Review
Biochemistry & Molecular Biology
Atiah H. Almalki
Summary: Lung cancer is the leading cause of cancer-related death worldwide. This review presents recent trends in the analytical techniques used for metabolome mapping of lung cancer, and discusses the potential applications of these techniques in the analysis of biological samples, providing new avenues for treatment strategies and monitoring drug responses.
Review
Pharmacology & Pharmacy
Abdul-Hamid Emwas, Kacper Szczepski, Inas Al-Younis, Joanna Izabela Lachowicz, Mariusz Jaremko
Summary: Fluxomics is an innovative research field that measures intracellular flux rates in biological systems, providing insights into molecular interactions and metabolic pathways. It has become increasingly relevant in studying metabolic phenotypes.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Pharmacology & Pharmacy
Anne Michelli Reis Silveira, Gustavo Henrique Bueno Duarte, Anna Maria Alves de Piloto Fernandes, Pedro Henrique Dias Garcia, Nelson Rogerio Vieira, Marcia Aparecida Antonio, Patricia de Oliveira Carvalho
Summary: Rosuvastatin, a lipid-lowering agent used for hypercholesterolemia treatment, exhibits significant inter-individual variability in absorption due to genetic polymorphisms. Investigating metabolic markers associated with this variability is crucial for optimizing drug therapy efficacy and minimizing side effects. The application of pharmacometabolomic strategies to predict pharmacokinetic parameters using plasma metabolites shows promising potential for personalized drug therapy.
FRONTIERS IN PHARMACOLOGY
(2021)
Review
Chemistry, Analytical
Muhammad Waris, Engin Kocak, Ekrem Murat Gonulalan, L. Omur Demirezer, Sedef Kir, Emirhan Nemutlu
Summary: Plant-based metabolomics studies aim to discover new active compounds, determine vegetation period, investigate adulteration, evaluate correlation activity and metabolite levels, and monitor quality control of medicinal plants. However, the chemical differences of primary and secondary metabolites in complex natural products present challenges for analysis, ranging from sample collection to preparation, and from analysis to metabolite annotation and quantification. A comprehensive evaluation of current and new trends in plant metabolomics helps researchers in designing their studies holistically.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Applied
Ahmed Zayed, Amr Abdelwareth, Tarik A. Mohamed, Heba A. Fahmy, Andrea Porzel, Ludger A. Wessjohann, Mohamed A. Farag
Summary: This study used a metabolomics approach to analyze commercial coffee products in the Middle East region, revealing changes in metabolites in these products which can aid in evaluating and standardizing coffee quality.
Review
Pharmacology & Pharmacy
Daisuke Saigusa, Naomi Matsukawa, Eiji Hishinuma, Seizo Koshiba
Summary: Metabolomics has been widely used for investigating disease expression and biomarker discovery. The unbiased techniques in metabolic profiling have been applied in pharmacological studies to predict drug therapeutic and adverse reactions.
DRUG METABOLISM AND PHARMACOKINETICS
(2021)
Article
Plant Sciences
Omar M. Khattab, Dina M. El-Kersh, Shaden A. M. Khalifa, Nermeen Yosri, Hesham R. El-Seedi, Mohamed A. Farag
Summary: Urginea maritima L. (squill) species, consisting of two main varieties (white squill and red squill), have various health potentials. Squill contains cardiac glycosides, flavonoids, and anthocyanins as major secondary metabolite classes. Metabolomics approaches including MS, NMR, and chromatography were used for varieties classification and revealed different metabolite profiles between white squill and red squill.
Article
Plant Sciences
Xiaoping Zhang, Zeng Li, Chuanpu Shen, Jinzhi He, Longfei Wang, Lei Di, Bin Rui, Ning Li, Zhicheng Liu
Summary: TSD improves depressive symptoms in CUMS rats by affecting relevant metabolites and protein expression.
PHARMACEUTICAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Dejan Godevac, Stefan Ivanovic, Katarina Simic, Boban Andelkovic, Zivko Jovanovic, Tamara Rakic
Summary: This study investigated the metabolic changes in Ramonda serbica and R. nathaliae during their desiccation and recovery process. The results showed a decrease in certain metabolite contents during dehydration, which were preserved in partially rehydrated plants. Additionally, accumulation of raffinose and myo-inositol was observed in dry samples.
PHYTOCHEMICAL ANALYSIS
(2022)
Article
Chemistry, Applied
Mohamed A. Farag, Sherif M. Afifi, Dalia M. Rasheed, Amira R. Khattab
Summary: Glossostemon bruguieri roots are known for their thick long-tapering dark colored roots, with studies showing high levels of phenolic content and various primary and secondary metabolites. Different origins of roots show variation in their metabolite profiles, with potential for future use in nutraceuticals. Roasting of the roots impacts the volatile composition, with specific compounds identified as markers for the roasting process.
