Publications

Featured Publication:


"Unraveling the Pathogenesis of Crimean-Congo Hemorrhagic Fever: A Novel Approach via Non-Targeted Metabolomics by NMR Spectroscopy." (2023).

The application of metabolomics for studying modifications in host metabolism due to viral infections has proven to be a game-changing approach. Prior to our study, only one other ‘omics’ study has been carried out that investigates the interplay between the host and CCHFV and its subsequent pathogenesis. We employed NMR spectroscopy, given its advantages in terms of reproducibility, minimal sample preparation, and capability to analyze complex biofluids. Our methodology builds upon the proven success of metabolomics in the research of other viral hemorrhagic fevers such as Ebola, Marburg, and Dengue. Our research underlines the critical role of SAH, a metabolite involved in numerous biochemical reactions. We provide new insights into the metabolic alterations occurring in CCHF patients. These alterations not only shed light on the disease’s pathogenesis but also pave the way for potential biomarkers and therapeutic targets. Among all the metabolites detected, S-Adenosyl-L-homocysteine and Carnosine stood out as the most prevalent, warranting further exploration of their roles in CCHFV pathogenesis and their potential as therapeutic targets.

Dag, Cagdas, Oktay Göcenler, Kerem Kahraman, Derya Yapar, Yaren Kahraman, Cengizhan Büyükdag, Gülen Esken et al.

View 2006 - 2022 Publications 

514) Zhao, Mingjian, Ruowen Li, Chengxu Miao, Paolo Miccoli, and Jinghui Lu. "Non-invasive diagnosis of papillary thyroid microcarcinoma using a novel metabolomics analysis of urine." Endocrine (2024): 1-12.

513) Kaihara, Julyane NS, Fabio Rogerio de Moraes, Priscila Rezeck Nunes, Marco G. Alves, Ricardo C. Cavalli, Ljubica Tasic, and Valeria Cristina Sandrim. "Plasma metabolic profile reveals signatures of maternal health during gestational hypertension and preeclampsia without and with severe features." PloS one 19, no. 11 (2024): e0314053.

512) Ugwuodo, Chika Jude, Fabrizio Colosimo, Jishnu Adhikari, Samuel O. Purvine, Elizabeth K. Eder, David W. Hoyt, Stephanie A. Wright, Mary S. Lipton, and Paula J. Mouser. "Aromatic amino acid metabolism and active transport regulation are implicated in microbial persistence in fractured shale reservoirs." ISME Communications (2024): ycae149.

511) Barekat, Kayla, Emanuela Ricciotti, Soumita Ghosh, Christin Herrmann, Karl Keat, Charles-Antoine Assenmacher, Ceylan Tanes et al. "Concomitant suppression of COX-1 and COX-2 is insufficient to induce enteropathy associated with chronic NSAID use." bioRxiv (2024): 2024-11.

510) Kumar, Umesh, Monika Sodhi, Dinesh Kumar, Prince Vivek, Saket K. Niranjan, Ranjit Singh Kataria, Sudarshan Kumar et al. "Characterizing metabolome signature of colostrum, transition and mature milk of indigenous cows (Bos indicus) adapted to high altitude environment of Leh-Ladakh." Food Chemistry 464 (2025): 141767.

509) Biswas, Anisha, Babasaheb Bhaskarrao Borse, and Sachin R. Chaudhari. "Quantitative NMR analysis of sugars in natural sweeteners: Profiling in honey, jaggery, date syrup, and coconut sugar." Food Research International (2024): 115358.

508) Hanyuda, Akiko, Yoshihiko Raita, Takahiro Ninomiya, Kazuki Hashimoto, Naoko Takada, Kota Sato, Jin Inoue et al. "Metabolomic Profiling of Open-Angle Glaucoma Etiologic Endotypes: Tohoku Multi-Omics Glaucoma Study." Investigative Ophthalmology & Visual Science 65, no. 13 (2024): 44-44.

507) Osthoff, Gernot, and Petronella Nieuwoudt. "Non-Targeted Metabolomics of White Rhinoceros Colostrum and Its Changes During Early Lactation by 1H Nuclear Magnetic Resonance Spectroscopy." Metabolites 14, no. 11 (2024): 637.

506) Sangermani, Matteo, Indri Desiati, Solveig M. Jørgensen, Jia V. Li, Trygve Andreassen, Tone F. Bathen, and Guro F. Giskeødegård. "Stability in fecal metabolites amid a diverse gut microbiome composition: a one-month longitudinal study of variability in healthy individuals." Gut Microbes 16, no. 1 (2024): 2427878.

505) Cerulli, Antonietta, Luciana Maria Polcaro, Milena Masullo, and Sonia Piacente. "Spinacia oleracea L. Baby Leaves as a Source of Bioactive Principles: The Chemical Profiling of Eco-Sustainable Extracts by Using LC-ESI/HRMS-and 1H NMR-Based Metabolomics." Foods 13, no. 22 (2024): 3699.

504) Polcaro, Luciana Maria, Antonietta Cerulli, Milena Masullo, and Sonia Piacente. "Metabolomics of Withania somnifera L. extracts by an integrated LC-MS and NMR approach and evaluation of their tyrosinase inhibitory activity." Journal of Pharmaceutical and Biomedical Analysis 253 (2025): 116520.

503) Giménez-Valero, Carlos, Alejandro Andy Maciá-Vázquez, Dámaris Núñez-Gómez, Juan José Martínez-Nicolás, Pilar Legua, and Pablo Melgarejo. "Metabolic Profile Evolution of Citrus sinensis ‘Navelina’Under Different Cultivation Techniques and Water-Saving Strategies." Horticulturae 10, no. 11 (2024): 1187.

