Review
Biochemistry & Molecular Biology
Zhiyong Ding, Nan Wang, Ning Ji, Zhe-Sheng Chen
Summary: The complexity of proteomes in liquid biopsy samples and the limitations of proteomic technologies compared to high-plex sequencing technologies have hindered the development of proteomics. However, novel protein technologies are urgently needed for biomarker discovery in cancer liquid biopsies. Traditional and innovative proteomic technologies are being rapidly developed and have greatly facilitated early detection, diagnosis, prognosis, and monitoring of cancer evolution.
Article
Neurosciences
Meng Jin, Ruidie Shi, Daili Gao, Baokun Wang, Ning Li, Xia Li, Attila Sik, Kechun Liu, Xiujun Zhang
Summary: This study aims to identify a promising biomarker for Parkinson's disease (PD) using reverse phase protein array (RPPA) technology and in vivo verification. The biomarker discovered can facilitate early intervention in PD, leading to improved treatment effectiveness and reduced disease morbidity.
CNS NEUROSCIENCE & THERAPEUTICS
(2023)
Article
Engineering, Chemical
Miao Tian, HuiJuan Xu, Lei Yao, Rong Wang
Summary: A green antimicrobial lysozyme nanofilm was developed and successfully reduced membrane fouling by introducing remarkable antibacterial and antifouling properties. The protein-based biomaterial demonstrated a safe and environmentally friendly way of antimicrobials, showing significant potential for reducing membrane fouling in membrane filtration applications.
Article
Chemistry, Medicinal
Laura J. Kingsley, Xiaohui He, Matthew McNeill, John Nelson, Victor Nikulin, Zhiwei Ma, Wenshuo Lu, Vicki W. Zhou, Mari Manuia, Andreas Kreusch, Mu-Yun Gao, Darbi Witmer, Mei-Ting Vaillancourt, Min Lu, Sarah Greenblatt, Christian Lee, Ajay Vashisht, Steven Bender, Glen Spraggon, Pierre-Yves Michellys, Yong Jia, Jacob R. Haling, Gerald Lelais
Summary: LONP1 is an AAA+ protease essential for maintaining mitochondrial homeostasis, with its inhibitors potentially promoting cancer cell proliferation. This study describes the development of selective boronic acid-based LONP1 inhibitors and the structures of human LONP1 in complex with various inhibitors, providing valuable tools for investigating LONP1 biology.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Oncology
Caroline Xue, Eva Corey, Taranjit S. Gujral
Summary: Metastatic prostate cancer is a leading cause of male cancer deaths and has limited treatment options. The lack of preclinical models for advanced stage prostate cancer is a major barrier to understanding aggressive subtypes. In this study, we used LuCaP patient-derived xenograft models to represent the genomic and phenotypic features of human disease. Through comprehensive transcriptomic and proteomic profiling, we identified molecular markers associated with androgen receptor-positive and androgen receptor-null castration-resistant prostate cancers. Our findings suggest activation of specific pathways in these subtypes and highlight the importance of integrating transcriptomic and proteomic approaches in preclinical models for understanding poorly understood signaling pathways in metastatic prostate cancer.
Review
Chemistry, Multidisciplinary
Saurabh Shah, Mahavir Bhupal Chougule, Arun K. Kotha, Rama Kashikar, Chandraiah Godugu, Rajeev Singh Raghuvanshi, Shashi Bala Singh, Saurabh Srivastava
Summary: Millions of people die each year from viral infections, highlighting the urgent need to overcome current pitfalls in antiviral therapy. Nanomedicine offers a promising solution by using different types of nanoformulations to target the drawbacks in antiviral treatment.
JOURNAL OF CONTROLLED RELEASE
(2021)
Review
Fisheries
T. Encinas-Garcia, F. Mendoza-Cano, A. Muhlia-Almazan, Marco Porchas-Cornejo, A. Sanchez-Paz
Summary: The white spot syndrome virus (WSSV) has caused high mortalities and significant economic losses for the global shrimp aquaculture industry. This review provides a comprehensive understanding of the interaction between WSSV proteins and cell receptors, highlighting the importance of these molecules for WSSV pathogenesis. The findings suggest strategies for the development of therapeutic antivirals targeting critical components, which can be used in shrimp farming.
