Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes

Thomas, Stefani N.; Friedrich, Betty; Schnaubelt, Michael; Chan, Daniel W.; Zhang, Hui; Aebersold, Ruedi

doi:10.1016/j.isci.2020.101079

Cited by 27 publications

(30 citation statements)

References 107 publications

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“…A similar range of FCs has been previously reported by studies using isobaric labeling. 31 − 35 Rotenone treatment highlighted 421 differentially regulated proteins (FC ≥1.25 or ≤0.8), of which 144 were significantly altered ( q ≤ 0.05, with respect to untreated cell control, Figure 3 B). Yashtimadhu choorna extract cotreatment was found to significantly regulate 88 proteins ( q ≤ 0.05, with respect to rotenone), which included restoration of 84 proteins that were dysregulated by rotenone and an additional regulation of 4 proteins ( Figure 3 C).…”

Section: Results and Discussionmentioning

confidence: 99%

Identification of Molecular Network Associated with Neuroprotective Effects of Yashtimadhu (Glycyrrhiza glabra L.) by Quantitative Proteomics of Rotenone-Induced Parkinson’s Disease Model

et al. 2020

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Parkinson’s disease (PD) is a progressive neurodegenerative disorder, whose treatment with modern therapeutics leads to a plethora of side effects with prolonged usage. Therefore, the management of PD with complementary and alternative medicine is often pursued. In the Ayurveda system of alternative medicine, Yashtimadhu choorna, a Medhya Rasayana (nootropic), prepared from the dried roots of Glycyrrhiza glabra L. (licorice), is prescribed for the management of PD with a favorable outcome. We pursued to understand the neuroprotective effects of Yashtimadhu choorna against a rotenone-induced cellular model of PD using differentiated IMR-32 cells. Cotreatment with Yashtimadhu choorna extract rescued rotenone-induced apoptosis and hyperphosphorylation of ERK-1/2. Quantitative proteomic analysis of six peptide fractions from independent biological replicates acquired 1,561,169 mass spectra, which when searched resulted in 565,008 peptide-spectrum matches mapping to 30,554 unique peptides that belonged to 4864 human proteins. Proteins commonly identified in biological replicates and >4 PSMs were considered for further analysis, leading to a refined set of 3720 proteins. Rotenone treatment differentially altered 144 proteins (fold ≥1.25 or ≤0.8), involved in mitochondrial, endoplasmic reticulum, and autophagy functions. Cotreatment with Yashtimadhu choorna extract rescued 84 proteins from the effect of rotenone and an additional regulation of 4 proteins. Network analysis highlighted the interaction of proteins and pathways regulated by them, which can be targeted for neuroprotection. Validation of proteomics data highlighted that Yashtimadhu confers neuroprotection by preventing mitochondrial oxidative stress and apoptosis. This discovery will pave the way for understanding the molecular action of Ayurveda drugs and developing novel therapeutics for PD.

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Section: Results and Discussionmentioning

confidence: 99%

Identification of Molecular Network Associated with Neuroprotective Effects of Yashtimadhu (Glycyrrhiza glabra L.) by Quantitative Proteomics of Rotenone-Induced Parkinson’s Disease Model

et al. 2020

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“…Specifically, we show that TCEP improves lysis at acidic pH. TCEP is also used to stabilize extracted RNA, for the reduction of proteomic samples and the preparation of protein:RNA crystallization samples (Rhee and Burke, 2004;Ripin et al, 2019;Thomas et al, 2020).…”

Section: Discussionmentioning

confidence: 97%

High Efficiency RNA Extraction From Sperm Cells Using Guanidinium Thiocyanate Supplemented With Tris(2-Carboxyethyl)Phosphine

Roszkowski

Mansuy

2021

Front. Cell Dev. Biol.

