Article
Biochemical Research Methods
Jeffrey Molendijk, Rui Yip, Benjamin L. Parker
Summary: We have developed a database for underrepresented post-translational modifications (PTMs) to accelerate the discovery of enriched protein modifications in experimental data. The database provides curated lists of proteins reported to be substrates of underrepresented modifications. We demonstrated the utility of the database through the analysis of previously published data. Additionally, we developed an online tool that integrates upstream transcription factor enrichment analysis with downstream pathway analysis through an easy-to-use interactive interface.
JOURNAL OF PROTEOME RESEARCH
(2022)
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: Microbial molecules from soil, seawater, and human bodies are among the least understood substances on Earth.
Article
Biochemical Research Methods
Frank Koopmans, Ka Wan Li, Remco V. Klaassen, August B. Smit
Summary: This article introduces a mass spectrometry downstream analysis pipeline (MS-DAP) that integrates popular and recently developed algorithms for data normalization and statistical analysis. It generates extensive data visualizations and quality reporting in standardized PDF reports, promoting transparent and reproducible proteome science.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Health Care Sciences & Services
Denis V. Petrovsky, Arthur T. Kopylov, Vladimir R. Rudnev, Alexander A. Stepanov, Liudmila I. Kulikova, Kristina A. Malsagova, Anna L. Kaysheva
Summary: The study demonstrates that using neural networks for analyzing metabolomic-proteomic HPLC-MS/MS data can effectively classify cancer pathologies and provide information on the proximity of studied phenotypes.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Review
Biochemical Research Methods
Rebecca Elizabeth Kattan, Deena Ayesh, Wenqi Wang
Summary: During intracellular signal transduction, protein-protein interactions (PPIs) play a critical role in regulating protein localization and function. Mass spectrometry-based interactome analysis has become a popular method for studying PPI networks, but the analysis of large datasets can be challenging. In this review, we discuss the methods and resources commonly used for analyzing large interactome-related proteomic data and propose a guideline for identifying novel interacting proteins.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Microbiology
Maciej Kochanowski, Joanna Dabrowska, Miroslaw Rozycki, Jacek Sroka, Jacek Karamon, Aneta Belcik, Weronika Korpysa-Dzirba, Tomasz Cencek
Summary: This study identified and characterized the excretory-secretory (ES) proteins of Anisakis simplex L3 larvae. A total of 158 proteins were detected, including allergens and pathogenicity-related proteins. Predicted host-parasite interactions between Anisakis ES proteins and both human and fish proteins were also identified.
Article
Biochemical Research Methods
Andrea Laguillo-Gomez, Enrique Calvo, Noa Martin-Cofreces, Marta Lozano-Prieto, Francisco Sanchez-Madrid, Jesus Vazquez
Summary: Open-search methods with prior knowledge improve identification performance of protein post-translational modifications by minimizing experimental errors and precursor mass assignation. The introduction of a novel approach enables the study of a wider variety of PTMs, including unknown or unexpected modifications.
JOURNAL OF PROTEOMICS
(2023)
Article
Mechanics
Paolo Boldi, Ian Leifer, Hernan A. Makse
Summary: Graph fibrations are useful tools to uncover symmetries and cluster synchronization in biological networks, but the incompleteness and disordered nature of biological data make it challenging to apply the traditional definition and algorithms. This paper introduces the theory of quasifibrations to capture quasi-symmetry in such networks and provides an algorithmic solution for finding quasifibrations in networks with missing links and variability across samples. The algorithm is tested using real connectome data and synthetic networks, and it can help researchers find hidden symmetries in unknown or partially known networks, particularly in biological networks.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Engineering, Environmental
Dachuan Zhang, Ye Tian, Yu Tian, Huadong Xing, Sheng Liu, Haoyang Zhang, Shaozhen Ding, Pengli Cai, Dandan Sun, Tong Zhang, Yanhong Hong, Hongkun Dai, Weizhong Tu, Junni Chen, Aibo Wu, Qian-Nan Hu
Summary: The article introduces a new platform that integrates data-driven computational methods with experimental validation to predict toxin biotransformation and discover new metabolites. This platform will help explore the "dark matter" of toxin metabolites and promote the discovery of detoxification enzymes.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Jingrong Ma, Chuang Pan, Haiming Chen, Weijun Chen, Wenxue Chen, Ming Zhang, Qiuping Zhong
Summary: This study investigated the proteome of coconut meat using shotgun proteomics and protein-based bioinformatic analysis. A total of 1686 proteins were identified, including antioxidant proteins and globulins. Network analysis revealed the associations of globulins with Cupin and Oleosin sub-networks, and antioxidant proteins with glutathione metabolism and peroxisome sub-networks. The study also discovered that bioactive peptides, with antioxidant and emulsifying properties, can be obtained through in-silico digestion.
