bims-prodis 2019-03-10 papers

bims-prodis

Biomed News

on Proteomics in disease

Issue of 2019–03–10
25 papers selected by
Nancy Gough, Bioserendipity

Serum Proteomic Signatures of Male Breast Cancer.
Transcriptome-proteome integration of archival human renal cell carcinoma biopsies enable identification of molecular mechanisms.
Glycation profile of minor abundant erythrocyte proteome across varying glycemic index in diabetes mellitus.
Are formalin-fixed and paraffin-embedded tissues fit for proteomic analysis?
Individual and stable autoantibody repertoires in healthy individuals.
Circulating Markers of Inflammation Persist in Children and Adults with Giant Aneurysms after Kawasaki Disease.
Proteomics in Psoriasis.
The imbalance in the complement system and its possible physiological mechanisms in patients with lung cancer.
Proteomics Profiling and Risk of New-Onset Atrial Fibrillation: Framingham Heart Study.
Recent Advances on the Molecular Mechanism of Cervical Carcinogenesis Based on Systems Biology Technologies.
APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors.
Quantitative proteomic analysis of dermal papilla from male androgenetic alopecia comparing before and after treatment with low-level laser therapy.
Blood Biomarkers for Stroke Diagnosis and Management.
Proteomic analysis of the aqueous humour in eyes with pseudoexfoliation syndrome.
MALDI-TOF MS-based total serum protein fingerprinting for liver cancer diagnosis.
Modified lipoproteins in periodontitis - a link to cardiovascular disease?
Mass Spectrometry Amyloid Typing Is Reproducible across Multiple Organ Sites.
The integration of emerging omics approaches to advance precision medicine: How can regulatory science help?
NrCAM is a marker for substrate-selective activation of ADAM10 in Alzheimer's disease.
Identification of an Antigenic Determinant of Clavulanic Acid Responsible for IgE-mediated Reactions.
Tumor endothelial cell-derived cadherin-2 promotes angiogenesis and has prognostic significance for lung adenocarcinoma.
Discovery and Validation of a Novel Neutrophil Activation Marker Associated with Obesity.
An interpretable machine learning model for diagnosis of Alzheimer's disease.
Occupational exposure to urinary bladder carcinogens - risk factors, molecular mechanisms and biomarkers.
Differential miRNA expression profile and proteome in plasma exosomes from patients with paroxysmal nocturnal hemoglobinuria.

Cancer Genomics Proteomics. 2019 Mar-Apr;16(2):16(2): 129-137

Serum Proteomic Signatures of Male Breast Cancer.

Eleni Zografos, Athanasios K Anagnostopoulos, Aggeliki Papadopoulou, Evangelia Legaki, Flora Zagouri, Evangelos Marinos, George T Tsangaris, Maria Gazouli.

   BACKGROUND: To date, the elucidation of serum protein alterations in male breast cancer (MBC) has not been extensively studied, due to the rarity of the disease.
MATERIALS AND METHODS: In the present work, two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) were employed to detect differences in serum protein expression between patients with MBC and healthy controls.
RESULTS: A panel of differentially expressed serum proteins was identified, including proteins involved in the regulation of the cell cycle [e.g. cell division cycle 7-related protein kinase (CDC7)], in mitochondrial function [e.g. mitochondrial aldehyde dehydrogenase (ALDH2) and dimethyladenosine transferase 1 (TFB1M)], in lipid metabolism and transport [e.g. apolipoprotein A-I (APOA1) and E (APOE)], in apoptosis and immune response [e.g. CD5 antigen-like (CD5L), clusterin (CLUS) and C-C motif chemokine 14 (CCL14)], in transcription (e.g. protein SSX3 and signal transducer and activator of transcription 3 (STAT3)], in invasion and metastasis (e.g. alpha-2-HS-glycoprotein (FETUA)], in estrogen synthesis [aromatase (CYP19A1)] and other diverse biological roles [e.g. actin-related protein 2/3 complex subunit 4 (ARPC4), dual specificity mitogen-activated protein kinase kinase 4 (MP2K4), ectoderm-neural cortex protein 1 (ENC1), and matrix metalloproteinase-27 (MMP27)].
CONCLUSION: These findings provide valuable insight into the distinct clinicopathological features of MBC and indicate that select serum proteomic markers may help improve MBC management.

Keywords:  Male breast cancer; mass spectrometry; proteomics; serum biomarkers

DOI:  https://doi.org/10.21873/cgp.20118
Am J Physiol Renal Physiol. 2019 Mar 06.

