Article
Dermatology
Dana Westphal, Matthias Meinhardt, Konrad Gruetzmann, Lisa Schoene, Julian Steininger, Lena T. Neuhaus, Miriam Wiegel, Daniel Schrimpf, Daniela E. Aust, Evelin Schroeck, Gustavo B. Baretton, Stefan Beissert, Tareq A. Juratli, Gabriele G. Schackert, Jan Gravemeyer, Juergen C. Becker, Andreas von Deimling, Christian Koelsche, Barbara Klink, Friedegund Meier, Alexander Schulz, Michael H. Muders, Michael Seifert
Summary: This study integrated omics data analysis to evaluate the methylomes and transcriptomes of matched melanoma metastases, identifying 38 candidate genes with distinct promoter methylation and gene expression changes in intracranial compared with extracranial metastases. The protein expression of the 11 most promising genes was validated using immunohistochemistry, and significant differences were observed in intracranial metastases. Knockdown of PRKCZ or GRB10 altered protein kinase B expression and decreased the viability of a brain-specific melanoma cell line. These findings provide insights into the molecular mechanisms that differentiate brain metastases and could be targeted for therapy.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Multidisciplinary Sciences
Yuta Yamamura, Kengo Furuichi, Yasuhiro Murakawa, Shigeki Hirabayashi, Masahito Yoshihara, Keisuke Sako, Shinji Kitajima, Tadashi Toyama, Yasunori Iwata, Norihiko Sakai, Kazuyoshi Hosomichi, Philip M. Murphy, Atsushi Tajima, Keisuke Okita, Kenji Osafune, Shuichi Kaneko, Takashi Wada
Summary: This study analyzed gene expression in iPSCs from patients with RCS carrying PAX2 mutations, identifying differentially activated candidate promoters and enhancers, and prioritized 17 candidate genes, with PBX1, POSTN, and ITGA9 ranked as the top three. The identification of these genes may provide important information for clarifying the pathogenesis of RCS, human kidney development, and kidney regeneration.
SCIENTIFIC REPORTS
(2021)
Article
Medicine, General & Internal
Xiuyun Xuan, Yuqi Wang, Yanhong Sun, Changzheng Huang
Summary: In this study, 295 overlapping DEGs and 9 hub genes were identified between primary melanoma and normal skin tissues through various bioinformatics analyses. Functional analysis of these hub genes showed enrichment in cell chemotaxis and the chemokine signaling pathway. The upregulated chemokines CCL5, CCL4, CXCL9 and CXCL10 demonstrated good overall survival in melanoma, with a positive correlation between their expression and immune cell infiltration. Drug-gene interaction analysis identified 46 interactions, and in vitro data confirmed higher levels of these chemokines in melanoma tissues compared to normal skin.
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Dabin Choi, Wesuk Kang, Soyoon Park, Bomin Son, Taesun Park
Summary: For several decades, excessive glucocorticoids (GCs) have been known to inhibit collagen synthesis and accelerate skin aging, but the molecular mechanisms involved are not well understood. In this study, the researchers identified potential glucocorticoid receptor (GR) target genes that may contribute to the inhibition of collagen synthesis. They confirmed that dexamethasone, a synthetic GC, activates canonical GR signaling in dermal fibroblasts and identified six candidate genes involved in the GC-mediated inhibition of collagen synthesis. This study provides insights into the molecular mechanisms of GC-mediated skin aging and lays the foundation for further research on the biological characteristics of individual GR target genes.
Article
Multidisciplinary Sciences
Federica A. Falchi, Francesca Forti, Cristina Carnelli, Aurelia Genco, Roberto Pizzoccheri, Caterina Manzari, Giulio Pavesi, Federica Briani
Summary: This study demonstrates that expression of human PNPase in E. coli leads to oxidative stress, activation of SOS response, and accumulation of R-loops. It also affects the stability of E. coli RNA and its phenotypic traits.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Paula Clemente, Javier Calvo-Garrido, Sarah F. Pearce, Florian A. Schober, Megumi Shigematsu, Stefan J. Siira, Isabelle Laine, Henrik Spahr, Christian Steinmetzger, Katja Petzold, Yohei Kirino, Rolf Wibom, Oliver Rackham, Aleksandra Filipovska, Joanna Rorbach, Christoph Freyer, Anna Wredenberg
Summary: Using Drosophila and mouse models, this study demonstrates that non-canonical RNA processing in mammalian mitochondria results in the formation of 3' phosphates, which are hydrolyzed by the phosphatase activity of the carbon catabolite repressor 4 domain-containing family member ANGEL2. The findings also suggest the involvement of the FAST kinase domain-containing protein family in the generation of these 3' phosphates.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Tobias Strunz, Martin Kellner, Christina Kiel, Bernhard H. F. Weber
Summary: This study identified clusters of co-regulated genes across multiple tissues using eQTL analysis and colocalization studies, highlighting the importance of understanding common effects on biological pathways and treatment implications when targeting co-regulated disease genes.