Article
Biochemistry & Molecular Biology
Yosui Nojima, Masahiko Aoki, Suyong Re, Hidekazu Hirano, Yuichi Abe, Ryohei Narumi, Satoshi Muraoka, Hirokazu Shoji, Kazufumi Honda, Takeshi Tomonaga, Kenji Mizuguchi, Narikazu Boku, Jun Adachi
Summary: This study investigated the anti-tumor efficacy of apatinib against gastric cancer cell lines and found that it differed among different cell lines. The study also revealed that apatinib acts as a multi-kinase inhibitor, predominantly targeting c-Kit. These findings contribute to a deeper understanding of the mechanism of action of apatinib in gastric cancer cells.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Computer Science, Artificial Intelligence
Hussain Ahmed Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita
Summary: This paper proposes an effective clustering method for scRNA-seq data, which integrates preprocessing steps and robust cell group identification. The method requires no user input, except for setting thresholds, and outperforms most other existing methods.
KNOWLEDGE-BASED SYSTEMS
(2022)
Article
Genetics & Heredity
Kimia Sadat Hashemi, Mohadese Koohi Aliabadi, Arian Mehrara, Elham Talebi, Ali Akbar Hemmati, Radin Dabbagh Rezaeiye, Mohammad Javad Ghanbary, Maryam Motealleh, Behnaz Dayeri, Shayan Khalili Alashti
Summary: This study utilized microarray bioinformatic analysis to identify potential biomarkers of AD by analyzing six microarray datasets of AD patients and control groups. The results identified CXCR4, TGFB1, ITGB1, MYH11, and SELE genes as hub genes in this study. These genes were significantly enriched in actin cytoskeleton regulation, ECM-receptor interaction, and hypertrophic cardiomyopathy. Additionally, multiple miRNAs exhibited significant interactions with most of the hub genes.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Kevin Klann, Christian Muench
Summary: We introduce a peptide-based linear mixed models tool, PBLMM, as a standalone desktop application for differential expression analysis of proteomics data. We also offer a Python package that enables streamlined data analysis workflows implementing the PBLMM algorithm. PBLMM, which uses peptide-based linear mixed regression models, is user-friendly and does not require scripting experience. Our study demonstrates that peptide-based models outperform classical methods in statistically inferring differentially expressed proteins. Furthermore, PBLMM exhibits superior statistical power, especially in situations with low effect size and/or low sample size.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2022)
Article
Biology
Hussain Ahmed Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita
Summary: scRNA-seq data analysis allows for identification of novel cells, specific characterization of known cells, and study of cell heterogeneity. Most clustering methods are influenced by user input, but UICPC shows excellent performance without requiring user input.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Oncology
Tiziana Triulzi, Giampaolo Bianchini, Serena Di Cosimo, Tadeusz Pienkowski, Young-Hyuck Im, Giulia Valeria Bianchi, Barbara Galbardi, Matteo Dugo, Loris De Cecco, Ling-Ming Tseng, Mei-Ching Liu, Begona Bermejo, Vladimir Semiglazov, Giulia Viale, Juan de la Haba-Rodriguez, Do-Youn Oh, Brigitte Poirier, Pinuccia Valagussa, Luca Gianni, Elda Tagliabue
Summary: In HER2-positive/ER-positive breast cancer, the 41-gene classifier TRAR has been identified as an independent predictor of pCR, serving as a promising tool to select patients responsive to anti-HER2-based neoadjuvant therapy and to assist in treatment escalation and de-escalation strategies.