Transcriptome-proteome integration of archival human renal cell carcinoma biopsies enable identification of molecular mechanisms.

Even Evjen Koch, Kenneth Finne, Oystein Eikrem, Lea Landolt, Christian Beisland, Sabine Leh, Nicolas Delaleu, Magnus Granly, Bjorn Egil Vikse, Tarig Osman, Andreas Scherer, Hans-Peter Marti.

  Renal cell cancer is among the most common forms of cancer in humans, with around 35,000 deaths attributed to kidney carcinoma in the European Union (EU) in 2012 alone. Clear cell renal cell carcinoma (ccRCC) represents the most common form of kidney cancer and the most lethal of all genitourinary cancers. Here we apply omics technologies to archival core biopsies to investigate the biology underlying ccRCC. Knowledge of these underlying processes should be useful for the discovery and/or confirmation of novel therapeutic approaches and ccRCC biomarker development. From partial or full nephrectomies of 11 patients, paired core biopsies of ccRCC affected tissue and adjacent ("peritumorous") non-tumor tissue were both sampled and subjected to proteomics analyses. We combined proteomics results with our published mRNA-seq from the same patients and with published miRNA-seq data from an overlapping patient cohort from our institution. Statistical analysis and pathway analysis were performed with JMP Genomics (SAS) and Ingenuity Pathway Analysis (IPA, Qiagen), respectively. Proteomics analysis confirmed the involvement of metabolism and oxidative stress-related pathways in ccRCC, while the most affected pathways in the mRNA-seq data were related to the immune system. Unlike proteomics or mRNA-seq alone, a combinatorial cross-omics pathway analysis approach captured a broad spectrum of biological processes underlying ccRCC, such as mitochondrial damage, repression of apoptosis, and immune system pathways. Sirtuins, immunoproteasome genes and CD74 are proposed as potential targets for the treatment of ccRCC.

Keywords:  CD74; cross-omics; immunoproteasome; kidney cancer; proteomics

DOI:  https://doi.org/10.1152/ajprenal.00424.2018
Anal Biochem. 2019 Mar 01. pii: S0003-2697(19)30045-4. [Epub ahead of print]

Glycation profile of minor abundant erythrocyte proteome across varying glycemic index in diabetes mellitus.

Monita Muralidharan, Vijay Bhat, Y S Bindu, Amit Kumar Mandal.

PURPOSE: Long-term glycemic index in patients with diabetes mellitus (DM) is measured by glycated hemoglobin (HbA1c) besides blood glucose. In DM, the primary amino groups of proteins get glycated via non-enzymatic post-translational modification. This study aims at identifying and characterizing site-specific glycation of erythrocyte proteome across varying glycemic index in patients with DM.
EXPERIMENTS: We isolated the glycated erythrocyte proteome devoid of hemoglobin from control and diabetic samples using boronate affinity chromatography. Proteomic analysis was performed using nanoLC/ESI-MS proteomics platform. The site-specific modification on different proteins was deciphered using a customized database.
RESULTS: We report 37 glycated proteins identified and characterized from samples with HbA1c of 6%, 8%, 12%, and 16%. Our results show that both extent and site-specific modification of proteins increased with increasing HbA1c. The observed residue-specific modifications of catalase, peroxiredoxin, carbonic anhydrase, lactate dehydrogenase B and delta-aminolevulinic acid dehydratase were correlated with the literature report on their functional disorder in DM.
CONCLUSIONS: and clinical relevance: 37 glycated erythrocyte proteins apart from hemoglobin were characterized from DM patient samples with varying HbA1c values. We correlated the site-specific glycation and associated functional disorder of five representative proteins. However, the clinical correlation with the observed modifications needs further investigation.

DOI: https://doi.org/10.1016/j.ab.2019.02.026
J Mass Spectrom. 2019 Mar 03.

Are formalin-fixed and paraffin-embedded tissues fit for proteomic analysis?

Malte Bayer, Linus Angenendt, Christoph Schliemann, Wolfgang Hartmann, Simone König.

