Complex Proteomes Research Articles

LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes

Background: Target identification is a critical step in elucidating the mechanism of action (MoA) for bioactive compounds. For phenotypic drug discovery pipelines, current unbiased, label-free chemoproteomics-based methods rely predominantly on the modulation of target thermal stability upon drug binding. We developed an automated drug target deconvolution workflow combining limited proteolysis with mass spectrometry (LiP-Quant) that exploits protein structural alterations, as well as steric effects driven by drug binding. A major advantage of LiP-Quant is its unique focus on the detection of signature peptides that discern ligand binding, peptides that are generated by a limited digestion and identified by proteomic analysis. Here we demonstrate the performance of LiP-Quant using two well-characterized kinase inhibitors (KIs), Selumetinib (SE) and Staurosporine (ST), as well as two natural product-derived phosphatase inhibitors (PIs) Calyculin A and Fostriecin in human cell lysate. Furthermore, LiP-Quant can be deployed to estimate in-lysate EC50 value of compound binding.

Rhinology on the move despite Covid-19!

The October 2020 issue of Rhinology is a very interesting edition as it illustrates how world-wide colleagues pave the way for a better future of patients affected by nose and sinus diseases. After the successful launch of EPOS2020 in Spring 2020, the editorial team of Rhinology is proud to present to you the latest and most exciting data in Rhinology research. Getting insight into the complexity and relevance of proteomics in CRS, epithelial-mesenchymal contribution to CRS, zinc levels in nasal and systemic compartment of CRS, nasal biomarkers of CRSwNP that predict recurrence of disease after sinus surgery, and the odor identification test for children, called "U-Sniff", and FID scores (Frequency, Intensity and Duration) scores for epistaxis are all in the 2020 October issue and highly relevant for Rhinology practice. These studies build further on the solid grounds of previous Rhinology research meeting the unmets needs in the field.

Circular RNA Encoded Amyloid Beta peptides-A Novel Putative Player in Alzheimer's Disease.

Alzheimer’s disease (AD) is an age-related detrimental dementia. Amyloid beta peptides (Aβ) play a crucial role in the pathology of AD. In familial AD, Aβ are generated from the full-length amyloid beta precursor protein (APP) via dysregulated proteolytic processing; however, in the case of sporadic AD, the mechanism of Aβ biogenesis remains elusive. circRNAs are a class of transcripts preferentially expressed in brain. We identified a circRNA harboring the Aβ-coding region of the APP gene termed circAβ-a. This circular RNA was detected in the brains of AD patients and non-dementia controls. With the aid of our recently established approach for analysis of circRNA functions, we demonstrated that circAβ-a is efficiently translated into a novel Aβ-containing Aβ175 polypeptide (19.2 KDa) in both cultured cells and human brain. Furthermore, Aβ175 was shown to be processed into Aβ peptides—a hallmark of AD. In summary, our analysis revealed an alternative pathway of Aβ biogenesis. Consequently, circAβ-a and its corresponding translation product could potentially represent novel therapeutic targets for AD treatment. Importantly, our data point to yet another evolutionary route for potentially increasing proteome complexity by generating additional polypeptide variants using back-splicing of primary transcripts that yield circular RNA templates.

Characterizing the Relapse Potential in Different Luminal Subtypes of Breast Cancers with Functional Proteomics.

Poor prognosis due to the high relapse and metastasis rates of breast cancer has been particularly linked to the luminal B subtype. The current study utilized MCF-7 and ZR-75-1 to investigate various luminal subtypes of breast cancers that have discrepant expressions in the estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2). Understanding of the differential protein profiles and the associated pathways could help alleviate the malignance and promote the long-term survival rate of breast cancer patients. Functional proteome tools were applied to comprehensively delineate the global protein alterations that reflect the varieties of biological features between the two subtypes. In this study, a total of 11 proteins with significant and meaningful changes were identified. These protein targets including PRX2, CK19, nucleophosmin and cathepsin D were mostly involved in cell differentiation or proliferation. Particularly, cathepsin D was highly expressed in the luminal B subtype. Moreover, the level of cathepsin-D was also upregulated in the clinical metastatic tissues. Accordingly, the RNA interference-mediated silencing of cathepsin D stimulated ER expression but suppressed the level of HER2. The knockdown of cathepsin D enhanced the level of ZO-1 and a remarkable decrease in N-cadherin was also detected. Again, the matrix metalloproteinases (MMP) activity was impaired under the cathepsin D abolishment. Collectively, this study represented a modality to explore novel relationships in a proteome complex and highlighted the functional roles of cathepsin D in treatment options for different subtypes of breast cancer.