JOURNAL OF FOOD COMPOSITION AND ANALYSIS
(2021)
Article
Oncology
Lihong Mei, Zhihua Zhang, Xushuo Li, Ying Yang, Ruixue Qi
Summary: This study aimed to explore potential metabolomics biomarkers for predicting the efficiency of chemo-immunotherapy in NSCLC patients. Metabolomics profiling analyses using GC-MS identified seven key metabolites, including pyruvate, threonine, alanine, urea, oxalate, elaidic acid, and glutamate, which were associated with the chemo-immunotherapy response. Pathway analyses revealed that urea cycle, glucose-alanine cycle, glycine and serine metabolism, alanine metabolism, and glutamate metabolism were the key metabolic pathways involved.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hongbin Wang, Qiyu Tian, Zhixin Xu, Min Du, Mei-Jun Zhu
Summary: Grape pomace (GP), a rich source of bioactive compounds, has protective effects against colorectal cancer (CRC) development by suppressing cell proliferation and modulating DNA methylation. This study used metabolomic analysis to profile fecal metabolomic changes in a mouse CRC model in response to GP supplementation. GP supplementation led to significant changes in various metabolites, including bile acids, amino acids, fatty acids, phenols/flavonoids, glycerolipids, carbohydrates, organic acids, and others. GP supplementation upregulated the expression of farnesoid X receptor (FXR) downstream genes, decreased fecal urease activity, upregulated the DNA repair enzyme MSH2, decreased the DNA damage marker gamma-H2AX, and decreased the ATM pathway protein MDM2. These findings provide valuable metabolic clues for understanding the protective effects of GP supplementation against CRC development.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2023)
Review
Oncology
Andrew Gold, Fouad Choueiry, Ning Jin, Xiaokui Mo, Jiangjiang Zhu
Summary: Colorectal Cancer (CRC) is a leading cause of cancer-related death in the United States and current diagnosis techniques lack sufficient sensitivity. Metabolomics is a promising technique for identifying CRC biomarkers with high sensitivity and specificity, but it is rarely used in clinical settings. This study conducted a systematic review of recent literature on the detection of CRC biomarkers through metabolomics, identifying dysregulated metabolites across different biospecimens. The study also highlighted the interplay between the gut microbiome and perturbed metabolites in CRC. The findings demonstrate the value of metabolomics as a promising diagnostic technique for CRC.
Article
Chemistry, Applied
Ting Zeng, Baohua Fang, Fenglin Huang, Li Dai, Zhi Tang, Jinglin Tian, Guodong Cao, Xuanlin Meng, Yuanchen Liu, Bo Lei, Minghua Lu, Zongwei Cai
Summary: Through metabolomics analysis, it was found that under cadmium stress, most carbohydrates and amino acids were down-regulated as the cadmium concentration increased in rice grains, except for myoinositol which can prevent cadmium toxicity. D-Mannitol and L-cysteine were up-regulated in low-cadmium-accumulating rice with the increase of cadmium concentration. Organic acids, especially 13-(S)-hydroperoxy-9(Z),11(E),15(Z)-octadecatrienoic acid related to alphalinolenic acid metabolism and jasmonic acid production, were activated.
Review
Biochemistry & Molecular Biology
Alessia Vignoli, Emanuela Risi, Amelia McCartney, Ilenia Migliaccio, Erica Moretti, Luca Malorni, Claudio Luchinat, Laura Biganzoli, Leonardo Tenori
Summary: Precision oncology focuses on selecting the optimal therapy for individual patients with breast cancer, who need appropriate stratification for maximizing survival and quality of life. Gene-expression tools assist in estimating risk and benefit from chemotherapy, while NMR metabolomics has shown promising results in BC research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Shahil Amin, Jodi Rattner, Mohammad Reza Keramati, Farshad Farshidfar, Mairead G. McNamara, Jennifer J. Knox, Karen Kopciuk, Hans J. Vogel, Oliver F. Bathe
Editorial Material
Oncology
Ai Wen Tan, Aalim M. Weljie
Article
Immunology
Rosalyn W. Sayaman, Mohamad Saad, Vesteinn Thorsson, Donglei Hu, Wouter Hendrickx, Jessica Roelands, Eduard Porta-Pardo, Younes Mokrab, Farshad Farshidfar, Tomas Kirchhoff, Randy F. Sweis, Oliver F. Bathe, Carolina Heimann, Michael J. Campbell, Cynthia Stretch, Scott Huntsman, Rebecca E. Graff, Najeeb Syed, Laszlo Radvanyi, Simon Shelley, Denise Wolf, Francesco M. Marincola, Michele Ceccarelli, Jerome Galon, Elad Ziv, Davide Bedognetti
Summary: Understanding the host's genetic background's contribution to cancer immunity has significant impact on the composition and functional orientation of the tumor immune microenvironment, with certain genes potentially acting as immune modulators. Investigating the effects of germline variants on immune traits provides a resource toward further understanding tumor-immune interactions.