REVIEWS IN FISHERIES SCIENCE & AQUACULTURE
(2023)
Review
Biochemical Research Methods
Shaofeng Liao, Yujun Zhang, Yifei Qi, Zhuqing Zhang
Summary: Liquid-liquid phase separation (LLPS) of proteins and nucleic acids is crucial for the formation of biomolecular condensates in cells. Dysregulation of protein LLPS is associated with various difficult-to-treat diseases. Several tools have been developed to predict phase-separating proteins (PSPs) using different algorithms and datasets. In this study, we evaluated eleven PSPs predictors and found that FuzDrop, DeePhase, and PSPredictor performed well on folded proteins, while LLPhyScore was the best predictor for the human proteome. However, none of the predictors accurately identified experimentally verified non-PSPs. More diverse training sequences and the consideration of refined sequence patterns reflecting molecular interactions may improve the performance of PSPs prediction.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Oncology
John C. Dawson, Alison Munro, Kenneth Macleod, Morwenna Muir, Paul Timpson, Robert J. Williams, Margaret Frame, Valerie G. Brunton, Neil O. Carragher
Summary: Studied the mechanism of action of SRC inhibitor AZD0424 in cancer cells, confirming its ability to inhibit cell viability and reduce cell signaling pathway activation, especially with synergistic effects when used in combination with MEK inhibitors. Additionally, demonstrated that SRC inhibition is an effective way to block resistance to MEK inhibitors.
MOLECULAR ONCOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Chhavi Choudhary, Keshav Kumar Meghwanshi, Nidhi Shukla, Jayendra Nath Shukla
Summary: RNA interference (RNAi) is a post-transcriptional gene silencing process that has potential applications in gene function exploration and pest control. However, differential RNAi efficiency in insects poses a major challenge in developing RNAi-based pesticides.
Article
Cell Biology
Demin Xu, Xiangyang Chen, Yan Kuang, Minjie Hong, Ting Xu, Ke Wang, Xinya Huang, Chuanhai Fu, Ke Ruan, Chengming Zhu, Xuezhu Feng, Shouhong Guang
Summary: Two types of nucleoli exist in C. elegans, with one type lacking nucleolar vacuoles and having evenly distributed rRNA transcription and processing factors, while the other type contains nucleolar vacuoles and accumulates these factors exclusively in the periphery rim. The nucleolar vacuoles contain nucleoplasmic proteins and can exchange contents with the nucleoplasm. This finding reveals the dynamic regulation of nucleolar structure in C. elegans.
Article
Chemistry, Multidisciplinary
Molly Kozminsky, Thomas R. Carey, Lydia L. Sohn
Summary: DNA-directed patterning offers versatility in immobilizing and segregating lipid-based nanoparticles for subsequent analysis, providing a wide variety of custom assays for the characterization of any lipid-based nanoparticle with high control and precision.
Review
Agronomy
Ritesh G. Jain, Karl E. Robinson, Sassan Asgari, Neena Mitter
Summary: RNA interference (RNAi) is a promising approach for managing hemipteran pests, but commercial implementation faces challenges such as limited knowledge about dsRNA uptake mechanisms and RNAi gene functions. This review highlights recent progress in RNAi-based studies aimed at reducing insect populations, viral transmission, and insecticide resistance in hemipteran pests. It also explores potential solutions to improve RNAi-mediated management of hemipteran insects, including in silico approaches and formulation of dsRNA effector to minimize off-target effects and improve broad-spectrum pest control.
