Article
Biochemistry & Molecular Biology
Karen G. Soans, Ana Patricia Ramos, Jaydeep Sidhaye, Abhijeet Krishna, Anastasia Solomatina, Karl B. Hoffmann, Raimund Schluessler, Jochen Guck, Ivo F. Sbalzarini, Carl D. Modes, Caren Norden
Summary: Cell migration is crucial for organismal development, but the influence of physical properties on migration phenomena in vivo remains unclear. In this study, the researchers used zebrafish optic cup formation to investigate the role of extracellular matrix (ECM) properties in cell migration. They found that rim cells migrate over an immobile ECM and require cryptic lamellipodia for movement. The topology of the ECM changes along the migration path and is accompanied by changes in cell-matrix interactions. Matrix porosity is linked to efficient migration.
Article
Biochemical Research Methods
Gaetan De Waele, Jim Clauwaert, Gerben Menschaert, Willem Waegeman
Summary: The adoption of current single-cell DNA methylation sequencing protocols is hindered by incomplete coverage, outlining the need for effective imputation techniques. By adapting the Transformer neural network architecture and combining axial attention with sliding window self-attention, the CpG Transformer shows state-of-the-art performances on various datasets. The CpG Transformer also demonstrates interpretability and rapid transfer learning properties, making it efficient for practitioners to train models on new datasets with limited computational resources and time constraints.
Article
Oncology
Aliki Ntzifa, Dora Londra, Theodoros Rampias, Athanasios Kotsakis, Vassilis Georgoulias, Evi Lianidou
Summary: In this study, DNA methylation analysis in plasma-cfDNA and paired CTCs of NSCLC patients during osimertinib therapy revealed that DNA methylation of selected genes could be a possible resistance mechanism. There was a low concordance between DNA methylation in plasma-cfDNA and CTC samples, indicating that they provide complementary information. When at least one of the selected genes was methylated, there was a statistically significant increase at PD compared to baseline, suggesting a potential role in osimertinib resistance.
Article
Chemistry, Physical
Yuxi Cheng, Junji Ren, Shumin Fan, Peiyao Wu, Wenshu Cong, Yuxing Lin, Shaojie Lan, Siyang Song, Bin Shao, Wenbing Dai, Xueqing Wang, Hua Zhang, Bo Xu, Wenzhe Li, Xia Yuan, Bing He, Qiang Zhang
Summary: It is observed that nanoparticles bind closely to specific types of extracellular matrix components, namely retraction fibers and migrasomes, which are located at the rear of tumor cells during their migration. This interaction alters cell morphology, limits cell motion range, and changes cell adhesion. Nanoparticles inhibit tumor cell removal and anti-metastasis potential is confirmed in vitro. Mechanically, nanoparticles form a rigid shell on the surface of migrasomes and retraction fibers, blocking their recognition, endocytosis, and elimination by surrounding tumor cells. This interference reduces the promotion effect of migrasomes on cell movement.
NANOSCALE HORIZONS
(2022)
Article
Biochemistry & Molecular Biology
Suza Mohammad Nur, Mohammed Razeeth Shait Mohammed, Mazin A. Zamzami, Hani Choudhry, Aamir Ahmad, Bushra Ateeq, Irfan A. Rather, Mohammad Imran Khan
Summary: In this study, it was found that tumor cells undergo metabolic reprogramming, including methylation regulation and changes in 1C metabolism, after detachment from the extracellular matrix, promoting cancer cell survival and metastasis.
Article
Chemistry, Multidisciplinary
Agnieszka Maria Jelen, Bartlomiej Strehl, Dagmara Szmajda-Krygier, Milena Pazik, Ewa Balcerczak
Summary: P-glycoprotein (P-gp) plays a role in lung cancer development, progression, and patient survival. Changes in ABCB1 expression level may be related to tumorigenesis and multidrug resistance (MDR). Epigenetic modifications, such as DNA methylation, also regulate the gene's activity. Our analysis found downregulated ABCB1 expression and associated methylation changes in lung cancer cells, with variations based on age, gender, ethnicity, and smoking cessation. Decreased transcript levels were linked to advanced cancer stage and lower survival probability. Notably, ABCB1 expression changes were often unique to specific tumor subtypes. Methylation promoter was identified as a cause of decreased gene expression in lung cancer cells. These findings establish ABCB1 as an important prognostic factor in lung cancer.
APPLIED SCIENCES-BASEL
(2023)
Article
Oncology
Weipeng Liu, Yunyun Zhang, Fengdan Huang, Qianli Ma, Chuanyin Li, Shuyuan Liu, Yan Liang, Li Shi, Yufeng Yao
Summary: The expression of EGFL7 and miR-126 is downregulated in non-small cell lung cancer (NSCLC) through methylation. The EGFL7/miR-126 polymorphism rs2297538 is associated with NSCLC risk.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemical Research Methods
Christos Maniatis, Catalina Vallejos, Guido Sanguinetti
Summary: Single-cell multi-omics assays provide unprecedented opportunities to explore epigenetic regulation at the cellular level. However, high levels of technical noise and data sparsity often result in a lack of statistical power in correlative analyses. SCRaPL is a novel computational tool that addresses this issue by carefully modeling noise in the experimental systems.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Mary L. Stackpole, Weihua Zeng, Shuo Li, Chun-Chi Liu, Yonggang Zhou, Shanshan He, Angela Yeh, Ziye Wang, Fengzhu Sun, Qingjiao Li, Zuyang Yuan, Asli Yildirim, Pin-Jung Chen, Paul Winograd, Benjamin Tran, Yi-Te Lee, Paul Shize Li, Zorawar Noor, Megumi Yokomizo, Preeti Ahuja, Yazhen Zhu, Hsian-Rong Tseng, James S. Tomlinson, Edward Garon, Samuel French, Clara E. Magyar, Sarah Dry, Clara Lajonchere, Daniel Geschwind, Gina Choi, Sammy Saab, Frank Alber, Wing Hung Wong, Steven M. Dubinett, Denise R. Aberle, Vatche Agopian, Steven-Huy B. Han, Xiaohui Ni, Wenyuan Li, Xianghong Jasmine Zhou
Summary: Early cancer detection using cell-free DNA faces challenges of low tumor DNA fraction, molecular heterogeneity, and limited sample sizes. In this study, the authors developed a cost-effective method called cfMethyl-Seq to profile the methylome of cell-free DNA and detect and locate cancer. The approach achieved high sensitivity and accuracy for detecting and identifying the tissue-of-origin of various cancer types.
