Isobaric Labeling Strategy Utilizing 4-Plex N,N-Dimethyl Leucine (DiLeu) Tags Reveals Proteomic Changes Induced by Chemotherapy in Cerebrospinal Fluid of Children with B-Cell Acute Lymphoblastic Leukemia

Abstract

The use of mass spectrometry for protein identification and quantification in cerebrospinal fluid (CSF) is at the forefront of research efforts to identify and explore biomarkers for the early diagnosis and prognosis of neurologic disorders. Here, we implemented 4-plex N,N-dimethyl leucine (DiLeu) isobaric labeling strategy in a longitudinal study aiming to investigate protein dynamics in children with B-cell acute lymphoblastic leukemia (B-cell ALL) undergoing chemotherapy. The temporal profile of CSF proteome during chemotherapy treatment at weeks 5, 10-14 and 24-28 highlighted many differentially expressed proteins, such as neural cell adhesion molecule, neuronal growth regulator 1, and secretogranin-3, all of which play important roles in neurodegenerative diseases. A total of 63 proteins were significantly altered across all the time *

12-Plex DiLeu Isobaric Labeling Enabled High-Throughput Investigation of Citrullination Alterations in the DNA Damage Response

“…Alternatively, stable isotope labeling, especially isobaric labeling techniques, such as the commercially available tandem mass tags (TMTs) , and our custom-developed N,N -dimethyl leucine tags (DiLeu), , have become popular for comparative studies of different biological states. Although these strategies have been shown to generate accurate quantitative results with great multiplexing capability and analytical throughput in many proteomics works, , their applications in PTM research are relatively limited . This is because each PTM analysis involves specific enrichment and a preferred acquisition method, and therefore, the integration with isobaric labeling often requires delicate optimization during workflow design, sample preparation, and liquid chromatography (LC)–MS analysis.…”

In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease

“…It is the only body fluid that directly interchanges with the extracellular fluid of CNS and reflects the ongoing pathological changes in the CNS most directly ( 4 , 5 ). Thus, biochemical analysis of CSF has great potential for CNS-related disease diagnostics, including biomarker discovery in many neurological disorders ( 6 , 7 ).…”

A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics

“…Isotope labeling techniques are widely used in neuroproteomics to address various biological questions. These techniques are primarily used to characterize the proteomes of neurological disorders, drug responses, or different regions of the brain. , For instance, isobaric labels such as DiLeu, iTRAQ, and TMT have been utilized to study dynamic protein changes in children with B-cell acute lymphoblastic leukemia during chemotherapy, investigate the proteomics of serum in Parkinson’s patients, and analyze circuit-specific proteomes and phosphoproteomes in the corticostriatal system of the mouse brain during development. − Additionally, numerous reports have focused on the studies of protein expression in the thalamus and cerebrospinal fluid of schizophrenia patients, investigation of variations in protein expression levels in human brains after severe traumatic brain injury, and even exploring the mechanisms of memory formation in the hippocampus. ,, Overall, neuroproteomics provides deep insights into the complexity of the nervous system and its related diseases by revealing potential molecular linkages through the comparative quantification of proteome alterations.…”