Article
Integrative & Complementary Medicine
Xuejiao Liao, Shuai Guo, Xianmei Yin, Baosheng Liao, Mingqian Li, He Su, Qiushi Li, Jin Pei, Jihai Gao, Juan Lei, Xiwen Li, Zhihai Huang, Jiang Xu, Shilin Chen
Summary: The study revealed that intra-chromosomal interactions are more intense than inter-chromosomal interactions in the control group, 3-day venom glands, and muscles group. The findings also indicated that compartmental transition is correlated with chromatin interactions, with up-regulated genes in switch regions reflecting toxin activity.
Article
Biology
Qing Ma, Liuyi Yang, Karen Tolentino, Guiping Wang, Yang Zhao, Ulrike M. Litzenburger, Quanming Shi, Lin Zhu, Chen Yang, Huiyuan Jiao, Feng Zhang, Rui Li, Miao-Chih Tsai, Jun-An Chen, Ian Lai, Hong Zeng, Lingjie Li, Howard Y. Chang
Summary: This study demonstrates the significant role of human HOTAIR lncRNA in promoting breast cancer progression, including increased metastatic capacity and invasiveness in breast cancer cells, and alterations in the transcriptome and chromatin accessibility landscape.
Article
Genetics & Heredity
Shan Wang, Pei Shang, Guangyu Yao, Changsheng Ye, Lujia Chen, Xiaolei Hu
Summary: This study delved into the molecular mechanisms of breast cancer at the genomic and transcriptomic levels in different subtypes, aiming to provide a theoretical basis for personalized treatments and precision medicine. It was found that carcinogenesis and development of triple-negative breast cancer were the most important and complex processes, and the luminal A subtype exhibited a different pathogenesis compared to the other subtypes. Additionally, 16 hub genes related to good prognosis in triple-negative breast cancer were identified, and new transcription factors and microRNAs were introduced, offering novel perspectives for breast cancer research and treatment.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Samah El Ghamrasni, Rene Quevedo, James Hawley, Parisa Mazrooei, Youstina Hanna, Iulia Cirlan, Helen Zhu, Jeff P. Bruce, Leslie E. Oldfield, S. Y. Cindy Yang, Paul Guilhamon, Juri Reimand, Dave W. Cescon, Susan J. Done, Mathieu Lupien, Trevor J. Pugh
Summary: By analyzing primary breast tumors through whole-genome sequencing, we identified transcription factors and cis-regulatory elements associated with the development of breast cancer, providing insights into the driver mechanisms of breast cancer.
MOLECULAR CANCER RESEARCH
(2022)
Article
Multidisciplinary Sciences
Jeremy Poulet-Benedetti, Caroline Tonnerre-Doncarli, Anne-Laure Valton, Marc Laurent, Marie Gerard, Natalja Barinova, Nikolaos Parisis, Florian Massip, Franck Picard, Marie-Noelle Prioleau
Summary: In this study, the involvement of three elements (guanine-rich motifs potentially forming G-quadruplexes, nucleosome-free regions, and the histone variant H2A.Z) in the firing of replication origins in vertebrates were investigated. It was found that two guanine-rich motifs on the same DNA strand were sufficient to assemble a functional replication origin without inducing transcription. The guanine-rich motifs were associated with the formation of nucleosome-free regions and enrichment of H2A.Z. These findings suggest the importance of guanine-rich motifs in the organization and duplication of vertebrate genomes.
NATURE COMMUNICATIONS
(2023)
Review
Oncology
Siwei Deng, Yuliang Feng, Siim Pauklin
Summary: This review discusses the importance of three-dimensional chromatin structures in biological processes and diseases, as well as the key structural protein elements involved in chromatin interactions. The recent development of technologies and bioinformatics approaches for studying chromatin interactions in gene expression regulation is also summarized.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2022)
Article
Oncology
Sheetal Parida, Sumit Siddharth, Yuqing Xia, Dipali Sharma
Summary: Racial disparities in breast cancer are evident, with Black women having a lower risk of incidence but the highest mortality. This study investigates the genomic and metagenomic features of breast tumors from Asian, Black and white women, revealing distinctive microbial compositions and tumor immune microenvironment-related traits. The findings provide a comprehensive understanding of racial disparities in breast cancer and suggest potential race-specific microbial biomarkers.