  Formalin-fixed and paraffin-embedded (FFPE)-tissue archives are potential treasure troves in the search for clinically interesting specimens. However, while the FFPE-treatment provides excellent conservation of the three-dimensional structure of the tissue and prevents degradation over decades, it also introduces numerous non-specific and irreversible protein modifications. In this study, we have evaluated several published workflows for FFPE-tissue by fit-for-purpose proteomics technologies. We demonstrate that many protein modifications and cross-links remain after treatment and conclude that the proteomics of FFPE-tissue is of value, but clear-cut limitations must be kept in mind. The analysis of abundant proteins in FFPE is straightforward, but confident identification of low-level proteins and/or biologically relevant modifications is seriously hampered by the FFPE-treatment. Peptide assignment should only be performed on high quality spectra, even if this is at the cost of lower numbers of protein IDs. As Yergey and Coorssen stated in 2015: "Data quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis."

Keywords:  FFPE-tissue; cross-links; formaldehyde-induced modifications; proteomics

DOI:  https://doi.org/10.1002/jms.4347
Autoimmunity. 2019 Mar 05. 1-11

Individual and stable autoantibody repertoires in healthy individuals.

Maja Neiman, Cecilia Hellström, David Just, Cecilia Mattsson, Linn Fagerberg, Ina Schuppe-Koistinen, Anders Gummesson, Göran Bergström, Olli Kallioniemi, Adnane Achour, Riitta Sallinen, Mathias Uhlén, Peter Nilsson.

  In the era towards precision medicine, we here present the individual specific autoantibody signatures of 193 healthy individuals. The self-reactive IgG signatures are stable over time in a way that each individual profile is recognized in longitudinal sampling. The IgG autoantibody reactivity towards an antigen array comprising 335 protein fragments, representing 204 human proteins with potential relevance to autoimmune disorders, was measured in longitudinal plasma samples from 193 healthy individuals. This analysis resulted in unique autoantibody barcodes for each individual that were maintained over one year's time. The reactivity profiles, or signatures, are person specific in regards to the number of reactivities and antigen specificity. Two independent data sets were consistent in that each healthy individual displayed reactivity towards 0-16 antigens, with a median of six. Subsequently, four selected individuals were profiled on in-house produced high-density protein arrays containing 23,000 protein fragments representing 14,000 unique protein coding genes. Based on a unique, broad and deep longitudinal profiling of autoantibody reactivities, our results demonstrate a unique autoreactive profile in each analyzed healthy individual. The need and interest for broad-ranged and high-resolution molecular profiling of healthy individuals is rising. We have here generated and assessed an initial perspective on the global distribution of the self-reactive IgG repertoire in healthy individuals, by investigating 193 well-characterized healthy individuals. Highlights A unique longitudinal profiling of autoantibody repertoires in healthy individuals Autoantibody profiles are highly individual and stable over time All individuals display IgG binding to human protein fragments The specificity of disease associated autoantigens needs to be thoroughly characterized The identification of a small set of highly reactive autoantigens Importance of stringent antigen and sample specific cut-offs for defining reactivity.

Keywords:  Autoantibody repertoire; affinity proteomics; autoantibody profile; precision medicine; protein array

DOI:  https://doi.org/10.1080/08916934.2019.1581774
Circ Genom Precis Med. 2019 Mar 07.

Circulating Markers of Inflammation Persist in Children and Adults with Giant Aneurysms after Kawasaki Disease.

Miroslaw Lech, Jamey Guess, Jay Duffner, Jun Oyamada, Chisato Shimizu, Shinsuke Hoshino, Victor Farutin, Dorota A Bulik, Bryan Gutierrez, Hetal Sarvaiya, Bulbul Kapoor, Laura Koppes, Radka Saldova, Henning Stockmann, Simone Albrecht, Ciara McManus, Pauline M Rudd, Ganesh V Kaundinya, Anthony M Manning, Carlos J Bosques, Andrew M Kahn, Lori B Daniels, John B Gordon, Adriana H Tremoulet, Ishan Capila, Nur Sibel Gunay, Leona E Ling, Jane C Burns.

