Article
Medicine, Research & Experimental
Elham Fakhr, Fatemeh Zare, Kayhan Azadmanesh, Ladan Teimoori-Toolabi
Summary: LEF1 plays an important role in the chemo-resistance of colorectal cancer cells, with downregulation of the long isoform making cells more sensitive to chemotherapy through reduced proliferation, increased apoptosis, or cell cycle arrest. Balancing the expression of long and short isoforms of LEF1 is crucial in overcoming chemo-resistance.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Multidisciplinary Sciences
Lishan Fang, Dane Ford-Roshon, Max Russo, Casey O'Brien, Xiaozhe Xiong, Carino Gurjao, Maximilien Grandclaudon, Srivatsan Raghavan, Steven M. Corsello, Steven A. Carr, Namrata D. Udeshi, James Berstler, Ewa Sicinska, Kimmie Ng, Marios Giannakis
Summary: The RNF43 G659fs mutation is an oncogenic mutation in colorectal cancer and sensitizes tumor cells to PI3K/mTOR inhibition. PI3K/mTOR inhibitors demonstrate promising antitumor activity in cells and models carrying RNF43_p.G659fs mutations, possibly by regulating PI3K signaling and interferon response gene expression.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Fangyuan Zhou, Haiyang Gao, Luorui Shang, Jinxiao Li, Mengqi Zhang, Shuhan Wang, Runze Li, Lin Ye, Shenglan Yang
Summary: Traditional Chinese medicine therapy has a unique effect in prolonging survival time and improving the prognosis of patients with colorectal cancer. Oridonin has anti-cancer effects, possibly through inducing ER stress, upregulating TP53, and inhibiting TCF4 transactivation in colorectal cancer cells.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2023)
Article
Multidisciplinary Sciences
Jing Li, Yuchen Sun, Xuanzi Sun, Xu Zhao, Yuan Ma, Yuzhu Wang, Xiaozhi Zhang
Summary: The study found that AEG-1 is overexpressed in glioma tissues, and its silencing can increase the sensitivity of glioma cells to TMZ and promote DNA damage. Silencing AEG-1 can also reduce M2 polarization of microglia and decrease the secretion of tumor supportive cytokines IL-6 and TGF-beta 1.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Hao Wang, Wei Wei, Zhong-Yuan Zhang, Yao Liu, Bin Shi, Wen Zhong, Hou-Shun Zhang, Xin Fang, Chun-Lei Sun, Jia-Bei Wang, Lian-Xin Liu
Summary: Metastasis in colorectal cancer (CRC) remains a major challenge, and dysregulation of N6-methyladenosine (m6A) is associated with this process. This study reveals that METTL14, a key component of m6A methylation, plays a role in inhibiting CRC metastasis by regulating the ARRDC4/ZEB1 signaling pathway. METTL14 regulates ARRDC4 mRNA stability through YHTDF2, and its protein expression is controlled by TCF4 and HuR. Clinical studies show that decreased METTL14 is associated with poor prognosis in CRC patients.
CELL DEATH & DISEASE
(2022)
Article
Genetics & Heredity
Yanming Lin, Jinmei Li, Shujun Li, Yuting Chen, Yiping Luo, Yongcun Wang, Zhixiong Yang
Summary: This study found that LINC00482 is upregulated in NSCLC tissues and cells, and it enhances the expression of CLASRP by recruiting E2F1, thereby affecting cell proliferation, apoptosis, and DDP sensitivity in NSCLC. Knockdown of LINC00482 can restrict tumor growth and enhance DDP sensitivity in NSCLC.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Multidisciplinary Sciences
Mohammad Shariq, Vinaya Sahasrabuddhe, Sreevatsan Krishna, Swathi Radha, Nruthyathi, Ravishankara Bellampalli, Anukriti Dwivedi, Rajit Cheramangalam, Boris Reizis, Jean Hebert, Hiyaa S. Ghosh
Summary: In this study, it was found that adult hippocampal neural progenitors have a latent inflammatory potential that is proactively suppressed by the transcription factor Tcf4. Deletion of Tcf4 leads to loss of proliferative capacity and acquisition of myeloid inflammatory properties in progenitors, ultimately resulting in inflammation in the niche. Tcf4 is identified as a critical regulator that facilitates adult neurogenesis by suppressing this detrimental potential.
