Proteogenomics
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The allergen repertoire of the house dust mite, Dermatophagoides farinae, is incomplete despite most mite allergens having been described in this species. Using proteogenomics, we aimed to compare proteins and allergens between sexes and provide a foundation for the identification of novel allergens. Overall, 6297 protein hits were identified, and 2899 and 886 were male- and female-specific, respectively. Removal of trace results narrowed the dataset to 3478 hits, including 275 and 157 male- and female-specific hits, respectively. All 34 WHO/IUIS-approved D. farinae allergens (omitting Der f 17) were identified, and we also identified homologs of the yet undescribed Der f 9 and 38. Der f 27/serpin exhibited the largest sex-dependent difference and was dominant in females. Using official protein sequences, Der f 11, 14, 23, 28 and 30 were identified with low success. However, identification success of Der f 11 and 14 was greatly increased by using longer/complete sequences. Der f 30 is characterized by the same tryptic digests as the more abundant Der f 30 (isoform) identified here. Der f 23 appears to be of low abundance in mite bodies. Der f 28.0101 and Der f 28.0201 were detected at low abundance and in trace amounts, respectively. SIGNIFICANCE: In this work, we performed a proteogenomic annotation of the house dust mite, Dermatophagoides farinae, which is the most important source of house dust allergens. The proteogenomic analysis performed here provides a foundation for not only understanding the biology of the mite but also the identification of novel allergens. This study generated a robust proteomic dataset for D. farinae and reviewed existing and candidate allergens in this species. We stress some pitfalls of high-throughput analyses, especially that improper headers of allergen protein records provided in databases can lead to confusion. Using partial sequences in proteomic identification and quantification can lead to low identification success (low signal intensity or MS/MS counts). Thus, we individually curated the protein sequences for proper identification and quantification. The discovered sex differences can be one factor affecting allergen/immunogen variations in mite extracts. Overall, this work provides a benchmark for accurate identification of mite immunogenic proteins using proteomics.
- MeSH
- alergeny genetika imunologie metabolismus MeSH
- Dermatophagoides farinae genetika imunologie metabolismus MeSH
- proteiny členovců genetika imunologie metabolismus MeSH
- proteogenomika metody MeSH
- proteom metabolismus MeSH
- Pyroglyphidae genetika imunologie metabolismus MeSH
- sekvence aminokyselin MeSH
- sekvenční homologie MeSH
- sexuální faktory MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
The pollen beetle is a major pest of oilseed rape. Although various resistance mechanisms have been identified, such as kdr (mutation in the sodium channel) and metabolic resistance (CYP overexpression), other "hidden" factors also exist. Some studies have stressed the importance of epistasis as a genetic background. The combination of kdr and metabolic resistance appears to be unfavorable under field conditions in the absence of pesticide selection. The regulation of detoxification enzymes can play an important role, but we highlight different detoxification markers compared to those emphasized in other studies. We also stress the importance of studying the role of markers identified as pathogenesis-related protein 5-like (PR5; upregulated by insecticides) and highlight the role of RNA (DEAD-box) helicases (downregulated by insecticides). Thus, we suggest the importance of epigenetic drivers of resistance/tolerance to pesticides. The key results are similar to those of our previous study, in which deltamethrin treatment of the pollen beetle was also investigated by a proteogenomic approach. Indeed, the mechanism leading to resistance of the pollen beetle may be an innate mechanism that the pollen beetle can also employ in natural habitats, but under field conditions (pesticide exposure), this mechanism is used to survive in response to insecticides. SIGNIFICANCE: Pesticide resistance is a serious problem that hampers the successful production of crops. Understanding the mechanisms of insecticide resistance is highly important for successful pest control, especially when considering integrated pest management. Here, using a proteogenomic approach, we identified novel markers for understanding pollen beetle resistance to pesticides. In addition, future studies will reveal the role of these markers in the multiresistance of pollen beetle populations. We highlight that the proteins identified as PR5, which are known to occur in beetles and are similar to those in plants, may be responsible for tolerance to multiple stresses. In addition, our results indicate that the RNA helicases that exhibited changes in expression may be the epigenetic drivers of multiresistance. The nature of these changes remains an open question, and their relevance in different situations (responses to different stresses) in natural habitats in the absence of pesticides can be proposed.
