Article
Biochemistry & Molecular Biology
Yanhong Wang, Na Li, Yanping Zheng, Anqing Wang, Chunlei Yu, Zhenbo Song, Shuyue Wang, Ying Sun, Lihua Zheng, Guannan Wang, Lei Liu, Jingwen Yi, Yanxin Huang, Muqing Zhang, Yongli Bao, Luguo Sun
Summary: KIAA1217 plays a crucial role in hepatocellular carcinoma (HCC) metastasis by promoting cell migration and invasion through inducing epithelial-mesenchymal transition (EMT), and activating JAK1/2 and STAT3. It interacts with the Notch and Wnt/β-catenin pathways to facilitate HCC metastasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Eunjeong Kang, Jihye Seo, Haelim Yoon, Sayeon Cho
Summary: Epithelial-mesenchymal transition (EMT) plays a key role in both normal development and pathology, regulated by EMT-inducing transcription factors (EMT-TFs) to control the up- and down-regulation of specific proteins. This process is crucial for cancer metastasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Medicinal
Paola De Cicco, Giuseppe Ercolano, Gian Carlo Tenore, Angela Ianaro
Summary: This study investigated the effects of an extract from olive tree leaves (OLE) on metastatic melanoma, a highly aggressive and deadly form of skin cancer. The results showed that OLE inhibited melanoma cell proliferation, migration, invasion, and colonies formation both in vitro and in vivo. These effects were attributed to the targeting of mitogen-activated protein kinase and PI3K pathways. The findings suggest that OLE has the potential to be a new add-on therapy for the management of metastatic melanoma.
PHYTOTHERAPY RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Fernando Toshio Ogata, Alex Yuri Simoes Sato, Lucia Coppo, Roberto Jun Arai, Arnold Ira Stern, Hugo Pequeno Monteiro
Summary: The epithelial/mesenchymal transition (EMT) is associated with tumor metastasis. Cancer cells have high levels of antioxidants, such as the Trx/TrxR and GSH/Grx systems, to counteract oxidative and nitrosative stress. These systems play a significant role in EMT signaling and cancer cell progression.
ANTIOXIDANTS & REDOX SIGNALING
(2022)
Article
Biotechnology & Applied Microbiology
Hao-Ming Shen, Di Zhang, Ping Xiao, Bin Qu, Yi-Fan Sun
Summary: In this study, researchers investigated the role of long non-coding RNA KDM4A-AS1 in hepatocellular carcinoma (HCC). They found that elevated levels of KDM4A-AS1 were associated with poor prognosis in HCC. It was discovered that KDM4A-AS1 maintained the stability of AURKA mRNA by recruiting ILF3, thus regulating HCC progression through the PI3K/AKT pathway. The findings suggest that E2F1 and KDM4A-AS1 may serve as potential prognostic targets for HCC treatment.
CANCER GENE THERAPY
(2023)
Review
Oncology
Meina Jiang, Shuai Fang, Xiaodong Zhao, Chengwei Zhou, Zhaohui Gong
Summary: EMT plays a crucial role in cancer development, especially in lung carcinoma. CircRNAs are involved in EMT-related cell invasion and metastasis, and may become promising biomarkers and therapeutic targets in cancer management.
