuanqiang Zhang, Jie Shi, Qing Xie, Lei Cheng
Summary: The study found that Fexofenadine protects against TNF-alpha-induced inflammatory disc degeneration and promotes disc integrity through inhibiting ECM degradation and rescuing inflammation. Additionally, Fexofenadine may serve as a potential target for treating other inflammatory-related diseases, including IVD degeneration, by modulating various pathways and signaling mechanisms.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Michittra Boonchan, Hideki Arimochi, Kunihiro Otsuka, Tomoko Kobayashi, Hisanori Uehara, Thiranut Jaroonwitchawan, Yuki Sasaki, Shin-ichi Tsukumo, Koji Yasutomo
Summary: The study demonstrates that RIPK3 and MLKL-mediated necroptosis has protective effects in acute pancreatitis, cautioning against the use of necroptosis inhibitors as a treatment for acute pancreatitis.
CELL DEATH & DISEASE
(2021)
Article
Immunology
Robin Caire, Elisa Dalix, Marwa Chafchafi, Mireille Thomas, Marie-Therese Linossier, Myriam Normand, Alain Guignandon, Laurence Vico, Hubert Marotte
Summary: This study reveals the critical role of transcription co-factors YAP/TAZ in the signaling of pro-inflammatory cytokine TNF, and their involvement in biological effects associated with cancer and inflammatory disorders.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Hui-yun Ye, Ya-li Song, Wen-ting Ye, Chong-xiang Xiong, Jie-mei Li, Jin-hua Miao, Wei-wei Shen, Xiao-long Li, Li-li Zhou
Summary: This study investigated the mediators responsible for PCOS-related kidney injury and found that TNF-alpha plays a key role in mediating inflammation and apoptosis in renal tubular cells associated with PCOS-related kidney injury. Increased levels of TNF-alpha were observed in serum and ovarian tissue of PCOS patients, and these levels were positively correlated with the severity of PCOS and markers of renal tubular cell-derived proteinuria.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Oncology
Yan Zhang, Hui Yang, Jun Zhao, Ping Wan, Ye Hu, Lv Kun, YiRen Hu, Xi Yang, Mingzhe Ma
Summary: The study revealed that in TAMs in gastric cancer patients, increased levels of MAT2A play a role in the activation and maintenance of TAMs phenotype, mediating the upregulation of RIP1. This finding sheds light on the regulatory role of methionine metabolism in the anti-inflammatory function of monocytes in GC, with MAT2A potentially serving as a therapeutic target.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)
Article
Multidisciplinary Sciences
Thuy Tien Bui, Kumar Selvarajoo
SCIENTIFIC REPORTS
(2020)
Article
Multidisciplinary Sciences
Thuy Tien Bui, Daniel Lee, Kumar Selvarajoo
SCIENTIFIC REPORTS
(2020)
Editorial Material
Biology
Kumar Selvarajoo
PHYSICS OF LIFE REVIEWS
(2021)
Article
Multidisciplinary Sciences
Anna Kychygina, Marina Dall'Osto, Joshua A. M. Allen, Jean-Charles Cadoret, Vincent Piras, Hilda A. Pickett, Laure Crabbe
Summary: The study reveals that defects in the nuclear lamina in HGPS cells lead to changes in telomere organization and chromatin state, affecting replication timing and DNA synthesis process. Increasing dNTP levels in HGPS cells can rescue fragile telomeres and enhance replicative capacity, highlighting a functional connection between NE dysfunction and telomere homeostasis in the context of premature aging.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Alessandro Giuliani, Thuy Tien Bui, Mohamed Helmy, Kumar Selvarajoo
Summary: The study investigates the transcriptome-wide scatter of 23 cell types and conditions across different levels of biological complexity, focusing on genes that act as toggle switches between pairwise replicates of the same cell type. It is found that the proportion of toggle genes dramatically increases from unicellular to multicellular organization, with a significant portion being non-coding genes such as tRNA, rRNA, lncRNA, sncRNA, and pseudogenes. The presence of disease associated microRNAs, pseudogenes, and uncharacterized transcripts in both development and cancer cells suggests toggle genes as a novel component creating transcriptome-wide variability.
