Article
Multidisciplinary Sciences
Yan Wang, Xiong Xiao, Xiaobo Wang, Feng Guo, Xiaozhong Wang
Summary: By analyzing lncRNAs and genes in fibrotic rat liver tissues induced by CCl4, 10 novel DE-lncRNAs were identified, with potential roles in oxidation-reduction processes and the PI3K/Akt signaling pathway. The cis target genes of these DE-lncRNAs were found to be Met and Nox4, suggesting new therapeutic strategies for hepatic fibrosis.
Article
Multidisciplinary Sciences
Yan Wang, Xiong Xiao, Xiaobo Wang, Feng Guo, Xiaozhong Wang
Summary: Through RNA sequencing and qRT-PCR validation, we identified 10 differentially expressed lncRNAs related to hepatic fibrosis, with involvement in oxidation-reduction processes and the PI3K/Akt signaling pathway.
Article
Biochemical Research Methods
Olga Zolotareva, Sahand Khakabimamaghani, Olga I. Isaeva, Zoe Chervontseva, Alexey Savchik, Martin Ester
Summary: The study highlights the importance of identifying differentially expressed genes in diseases for understanding disease pathogenesis. DESMOND, a new method, performs network-constrained biclustering on gene expression data to identify disease-related gene modules, improving the reproducibility of results.
Article
Genetics & Heredity
Guofeng Zhou, Shaoyan Sun, Qiuyue Yuan, Run Zhang, Ping Jiang, Guangyu Li, Yong Wang, Xiao Li
Summary: Heart failure with preserved ejection fraction (HFpEF) is a complex disease characterized by dysfunctions in the heart, adipose tissue, and cerebral arteries. This study utilized a multilevel comparative framework to investigate the shared and unique pathological features among the three tissues in HFpEF, revealing potential therapeutic targets for personalized medicine.
FRONTIERS IN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Yufang Liu, Guiling Cao, Yujing Xie, Mingxing Chu
Summary: The study aimed to identify genes related to precocious puberty in goats by SSH, using pituitary tissues from goats at different growth stages. DEGs were annotated and enriched in GO terms related to ribosome structure, translation, and GTP binding, as well as in KEGG pathways related to Jak-STAT signaling and oocyte meiosis. Candidate genes associated with precocious puberty were screened from the SSH libraries, providing valuable insights for further research into goat reproductive biology.
ANIMAL BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Mingxing Liao, Zhuqing Ren, Yuanxin Miao
Summary: This study identified miRNAs in adipose tissues that are differentially expressed in pigs with extreme differences in feed efficiency. These miRNAs were found to modulate feed efficiency by regulating lipid metabolism. The study also obtained differentially expressed target genes of these miRNAs and constructed interaction networks. The down-regulated miRNAs, ssc-miR-122-5p and ssc-miR-192, may be key miRNAs for feed efficiency.
Article
Multidisciplinary Sciences
Juan Zhang, Ying Ma, Daojun Xie, Yuancheng Bao, Wenming Yang, Han Wang, Huaizhou Jiang, Hui Han, Ting Dong
Summary: This study investigated the lncRNA-mRNA regulation network in a TX WD mouse model, identifying differentially expressed lncRNAs and mRNAs associated with WD liver injury. Functional and pathway analyses revealed enrichment in key processes such as apoptosis and pathways including drug metabolism and signaling pathways. The differential lncRNAs identified may play a role in the pathogenesis and development of WD liver injury.
SCIENTIFIC REPORTS
(2021)
Article
Oncology
Yange Wang, He Shi, Yulu Zhang, Qian Zeng, Tingmei Chen, Chengsen Chai
Summary: This study explored differentially expressed hub genes associated with tumor-infiltrating immune cells in a subtype of breast cancer called claudin-low breast cancer (CL-BCa), using a multi-approach bioinformatics analysis. The results showed an increase in tumor-infiltrating immune cells, especially CD8+ T cells and macrophages, in CL-BCa. Differentially expressed cytokines and claudins were found to be associated with overall survival. The study sheds light on the molecular features of CL-BCa in the immune microenvironment and contributes to the identification of prognosis biomarkers for CL-BCa patients.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Jinyu Li, Gena Huang, Caixia Ren, Ning Wang, Silei Sui, Zuowei Zhao, Man Li
Summary: This study identified the most common differentially expressed genes in various subtypes of BRCA and established a 12-gene prognostic risk model. Evaluation of the risk model using K-M curves, ROC curves, and Cox regression showed good predictive performance and improved accuracy and sensitivity in prognosis. The risk model can assist in individualizing treatment for patients and proposing precise strategies for BRCA therapy.