502) Sievers, Michael, Jasmine A. Rasmussen, Benjamin Nielsen, Rune C. Steinfurth, Mogens R. Flindt, Steven D. Melvin, and Rod M. Connolly. "Restored seagrass rapidly provides high‐quality habitat for mobile animals." Restoration Ecology (2024): e14343.

501) Bhattacharyya, Dipanjan, Marcia A. LeVatte, Upasana Singh, Fleur Issac, Mahmoud Karim, Saira Ali, August Sieben, Suyenna Huang, and David S. Wishart. "A novel colorimetric assay for the detection of urinary N1, N12-diacetylspermine, a known biomarker for colorectal cancer." Analytical Biochemistry (2024): 115717.

500) McNeil, Jordyn. "Differential Metabolomic Response of the Red Eared Slider Turtle (Trachemys scripta) Ventricle and Brain to Prolonged Anoxia Exposure." Master's thesis, University of Alaska Anchorage, 2024.

499) de Sousa, Ashelley Kettyllem Alves, Keyla Silva Nobre Pires, Isadora Hart Cavalcante, Iasmin Cristina Lira Cavalcante, Julia Domingues Santos, Maiara Ingrid Cavalcante Queiroz, Ana Catarina Rezende Leite et al. "Polystyrene microplastics exposition on human placental explants induces time-dependent cytotoxicity, oxidative stress and metabolic alterations." Frontiers in Endocrinology 15 (2024): 1481014.

498) Botello-Marabotto, Marina, Emma Plana, M. Carmen Martínez-Bisbal, Pilar Medina, Andrea Bernardos, Ramón Martínez-Máñez, and Manuel Miralles. "Metabolomic study for the identification of symptomatic carotid plaque biomarkers." Talanta (2024): 127211.

497) Islam, Md Shiful. "Catechol-Escherichia coli UM146 interaction revealed through multi-omics." (2024).

496) Randall, David, Asil Alsam, Julius Kieswich, Susan Joseph, Joseph Aduse-Opoku, Jonathan Swann, Alan Boyde et al. "Oral dysbiosis initiates periodontal disease in experimental kidney disease." Nephrology Dialysis Transplantation (2024): gfae266.

495) Humphries, Josephine E., Steven D. Melvin, Chantal Lanctôt, Hamish McCallum, David Newell, and Laura F. Grogan. "Chytridiomycosis disrupts metabolic responses in amphibians at metamorphic climax." Microbes and Infection (2024): 105438.

494) SINGH, ANANYA. "METABOLOMICS IN BIOMEDICAL RESEARCH." Omics Applications and Avenues (2024): 190.

493) Ferreira, Osania Emerenciano, Halax Duart Martins Silva, Adriana Barboza Alves, Mariana Guerra de Aguilar, Lúcia Pinheiro Santos Pimenta, Gustavo Henrique Gravatim Costa, Mara Cristina Pessôa da Cruz, Augusto Cesar da Silva Bezerra, and Alan Rodrigues Teixeira Machado. "Biochar enhances soil interactions and the initial development of sugarcane." Scientific Reports 14, no. 1 (2024): 27610.

492) Wijaya, I. Dewa Made Rizky, Izwandy Idris, Wan Iryani Wan Ismail, Asnuzilawati Asari, Noor Aniza Harun, R. Rudiyanto, Kustiariyah Tarman, Faridah Abas, and M. Maulidiani. "Discrimination of Marine Polychaete Species of Different Harvest Times Using FTIR Metabolomics."

491) da Silva, Gustavo H. Rodrigues, Luís F. Mendes, Gabriela Geronimo, Ludmilla D. de Moura, Juliana S. Ruas, Roger F. Castilho, Helon G. Cordeiro, Carmen V. Ferreira, Eneida de Paula, and Iola F. Duarte. "Schwann Cells Exposed to Articaine Display Distinct Toxic Pathways Compared to Lidocaine." Chemico-Biological Interactions (2024): 111315.

490) Casarrubios, Laura, Mónica Cicuéndez, Alberto Polo-Montalvo, María José Feito, Álvaro Martínez-del-Pozo, Daniel Arcos, Iola F. Duarte, and María Teresa Portolés. "Metabolomic characterization of MC3T3-E1pre-osteoblast differentiation induced by ipriflavone-loaded mesoporous nanospheres." Biomaterials Advances 166 (2025): 214085.

489) Luo, Yunqing, Chengjun Zhao, and Fei Chen. "Multi-omics research: principles and challenges in integrated analysis." BioDesign Research.

488) Nolis, Pau. "NMR spectroscopy of small molecules in solution." (2024).

487) Mendes, Luiza Tomé, Marcos C. Gama-Almeida, Desirée Lopes Reis, Ana Carolina Pires E. Silva, Rômulo Leão Silva Neris, Rafael Mello Galliez, Terezinha Marta Pereira Pinto Castiñeiras et al. "Longitudinal 1H NMR-Based Metabolomics in Saliva Unveils Signatures of Transition from Acute to Post-Acute Phase of SARS-CoV-2 Infection." Viruses 16, no. 11 (2024): 1769.

486) Pasam, Tulasi, Hara Prasad Padhy, and Manoj P. Dandekar. "Lactobacillus Helveticus Improves Controlled Cortical Impact Injury-Generated Neurological Aberrations by Remodeling of Gut-Brain Axis Mediators." Neurochemical Research 50, no. 1 (2025): 3.

485) Surwaich, Arhana, Ali Maqbool, Sajid Ali Majeedaro, Agha Taymoor Ali, Bushra Arain, Khurram Anwar, Shaharyar Ahsan, and Maheen Ejaz. "Evaluating Preventive Health Strategies: Salivary Biomarkers as Non-Invasive Indicators of Caries Risk in School Children: Salivary Biomarkers for Caries Risk in Children." Pakistan Journal of Health Sciences (2024).

