Article
Neurosciences
Maxime Francois, Avinash Karpe, Jian-Wei Liu, David Beale, Maryam Hor, Jane Hecker, Jeff Faunt, John Maddison, Sally Johns, James Doecke, Stephen Rose, Wayne R. Leifert
Summary: This study compared the metabolomic and proteomic signature of saliva from cognitively normal individuals and patients with MCI or AD. Significant alterations in multiple cellular pathways were found, indicating that disease progression impacts various cellular processes at the omics level. The study suggests that integration of multi-omics parameters could be useful in identifying new biomarkers for AD.
JOURNAL OF ALZHEIMERS DISEASE
(2021)
Review
Biochemistry & Molecular Biology
Qiaolifan Aerqin, Zuo-Teng Wang, Kai-Min Wu, Xiao-Yu He, Qiang Dong, Jin-Tai Yu
Summary: This review summarizes the progress made in the discovery of reliable Alzheimer's disease (AD) biomarkers using genomics, transcriptomics, proteomics, and metabolomics. The importance of these biomarkers in the diagnosis and treatment of AD is discussed.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Review
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Jodie Lord, Bradley Jermy, Rebecca Green, Andrew Wong, Jin Xu, Cristina Legido-Quigley, Richard Dobson, Marcus Richards, Petroula Proitsi
Summary: This study explored the causal relationship between metabolites associated with midlife cognition and AD, highlighting XL.HDL.FC, total lipids, phospholipids, and XL.HDL particle concentration as potential causal candidates. Evidence suggests that GP may also play a role in AD pathology and warrants further investigation. Understanding these relationships could inform risk reduction strategies for AD, which is believed to develop decades before symptoms appear.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Marina Amaral Alves, Santosh Lamichhane, Alex Dickens, Aidan McGlinchey, Henrique Caracho Ribeiro, Partho Sen, Fang Wei, Tuulia Hyotylainen, Matej Oresic
Summary: Lipids play important roles in biology, such as energy storage and cell membrane structure. Lipid metabolism is tightly regulated, and disturbances in lipid-related pathways are involved in the pathogenesis of common diseases. Advances in lipidomics provide new methods for lipid research.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2021)
Article
Biochemistry & Molecular Biology
Yafei Zheng, Qingqing Xu, Qihao Jin, Yao Du, Junjie Yan, Hongchang Gao, Hong Zheng
Summary: In this study, the urinary and faecal metabolic profiles in APP/PS1 mice were investigated, revealing disrupted metabolic phenotypes and potential biomarkers at earlier stage of AD.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Paniz Jasbi, Xiaojian Shi, Ping Chu, Natalie Elliott, Haley Hudson, Douglas Jones, Geidy Serrano, Brandon Chow, Thomas G. Beach, Li Liu, Garilyn Jentarra, Haiwei Gu
Summary: This study conducted metabolomics analysis on brain tissues of dementia patients, identifying metabolite markers that can distinguish different cases, providing important clues for understanding disease mechanisms and identifying therapeutic targets, laying the foundation for future research on the diagnosis and treatment of Alzheimer's disease.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Neurosciences
Elena Puris, Stepan Kouril, Lukas Najdekr, Seppo Auriola, Sanna Loppi, Paula Korhonen, Mireia Gomez-Budia, Gert Fricker, Katja M. Kanninen, Tarja Malm, David Friedecky, Mikko Gynther
Summary: Neuroinflammation is an important feature in the pathogenesis and progression of central nervous system diseases. In this study, a lipopolysaccharide-induced inflammation mouse model was used to investigate the effects of systemic inflammation on the metabolome, lipidome, and protein expression in the mouse brain and plasma. The study found that the hippocampus was more vulnerable to LPS-induced inflammation, and identified specific changes in metabolism and lipids in the brain regions.
Article
Pharmacology & Pharmacy
Jericha Mill, Vihar Patel, Ozioma Okonkwo, Lingjun Li, Thomas Raife
Summary: Diagnosing Alzheimer's disease in the early stage is challenging. This study explores the potential utility of erythrocyte metabolite profiles as biomarkers for screening AD. Comparing the metabolomes of AD patients and control group, increased amino acid metabolism and decreased lipid metabolism were observed in AD. Sphingolipids, previously implicated in AD, were consistently decreased in AD patients, suggesting their potential as risk markers for AD development.