A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes

Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in the development of optimized small-molecule compounds. Current approaches cannot identify the protein targets of a compound and also detect the interaction surfaces between ligands and protein targets without prior labeling or modification. To address this limitation, we here develop LiP-Quant, a drug target deconvolution pipeline based on limited proteolysis coupled with mass spectrometry that works across species, including in human cells. We use machine learning to discern features indicative of drug binding and integrate them into a single score to identify protein targets of small molecules and approximate their binding sites. We demonstrate drug target identification across compound classes, including drugs targeting kinases, phosphatases and membrane proteins. LiP-Quant estimates the half maximal effective concentration of compound binding sites in whole cell lysates, correctly discriminating drug binding to homologous proteins and identifying the so far unknown targets of a fungicide research compound.

Abstract 6404: LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes

Abstract Background Target identification is a critical step in elucidating the mechanism of action (MoA) for bioactive compounds. For phenotypic drug discovery pipelines, current unbiased, label-free chemoproteomics-based methods rely predominantly on the modulation of target thermal stability upon drug binding. We developed an automated drug target deconvolution workflow combining limited proteolysis with mass spectrometry (LiP-Quant) that exploits protein structural alterations, as well as steric effects driven by drug binding. A major advantage of LiP-Quant is its unique focus on the detection of signature peptides that discern ligand binding, peptides that are generated by a limited digestion and identified by proteomic analysis. Here we demonstrate the performance of LiP-Quant using two well-characterized kinase inhibitors (KIs), Selumetinib (SE) and Staurosporine (ST), as well as two natural product-derived phosphatase inhibitors (PIs) Calyculin A and Fostriecin in human cell lysate. Furthermore, LiP-Quant can be deployed to estimate in-lysate EC50 value of compound binding. Methods Mechanically sheared HeLa cell lysate was incubated with compound at multiple concentrations. Next, a limited digest was performed using proteinase K. Finally, the limited digests were processed to peptides with trypsin for mass spectrometry analysis. A project-specific spectral library was generated using data-dependent acquisition (DDA) mass spectrometry and for quantitative analysis data-independent acquisition (DIA) data were recorded and analyzed using Spectronaut Pulsar X. Results Herein, we demonstrate the ability of our LiP-Quant approach to identify unique peptides generated by the binding of either a highly specific (selumetinib) or broad specificity (staurosporine) KI in human cell line lysate. While > 20 kinases met the qualifying LiP-score cutoff for staurosporine, the direct targets MEK1 and MEK2 were clearly identified as main hits in the unbiased ranking by LiP scores. Both cases represent a highly specific enrichment given that we quantified > 100,000 peptides in each of the experiments. These findings confirm our approach's ability to identify genuine drug targets regardless of drug specificity in a complex biological matrix. To characterize the specificity of LiP-Quant, we treated lysate with two separate protein PIs. According to literature calyculin A targets protein phosphatase 1 and 2 (PP1A and PP2A) and fostriecin also targets PP2A, in addition to protein phosphatase 4 (PP4C) but does not bind PP1A. Robust phosphatase identification was achieved for both calyculin A and fostriecin treatment. Importantly, with LiP-Quant, we could recapitulate the known relative affinities of the PIs towards their respective targets. Conclusions Collectively, this data demonstrate that LiP-Quant can be used to effectively identify protein drug targets and characterize the binding properties in complex proteomes, without compound modification or labeling, and regardless of the specificity of the compound. These capabilities make LiP-Quant a powerful target deconvolution and identification strategy. Citation Format: Yuehan Feng, Nigel Beaton, Roland Bruderer, Ilaria Piazza, Paola Picotti, Lukas Reiter. LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6404.