Article
Cell Biology
Yao Chen, Xiaozhen Chen, Xianggui Wang
Summary: This study analyzed 10 CRGs in 80 UVM patients and constructed a prognostic gene model. It was found that the alteration of CRGs is related to UVM patients and can predict their prognosis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Renjian Xie, Bifei Li, Lee Jia, Yumei Li
Summary: This study identified core genes and molecular mechanisms related to melanoma metastasis using gene expression profiles and bioinformatics analysis. Experimental validation showed that KRT5 plays an inhibitory role in melanoma metastasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Meredith B. Finn, Kathryn M. Ramsey, Simon L. Dove, Michael R. Wessels
Summary: The study reveals that the CsrRS system in Group A Streptococcus regulates gene expression by modulating the phosphorylation of CsrR, affecting the bacteria's ability to adapt to the human host. Analysis indicates that CsrR influences the expression of multiple genes by binding to regulated promoters and controlling the expression of intermediate transcription regulators.
Article
Biochemistry & Molecular Biology
Tatyana Liburkin-Dan, Inbal Nir-Zvi, Hila Razon, Ofra Kessler, Gera Neufeld
Summary: The five lysyl-oxidase genes were knocked out in MDA-MB-231 breast cancer cells to identify LOX-regulated genes and study their mechanism. Re-expression experiments revealed four downregulated genes rescued by LOX re-expression. LOX variants with point mutations induced gene expression, suggesting unrecognized functions of LOX pro-enzyme.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Xinbao Ding, Priti Singh, Kerry Schimenti, Tina N. Tran, Robert Fragoza, Jimmaline Hardy, Kyle E. Orwig, Marta Olszewska, Maciej K. Kurpisz, Alexander N. Yatsenko, Donald F. Conrad, Haiyuan Yu, John C. Schimenti
Summary: Infertility is a heterogeneous condition that can be caused by genetic factors. Genome sequencing is important for genetic diagnosis, but most rare variants found in patients have uncertain significance. Researchers evaluated the effects of these variants in key fertility genes using genome-edited mouse models and found that the predictions made by widely used algorithms were not accurate. Therefore, alternative and efficient functional validation models are needed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Medicine, Research & Experimental
Onat Kadioglu, Mohamed E. M. Saeed, Nuha Mahmoud, Shaymaa S. Hussein Azawi, Martina Rincic, Thomas Liehr, Thomas Efferth
Summary: Several genes were found to be overexpressed in B16-F10 cells, including Nr5a1/sf1 and Hoxb8 which are known to be linked with tumor progression and metastasis. Additionally, B16-F10 cells acquired additional chromosomal aberrations compared to B16-F1 cells. The study identified numerous novel genes and genomic aberrations that may serve as potential targets for future treatment strategies.
Article
Oncology
Jie Jiang, Chong Liu, Guoyong Xu, Tuo Liang, Chaojie Yu, Shian Liao, Zide Zhang, Zhaojun Lu, Zequn Wang, Jiarui Chen, Tianyou Chen, Hao Li, Xinli Zhan
Summary: A total of 435 differentially co-expressed genes were identified. Survival curves showed that high expression of FOXM1, EXO1, KIF20A, TPX2, and CDC20 in melanoma patients was associated with reduced overall survival. Immunohistochemistry confirmed higher protein levels of these genes in melanoma compared to normal tissues, indicating their potential as prognostic biomarkers.
FRONTIERS IN ONCOLOGY
(2021)
Article
Microbiology
Zhe Zhao, Ying Xu, Bo Jiang, Qingsheng Qi, Ya-Jie Tang, Mo Xian, Jichao Wang, Guang Zhao
Summary: The CpxRA system senses environmental stresses and regulates gene transcription for adaptation. This study identified over 10,000 putative CpxR binding sites and confirmed experimentally that 73 candidate genes are regulated by CpxR. These findings greatly expand our understanding of the CpxRA-dependent stress response network in Escherichia coli.
Article
Oncology
Manny D. Bacolod, Francis Barany
Summary: The study used a bioinformatic approach to investigate the epigenetic regulation of the MGMT gene, revealing contrasting influences of CpG methylation at the promoter region and at the gene body on MGMT transcription. These findings may contribute to improving diagnostic assays for MGMT in the future.