484) Kanagaraja, Abinaya, and Pachaiappan Raman. "Microbial Biotechniques Progressions: Fundamental of Analytic Techniques." In Industrial Microbiology and Biotechnology: A New Horizon of the Microbial World, pp. 183-245. Singapore: Springer Nature Singapore, 2024.

483) Chena, Hu, Patrick C. Blaufussa, Dong-Fang Denga, Fabio Casub, Emma K. Kracod, Brian Shepherdd, Wendy M. Sealeye, Aaron M. Watsonc, Matthew F. Digmanf, and Deborah A. Samacg. "Impacts of alfalfa nutrient concentrate on pellet physical attributes, growth performance, metabolism and nutritional quality of rainbow trout, Oncorhynchus mykiss 2."

482) Kumar, Umesh, Monika Sodhi, Dinesh Kumar, Prince Vivek, Saket K. Niranjan, Ranjit Singh Kataria, Sudarshan Kumar et al. "Characterizing metabolome signature of colostrum, transition and mature milk of indigenous cows (Bos indicus) adapted to high altitude environment of Leh-Ladakh." Food Chemistry (2024): 141767.

481) Chen, Guixia, Lifeng Chen, Huiya Wang, Jiyong Zhang, Xiaoling Sun, Xiaoxin Chen, Jianxia Fan, Zhiwei Jia, and Yinying Huang. "1H NMR-Based Metabolomic Profiling and Comparison of Human Milk Across Different Lactation Stages in Secretors and Non-Secretors: A Study of Chinese Lactating Women." The Journal of Nutrition (2024).

480) Kandasamy, Sujatha, Won-Seo Park, In-Seon Bae, Jayeon Yoo, Jeonghee Yun, Van-Ba Hoa, and Jun-Sang Ham. "HRMAS-NMR-Based Metabolomics Approach to Discover Key Differences in Cow and Goat Milk Yoghurt Metabolomes." Foods 13, no. 21 (2024): 3483.

479) Marokane-Radebe, Cynthia, Adekunle Raimi, Stephen Amoo, and Rasheed Adeleke. "Metabolomic profiling and 16 S rRNA metabarcoding of endophytes of two Aloe species revealed diverse metabolites." AMB Express 14, no. 1 (2024): 122.

478) Gowen, Niamh, Nan Gai, Seamus James A. O'Mahony, Jonathan O’Regan, and David Anthony Goulding. "Non-Protein Nitrogen in Dairy Ingredients: A Closer Look at its Contribution in Infant Nutritional Product Formulation." Jonathan and Goulding, David Anthony, Non-Protein Nitrogen in Dairy Ingredients: A Closer Look at its Contribution in Infant Nutritional Product Formulation.

477) Polcaro, Luciana Maria, Antonietta Cerulli, Milena Masullo, and Sonia Piacente. "Metabolomics of Withania somnifera L. extracts by an integrated LC-MS and NMR approach and evaluation of their tyrosinase inhibitory activity." Journal of Pharmaceutical and Biomedical Analysis (2024): 116520.

476) Hasan, Sk, Nafizul Alam, Gazi Abdullah Mashud, and Subodh Bhujel. "Neural Network for Enhancing Robot Assisted Rehabilitation: A Systematic Review." (2024).

475) D’Elia, Maria, Carmen Marino, Rita Celano, Enza Napolitano, Anna Maria D’Ursi, Mariateresa Russo, and Luca Rastrelli. "Impact of a Withania somnifera and Bacopa monnieri Formulation on SH-SY5Y Human Neuroblastoma Cells Metabolism Through NMR Metabolomic." (2024).

474) Laghi, Luca, Maria Àngels Ortiz, Giacomo Rossi, Eva Román, Carlo Mengucci, Elisabet Cantó, Lucia Biagini et al. "Biomarkers of Frailty in Patients with Advanced Chronic Liver Disease Undergoing a Multifactorial Intervention Consisting of Home Exercise, Branched-Chain Amino Acids, and Probiotics." Biomolecules 14, no. 11 (2024): 1410.

473) Katherinatama, Aldia, Yonathan Asikin, Kazuki Shimoda, Momoko Shimomura, Fumimasa Mitsube, Kensaku Takara, and Koji Wada. "Characterization of Free and Glycosidically Bound Volatile and Non-Volatile Components of Shiikuwasha (Citrus depressa Hayata) Fruit." Foods 13, no. 21 (2024): 3428.

472) Kumar, Sazal, Rafiquel Islam, Wayne O'Connor, Steve D. Melvin, Frederic DL Leusch, Allison Luengen, and Geoff R. MacFarlane. "A metabolomic analysis on the toxicological effects of the universal solvent, dimethyl sulfoxide." Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology (2024): 110073.

471) Dağ, Çağdaş, and Kerem Kahraman. "Exploring the Biochemical Landscape of Bacterial Medium with Pyruvate as the Exclusive Carbon Source for NMR Studies." bioRxiv (2024): 2024-10.

470) Yang, Zhibo, Chuan Song, Qiuyu Lan, Bin Hu, Zonghua Ao, Xiaole Jiang, Suyi Zhang et al. "High-Throughput Metabolomics Reveals Effect of Glutathione-Enriched Inactive Dry Yeast on Volatile and Non-Volatile Compounds of Kiwi Wine." Available at SSRN 4979109.

