Inflammation in multiple system atrophy

Leńska-Mieciek, Marta; Madetko, Natalia; Alster, Piotr; Królicki, Leszek; Fiszer, Urszula; Koziorowski, Dariusz

doi:10.3389/fimmu.2023.1214677

Cited by 11 publications

(3 citation statements)

References 104 publications

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“…Therefore, a more detailed investigation is necessary, including experimental groups categorized by both clinical criteria and brain regions. A more comprehensive review of the issue can be found elsewhere. − …”

Section: Resultsmentioning

confidence: 99%

Reanalysis of DIA Data Demonstrates the Capabilities of MS/MS-Free Proteomics to Reveal New Biological Insights in Disease-Related Samples

Ivanov,

Kopeykina,

Gorshkov

2024

J. Am. Soc. Mass Spectrom.

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Data-independent acquisition (DIA) at the shortened data acquisition time is becoming a method of choice for quantitative proteomic applications requiring high throughput analysis of large cohorts of samples. With the advent of the combination of high resolution mass spectrometry with an asymmetric track lossless analyzer, these DIA capabilities were further extended with the recent demonstration of quantitative analyses at the speed of up to hundreds of samples per day. In particular, the proteomic data for the brain samples related to multiple system atrophy disease were acquired using 7 and 28 min chromatography gradients (Guzman et al., Nat. Biotech. 2024). In this work, we applied the recently introduced DirectMS1 method to reanalysis of these data using only MS1 spectra. Both DirectMS1 and DIA results were matched against long gradient DDA analysis from the earlier study of the same sample cohort. While the quantitation efficiency of DirectMS1 was comparable with DIA on the same data sets, we found an additional five proteins of biological significance relevant to the analyzed tissue samples. Among the findings, DirectMS1 was able to detect decreased caspase activity for Vimentin protein in the multiple system atrophy samples missed by the MS/MS-based quantitation methods. Our study suggests that DirectMS1 can be an efficient MS1-only addition to the analysis of DIA data in high-throughput quantitative proteomic studies.

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Section: Resultsmentioning

confidence: 99%

Reanalysis of DIA Data Demonstrates the Capabilities of MS/MS-Free Proteomics to Reveal New Biological Insights in Disease-Related Samples

Ivanov,

Kopeykina,

Gorshkov

2024

J. Am. Soc. Mass Spectrom.

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“…Chronic inflammation induces cancer, autoimmune disorders, metabolic disorders, and neurological diseases, such as AD, PD, and ALS. In the brain, inflammation induces the reactions of glial cells (astrocyte and microglial acti-vation) and an increase in the production of proinflammatory cytokines, such as IL-2 and IL-13 [40], by circulating immune cells, including monocytes, neutrophils, and lymphocytes. In addition, neurodegenerative diseases are characterized by the impairment of inflammatory events.…”

Section: Discussionmentioning

confidence: 99%

Protective Effects of a Combined Herbal Medicine against Amyotrophic Lateral Sclerosis-Associated Inflammation and Oxidative Stress

Yang

2024

Applied Sciences

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Despite extensive studies to identify effective curative drugs for amyotrophic lateral sclerosis (ALS), only riluzole and edaravone have been approved by the Food and Drug Administration. However, these drugs only delay disease progression and exhibit adverse effects, necessitating the development of more effective drugs. Herbal medicines are effective against incurable diseases with various pathogenic factors owing to their low toxicity and presence of multiple components, which target multiple organs. Therefore, we aimed to investigate whether a combined herbal medicine (CHM), comprising Gastrodia elata, Cnidium officinale Makino, and Ostericum koreanum, affects muscle function and motor neuron death in an animal model of ALS. We treated 8-week-old hSOD1G93A mice with 1 mg/g CHM, administered orally once daily for 6 weeks. Muscle function was measured via a footprint test. Biochemical analyses, including immunoblotting, western blotting, and immunohistochemistry, of the muscles (tibialis anterior and gastrocnemius) and spinal cord of hSOD1G93A mice were performed. The CHM treatment improved movement and reduced motor neuron loss in the mouse spinal cord. It also enhanced anti-inflammatory and anti-oxidant activities and regulated autophagy in the mouse muscles and spinal cord. These findings suggest that CHM has multi-active components that effectively target muscles and the spinal cord, delaying disease progression.

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“…A more comprehensive review of the issue can be found elsewhere. [47][48][49][50][51] More on the Vimentin protein in view of caspase activity. During manual inspection of DEPs reported by DirectMS1 method, we noticed that most valuable information showing differential expression of Vimentin protein comes from peptides from the middle (104-236 amino acid positions) and last part (294-410) of the protein sequence (Supplementary Table 2).…”

Section: P06576 Proteinmentioning

confidence: 99%

Reanalysis of Orbitrap Astral DIA data demonstrates the capabilities of MS/MS-free proteomics to reveal new biological insights in disease-related samples

Ivanov,

Kopeykina,

Gorshkov

2024

Preprint

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Data-independent acquisition (DIA) became a method of choice for quantitative proteomics. With the advent of the combination of Orbitrap FTMS and asymmetric track lossless analyzer Astral these DIA capabilities were further extended with the recent demonstration of quantitative proteomic sample analyses at the speed of up to hundreds of samples per day. In particular, the dataset containing brain samples related to the multiple system atrophy was acquired using 7 and 28 min chromatography gradients and the Orbitrap Astral mass spectrometer (Guzman et al., Nat. Biotech.2024). In this work, we reanalysed the Orbitrap Astral DIA data using MS1 spectra without applying to fragmentation information using the recently introduced DirectMS1 approach. The results were compared with previous study of the same sample cohort by traditional long gradient DDA analysis. While the quantitation efficiency of DirectMS1 was comparable, we found additional five proteins of biological significance relevant to the analyzed tissue samples. Among the findings, DirectMS1 was able to detect decreased caspase activity for Vimentin protein in the multiple system atrophy samples which was barely observed from MS/MS-based methods. Our study suggests that DirectMS1 can be an efficient MS1-only addition to the analysis of DIA data in quantitative proteomic studies.

show abstract

Inflammation in multiple system atrophy

Cited by 11 publications

References 104 publications

Reanalysis of DIA Data Demonstrates the Capabilities of MS/MS-Free Proteomics to Reveal New Biological Insights in Disease-Related Samples

Reanalysis of DIA Data Demonstrates the Capabilities of MS/MS-Free Proteomics to Reveal New Biological Insights in Disease-Related Samples

Protective Effects of a Combined Herbal Medicine against Amyotrophic Lateral Sclerosis-Associated Inflammation and Oxidative Stress

Reanalysis of Orbitrap Astral DIA data demonstrates the capabilities of MS/MS-free proteomics to reveal new biological insights in disease-related samples

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