BACKGROUND: The sequelae of Kawasaki disease (KD) vary widely with the greatest risk for future cardiovascular events among those who develop giant coronary artery aneurysms (CAA). We sought to define the molecular signature associated with different outcomes in pediatric and adult KD patients.
METHODS: Molecular profiling was conducted using mass spectrometry-based shotgun proteomics, transcriptomics, and glycomics methods on eight pediatric KD patients at the acute, sub-acute and convalescent time points. Shotgun proteomics was performed on nine KD adults with giant CAA and matched healthy controls. Plasma calprotectin was measured by ELISA in 28 pediatric KD patients one-year post-KD, 70 adult KD patients, and 86 healthy adult volunteers.
RESULTS: A characteristic molecular profile was seen in pediatric patients during the acute disease, which resolved at the subacute and convalescent periods in patients with no coronary artery sequelae but persisted in two patients who developed giant CAA. We therefore investigated persistence of inflammation in KD adults with giant CAA by shotgun proteomics that revealed a signature of active inflammation, immune regulation, and cell trafficking. Correlating results obtained using shotgun proteomics in the pediatric and adult KD cohorts identified elevated calprotectin levels in the plasma of patients with CAA. Investigation of expanded pediatric and adult KD cohorts revealed elevated levels of calprotectin in pediatric patients with giant CAA one-year post-KD and in adult KD patients who developed giant CAA in childhood.
CONCLUSIONS: Complex patterns of biomarkers of inflammation and cell trafficking can persist long after the acute phase of KD in patients with giant CAA. Elevated levels of plasma calprotectin months to decades after acute KD and infiltration of cells expressing S100A8 and A9 in vascular tissues suggest ongoing, sub-clinical inflammation. Calprotectin may serve as a biomarker to inform the management of KD patients following the acute illness.

DOI: https://doi.org/10.1161/CIRCGEN.118.002433
Int J Mol Sci. 2019 Mar 06. pii: E1141. [Epub ahead of print]20(5):

Proteomics in Psoriasis.

Leena Chularojanamontri, Norramon Charoenpipatsin, Narumol Silpa-Archa, Chanisada Wongpraparut, Visith Thongboonkerd.

  Psoriasis has been thought to be driven primarily by innate and adaptive immune systems that can be modified by genetic and environmental factors. Complex interplay between inflammatory cytokines and T-cells, especially Th1 and Th17 cells, leads to abnormal cell proliferation and psoriatic skin lesions. Nevertheless, such mechanisms do not entirely represent the pathogenesis of psoriasis. Moreover, earlier and better biomarkers in diagnostics, prognostics, and monitoring therapeutic outcomes of psoriasis are still needed. During the last two decades, proteomics (a systematic analysis of proteins for their identities, quantities, and functions) has been widely employed to psoriatic research. This review summarizes and discusses all of the previous studies that applied various modalities of proteomics technologies to psoriatic skin disease. The data obtained from such studies have led to (i) novel mechanisms and new hypotheses of the disease pathogenesis; (ii) biomarker discovery for diagnostics and prognostics; and (iii) proteome profiling for monitoring treatment efficacy and drug-induced toxicities.

Keywords:  biomarker discovery; dermatology; diagnostics; mass spectrometry; prognostics; proteome; psoriatic skin

DOI:  https://doi.org/10.3390/ijms20051141
BMC Cancer. 2019 Mar 06. 19(1): 201

The imbalance in the complement system and its possible physiological mechanisms in patients with lung cancer.

Ping Zhao, Jun Wu, Feiteng Lu, Xuan Peng, Chenlin Liu, Nanjin Zhou, Muying Ying.

   BACKGROUND: The clinical and experimental evidences for complement-cancer relationships are solid, whereas an epidemiological study reporting the imbalance of complement system in patients is still lacking.
METHODS: Using publicly available databases, we jointly compared the levels of complement components in plasma and lung cancer tissues. With iTRAQ proteomics, quantitative RT-PCR and western blotting, we analysed the differences in complement levels in lung cancer tissues and normal control tissues. Complement components are mainly synthesized by the liver and secreted into the blood. Using paired co-cultures of human normal QSG-7701 hepatocytes with lung cancer cells (A549, LTEP-α-2 or NCI-H1703) or human normal bronchial epithelial (HBE) cells, we examined the effects of lung cancer cells on complement synthesis and secretion in QSG-7701 hepatocytes.
RESULTS: An integrated analysis of transcriptome and proteome datasets from 43 previous studies revealed lower mRNA and protein levels of 25 complement and complement-related components in lung cancer tissues than those in normal control tissues; conversely, higher levels of complement proteins were detected in plasma from patients than those in healthy subjects. Our iTRAQ proteome study identified decreased and increased levels of 31 and 2 complement and complement-related proteins, respectively, in lung cancer tissues, of which the reduced levels of 10 components were further confirmed using quantitative RT-PCR and western blotting. Paired co-cultures of QSG-7701 hepatocytes with A549, LTEP-α-2, NCI-H1703 or HBE cells indicated that lung cancer cells increased complement synthesis and secretion in QSG-7701 cells compared to HBE cells.
CONCLUSIONS: The opposite associations between the levels of complement and complement-related components in lung cancer tissues and plasma from patients that have been repeatedly reported by independent publications may indicate the prevalence of an imbalance in the complement system of lung cancer patients. The possible mechanism of the imbalance may be associated not only with the decreased complement levels in lung cancer tissues but also the concurrent lung cancer tissue-induced increase in hepatocyte complement synthesis and plasma secretion in patients. And the imbalance should be accompanied by a suppression of complement-dependent immunity in lung cancer tissues coupled with a burden of complement immunity in the circulation of patients.