469) Wang, Gangqi, Bernard M. van den Berg, Sarantos Kostidis, Kelsey Pinkham, Marleen E. Jacobs, Arthur Liesz, Martin Giera, and Ton J. Rabelink. "Spatial quantitative metabolomics enables identification of remote and sustained ipsilateral cortical metabolic reprogramming after stroke." bioRxiv (2024): 2024-10.

468) Boisen, Gabriella, Susanne Brogårdh-Roth, Jessica Neilands, Alex Mira, Miguel Carda-Diéguez, and Julia R. Davies. "Oral biofilm composition and phenotype in caries-active and caries-free children." Frontiers in Oral Health 5 (2024): 1475361.

467) Msomi, Mhlonipheni, Garland More, Noluyolo Nogemane, and Gerhard Prinsloo. "1h-Nmr-Based Metabolomics and Antioxidant Enzymes of Maize (Zea Mays) in Response to Exogenously Applied Dicarboxylic Acids (Photon)." Available at SSRN 4891435.

466) McGivern, Bridget B., Jared B. Ellenbogen, David W. Hoyt, John A. Bouranis, Brooke P. Stemple, Rebecca A. Daly, Samantha H. Bosman et al. "Polyphenol rewiring of the microbiome reduces methane emissions." bioRxiv (2024): 2024-10.

465) Sink, Warren John, Russell Fling, Ali Yilmaz, Rance Nault, Delanie Goniwiecha, Jack Harkema, Stewart Graham, and Tim Zacharewski. "2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin (TCDD) elicited dose-dependent shifts in the murine urinary metabolome associated with hepatic AHR-mediated differential gene expression." bioRxiv (2024): 2024-10.

464) Quifer-Rada, Paola, Laia Aguilar-Camprubí, Sara Samino, Nuria Amigó, Oria Soler, and Alba Padró-Arocas. "Metabolomics Approach to Identify Biomarkers of Acute and Subacute Mastitis in Milk Samples: A Pilot Case–Control Study." Metabolites 14, no. 10 (2024): 566.

463) Dias, Ana S., Catarina R. Almeida, Luisa Helguero, and Iola F. Duarte. "Antitumoral Activity and Metabolic Signatures of Dichloroacetate, 6-Aminonicotinamide and Etomoxir in Breast-Tumor-Educated Macrophages." Journal of Proteome Research (2024).

462) Lu, Jie, Jiawen Wang, Tuo Yao, Shengli Fu, Xiao Hu, and Lingtong Ye. "Metabolomic and enzymatic markers reveal critical air exposure threshold for Crassostrea hongkongensis quality." Food Research International (2024): 115309.

461) Young, Megan, Malene Aastrup, Nikayla Patel, Fenn Cullen, Esben SS Hansen, James E. Clark, Thomas R. Eykyn et al. "Altered systemic bioenergetic reserve in chronic kidney disease predisposes hearts to worse functional outcomes." bioRxiv (2024): 2024-10.

460) Brai, Annalaura, Cassia Neri, Franca Tarchi, Federica Poggialini, Chiara Vagaggini, Riccardo Frosinini, Sauro Simoni, Valeria Francardi, and Elena Dreassi. "Upcycling Milk Industry Byproducts into Tenebrio molitor Larvae: Investigation on Fat, Protein, and Sugar Composition." Foods 13, no. 21 (2024): 3450.

459) Martins, Cátia Falcão, Manolis Matzapetakis, David M. Ribeiro, Josipa Kuleš, Anita Horvatić, Nicholas Guillemin, Peter David Eckersall, João PB Freire, André M. Almeida, and José AM Prates. "Metabolomics and proteomics insights into hepatic responses of weaned piglets to dietary Spirulina inclusion and lysozyme supplementation." BMC Veterinary Research 20, no. 1 (2024): 505.

458) Casarrubios, Laura, Mónica Cicuéndez, Alberto Polo-Montalvo, María José Feito, Alvaro Martínez-del-Pozo, Daniel Arcos, Iola F. Duarte, and María Teresa Portolés. "Metabolomic characterization of MC3T3-E1pre-osteoblast differentiation induced by ipriflavone-loaded mesoporous nanospheres." Biomaterials Advances (2024): 214085.

457) Paglione, Marco, David CS Beddows, Anna Jones, Thomas Lachlan-Cope, Matteo Rinaldi, Stefano Decesari, Francesco Manarini et al. "Simultaneous organic aerosol source apportionment at two Antarctic sites reveals large-scale and eco-region specific components." Atmospheric Chemistry and Physics 24, no. 10 (2024): 6305-6322.

456) Li, Da-Wei, Rodrigo Cabrera Allpas, Munki Choo, Lei Bruschweiler-Li, Alexandar L. Hansen, and Rafael Brüschweiler. "COLMAR1d: A Web Server for Automated, Quantitative One-Dimensional Nuclear Magnetic Resonance-Based Metabolomics at Arbitrary Magnetic Fields." Analytical Chemistry (2024).

455) Singh, Rita, Sneh Bajpai, Amardeep Singh, Phulwanti Sharma, Yashwant Kumar, and Niraj Kumar. "Metabolomics of Chinese Hamster Ovary Cells." In Heterologous Protein Production in CHO Cells: Methods and Protocols, pp. 205-234. New York, NY: Springer US, 2024.

454) Qiu, Xu, and Xixiang Tang. "Metabolic adaptations of Shewanella eurypsychrophilus YLB-09 for survival in the high-pressure environment of the deep sea." Frontiers in Microbiology 15 (2024): 1467153.

453) Casarrubios Molina, Laura, Mónica Cicuéndez Maroto, Alberto Polo Montalvo, María José Feito Castellano, Álvaro Martínez Del Pozo, Daniel Arcos Navarrete, Iola F. Duarte, and María Teresa Portolés Pérez. "Metabolomic characterization of MC3T3-E1pre-osteoblast differentiation induced by ipriflavone-loaded mesoporous nanospheres." (2025).

