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JOURNAL ARTICLE
Francesco Di Mauro, Giuseppina Arbore
Chemotherapeutics, radiation, targeted therapeutics and immunotherapeutics each demonstrate clinical benefits for a small subset of patients with solid malignancies. Immune cells infiltrating the tumor and the surrounding stroma play a critical role in shaping cancer progression and modulating therapy response. They do this by interacting with the other cellular and molecular components of the tumor microenvironment (TME). Spatial multi-OMICs technologies are rapidly evolving. Currently, such technologies allow high-throughput RNA and protein profiling and retain geographical information about the TME cellular architecture and the functional phenotype of tumor, immune and stromal cells...
April 24, 2024: Cancer Immunology Research
#2
JOURNAL ARTICLE
Viviana Nguyen, Yifei Li, Ting Lu
Microbial metabolism is a fundamental cellular process that involves many biochemical events and is distinguished by its emergent properties. While the molecular details of individual reactions have been increasingly elucidated, it is not well understood how these reactions are quantitatively orchestrated to produce collective cellular behaviors. Here we developed a coarse-grained, systems, and dynamic mathematical framework, which integrates metabolic reactions with signal transduction and gene regulation to dissect the emergent metabolic traits of Saccharomyces cerevisiae ...
April 24, 2024: ACS Synthetic Biology
#3
JOURNAL ARTICLE
Yuta Ito, Amira Marouf, Yasunori Kogure, Junji Koya, Raphaël Liévin, Julie Bruneau, Mariko Tabata, Yuki Saito, Sumito Shingaki, Mitsuhiro Yuasa, Kentaro Yamaguchi, Koichi Murakami, Robert Weil, Manon Vavasseur, Guillaume P Andrieu, Mehdi Latiri, Layla Veleanu, Michaël Dussiot, Isabelle André, Akshay Joshi, Chantal Lagresle-Peyrou, Aude Magerus, Sammara Chaubard, David Lavergne, Emmanuel Bachy, Erika Brunet, Virginie Fataccioli, Chantal Brouzes, Camille Laurent, Laurence De Leval, Alexandra Traverse-Glehen, Céline Bossard, Marie-Cécile Parrens, Véronique Meignin, Laure Philippe, Julien Rossignol, Felipe Suarez, Jean-Marie Michot, Olivier Tournilhac, Gandhi Damaj, François Lemonnier, Christine Bôle-Feysot, Patrick Nitschké, Bruno Tesson, Cécile Laurent, Thierry Molina, Vahid Asnafi, Yosaku Watatani, Kenichi Chiba, Ai Okada, Yuichi Shiraishi, Sachiko Tsukita, Koji Izutsu, Hiroaki Miyoshi, Koichi Ohshima, Seiji Sakata, Akito Dobashi, Kengo Takeuchi, Masashi Sanada, Philippe Gaulard, Arnaud Jaccard, Seishi Ogawa, Olivier Hermine, Keisuke Kataoka, Lucile Couronné
Extranodal NK/T-cell lymphoma (ENKTCL) is an Epstein-Barr virus (EBV)-related neoplasm with male dominance and a poor prognosis. A better understanding of the genetic alterations and their functional roles in ENKTCL could help improve patient stratification and treatments. Here, we performed comprehensive genetic analysis of 177 ENKTCL cases to delineate the landscape of mutations, copy number alterations (CNAs), and structural variations, identifying 34 driver genes including six previously unappreciated ones, namely HLA-B, HLA-C, ROBO1, CD58, POT1, and MAP2K1...
April 24, 2024: Cancer Research
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JOURNAL ARTICLE
Chisato Sakuma, Sayaka Shizukuishi, Michinaga Ogawa, Yuko Honjo, Haruko Takeyama, Jun-Lin Guan, Jeffery Weiser, Miwa Sasai, Masahiro Yamamoto, Makoto Ohnishi, Yukihiro Akeda
Atg8 paralogs, consisting of LC3A/B/C and GBRP/GBRPL1/GATE16, function in canonical autophagy; however, their function is controversial because of functional redundancy. In innate immunity, xenophagy and non-canonical single membranous autophagy called "conjugation of Atg8s to single membranes" (CASM) eliminate bacteria in various cells. Previously, we reported that intracellular Streptococcus pneumoniae can induce unique hierarchical autophagy comprised of CASM induction, shedding, and subsequent xenophagy...