Keywords:  Hepatocyte complement synthesis and secretion; Integrated analysis of transcriptome and proteome datasets; Paired co-cultures of hepatocytes and lung cancer cells; The imbalance in the complement system

DOI:  https://doi.org/10.1186/s12885-019-5422-x
J Am Heart Assoc. 2019 Mar 19. 8(6): e010976

Proteomics Profiling and Risk of New-Onset Atrial Fibrillation: Framingham Heart Study.

Darae Ko, Mark D Benson, Debby Ngo, Qiong Yang, Martin G Larson, Thomas J Wang, Ludovic Trinquart, David D McManus, Steven A Lubitz, Patrick T Ellinor, Ramachandran S Vasan, Robert E Gerszten, Emelia J Benjamin, Honghuang Lin.

  Background Prior studies relating proteomics markers to incident AF screened for limited numbers of proteins. Methods and Results We performed proteomics assays among participants from the Framingham Heart Study Offspring attending their fifth examination. Plasma protein levels (n=1373) were measured by the SOMAscan proteomic profiling platform. We used robust inference for the Cox proportional hazards model to relate each protein level with incident AF. In addition, we examined the association between AF-related genetic loci and levels of proteins associated with AF. Our study included 1885 participants (mean age 55±10 years, 54% women) who had proteomic profiles measured. A total of 349 participants developed AF during follow-up (mean follow-up 18.3 years). We observed that 8 proteins were significantly associated with incident AF after adjusting for age, sex, technical covariates, and correction for multiple testing ( P<0.05/1373=3.6×10-5). After additional adjustments for clinical factors associated with AF, ADAMTS13 and N-terminal pro-B-type natriuretic peptide remained significantly associated with the risk of incident AF (hazard ratio, 0.78; 95% CI, 0.70-0.88; and 1.44; 95% CI, 1.22-1.70, respectively; P<3.6×10-5 for both). None of the 8 proteins were encoded by genes at AF-related genetic loci previously identified by genome-wide association studies. Conclusions We identified 8 proteins associated with risk of incident AF after adjustment for age and sex; 2 proteins were associated with AF after adjustment for AF risk factors. Future studies are needed to replicate our findings, identify whether the markers are mechanistically related to AF development, and whether they are clinically useful for identification of future AF risk.

Keywords:  atrial fibrillation; biomarker; proteomics; risk

DOI:  https://doi.org/10.1161/JAHA.118.010976
Comput Struct Biotechnol J. 2019 ;17 241-250

Recent Advances on the Molecular Mechanism of Cervical Carcinogenesis Based on Systems Biology Technologies.

Min Lin, Miaomiao Ye, Junhan Zhou, Z Peter Wang, Xueqiong Zhu.

  Cervical cancer is one of the common malignancies in women worldwide. Exploration of pathogenesis and molecular mechanism of cervical cancer is pivotal for development of effective treatment for this disease. Recently, systems biology approaches based on high-throughput technologies have been carried out to investigate the expression of some genes and proteins in genomics, transcriptomics, proteomics, and metabonomics of cervical cancer. Compared with traditional methods，systems biology technology has been shown to provide large of information regarding prognostic biomarkers and therapeutic targets for cervical cancer. These molecular signatures from system biology technology could be useful to understand the molecular mechanisms of cervical cancer development and progression, and help physicians to design targeted therapeutic strategies for patients with cervical cancer.

Keywords:  Cervical cancer; Genomics; Proteomics; Systems biology; Transcriptomics

DOI:  https://doi.org/10.1016/j.csbj.2019.02.001
Cell Rep. 2019 Mar 05. pii: S2211-1247(19)30199-8. [Epub ahead of print]26(10): 2651-2666.e6

APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors.

Nitin Roper, Shaojian Gao, Tapan K Maity, A Rouf Banday, Xu Zhang, Abhilash Venugopalan, Constance M Cultraro, Rajesh Patidar, Sivasish Sindiri, Anna-Leigh Brown, Alexander Goncearenco, Anna R Panchenko, Romi Biswas, Anish Thomas, Arun Rajan, Corey A Carter, David E Kleiner, Stephen M Hewitt, Javed Khan, Ludmila Prokunina-Olsson, Udayan Guha.