CANCER BIOLOGY & MEDICINE
(2021)
Article
Oncology
Yuxiang Liu, Taolin Chen, Mingyue Guo, Yu Li, Qian Zhang, Guixiang Tan, Li Yu, Yongjun Tan
Summary: FOXP2, a language-related gene, interacts with FOXA2 in breast cancer cells to inhibit EMT by activating the transcription of certain genes like E-cadherin and PHF2. The results suggest a collaborative role of FOXP2 and FOXA2 in regulating EMT in breast cancer cells.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jayashree Jayachandran, Harini Srinivasan, Krishna Priya Mani
Summary: Epithelial to mesenchymal transition (EMT) is a crucial biological process that plays a significant role in both embryonic development and various diseases. During EMT, epithelial cells lose their characteristics and acquire mesenchymal properties, with involvement of various transcription factors and miRNAs.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Review
Biochemistry & Molecular Biology
Fu Peng, Huali Fan, Sui Li, Cheng Peng, Xiaoqi Pan
Summary: MicroRNAs have been utilized as negative regulators in cancer treatment by down-regulating their targets, especially in the EMT process. Natural plant compounds can modulate deregulated microRNAs to inhibit EMT, which could potentially lead to the inhibition of cancer development. This review article highlights the significance of microRNAs in EMT as oncogenes and tumor suppressor genes, providing evidence for target therapy in cancer treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Bingfeng Luo, Yuan Yuan, Yifei Zhu, Songwu Liang, Runan Dong, Jian Hou, Ping Li, Yaping Xing, Zhenquan Lu, Richard Lo, Guan-Ming Kuang
Summary: miRNA-145-5p was found to negatively regulate EMT, inhibit Pca bone metastasis, and promote apoptosis. It may serve as a potential target for treating Pca with bone metastases.
FRONTIERS IN ONCOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Agata Poniewierska-Baran, Sylwia Sluczanowska-Glabowska, Paulina Malkowska, Olga Sierawska, Lukasz Zadroga, Andrzej Pawlik, Paulina Niedzwiedzka-Rystwej
Summary: Melanoma is an aggressive and progressive skin cancer that develops from melanocytes. Understanding the mechanisms behind its transformation is crucial. The study of metastasis mechanisms is important for comprehending neoplastic cell biology. MicroRNA (miRNA) plays a role in various steps of the metastatic process. This review discusses the involvement of miRNA molecules in the development and progression, as well as the immune response, to melanoma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, Research & Experimental
Shuang Liu, Xi Chen, Siqing Zhang, Xinyu Wang, Xiaoliu Du, Jiahe Chen, Guoping Zhou
Summary: This study revealed that miR-106b-5p plays a role in regulating pulmonary fibrosis and epithelial-mesenchymal transition in asthma by targeting SIX1 through E2F1, suggesting a potential therapeutic target for asthma treatment.
INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE
(2021)
Article
Cell Biology
Katharina Scheibner, Silvia Schirge, Ingo Burtscher, Maren Buettner, Michael Sterr, Dapeng Yang, Anika Boettcher, Ansarullah, Martin Irmler, Johannes Beckers, Filippo M. Cernilogar, Gunnar Schotta, Fabian J. Theis, Heiko Lickert
Summary: The mesoderm is formed by classical EMT, while the endoderm is formed independently of Snail1 through epithelial cell plasticity mechanisms. Foxa2 acts as an epithelial gatekeeper and EMT suppressor, protecting the endoderm from undergoing a mesenchymal transition.
NATURE CELL BIOLOGY
(2021)
Article
Oncology
Ana Pavlic, Kristian Urh, Katarina Stajer, Emanuela Bostjancic, Nina Zidar
Summary: The study analyzed the expression of the miR-200 family as EMT markers and their target genes in colorectal carcinoma. It found partial EMT at the invasive tumor front and partial MET in metastases based on miR-200 family and its target genes expression.
FRONTIERS IN ONCOLOGY
(2021)
Article
Medicine, Research & Experimental
Vignesh Ramesh, Paradesi Naidu Gollavilli, Luisa Pinna, Mohammad Aarif Siddiqui, Adriana Martinez Turtos, Francesca Napoli, Yasmin Antonelli, Aldo Leal-Egana, Jesper Foged Havelund, Simon Toftholm Jakobsen, Elisa Le Boiteux, Marco Volante, Nils Joakim Faergeman, Ole N. Jensen, Rasmus Siersbaek, Kumar Somyajit, Paolo Ceppi
Summary: This study found an inverse association between short-chain fatty acids and EMT in non-small cell lung cancer patients. In vitro experiments showed that propionate treatment enhanced the epithelial transcriptional program and reduced the EMT phenotype in lung cancer cell lines. Animal experiments also confirmed that propionate can reduce lung cancer metastasis and lymph node spread. Further mechanistic investigation revealed that propionate treatment caused chromatin remodeling through p300-mediated histone acetylation.