April 23, 2024: Cell Reports
#5
REVIEW
Pernilla Wikström, Anders Bergh, Andreas Josefsson, Elin Thysell, Karin Welén
Increased molecular knowledge makes it possible to consider not only genetic defects but also expression profiles for precision medicine in advanced prostate cancer. Several prognostic and treatment-predictive classifiers for prostate cancer have been described, such as Prolaris, OncotypeDx, Decipher, Prostatype, PAM50, PCS1-2, and MetA-C, which all build upon transcript profiles. In research studies, the MetA-C classifier has shown clear prognostic information for patients with metastatic disease, in relation to outcome after androgen receptor targeting therapies, and so has immunohistochemical evaluation of tumor cell proliferation (Ki67) and PSA expression...
April 24, 2024: Läkartidningen
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REVIEW
Sara Arfan, Khin Thway, Robin L Jones, Paul H Huang
Leiomyosarcoma (LMS) is one of the more common subtypes of soft tissue sarcomas (STS), accounting for about 20% of cases. Differences in anatomical location, risk of recurrence and histomorphological variants contribute to the substantial clinical heterogeneity in survival outcomes and therapy responses observed in patients. There is therefore a need to move away from the current one-size-fits-all treatment approach towards a personalised strategy tailored for individual patients. Over the past decade, tissue profiling studies have revealed key genomic features and an additional layer of molecular heterogeneity among patients, with potential utility for optimal risk stratification and biomarker-matched therapies...
April 24, 2024: Current Treatment Options in Oncology
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JOURNAL ARTICLE
Rasha Mohamed Hassan, Heba Yehia, Mohammed F El-Behairy, Aida Abdel-Sattar El-Azzouny, Mohamed Nabil Aboul-Enein
New quinazolin-4-ones 9-32 were synthesized in an attempt to overcome the life-threatening antibiotic resistance phenomenon. The antimicrobial screening revealed that compounds 9, 15, 16, 18, 19, 20 and 29 are the most broad spectrum antimicrobial agents in this study with safe profile on human cell lines. Additionally, compounds 19 and 20 inhibited biofilm formation in Pseudomonas aeruginosa, which is regulated by quorum sensing system, at sub-minimum inhibitory concentrations (sub-MICs) with IC50 values 3...
April 24, 2024: Molecular Diversity
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JOURNAL ARTICLE
Muhammad Ahmad
Plants produce diverse specialized metabolites (SMs) that do not participate in plant growth and development but help them adapt to various environmental conditions. In addition to aiding in plant adaptation, different SMs serve as active ingredients for pharmaceutical and cosmetics products. However, despite their significant role in plant adaptation and industrial importance, the genes involved in the biosynthesis and regulation of many SMs remain largely unknown. This hinders deciphering the specific role of SMs in plant adaptation and limits their industrial utilization...
2024: Methods in Molecular Biology
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JOURNAL ARTICLE
Thiely Patricia Fabian Dos Santos, Elodia Sánchez-Barrantes, Luiz Filipe Pereira, Andrés Gatica-Arias
Coffee, an important agricultural product for tropical producing countries, is facing challenges due to climate change, including periods of drought, irregular rain distribution, and high temperatures. These changes result in plant water stress, leading to significant losses in coffee productivity and quality. Understanding the processes that affect coffee flowering is crucial for improving productivity and quality. In this chapter, we describe a protocol for transcriptome analysis using available Internet software, mainly in the Galaxy Platform, using RNA-Seq data from flowers collected from different parts of the coffee tree...
2024: Methods in Molecular Biology
#10
JOURNAL ARTICLE
Andrés Gatica-Arias, Carolina Muñoz-Flores, Alejandro Bolívar-González
Coffea spp. is the source of one of the most widely consumed beverages in the world. However, the cultivation of this crop is threatened by Hemileia vastatrix Berk & Broome, a fungal disease, which reduces the productivity and can cause significant economic losses. In this protocol, coffee leaf segment derived from a chemical mutagenesis process are inoculated with uredospores of the pathogen. Subsequently, the gene expression changes are analyzed over the time (0, 5, 24, 48, and 120 h) using quantitative real-time polymerase chain reaction (RT-qPCR)...