  Intratumor mutational heterogeneity has been documented in primary non-small-cell lung cancer. Here, we elucidate mechanisms of tumor evolution and heterogeneity in metastatic thoracic tumors (lung adenocarcinoma and thymic carcinoma) using whole-exome and transcriptome sequencing, SNP array for copy-number alterations (CNAs), and mass-spectrometry-based quantitative proteomics of metastases obtained by rapid autopsy. APOBEC mutagenesis, promoted by increased expression of APOBEC3 region transcripts and associated with a high-risk APOBEC3 germline variant, correlated with mutational tumor heterogeneity. TP53 mutation status was associated with APOBEC hypermutator status. Interferon pathways were enriched in tumors with high APOBEC mutagenesis and IFN-γ-induced expression of APOBEC3B in lung adenocarcinoma cells, suggesting that the immune microenvironment may promote mutational heterogeneity. CNAs occurring late in tumor evolution correlated with downstream transcriptomic and proteomic heterogeneity, although global proteomic heterogeneity was significantly greater than transcriptomic and CNA heterogeneity. These results illustrate key mechanisms underlying multi-dimensional heterogeneity in metastatic thoracic tumors.

Keywords:  APOBEC; copy number alterations; evolution; heterogeneity; lung adenocarcinoma; proteogenomics; rapid autopsy; thymic carcinoma

DOI:  https://doi.org/10.1016/j.celrep.2019.02.028
Lasers Surg Med. 2019 Mar 07.

Quantitative proteomic analysis of dermal papilla from male androgenetic alopecia comparing before and after treatment with low-level laser therapy.

Ratchathorn Panchaprateep, Trairak Pisitkun, Nuttiya Kalpongnukul.

   BACKGROUND: Currently, low-level laser therapy (LLLT) has been approved as a new treatment for androgenetic alopecia (AGA). However, it has not been elucidated how LLLT promotes hair growth in vivo.
OBJECTIVES: To investigate the change in protein expression from dermal papilla (DP) tissues in male AGA patients after LLLT treatment using liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis.
METHODS: This is an open-label, prospective, single-arm study obtained punch scalp biopsy specimens from patients with AGA before and after LLLT treatment. Each subject was self-treated with helmet type of LLLT (655 nm, 5 mW) device at home for 25 minutes per treatment every other day for 24 weeks. LC-MS/MS analysis based on the dimethyl labeling strategy for protein quantification was used to identify proteins expressed in DP tissues from AGA patients.
RESULTS: Proteomic analysis revealed 11 statistically significant up-regulated and 2 down-regulated proteins in LLLT treated DP compared with baseline (P < 0.05). A bioinformatic analysis signifies that these proteins are involved in several biological processes such as regulation of cellular transcription, protein biosynthesis, cell energy, lipid homeostasis, extracellular matrix (ECM), ECM structural constituent, cell-cell/cell-matrix adhesion as well as angiogenesis. ATP-binding cassette sub-family G member, a transporter involved in cellular lipid homeostasis, was the most up-regulated protein. Additionally, LLLT increased the main ECM proteins in DP which results in a bigger volume of DP and a clinical improvement of hair diameter in AGA patients.
CONCLUSION: We identified the proteome set of DP proteins of male patients with AGA treated with LLLT which implicates the role of LLLT in promoting hair growth and reversing of miniaturization process of AGA by enhancing DP cell function. Our results strongly support the benefit of LLLT in the treatment of AGA. Lasers Surg. Med. © 2019 Wiley Periodicals, Inc.

Keywords:  androgenetic alopecia; dermal papilla; liquid chromatography-tandem mass spectrometry; low-level laser therapy; proteomic analysis

DOI:  https://doi.org/10.1002/lsm.23074
Neuromolecular Med. 2019 Mar 04.

Blood Biomarkers for Stroke Diagnosis and Management.

Joseph Kamtchum-Tatuene, Glen C Jickling.