PEST MANAGEMENT SCIENCE
(2021)
Article
Microbiology
Qun Wang, Qi Su, Bowen Liu, Yan Li, Wanli Sun, Yanxue Liu, Ruyu Xue, Shuang Chang, Yixin Wang, Peng Zhao
Summary: This study developed a treatment method for combating ALV in vitro culture system by using a combination of AZT and shRNA targeting ALV. The results showed that this method significantly improved antiviral efficacy with low cytotoxicity.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Veterinary Sciences
Elspeth M. Waugh, Hayley Haining, James Harvie, Alison E. Ridyard, P. David Eckersall
Summary: The automated VET-SAA assay is a robust, precise, and accurate method for measuring feline SAA levels, providing valuable insights into identifying patients with inflammatory diseases in feline medicine.
BMC VETERINARY RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Esra Cicek, Ayca Circir, Merve Oyken, Ozge Akbulut Caliskan, Didem Naz Dioken, Sezen Guntekin Ergun, Rengul Cetin-Atalay, Aysegul Sapmaz, Huib Ovaa, Ozgur Sahin, Ayse Elif Erson-Bensan
Summary: SNX3 plays a critical role in the EGFR network in triple-negative breast cancer, with increased interaction between SNX3 and EGFR upon EGF stimulation, affecting cell proliferation and migration, and correlating with relapse-free survival in breast cancer patients.
Article
Oncology
Ridho Assidicky, Unal Metin Tokat, Ibrahim Oguzhan Tarman, Ozge Saatci, Pelin Gulizar Ersan, Umar Raza, Hasan Ogul, Yasser Riazalhosseini, Tolga Can, Ozgur Sahin
Summary: In this study, we identified fibronectin (FN1) as a central driver gene in chemoresistance. Overexpression of miR-326 reversed FN1-driven chemoresistance by targeting the FN1 receptor, ITGA5. miR-326 expression was downregulated by increased hypoxia/HIF1A and ECM stiffness in chemoresistant tumors, leading to upregulation of ITGA5 and activation of the downstream FAK/Src signaling pathways. Overexpression of miR-326 or inhibition of ITGA5 overcame FN1-driven chemotherapy resistance in vitro by inhibiting the FAK/Src pathway and potentiated the efficacy of chemotherapy in vivo. Importantly, lower expression of miR-326 or higher levels of predicted miR-326 target genes were significantly associated with worse overall survival in chemotherapy-treated TNBC patients.
BREAST CANCER RESEARCH AND TREATMENT
(2022)
Meeting Abstract
Oncology
Marcus Bauer, Martina Vetter, Ana Maia, Efstathios Vlachavas, Brigitta Michels, Mireia Berdiel-Acer, Kathleen Schuler, Alessandra Morselli, Manio Skarlatou, Christoph Thomssen, Stefan Wiemann
Article
Oncology
Xiaoya Li, Birgitta Elisabeth Michels, Oyku Ece Tosun, Janine Jung, Jolane Kappes, Susanne Ibing, Nishanth Belugali Nataraj, Shashwat Sahay, Martin Schneider, Angelika Woerner, Corinna Becki, Naveed Ishaque, Lars Feuerbach, Bernd Hessling, Dominic Helm, Rainer Will, Yosef Yarden, Karin Muller-Decker, Stefan Wiemann, Cindy Koerner
Summary: This study investigates the functions of miRNAs and their 5'isomiRs. The results show that three variants of miR-183-5p are highly expressed and regulate cell proliferation and invasion in different ways. Proteomic analysis reveals that miR-183-5p vertical bar+2 modulates the cell cycle by directly targeting E2F1. Gene set enrichment analysis suggests that the activity of E2F correlates with the expression of miR-183-5p. This study demonstrates that different isomiRs from the same pre-miRNA may have different functions, collectively contributing to the same phenotype.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Multidisciplinary Sciences
Josefine Radke, Naveed Ishaque, Randi Koll, Zuguang Gu, Elisa Schumann, Lina Sieverling, Sebastian Uhrig, Daniel Huebschmann, Umut H. Toprak, Cristina Lopez, Xavier Pastor Hostench, Simone Borgoni, Dilafruz Juraeva, Fabienne Pritsch, Nagarajan Paramasivam, Gnana Prakash Balasubramanian, Matthias Schlesner, Shashwat Sahay, Marc Weniger, Debora Pehl, Helena Radbruch, Anja Osterloh, Agnieszka Korfel, Martin Misch, Julia Onken, Katharina Faust, Peter Vajkoczy, Dag Moskopp, Yawen Wang, Andreas Joedicke, Lorenz Truemper, Ioannis Anagnostopoulos, Dido Lenze, Ralf Kueppers, Michael Hummel, Clemens A. Schmitt, Otmar D. Wiestler, Stephan Wolf, Andreas Unterberg, Roland Eils, Christel Herold-Mende, Benedikt Brors, Reiner Siebert, Stefan Wiemann, Frank L. Heppner
Summary: This study profiles the genomic and transcriptomic landscape of primary lymphomas of the central nervous system (PCNSL) and identifies common mutations in immune pathways and upregulated TERT gene expression. It also reveals distinct pathway differences between PCNSL and other primary CNS lymphomas, as well as DLBCL.
