Article
Nuclear Science & Technology
Fang Wang, Yi Xiao, Jun-Fang Yan, Guo-Min Huang, Jin-Hua Zhang, Cui-Xia Di, Jing Si, Hong Zhang, Ai-Hong Mao
Summary: Carbon ion radiotherapy shows more effective impact on DNA damage, cell cycle, survival capability, and apoptosis of prostate cancer cells, possibly inducing cell cycle arrest and apoptosis through the pRb/E2F1/c-Myc signaling pathway to enhance the radiosensitivity of p53-deficient prostate cancer cells.
NUCLEAR SCIENCE AND TECHNIQUES
(2021)
Article
Oncology
Amy C. Mandigo, Wei Yuan, Kexin Xu, Peter Gallagher, Angel Pang, Yi Fang Guan, Ayesha A. Shafi, Chellappagounder Thangavel, Beshara Sheehan, Denisa Bogdan, Alec Paschalis, Jennifer J. McCann, Talya S. Laufer, Nicolas Gordon, Irina A. Vasilevskaya, Emanuela Dylgjeri, Saswati N. Chand, Matthew J. Schiewer, Josep Domingo-Domenech, Robert B. Den, Jeff Holst, Peter A. McCue, Johann S. de Bono, Christopher McNair, Karen E. Knudsen
Summary: This study identifies the stage-specific consequences of RB loss across cancer progression, which directly impact tumor response to clinically utilized therapeutics. It is the first to investigate the effect of RB loss on global metabolic regulation and link RB/E2F1 to redox control in multiple advanced diseases.
Article
Cell Biology
Xiaoling Xu, Tao Zhang, Meiju Zhang, Lanlan Li, Ge Deng, Zheng Lu, Zhenyu Zhang, Yan Du, Yubin Feng, Xiaowen Feng, Xiaoqing Peng, Feihu Chen
Summary: This study found that ATPR can promote the differentiation of MCL cells and achieve it through regulating the SOX11/CyclinD1/Rb/E2F1 pathway. This provides experimental foundation for developing differentiation therapy for MCL using ATPR.
CELLULAR SIGNALLING
(2022)
Article
Biochemistry & Molecular Biology
Juntae Kwon, Jinmin Zhang, Boram Mok, Samuel Allsup, Chul Kim, Jeffrey Toretsky, Cecil Han
Summary: This study established a mouse model of LUSC and found that USP13 is a molecular driver of lineage plasticity in club cells and is associated with upregulation of squamous programs in lung cancer cells.
Article
Oncology
Jing Xu, Lei Liu, Ranran Ma, Yawen Wang, Xu Chen, Haiting Liu, Youxin Ji, Tiantian Liu, Peng Gao
Summary: This study revealed that elevated KIF26A expression in breast cancer tissues is associated with lymph node metastasis. KIF26A promotes cell proliferation and cell cycle progression in breast cancer cells. The core promotor region of human KIF26A gene is located at position -395 to -385, upstream of the transcription start site. The transcriptional factor E2F1 activates KIF26A expression, leading to cell cycle progression through the CDK-RB-E2Fs pathway.
FRONTIERS IN ONCOLOGY
(2021)
Article
Cell Biology
Chad Liu, Takamasa Kudo, Xin Ye, Karen Gascoigne
Summary: Cell-to-cell heterogeneity is crucial for tumor evolution and survival, and cancer cells achieve this heterogeneity by expressing the highly heterogeneous transcription factor c-Myc. We have discovered that the expression of c-Myc displays a pulsatile nature and exhibits extensive cell-to-cell variability. This heterogeneity in c-Myc dynamics leads to variable transcription of target genes, and the timing of c-Myc expression predicts cell-cycle progression rates and drug sensitivities. Our findings suggest that cancer cells increase the heterogeneity of transcription factors, such as c-Myc, to adapt to stress and rapidly explore transcriptional landscapes.
Article
Medicine, Research & Experimental
Haylee A. Cosgrove, Sebastien Gingras, Minjung Kim, Sheldon Bastacky, Jeremy S. Tilstra, Mark J. Shlomchik
Summary: The regulatory role of Toll-like receptor 7 (TLR7) in the pathogenesis of lupus and its potential therapeutic strategy have been studied. The study found that TLR7 deficiency in B cells greatly improved the disease progression in TLR9-deficient mice with accelerated systemic lupus erythematosus, suggesting the importance of B cell-directed TLR7 regulation in lupus.