452) de la Cabeza Fernández, María, Marta Sánchez, Laura Lozano-Chamizo, Ana Cristina Abreu, Ana Anguís-Morillas, Padreep K. Divakar, Marzia Marciello et al. "Electrospun nanofibers for localized drug release of a neuroprotective natural extract of USNEA ghattensis." European Journal of Pharmaceutics and Biopharmaceutics (2024): 114552.

451) Sahoo, Ashutosh, Deepanshu Verma, and Prajnadipta Panda. "A Gateway to Multi‐Omics‐Based Clinical Research." Applied Biotechnology and Bioinformatics: Agriculture, Pharmaceutical Research and Environment (2024): 235-256.

450) Hong, Natalie E., Alice Chaplin, Lin Di, Anastasia Ravodina, Graham H. Bevan, Huiyun Gao, Courteney Asase et al. "Nanoparticle-based itaconate treatment recapitulates low-cholesterol/low-fat diet-induced atherosclerotic plaque resolution." Cell Reports 43, no. 11 (2024).

449) Ruiz Coca, Mario, Cristian Perez-Fernandez, Ana Abreu, Ana Salmeron, Miguel Morales-Navas, Diego Ruiz-Sobremazas, Teresa Colomina, Ignacio Fernandez, and Fernando Sanchez-Santed. "Modulating Neurotoxic Effects of Prenatal Chlorpyrifos Exposure Through Probiotic and Vitamin D Gestational Supplementation: Unexpected Effects on Neurodevelopment and Sociability." bioRxiv (2024): 2024-11.

448) Artacho, Alejandro, Cintya González-Torres, Nuria Gómez-Cebrián, Paula Moles-Poveda, Javier Pons, Nuria Jiménez, María Jinglei Casanova et al. "Multimodal analysis identifies microbiome changes linked to stem cell transplantation-associated diseases." Microbiome 12, no. 1 (2024): 229.

447) Liu, Yongjian, Hao Liu, Shuqi Li, Shaojun Yu, and Heng Chen. "Synthesis of Harmaline N-9 Derivatives and Investigation of in Vitro Anticancer Activity."

446) Lima, Bruna R. de, Vanessa de Souza Marinho, Midori Nakamura Marques, Anne Caroline Gouvêa Ferreira, Edgar Aparecido Sanches, Jaqueline A. Bezerra, Pedro Henrique Campelo Felix, Jaime Paiva Lopes Aguiar, and Francisca Amaral Souza. "Influence of Thermosonication on Bioactive Compounds and Quality of Albertia Edulis Nectar." Available at SSRN 4998093 .

445) Saparuddin, Fatin, Mohd Naeem Mohd Nawi, Liyana Ahmad Zamri, Fazliana Mansor, Mohd Fairulnizal Md Noh, Mohd Azahadi Omar, Nur Shahida Abdul Aziz et al. "Metabolite, Biochemical, and Dietary Intake Alterations Associated with Lifestyle Interventions in Obese and Overweight Malaysian Women." Nutrients 16, no. 20 (2024): 3501.

444) Resendiz-Acevedo, Karen, Nuria Esturau-Escofet, Martha E. García-Aguilera, and Lena Ruiz-Azuara. "Casiopeinas®, CasIIIia and CasIIgly, Potent Anticancer Drugs and Their Metabolomic Effect in Triple-Negative Mesenchymal Breast Cancer. A Study by 1H-NMR." A Study by 1H-NMR.

443) Combe, Michelle, Kathy Sharon Isaac, Greg Potter, and Stanislav Sokolenko. "Current Research in Food Science." Current Research in Food Science 9 (2024): 100855.

442) Lu, Zhen, Na Gao, Junfei Zhan, Shuang Wang, Chenglong Ji, Li Zhang, and Huifeng Wu. "Comparative investigations on the metabolomic responses to cadmium in clams Ruditapes philippinarum from the Bohai Sea and South China Sea." Marine Pollution Bulletin 209 (2024): 117100.

441) Fresneda Alarcon, Michele, Yun Xu, Cassio Lima, Susanna Ford, Royston Goodacre, Marie Phelan, and Helen L. Wright. "Serum metabolomics identifies unique inflammatory signatures to distinguish rheumatoid arthritis responders and non-responders to TNF inhibitor therapy." medRxiv (2024): 2024-10.

440) Baud, Véronique, Leonardo Lordello, Stéphanie Nuan-Aliman, Karoline Kielbassa-Elkadi, Aurélie Montagne, Konstantina Kotta, Isabelle Martins et al. "Metabolic heterogeneity in DLBCL cells reveals an innovative antimetabolic combination strategy." (2024).

439) Trivedi, Rimjhim, Smita Singh, Vivek Singh, Sachin Yadav, Avinash Chandra Singh, Anup Singh, Rameshwar Nath Chaurasia, Abhai Kumar, and Dinesh Kumar. "Unravelling Neuroinflammation-Mediated Mitochondrial Dysfunction in Mild Cognitive Impairment: Insights from Targeted Metabolomics." Brain Organoid and Systems Neuroscience Journal.

438) Paudel, Devendra, Fuhua Hao, Umesh K. Goand, Sangshan Tian, Anthony M. Koehle, Loi V. Nguyen, Yuan Tian, Andrew D. Patterson, and Vishal Singh. "Elevated systemic total bile acids escalate susceptibility to alcohol-associated liver disease." iScience 27, no. 10 (2024).