Article
Oncology
Fanqi Meng, Chunlong Ai, Guoqiang Yan, Guangyi Wang
Summary: This study reveals the potential role of ZNF24 in reducing 5-FU resistance in CRC cells by suppressing the Wnt pathway and activating p53 signaling, offering a potential strategy for managing chemoresistance in CRC.
EXPERIMENTAL CELL RESEARCH
(2023)
Article
Medicine, Research & Experimental
Federica Laudisi, Teresa Pacifico, Claudia Maresca, Anderson Luiz-Ferreira, Sara Antonelli, Angela Ortenzi, Alfredo Colantoni, Antonio Di Grazia, Eleonora Franze, Marco Colella, Davide Di Fusco, Giuseppe S. Sica, Ivan Monteleone, Giovanni Monteleone, Carmine Stolfi
Summary: Colorectal cancer is a major cause of cancer-related death, and current treatments are not effective against advanced disease. Researchers have found that the anthelmintic drug rafoxanide can enhance the sensitivity of colorectal cancer cells to TRAIL, a targeted therapy. This discovery suggests that rafoxanide could be a potential treatment option for overcoming TRAIL resistance in colorectal cancer.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Multidisciplinary Sciences
Simone Di Franco, Barbara Parrino, Miriam Gaggianesi, Vincenzo Davide Pantina, Paola Bianca, Annalisa Nicotra, Laura Rosa Mangiapane, Melania Lo Iacono, Gloria Ganduscio, Veronica Veschi, Ornella Roberta Brancato, Antonino Glaviano, Alice Turdo, Irene Pillitteri, Lorenzo Colarossi, Stella Cascioferro, Daniela Carbone, Camilla Pecoraro, Micol Eleonora Fiori, Ruggero De Maria, Matilde Todaro, Isabella Screpanti, Girolamo Cirrincione, Patrizia Diana, Giorgio Stassi
Summary: Limited therapeutic options are available for advanced colorectal cancer (CRC). Exposure to NORA234 initially reduces the proliferative and clonogenic potential of CR-CSphCs but leads to the selection of a resistant compartment expressing high levels of CD44v6 and Wnt pathway activity. The combination of NORA234 and CHK1 targeting induces synthetic lethality in both CD44v6-negative and CD44v6-positive CRC stem cell fractions.
Article
Multidisciplinary Sciences
Jana Koch, Dina Moench, Annika Maass, Christian Gromoll, Thomas Hehr, Tobias Leibold, Hans J. Schlitt, Marc-H. Dahlke, Philipp Renner
Summary: The study demonstrates that 3D cell cultures exhibit higher resistance to radiation therapy and certain chemotherapeutic drugs compared to 2D cell cultures, underscoring the importance of considering these differences in future approaches to modeling human diseases.
Article
Cell Biology
Weijia Li, Xibo Zhao, Rujian Zhang, Jiabin Xie, Guangmei Zhang
Summary: This study aims to investigate the role of NLRP3 in cisplatin resistance in ovarian cancer. It was found that NLRP3 is overexpressed in ovarian cancer and is associated with poor survival. Silencing NLRP3 gene can inhibit the malignant process of cisplatin-resistant ovarian cancer cells.
MEDIATORS OF INFLAMMATION
(2023)
Article
Biochemistry & Molecular Biology
Abdulraheem Alshareef, Anthea C. Peters, Pascal Gelebart, Will Chen, Raymond Lai
Summary: The constitutive activation of the Wnt canonical pathway (WCP) in mantle cell lymphoma (MCL) is mainly due to gene methylation/silencing of WIF1, which promotes cell growth. Gene transfection of WIF1 into cells significantly reduces cell growth and results in downregulation of various proteins in WCP.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Food Science & Technology
Jinkyung Lee, Chan Ho Jang, Yoonsu Kim, Jisun Oh, Jong-Sang Kim
Summary: This study examined the ability of quercetin to sensitize colorectal cancer cells to oxaliplatin by inhibiting glutathione reductase activity. The combination of quercetin and oxaliplatin was found to synergistically inhibit glutathione reductase activity, reduce cell viability, and increase reactive oxygen species production. Addition of sulforaphane further enhanced the anti-cancer efficacy of this combination therapy in a mouse model.