Article
Oncology
Zuolei Jing, Qianmei Liu, Xinyuan He, Zhirong Jia, Zhizhong Xu, Bolin Yang, Ping Liu
Summary: Our study demonstrates that NCAPD3 promotes glucose metabolism reprogramming and enhances the Warburg effect in colorectal tumorigenesis and CRC progression. We found that NCAPD3 is overexpressed in CRC tissues and is associated with poor prognosis in CRC patients. Knockout of NCAPD3 suppressed CRC development in mouse models and we identified the underlying molecular mechanism by which NCAPD3 regulates glucose metabolism.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jasmine Chen, Aleks Guanizo, Quinton Luong, W. Samantha N. Jayasekara, Dhilshan Jayasinghe, Chaitanya Inampudi, Anette Szczepny, Daniel J. Garama, Prudence A. Russell, Vinod Ganju, Jason E. Cain, D. Neil Watkins, Daniel J. Gough
Summary: The study shows that MYC overexpression can induce carcinoma in situ but not progress to invasive disease, while the formation of SCLC depends on the cell of origin. The combination of MYC with deletion of Trp53 and Rb1 exclusively gives rise to SCLC, regardless of the cell lineage, impacting disease latency, metastatic potential, and the transcriptional profile of the SCLC phenotype.
Article
Cell Biology
Deyan Jiao, Renhui Sun, Xiaolei Ren, Yingchun Wang, Panpan Tian, Yuzhen Wang, Detian Yuan, Xuetian Yue, Zhuanchang Wu, Chunyang Li, Lifen Gao, Chunhong Ma, Xiaohong Liang
Summary: This study reveals the persistent dysfunction of NK cells in a hyperlipidemia environment and demonstrates that exposure to oleic acid impairs NK cell function by inhibiting c-Myc acetylation. Moreover, it shows that engineered NK cells with hyperacetylated c-Myc mutants display superior anti-tumor activity.
Article
Oncology
Cansu Tekin, Brendon P. Scicluna, Sophie C. Lodestijn, Kun Shi, Maarten F. Bijlsma, C. Arnold Spek
Summary: The PAR1-Myc axis is identified as a driver of ductal cell fates in premalignant pancreas and PDAC, with macrophages playing a key role in ADM. Deficiency of PAR1 affects the fate of pancreatic cells.
MOLECULAR ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Chunfei Chen, Michael W. Forster, Stephen F. Foley, Svyatoslav S. Shcheka
Summary: Our new high-pressure experiments show that most carbonates in carbonate-rich crustal rocks survive devolatilization and hydrous melting in subduction zones, indicating their important role in the deep carbon cycle. In warm and hot subduction zones, KCl and NaCl become stable phases crystallizing from hydrous carbonatite melts, leading to the sequestration of chlorine in downwelling slabs. Therefore, the subduction of carbonate-rich rocks has facilitated the recycling of both chlorine and carbon into the deep mantle, shaping Earth's geological history.
Article
Multidisciplinary Sciences
Stella Amanda, Tze King Tan, Jolynn Zu Lin Ong, Madelaine Skolastika Theardy, Regina Wan Ju Wong, Xiao Zi Huang, Muhammad Zulfaqar Ali, Yan Li, Zhiyuan Gong, Hiroshi Inagaki, Ee Yong Foo, Brendan Pang, Soo Yong Tan, Shinsuke Iida, Takaomi Sanda
Summary: This study demonstrates the oncogenicity of IRF4 in zebrafish models and its potential effects on T-cell development and clonal evolution. The majority of IRF4-driven tumors are composed of double-negative T cells and show sensitivity to a BRD inhibitor.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Juhee Pae, Jonatan Ersching, Tiago B. R. Castro, Marta Schips, Luka Mesin, Samuel J. Allon, Jose Ordovas-Montanes, Coraline Mlynarczyk, Ari Melnick, Alejo Efeyan, Alex K. Shalek, Michael Meyer-Hermann, Gabriel D. Victora
Summary: During affinity maturation, GC B cells undergo proliferation and hypermutation in the dark zone, followed by selection in the light zone. Cyclin D3 plays a crucial role in controlling the anatomical segregation and cell cycle of GC B cells, and a specific mutation can lead to clonal B cell lymphoproliferation.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Hanjun Li, Xiuguo Han, Shengbing Yang, Yongjie Wang, Yang Dong, Tingting Tang
Summary: FOXP1, transactivated by ERK/JNK-c-JUN/c-FOS, drives osteosarcoma development by regulating the p53-P21/RB signaling cascade, suggesting it as a potential therapeutic target.