- MeSH
- brouci * genetika MeSH
- insekticidy * farmakologie MeSH
- proteogenomika * MeSH
- pyl MeSH
- pyrethriny * farmakologie MeSH
- rezistence k insekticidům genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Mass spectrometry proteomics data are typically evaluated against publicly available annotated sequences, but the proteogenomics approach is a useful alternative. A single genome is commonly utilized in custom proteomic and proteogenomic data analysis. We pose the question of whether utilizing numerous different genome assemblies in a search database would be beneficial. We reanalyzed raw data from the exoprotein fraction of four reference Enterobacterial Repetitive Intergenic Consensus (ERIC) I-IV genotypes of the honey bee bacterial pathogen Paenibacillus larvae and evaluated them against three reference databases (from NCBI-protein, RefSeq, and UniProt) together with an array of protein sequences generated by six-frame direct translation of 15 genome assemblies from GenBank. The wide search yielded 453 protein hits/groups, which UpSet analysis categorized into 50 groups based on the success of protein identification by the 18 database components. Nine hits that were not identified by a unique peptide were not considered for marker selection, which discarded the only protein that was not identified by the reference databases. We propose that the variability in successful identifications between genome assemblies is useful for marker mining. The results suggest that various strains of P. larvae can exhibit specific traits that set them apart from the established genotypes ERIC I-V.
- MeSH
- bakteriální proteiny * genetika metabolismus MeSH
- databáze proteinů MeSH
- faktory virulence * genetika metabolismus MeSH
- genom bakteriální * genetika MeSH
- Paenibacillus larvae * genetika patogenita metabolismus MeSH
- proteogenomika * metody MeSH
- proteomika metody MeSH
- včely mikrobiologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: The identification of mutated proteins in human cancer cells-termed proteogenomics, requires several technologically independent research methodologies including DNA variant identification, RNA sequencing, and mass spectrometry. Any one of these methodologies are not optimized for identifying potential mutated proteins and any one output fails to cover completely a specific landscape. METHODS: An isogenic melanoma cell with a p53-null genotype was created by CRISPR/CAS9 system to determine how p53 gene inactivation affects mutant proteome expression. A mutant peptide reference database was developed by comparing two distinct DNA and RNA variant detection platforms using these isogenic cells. Chemically fractionated tryptic peptides from lysates were processed using a TripleTOF 5600+ mass spectrometer and their spectra were identified against this mutant reference database. RESULTS: Approximately 190 mutated peptides were enriched in wt-p53 cells, 187 mutant peptides were enriched in p53-null cells, with an overlap of 147 mutated peptides. STRING analysis highlighted that the wt-p53 cell line was enriched for mutant protein pathways such as CDC5L and POLR1B, whilst the p53-null cell line was enriched for mutated proteins comprising EGF/YES, Ubiquitination, and RPL26/5 nodes. CONCLUSION: Our study produces a well annotated p53-dependent and p53-independent mutant proteome of a common melanoma cell line model. Coupled to the application of an integrated DNA and RNA variant detection platform (CLCbio) and software for identification of proteins (ProteinPilot), this pipeline can be used to detect high confident mutant proteins in cells. GENERAL SIGNIFICANCE: This pipeline forms a blueprint for identifying mutated proteins in diseased cell systems.
- MeSH
- lidé MeSH
- melanom genetika MeSH
- mutace MeSH
- nádorové buněčné linie MeSH
- nádorový supresorový protein p53 genetika MeSH
- proteogenomika MeSH
- proteom genetika MeSH
- regulace genové exprese u nádorů MeSH
- umlčování genů * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Circulating tumor cells (CTCs) are rare cells that can be found in the peripheral blood of cancer patients. They have been demonstrated to be useful prognostic markers in many cancer types. Within the last decade various methods have been developed to detect rare cells within a liquid biopsy from a cancer patient. These methods have revealed the phenotypic diversity of CTCs and how they can represent the complement of cells that are found in a tumor. Single-cell proteogenomics has emerged as an all-encompassing next-generation technological approach for CTC research. This allows for the deconstruction of cellular heterogeneity, dynamics of metastatic initiation and progression, and response or resistance to therapeutics in the clinical settings. We take advantage of this opportunity to investigate CTC heterogeneity and understand their full potential in precision medicine.The high-definition single-cell analysis (HD-SCA) workflow combines detection of the entire population of CTCs and rare cancer related cells with single-cell genomic analysis and may therefore provide insight into their subpopulations based on molecular as well as morphological data. In this chapter we describe in detail the protocols from isolation of a candidate cell from a microscopy slide, through whole-genome amplification and library preparation, to CNV analysis of identified cells from the HD-SCA workflow. This process may also be applicable to any platform starting with a standard microscopy slide or isolated cell of interest.
