Article
Oncology
Jing Zhang, Zhimin Hu, Calista A. Horta, Jing Yang
Summary: Epithelial-mesenchymal transition (EMT) is involved in various aspects of tumor development. The tumor microenvironment, consisting of different stroma cells and biochemical factors, influences the EMT program and tumor progression. This review explores the effects of tumor microenvironmental signals on EMT regulation, discusses the molecular mechanisms of EMT in therapy resistance, and proposes new therapeutic approaches targeting the tumor microenvironment to impact EMT and tumor progression.
SEMINARS IN CANCER BIOLOGY
(2023)
Article
Immunology
Sarthak Sahoo, Sonali Priyadarshini Nayak, Kishore Hari, Prithu Purkait, Susmita Mandal, Akash Kishore, Herbert Levine, Mohit Kumar Jolly
Summary: Recent research shows that cells with hybrid epithelial/mesenchymal characteristics can have high levels of PD-L1, important for immune evasion, without needing to fully undergo epithelial-mesenchymal transition. This cellular state in breast cancer is associated with resistance to anti-estrogen therapy.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Juliane Strietz, Stella S. Stepputtis, Marie Follo, Peter Bronsert, Elmar Stickeler, Jochen Maurer
Summary: Primary breast cancer stem cell (BCSC) cultures isolated from TNBC specimens have been established and shown to grow as tumor spheres under anchorage-independent culture conditions in vitro, while reliably forming tumors in mice when transplanted in limiting dilutions in vivo. Additionally, these BCSC xenograft tumors exhibit similar architecture and gene expression to the original patient tumor, suggesting a promising model for researching BCSC biology and testing new treatment options for TNBC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Daner Acunha Silveira, Shantanu Gupta, Marialva Sinigaglia, Jose Carlos Merino Mombach
Summary: The Wnt pathway plays a crucial role in regulating biochemical functions and cancer development. This study proposes a Boolean model of Wnt signaling in hepatocarcinoma and identifies new molecular circuits as well as their cooperation with known circuits. These findings provide insights into the mechanisms of Wnt signaling and offer potential therapeutic strategies for controlling cancer metastasis.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Ayalur Raghu Subbalakshmi, Bazella Ashraf, Mohit Kumar Jolly
Summary: The epithelial-mesenchymal transition (EMT) is a biological phenomenon that involves significant changes in cellular traits. EMT is now seen as a transition process involving diverse hybrid E/M phenotypes. These hybrid cells possess both epithelial and mesenchymal markers and/or functional traits and exhibit characteristics such as collective cell migration, enhanced tumor-initiating ability, and immune/targeted therapy-evasive features.
Article
Cell Biology
Wen Jia, Mohit Kumar Jolly, Herbert Levine
Summary: The epithelial-mesenchymal transition (EMT) is a crucial cellular process for wound healing, cancer metastasis, and embryonic development. Recent studies have shown that hybrid epithelial/mesenchymal states, possessing both epithelial and mesenchymal traits, play a significant role in cancer metastasis and resistance to therapies. NRF2 has been identified as a stabilizing factor for these hybrid states. This research incorporates a phenomenological epigenetic feedback effect into a computational model for EMT signaling and demonstrates its stabilizing effect on the hybrid state if NRF2 influences SNAIL at an epigenetic level.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Daner A. Silveira, Shantanu Gupta, Mariane da Cunha Jaeger, Caroline Brunetto de Farias, Jose Carlos Merino Mombach, Marialva Sinigaglia
Summary: This study proposes a logical EMT model for ES and highlights the involvement of ZEB2, miR-200, and miR-145 circuits in maintaining the hybrid states.
Article
Oncology
Ayalur Raghu Subbalakshmi, Sarthak Sahoo, Isabelle McMullen, Aaditya Narayan Saxena, Sudhanva Kalasapura Venugopal, Jason A. Somarelli, Mohit Kumar Jolly
Summary: Research shows that the transcription factor KLF4 can delay the onset of EMT by suppressing multiple EMT-TFs and promote a phenotypic shift towards a more epithelial state. KLF4 can also strengthen its influence on modulating EMT dynamics by inhibiting cell-state transitions at the epigenetic level.
Article
Biology
Thanh Thi Vuong-Brender, Sean Flynn, Yvonne Vallis, Mario de Bono
Summary: CAMTAs are ancient proteins expressed broadly in nervous systems, controlling neuronal CaM levels. Loss of CAMT-1, the sole C. elegans CAMTA, results in behavioral and neuronal Ca2+ signaling defects.