Article
Biochemistry & Molecular Biology
Ying Zhang, Guoting Chen, Li Deng, Baibai Gao, Jing Yang, Cheng Ding, Qing Zhang, Weizhi Ouyang, Minrong Guo, Wenxia Wang, Beibei Liu, Qinghua Zhang, Wing-Kin Sung, Jiapei Yan, Guoliang Li, Xingwang Li
Summary: Photoperiods and the circadian clock coordinate gene expression rhythms in plants, ensuring their fitness to the environment. Rice gene expression was found to be delayed under constant darkness and reduced under constant light. The study also revealed synchronous circadian oscillation in H3K9ac modifications and long non-coding RNAs expression at the loci of rhythmic genes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Qian Liu, Pingzhao Hu
Summary: This study aimed to predict clinical characteristics of breast cancer using deep radiomic features extracted from MRI images through deep learning technology. The results showed that deep radiomic features performed better in predicting clinical characteristics and had significant associations with genomic factors.
BIOMARKER RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Hyunsoo Kim, Kamila Wisniewska, Matthew J. Regner, Aatish Thennavan, Philip M. Spanheimer, Hector L. Franco
Summary: Male breast cancer, although rare, presents unique gene expression patterns compared to female breast cancer. This study utilizes single-cell analysis to identify differentially expressed genes and regulatory landscape in male breast tumors, highlighting potential therapeutic targets. The findings expand our understanding of the biology of male breast cancer and provide valuable resources for future therapeutic interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Huaipeng Xing, Reiya Taniguchi, Iskander Khusainov, Jan Philipp Kreysing, Sonja Welsch, Beata Turonova, Martin Beck
Summary: Using cryo-electron tomography, we resolved high-resolution ribosome structures inside human cells, revealing their distribution of functional states, including the elongation cycle, Z transfer RNA binding site, and ribosome expansion segments dynamics. Studying ribosome structures from cells treated with Homoharringtonine, a drug used against chronic myeloid leukemia, we discovered how translation dynamics were altered in situ and identified small molecules within the active site of the ribosome. Thus, we can assess structural dynamics and drug effects at high resolution within human cells.
Article
Multidisciplinary Sciences
Varvara Lukyanchikova, Miroslav Nuriddinov, Polina Belokopytova, Alena Taskina, Jiangtao Liang, Maarten J. M. F. Reijnders, Livio Ruzzante, Romain Feron, Robert M. Waterhouse, Yang Wu, Chunhong Mao, Zhijian Tu, Igor Sharakhov, Veniamin Fishman
Summary: This study comprehensively profiles the genome organizations of five Anopheles mosquito species and demonstrates the influence of chromatin architecture at different levels. The study reveals the conservation of chromatin architecture over millions of years and the causal relationship between gene density and chromatin structure.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Ken Chen, Huiying Zhao, Yuedong Yang
Summary: This study presents a Transformer-based model, TransEPI, for predicting enhancer-promoter interactions (EPI) by capturing large genomic contexts. TransEPI consistently outperforms other machine learning and deep learning models on datasets from different cell types.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Mark Kittisopikul, Takeshi Shimi, Meltem Tatli, Joseph Riley Tran, Yixian Zheng, Ohad Medalia, Khuloud Jaqaman, Stephen A. Adam, Robert D. Goldman
Summary: The study demonstrates that lamin isoforms and nucleoporins work together to maintain the normal organization of lamin meshworks and NPC within the nuclear envelope; Specific lamin isoforms are involved in regulating the number of NPCs;
The spatial association between lamin isoform fibers and NPCs remains intact in nuclei with knockout lamin isoforms.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Oncology
Maysa Abu-Khalaf, Chun Wang, Zhenchao Zhang, Rui Luo, Weelic Chong, Daniel P. Silver, Frederick Fellin, Rebecca Jaslow, AnaMaria Lopez, Terrence Cescon, Wei Jiang, Ronald Myers, Qiang Wei, Bingshan Li, Massimo Cristofanilli, Hushan Yang
Summary: The combination of CDK4/6 inhibitors and endocrine therapy has become the standard of care for ER+ breast cancer, but resistance to CDK4/6 inhibitors is a growing concern. This study used gene panel sequencing to profile circulating cell-free DNA in ER+ metastatic breast cancer patients before and after palbociclib treatment. The results identified CCNE1 mutations and TSC2 loss as potential genomic biomarkers for treatment resistance and poor prognosis. Further large-scale studies and mechanism-focused research are needed to confirm these findings and understand the underlying molecular mechanisms.