MOLECULAR ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Marco Silvestri, Matteo Dugo, Marta Vismara, Loris De Cecco, Davide Lanzoni, Andrea Vingiani, Secondo Folli, Maria Carmen De Santis, Filippo de Braud, Giancarlo Pruneri, Serena Di Cosimo, Vera Cappelletti
Summary: This study analyzed the copy number alterations (CNAs) of triple negative breast cancer (TNBC) patients before and after neoadjuvant chemotherapy (NAC) using next-generation sequencing. The study revealed common CNAs on chromosomes 1, 2, and 8 in pre-treatment tumor samples, and identified MSH2, PRDM1, and PAX3 as genes associated with pathological complete response. CNAs detected after treatment involved genes within druggable pathways. Furthermore, the analysis of circulating tumor cells (CTCs) showed the impact of NAC on tumor evolution and driver event selection.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Rihan El Bezawy, Stefano Percio, Chiara Maura Ciniselli, Michelandrea De Cesare, Gennaro Colella, Matteo Dugo, Silvia Veneroni, Valentina Doldi, Silvia Martini, Dario Baratti, Shigeki Kusamura, Paolo Verderio, Marcello Deraco, Paolo Gandellini, Nadia Zaffaroni, Valentina Zuco
Summary: In this study, miR-550a-3p was found to be downregulated in DMPM patients and its expression levels were associated with patient outcome. Functional experiments showed that miR-550a-3p inhibited proliferation and invasiveness, enhanced apoptosis, and reduced tumor growth in DMPM cell lines and xenograft models. Similar antitumor effects were observed in prostate and ovarian cancer cell lines. The effects of miR-550a-3p were mediated, at least in part, by the inhibition of HSP90AA1 and its target proteins.
CANCER GENE THERAPY
(2022)
Meeting Abstract
Oncology
Maurizio Callari, Marco Barreca, Matteo Dugo, Barbara Galbardi, Lucia Vigano, Alberta Locatelli, Luca Licata, Giulia Viale, Pinuccia Valagussa, Giuseppe Viale, Luca Gianni, Giampaolo Bianchini
Meeting Abstract
Oncology
Matteo Dugo, Chiun-Sheng Huang, Daniel Egle, Begona Bermejo, Claudio Zamagni, Robert S. Seitz, Tyler J. Nielsen, Marc Thill, Antonio Anton, Stefania Russo, Eva Maria Ciruelos, Brock L. Schweitzer, Douglas T. Ross, Barbara Galbardi, Richard Greil, Vladimir Semiglazov, Balazs Gyorffy, Marco Colleoni, Catherine Kelly, Gabriella Mariani, Lucia Del Mastro, Pinuccia Valagussa, Giuseppe Viale, Maurizio Callari, Luca Gianni, Giampaolo Bianchini
Meeting Abstract
Oncology
Matteo Dugo, Chiun-Sheng Huang, Daniel Egle, Begona Bermejo, Claudio Zamagni, Robert S. Seitz, Tyler J. Nielsen, Marc Thill, Antonio Anton, Stefania Russo, Eva Maria Ciruelos, Brock L. Schweitzer, Douglas T. Ross, Barbara Galbardi, Richard Greil, Vladimir Semiglazov, Balazs Gyorffy, Marco Colleoni, Catherine Kelly, Gabriella Mariani, Lucia Del Mastro, Pinuccia Valagussa, Giuseppe Viale, Maurizio Callari, Luca Gianni, Giampaolo Bianchini
Meeting Abstract
Oncology
Maurizio Callari, Chiun-Sheng Huang, Daniel Egle, Begona Bermejo, Claudio Zamagni, Matteo Dugo, Marc Thill, Antonio Anton, Marco Barreca, Stefania Russo, Eva Maria Ciruelos, Richard Greil, Stefania Zambelli, Balazs Gyorffy, Chanel Smart, Olivia Biasi, Pinuccia Valagussa, Giuseppe Viale, Luca Gianni, Giampaolo Bianchini
Article
Oncology
Lucia Vigano, Alberta Locatelli, Adele Ulisse, Barbara Galbardi, Matteo Dugo, Diego Tosi, Carlo Tacchetti, Tiziana Daniele, Balazs Gyorffy, Lorenzo Sica, Marina Macchini, Milvia Zambetti, Stefania Zambelli, Giampaolo Bianchini, Luca Gianni
Summary: This study investigates the interplay between ER and HER2 and its impact on the growth and progression of ER-positive breast cancer. It finds that combination therapy can bypass resistance mechanisms and that RTK functional activation may be an alternative survival pathway in ER+/HER2(low) tumors.