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The extraction of high-quality ribonucleic acid (RNA) from tissues and cells is a key step in many biological assays. Guanidinium thiocyanate-phenol-chloroform (AGPC) is a widely used and efficient method to obtain pure RNA from most tissues and cells. However, it is not efficient with some cells like sperm cells because they are resistant to chaotropic lysis solutions containing guanidinium thiocyanate such as Buffer RLT+ and Trizol. Here, we show that disulfide bonds are responsible for the chemical resistance of sperm cells to RNA extraction reagents. We show that while β-mercaptoethanol (βME) can increase sperm lysis in Buffer RLT+, it has no effect in Trizol and leaves sperm cells intact. We measured the reduction of disulfide bonds in 2,2′-dithiodipyridine (DTDP) and observed that βME has a pH-dependent activity in chaotropic solutions, suggesting that pH is a limiting factor. We identified tris(2-carboxyethyl)phosphine (TCEP) as an efficient lysis enhancer of AGPC solutions that can retain reducing activity even at acidic pH. Trizol supplemented with TCEP allows the complete and rapid lysis of sperm cells, increasing RNA yield by 100-fold and resulting in RNA with optimal quality for reverse transcription and polymerase chain reaction. Our findings highlight the importance of efficient cell lysis and extraction of various macromolecules for bulk and single-cell assays, and can be applied to other lysis-resistant cells and vesicles, thereby optimizing the amount of required starting material and animals.

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“…Single-platform genomic and proteomic analyses have allowed for the identification and cataloging of mutations; copy number alterations; and altered gene, miRNA, protein, or phosphoprotein expression profiles [ 2 , 3 , 7 , 12 , 23 , 145 , 146 , 147 , 148 , 149 , 150 , 151 , 152 ]. As we have outlined above, patterns of genomic and proteomic alterations can define tissue- and histological-specific differences in underlying biology and can be used to define molecularly distinct subtypes of cancer, including breast and ovarian cancer [ 2 , 3 , 11 , 23 , 97 , 118 , 119 , 120 , 136 , 153 , 154 , 155 ]. These genomic and proteomic patterns can identify oncogenic mechanisms that contribute to disease development, progression and in some instance can serve as therapeutic targets or markers of therapeutic response [ 10 , 62 , 63 , 99 , 102 , 113 , 126 , 128 , 129 , 135 , 137 , 142 , 156 , 157 , 158 , 159 , 160 , 161 , 162 , 163 , 164 , 165 , 166 , 167 , 168 , …”

Section: Advances In Genomic Analyses Of Breast and Ovarian Cancermentioning

confidence: 99%

Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer

Khella

Mehta

et al. 2021

JPM

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The underlying molecular heterogeneity of cancer is responsible for the dynamic clinical landscape of this disease. The combination of genomic and proteomic alterations, including both inherited and acquired mutations, promotes tumor diversity and accounts for variable disease progression, therapeutic response, and clinical outcome. Recent advances in high-throughput proteogenomic profiling of tumor samples have resulted in the identification of novel oncogenic drivers, tumor suppressors, and signaling networks; biomarkers for the prediction of drug sensitivity and disease progression; and have contributed to the development of novel and more effective treatment strategies. In this review, we will focus on the impact of historical and recent advances in single platform and integrative proteogenomic studies in breast and ovarian cancer, which constitute two of the most lethal forms of cancer for women, and discuss the molecular similarities of these diseases, the impact of these findings on our understanding of tumor biology as well as the clinical applicability of these discoveries.

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Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes

Cited by 27 publications

References 107 publications

Identification of Molecular Network Associated with Neuroprotective Effects of Yashtimadhu (Glycyrrhiza glabra L.) by Quantitative Proteomics of Rotenone-Induced Parkinson’s Disease Model

Identification of Molecular Network Associated with Neuroprotective Effects of Yashtimadhu (Glycyrrhiza glabra L.) by Quantitative Proteomics of Rotenone-Induced Parkinson’s Disease Model

High Efficiency RNA Extraction From Sperm Cells Using Guanidinium Thiocyanate Supplemented With Tris(2-Carboxyethyl)Phosphine

Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer

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