Article
Oncology
Yan Zhou, Leping Yang, Li Xiong, Kunpeng Wang, Xuyang Hou, Qinglong Li, Fanhua Kong, Xi Liu, Jun He
Summary: Colorectal cancer is a common cancer of the digestive tract, often treated with chemotherapy drugs like oxaliplatin. KIF11, a key protein in cell division, is overexpressed in CRC tissues and its knockdown leads to tumor growth arrest and increased sensitivity to oxaliplatin. This suggests KIF11 could potentially serve as an oncogene and biomarker for assessing chemotherapy sensitivity in CRC.
Article
Oncology
Kristin Koerdel, Melanie Spitzner, Thomas Meyer, Niklas Engels, Florian Krause, Jochen Gaedcke, Lena-Christin Conradi, Martin Haubrock, Tim Beissbarth, Andreas Leha, Steven A. Johnsen, B. Michael Ghadimi, Stefan Rose-John, Marian Grade, Jurgen Wienands
Summary: Resistance of tumor cells to chemoradiotherapy represents a fundamental problem in clinical oncology. This study shows that blocking inflammatory cytokine receptor signaling via STAT3 can re-sensitize treatment-refractory cancer cells and inhibit tumor growth. STAT3 triggers treatment resistance by regulating the expression of RBPJ, the key transcriptional regulator of the NOTCH pathway.
Article
Education, Scientific Disciplines
Binia-Laureen Grebener, Janina Barth, Sven Anders, Tim Beissbarth, Tobias Raupach
Summary: This study investigated whether a prediction-based method can be used to evaluate student learning outcomes, finding that both self-assessments and predictions are valid sources of learning outcome measures and that low response rates are sufficient to produce stable results. Female students tend to overestimate their peers' performance, which should be taken into account when using a prediction-based approach.
Article
Biochemistry & Molecular Biology
Melanie Spitzner, Georg Emons, Karl Burkhard Schuetz, Hendrik A. Wolff, Stefan Rieken, B. Michael Ghadimi, Gunter Schneider, Marian Grade
Summary: The standard treatment for locally advanced esophageal cancer includes preoperative chemoradiotherapy followed by surgical resection, but 5-year survival rates remain low. New strategies are needed to improve outcomes. Inhibition of Wnt/β-catenin signaling can enhance the sensitivity of cancer cells with robust pathway activity to chemoradiotherapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Georg Emons, Noam Auslander, Peter Jo, Julia Kitz, Azadeh Azizian, Yue Hu, Clemens F. Hess, Claus Roedel, Ulrich Sax, Gabriela Salinas, Philipp Stroebel, Frank Kramer, Tim Beissbarth, Marian Grade, Michael Ghadimi, Eytan Ruppin, Thomas Ried, Jochen Gaedcke
Summary: A gene-expression based classifier was developed to identify over 1/3 of rectal cancer patients with a pathological complete response (pCR), while ensuring no non-complete-responders were misclassified. The classifier's performance was validated in three independent datasets, suggesting it could help select patients for a watch and wait strategy.
BRITISH JOURNAL OF CANCER
(2022)
Article
Oncology
Kerstin Menck, Darius Wlochowitz, Astrid Wachter, Lena-Christin Conradi, Alexander Wolff, Andreas H. Scheel, Ulrike Korf, Stefan Wiemann, Hans-Ulrich Schildhaus, Hanibal Bohnenberger, Edgar Wingender, Tobias Pukrop, Kia Homayounfar, Tim Beissbarth, Annalen Bleckmann
Summary: In this study, the inter- and intra-patient heterogeneity of colorectal cancer liver metastases (CRLM) was comprehensively characterized. The study found high heterogeneity in the WNT and EGFR pathways among the metastases. Through analyzing the associated master regulators and effectors, a specific gene signature was identified and correlated with clinical outcome in a large cohort of colorectal cancer patients and CRLM samples.
Article
Biochemical Research Methods
Florian Auer, Simone Mayer, Frank Kramer
Summary: Networks are commonly used to capture complex associations between biological entities. Cytoscape is a popular software for visualizing biological networks. The NDEx platform allows users to upload and share networks.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Editorial Material
Biology
Dominik Mueller, Inaki Soto-Rey, Frank Kramer
Summary: This paper provides an overview and interpretation guide for various metrics in medical image segmentation evaluation, and discusses common issues in evaluation. It proposes a guideline for standardized medical image segmentation evaluation to improve evaluation quality, reproducibility, and comparability.