Východiská: Potenciál neoantigénov v indukcii protinádorovej imunitnej odpovede je už desaťročia známy, avšak prvé neoantigénové vakcíny boli vyvinuté len nedávno. Rozvoj genomických a proteomických metód umožnil popis somatických mutácií v nádore a imunogénnosť korešpondujúcich neoantigénov môže byť predpovedaná in silico prípadne in vitro. Kombinácia neoantigénovej vakcinácie so správnym imunologickým postupom umožňuje docieliť regresiu nádoru. Štúdie neoantigénových vakcín na modelových organizmoch dokazujú vysokú účinnosť postupu a dokonca prvé klinické štúdie zaznamenávajú úspech. Cieľ: Cieľom je priblížiť význam neoantigénových vakcín v personalizovanej protinádorovej liečbe a objasniť mechanizmus ich prípravy. Článok popisuje typy mutácií s potenciálom expresie imunogénnych neoantigénov nutných pre tvorbu efektívnej vakcíny a približuje aj ostatné procesy nutné k aktivácii T bunkovej protinádorovej odpovede pacienta. Predovšetkým je zameraný na identifikáciu vysokopravdepodobných neoantigénových sekvencií aplikáciou metód sekvenovania novej generácie a hmotnostnej spektrometrie (mass spectrometry - MS), čo je pre tvorbu vakcíny kľúčové. V článku je popísaný princíp proteogenomickej platformy, ktorá vznikla na našom pracovisku za účelom konfidentnej identifikácie mutantných peptidov v biologickom materiáli. Zmieňuje sa aj o možnosti kvantifikácie neoantigénov MS metódami monitorovania vybraných reakcií (selected reaction monitoring - SRM) a SWATH (sequential windowed acquisition of all theoretical fragment ion spectra). Potenciál neoantigénovej vakcinácie v protinádorovej terapii dokazujú úspešné klinické štúdie zhrnuté v závere článku.
Background: Although immune responses to "cancer neoantigens" have been known for decades, the first neoantigen vaccines emerged only very recently. Current developments in genomics and proteomics have enabled descriptions of tumor mutational landscapes, and the immunogenicity of corresponding neoantigens can now be predicted either in silico or in vitro. Cancer regression could be achieved via a combination of neoantigen vaccination and an appropriate immunology approach. Research in model organisms and the results of initial clinical trials of neoantigen vaccines have shown them to be effective. Purpose: We aim to emphasize the importance of neoantigen vaccines in personalized cancer treatment and describe their preparation. We summarize mutations leading to expression of an immunogenic antigen necessary for vaccine development. The processes leading to activation of T-cell anticancer immunity in a patient are briefly introduced. We especially focus on the identification of high confidence neoantigens by next-generation sequencing (NGS) and mass spectrometry (MS), which is key element in the process of designing neoantigen vaccines. Briefly, we describe a proteogenomic platform for confident identification of mutant peptides in biological material. We mention the possibility of neoantigen quantification in biological material using mass spectrometry such as SRM (selected reaction monitoring) and SWATH (sequential windowed acquisition of all theoretical fragment ion spectra). Successful clinical studies demonstrating the potential of neoantigen vaccination in personalized cancer treatment are summarized at the end of the paper.