NATURE COMMUNICATIONS
(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
Biochemistry & Molecular Biology
Mithil Soni, Ozge Saatci, Gourab Gupta, Yogin Patel, Manikanda Raja Keerthi Raja, Jie Li, Xinfeng Liu, Peisheng Xu, Hongjun Wang, Daping Fan, Ozgur Sahin, Hexin Chen
Summary: The study reveals the crucial role of miR-489 in regulating estrogen signaling and tamoxifen resistance in breast cancer. miR-489 negatively regulates estrogen receptor signaling and overexpression of miR-489 can restore tamoxifen sensitivity in resistant cells. Additionally, miR-489 disrupts the positive feed-forward loop in breast cancer cells and functions as a transcription factor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Ashish Noronha, Nishanth Belugali Nataraj, Joo Sang Lee, Benny Zhitomirsky, Yaara Oren, Sara Oster, Moshit Lindzen, Saptaparna Mukherjee, Rainer Will, Soma Ghosh, Arturo Simoni-Nieves, Aakanksha Verma, Rishita Chatterjee, Simone Borgoni, Welles Robinson, Sanju Sinha, Alexander Brandis, D. Lucas Kerr, Wei Wu, Arunachalam Sekar, Suvendu Giri, Youngmin Chung, Diana Drago-Garcia, Brian P. Danysh, Mattia Lauriola, Michelangelo Fiorentino, Andrea Ardizzoni, Moshe Oren, Collin M. Blakely, Jideofor Ezike, Stefan Wiemann, Laxmi Parida, Trever G. Bivona, Rami Aqeilan, Joan S. Brugge, Aviv Regev, Gad Getz, Eytan Ruppin, Yosef Yarden
Summary: EGFR inhibitors activate endogenous mutators in lung cancer cells, leading to drug resistance. Inhibiting this process can prevent drug resistance.
Article
Multidisciplinary Sciences
Madeleine Reilly, Iryna Benilova, Azadeh Khalili-Shirazi, Christian Schmidt, Parvin Ahmed, Daniel Yip, Parmjit S. Jat, John Collinge
Summary: There is an urgent need to develop disease-modifying therapies for neurodegenerative diseases. Prion diseases serve as a paradigm to study such diseases and understand their common mechanisms. The study shows that highly purified prions are not directly neurotoxic and develops a cell-based assay to specifically detect prion disease-associated neurotoxicity. The findings have important implications for the development of prion disease therapeutics.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Savroop Bhamra, Parineeta Arora, Szymon W. Manka, Christian Schmidt, Craig Brown, Melissa L. D. Rayner, Peter-Christian Klohn, Anthony R. Clarke, John Collinge, Parmjit S. Jat, Louise C. Serpell
Summary: The N-terminal residues within PrPC, specifically amino acids 105-111 in CC2, are necessary for the propagation of four different mouse prion strains. These residues mediate the ordering of unstructured CC2 into infectious prion fibrils.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Cell Biology
Alhaji H. Janneh, Mohamed Faisal Kassir, F. Cansu Atilgan, Han Gyul Lee, Megan Sheridan, Natalia Oleinik, Zdzislaw Szulc, Christina Voelkel-Johnson, Hung Nguyen, Hong Li, Yuri K. Peterson, Elisabetta Marangoni, Ozge Saatci, Ozgur Sahin, Michael Lilly, Carl Atkinson, Stephen Tomlinson, Shikhar Mehrotra, Besim Ogretmen
Summary: This study reveals how oncogenic sphingosine 1-phosphate (S1P) metabolism activates C3 complement and induces NLRP3/inflammasome activation, enhancing cell migration/metastasis. Furthermore, activation of the S1PR1/C3/PPIL1/NLRP3 signaling axis is associated with metastatic melanoma, and targeting this axis can prevent lung colonization/metastasis.