EMBO MOLECULAR MEDICINE
(2023)
Review
Oncology
Geoffray Monteuuis, Ulf Schmitz, Veronika Petrova, Padraic S. Kearney, John E. J. Rasko
Summary: Intron retention in cancer, previously overlooked as an artifact, is now recognized as a widespread phenomenon contributing to the transcriptional diversity of many cancers. Dysregulation of cellular mechanisms leading to aberrant intron retention has been highlighted in numerous studies in cancer, emphasizing its role in cancer pathogenesis and therapeutic resistance.
Article
Biochemistry & Molecular Biology
Adel B. Alharbi, Ulf Schmitz, Amy D. Marshall, Darya Vanichkina, Rajini Nagarajah, Melissa Vellozzi, Justin J. L. Wong, Charles G. Bailey, John E. J. Rasko
Summary: CTCF acts as a master regulator of gene transcription and chromatin organisation, with haploinsufficiency linked to tumor development and hypermethylation. Reduced levels of CTCF in different tissues led to tissue-specific differences in gene expression and alternative splicing. In liver and kidney, CTCF haploinsufficiency resulted in increased intron retention, particularly affecting genes related to cytoskeletal organization, splicing, and metabolism.
Article
Genetics & Heredity
Bhavani S. Kowtharapu, Jyoti Damaraju, Nitesh Kumar Singh, Josefin Ziebart, Rainer Bader, Dirk Koczan, Oliver Stachs
Summary: In this study, the effects of AC EFs on corneal epithelial cell gene and protein expression profiles were investigated. The results show that AC EFs have no harmful effects on epithelial cell function, and influence biological processes related to organic substances, chemicals, or external stimuli. Both gene and protein arrays activate pathways such as cytokine-cytokine receptor interaction, MAPK, and IL-17 signaling pathways. The protein array data demonstrate enrichment of various signaling pathways through interconnected networks.
Review
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Adel B. Alharbi, Ulf Schmitz, Charles G. Bailey, John E. J. Rasko
Summary: Decades of research have identified CTCF as a ubiquitous chromatin organizing factor and master regulator of gene expression, with a newly discovered role in regulating alternative splicing. CTCF's regulation of AS involves mechanisms such as transcriptional elongation, DNA methylation, histone modifications, and splicing factor expression, contributing to the complexity of the transcriptome. Further exploration of CTCF's role in splicing regulation may reveal it as a 'conductor of the splicing orchestra' due to its multiple connections.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Charles G. Bailey, Shailendra Gupta, Cynthia Metierre, Punkaja M. S. Amarasekera, Patrick O'Young, Wunna Kyaw, Tatyana Laletin, Habib Francis, Crystal Semaan, Mehdi Sharifi Tabar, Krishna P. Singh, Charles G. Mullighan, Olaf Wolkenhauer, Ulf Schmitz, John E. J. Rasko
Summary: The study shows that mutations in CTCF in cancer can have different impacts on its anti-proliferative effects and transcriptional regulatory activities, leading to disruption or enhancement of DNA binding. These mutations contribute to diverse cellular phenotypes by affecting cell growth regulation and gene regulatory activities.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Bijay P. Dhungel, Geoffray Monteuuis, Caroline Giardina, Mehdi S. Tabar, Yue Feng, Cynthia Metierre, Sarah Ho, Rajini Nagarajah, Angela R. M. Fontaine, Jaynish S. Shah, Divya Gokal, Charles G. Bailey, Ulf Schmitz, John E. J. Rasko
Summary: Chimeric RNA CLEC12A-MIR223HG, identified in CML patients, is widely expressed in both cancerous and normal tissues, potentially regulating the function of CLEC12A. Transcriptional activation of CLEC12A with the CRISPR/Cas9 system enhances the expression of CLEC12A-MIR223HG, leading to altered protein structure and function. This study provides insight into the characteristics and biological roles of chimeric RNAs and offers a template for further exploration in this field.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Eduard Gondas, Alzbeta Kralova Trancikova, Eva Baranovicova, Jakub Sofranko, Jozef Hatok, Bhavani S. Kowtharapu, Tomas Galanda, Dusan Dobrota, Peter Kubatka, Dietrich Busselberg, Radovan Murin
Summary: This study demonstrates that brain cancer cells have the ability to catabolize leucine and utilize it as a substrate for their metabolism. The results also suggest that leucine could potentially contribute to the synthesis of metabolites such as lipids in cancer cell metabolism. The findings provide new insights into the metabolic characteristics of brain cancer cells.