Article
Biology
Frederic Lavancier, Thierry Pecot, Liu Zengzhen, Charles Kervrann
Article
Biochemistry & Molecular Biology
Helene Bouvrais, Laurent Chesneau, Yann Le Cunff, Danielle Fairbrass, Nina Soler, Sylvain Pastezeur, Thierry Pecot, Charles Kervrann, Jacques Pecreaux
Summary: In C. elegans zygote, astral microtubules play a crucial role in generating forces to position the mitotic spindle by pushing against and pulling from the cortex. Two populations of microtubule dynamics, corresponding to pulling and pushing events, were identified. A threefold control of pulling force was proposed, with anteroposterior asymmetry in dynein on-rate being a key factor in posterior spindle displacement. Dynein processivity increases along mitosis, reflecting the temporal control of pulling forces, strengthening at anaphase onset independently from chromatid separation, while pushing force remains constant and symmetric during metaphase to maintain spindle position.
Review
Chemistry, Applied
Nick Fackler, Bjorn D. Heijstra, Blake J. Rasor, Hunter Brown, Jacob Martin, Zhuofu Ni, Kevin M. Shebek, Rick R. Rosin, Sean D. Simpson, Keith E. Tyo, Richard J. Giannone, Robert L. Hettich, Timothy J. Tschaplinski, Ching Leang, Steven D. Brown, Michael C. Jewett, Michael Kopke
Summary: Rising levels of greenhouse gases have led to significant environmental, economic, and social challenges globally. Technology that converts greenhouse gases into useful products can help mitigate climate change by enabling a circular carbon economy. Gas fermentation using carbon-fixing microorganisms is a commercially viable and scalable solution which offers unique feedstock and product flexibility.
ANNUAL REVIEW OF CHEMICAL AND BIOMOLECULAR ENGINEERING, VOL 12, 2021
(2021)
Article
Biochemical Research Methods
Xun Chen, Yang Li, Nicole Wyman, Zheng Zhang, Hongming Fan, Michael Le, Steven Gannon, Chelsea Rose, Zhao Zhang, Jeremy Mercuri, Hai Yao, Bruce Gao, Shane Woolf, Thierry Pecot, Tong Ye
Summary: Chondrocyte viability is crucial for evaluating cartilage health; deep learning significantly improves segmentation and classification with potential for 90% accuracy in viability measurement. Automated cell-based image processing methods can improve efficiency, making nonlinear optical imaging methods more feasible for biological or clinical studies.
BIOMEDICAL OPTICS EXPRESS
(2021)
Article
Multidisciplinary Sciences
Zhong Chen, William Hankey, Yue Zhao, Jeff Groth, Furong Huang, Hongyan Wang, Alexandre Rosa Campos, Jiaoti Huang, Robert G. Roeder, Qianben Wang
Summary: RNA Polymerase II (Pol II) recycling can impact transcription efficiency. An approach has been described to facilitate the identification of factors involved in Pol II recycling, with PAF1 complex components identified as mediators of recycling.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Shaaron Ochoa-Rios, Ian P. O'Connor, Lindsey N. Kent, Julian M. Clouse, Yannis Hadjiyannis, Christopher Koivisto, Thierry Pecot, Peggi M. Angel, Richard R. Drake, Gustavo Leone, Anand S. Mehta, Don C. Rockey
Summary: This study used imaging mass spectrometry to analyze the qualitative and quantitative N-glycome profile in NAFLD and NASH tissue. The results showed that the serum N-glycan profiles can be altered in NAFLD/NASH patients. Both animal models and human biopsy specimens demonstrated that the alterations in N-glycan structures were associated with the degree of fibrosis, and the spatial distribution of glycan alterations correlated with tissue steatosis.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Zhong Chen, Zhenqing Ye, Raymond E. Soccio, Tomoyoshi Nakadai, William Hankey, Yue Zhao, Furong Huang, Fuwen Yuan, Hongyan Wang, Zhifen Cui, Benjamin Sunkel, Dayong Wu, Richard K. Dzeng, Jennifer M. Thomas-Ahner, Tim H. M. Huang, Steven K. Clinton, Jiaoti Huang, Mitchell A. Lazar, Victor X. Jin, Robert G. Roeder, Qianben Wang
Summary: This study reveals a novel role of phosphorylated MED1 in driving Pol II recycling during transcription. The phosphorylated MED1, when dynamically moving along with Pol II, enhances mRNA output and its inhibition suppresses prostate tumor growth. These findings provide insights into dysregulated Pol II recycling in cancer and identify a potential therapeutic target.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Thierry Pecot, Maria C. Cuitino, Roger H. Johnson, Cynthia Timmers, Gustavo Leone
Summary: This study presents a deep learning-based approach for accurate nuclear segmentation and quantification of fluorescent labeling intensity. By applying this approach to 2D fluorescent still images of mouse tissues, the researchers successfully analyzed the cell cycle-dependent protein concentration.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Tianbao Li, Qi Liu, Zhong Chen, Kun Fang, Furong Huang, Xueqi Fu, Qianben Wang, Victor X. Jin
Summary: In this study, the authors conducted a multi-omic study on the nucleosome landscape in LNCaP cells, observing changes in nucleosome states and pioneer factors such as GATA2 upon androgen stimulation. They revealed a dual role of GATA2 as a pioneer and master transcription factor in mediating nucleosome dynamics and enhancing downstream signaling pathways.