Article
Cell Biology
Yichen Wang, Lin Jia, Cong Wang, Zhonghua Du, Shilin Zhang, Lei Zhou, Xue Wen, Hui Li, Huiling Chen, Yuanyuan Nie, Dan Li, Shanshan Liu, Daniela Salgado Figueroa, Ferhat Ay, Wei Xu, Songling Zhang, Wei Li, Jiuwei Cui, Andrew R. Hoffman, Hui Guo, Ji-Fan Hu
Summary: Wang et al. identify Peln1 as a key chromatin long non-coding RNA that controls pluripotency exit and intrachromosomal looping in stem cells. Peln1 interacts with the Oct4 promoter, recruits DNMT3A, and alters the epigenotype to disrupt the intrachromosomal loop, leading to pluripotency exit. Peln1 also targets multiple pathway genes associated with stem cell self-renewal.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Endocrinology & Metabolism
Margaret C. S. Boguszewski, Cesar L. Boguszewski, Wassim Chemaitilly, Laurie E. Cohen, Judith Gebauer, Claire Higham, Andrew R. Hoffman, Michel Polak, Kevin C. J. Yuen, Nathalie Alos, Zoltan Antal, Martin Bidlingmaier, Beverley M. K. Biller, George Brabant, Catherine S. Y. Choong, Stefano Cianfarani, Peter E. Clayton, Regis Coutant, Adriane A. Cardoso-Demartini, Alberto Fernandez, Adda Grimberg, Kolbeinn Gudmundsson, Jaime Guevara-Aguirre, Ken K. Y. Ho, Reiko Horikawa, Andrea M. Isidori, Jens Otto Lunde Jorgensen, Peter Kamenicky, Niki Karavitaki, John J. Kopchick, Maya Lodish, Xiaoping Luo, Ann McCormack, Lillian Meacham, Shlomo Melmed, Sogol Mostoufi Moab, Hermann L. Muller, Sebastian J. C. M. M. Neggers, Manoel H. Aguiar Oliveira, Keiichi Ozono, Patricia A. Pennisi, Vera Popovic, Sally Radovick, Lars Savendahl, Philippe Touraine, Hanneke M. van Santen, Gudmundur Johannsson
Summary: Growth hormone replacement therapy is not associated with primary tumor or cancer recurrence. The risk of secondary neoplasia from GH replacement is minimal compared to other factors. GH replacement may be considered in adult cancer survivors in remission after careful risk/benefit analysis.
EUROPEAN JOURNAL OF ENDOCRINOLOGY
(2022)
Article
Endocrinology & Metabolism
Peggy M. Cawthon, Katherine E. Peters, Steven R. Cummings, Eric S. Orwoll, Andrew R. Hoffman, Kristine E. Ensrud, Jane A. Cauley, William J. Evans
Summary: The study investigates the relationship between total skeletal muscle mass and incident fractures. The findings indicate that low D3Cr muscle mass is associated with an increased risk of hip and potentially other fractures in older men, and this association is partially mediated by physical performance.