2024: Methods in Molecular Biology
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JOURNAL ARTICLE
Rafael da Silva Rosa, João Pedro Rueda Furlan, Lucas David Rodrigues Dos Santos, Micaela Santana Ramos, Eduardo Angelino Savazzi, Eliana Guedes Stehling
During the COVID-19 pandemic, the occurrence of carbapenem-resistant Klebsiella pneumoniae increased in human clinical settings worldwide. Impacted by this increase, international high-risk clones harboring carbapenemase-encoding genes have been circulating in different sources, including the environment. The blaKPC gene is the most commonly disseminated carbapenemase-encoding gene worldwide, whose transmission is carried out by different mobile genetic elements. In this study, blaKPC-2 -positive Klebsiella pneumoniae complex strains were isolated from different anthropogenically affected aquatic ecosystems and characterized using phenotypic, molecular, and genomic methods...
April 24, 2024: World Journal of Microbiology & Biotechnology
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JOURNAL ARTICLE
Yang Zhao, Yiming Ma, Jianing Pei, Xiaoxuan Zhao, Yuepeng Jiang, Qingsheng Liu
Ulcerative colitis (UC) is an idiopathic, relapsing inflammatory disorder of the colonic mucosa. Pyroptosis contributes significantly to UC. However, the molecular mechanisms of UC remain unexplained. Herein, using transcriptome data and animal experimental validation, we sought to explore pyroptosis-related molecular mechanisms, signature genes, and potential drugs in UC. Gene profiles (GSE48959, GSE59071, GSE53306, and GSE94648) were selected from the Gene Expression Omnibus (GEO) database, which contained samples derived from patients with active and inactive UC, as well as health controls...
April 24, 2024: Inflammation
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JOURNAL ARTICLE
Yong'An Jiang, Peng Chen, YangYang Zhao, Yan Zhang
The cadherin family plays a pivotal role in orchestrating synapse formation in the central nervous system. Cadherin-related family member 1 (CDHR1) is a photoreceptor-specific calmodulin belonging to the expansive cadherin superfamily. However, its role in traumatic brain injury (TBI) remains largely unknown. CDHR1 expression across various brain tissue sites was analyzed using the GSE104687 dataset. Employing a summary-data-based Mendelian Randomization (SMR) approach, integrated analyses were performed by amalgamating genome-wide association study abstracts from TBI with public data on expressed quantitative trait loci and DNA methylation QTL from both blood and diverse brain tissues...
April 24, 2024: Cellular and Molecular Neurobiology
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JOURNAL ARTICLE
Harnoor Singh Sachar, Everett S Zofchak, Nico Marioni, Zidan Zhang, Venkat Ganesan
Membranes incorporating zwitterionic chemistries have recently emerged as promising candidates for facilitating challenging ion-ion separations. Transport of ions in such membranes predominantly occurs in hydrated nanopores lined with zwitterionic monomers. To shed light on the physics of ion-ion selectivity underlying such materials, we conducted molecular dynamics simulations of sodium halide transport in model nanopores grafted with sulfobetaine methacrylate molecules. Our results reveal that in both functionalized and unfunctionalized nanopores smaller ions prefer to reside near the pore center, while the larger ions tend to reside near the pore walls...
April 24, 2024: Langmuir: the ACS Journal of Surfaces and Colloids
#15
JOURNAL ARTICLE
Muhammet Tanc, Nicolò Filippi, Yentl Van Rymenant, Sergei Grintsevich, Isabel Pintelon, Marlies Verschuuren, Joni De Loose, Emile Verhulst, Euy Sung Moon, Lorenzo Cianni, Sigrid Stroobants, Koen Augustyns, Frank Roesch, Ingrid De Meester, Filipe Elvas, Pieter Van der Veken
Fibroblast activation protein (FAP) is a very reliable biomarker for tissue remodeling. FAP has so far mainly been studied in oncology, but there is growing interest in the enzyme in other diseases like fibrosis. Recently, FAP-targeting diagnostics and therapeutics have emerged, of which the so-called FAPIs are among the most promising representatives. FAPIs typically have a relatively high molecular weight and contain very polar, multicharged chelator moieties. While this is not limiting the application of FAPIs in oncology, more druglike FAPIs could be required to optimally study diseases characterized by denser, less permeable tissue...