Article
Biochemistry & Molecular Biology
Hadil Onallah, Sheethal Thomas Mannully, Ben Davidson, Reuven Reich
Summary: The study demonstrates the important role of PLD isoenzymes in regulating migration, invasion, metastasis, and EMT in HGSC cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Xue-Kun Guo, Jiali Wang, Vincent P. van Hensbergen, Jintao Liu, Huji Xu, Xiaoyu Hu
Summary: This study reveals a unique pattern of crypt occupation by mucus-associated biofilms during early colitis, which is genetically dependent on bacterial biofilm-forming capacity and restricted by host epithelial O 1,2-fucosylation. Deficiency in O 1,2-fucosylation leads to increased crypt occupation by biofilms and exacerbated intestinal inflammation. Mechanistically, fucose from biofilm-occupied mucus suppresses biofilm formation and related genes. Additionally, fucose administration ameliorates experimental colitis, suggesting the therapeutic potential of fucose for biofilm-related disorders.
Article
Cell Biology
Tamotsu Sugai, Noriyuki Yamada, Mitsumasa Osakabe, Mai Hashimoto, Noriyuki Uesugi, Makoto Eizuka, Yoshihito Tanaka, Ryo Sugimoto, Naoki Yanagawa, Takayuki Matsumoto
Summary: The study aimed to analyze the expression patterns of cancer cell- and CAF-related proteins in SiCRC and found that high expression of Ki-67, p53, FAP-1, PDGFR-alpha, PDGFR-beta, and TWIST1 was correlated with lymph node metastasis.
Article
Multidisciplinary Sciences
Pei-Li Yao, Vipul M. Parmar, Mayur Choudhary, Goldis Malek
Summary: The expression and activity of NURR1 play critical roles in the physiological and pathological functions of human RPE cells. Targeting NURR1 may have therapeutic potential for AMD by improving EMT, inflammation, and lipid homeostasis in RPE cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Developmental Biology
K. Kusama, Y. Fukushima, K. Yoshida, H. Sakakibara, N. Tsubata, M. Yoshie, J. Kojima, H. Nishi, K. Tamura
Summary: The study revealed that hypoxia and proinflammatory factors induce EMT, cell migration, and inflammation in EECs, and the effect is enhanced by CXCL12 released from ESCs.
MOLECULAR HUMAN REPRODUCTION
(2021)
Article
Cell Biology
Kalliopi Tzavlaki, Yae Ohata, Anita Moren, Yukihide Watanabe, Jens Eriksson, Maiko Tsuchiya, Yuki Kubo, Kouhei Yamamoto, Mikael E. Sellin, Mitsuyasu Kato, Laia Caja, Carl-Henrik Heldin, Aristidis Moustakas
Summary: LKB1 pathway limits TGF beta-induced epithelial-mesenchymal transition, maintaining mammary epithelial morphogenesis. Downregulation of LKB1 expression in breast cancer is predicted to lead to increased epithelial-mesenchymal transition induced by SNAI1 and TGF beta family members.
JOURNAL OF CELLULAR PHYSIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Gianluca Selvaggio, Claudine Chaouiya, Florence Janody
Summary: The use of logical computational models combined with experimental validations is an effective approach to identify cooperative mechanisms and therapeutic strategies in the context of cancer biology. This method helps overcome difficulties and challenges in experimental models, improving our understanding of oncogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Engineering, Manufacturing
Alexandre Lemos, Pedro T. Monteiro, Ines Lynce
Summary: This paper introduces the UniCorT tool designed for solving university course timetabling problems specifically tailored for the 2019 International Timetabling Competition. The proposed approach includes pre-processing, the use of a MaxSAT solver, and a local search procedure. The success of the tool is evidenced by its ranking among the top five finalists in the ITC 2019 competition, showcasing the effectiveness of the techniques employed.
JOURNAL OF SCHEDULING
(2022)
Article
Biology
John Zobolas, Pedro T. Monteiro, Martin Kuiper, Asmund Flobak
Summary: Computational models are powerful tools for analyzing complex biological processes. Logic-based modeling enhances our understanding of biological systems. Defining rules for regulating biological entities' output activity is challenging, but boolean function metrics provide a framework for analyzing model parameterizations.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Review
Oncology
Maria Manuela Bras, Susana R. Sousa, Fatima Carneiro, Manfred Radmacher, Pedro L. Granja
Summary: This review discusses the mechanobiology of colorectal cancer (CRC) and explores the relationship between biophysical cues and biochemical pathways. It emphasizes the importance of understanding how mechanical cues influence cell behavior and CRC progression. The role of the tumor microenvironment, extracellular matrix, and stroma are also discussed, as well as the impact of cancer-associated fibroblasts and flow shear stress on CRC metastasis. Insights into how the knowledge of biophysical mechanisms may contribute to the development of new therapeutic strategies and targeting molecules are also presented.