CLINICAL CANCER RESEARCH
(2022)
Article
Oncology
Emanuela Fina, Loredana Cleris, Matteo Dugo, Mara Lecchi, Chiara Maura Ciniselli, Daniele Lecis, Giulia Valeria Bianchi, Paolo Verderio, Maria Grazia Daidone, Vera Cappelletti
Summary: The study highlights the importance of understanding the hematogenous phase of breast cancer metastasis and identifies genes associated with metastasis through transcriptome analysis of circulating tumor cells. These findings provide valuable information on disease progression and potential therapeutic targets.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Dermatology
Elisabetta Vergani, Adele Busico, Matteo Dugo, Andrea Devecchi, Barbara Valeri, Mara Cossa, Lorenza Di Guardo, Loris De Cecco, Erika Feltrin, Giorgio Valle, Paola Deho, Simona Frigerio, Luca Lalli, Gianfrancesco Gallino, Michele Del Vecchio, Mario Santinami, Giancarlo Pruneri, Elena Tamborini, Licia Rivoltini, Marialuisa Sensi, Viviana Vallacchi, Monica Rodolfo
Summary: The genetic landscape of melanoma resistance to targeted therapy with small molecules inhibiting BRAF and MEK kinases was explored in this study. Somatic alterations in resistant melanoma were characterized and their integration with transcriptional profiles revealed enrichment in gene families involved in oncogenic signaling pathways and DNA repair. The analysis also showed positive modulation of gene signatures associated with anabolic processes, chromatin alterations, and IFN-a response. MTORC1 signaling was found to be enriched in poorly responsive patients and resistant tumors. These findings provide insights into the genetic patterns underlying melanoma resistance and have implications for personalized therapies.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
Article
Oncology
Emanuela Minna, Paola Romeo, Matteo Dugo, Loris De Cecco, Antonella Aiello, Federico Pistore, Andrea Carenzo, Angela Greco, Maria Grazia Borrello
Summary: Medullary thyroid carcinoma (MTC) is a rare but aggressive tumor. The mechanisms underlying MTC development and associated signaling pathways are not fully understood. In this study, we analyzed mutation and gene expression profiles of 17 MTCs, including primary and metastatic tumors, and identified uncommon gene alterations. We also identified distinct signaling subtypes based on gene expression signatures. Our findings suggest that there are emerging gene drivers in MTC and highlight the importance of understanding the molecular subtypes of MTC.
Article
Oncology
Lorenzo Castagnoli, Simona Corso, Alma Franceschini, Alessandra Raimondi, Sara Erika Bellomo, Matteo Dugo, Federica Morano, Michele Prisciandaro, Silvia Brich, Antonino Belfiore, Andrea Vingiani, Maria Di Bartolomeo, Giancarlo Pruneri, Elda Tagliabue, Silvia Giordano, Filippo Pietrantonio, Serenella M. Pupa
Summary: In this study, cotargeting HER2 and FASN was found to enhance the efficacy of anti-HER2 therapy, providing a new opportunity for treating trastuzumab-resistant HER2+ gastric cancer.
Article
Multidisciplinary Sciences
Arianna Bresci, Jeong Hee Kim, Silvia Ghislanzoni, Francesco Manetti, Lintong Wu, Federico Vernuccio, Chiara Ceconello, Salvatore Sorrentino, Ishan Barman, Italia Bongarzone, Giulio Cerullo, Renzo Vanna, Dario Polli
Summary: Screening for anticancer therapy in vitro can lead to the identification of additional treatments and improve clinical outcomes. This study demonstrates the potential of all-optical, label-free, and quantitative microscopy techniques in early detection of therapy-induced senescent cells in tumor cells, providing a rapid and accurate method for research in anticancer treatment.
Article
Chemistry, Analytical
Silvia Ghislanzoni, Jeon Woong Kang, Arianna Bresci, Andrea Masella, Koseki J. Kobayashi-Kirschvink, Dario Polli, Italia Bongarzone, Peter T. C. So
Summary: This study used optical diffraction tomography and Raman spectroscopy to analyze the structure of vacuoles in cancer cells and detect chemical species within them. The researchers found that the vacuoles contained diluted cell-derived macromolecules and could be distinguished from the surrounding medium and cells using their Raman fingerprint. This noninvasive approach is valuable for studying complex biological processes.