437) Pudełko-Malik, Natalia, Dominika Drulis-Fajdasz, Łukasz Pruss, Karolina Anna Mielko-Niziałek, Dariusz Rakus, Agnieszka Gizak, and Piotr Młynarz. "A single dose of glycogen phosphorylase inhibitor improves cognitive functions of aged mice and affects the concentrations of metabolites in the brain." Scientific Reports 14, no. 1 (2024): 24123.

436) Imperlini, Esther, Federica Massaro, Angelica Grifoni, Francesco Maiurano, Anna Rita Taddei, Stefano Borocci, Francesco Buonocore, and Fernando Porcelli. "Membrane alteration, anti-virulence properties and metabolomic perturbation of a chionodracine-derived antimicrobial peptide, KHS-Cnd, on two bacteria models." Peptides (2024): 171311.

435) Chae, Young Kee, Hakbeom Kim, and Emine Sonay Elgin. "Discrimination of Turkish Propolis from Different Geographical Origins by NMR Spectroscopy." Journal of the Korean Magnetic Resonance Society 28, no. 3 (2024): 20-24.

434) Baud, Véronique, Thomas Becquard, Clara Benatar, Charles Bretot, Baptiste Eluard, Didier Bordereaux, Laura Thirouard et al. "The alternative NF-κB RelB subunit is a novel critical sensor of lipid metabolism to promote tumor development." (2024).

433) Bedulina, Daria, Špela Korez Lupše, Lars Hildebrandt, Yaqing Duan, Ole Klein, Sebastian Primpke, Christian Bock et al. "Effect of Particles from Wind Turbine Blades Erosion on Blue Mussels Mytilus Edulis." Available at SSRN 4882025.

432) Wojtowicz, Wojciech, R. Tarkowski, A. Olczak, A. Szymczycha-Madeja, P. Pohl, A. Maciejczyk, Ł. Trembecki, R. Matkowski, and Piotr Młynarz. "Serum metabolite and metal ions profiles for breast cancer screening." Scientific Reports 14, no. 1 (2024): 24559.

431) Johnson, Hayden Tyler. "Developing Accurate and Automated High-Field and Benchtop NMR-Based Metabolomic Techniques Using Neural Networks." PhD diss., The University of Memphis, 2024.

430) Amigó, N., L. Cabau, S. Iftimie, R. Pavón, X. Gavaldó, X. Correig, S. Paredes, J. C. Vallvé, and A. Castro. "Lipidomic and Metabolomic Changes in Community-acquired and COVID-19 Pneumonia."

429) Krebs, Nina. "The effect of acute warming on protein turnover and oxygen demand in stenothermal and eurythermal eelpouts." PhD diss., Universität Bremen, 2024.

428) Alves, Gabriel Machado. "Chemical characterization of sour beers with added fruits by hydrogen nuclear magnetic resonance." (2024).

427) Ερμείδης, Δημήτριος. "Ταυτοποίηση ενώσεων σε δείγματα ανθρωπίνων κοπράνων που σχετίζονται μ ε τη λήψη φλαβονοειδών." (2024).

426) Parenti, Mariana, Rebecca J. Schmidt, Daniel J. Tancredi, Irva Hertz-Picciotto, Cheryl K. Walker, and Carolyn M. Slupsky. "Network lOpen."

425) Castro, Alex, Antonio Gilberto Ferreira, Aparecida Maria Catai, Matheus Alejandro Bolina Amaral, Claudia Regina Cavaglieri, and Mara Patrícia Traina Chacon-Mikahil. "Metabolic Predictors of Cardiorespiratory Fitness Responsiveness to Continuous Endurance and High-Intensity Interval Training Programs: The TIMES Study—A Randomized Controlled Trial." Metabolites 14, no. 9 (2024): 512.

424) Fei, Shuangwen, Xiangrong Wang, Xinling Qin, Yaqian Yuan, Yujuan Zheng, Xue Lin, Jiamu Kang, Sixin Liu, and Congfa Li. "Efficient nata de coco production of Komagataeibacter nataicola driven by microbiota-fermented coconut water: biological and structural characteristics." Food Bioscience (2024): 105184.

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627) Rodrigues, Barbara Martins, Ramon Costa Alvarenga, Dante Pazzanese Duarte Lanna, Afonso de Liguori Oliveira, Caroline Ceribeli, Banny Silva Barbosa Correia, Luiz Alberto Colnago, Daniel Rodrigues Cardoso, Fernando Antônio de Souza, and Leandro Sâmia Lopes. "Aged-beef quality and fatty acid profile of subcutaneous fat from Nellore and Nellore× Angus crossbred young bulls finished in the feedlot with a high-lipid diet." Animal Production Science (2023).

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623) Johnsen, Philip. "Application of Environmental Metabolomics for Assessment of Aquatic Invertebrate Sensitivity to Naphthenic Acids." Master's thesis, University of Waterloo, 2023.

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620) Ducros, Loïck, Mohamed Touaibia, Nicolas Pichaud, and Simon G. Lamarre. "Resilience and phenotypic plasticity of Arctic char (Salvelinus alpinus) facing cyclic hypoxia: insights into growth, energy stores and hepatic metabolism." Conservation Physiology 11, no. 1 (2023): coad099.

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617) Domżał, Barbara, Ewa Klaudia Nawrocka, Dariusz Gołowicz, Michał Aleksander Ciach, Błażej Miasojedow, Krzysztof Kazimierczuk, and Anna Gambin. "Magnetstein: An Open-Source Tool for Quantitative NMR Mixture Analysis Robust to Low Resolution, Distorted Lineshapes, and Peak Shifts." Analytical Chemistry (2023).