Article
Multidisciplinary Sciences
Farshad Farshidfar, Kahn Rhrissorrakrai, Chaya Levovitz, Cong Peng, James Knight, Antonella Bacchiocchi, Juan Su, Mingzhu Yin, Mario Sznol, Stephan Ariyan, James Clune, Kelly Olino, Laxmi Parida, Joerg Nikolaus, Meiling Zhang, Shuang Zhao, Yan Wang, Gang Huang, Miaojian Wan, Xianan Li, Jian Cao, Qin Yan, Xiang Chen, Aaron M. Newman, Ruth Halaban
Summary: Despite being the most common melanoma subtype among non-White individuals, the molecular drivers of acral melanoma remain unknown. In this study, the authors integrated genomic and clinical data from 104 patients and identified recurrent amplifications of cytoband 22q11.21 and LZTR1 as a key tumor promoter in this region.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
Farshad Farshidfar, Kahn Rhrissorrakrai, Chaya Levovitz, Cong Peng, James Knight, Antonella Bacchiocchi, Juan Su, Mingzhu Yin, Mario Sznol, Stephan Ariyan, James Clune, Kelly Olino, Laxmi Parida, Joerg Nikolaus, Meiling Zhang, Shuang Zhao, Yan Wang, Gang Huang, Miaojian Wan, Xianan Li, Jian Cao, Qin Yan, Xiang Chen, Aaron M. Newman, Ruth Halaban
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Jin Yang, Francis Grafton, Sara Ranjbarvaziri, Ana Budan, Farshad Farshidfar, Marie Cho, Emma Xu, Jaclyn Ho, Mahnaz Maddah, Kevin E. Loewke, Julio Medina, David Sperandio, Snahel Patel, Tim Hoey, Mohammad A. Mandegar
Summary: This study developed an in vitro model of dilated cardiomyopathy (DCM) using induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) and identified cardioprotective drugs by inhibiting histone deacetylase 6 (HDAC6). The findings were validated in a mouse model, and the effects of these drugs on mitochondrial function were further investigated.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Cell Biology
Zhen Lu, Noreen McBrearty, Jinyun Chen, Vivek S. Tomar, Hongru Zhang, Gianluca De Rosa, Aiwen Tan, Aalim M. Weljie, Daniel P. Beiting, Zhen Miao, Subin S. George, Allison Berger, Gurpanna Saggu, J. Alan Diehl, Constantinos Koumenis, Serge Y. Fuchs
Summary: The factors derived from tumors affect the activity and viability of tumor-specific cytotoxic T lymphocytes (CTLs), but the underlying mechanism is not well understood. These tumor-derived factors alter the lipid composition of cells and regulate the effector trogocytosis between cells. This process is controlled by the ATF3-CH25H axis, which affects tumor immunity, tumor growth, and the efficacy of CAR cell therapy.
Article
Clinical Neurology
Arjun Sengupta, Jennifer C. Tudor, Danielle Cusmano, Joseph A. Baur, Ted Abel, Aalim M. Weljie
Summary: This study examines the common molecular underpinnings of sleep deprivation and aging by analyzing metabolic features in young and aged mice after acute sleep deprivation. The results show that sleep deprivation primarily impacts peripheral plasma and liver metabolism, while the hippocampus is more affected by aging. Additionally, aged animals exhibit similar metabolic features to sleep deprivation even at baseline.
Article
Genetics & Heredity
Juliana Cazarin, Rachel E. Derollo, Siti Noor Ain Binti Ahmad Shahidan, Jamison B. Burchett, Daniel Mwangi, Saikumari Krishnaiah, Annie L. Hsieh, Zandra E. Walton, Rebekah Brooks, Stephano S. Mello, Aalim M. Weljie, Chi V. Dang, Brian J. Altman
Summary: MYC disrupts the molecular circadian clock, releasing metabolic and biosynthetic processes from circadian control, which may provide an advantage to cancer cells.
Article
Toxicology
Lisa N. Bottalico, Julia Korlyakova, Aalim M. Weljie, Hamid R. Habibi
Summary: The study found that exposure of goldfish to endocrine disrupting chemicals and natural hormones leads to changes in metabolic levels in different seasons and reproductive stages, with goldfish being most vulnerable to metabolic perturbations in February (mid-recrudescence). Responses induced by contaminants differed from those induced by natural hormones in a season-specific manner, and exposure to the tertiary mixture resulted in a functional gain at the level of biochemical pathways modeling in select tissues and seasons.
FRONTIERS IN TOXICOLOGY
(2021)
Meeting Abstract
Critical Care Medicine
B. W. Winston, M. Banoei, H. J. Vogel, A. M. Weljie, S. Yende, D. C. Angus
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2020)
Meeting Abstract
Critical Care Medicine
B. W. Winston, M. Banoei, H. J. Vogel, A. M. Weljie, S. Tende, D. C. Angus
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2019)
Meeting Abstract
Gastroenterology & Hepatology
Lillian Chau, Sarah A. Smith, Sayaka A. Ogawa, Kelly A. Whelan, Kathryn E. Hamilton, Jie Chen, Sue A. Keilbaugh, Franz Fogt, Meenakshi Bewtra, Barry Slaff, Aalim Weljie, Michael J. Bennett, Hiroshi Nakagawa, Gary D. Wu
Article
Biochemistry & Molecular Biology
Calena R. Marchand, Farshad Farshidfar, Jodi Rattner, Oliver F. Bathe
Article
Biology
Dania M. Malik, Seth Rhoades, Aalim Weljie