Article
Biochemistry & Molecular Biology
Hye-Mi Choi, Sang-Hyeop Lee, Min-Seok Lee, Donghyun Park, Sun Shim Choi
Summary: The study investigated the role of antisense transcripts in regulating their corresponding sense transcripts in colorectal cancer samples, finding that cancer-related genes were significantly enriched in the significantly correlated sense-antisense gene pairs. The research also showed that the correlation between sense-antisense gene pairs could distinguish between poor prognostic and good prognostic colorectal cancers.
Article
Dermatology
Yong Song, Yi Wang, Minjian Chen, Zhenni Wei
Summary: This study explored the expression patterns of HOTAIR and miR-30a-5p in scar tissues of hypertrophic scar (HS) patients and demonstrated the regulatory role of HOTAIR on fibroblast function through negative regulation of miR-30a-5p. These findings are of great importance for understanding the pathogenesis of scar formation, identifying therapeutic targets, and developing prevention strategies.
DERMATOLOGICA SINICA
(2023)
Article
Andrology
Jing Ma, Ruiyu Han, Bo Sun, Jiajie Lin, Peipei Deng, Shusong Wang, Shaoguang Sun
Summary: This study identified 39 differentially expressed miRNAs in testicular tissues of rats with hyperuricaemia-induced male infertility. These miRNAs could shed light on the mechanism of hyperuricaemia-induced male infertility.
Article
Biochemistry & Molecular Biology
Bai-Zhong Zhang, Gui-Lei Hu, Liu-Yang Lu, Shuai-Fei Hu, Ya-She Li, Xu Su, Wen-Yang Dong, Cong-Ai Zhen, Run-Qiang Liu, Fan-Bin Kong, Ming-Wang Shi, Xi-Ling Chen
Summary: The study revealed that miRNAs differentially expressed in response to Imidacloprid play a crucial regulatory role in the metabolism of S. miscanthi to Imidacloprid. Twenty-three miRNAs were significantly up-regulated and 54 miRNAs were significantly down-regulated in S. miscanthi nymphs treated with Imidacloprid, and changing the abundance of specific miRNAs can alter the susceptibility of S. miscanthi to Imidacloprid. Additionally, smi-miR-278 and smi-miR-316 are confirmed to be involved in post-transcriptional regulation.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2021)
Article
Oncology
Minghui Wang, Huilin Liu, Wenyao Wu, Jinxia Zhao, Guanghui Song, Xi Chen, Rong Wang, Changfeng Shao, Jing Li, Haiyan Wang, Qing Wang, Xiaodong Feng
Summary: This study identified three differentially expressed lncRNAs in plasma of breast cancer patients. The results suggest that these three lncRNAs could serve as potential diagnostic biomarkers for breast cancer.
CLINICAL BREAST CANCER
(2022)
Article
Agriculture, Dairy & Animal Science
Shaokang Zhao, Tingting Chen, Xinmao Luo, Shiyi Chen, Jie Wang, Songjia Lai, Xianbo Jia
Summary: Cattle-yak is an excellent hybrid of cattle and yak, characterized by better meat quality and stronger adaptability to harsh environments. However, male sterility of cattle-yak restricts the transmission of heterosis. By analyzing the mRNA and lncRNA expression profiles of cattle, yak, and cattle-yak, this study identified differentially expressed genes related to male sterility, providing a theoretical basis for breeding work.
Article
Oncology
O. Sipos, H. Tovey, J. Quist, S. Haider, S. Nowinski, P. Gazinska, S. Kernaghan, C. Toms, S. Maguire, N. Orr, S. C. Linn, J. Owen, C. Gillett, S. E. Pinder, J. M. Bliss, A. Tutt, M. C. U. Cheang, A. Grigoriadis
Summary: This study found that patients with triple negative breast cancer who had certain measures of structural chromosomal instability and lacked high-level amplifications benefited more from carboplatin treatment compared to docetaxel within the TNT trial.
ANNALS OF ONCOLOGY
(2021)
Article
Oncology
Jelmar Quist, Lawson Taylor, Johan Staaf, Anita Grigoriadis
Summary: Breast cancer is a complex disease where integrative analyses are needed to identify clinically relevant patterns. A computational framework was developed to identify subtypes of breast cancer with distinct molecular mechanisms. The approach demonstrated reproducibility and robustness in assessing clinical outcomes.
Article
Cell Biology
Liliana D. Ordonez, Lorenzo Melchor, Kirsty R. Greenow, Howard Kendrick, Giusy Tornillo, James Bradford, Peter Giles, Matthew J. Smalley
Summary: In this study, researchers targeted specific genetic alterations to mammary epithelial cells using CRE-activated HER2 orthologue, revealing that in a HER2 breast cancer model, factors such as cell-of-origin, reproductive history, gene amplification, and WNT signaling pathway activation interact to drive inter-tumour heterogeneity.