Non-porous thin dense layer coating: Key to achieving ultrahigh peak capacities using narrow open tubular columns

Chromatographic theory has predicted that narrow open tubular (OT) columns are essential toward achieving ultrahigh-efficiency liquid chromatographic separations. It is also well-recognized that low loadability is a major issue for capitalizing the benefits of open tubular liquid chromatography (OTLC). To mitigate this issue, researchers have tried to increase surface area of or create a thick porous coating on the column wall. In this work, we hypothesize that a thin dense non-porous coating is well-suited for us to achieve ultrahigh efficiency or ultrahigh peak capacity if the inner diameter of the OT column is small (e.g., 1−2 µm). We first discuss the rationale of this hypothesis. To provide evidence to further support the hypothesis, we prepare, optimize and characterize the coating for high-resolution separations. We utilize columns prepared under the optimized conditions to separate a peptide sample form E. coli lysate digested first by pepsin and then by trypsin, and we show ultrahigh-peak-capacity results (770 within 47 min using a 45-cm-long column and 2000 within 155 min using a 155-cm-long column). The coating is stable, and the coating method is reproducible. Ultrahigh-resolution separations and ultra-sensitive analyses are critically important and currently challenging for analyses of complex proteomics samples; employing narrow OT columns can alleviate this problem effectively.

Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona

Large-scale, unbiased proteomics studies are constrained by the complexity of the plasma proteome. Here we report a highly parallel protein quantitation platform integrating nanoparticle (NP) protein coronas with liquid chromatography-mass spectrometry for efficient proteomic profiling. A protein corona is a protein layer adsorbed onto NPs upon contact with biofluids. Varying the physicochemical properties of engineered NPs translates to distinct protein corona patterns enabling differential and reproducible interrogation of biological samples, including deep sampling of the plasma proteome. Spike experiments confirm a linear signal response. The median coefficient of variation was 22%. We screened 43 NPs and selected a panel of 5, which detect more than 2,000 proteins from 141 plasma samples using a 96-well automated workflow in a pilot non-small cell lung cancer classification study. Our streamlined workflow combines depth of coverage and throughput with precise quantification based on unique interactions between proteins and NPs engineered for deep and scalable quantitative proteomic studies.

A quantitative thiol reactivity profiling platform to analyze redox and electrophile reactive cysteine proteomes.

Cysteine is unique among all protein-coding amino acids, owing to its intrinsically high nucleophilicity. The cysteinyl thiol group can be covalently modified by a broad range of redox mechanisms or by various electrophiles derived from exogenous or endogenous sources. Measuring the response of protein cysteines to redox perturbation or electrophiles is critical for understanding the underlying mechanisms involved. Activity-based protein profiling based on thiol-reactive probes has been the method of choice for such analyses. We therefore adapted this approach and developed a new chemoproteomic platform, termed 'QTRP' (quantitative thiol reactivity profiling), that relies on the ability of a commercially available thiol-reactive probe IPM (2-iodo-N-(prop-2-yn-1-yl)acetamide) to covalently label, enrich and quantify the reactive cysteinome in cells and tissues. Here, we provide a detailed and updated workflow of QTRP that includes procedures for (i) labeling of the reactive cysteinome from cell or tissue samples (e.g., control versus treatment) with IPM, (ii) processing the protein samples into tryptic peptides and tagging the probe-modified peptides with isotopically labeled azido-biotin reagents containing a photo-cleavable linker via click chemistry reaction, (iii) capturing biotin-conjugated peptides with streptavidin beads, (iv) identifying and quantifying the photo-released peptides by mass spectrometry (MS)-based shotgun proteomics and (v) interpreting MS data by a streamlined informatic pipeline using a proteomics software, pFind 3, and an automatic post-processing algorithm. We also exemplified here how to use QTRP for mining H2O2-sensitive cysteines and for determining the intrinsic reactivity of cysteines in a complex proteome. We anticipate that this protocol should find broad applications in redox biology, chemical biology and the pharmaceutical industry. The protocol for sample preparation takes 3 d, whereas MS measurements and data analyses require 75 min and <30 min, respectively, per sample.