NATURE COMMUNICATIONS
(2022)
Article
Developmental Biology
Manon Lesage, Manon Thomas, Thierry Pecot, Tu -Ky Ly, Nathalie Hinfray, Remy Beaudouin, Michelle Neumann, Robin Lovell-Badge, Jerome Bugeon, Violette Thermes
Summary: Computational analysis of bio-images using deep learning algorithms has progressed significantly and become more accessible to non-specialists thanks to ready-to-use tools. Recent developments in three-dimensional (3D) imaging of ovaries have also benefited the study of oogenesis mechanisms and female reproductive success. However, analyzing these complex datasets has been a challenge due to the lack of efficient workflows. In this study, we integrated two open-source DL tools, Noise2Void and Cellpose, into an analysis pipeline for 3D follicular content analysis, which showed successful application in different types of ovaries. This pipeline enables automatic and accurate quantification of irregularly stained, low autofluorescence, or heterogeneous follicles sizes in 3D images.
Review
Medicine, General & Internal
Pierre Allaume, Noemie Rabilloud, Bruno Turlin, Edouard Bardou-Jacquet, Olivier Loreal, Julien Calderaro, Zine-Eddine Khene, Oscar Acosta, Renaud De Crevoisier, Nathalie Rioux-Leclercq, Thierry Pecot, Solene-Florence Kammerer-Jacquet
Summary: This study provides a systematic review of applications and performances of deep neural network algorithms in liver pathology. The results show that DNN models have diverse applications in this field, but most studies have a high risk of bias. Therefore, DNN models in liver pathology present both opportunities and limitations.
Article
Oncology
Peipei Lu, Joseph Foley, Chunfang Zhu, Katherine McNamara, Korsuk Sirinukunwattana, Sujay Vennam, Sushama Varma, Hamid Fehri, Arunima Srivastava, Shirley Zhu, Jens Rittscher, Parag Mallick, Christina Curtis, Robert West
Summary: This study utilizes spatially oriented genomic methods to identify transcriptomic and genetic changes in precursor neoplasia associated with invasive breast cancer at a single-duct level. The findings show that HER2 amplification in DCIS alters transcriptomic profiles and increases diversity of copy number variations, activating the interferon signaling pathway. Multiple subclones of HER2-amplified DCIS with distinct CNV profiles suggest that multiple events are involved in the acquisition of HER2 amplification. Additionally, DCIS acquires key transcriptomic changes and CNV events prior to HER2 amplification, indicating a cellular state primed for growth advantage.
BREAST CANCER RESEARCH
(2021)
Article
Biochemical Research Methods
Nicholas Fackler, James Heffernan, Alex Juminaga, Damien Doser, Shilpa Nagaraju, R. Axayacatl Gonzalez-Garcia, Sean D. Simpson, Esteban Marcellin, Michael Kopke
Summary: Gas fermentation by Clostridium autoethanogenum is a commercial process for sustainable biomanufacturing of fuels and chemicals using low-cost C1 feedstocks, but progress in pathway engineering and gene function elucidation is hindered by a lack of genetic tools.Efforts towards pathway engineering and elucidation of gene function in this microbe have been limited by a lack of genetic tools to control gene expression and arduous genome engineering methods.
Letter
Cell Biology
Furong Huang, Hongyan Chen, Xiaolin Zhu, Tongyang Gong, Xukun Li, William Hankey, Hongyan Wang, Zhong Chen, Qianben Wang, Zhihua Liu
Proceedings Paper
Biochemical Research Methods
Arunima Srivastava, Michael Sharpnack, Kun Huang, Parag Mallick, Raghu Machiraju
PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020
(2020)