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614) Litzenberg, Kerryanne Lenore. "The Physiological Effects of Age and Temperature on Blood Chemistry, Metabolism, and Mortality of Harvested Horseshoe Crabs (Limulus polyphemus)." PhD diss., College of Charleston, 2023.

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598) Govindasamy, Chandramohan, Khalid S. Al-Numair, Mohammed A. Alsaif, Abilash Valsala Gopalakrishnan, and Raja Ganesan. "Assessment of metabolic responses following silica nanoparticles in zebrafish models using 1H NMR analysis." Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology (2023): 109808.

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595) Hurtado, Joaquín I., Andrés López-Radcenco, José Luis Izquierdo-García, Fernando Rodríguez, Guillermo Moyna, Gonzalo Greif, and Nicolas Nin. "A comparative NMR-based metabolomics study of lung parenchyma of severe COVID-19 patients." Frontiers in Molecular Biosciences 10 (2023).

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24) Ruiz-Rico, María, Simone Renwick, Sarah J. Vancuren, Avery V. Robinson, Connor Gianetto-Hill, Emma Allen-Vercoe, and José M. Barat. "Impact of food preservatives based on immobilized phenolic compounds on an in vitro model of human gut microbiota." Food Chemistry 403 (2023): 134363.

23) Tripathi, Shweta, Manikyaprabhu Kairamkonda, Payal Gupta, and Krishna Mohan Poluri. "Dissecting the molecular mechanisms of producing biofuel and value-added products by cadmium tolerant microalgae as sustainable biorefinery approach." Chemical Engineering Journal 454 (2023): 140068.

22) Han, Dong Min, Ju Hye Baek, Byung Hee Chun, and Che Ok Jeon. "Fermentative features of Bacillus velezensis and Leuconostoc mesenteroides in doenjang-meju, a Korean traditional fermented soybean brick." Food Microbiology 110 (2023): 104186.

21) Baek, Ju Hye, Kyung Hyun Kim, Dong Min Han, Se Hee Lee, and Che Ok Jeon. "Effects of glutinous rice paste and fish sauce on kimchi fermentation." LWT 173 (2023): 114253.

20) Pereira, Tayla CS, Alzenir R. Souza, Paula B. Daltro, Maria GA Carosio, Antonio G. Ferreira, Regina V. Oliveira, Vitor Fortuna, and Paulo R. Ribeiro. "Blood plasma and bone marrow interstitial fluid metabolomics of sickle cell disease patients with osteonecrosis: An exploratory study to dissect biochemical alterations." Clinica Chimica Acta 539 (2023): 18-25.

19) Jiang, Lin, and Bo Wang. "Metabolomics study on southern hard clams (Mercenaria campechiensis) response to diclofenac exposure." Environmental Science: Advances (2023).

18) Bragulat, Ana P. Flores, Isabel Ortiz, Jaime Catalán, Jesus Dorado, Manuel Hidalgo, Luis Losinno, Marta Dordas-Perpinyà et al. "Time-lapse imaging and developmental competence of donkey eggs after ICSI: Effect of preovulatory follicular fluid during oocyte in vitro maturation." Theriogenology 195 (2023): 199-208.

17) Canella, Rita, Federica Brugnoli, Mariana Gallo, Jeffrey W. Keillor, Anna Terrazzan, Elena Ferrari, Silvia Grassilli et al. "A Multidisciplinary Approach Establishes a Link between Transglutaminase 2 and the Kv10. 1 Voltage-Dependent K+ Channel in Breast Cancer." Cancers 15, no. 1 (2023): 178.

16) Lee, Sheng-Han, Zhi-Yi Du, Wei-Chen Tseng, Wan-Yu Lin, Mei-Huei Chen, Ching-Chun Lin, Hao-Jan Liang et al. "Identification of serum metabolic signatures of environmental-leveled phthalate in the Taiwanese child population using NMR-based metabolomics." Environmental Pollution 316 (2023): 120454.

15) Yim, Dong-Gyun, Hyun Jun Kim, Sung-Su Kim, Hag Ju Lee, Jae-Kyung Kim, and Cheorun Jo. "Effects of different X-ray irradiation doses on quality traits and metabolites of marinated ground beef during storage." Radiation Physics and Chemistry 202 (2023): 110563.

14) Kunc, Martin, Pavel Dobeš, Rachel Ward, Saetbyeol Lee, Radim Čegan, Silvie Dostálková, Kateřina Holušová et al. "Omics-based analysis of honey bee (Apis mellifera) response to Varroa sp. parasitisation and associated factors reveals changes impairing winter bee generation." Insect Biochemistry and Molecular Biology 152 (2023): 103877.

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8) He, Ying, Bang Cheng, Bing-Jian Guo, Zheng Huang, Jing-Hua Qin, Qian-Yi Wang, Lin-Lin Feng et al. "Metabonomics and 16S rRNA gene sequencing to study the therapeutic mechanism of Danggui Sini decoction on collagen-induced rheumatoid arthritis rats with Cold Bi syndrome." Journal of Pharmaceutical and Biomedical Analysis 222 (2023): 115109.

7) Verlander, Jill W., Hyun-Wook Lee, Susan M. Wall, Autumn N. Harris, and I. David Weiner. "The proximal tubule through an NBCe1-dependent mechanism regulates collecting duct phenotypic and remodeling responses to acidosis." American Journal of Physiology-Renal Physiology 324, no. 1 (2023): F12-F29.

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1) Huang, Feng, Tong Zhang, Bin Li, Shaosong Wang, Chang Xu, Caihua Huang, and Donghai Lin. "NMR-based metabolomic analysis for the effects of moxibustion on imiquimod-induced psoriatic mice." Journal of Ethnopharmacology 300 (2023): 115626.