Zonal regulation of collagen-type proteins and posttranslational modifications in prostatic benign and cancer tissues by imaging mass spectrometry.

The emergence of reactive stroma is a hallmark of prostate cancer (PCa) progression and a potential source for prognostic and diagnostic markers of PCa. Collagen is a main component of reactive stroma and changes systematically and quantitatively to reflect the course of PCa, yet has remained undefined due to a lack of tools that can define collagen protein structure. Here we use a novel collagen-targeting proteomics approach to investigate zonal regulation of collagen-type proteins in PCa prostatectomies. Prostatectomies from nine patients were divided into zones containing 0%, 5%, 20%, 70% to 80% glandular tissue and 0%, 5%, 25%, 70% by mass of PCa tumor following the McNeal model. Tissue sections from zones were graded by a pathologist for Gleason score, percent tumor present, percent prostatic intraepithelial neoplasia and/or inflammation (INF). High-resolution accurate mass collagen targeting proteomics was done on a select subset of tissue sections from patient-matched tumor or nontumor zones. Imaging mass spectrometry was used to investigate collagen-type regulation corresponding to pathologist-defined regions. Complex collagen proteomes were detected from all zones. COL17A and COL27A increased in zones of INF compared with zones with tumor present. COL3A1, COL4A5, and COL8A2 consistently increased in zones with tumor content, independent of tumor size. Collagen hydroxylation of proline (HYP) was altered in tumor zones compared with zones with INF and no tumor. COL3A1 and COL5A1 showed significant changes in HYP peptide ratios within tumor compared with zones of INF (2.59 ± 0.29, P value: .015; 3.75 ± 0.96 P value .036, respectively). By imaging mass spectrometry COL3A1 showed defined localization and regulation to tumor pathology. COL1A1 and COL1A2 showed gradient regulation corresponding to PCa pathology across zones. Pathologist-defined tumor regions showed significant increases in COL1A1 HYP modifications compared with COL1A2 HYP modifications. Certain COL1A1 and COL1A2 peptides could discriminate between pathologist-defined tumor and inflammatory regions. Site-specific posttranslational regulation of collagen structure by proline hydroxylation may be involved in reactive stroma associated with PCa progression. Translational and posttranslational regulation of collagen protein structure has potential for new markers to understand PCa progression and outcomes.

Targeted identification of C-type lectins in snake venom by 2DE and Western blot

C-type lectins (CTL) and CTL-like proteins (snaclecs) are important toxins found in snake venom which can disrupt hemostasis by binding platelet membrane glycoproteins. Traditional identification of these toxins usually relies on an “activity-directed fractionation” approach which is very arduous. Here, we report a new method for rapid screening of these proteins in snake venom. MethodsA conserved and immunogenic peptide found in svCTLs (CTL and snaclecs) was identified by sequence alignment using DNAStar software. The peptide was de novo synthesized and conjugated to keyhole limpet hemocyanin (KLH). Rabbit antibodies were generated against the peptide by classical immunization. Deinagkistrodon acutus venom was separated by two-dimensional electrophoresis (2DE) followed by Western blot and CTLs immunodetected using the isolated polyclonal antibody. The same svCTL spots on a parallel 2DE gel were isolated and analyzed by MALDI-TOF-MS. ResultsA highly conserved peptide with the sequence “KTWDDAEKFCTEQ” was identified as a common epitope in svCTLs. The polyclonal antibody against the 13aa-peptide was successfully prepared and purified. Its usefulness to detect svCTLs in D. acutus venom was tested by 2DE-WB and we determined that it positively identified all known D. acutus venom CTLs. ConclusionsImmunodetection with antibodies against KTWDDAEKFCTEQ is an efficient strategy to identify novel svCTLs in the context of a complex proteome.