April 24, 2024: Journal of Medicinal Chemistry
#16
REVIEW
Tianlin Wang, Ke Xiong, Yanli He, Binbin Feng, Linbin Guo, Jingliang Gu, Hong Wang, Xiaohao Wu
Chronic pancreatitis (CP) is a progressive inflammatory disease with an increasing global prevalence. In recent years, a strong association between CP and metabolic bone diseases (MBDs), especially osteoporosis, has been identified, attracting significant attentions in the research field. Epidemiological data suggest a rising trend in the incidence of MBDs among CP patients. Notably, recent studies have highlighted a profound interplay between CP and altered nutritional and immune profiles, offering insights into its linkage with MBDs...
April 24, 2024: American Journal of Physiology. Endocrinology and Metabolism
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JOURNAL ARTICLE
Piotr A Serwacki, Dariusz A Hareza, Anna Kujawska, Anna Pałka, Estera Jachowicz-Matczak, Agata Rybka-Grymek, Wioletta Świątek-Kwapniewska, Iwona Pawłowska, Zofia Gniadek, Karolina Gutkowska, Mateusz Gajda, Jadwiga Wójkowska-Mach
INTRODUCTION: The complex interplay between Acinetobacter spp., patients, and the environment has made it increasingly difficult to optimally treat patients infected with Acinetobacter spp., mainly due to rising antimicrobial resistance and challenges with surveillance. OBJECTIVES: This study evaluated carbapenem-resistance Acinetobacter baumannii (CRAB) isolates to determine their resistance profiles and the presence of specific β-lactamase enzymes to inform the use of CRAB surveillance upon hospital admission and regional empiric antibiotic therapies...
April 23, 2024: Polish Archives of Internal Medicine
#18
JOURNAL ARTICLE
Patil Shivprasad Suresh, Xinguo Sun, Zhanxiang Zhou, Qibin Zhang
Alcohol consumption perturbs the gut immune barrier and ultimately results in alcoholic liver diseases, but little is known about how immune-related cells in the gut are perturbed in this process. In this study, we employed laser capture microdissection and a label-free proteomics approach to investigate the consequences of alcohol exposure to the proteomes of crypts and villi in the proximal small intestine. Intestinal tissues from alcohol-fed and pair-fed mice were microdissected to selectively capture cells in the crypts and villi regions, followed by one-pot protein digestion and data-independent LC-MS/MS analysis...
April 24, 2024: Journal of Proteome Research
#19
JOURNAL ARTICLE
Srinivasa Rao Kareti, Vivek Singh Rajpoot
Baccharoides anthelmintica (L.) Moench is a popular medicinal plant with a long history of use in several traditional remedies to cure a variety of diseases including; its effect on the central nervous system, gastrointestinal tract, metabolism, kidneys, gynecology, skin diseases, and general health. The present review aims to provide the latest, organized information on toxicological, pharmacological, phytochemical, and ethnomedicinal applications of Baccharoides anthelmintica. Several well-known searchable websites like; Web of Science, Google Scholar, Scopus-Elsevier, Taylor & Francis, Springer, and DOAJ, were used to empirically investigate the knowledge of this useful medicinal plant...
April 24, 2024: Chemistry & Biodiversity
#20
JOURNAL ARTICLE
Marcin Cybulski, Magdalena Zaremba-Czogalla, Bartosz Trzaskowski, Marek Kubiszewski, Joanna Tobiasz, Anna Jaromin, Piotr Krzeczyński, Jerzy Gubernator, Olga Michalak
New amide conjugates 1-6 of hydroxycinnamic acids (HCA) and 5'-deoxy-5-fluorocytidine (5-dFCR), the prodrug of 5-fluorouracil (5-FU), were synthesized and tested in vitro against pancreatic cancer lines (PDAC). The compounds showed slightly higher efficacy against primary BxPC-3 cells (IC50 values of 14-45 μM) than against metastatic AsPC-1 (IC50 values of 37-133 μM), and similar to that of 5-FU for both PDAC lines. Compound 1, which has a para -(acetyloxy)coumaroyl substituent, was found to be the most potent (IC50 = 14 μM) with a selectivity index of approximately 7 to normal dermal fibroblasts (IC50 = 96 μM)...
April 22, 2024: RSC Advances
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