Document text
Principal Investigator: Yehia Mechref
Organization: TEXAS TECH UNIVERSITY
Fiscal Year: 2022
Award: $302,855
Funding agency: National Institute of General Medical Sciences
Glycosylation is one of the most complex protein modifications; more than 50% of mammalian
proteins are glycosylated. The fact that there are 100,000 proteoforms coded by only ~20,300
genes identified in the human genome emphasizes the importance of posttranslational
modifications (PTMs) like glycosylation. Aberrant protein glycosylation has been implicated in
many diseases, such as Alzheimer’s disease, congenital/metabolic disorders, diabetes,
inflammation, Parkinson’s disease, bacterial/viral infectious diseases, and various cancers. More
recently, glycans have been associated with coronavirus spike glycoproteins, including the SARS-
CoV-2 virion. The diverse biological roles of glycans and their implications in diseases have
created a demand for reliable qualitative and quantitative glycomic approaches, which facilitates
sensitive investigation of glycan changes in different biological and biomedical samples. Mass
spectrometry (MS) is the most efficient technique in glycomics due to its high sensitivity and
capacity for acquiring structural information. However, glycomic research remains a challenge
because of the microheterogeneity of glycan compositions in complex biological samples; the
relatively low abundance in nature and low ionization efficiency in MS analysis; and the existence
of variant positional and linkage isomers caused by the biosynthesis process. To overcome these
challenges, several separation methods have been coupled to MS. Despite the development of
these separation techniques, isomeric separation of glycans remains insufficient. There is an
increasing demand for more efficient isomeric separation approaches since glycan isomers have
been related to different diseases.
The main aim of this proposal is to provide easily accessible, adaptable, and affordable
strategies for better separation and characterization of glycans and glycan isomers derived from
different glycoconjugates. Aim 1 is focused on finding a replacement for porous craphitic carbon
columns that sufferes from low reprodcubility and loss of resolution and efficiency with time. The
in-house mesoporous graphitic carbon (MGC)-LC-MS will be investigated for both permethylated
(Aim 1a) and native (Aim 2b) isomeric separation of N- and O-glycans, glycolipid glycans, and
free oligosaccharides. Other alternatives (also part of Aim 1a), such as 50 cm and 200 cm micro
pillar array columns (μPAC)-C18-LC-MS, and a 50 cm long capillary nanoC18-LC-MS, will also
be evaluated to achieve an improved isomeric separation of glycan isomers. Subsequently, GUI
will be utilized to improve the identification of glycan isomers. A GUI libraries for the separation
strategies developed in Aim 1 will be established to normalize the possible retention time shift
among different runs (Aim 2). LC-M based glycomics quantitative strategies will be developed
and assessed in Aim 3. The combination of permethylation and TMT will capitalize on the
advantages of both techniques, providing enhanced sensitivity and accuracy in glycan
quantitation (Aim 3a). Additionally, the combination of 8-plex isotopic permethylation and 6-plex
TMT will facilitate a reliable 48-plex, thus significantly increasing the throughput of analysis (Aim
3b). Furthermore, with the improved separation and identification (Aim 1 and 2), PRM will be
employed to assist the better quantitation of glycans and the differentiation of glycan isomers. A
library containing the fragments fingerprint of each glycan isomer will be created to aid the glycan
isomeric identification (Aim 3c). The development of automated software for easy, fast, and
accurate glycomic data processing is the main focus of Aim 4. Finally, the aforementioned
strategies and tools will be applied to clinical samples to address a variety of biological and
biomedical issues such as COVID-19, breast cancer brain metastasis, liver cancer vs. cirrhosis,
kidney diseases, algae development, and others (Aim 5). The development of the proposed
methods and algorithms will help us and our collaborators to better understand the attributes and
biomedical significance of glycan isomers in the development and progression of esophageal,
breast, and liver cancer. Furthermore, we expect the analytical tools and algorithms proposed
here to benefit researchers and scientists who are interested in understanding the biological