The Promise of Nanopore Technology: Advances in the Discrimination of Protein Sequences and Chemical Modifications

AbstractOnly a small percent of human genomic DNA encodes for proteins. Additionally, protein isoforms variants and chemical modifications are not coded in the genome read by the cell machinery. The resulting protein diversity is deeply involved in regular and diseased cellular processes. One challenge for the field of biotechnology, after human genome sequencing, will be to decipher the proteome at a single molecule scale to analyze single‐cell protein variability. In fact, cellular proteic information, often used as a source of biomarkers, is of great importance for early disease detection. This review discusses the proteome's complexity from its genetic source to fully modified proteins. It focuses on the principle of nanopore data analysis and how to obtain information from an electrical current trace. Specifically, the most recent developments in detection, sequencing and post‐translational discrimination of amino acids, peptides and proteins, are described. The main results obtained in this field are discussed and the nanopore techniques to other classical or single‐molecule approaches are compared.

Minimal deuterium isotope effects in quantitation of dimethyl-labeled complex proteomes analyzed with capillary zone electrophoresis/mass spectrometry.

Stable heavy‐isotope labeling is commonly used in quantitative proteomics. Several common techniques incorporate deuterium (2H) as the heavy isotopic label using reductive amination with formaldehyde. Compared with alternatives, dimethyl labeling reagents are inexpensive and the labeling chemistry is simple and rapid. However, the substitution of hydrogen by deuterium can introduce subtle changes in peptides’ polarities, leading to a shift in chromatographic retention times between deuterated and nondeuterated peptides that can lead to quantification deviations. Capillary zone electrophoresis has emerged as a complementary separation for ESI–MS‐based proteomics, including targeted and quantitative approaches. The extent to which the deuterium isotope effect impacts CZE‐based proteomics, which separates peptides based on their S/N ratios, has not been investigated. To address this issue, CZE was used to analyze dimethyl labeled E. coli tryptic digests in 100 min single‐shot analyses. The median migration time shift was 0.1 s for light versus heavy labeled peptides, which is 2.5% of the peak width. For comparison, nUHPLC–ESI–MS/MS was used to analyze the same sample. In UPLC, deuterated peptides tended to elute earlier than nondeuterated peptides, with a retention shift of 3 s for light versus heavy labeled peptides, which is roughly half the peak width. This shift in separation time did not have a significant effect on quantitation for either method for equal mixing ratios of the light‐intermediate‐heavy isotope labeled samples.

A single mutation in the ACTR8 gene associated with lineage-specific expression in primates

BackgroundAlternative splicing (AS) generates various transcripts from a single gene and thus plays a significant role in transcriptomic diversity and proteomic complexity. Alu elements are primate-specific transposable elements (TEs) and can provide a donor or acceptor site for AS. In a study on TE-mediated AS, we recently identified a novel AluSz6-exonized ACTR8 transcript of the crab-eating monkey (Macaca fascicularis). In the present study, we sought to determine the molecular mechanism of AluSz6 exonization of the ACTR8 gene and investigate its evolutionary and functional consequences in the crab-eating monkey.ResultsWe performed RT-PCR and genomic PCR to analyze AluSz6 exonization in the ACTR8 gene and the expression of the AluSz6-exonized transcript in nine primate samples, including prosimians, New world monkeys, Old world monkeys, and hominoids. AluSz6 integration was estimated to have occurred before the divergence of simians and prosimians. The Alu-exonized transcript obtained by AS was lineage-specific and expressed only in Old world monkeys and apes, and humans. This lineage-specific expression was caused by a single G duplication in AluSz6, which provides a new canonical 5′ splicing site. We further identified other alternative transcripts that were unaffected by the AluSz6 insertion. Finally, we observed that the alternative transcripts were transcribed into new isoforms with C-terminus deletion, and in silico analysis showed that these isoforms do not have a destructive function.ConclusionsThe single G duplication in the TE sequence is the source of TE exonization and AS, and this mutation may suffer a different fate of ACTR8 gene expression during primate evolution.