DISEASE MODELS & MECHANISMS
(2021)
Article
Oncology
Jessica Castro, Giusy Tornillo, Gerardo Ceada, Beatriz Ramos-Neble, Marlon Bravo, Marc Ribo, Maria Vilanova, Matthew J. Smalley, Antoni Benito
Summary: Despite significant improvements in cancer treatment over the past few decades, cancer remains a leading cause of death worldwide. Targeting cancer stem cells (CSCs) is crucial for improving clinical outcomes, as these cells can survive treatment, leading to cancer relapse, therapy resistance, and metastasis. Studying the effects of human ribonuclease variants on tumor cells and CSCs in 3D environments shows potential for inhibiting cell growth and metastasis.
Article
Genetics & Heredity
Esther H. Lips, Tapsi Kumar, Anargyros Megalios, Lindy L. Visser, Michael Sheinman, Angelo Fortunato, Vandna Shah, Marlous Hoogstraat, Emi Sei, Diego Mallo, Maria Roman-Escorza, Ahmed A. Ahmed, Mingchu Xu, Alexandra W. Van den Belt-Dusebout, Wim Brugman, Anna K. Casasent, Karen Clements, Helen R. Davies, Liping Fu, Anita Grigoriadis, Timothy M. Hardman, Lorraine M. King, Marielle Krete, Petra Kristel, Michiel de Maaker, Carlo C. Maley, Jeffrey R. Marks, Brian A. Menegaz, Lennart Mulder, Frank Nieboer, Salpie Nowinski, Sarah Pinder, Jelmar Quist, Carolina Salinas-Souza, Michael Schaapveld, Marjanka K. Schmidt, Abeer M. Shaaban, Rana Shami, Mathini Sridharan, John Zhang, Hilary Stobart, Deborah Collyar, Serena Nik-Zainal, Lodewyk F. A. Wessels, E. Shelley Hwang, Nicholas E. Navin, P. Andrew Futreal, Alastair M. Thompson, Jelle Wesseling, Elinor J. Sawyer
Summary: A genomic analysis of ductal carcinoma in situ (DCIS) samples reveals that a significant portion of invasive breast cancer recurrences are unrelated to the initial DCIS and have distinct clonal origins. This finding is crucial for accurately assessing the risk of DCIS, developing effective treatment strategies, and identifying predictive biomarkers.
Article
Biochemistry & Molecular Biology
Dalia Tarantino, Callum Walker, Daniel Weekes, Helen Pemberton, Kathryn Davidson, Gonzalo Torga, Jessica Frankum, Ana M. Mendes-Pereira, Cynthia Prince, Riccardo Ferro, Rachel Brough, Stephen J. Pettitt, Christopher J. Lord, Anita Grigoriadis, Andrew N. J. Tutt
Summary: HORMAD1 expression is usually limited to germline cells, but it becomes mis-expressed in epithelial cells in triple-negative breast cancers, leading to increased genomic instability. Through cell line modeling and small interfering RNA screening, we identified candidate genes associated with cellular growth in HORMAD1-expressing cells. Our study reveals the dependency of replication stress tolerance pathways on HORMAD1 expression, providing potential new approaches for treating this disease group.
Article
Oncology
Anthony Cheung, Alicia M. Chenoweth, Jelmar Quist, Heng Sheng Sow, Christina Malaktou, Riccardo Ferro, Ricarda M. Hoffmann, Gabriel Osborn, Eirini Sachouli, Elise French, Rebecca Marlow, Katie E. Lacy, Sophie Papa, Anita Grigoriadis, Sophia N. Karagiannis
Summary: This study demonstrates that suboptimal dosing of the CDK2 inhibitor SNS-032 reduces the viability of TNBC cells and upregulates PD-L1 expression in surviving cancer cells. Additionally, SNS-032 treatment promotes the infiltration of human immune cells in TNBC tumors. Combination therapy of suboptimal SNS-032 and anti-PD-L1 antibody significantly restricts tumor growth. These findings suggest that suboptimal CDK inhibition may enhance the effectiveness of checkpoint immunotherapy in TNBC.
Review
Oncology
Isobelle Wall, Victoire Boulat, Aekta Shah, Kim R. M. Blenman, Yin Wu, Elena Alberts, Dinis Pedro Calado, Roberto Salgado, Anita Grigoriadis
Summary: The tumor microenvironment (TME), lymph nodes (LNs), and peripheral blood form the interconnected immune sites in breast cancer. Understanding the dynamic interaction between these immune sites is crucial for improving anti-cancer responses and therapeutic outcomes in breast cancer patients.