attributes of glycan isomers in other systems.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><AD dementia><Address><Adhesions><Algae><Algorithms><Alzheimer><Alzheimer Type Dementia><Alzheimer disease><Alzheimer sclerosis><Alzheimer syndrome><Alzheimer's><Alzheimer's Disease><Alzheimer's disease dementia><Alzheimers Dementia><Alzheimers disease><Anabolism><Area><Bacterial Infections><Bio-Informatics><Bioinformatics><Biological><Biological Function><Biological Process><Blood capillaries><Brain Metastasis><Brain Trauma><Breast Cancer><COVID-19><COVID-19 virus><COVID19><COVID19 virus><CV-19><CV19><Cancers><Carbon><Cell Body><Cell Differentiation><Cell Differentiation process><Cells><Cirrhosis><Clinical><CoV S protein><CoV glycoprotein S><CoV spike glycoprotein><CoV spike protein><CoV-2><CoV2><Code><Coding System><Communicable Diseases><Communities><Complex><Computer Software Tools><Computer software><Coronaviridae><Coronavirus><Coronavirus glycoprotein S><Coronavirus spike protein><Coupled><Cystic Fibrosis><D-Glucose><Development><Dextrose><Diabetes Mellitus><Disease><Disorder><Drug Targeting><Esophageal Cancer><Esophagus Cancer><Fingerprint><Future><Gangliosides><Genes><Glucose><Glycans><Glycoconjugates><Glycolipids><Glycoproteins><Goals><Graphite><Hepatic Cancer><High temperature of physical object><Human Genome><Immune response><Immunological response><Infectious Disease Pathway><Infectious Diseases><Infectious Disorder><Inflammation><Investigation><Investigators><Ions><Isomerism><Isotopes><Kidney Diseases><Label><Libraries><Malignant Esophageal Neoplasm><Malignant Esophageal Tumor><Malignant Neoplasms><Malignant Tumor><Malignant Tumor of the Esophagus><Malignant neoplasm of esophagus><Malignant neoplasm of liver><Mass Photometry/Spectrum Analysis><Mass Spectrometry><Mass Spectroscopy><Mass Spectrum><Mass Spectrum Analyses><Mass Spectrum Analysis><Metabolic Diseases><Metabolic Disorder><Metabolic Glycosylation><Metastatic Neoplasm to the Brain><Metastatic Tumor to the Brain><Metastatic malignant neoplasm to brain><Methods><Monitor><Mucoviscidosis><Natural graphite><Nature><Nephropathy><Oligosaccharides><Outcome><Paralysis Agitans><Parkinson><Parkinson Disease><Parkinson's disease><Parkinsons disease><Pattern><Polysaccharides><Post-Translational Modification Protein/Amino Acid Biochemistry><Post-Translational Modifications><Post-Translational Protein Modification><Post-Translational Protein Processing><Posttranslational Modifications><Posttranslational Protein Processing><Primary Parkinsonism><Primary Senile Degenerative Dementia><Process><Protein Glycosylation><Protein Modification><Proteins><Public Health><Reaction><Recombinant Proteins><Renal Disease><Research><Research Activity><Research Personnel><Researchers><Resolution><Role><Running><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV2><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Sampling><Scientist><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome related corona virus 2><Sialoglycosphingolipids><Software><Software Tools><Symbiosis><System><Techniques><Thesaurismosis><Time><Traumatic Brain Injury><Variant><Variation><Viral><Viral Diseases><Virion><Virus Diseases><Virus Particle><Wuhan coronavirus><analytical tool><bacteria infection><bacterial disease><base><bio-informatics tool><bioinformatics tool><biologic><biosynthesis><brain micrometastasis><cancer biomarkers><cancer markers><capillary><carbohydrate structure><cirrhotic><clinical diagnostics><commensalism><computerized data processing><corona virus><corona virus disease 2019><coronavirus S protein><coronavirus disease 2019><coronavirus disease 2019 virus><coronavirus disease-19><coronavirus disease-19 virus><coronavirus infectious disease-19><coronavirus spike glycoprotein><data processing><dementia of the Alzheimer type><develop software><developing computer software><developmental><diabetes><drug development><glycosylation><hCoV19><high temperature><host response><human whole genome><immune system response><immunoresponse><implementation tool><improved><indexing><interest><ionization><isomer><kidney disorder><liver cancer><liver malignancy><machine learning based prediction model><machine learning based predictive model><machine learning prediction><machine learning prediction model><machine learning predictive model><malignancy><malignant breast neoplasm><malignant breast tumor><malignant liver tumor><medical diagnostic><metabolism disorder><nCoV2><nano><native protein drug><neoplasm/cancer><oesophageal cancer><pathogen><pharmaceutical protein><predictive signature><primary degenerative dementia><protein complex><protein drug agent><protein-based drug><renal disorder><senile dementia of the Alzheimer type><side effect><social role><software development><software toolkit><tandem mass spectrometry><therapeutic protein><tool><tool development><traumatic brain damage><viral infection><virus infection><virus-induced disease>