JOURNAL OF PHARMACEUTICAL ANALYSIS
(2022)
Review
Biochemistry & Molecular Biology
Chunyuan Yin, Amy C. C. Harms, Thomas Hankemeier, Alida Kindt, Elizabeth C. M. de Lange
Summary: Alzheimer's disease is an aging-related neurodegenerative disease that leads to progressive memory loss and cognitive decline. Understanding the pathogenesis and etiology of the disease is still limited, and there are no effective treatments available. Metabolomics offers a valuable approach to studying biochemical changes and discovering potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Alvaro Gonzalez-Dominguez, Raul Gonzalez-Dominguez
Summary: This review article discusses the challenges of identifying reliable biomarkers in metabolomics and examines the role of inter-individual variability in this process. Additionally, future perspectives for the applicability of metabolomics in biomedical research and clinical practice are provided.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2024)
Review
Immunology
Denise Battaglini, Miqueias Lopes-Pacheco, Hugo C. Castro-Faria-Neto, Paolo Pelosi, Patricia R. M. Rocco
Summary: This article summarizes the commonly used biomarkers in COVID-19, which play important roles in predicting disease severity, hospitalization, ICU admission, and mortality. It also discusses how novel analytical strategies can be applied in clinical practice, emphasizing the need for future research to focus on identifying a limited but essential number of laboratory biomarkers for predicting prognosis and outcomes in severe COVID-19.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Tomasz Pienkowski, Tomasz Kowalczyk, Noemi Garcia-Romero, Angel Ayuso-Sacido, Michal Ciborowski
Summary: The diagnosis of glioma relies on imaging methods that cannot differentiate between different stages and subtypes. Patients are usually diagnosed in the symptomatic stage. Molecular alterations and tumor biomarkers can be used to diagnose asymptomatic gliomas. A multiomics approach can track physiological changes and serve as a non-invasive diagnostic method.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2022)
Article
Biochemistry & Molecular Biology
Pratishtha Chatterjee, Yeo-Jin Cheong, Atul Bhatnagar, Kathryn Goozee, Yunqi Wu, Matthew McKay, Ian J. Martins, Wei L. F. Lim, Steve Pedrini, Michelle Tegg, Victor L. Villemagne, Prita R. Asih, Preeti Dave, Tejal M. Shah, Cintia B. Dias, Stephanie J. Fuller, Heidi Hillebrandt, Sunil Gupta, Eugene Hone, Kevin Taddei, Henrik Zetterberg, Kaj Blennow, Hamid R. Sohrabi, Ralph N. Martins
Summary: The study identified associations between plasma neurofilament light chain, a marker of neurodegeneration, and plasma metabolites, suggesting a link between neurodegeneration and biological pathways associated with Alzheimer's disease pathology. Further validation in independent cohorts is needed to explore the potential of these metabolites as prognostic markers for neurodegenerative diseases.
JOURNAL OF NEUROCHEMISTRY
(2021)
Article
Medicine, Research & Experimental
Pengyu Liu, Wenxuan Wang, Fei Wang, Jiaqi Fan, Jinan Guo, Tao Wu, Dongliang Lu, Qingchun Zhou, Zhuohao Liu, Yuliang Wang, Zhiqun Shang, Franky Leung Chan, Wei Yang, Xin Li, Shan-Chao Zhao, Qingyou Zheng, Dinglan Wu
Summary: In this study, proteomic and metabolomic analysis of exosomes from prostate cancer (PCa) patients was performed. Several potential biomarkers for PCa and castration resistant prostate cancer (CRPC) were identified, including the proteins LRG1 and ITIH3. Metabolomic evaluation also revealed differentially expressed metabolites. These findings suggest the potential of exosomal proteins and metabolites as markers for CRPC and confirm the important role of the protein LRG1 in PCa progression.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Medicine, General & Internal
Ali Eqbal, Alicia Martin, James D. Doecke, Desmond Patrick
Summary: This study evaluated the short-term efficacy and safety of low-dose therapeutic drug-monitored (TDM) thioguanine in patients with inflammatory bowel disease. The results showed that thioguanine was well tolerated in 63% of patients, with a clinical response rate of 62% and a high maintenance of remission rate at 76%.
INTERNAL MEDICINE JOURNAL
(2023)
Article
Clinical Neurology
Pratishtha Chatterjee, Steve Pedrini, James D. Doecke, Rohith Thota, Victor L. Villemagne, Vincent Dore, Abhay K. Singh, Penghao Wang, Stephanie Rainey-Smith, Christopher Fowler, Kevin Taddei, Hamid R. Sohrabi, Mark P. Molloy, David Ames, Paul Maruff, Christopher C. Rowe, Colin L. Masters, Ralph N. Martins
Summary: This study investigated the changes in several blood biomarkers across the AD continuum and their associations with cognitive decline and brain Aβ-PET load. The results showed that plasma Aβ1-42/Aβ1-40 ratio decreased, p-tau181 and GFAP increased in predicting the β-amyloid positive/negative status across the AD continuum.
