Proteomics approaches to characterize the immune responses in cancer

Urbiola-Salvador, Víctor; Miroszewska, Dominika; Jabłońska, Agnieszka; Qureshi, Talha; Chen, Zhi

doi:10.1016/j.bbamcr.2022.119266

Cited by 11 publications

(4 citation statements)

References 168 publications

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“…The GOLM2 gene, also referred to as CASC4 and identi ed as a potential cancer susceptibility gene 39 , has been linked to reduced overall survival rates in ovarian cancer 40 . Recent studies conducted during the pandemic have highlighted the GOLM gene family, including GOLM1 and GOLM2, identifying them as potential causal plasma proteins associated with SARS-CoV-2 and suggesting their involvement in increased susceptibility to COVID-19 infection 41,42 .…”

Section: Discussionmentioning

confidence: 99%

Unveiling Genetic Signatures Associated with Resilience to Neonatal Diarrhea in Lambs Through Dual GWAS Approaches

Yaman,

Kişi,

Şengül

et al. 2024

Preprint

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Neonatal diarrhea poses a particularly daunting challenge due to its multifactorial etiology, resulting in high morbidity and mortality rates and substantial economic consequences worldwide. Moreover, the zoonotic potential of neonatal diarrhea underscores its importance in public health concerns. Although no molecular-level study has evaluated genetic resistance/susceptibility to neonatal diarrhea in farm animals, previous observations suggest potential avenues for further research. The present study employs two genome-wide association approaches, namely the nonparametric multi-locus (pKWmEB) and the single-locus Mixed Linear Model (MLM), to explore potential associations between genetic variations in innate immunity and neonatal diarrhea in Karacabey Merino lambs. A total of 707 lambs, comprising 180 cases and 527 controls, were analyzed, revealing an overall prevalence rate of 25.5%. Using a multi-locus (pKWmEB) GWA analysis, 13 SNPs surpassing the threshold of ≥ LOD 3 were identified. Additionally, the single-locus MLM approach identified one SNP with an exact p-value of 1.85e-7, and this SNP (s61781.1) in the SLC22A8 gene was co-detected by both methods. Our results demonstrate that besides environmental conditions and management practices, the manifestation of neonatal diarrhea can be explained to some degree by genetic backgrounds, and marker-assisted selection can be a useful complementary tool in the struggle against neonatal diarrhea.

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Section: Discussionmentioning

confidence: 99%

Unveiling Genetic Signatures Associated with Resilience to Neonatal Diarrhea in Lambs Through Dual GWAS Approaches

Yaman,

Kişi,

Şengül

et al. 2024

Preprint

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“…The correlation between epigenetic and genetic information, along with the analysis of phenotype through proteomic analysis, plays a critical role in uncovering the complex associations between molecular variations and observable traits. Integrating these diverse layers of molecular data allows for a comprehensive analysis of the interplay between genotype [ 9 ] and phenotype [ 10 , 11 , 12 ]. Consequently, the development of novel tools that enhance the precision and output of genotyping and phenotyping techniques holds substantial importance.…”

Section: Introductionmentioning

confidence: 99%

Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling

Sandoval

Ismail

Mazzone

et al. 2023

Genes

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The snATAC + snRNA platform allows epigenomic profiling of open chromatin and gene expression with single-cell resolution. The most critical assay step is to isolate high-quality nuclei to proceed with droplet-base single nuclei isolation and barcoding. With the increasing popularity of multiomic profiling in various fields, there is a need for optimized and reliable nuclei isolation methods, mainly for human tissue samples. Herein we compared different nuclei isolation methods for cell suspensions, such as peripheral blood mononuclear cells (PBMC, n = 18) and a solid tumor type, ovarian cancer (OC, n = 18), derived from debulking surgery. Nuclei morphology and sequencing output parameters were used to evaluate the quality of preparation. Our results show that NP-40 detergent-based nuclei isolation yields better sequencing results than collagenase tissue dissociation for OC, significantly impacting cell type identification and analysis. Given the utility of applying such techniques to frozen samples, we also tested frozen preparation and digestion (n = 6). A paired comparison between frozen and fresh samples validated the quality of both specimens. Finally, we demonstrate the reproducibility of scRNA and snATAC + snRNA platform, by comparing the gene expression profiling of PBMC. Our results highlight how the choice of nuclei isolation methods is critical for obtaining quality data in multiomic assays. It also shows that the measurement of expression between scRNA and snRNA is comparable and effective for cell type identification.

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“…Proteomics plays an increasingly important role in biology and medical fields. − The combination of mass spectrometry (MS) and separation methods is the principal tool for proteomics. − Bottom-up and top-down are the two approaches currently used in proteomics. − In bottom-up proteomics, proteins are first digested into peptides, which are usually analyzed by liquid chromatography-tandem MS (LC-MS/MS). − Compared to intact proteins, peptides could be better separated and accurately analyzed. ,− Thus, bottom-up proteomics remains the most mature and widely used approach for protein characterization. Great progresses have been made in the past decade, and the performance of commercial mass spectrometers has been boosted in terms of speed, mass resolution, sensitivity, and mass accuracy. ,− Due to the complexity and large number of peptides, it is still demanding to have highly efficient front-end separations to achieve deep bottom-up proteomics. − …”

Section: Introductionmentioning

confidence: 99%

Deep Bottom-up Proteomics Enabled by the Integration of Liquid-Phase Ion Trap

Hong

Zhai

et al. 2023

Anal. Chem.

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In bottom-up proteomics, the complexity of the proteome requires advanced peptide separation and/or fractionation methods to acquire an in-depth understanding of protein profiles. Proposed earlier as a solution-phase ion manipulation device, liquid phase ion traps (LPITs) were used in front of mass spectrometers to accumulate target ions for improved detection sensitivity. In this work, an LPIT-reversed phase liquid chromatography-tandem mass spectrometry (LPIT-RPLC-MS/MS) platform was established for deep bottom-up proteomics. LPIT was used here as a robust and effective method for peptide fractionation, which also shows good reproducibility and sensitivity on both qualitative and quantitative levels. LPIT separates peptides based on their effective charges and hydrodynamic radii, which is orthogonal to that of RPLC. With excellent orthogonality, the integration of LPIT with RPLC-MS/MS could effectively increase the number of peptides and proteins being detected. When HeLa cells were analyzed, peptide and protein coverages were increased by ∼89.2% and 50.3%, respectively. With high efficiency and low cost, this LPIT-based peptide fraction method could potentially be used in routine deep bottom-up proteomics.

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Proteomics approaches to characterize the immune responses in cancer

Cited by 11 publications

References 168 publications

Unveiling Genetic Signatures Associated with Resilience to Neonatal Diarrhea in Lambs Through Dual GWAS Approaches

Unveiling Genetic Signatures Associated with Resilience to Neonatal Diarrhea in Lambs Through Dual GWAS Approaches

Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling

Deep Bottom-up Proteomics Enabled by the Integration of Liquid-Phase Ion Trap

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