BMC RESEARCH NOTES
(2022)
Article
Medicine, General & Internal
Fabian Bockhop, Katrin Cunitz, Marina Zeldovich, Anna Buchheim, Tim Beissbarth, York Hagmayer, Nicole von Steinbuechel
Summary: Psychopathological symptoms often occur after traumatic brain injury (TBI), causing increased burden on individuals and society. Previous studies on factors influencing PTSD, GAD, and MDD after TBI have been inconclusive due to methodological limitations. This study examined the impact of various factors on the clinical impairment and occurrence of PTSD, GAD, and MDD. The findings suggest that education level, pre-injury psychiatric history, injury cause, and functional recovery are associated with the severity and frequency of these symptoms.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Health Care Sciences & Services
Johann Frei, Frank Kramer
Summary: This study demonstrated the feasibility of obtaining and training a German medical NER model using a publicly available English data set through translation and word alignment. The NER model achieved an F-1 score of 0.82 on the test set using a simple network architecture. The limitations of this approach and potential solutions for future work were discussed.
JMIR FORMATIVE RESEARCH
(2023)
Article
Computer Science, Interdisciplinary Applications
Johann Frei, Frank Kramer
Summary: Obtaining text datasets with semantic annotations is crucial for supervised training in NLP, but it is a laborious process. Domain-specific NLP tasks often require custom-designed datasets to address task-specific needs. When working with non-English languages in medical data processing, issues arise with the lack of task-matching datasets and task-specific pre-trained models.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Article
Computer Science, Interdisciplinary Applications
Johann Frei, Ludwig Frei-Stuber, Frank Kramer
Summary: This article presents GERNERMED++, a statistical model for German medical natural language processing that achieves strong entity recognition performance by combining multiple techniques. It offers a baseline model for the German research community on medical NLP, addressing the scarcity of open, public medical entity recognition models for German texts.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Dominik Mueller, Silvan Mertes, Niklas Schroeter, Fabio Hellmann, Miriam Elia, Bernhard Bauer, Wolfgang Reif, Elisabeth Andre, Frank Kramer
Summary: COVID-19 presence classification and severity prediction are crucial for capacity planning of intensive care units. This study presents an approach that uses advanced techniques and models to predict the future severity of COVID-19 patients, achieving comparable results with other popular methods.
CARING IS SHARING-EXPLOITING THE VALUE IN DATA FOR HEALTH AND INNOVATION-PROCEEDINGS OF MIE 2023
(2023)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Florian Auer, Nadja Bramkamp (Beckmann), Simone Mayer, Dominik Mueller, Frank Kramer
Summary: Public repositories provide access and distribution of network-encoded biomedical results, but customized data structures and implementations are needed for integrating complementary information. The RCX extension hub offers overview and access to Cytoscape exchange format extensions implemented in R, supporting self-customized extensions through guides, example implementations, and a template for R extension packages creation.
CARING IS SHARING-EXPLOITING THE VALUE IN DATA FOR HEALTH AND INNOVATION-PROCEEDINGS OF MIE 2023
(2023)
Article
Computer Science, Software Engineering
Johann Frei, Frank Kramer
Summary: Recent advancements in natural language processing (NLP) have been achieved through the use of increasingly complex neural networks. In a clinical context, NLP is a crucial technique for extracting relevant information from unstructured texts such as clinical notes. This study evaluates the feasibility of training the neural model GERNERMED on annotated German training data generated by automated translation from a publicly available English dataset. The findings provide guidance to other researchers regarding the use of machine translation methods for dataset acquisition. The fact that the dataset is publicly available allows fellow researchers to use our trained software without any legal access restrictions.
Article
Computer Science, Information Systems
Dominik Mueller, Inaki Soto-Rey, Frank Kramer
Summary: This study analyzed the performance impact of three ensemble learning techniques (Augmenting, Stacking, and Bagging) in deep learning based medical image classification pipelines. The results showed that Stacking achieved the largest performance gain, with up to 13% F1-score increase. Augmenting and Bagging also showed consistent improvement capabilities.