Review
Biochemical Research Methods
Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noel, Henning Hermjakob, Tomas Helikar, Sylvain Soliman, Laurence Calzone
Summary: This article highlights the importance of using computational models in systems biology to study complex system dynamics. It discusses the need for improving the reusability of these models and their ability to reproduce virtual experiments through proper model annotation in community-supported and standardized formats.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Anna Niarakis, Juilee Thakar, Matteo Barberis, Maria Rodriguez Martinez, Tomas Helikar, Marc Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Draeger
Summary: The SysMod meeting is an interdisciplinary annual conference that brings together scientists interested in data-driven computational modeling, multi-scale mechanistic frameworks, large-scale -omics data, and bioinformatics. The 2021 meeting was conducted virtually and focused on the development and application of computational tools, approaches, and predictive models in biological systems, with an emphasis on disease mechanisms.
Article
Biochemical Research Methods
Elena Piretto, Gianluca Selvaggio, Damiano Bragantini, Enrico Domenici, Luca Marchetti
Summary: In this paper, a logical-based mathematical model was developed to study the cellular pathways involved in COVID-19 infection and analyze various drug treatments. The research found that single drugs have limited effects, while combination therapy can achieve better results. Specifically, the combination of the anti-inflammatory drug Baricitinib and the anti-viral drug Remdesivir showed significant benefits, and the triple combination of Baricitinib, Remdesivir, and the corticosteroid Dexamethasone demonstrated even stronger efficacy.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Oncology
M. Manuela Bras, Tania B. Cruz, Andre F. Maia, Maria Jose Oliveira, Susana R. Sousa, Pedro L. Granja, Manfred Radmacher
Summary: This study investigated the mechanical properties of colorectal cancer cells using atomic force microscopy and found a correlation between the mechanical properties and the migratory behavior of the cells.
Article
Biochemistry & Molecular Biology
Miguel Cacho Teixeira, Romeu Viana, Margarida Palma, Jorge Oliveira, Monica Galocha, Marta Neves Mota, Diogo Couceiro, Maria Galhardas Pereira, Miguel Antunes, Ines Costa, Pedro Pais, Carolina Parada, Claudine Chaouiya, Isabel Sa-Correia, Pedro Tiago Monteiro
Summary: YEASTRACT+ is a tool for analyzing, predicting, and modeling transcription regulatory data in yeasts at the gene and genomic levels. It incorporates three integrated databases and a community platform. It provides information on transcription regulation and DNA binding sites for multiple yeast species, and offers tools combining regulatory information with genome-scale metabolic models.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Lidia Faria, Sara Canato, Tito T. Jesus, Margarida Goncalves, Patricia S. Guerreiro, Carla S. Lopes, Isabel Meireles, Eurico Morais-de-Sa, Joana Paredes, Florence Janody
Summary: Alterations in P-cadherin expression or function influence tumor progression. P-cadherin is highly expressed in basal-like breast carcinomas and is involved in cancer cell renewal, migration, and invasion. In this study, a humanized P-cadherin Drosophila model was generated to investigate its role in vivo. The results showed that actin nucleators Mrtf and Srf are main effectors of P-cadherin in flies. These findings were validated in a human mammary epithelial cell line with conditional activation of the SRC oncogene. Knocking down P-cadherin or inhibiting F-actin polymerization impaired SRF transcriptional activity, while blocking Mrtf-A nuclear translocation hindered proliferation, self-renewal, and invasion.
DISEASE MODELS & MECHANISMS
(2023)
Review
Biochemistry & Molecular Biology
Komal Khalil, Alice Eon, Florence Janody
Summary: Animal cells exhibit diverse shapes, which result from the interaction between the plasma membrane and cytoskeleton macromolecules. Changes in cell shape are not only passive effects but also actively influence cell fate decisions. Alterations in cell shape can impact the transcriptional program through various mechanisms, including the regulation of physical links and signaling molecules. Anomalies in cell shape contribute to diseases, such as cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Proceedings Paper
Computer Science, Information Systems
Paulo Dias, Pedro T. Monteiro, Andreia Sofia Teixeira
Summary: Transcriptional regulatory networks control gene expression and allow organisms to respond to environmental disturbances. This study focuses on yeast species and aims to uncover the functions encoded in the regulatory network by detecting and comparing functional modules.
NETWORK SCIENCE (NETSCI-X 2022)
(2022)