JOURNAL OF BONE AND MINERAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Simon Eschweiler, Ciro Ramirez-Suastegui, Yingcong Li, Emma King, Lindsey Chudley, Jaya Thomas, Oliver Wood, Adrian von Witzleben, Danielle Jeffrey, Katy McCann, Hayley Simon, Monalisa Mondal, Alice Wang, Martina Dicker, Elena Lopez-Guadamillas, Ting-Fang Chou, Nicola A. Dobbs, Louisa Essame, Gary Acton, Fiona Kelly, Gavin Halbert, Joseph J. Sacco, Andrew Graeme Schache, Richard Shaw, James Anthony McCaul, Claire Paterson, Joseph H. Davies, Peter A. Brennan, Rabindra P. Singh, Paul M. Loadman, William Wilson, Allan Hackshaw, Gregory Seumois, Klaus Okkenhaug, Gareth J. Thomas, Terry M. Jones, Ferhat Ay, Greg Friberg, Mitchell Kronenberg, Bart Vanhaesebroeck, Pandurangan Vijayanand, Christian H. Ottensmeier
Summary: This study assessed the effects of PI3K delta inhibitors in patients with head and neck cancer, finding that it reduced the number of regulatory T cells in tumors and enhanced the cytotoxic potential of tumor-infiltrating T cells. However, high doses of the inhibitors led to immune-related adverse events, indicating the need for alternative dosing regimens to limit toxicity.
Article
Ophthalmology
Connie M. Sears, Amee D. Azad, Linus Amarikwa, Brandon H. Pham, Clara J. Men, Daniel N. Kaplan, Jocelyn Liu, Andrew R. Hoffman, Austin Swanson, Jennifer Alyono, Jennifer Y. Lee, Chrysoula Dosiou, Andrea L. Kossler
Summary: This study aims to characterize the frequency, severity, and resolution of hearing dysfunction in patients treated with teprotumumab for TED. The study found that hearing loss is a concerning adverse event of teprotumumab, and further studies are needed to understand its mechanism and reversibility. Baseline audiometry and repeat testing are recommended for monitoring and prevention.
AMERICAN JOURNAL OF OPHTHALMOLOGY
(2022)
Review
Cell Biology
Yudi Liu, Jiuwei Cui, Andrew R. Hoffman, Ji-Fan Hu
Summary: Protein translation is a critical regulatory event involved in various physiological and pathological processes. The eukaryotic translation initiation factor 4G2 (eIF4G2) is important for cap-independent translation initiation via internal ribosome entry sites (IRESs), but recent findings suggest that it plays a role in other translation initiation pathways as well. This review summarizes the role of eIF4G2 in different translation initiation events and its involvement in apoptosis, cell survival, cell differentiation, and embryonic development.
CELL PROLIFERATION
(2023)
Article
Allergy
Haruka Miki, William B. Kiosses, Mario C. Manresa, Rinkesh K. Gupta, Gurupreet S. Sethi, Rana Herro, Ricardo Da Silva Antunes, Paramita Dutta, Marina Miller, Kai Fung, Ashu Chawla, Katarzyna Dobaczewska, Ferhat Ay, David H. Broide, Alexei V. Tumanov, Michael Croft
Summary: This study found that signaling through lymphotoxin beta receptor and herpesvirus entry mediator from LIGHT directly controls the dysregulation of airway smooth muscle cells in asthma. By using animal models and in vitro experiments, it was discovered that these receptors play a crucial role in airway smooth muscle hyperresponsiveness and remodeling.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Yanbo Zhu, Zi Yan, Changhao Fu, Xue Wen, Lin Jia, Lei Zhou, Zhonghua Du, Cong Wang, Yichen Wang, Jingcheng Chen, Yuanyuan Nie, Wenjun Wang, Jiuwei Cui, Guixia Wang, Andrew R. Hoffman, Ji-Fan Hu, Wei Li
Summary: By combining CRIST-seq and RNA sequencing, researchers identified a pluripotency-associated lncRNA Osilr9, which plays a critical role in maintaining the pluripotency of stem cells by coordinating the promoter activity of core stem cell factor genes. Osilr9 binds to the Oct4 promoter and recruits a DNA demethylase to induce promoter demethylation, thus facilitating the maintenance of pluripotency.
Review
Critical Care Medicine
Tamara L. Wexler, Kent Reifschneider, Philippe Backeljauw, Javier F. Cardenas, Andrew R. Hoffman, Bradley S. Miller, Kevin C. J. Yuen
Summary: Traumatic brain injury (TBI) is a serious condition that can lead to various consequences, including deficiencies in pituitary hormones. Growth hormone deficiency (GHD) is the most common pituitary hormone deficiency post-TBI and is associated with numerous adverse effects on health outcomes. However, research on post-TBI GHD in pediatric and adolescent patients is limited, and diagnostic and treatment recommendations are lacking. This review addresses the occurrence and diagnosis of TBI, analyzes the prevalence rates of post-TBI hypopituitarism and GHD in pediatric and adolescent patients, and discusses appropriate testing strategies and dosage recommendations for GH treatment.