Ultrasonic-Based Filter Aided Sample Preparation as the General Method to Sample Preparation in Proteomics

We propose a new high-throughput ultrafast method for large-scale proteomics approaches by speeding up the classic filter aided sample preparation protocol, FASP, from overnight to 2.5 h. Thirty-six samples can be treated in 2.5 h, and the method is scalable to 96-well plate-based pipelines. After a modification of the FASP-tube, the steps of protein reduction, protein alkylation, and protein digestion of complex proteomes are done in just 5.25 min, each one under the effects of an ultrasonic field (7 cycles: 30 s on and 15 s off). The new method was compared to the standard overnight digestion FASP protocol, and no statistical differences were found for more than 92.4%, 92%, and 93.3% of the proteins identified by studying the proteome of E. coli, mouse brain, and mouse liver tissue samples, respectively. Furthermore, the successful relative label-free quantification of four spiked proteins in E. coli samples, BSA, β-lactoglobulin, α-casein, and α-lactalbumin, was achieved, using either the ultrasonic-based FASP protocol or the classic overnight one. The new US-FASP method matches the analytical minimalism rules as time, cost, sample requirement, reagent consumption, energy requirements, and production of waste products are reduced to a minimum while maintaining high sample throughput in a robust manner as all of the advantages of the filter aided sample preparation protocol are maintained.

Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines.

Ribosome profiling and mass spectrometry have revealed thousands of small and alternative open reading frames (sm/alt-ORFs) that are translated into polypeptides variously termed as microproteins and alt-proteins in mammalian cells. Some micro-/alt-proteins exhibit stress-, cell-type-, and/or tissue-specific expression; understanding this regulated expression will be critical to elucidating their functions. While differential translation has been inferred by ribosome profiling, quantitative mass spectrometry-based proteomics is needed for direct comparison of microprotein and alt-protein expression between samples and conditions. However, while label-free quantitative proteomics has been applied to detect stress-dependent expression of bacterial microproteins, this approach has not yet been demonstrated for analysis of differential expression of unannotated ORFs in the more complex human proteome. Here, we present global micro-/alt-protein quantitation in two human leukemia cell lines, K562 and MOLT4. We identify 12 unannotated proteins that are differentially expressed in these cell lines. The expression of six micro/alt-proteins from cDNA was validated biochemically, and two were found to localize to the nucleus. Thus, we demonstrate that label-free comparative proteomics enables quantitation of micro-/alt-protein expression between human cell lines. We anticipate that this workflow will enable the discovery of regulated sm/alt-ORF products across many biological conditions in human cells.

Heterogeneity of proteome dynamics between connective tissue phases of adult tendon.

Maintenance of connective tissue integrity is fundamental to sustain function, requiring protein turnover to repair damaged tissue. However, connective tissue proteome dynamics remain largely undefined, as do differences in turnover rates of individual proteins in the collagen and glycoprotein phases of connective tissue extracellular matrix (ECM). Here, we investigate proteome dynamics in the collagen and glycoprotein phases of connective tissues by exploiting the spatially distinct fascicular (collagen-rich) and interfascicular (glycoprotein-rich) ECM phases of tendon. Using isotope labelling, mass spectrometry and bioinformatics, we calculate turnover rates of individual proteins within rat Achilles tendon and its ECM phases. Our results demonstrate complex proteome dynamics in tendon, with ~1000 fold differences in protein turnover rates, and overall faster protein turnover within the glycoprotein-rich interfascicular matrix compared to the collagen-rich fascicular matrix. These data provide insights into the complexity of proteome dynamics in tendon, likely required to maintain tissue homeostasis.