  Biomarkers are objective indicators used to assess normal or pathological processes, evaluate responses to treatment and predict outcomes. Many blood biomarkers already guide decision-making in clinical practice. In stroke, the number of candidate biomarkers is constantly increasing. These biomarkers include proteins, ribonucleic acids, lipids or metabolites. Although biomarkers have the potential to improve the diagnosis and the management of patients with stroke, there is currently no marker that has demonstrated sufficient sensitivity, specificity, rapidity, precision, and cost-effectiveness to be used in the routine management of stroke, thus highlighting the need for additional work. A better standardization of clinical, laboratory and statistical procedures between centers is indispensable to optimize biomarker performance. This review focuses on blood biomarkers that have shown promise for translation into clinical practice and describes some newly reported markers that could add to routine stroke care. Avenues for the discovery of new stroke biomarkers and future research are discussed. The description of the biomarkers is organized according to their expected application in clinical practice: diagnosis, treatment decision, and outcome prediction.

Keywords:  Biomarker; Diagnosis; Genomics; Management; Proteomics; Stroke

DOI:  https://doi.org/10.1007/s12017-019-08530-0
Br J Ophthalmol. 2019 Mar 06. pii: bjophthalmol-2017-310416. [Epub ahead of print]

Proteomic analysis of the aqueous humour in eyes with pseudoexfoliation syndrome.

Amelie Botling Taube, Anne Konzer, Albert Alm, Jonas Bergquist.

   BACKGROUND/AIMS: Pseudoexfoliation syndrome (PEX) is characterised by the production and accumulation of extracellular fibrillar material in the anterior segment of the eye. The pathogenesis of PEX is multifactorial with genetic factors and ageing as contributing factors. Previously, an increased concentration of beta-crystalline B2 (CRYBB2) was observed in the aqueous humour (AH) in eyes with PEX in a pooled material. Here, the protein content was examined on individual basis.
METHODS: During cataract surgery, AH was sampled from patients with and without PEX, 10 eyes in each group. The proteins were digested and labelled with isotopomeric dimethyl labels, separated with high-pressure liquid chromatography and analysed in an Orbitrap mass analyzer.
RESULTS: The concentration of complement factor 3, kininogen-1, antithrombin III and vitamin D-binding protein was increased in all eyes with PEX. Retinol-binding protein 3, glutathione peroxidase, calsyntenin-1 and carboxypeptidase E were decreased in eyes with PEX. Beta-crystalline B1 and CRYBB2 and gamma-crystalline D were up to eightfold upregulated in 4 of 10 in eyes with PEX. CONCLUSION : The results indicate that oxidative stress and inflammation are contributing factors in the formation of PEX. Knowledge about the proteome in PEX is relevant for understanding this condition.

Keywords:  aqueous humour; diagnostic tests/Investigation

DOI:  https://doi.org/10.1136/bjophthalmol-2017-310416
Analyst. 2019 Mar 08.

MALDI-TOF MS-based total serum protein fingerprinting for liver cancer diagnosis.

Han-Gyu Park, Kyoung-Soon Jang, Hae-Min Park, Won-Suk Song, Yoon-Yi Jeong, Da-Hee Ahn, Seong-Min Kim, Yung-Hun Yang, Yun-Gon Kim.

Serum is one of the most commonly used samples in many studies to identify protein biomarkers to diagnose cancer. Although conventional enzyme-linked immunosorbent assay (ELISA) or liquid chromatography-mass spectrometry (LC-MS)-based methods have been applied as clinical tools for diagnosing cancer, there have been troublesome problems, such as inferior multiplexing capabilities, high development costs and long turnaround times, which are inappropriate for high-throughput analytical platforms. Here, we developed a simple and robust cancer diagnostic method using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based total serum protein fingerprinting. First, serum samples were simply diluted with distilled water and subsequently spotted onto a MALDI plate without prior chromatographic purification or separation. The sample preparation method was enough to collect reproducible total serum protein fingerprints and would be highly advantageous for high-throughput assay. Each of the integrated main spectrum profiles (MSPs), which are representative of liver cancer patients (n = 40) or healthy controls (n = 80), was automatically generated by the MALDI Biotyper 3 software. The reliability of the integrated MSPs was successfully evaluated in comparison with a blind test set (n = 31), which consisted of 13 liver cancer patients and 18 healthy controls. Additionally, our partial least squares discriminant analysis (PLS-DA) demonstrated a statistically significant difference in MALDI-TOF MS-based total serum protein fingerprints between liver cancer patients and healthy controls. Taken together, this work suggests that this method may be an effective high-throughput platform technology for various cancer diagnoses and disease evaluations.

DOI: https://doi.org/10.1039/c8an02241k
Biosci Rep. 2019 Mar 06. pii: BSR20181665. [Epub ahead of print]

Modified lipoproteins in periodontitis - a link to cardiovascular disease?