Case Studies

The case studies below showcase various studies that were performed using Chenomx technology and services.

 

Analyzing the Metabolic Effects of Acetaminophen

 

Developing Biomarkers for Adverse Drug Responses

 

Pathways From Serological Metabolite Profiles

Acetaminophen is the most common identifiable cause of acute liver failure, and is an excellent model compound for studying liver toxicity. Acetaminophen toxicity has thus become a very active area of research. Identifying and quantifying metabolites associated with acetaminophen toxicity is an integral part of this research, and Chenomx is uniquely equipped to extract this information from biofluid samples.

Drug-induced liver injury is the leading reason that drug candidates fail. Identifying a suite of toxicity biomarkers for use in preclinical screening of drug candidates will allow drugs with harmful side effects to be identified earlier. Biomarkers that can be used to monitor or stage diseases will also offer insight into the net metabolic effect of a drug and can provide information for developing new drugs or adjusting treatment. Chenomx software offers powerful tools to aid in identifying these biomarkers.

Metabolomic data sets obtained using Chenomx NMR Suite often require additional analysis to place them in proper context. The GeneGo pathway analysis platform can help establish this context. In this note, we present an example analysis using serological metabolic profiles from Chenomx NMR Suite, known inflammatory markers from prior studies of the K/BxN mouse model and the GeneGo platform to generate a mechanistic hypothesis for the K/BxN mouse model.

Application Notes

Methods

Accurate CSI Quantification for Targeted Profiling

Accurately quantifying metabolites using targeted profiling in Chenomx NMR Suite requires using a chemical shape and shift indicator (CSI) of known concentration. As a result, the accuracy of the CSI concentration has a significant influence on quantification accuracy using this technique. Measuring ratios of the CSI peak area with that of a second, commercially available standard under optimal acquisition conditions offers a simple method of accurately measuring the concentration of the CSI.

 Optimizing Spectra for Metabolomics

Chenomx Processor allows you to work with NMR spectra from a variety of sources, helping you apply phasing and baseline correction through manual and semi-automated tools, and offering advanced lineshape correction through reference deconvolution. Processor also allows you to define chemical shape indicator (CSI) parameters and determine sample pH via indicator compounds. These are necessary prerequisites to analyzing your spectra with Chenomx Profiler.

Sample Types

Targeted Profiling of Common Metabolites in Saliva

Saliva is an excellent biofluid for analysis by targeted profiling. It is easily collected by individuals with minimal training, using noninvasive techniques. Targeted profiling of saliva samples can provide identification and quantification of many of the small molecule metabolites commonly found in saliva, and may allow the development of simple screening procedures for a variety of diseases. In this note we present a list of common metabolites found in human saliva, and techniques for targeted profiling of saliva spectra with Chenomx NMR Suite.

Metabolites in Blood Serum and Plasma

Blood serum and plasma are biofluids that are increasingly important in NMR-based metabolomics analysis. In this note we discuss several approaches to the analysis of serum using Chenomx NMR Suite, focusing on relaxation-edited NMR (CPMG) and physical separation of protein and metabolites using ultrafiltration. The CPMG method is simpler to apply, but the spectra are easier to analyze when protein is removed from a sample.

 

Targeted Profiling of Common Metabolites in Urine

Urine is a readily-collected, information-rich biofluid that can provide insight into the metabolic state of an organism. As a result, urine is often a focus in metabolomics investigations using NMR and MRI spectroscopy, in both diagnostic and monitoring applications. Targeted profiling is a powerful tool that can drive such studies, providing direct identification and quantification of a variety of metabolites. In this note we present a list of common metabolites found in many NMR spectra of human urine and several strategies for approaching targeted profiling of such spectra with Chenomx NMR Suite.

 

Identifying Metabolites in Biofluids

In this note we present a rapid, efficient method for identifying metabolites in biofluid NMR spectra using targeted profiling. Conventional techniques for identifying and quantifying metabolites in such spectra are labor-intensive and error-prone, as positions and linewidths of peaks can vary widely with changes in pH and other solution matrix effects. The length of time and level of operator skill needed to analyze large numbers of these complex spectra are significant barriers to the widespread application of NMR in metabolomics.

Statistical Analysis

Statistical Analysis of Targeted Profiling Data

Analysis of 1H NMR spectra in metabolomics studies often requires multivariate pattern recognition techniques to extract meaningful results. Targeted profiling offers the ability to analyze spectra based directly on the identity and quantities of individual compounds. Profiles created using targeted profiling in Chenomx NMR Suite can be used as input in statistical software packages such as Umetrics SIMCA-P. Performing PCA on Chenomx targeted profiles yields information-rich results that allow rapid biological interpretation, since group separation can be directly correlated to variations in specific metabolite concentrations.

Correcting Lineshapes in NMR Spectra

In this note we present a method for removing lineshape distortions from nuclear magnetic resonance (NMR) spectra prior to more detailed analysis. Reference deconvolution is a method of reconstructing an ideal spectrum by removing lineshape distortions caused by field inhomogeneity. Applying reference deconvolution has been found to improve the quality of fit of a spectrum using targeted profiling in Chenomx NMR Suite. However, successful application of reference deconvolution to a spectrum requires some preprocessing and the presence of an appropriate reference peak.

 

Statistical Analysis of Spectral Binning Data

Analysis of 1H NMR spectra in metabolomics studies often requires multivariate pattern recognition techniques to extract meaningful results. Spectral binning is an effective data reduction technique commonly used to prepare spectra for multivariate analysis. Spectral binning output from the Profiler module of Chenomx NMR Suite can readily be analyzed with multivariate analysis software packages like Umetrics SIMCA-P.