Sample preparation of blood plasma enables baseline separation of iron metalloproteins by SEC-GFAAS

The analysis of human plasma for biomarkers holds promise to revolutionize disease diagnosis, but is hampered by the inherent complexity of the plasma proteome. One way to overcome this problem is to analyze plasma for a sub-proteome, such as the metalloproteome. Previous studies employing size-exclusion chromatography (SEC) coupled on-line to an inductively coupled plasma-atomic emission spectrometer (ICP-AES) have revealed that plasma contains ~12 copper, iron and zinc metalloproteins. This included the iron metalloproteins transferrin (Tf) and a recently identified haptoglobin-hemoglobin (Hp-Hb) complex, which is formed in plasma when red blood cells rupture. Since this SEC-ICP-AES method required a sample volume of 500 µL to generate diagnostically useful results, we sought to develop an alternative SEC-based hyphenated approach using a smaller SEC column (150 × 5 mm I.D.) and a graphite furnace atomic absorption spectrometer (GFAAS) as the iron-specific detector. A designed interface enabled the integration of the SEC system with the GFAAS. Baseline separation between the Hp-Hb complex and Tf was achieved by developing a sample preparation procedure which involved the chelating agent-based mobilization of Fe from Tf to a small molecular weight Fe complex. Spiking of human plasma (1.0 mL) with red blood cell lysate (1–2 µL) increased only the intensity of the Fe peak corresponding to the Hp-Hb complex, but not that of Tf. Since the developed SEC-GFAAS method requires only 50 µL of plasma for analysis, it can now be employed for the cost-effective quantification of the clinically relevant Hb-Hp complex in human plasma in <50 min.

Alternative proteins are functional regulators in cell reprogramming by PKA activation.

It has been recently shown that many proteins are lacking from reference databases used in mass spectrometry analysis, due to their translation templated on alternative open reading frames. This questions our current understanding of gene annotation and drastically expands the theoretical proteome complexity. The functions of these alternative proteins (AltProts) still remain largely unknown. We have developed a large-scale and unsupervised approach based on cross-linking mass spectrometry (XL-MS) followed by shotgun proteomics to gather information on the functional role of AltProts by mapping them back into known signalling pathways through the identification of their reference protein (RefProt) interactors. We have identified and profiled AltProts in a cancer cell reprogramming system: NCH82 human glioma cells after 0, 16, 24 and 48 h Forskolin stimulation. Forskolin is a protein kinase A activator inducing cell differentiation and epithelial–mesenchymal transition. Our data show that AltMAP2, AltTRNAU1AP and AltEPHA5 interactions with tropomyosin 4 are downregulated under Forskolin treatment. In a wider perspective, Gene Ontology and pathway enrichment analysis (STRING) revealed that RefProts associated with AltProts are enriched in cellular mobility and transfer RNA regulation. This study strongly suggests novel roles of AltProts in multiple essential cellular functions and supports the importance of considering them in future biological studies.

Preoperative Radiotherapy Leads to Significant Differences in the Plasma Protein Profile of Rectal Cancer Patients

Introduction: Colorectal cancer (CRC) is the third most common cancer worldwide, accounting for 10% of the global cancer burden. Rectal cancer accounts for around 30% of CRC cases, and patients with resectable rectal cancer are often given preoperative radiotherapy (PRT) to reduce the rate of local recurrence. The human plasma proteome is an exceptionally complex proteome and ideal to study due to its ability to reflect the presence of diseases such as cancer and the ease of obtaining blood samples. Previous proteomic studies involving rectal cancer patients have mostly focused on the identification of proteins involved in resistance to radiotherapy. Objective: The aim of this study was to investigate the overall effects of PRT on plasma protein expression in rectal cancer patients, as there is a lack of such studies. Methods: Here, we have used mass spectrometry and subsequent statistical analyses to analyze the plasma samples of 30 rectal cancer patients according to PRT status (positive or negative) and tumor stage (II or III). Results and Conclusions: We discovered 42 proteins whose levels differed significantly between stage II and III rectal cancer patients who did or did not receive PRT. This study shows that PRT, although localized to the pelvis, leads to measurable, tumor stage-specific changes in plasma protein expression. Future studies of plasma proteins should, when relevant, take this into account and be aware of the widespread effects that PRT has on the plasma proteome.