CURRENT CANCER DRUG TARGETS
(2021)
Article
Biochemistry & Molecular Biology
Mohammed A. Ibrahim Al-Obaide, Viswanath Arutla, Manny D. Bacolod, Wei Wang, Ruiwen Zhang, Kalkunte S. Srivenugopal
Summary: This study identified new regulatory elements in the MGMT gene locus, indicating complex transcriptional and posttranscriptional controls, with potential for new therapeutic avenues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Erika T. Rhone, Elissa Bardhi, Sai Vineela Bontha, Patrick D. Walker, Jorge A. Almenara, Catherine I. Dumur, Helen Cathro, Daniel Maluf, Valeria Mas
Summary: The study evaluated gene expression profiles in pediatric kidney transplant recipients and found oxidative phosphorylation and mitochondrial dysfunction, decreased ATP synthesis, and other toxicology pathways in CNIT patients. An integrative analysis identified a panel of 13 significant miRNAs and their 33 CNIT-specific gene targets, which may serve as future molecular markers for CNIT diagnosis and potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Endocrinology & Metabolism
Yunwei Xia, Upneet K. Sokhi, Richard D. Bell, Tania Pannellini, Kathleen Turajane, Yingzhen Niu, Laura Frye, Max Chao, Ugur Ayturk, Miguel Otero, Mathias Bostrom, David Oliver, Xu Yang, Lionel B. Ivashkiv
Summary: The study found that injured tissues actively sensed in secondary lymphoid organs may activate adaptive immunity. Joint tissues exhibited three temporally distinct immune response components, including a novel interferon (IFN) response with activation of signal transducer and activator of transcription (STAT) and interferon regulatory factor (IRF) pathways.
JOURNAL OF BONE AND MINERAL RESEARCH
(2021)
Article
Pathology
Umberto Malapelle, Francesco Pepe, Pasquale Pisapia, Annalisa Altimari, Claudio Bellevicine, Hans Brunnstrom, Rossella Bruno, Reinhard Buttner, Luis Cirnes, Carlos E. De Andrea, Dario de Biase, Catherine Dumur, Kajsa Ericson Lindquist, Gabriella Fontanini, Eugenio Gautiero, David Gentien, Paul Hofman, Veronique Hofman, Antonino Iaccarino, Maria Dolores Lozano, Clara Mayo-de-Las-Casas, Sabine Merkelbach-Bruse, Fabio Pagni, Ruth Roman, Fernando C. Schmitt, Janna Siemanowski, Sinchita Roy-Chowdhuri, Giovanni Tallini, Francesc Tresserra, Sara Vander Borght, Philippe Vielh, Elena Vigliar, Giulia Anna Carmen Vita, Birgit Weynand, Rafael Rosell, Miguel Angel Molina Vila, Giancarlo Troncone
Summary: Gene fusion assays are crucial for personalized treatments of advanced human cancers. This study developed and validated gene fusion reference standards using cell line slides, finding that better results were obtained with Pap staining and amplicon-based assays. Further optimization is required for MGG stained cells and hybridisation-based approaches.
JOURNAL OF CLINICAL PATHOLOGY
(2023)
Article
Biochemical Research Methods
Leon Avery, Brian Ingalls, Catherine Dumur, Alexander Artyukhin
Summary: Collective behaviors in Starved first-stage larvae of the nematode Caenorhabditis elegans are known to produce large-scale organization. A mathematical model was developed to explain how and why the larvae aggregate, focusing on chemotaxis and the role of two chemical signals. Knocking out the sensory receptor gene srh-2 resulted in irregularly shaped aggregates, suggesting that mutant worms moved slower than wild type.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Endocrinology & Metabolism
Upneet K. Sokhi, Yunwei Xia, Branden Sosa, Kathleen Turajane, Sita N. Nishtala, Tania Pannellini, Mathias P. Bostrom, Alberto Carli, Xu Yang, Lionel B. Ivashkiv
Summary: This study characterized the immune response in orthopedic periprosthetic joint infection (PJI) using histology, flow cytometry, and gene expression analysis. The results showed that persistent S. aureus infection leads to robust activation of both innate and adaptive immunity, as well as ongoing inflammation and lymph node and bone marrow reactions. However, there are feedback mechanisms that suppress immune cell activation and inhibit T-cell proliferation and tissue infiltration. These findings provide insights into the immune response to persistent S. aureus PJI and suggest potential targets for immunotherapeutic strategies.
JOURNAL OF BONE AND MINERAL RESEARCH
(2022)
Review
Chemistry, Multidisciplinary
Liviu Duta, Gabriela Dorcioman, Valentina Grumezescu
Summary: This review summarizes the results on the production of biphasic calcium phosphate (BCP) materials derived from fish wastes and discusses their potential applications in the biomedical field. Transforming waste into valuable products can have significant social, economic, and environmental benefits. The use of fish discards for BCP materials has shown promising results and is a safe, cheap, and simple procedure.