Editorial Material
Genetics & Heredity
Justin J. -L. Wong, Ulf Schmitz
Summary: Recent research has highlighted the physiological significance of intron retention (IR) in various domains of life and has uncovered unexpected functions in a wide range of biological processes. Despite significant progress in the field, there are still some challenges to be addressed, which, once overcome, will enable the discovery of more functions of IR.
TRENDS IN GENETICS
(2022)
Review
Biochemical Research Methods
Ryley Dorney, Bijay P. Dhungel, John E. J. Rasko, Lionel Hebbard, Ulf Schmitz
Summary: This review highlights the importance of gene fusions in cancer, including chromosomal rearrangement-independent fusion transcripts and complex fusion structures. It proposes a classification system for gene and transcript fusions and discusses the use of long-read sequencing and bioinformatic tools to detect and characterize fusions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Veronika Petrova, Renhua Song, Karl J. Nordstroem, Joern Walter, Justin J. L. Wong, Nicola J. Armstrong, John E. J. Rasko, Ulf Schmitz
Summary: This study investigates the regulation of intron retention in cells of the innate immune system and identifies the importance of chromatin accessibility and intrinsic characteristics of introns. The findings provide insights for understanding the pathogenic alterations linked to RNA processing and may contribute to the development of novel therapeutic approaches.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Mehdi Sadeghi, Mohammad Reza Karimi, Amir Hossein Karimi, Nafiseh Ghorbanpour Farshbaf, Abolfazl Barzegar, Ulf Schmitz
Summary: In this study, a differentially expressed co-expression module of mRNAs in EMT-type gastric tumors was identified using Weighted Gene Co-expression Network Analysis (WGCNA). Through network analysis and linear discriminant analysis, mRNA motifs and microRNA-based models with strong prognostic and diagnostic relevance were determined. Additionally, the DMD/ITGA1/CAV1 motif was identified as the top motif with consistent relevance to prognosis. The molecular functions of the identified models indicate the central roles of MAPK, Hh, and cGMP/cAMP signaling in the pathology of the EMT subtype of gastric cancer and highlight their potential utility in precision therapeutic approaches.
Review
Biochemistry & Molecular Biology
Siyuan Wu, Ulf Schmitz
Summary: Single-cell sequencing technologies have revolutionized life sciences and biomedical research by providing high-resolution data on cell heterogeneity. Computational algorithms and mathematical models have been developed to make sense of the data and simulate biological processes, leading to breakthroughs in understanding cell differentiation and tissue composition. Long-read sequencing technologies have further enhanced the investigation of alternative splicing, isoform expression, genome assembly, and the detection of complex structural variants.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Rhys Gillman, Matt A. Field, Ulf Schmitz, Rozemary Karamatic, Lionel Hebbard
Summary: Cancer, a heterogeneous disease with a strong genetic component, can benefit from precision medicine approaches to identify molecular drivers. Single-tumour methods based on gene interaction networks have limitations and require further research for evaluation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Oncology
Jaynish S. S. Shah, Michael J. G. Milevskiy, Veronika Petrova, Amy Y. M. Au, Justin J. L. Wong, Jane E. E. Visvader, Ulf Schmitz, John E. J. Rasko
Summary: After years of neglect, the importance of intron retention (IR) in cancer has been recognized. Many tumors are associated with increased IR, while breast cancer is the only tumor type with reduced IR. It was found that normal breast tissue has unusually high IR, and low IR in breast tumors is associated with poor prognosis.
BREAST CANCER RESEARCH
(2022)