Article
Oncology
Grace Edmunds, Sam Beck, Kedar Umakant Kale, Irena Spasic, Dan O'Neill, David Brodbelt, Matthew J. Smalley
Summary: This study found associations between breed, age, and neuter status with the development and characteristics of canine mammary neoplasms. Smaller breeds were more likely to have mammary epithelial-origin tumors, while neutered dogs had a higher risk of malignant diseases. However, there was no breed with increased odds of both malignant disease and multiple lesions. This analysis supports the hypothesis that age, neuter status, and intrinsic biological and genetic factors contribute to the biological heterogeneity of canine mammary neoplasms.
JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA
(2023)
Review
Oncology
Mengyuan Li, Angela Quintana, Elena Alberts, Miu Shing Hung, Victoire Boulat, Merce Marti Ripoll, Anita Grigoriadis
Article
Oncology
Hannah Si Hui Lau, Veronique Kiak Mien Tan, Benita Kiat Tee Tan, Yirong Sim, Jelmar Quist, Aye Aye Thike, Puay Hoon Tan, Shazib Pervaiz, Anita Grigoriadis, Kanaga Sabapathy
Summary: This study reveals the regional heterogeneity in both tumors and peri-tumoral stroma of invasive breast carcinomas, providing insights into the importance of peri-tumoral heterogeneity in the evolution and treatment of breast cancers. A pro-inflammatory adipose-enriched peri-tumoral subtype is identified, which is significantly associated with poorer overall survival in breast cancer patients.
Proceedings Paper
Engineering, Biomedical
Nikhil Cherian Kurian, Amit Lohan, Gregory Verghese, Nimish Dharamshi, Swati Meena, Mengyuan Li, Fangfang Liu, Cheryl Gillet, Swapnil Rane, Anita Grigoriadis, Amit Sethi
Summary: In this work, we address two shortcomings of the U-Net architecture for medical image segmentation. Firstly, we propose adding multiscale feature maps to improve accuracy for target regions with significant variations in shape and size. Secondly, we introduce auxiliary confidence maps and utilize bootstrapping properties to improve accuracy when annotations are noisy or incomplete. Experimental results on a private dataset show substantial improvement over baselines.
2022 IEEE 22ND INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING (BIBE 2022)
(2022)
Article
Oncology
Micaela Harrasser, Satyen Harish Gohil, Hiu Lau, Marco Della Peruta, Vincent Muczynski, Dominic Patel, Elena Miranda, Kristiana Grigoriadis, Anita Grigoriadis, David Granger, Rachel Evans, Amit Chunilal Nathwani
Summary: The research team developed a new generation of ROR1-targeting inducible armored CAR platform, which can release an immune stimulating payload only in the presence of target tumor cells, enhancing the therapeutic activity of CAR-T cells and showing significant survival advantages in TNBC mouse models.
BREAST CANCER RESEARCH
(2022)
Article
Cell Biology
Richard E. Beatson, Ana C. Parente-Pereira, Leena Halim, Domenico Cozzetto, Caroline Hull, Lynsey M. Whilding, Olivier Martinez, Chelsea A. Taylor, Jana Obajdin, Kim Ngan Luu Hoang, Benjamin Draper, Ayesha Iqbal, Tom Hardiman, Tomasz Zabinski, Francis Man, Rafael T. M. de Rosales, Jinger Xie, Fred Aswad, Daniela Achkova, Chung-Yang Ricardo Joseph, Sara Ciprut, Antonella Adami, Helge G. Roider, Holger Hess-Stumpp, Balazs Gyorffy, Jelmar Quist, Anita Grigoriadis, Anette Sommer, Andrew N. J. Tutt, David M. Davies, John Maher
Summary: Expanding circulating Vγ9Vδ2 T cells in specific culture medium can enhance the therapeutic efficacy and activity of γδT cells in cancer immunotherapy, particularly showing potential treatment activity in leukemia and solid tumor models.
CELL REPORTS MEDICINE
(2021)
Article
Cell Biology
Tamara Muliaditan, Leena Halim, Lynsey M. Whilding, Benjamin Draper, Daniela Y. Achkova, Fahima Kausar, Maya Glover, Natasha Bechman, Appitha Arulappu, Jenifer Sanchez, Katie R. Flaherty, Jana Obajdin, Kristiana Grigoriadis, Pierre Antoine, Daniel Larcombe-Young, Caroline M. Hull, Richard Buus, Peter Gordon, Anita Grigoriadis, David M. Davies, Anna Schurich, John Maher
Summary: Second generation (2G) and third generation (3G) chimeric antigen receptors (CARs) show remarkable efficacy in treating hematological malignancies, but the clinical impact of 3G CARs has been somewhat muted. Designing and using parallel (p)CARs, which co-express a CD28+CD3z CAR with a 41BB-containing chimeric co-stimulatory receptor, optimally harnesses synergistic and tumor-dependent co-stimulation to resist T cell exhaustion and senescence, maintaining proliferation, cytokine release, cytokine signaling, and metabolic fitness upon repeated stimulation.
CELL REPORTS MEDICINE
(2021)