Article
Oncology
Manny D. Bacolod, Francis Barany
Summary: This study utilized integrated bioinformatic and statistical reanalysis of publicly available genomic datasets to identify molecular pathways and biomarkers relevant to metastatic prostate cancer progression. The transition from primary prostate cancer to mPrCa is characterized by upregulation of processes associated with DNA replication, metastasis, and events regulated by the serine/threonine kinase PLK1. Over-expressed genes identified may be potential targets for therapeutic interventions and minimally invasive diagnostics for mPrCa.
Article
Genetics & Heredity
Jose Marie Antonio Minoza, Jonathan Adam Rico, Pia Regina Fatima Zamora, Manny Bacolod, Reinhard Laubenbacher, Gerard G. Dumancas, Romulo de Castro
Summary: In this study, a transfer learning-based biomarker discovery model was developed to aid in the diagnosis and prognosis of melanoma. The model achieved high performance on an independent validation dataset and identified potential genes for diagnostic classification and diagnostic prognostic biomarkers.
Article
Materials Science, Multidisciplinary
L. Duta, G. E. Stan, G. Popescu-Pelin, I. Zgura, M. Anastasescu, F. N. Oktar
Summary: In this study, hydroxyapatite coatings of biological-origin doped with lithium carbonate and lithium phosphate were synthesized on Ti6Al4V substrates using pulsed laser deposition. A comparison was made between as-deposited and post-deposition thermal-treated coatings at various temperatures. The results showed that increasing the temperature led to complete crystallization of the coatings and increased roughness of the surfaces. Thermal treatments at higher temperatures were found to improve the physical-chemical and mechanical properties of the coatings.
Article
Materials Science, Multidisciplinary
Liviu Duta, Ion N. Mihailescu
Article
Pharmacology & Pharmacy
Gabriela Dorcioman, Valentina Grumezescu, George E. Stan, Mariana Carmen Chifiriuc, Gratiela Pircalabioru Gradisteanu, Florin Miculescu, Elena Matei, Gianina Popescu-Pelin, Irina Zgura, Valentin Craciun, Faik Nuzhet Oktar, Liviu Duta
Summary: Novel biomaterials with excellent bone regeneration potential were synthesized from marine-derived hydroxyapatite by pulsed laser deposition. The rough surfaces of the thin films promoted cell adhesion and implant anchorage. The thin films exhibited strong hydrophilic behavior, superior bonding strength adherence, low cytotoxicity, and effective antimicrobial activity. These cost-effective materials from sustainable sources are recommended for the development of innovative coatings for metallic dental implants.
Article
Endocrinology & Metabolism
Takayuki Fujii, Susumu Wada, Camila B. Carballo, Richard D. Bell, Wataru Morita, Yusuke Nakagawa, Yake Liu, Daoyun Chen, Tania Pannellini, Upneet K. Sokhi, Xiang-hua Deng, Kyung Hyung Park-Min, Scott A. Rodeo, Lionel B. Ivashkiv
Summary: In this study, the role of macrophages in the healing process after surgical repair of musculoskeletal tissues was investigated using single-cell RNA sequencing and other techniques. Two distinct populations of macrophages were identified, one highly inflammatory and the other expressing interferon signals. Deletion of a specific gene was shown to improve healing. These findings provide new insights into the role of surgery-induced macrophages in the healing process and suggest potential therapeutic strategies.
Article
Pathology
Umberto Malapelle, Francesco Pepe, Pasquale Pisapia, Roberta Sgariglia, Mariantonia Nacchio, Massimo Barberis, Michel Bilh, Lukas Bubendorf, Reinhard Buettner, Daniela Cabibi, Marta Castiglia, Carlos E. De Andrea, Dario de Biase, Catherine Dumur, Gabriella Fontanini, Javier Freire, Valerio Gristina, Paul Hofman, Marius Ilie, Maria Dolores Lozano, Sabine Merkelbach-Bruse, Roberto Pappesch, Natalie Pelusi, Gianluca Roma, Antonio Russo, Spasenija Savic, Janna Siemanowski, Giovanni Tallini, Verena Tischler, Sara Vander Borght, Birgit Weynand, Tom Xu, Giancarlo Troncone
Summary: The TargetPlex FFPE-Direct DNA Library Preparation Kit was validated for NGS analysis in cancer care, eliminating the complex manual workflow and providing a convenient and cost-saving solution for routine practice. With a success rate of 92.8%, the kit was able to detect 90.5% of variants compared to standard protocols.
JOURNAL OF CLINICAL PATHOLOGY
(2022)