ALZHEIMERS & DEMENTIA
(2023)
Article
Gastroenterology & Hepatology
Sally Mortlock, Anton Lord, Grant Montgomery, Martha Zakrzewski, Lisa A. Simms, Krupa Krishnaprasad, Katherine Hanigan, James D. Doecke, Alissa Walsh, Ian C. Lawrance, Peter A. Bampton, Jane M. Andrews, Gillian Mahy, Susan J. Connor, Miles P. Sparrow, Sally Bell, Timothy H. Florin, Jakob Begun, Richard B. Gearry, Graham L. Radford-Smith
Summary: This study identified genetic loci associated with medically refractory ulcerative colitis (UC) through a genome wide association analysis. The findings suggest different genetic risk factors for medically refractory UC compared to non-medically refractory UC. Further research may uncover additional loci related to disease severity.
JOURNAL OF CROHNS & COLITIS
(2023)
Article
Clinical Neurology
Xin Huang, Yihan Li, Christopher Fowler, James D. Doecke, Yen Ying Lim, Candace Drysdale, Vicky Zhang, Keunha Park, Brett Trounson, Kelly Pertile, Rebecca Rumble, John W. Pickering, Robert A. Rissman, Floyd Sarsoza, Sara Abdel-Latif, Yong Lin, Vincent Dore, Victor Villemagne, Christopher C. Rowe, Jurgen Fripp, Ralph Martins, James S. Wiley, Paul Maruff, Jacobo E. Mintzer, Colin L. Masters, Ben J. Gu
Summary: This study examined leukocyte antigens in sporadic Alzheimer's disease (AD) and identified differentially expressed markers. A proposed panel of four leukocyte markers showed high predictive accuracy for PET A beta status. These findings were validated in independent cohorts, demonstrating the utility of leukocyte-based biomarkers for AD screening and diagnosis.
ALZHEIMERS & DEMENTIA
(2023)
Article
Biochemical Research Methods
Licai Huang, James P. Long, Ehsan Irajizad, James D. Doecke, Kim-Anh Do, Min Jin Ha
Summary: This study introduces a mediation analysis framework for multilevel molecular tumor profiling, which can handle various types of outcome variables and is suitable for high-throughput molecular profiling data. By analyzing kidney renal clear cell carcinoma proteogenomic data, genes that are mediated by proteins and the underlying mechanisms for various survival outcomes are identified, capturing disease-specific clinical characteristics in both short and long-term.
Article
Environmental Sciences
Katie E. Hillyer, Utpal Bose, James A. Broadbent, Andrew Bissett, David J. Beale
Summary: Legacy contamination from human use is a major concern for estuaries worldwide. This study utilizes multi-omics techniques and traditional sediment quality analysis to investigate the molecular and cellular responses of invertebrate communities in estuaries exposed to complex contaminants. The research provides insights into the different modes of toxicity and local adaptation to multiple pollutants in a complex estuarine environment.
ENVIRONMENTAL POLLUTION
(2023)
Article
Environmental Sciences
Katie E. Hillyer, Eric Raes, Andrew Bissett, David J. Beale
Summary: The study characterized bacterial communities in a metal-contaminated estuary sediment using multiple methods, and found additional contamination in areas with high metal concentrations. The dominant bacterial phyla included Proteobacteria and Desulfobacteria, and high concentration areas were enriched with metabolically versatile and biofilm forming phyla. The results can be used to inform management decisions and predictive models.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biochemistry & Molecular Biology
Avinash V. Karpe, Melanie L. Hutton, Steven J. Mileto, Meagan L. James, Chris Evans, Amol B. Ghodke, Rohan M. Shah, Suzanne S. Metcalfe, Jian-Wei Liu, Tom Walsh, Dena Lyras, Enzo A. Palombo, David J. Beale
Summary: This study investigated the impact of giardiasis on the host's body and the effects of changes in gut microbiota on metabolic pathways. The results revealed significant alterations in energy and oxidative stress pathways in the gut and liver during giardiasis and identified changes in bacterial populations. These findings contribute to the discovery of new biomarkers and the development of precision health solutions for giardiasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Neurosciences
Charisse N. Winston, Oliver Langford, Natalie Levin, Rema Raman, Kevin Yarasheski, Tim West, Sara Abdel-Latif, Michael Donohue, Akinori Nakamura, Kenji Toba, Colin L. Masters, James Doecke, Reisa A. Sperling, Paul S. Aisen, Robert A. Rissman
Summary: The study aimed to determine whether a blood-based screening test can accurately identify patients' amyloid burden and improve screening efficiency. The results showed that plasma A beta (42)/A beta (40) is the best biomarker for predicting amyloid accumulation in the brain, and blood samples processed within 2 hours after collection had better predictive performance.