Article
Immunology
Mohamed Helmy, Kumar Selvarajoo
Summary: The majority of human genome consists of non-coding genes, with about half made up of transposable elements, including endogenous retroviruses. While generally harmless, endogenous retroviruses have been linked to inflammatory diseases and cancer, posing a challenge in elucidating the mechanistic understanding between them.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Food Science & Technology
Derek J. Smith, Mohamed Helmy, Nicholas D. Lindley, Kumar Selvarajoo
Summary: This article highlights the progress and global interest in alternative proteins, cultured meat, and nutrition. It discusses the efforts made by governments, industries, and researchers to address the impending worldwide food crisis. The findings reveal that there is significant investment and potential in this field, covering various aspects of the food system. However, concerns regarding religion, safety, and taste/texture still need to be addressed.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2022)
Article
Biochemical Research Methods
Hock Chuan Yeo, Kumar Selvarajoo
Summary: In recent years, artificial intelligence (AI)/machine learning has become a viable alternative to systems biology for understanding biological phenomena and achieving design objectives in synthetic biology. However, there are fundamental and practical challenges in using AI for studying emergent behaviors in chaotic or stochastic biological systems. Without proper consideration of suitability, data quality, and preprocessing approaches, the research and development community may face similar challenges experienced in other fields, known as 'AI winters'. Instead, an integration or combination of both approaches is anticipated for future advancements.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Nutrition & Dietetics
Mohamed Helmy, Hosam Elhalis, Yan Liu, Yvonne Chow, Kumar Selvarajoo
Summary: Food security is a pressing issue due to population growth, the COVID-19 pandemic, political conflicts, and climate change. Fundamental changes to the current food system and exploring alternative food sources are necessary. Microalgae are gaining attention as a lab-based source of nutrition and their potential in the circular economy. Overcoming challenges and limitations, such as toxicity, can be achieved through systems biology and artificial intelligence, with the help of data-driven metabolic optimization and advanced analytics methods using microalgal databases.
ADVANCES IN NUTRITION
(2023)
Review
Biotechnology & Applied Microbiology
Jasmeet Kaur Khanijou, Hanna Kulyk, Cecilia Berges, Leng Wei Khoo, Pnelope Ng, Hock Chuan Yeo, Mohamed Helmy, Floriant Bellvert, Wee Chew, Kumar Selvarajoo
Summary: Metabolic engineering manipulates microbes to produce desired compounds, while metabolomics quantifies intracellular and extracellular metabolites. Dynamic models and machine learning algorithms can be used in conjunction with time-series metabolomics data to advance metabolic engineering research.
METABOLIC ENGINEERING COMMUNICATIONS
(2022)
Article
Mathematical & Computational Biology
Olga Sirbu, Mohamed Helmy, Alessandro Giuliani, Kumar Selvarajoo
Summary: Cancer is considered a genetic disease, and recent studies have shown that every human gene may be associated with cancer. The distinction between oncogenes that drive cancer and those that are associated but do not play a role is important. Through analysis of single-cell and bulk datasets of cancer transcriptomes and proteomes, it was found that oncogenes have higher connectivity in protein-protein interaction networks compared to random genes. Additionally, at the single-cell level, there is variant behavior in a subset of oncogenes for each cancer type. Further study using protein causality and higher-resolution single-cell analysis is needed to understand the role of oncogenes.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Kumar Selvarajoo, Alessandro Giuliani
Article
Mathematical & Computational Biology
Mohamed Helmy, Rahul Agrawal, Javed Ali, Mohamed Soudy, Thuy Tien Bui, Kumar Selvarajoo
Summary: Gene expression profiling techniques, such as DNA microarray and RNA-Sequencing, have significantly impacted biomedical research. GeneCloudOmics is a user-friendly web server that extends the functionality of previous tools, allowing rapid execution of various bioinformatics tasks with comprehensive data analytics tools.
FRONTIERS IN BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Mohamed Helmy, Derek Smith, Kumar Selvarajoo
METABOLIC ENGINEERING COMMUNICATIONS
(2020)
Article
Biotechnology & Applied Microbiology
David Lleres, Benoit Moindrot, Rakesh Pathak, Vincent Piras, Melody Matelot, Benoit Pignard, Alice Marchand, Mallory Poncelet, Aurelien Perrin, Virgile Tellier, Robert Feil, Daan Noordermeer