- MeSH
- antigeny nádorové terapeutické užití MeSH
- lidé MeSH
- nádory * imunologie terapie MeSH
- protinádorové vakcíny * MeSH
- vakcinace metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- přehledy MeSH
In this study, we conducted an extensive investigation of the biodegradation capabilities and stress response of the newly isolated strain Pseudomonas veronii SM-20 in order, to assess its potential for bioremediation of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Initially, phenotype microarray technology demonstrated the strain's proficiency in utilizing various carbon sources and its resistance to certain stressors. Genomic analysis has identified numerous genes involved in aromatic hydrocarbon metabolism. Biodegradation assay analyzed the depletion of phenanthrene (PHE) when it was added as a sole carbon and energy source. We found that P. veronii strain SM-20 degraded approximately 25% of PHE over a 30-day period, starting with an initial concentration of 600 μg/mL, while being utilized for growth. The degradation process involved PHE oxidation to an unstable arene oxide and 9,10-phenanthrenequinone, followed by ring-cleavage. Comparative proteomics provided a comprehensive understanding of how the entire proteome responded to PHE exposure, revealing the strain's adaptation in terms of aromatic metabolism, surface properties, and defense mechanism. In conclusion, our findings shed light on the promising attributes of P. veronii SM-20 and offer valuable insights for the use of P. veronii species in environmental restoration efforts targeting PAH-impacted sites.
- Publikační typ
- časopisecké články MeSH
Genetic variations in protein expression are implicated in a broad spectrum of common diseases and complex traits but remain less explored compared to mRNA and classical phenotypes. This study systematically analyzed brain proteomes in a rat family using tandem mass tag (TMT)-based quantitative mass spectrometry. We quantified 8,119 proteins across two parental strains (SHR/Olalpcv and BN-Lx/Cub) and 29 HXB/BXH recombinant inbred (RI) strains, identifying 597 proteins with differential expression and 464 proteins linked to cis-acting quantitative trait loci (pQTLs). Proteogenomics identified 95 variant peptides, and sex-specific analyses revealed both shared and distinct cis-pQTLs. We improved the ability to pinpoint candidate genes underlying pQTLs by utilizing the rat pangenome and explored the connections between pQTLs in rats and human disorders. Collectively, this study highlights the value of large proteo-genetic datasets in elucidating protein modulation in the brain and its links to complex central nervous system (CNS) traits.
- Publikační typ
- časopisecké články MeSH
Reakce buňky na chemoterapii spočívá na určitých obecných biologických principech. Genetická struktura buněčných populací, jejich aktuální reakce na chemoterapii a prognóza jejich vývoje nejsou náhodné. Jsou determi- novány předchozími expozicemi chemoterapeutiky, a tudíž jejich evoluční zkušeností na darwinovském principu. Chemoterapie se vždy uplatňuje v konkrétním prostředí hostitele za jeho aktivní spoluúčasti. V reakci hostitele na chemoterapeutické zásahy existuje genetická variabilita, je také evoluční povahy v dlouhodobé perspektivě. Do komplexu posouzení terapeutických postupů tedy patří i posouzení a ovlivnění hostitele a jeho variability (imuno- terapie). Pochopení molekulárních mechanizmů patogeneze nemocí, definice specifických genů, jejich exprese, úlohy jejich produktů a vymezení možných terčů cílené chemoterapie je v současné době realistickým cílem využití genomiky a proteogenomiky v medicíně. Nová filozofie v medicíně je tedy založena na respektování individuality v diagnostice, terapii a prognóze. Lze si jen přát, aby se trend respektování individuality v budoucnu skutečně uplatnil, a to nejen v medicíně.
The cell reaction to chemotherapy is based on certain general biological principles. The genetic structure of cell populations, their actual reaction to chemotherapy and the prognosis of their development are not accidental. They are determined by previous exposures to chemotherapeutic agents and thus their evolutional experience on Darwinian principles. Chemotherapy occurs always in a defined environment of the host with his active participation. A genetic variability in the host reaction to chemotherapeutic interference also exists and which in the long-term perspective is also of evolutional nature. The complex of evaluation of therapeutic procedures thus involves evaluation and influencing of the host and his variability (immunotherapy). Understanding of molecular mechanisms of the pathogenesis of disease, definition of specific genes, their expression, the role of their products and definition of possible targets of chemotherapy is at present a realistic goal of application of genomics and proteogenomics in medicine. The new philosophy in medicine is thus based on respecting individuality in diagnosis, treatment and prognosis. We only can wish that the trend of respecting individuality will be applied in the future, and not only in medicine.