Article
Biochemistry & Molecular Biology
Ozge Saatci, Ozge Akbulut, Metin Cetin, Vitali Sikirzhytski, Meral Uner, Deniz Lengerli, Elizabeth C. C. O'Quinn, Martin J. J. Romeo, Burcu Caliskan, Erden Banoglu, Sercan Aksoy, Aysegul Uner, Ozgur Sahin
Summary: Centrosome amplification (CA) is a key characteristic of cancer, associated with aggressive disease and poor clinical outcomes. Transforming Acidic Coiled-Coil Containing Protein 3 (TACC3) is overexpressed in tumors with CA and plays a crucial role in ensuring proliferation and survival of cancer cells with CA. TACC3 forms distinct functional interactomes in mitosis and interphase, interacting with Kinesin Family Member C1 (KIFC1) and nucleosome remodeling and deacetylase (NuRD) complex to regulate mitotic progression and G1/S progression, respectively.
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Engineering, Electrical & Electronic
Arda Secme, Uzay Tefek, Burak Sari, Hadi Sedaghat Pisheh, H. Dilara Uslu, Ozge Akbulut Caliskan, Berk Kucukoglu, Ramazan Tufan Erdogan, Hashim Alhmoud, Ozgur Sahin, M. Selim Hanay
Summary: Microwave sensors combined with optical sensing can be used to probe material properties and track size changes of microscale objects. In this study, we designed and fabricated two types of planar sensors, the CPW resonator and the SRR, to detect single cells and particles. The results show that microwave sensing technology can serve as a complementary technique for single-cell biophysical experiments and microscale pollutant screening.
IEEE SENSORS JOURNAL
(2023)
Article
Clinical Neurology
Simon Mead, Azadeh Khalili-Shirazi, Caroline Potter, Tzehow Mok, Akin Nihat, Harpreet Hyare, Stephanie Canning, Christian Schmidt, Tracy Campbell, Lee Darwent, Nicola Muirhead, Nicolette Ebsworth, Patrick Hextall, Madeleine Wakeling, Jacqueline Linehan, Vincenzo Libri, Bryan Williams, Zane Jaunmuktane, Sebastian Brandner, Peter Rudge, John Collinge
Summary: This study evaluated the use of an anti-PrPC monoclonal antibody (PRN100) as a treatment for human prion diseases. The results showed that PRN100 treatment was safe and achieved encouraging concentrations in the cerebrospinal fluid and brain tissue.
Article
Oncology
Svenja Kemmer, Mireia Berdiel-Acer, Eileen Reinz, Johanna Sonntag, Nooraldeen Tarade, Stephan Bernhardt, Mirjam Fehling-Kaschek, Max Hasmann, Ulrike Korf, Stefan Wiemann, Jens Timmer
Summary: Breast cancer subtypes differ in their treatment and prognosis due to the expression and activity of different receptors. The HER2 subtype has been successfully targeted with anti-HER2 therapies, and this study explores whether the HER2 receptor and downstream signaling network could be potential therapeutic targets beyond the HER2-positive subtype. The findings suggest that major parts of the intracellular signal transduction network are unchanged between subtypes, and alterations in this network could render anti-HER therapies relevant beyond the HER2-positive subtype.