NATURE COMMUNICATIONS
(2022)
Article
Materials Science, Biomaterials
Eunji Shin, Tae Yoon Kwon, Youngbin Cho, Youngjin Kim, Jennifer H. Shin, Yong-Mahn Han
Summary: Changes in the extracellular matrix (ECM) influence stem cell fate. Differentiation of human embryonic stem cells (hESCs) on Matrigel coated onto PDMS (Matrigel_PDMS) resulted in an increase in focal adhesion and YAP/TEF1 activation, promoting pancreatic endoderm (PE)-associated gene transcription. YAP activation in PE cells was mediated by integrin alpha 3-FAK-CDC42-PP1A signaling, and pancreatic islet-like organoids (PIOs) generated on Matrigel_PDMS secreted more insulin than those on Matrigel_TCPS. The unique mucus-like network structure of Matrigel_PDMS directly upregulated focal adhesion, leading to better maturation of hESCs' pancreatic development in vitro.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2023)
Article
Biochemical Research Methods
Sapir Margalit, Yotam Abramson, Hila Sharim, Zohar Manber, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Hayk Barseghyan, Ran Elkon, Roded Sharan, Yuval Ebenstein
Summary: This study explored the methylation status of enhancer-promoter pairs using long-read optical methylome data, and developed various analysis approaches for deconvolving cell-type mixtures. Results showed that these pairs can be used for detecting rare cancerous transformations in a given cell population, with accurate estimates obtained through promoter methylation and enhancer-promoter pairwise methylation analysis. Additionally, the analysis can be applied to resolve different cell populations of the same cell type in subtle scenarios.
Review
Cell Biology
Anetta Sulewska, Lothar Pilz, Christian Manegold, Rodryg Ramlau, Radoslaw Charkiewicz, Jacek Niklinski
Summary: Epigenetic research has the potential to improve our understanding of the pathogenesis of non-small-cell lung cancer and personalize the management of the disease. Epigenetic alterations are relevant for early detection, diagnosis, outcome prediction, and tumor response to therapy. Epi-drugs as therapeutic modalities may recover genes delaying tumor growth and be effective against tumors without druggable mutations.
Review
Biochemistry & Molecular Biology
Jongseong Ahn, Sunghoon Heo, Jihyun Lee, Duhee Bang
Summary: DNA methylation is an important epigenetic mechanism linked to mammalian cellular differentiation, gene expression regulation, and diseases. This review outlines single-cell DNA methylation profiling methods, including experimental strategies and computational data analysis, as well as highlights blind spots in basic analysis and recent alternatives. It also introduces well-known applications and discusses future developments in the field.
Article
Multidisciplinary Sciences
Elham Sheykhi, Behnaz Shojaedin-Givi, Batool Sajad, Hossein Naderi-Manesh, Sharareh Tavaddod
Summary: Total-internal reflection fluorescence (TIRF) microscope is a unique technique that selectively excites fluorophore molecules at specific positions in a cellular environment. Quantitative analysis has been a challenge due to the strong dependence of excitation intensity on the axial position of the molecules. This study presents an easy-implemented data analysis method that characterizes fluorescent signals quantitatively without considering intensity values. The proposed method is applicable for characterizing F-actin patches and analyzing their spatio-temporal distribution at the cell's contact area.
SCIENTIFIC REPORTS
(2022)
Review
Oncology
Vasiliki Zolota, Vasiliki Tzelepi, Zoi Piperigkou, Helen Kourea, Efthymia Papakonstantinou, Maria-Ioanna Argentou, Nikos K. Karamanos
Summary: Current data suggest that epigenetic alterations play a key role in the initiation and subclonal evolution of breast cancer, especially in the aggressive molecular subgroup of triple-negative breast cancer. The extracellular matrix undergoes significant structural alterations during cancer progression, which are closely linked with epigenetic modifiers. Targeting tumor microenvironment and epigenetic pathways may provide potential therapeutic strategies, particularly in triple-negative breast cancer where standard chemotherapy is limited.
Article
Biochemistry & Molecular Biology
Yunxia Ma, Desiree Charlotte Schroeder, Miljana Nenkov, Maryam Noor Rizwan, Mohamed Abubrig, Juergen Sonnemann, Jose M. Murrieta-Coxca, Diana M. Morales-Prieto, Martin Westermann, Nikolaus Gassler, Yuan Chen
Summary: The study suggests that decreased EMP1 expression is significantly associated with increased tumor size in NSCLC, while overexpression of EMP2 can suppress tumor cell growth, migration, and invasion, and affect cell cycle.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Miljana Nenkov, Yunxia Ma, Nikolaus Gassler, Yuan Chen
Summary: Colorectal carcinoma is a common cancer characterized by metabolic reprogramming that provides tumor cells with energy and nutrients for malignant growth. The metabolic crosstalk between tumor cells, the tumor microenvironment, and gut microbiota facilitates the development and therapy resistance of colorectal carcinoma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