Article
Oncology
Luca Licata, Marco Barreca, Barbara Galbardi, Matteo Dugo, Giulia Viale, Balazs Gyorffy, Thomas Karn, Lajos Pusztai, Luca Gianni, Maurizio Callari, Giampaolo Bianchini
Summary: Luminal breast cancers with high proliferation and low ER signaling have poor prognosis. These tumors show high response to chemotherapy, but resistance to endocrine therapy and palbociclib. Immunotherapy may play a potential role in treating these tumors.
BRITISH JOURNAL OF CANCER
(2023)
Article
Biochemistry & Molecular Biology
Trang Van Tran, Hoa Nguyen, Luyen Vu, ChangWoo Lee
Summary: Glutaredoxin 3 (Grx3) is a redox protein that maintains structural integrity and glutathione (GSH) binding capabilities across different temperatures. This study investigates the roles of specific bonds in Grx3's structure and function, and how psychrophilic Grx3 variants adapt to cold environments. The highly conserved Arg51-Asp69 salt bridge and Gln56-His63 hydrogen bond are crucial for stabilizing the structure and catalytic activity of Grx3. Psychrophilic variants of Grx3 have adapted to cold environments by reducing GSH binding and increasing structural flexibility.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Amanda Lais de Souza Coto, Arthur Alexandre Pereira, Sabrina Dorta Oliveira, Milene Nobrega de Oliveira Moritz, Arthur Moraes Franco da Rocha, Paulo Roberto Dores-Silva, Noeli Soares Melo da Silva, Ana Rita de Araujo Nogueira, Lisandra Marques Gava, Thiago Vagas Seraphim, Julio Cesar Borges
Summary: J-domain proteins form a large molecular chaperone family involved in proteostasis processes, with hDjC20 playing a vital role in mitochondria and being heavily influenced by the presence of Zn+2.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Meiling Zhang, Jiaxiang Zhang, Yan Liang, Shicheng Tian, Shuyang Xie, Tong Zhou, Qin Wang
Summary: This study determined the crystal structures of RGLG2 VWA domain in Arabidopsis thaliana, revealing that Ca2+ ions act as regulators and affect the conformational change of RGLG2-VWA domain.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Alexandra Bork, Sander H. J. Smits, Lutz Schmitt
Summary: This study reveals the structure and calcium ion binding properties of CBL1 protein, and proposes a binding model of CBL1 for Ca2+. Additionally, it provides preliminary insights into the formation of the dimer interface of CBL1.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Evgeniia V. Leisi, Andrey V. Moiseenko, Sofia S. Kudryavtseva, Denis V. Pozdyshev, Vladimir I. Muronetz, Lidia P. Kurochkina
Summary: The pathogenesis of prion diseases involves the transformation of prion protein into an insoluble form. This study found that two phage chaperonins can promote the fibrillation of prion protein in an ATP-dependent manner, resulting in the formation of less toxic large clusters. These fibrils differ in morphology and properties from those formed spontaneously in acidic pH with denaturants.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Gaurab Chowdhury, Saroj Biswas, Yuthika Dholey, Puja Panja, Sumit Das, Subrata Adak
Summary: Magnesium is an important divalent cation for regulating enzyme activity. The binding of Mg2+ through the PAS domain inhibits phosphoglycerate kinase (PGK) activity in LmPAS-PGK at neutral pH, but PGK activity is derepressed at acidic pH. Mutation studies revealed that the Asp-4 residue is crucial for Mg2+ binding at neutral pH.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Shima Ghaedizadeh, Majid Zeinali, Bahareh Dabirmanesh, Behnam Rasekh, Khosrow Khajeh, Ali Mohammad Banaei-Moghaddam
Summary: Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies can increase the rate of CO2 absorption from industrial flue gases. This study successfully improved the thermostability of a known hyperthermostable carbonic anhydrase through rational engineering of a single-point mutation.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Khaled A. Elnahriry, Dorothy C. C. Wai, Lauren M. Ashwood, Muhammad Umair Naseem, Tibor G. Szanto, Shaodong Guo, Gyorgy Panyi, Peter J. Prentis, Raymond S. Norton
Summary: Sea anemone venom contains a peptide called Tst2, which shows sequence similarity to peptides that interact with various ion channels. Recombinant Tst2 was successfully produced and its structure and function were studied. The results showed that Tst2 is an inhibitor of the TRPV1 channel.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)