JOURNAL OF NEUROTRAUMA
(2023)
Article
Multidisciplinary Sciences
Konstantin Okonechnikov, Aylin Camgoez, Owen Chapman, Sameena Wani, Donglim Esther Park, Jens-Martin Huebner, Abhijit Chakraborty, Meghana Pagadala, Rosalind Bump, Sahaana Chandran, Katerina Kraft, Rocio Acuna-Hidalgo, Derek Reid, Kristin Sikkink, Monika Mauermann, Edwin F. Juarez, Anne Jenseit, James T. Robinson, Kristian W. Pajtler, Till Milde, Natalie Jaeger, Petra Fiesel, Ling Morgan, Sunita Sridhar, Nicole G. Coufal, Michael Levy, Denise Malicki, Charlotte Hobbs, Stephen Kingsmore, Shareef Nahas, Matija Snuderl, John Crawford, Robert J. Wechsler-Reya, Tom Belle Davidson, Jennifer Cotter, George Michaiel, Gudrun Fleischhack, Stefan Mundlos, Anthony Schmitt, Hannah Carter, Kulandaimanuvel Antony Michealraj, Sachin A. Kumar, Michael D. Taylor, Jeremy Rich, Frank Buchholz, Jill P. Mesirov, Stefan M. Pfister, Ferhat Ay, Jesse R. Dixon, Marcel Kool, Lukas Chavez
Summary: This study investigates the chromosomal conformations and regulatory mechanisms associated with aberrant gene expression in ependymoma tumors. The researchers identified new topologically associating domains, group-specific chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Inhibition experiments confirmed that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Lei Zhou, Hui Li, Tingge Sun, Xue Wen, Chao Niu, Min Li, Wei Li, Miguel A. Esteban, Andrew R. Hoffman, Ji-Fan Hu, Jiuwei Cui
Summary: This study investigates the factors regulating inter-organelle crosstalk in pluripotent stem cells through the analysis of long non-coding RNAs and identifies non-coding RNAs related to stem cell reprogramming and exit from pluripotency. This research provides a valuable resource for understanding the molecular mechanisms underlying pluripotency.
Meeting Abstract
Urology & Nephrology
Julia H. Yuan, Dena E. Rifkin, Charles Ginsberg, Peggy Cawthon, Deborah M. Kado, Scott R. Bauer, Kristine Ensrud, Andrew Hoffman, O. Alison Potok
AMERICAN JOURNAL OF KIDNEY DISEASES
(2023)
Meeting Abstract
Endocrinology & Metabolism
Suet Ching Chen, Evangelia Charmandari, Jin-Ho Choi, Xinyu Dou, Chunxiu Gong, Rasha Hamza, Jamie Harvey, Andrew R. Hoffman, Reiko Horikawa, Gudmundur Johannson, Alexander Jorje, Bradley Miller, Lars Savendahl, Xanthippi Tseretopoulou, Diana Vitali, S. Faisal Ahmed
HORMONE RESEARCH IN PAEDIATRICS
(2023)
Meeting Abstract
Endocrinology & Metabolism
Bradley S. Miller, Suet Ching Chen, Evangelia Charmandari, Jin Ho Choi, Xinyu Dou, Chunxiu Gong, Rasha Hamza, Jamie Harvey, Andrew R. Hoffman, Reiko Horikawa, Gudmundur Johannsson, Alexander Jorge, Ryan S. Miller, Sebastian Roehrich, Lars Savendahl, Xanthippi Tseretopoulou, Diana Vitali, Michael P. Wajnrajch, S. Faisal Ahmed
HORMONE RESEARCH IN PAEDIATRICS
(2023)
Meeting Abstract
Immunology
Rinkesh Kumar Gupta, Donald Gracias, Daniela Salgado Figueroa, Haruka Miki, Jacqueline Miller, Kai Fung, Ferhat Ay, Linda C. Burkly, Michael Croft
JOURNAL OF IMMUNOLOGY
(2022)