JOURNAL OF ALZHEIMERS DISEASE
(2023)
Article
Neurosciences
Alex M. Pagnozzi, Liza van Eijk, Kerstin Pannek, Roslyn N. Boyd, Susmita Saha, Joanne George, Samudragupta Bora, DanaKai Bradford, Michael Fahey, Michael Ditchfield, Atul Malhotra, Helen Liley, Paul B. Colditz, Stephen Rose, Jurgen Fripp
Summary: Infants born very preterm face neurodevelopmental challenges and early identification through clinical assessment and MRI can enable targeted interventions. This study used a prospective cohort of preterm infants and identified early MRI biomarkers for neurodevelopmental outcomes using advanced imaging techniques. The results demonstrated the utility of MRI prior to term equivalent age for predicting outcomes and initiating early interventions.
Article
Environmental Sciences
Rohan Shah, Thao V. Nguyen, Anna Marcora, Angela Ruffell, Andrew Hulthen, Khoa Pham, Gene Wijffels, Cate Paull, David J. Beale
Summary: Insect biodegradation of plastics has shown significant progress, providing new possibilities for plastic waste treatment. This study focused on the metabolism of greater wax moth larvae fed on polylactic acid plastic (PLA) blocks. The results revealed metabolic disturbances and oxidative stress in the larvae due to PLA ingestion.
ENVIRONMENTAL RESEARCH
(2023)
Review
Chemistry, Analytical
Joost L. D. Nelis, Veronika J. Schacht, Amanda L. Dawson, Utpal Bose, Aristeidis S. Tsagkaris, Darina Dvorakova, David J. Beale, Ali Can, Christopher T. Elliott, Kevin V. Thomas, James A. Broadbent
Summary: Agricultural systems are facing increasing concerns over food safety and security due to the impact of micro-and nanoplastic (MNP) pollution. To address this issue, it is necessary to understand the effects and impacts of MNP and develop mitigation strategies. This article discusses the entry pathways of MNP into the human food chain and their effects on food and feed sources, as well as identifies research gaps hindering accurate risk assessments. Emerging analytical methods and interdisciplinary approaches can help close these gaps and accurately quantify MNP pollution risks, providing essential data for policy development and legislation to prevent further food safety and security problems caused by MNP pollution.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Clinical Neurology
Matteo Senesi, Victoria Lewis, Shiji Varghese, Christiane Stehmann, Amelia McGlade, James D. Doecke, Laura Ellett, Shannon Sarros, Christopher J. Fowler, Colin L. Masters, Qiao-Xin Li, Steven J. Collins
Summary: The most frequently used biomarkers for pre-mortem clinical diagnosis of sporadic Creutzfeldt-Jakob disease (sCJD) include concentrations of the 14-3-3 and total tau (T-tau) proteins, as well as the application of protein amplification techniques. Combining the results of these three cerebrospinal fluid biomarkers can increase the sensitivity and accuracy in diagnosing sCJD before death, providing the best chance for early detection.
FRONTIERS IN NEUROLOGY
(2023)
Review
Microbiology
Avinash V. Karpe, David J. Beale, Cuong D. Tran
Summary: Enteric protozoan pathogenic infections contribute significantly to gastrointestinal illnesses globally, particularly in remote and indigenous communities with limited access to clean water and sanitation. Medicinal treatments for these robust pathogens often lead to dysbiosis and subsequent opportunistic pathogen invasion, antimicrobial resistance, and functional gastrointestinal disorders. Nutritional supplementation, including proteins, prebiotics, probiotics, synbiotics, and food formulations, can help recover from dysbiosis and build resilience against future infections. Systems biology techniques are effective in understanding the biochemistry of these processes and tracking the impact of gut microbiome remediation. This study discusses infection mechanisms, cross-organ impacts, and nutritional interventions, highlighting the importance of addressing anti-microbial resistance and the role of nutrition in resilience.
Article
Environmental Sciences
D. C. Lettoof, T. V. Nguyen, W. R. Richmond, H. E. Nice, M. M. Gagnon, D. J. Beale
Summary: This study investigates the potential impacts of PFAS on a top predator of wetlands, the tiger snake, using exposure and bioaccumulation patterns, whole organism responses, and omics-based ecosurveillance methods. The results demonstrate the bioavailability of urban wetland PFAS in higher-order reptilian predators and suggest a negative impact on snake health and metabolic processes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)