Stefan Ljunggren, Torbjörn Bengtsson, Helen Karlsson, Carin Johansson Starkhammar, Eleonor Palm, Fariba Nayeri, Bijar Ghafouri, Julia Davies, Gunnel Svensäter, Johanna Lönn.

  There is a strong association between periodontal disease and atherosclerotic cardiovascular disorders. A key event in the development of atherosclerosis is accumulation of modified lipoproteins within the arterial wall. We hypothesize that patients with periodontitis have an altered lipoprotein profile towards an atherogenic form. Therefore, this study aims at identifying modifications of plasma lipoproteins in periodontitis. Lipoproteins from ten female patients with periodontitis and gender- and age-matched healthy controls were isolated by density-gradient-ultracentrifugation. Proteins were separated by two-dimensional gel-electrophoresis and identified by map-matching or by nano-liquid chromatography followed by mass spectrometry. ApoA-I methionine oxidation, Oxyblot, total antioxidant capacity and a multiplex of 71 inflammation-related plasma proteins were assessed.Reduced levels of apoJ, phospholipid transfer protein, apoF, complement C3, paraoxonase 3 and increased levels of alpha-1-antichymotrypsin, apoA-II, apoC-III were found in HDL from the patients. In LDL/VLDL, the levels of apoL-1 and platelet-activating factor acetylhydrolase as well as apo-B fragments were increased. Methionine oxidation of apoA-I was increased in HDL and showed a relationship with periodontal parameters. Alpha-1 antitrypsin and alpha-2-HS glycoprotein were oxidised in LDL/VLDL and antioxidant capacity was increased in the patient group. 17 inflammation-related proteins were important for group separation with the highest discriminating proteins identified as IL-21, Fractalkine, IL-17F, IL-7, IL-1RA and IL-2.Patients with periodontitis have an altered plasma lipoprotein profile, defined by altered protein levels as well as posttranslational and other structural modifications towards an atherogenic form, which supports a role of modified plasma lipoproteins as central in the link between periodontal and cardiovascular disease.

Keywords:  lipoproteins; nLC-MS/MS; periodontal microbiota; periodontitis; two-dimensional gel electrophoresis

DOI:  https://doi.org/10.1042/BSR20181665
Biomed Res Int. 2019 ;2019 3689091

Mass Spectrometry Amyloid Typing Is Reproducible across Multiple Organ Sites.

Dusan Holub, Pavla Flodrova, Tomas Pika, Patrik Flodr, Marian Hajduch, Petr Dzubak.

We have determined patient's amyloid subtype through immunohistochemical and proteomic analyses of formalin-fixed, paraffin-embedded (FFPE) tissue samples from two affected organs per patient. Amyloid typing, via immunohistochemistry (IHC) and laser microdissection followed by the combination of liquid chromatography with mass spectrometry (LMD-LC-MS), was performed using tissue samples of the human heart, liver, kidney, tongue, and small intestine from 11 patients, and the results were compared with clinical data. LMD-LC-MS correctly typed AL amyloidosis in all 22 FFPE tissue samples despite tissue origin. In contrast, IHC was successful only in the analysis of eight FFPE tissue samples with differences between the examined organs. In the majority of LMD-LC-MS typed samples, the level of IHC staining intensity for transthyretin and serum amyloid A was the same as that for Ig κ and Ig λ antibodies, suggesting low Ig κ or Ig λ antibodies reactivity and the additional antibody clones were essential for correct typing. Both methods used in the study were found to be suitable for amyloid typing, although LMD-LC-MS yielded more promising results than IHC.

DOI: https://doi.org/10.1155/2019/3689091
J Clin Transl Sci. 2018 Oct;2(5): 295-300

The integration of emerging omics approaches to advance precision medicine: How can regulatory science help?

Joan E Adamo, Robert V Bienvenu, F Owen Fields, Soma Ghosh, Christina M Jones, Michael Liebman, Mark S Lowenthal, Scott J Steele.

  Building on the recent advances in next-generation sequencing, the integration of genomics, proteomics, metabolomics, and other approaches hold tremendous promise for precision medicine. The approval and adoption of these rapidly advancing technologies and methods presents several regulatory science considerations that need to be addressed. To better understand and address these regulatory science issues, a Clinical and Translational Science Award Working Group convened the Regulatory Science to Advance Precision Medicine Forum. The Forum identified an initial set of regulatory science gaps. The final set of key findings and recommendations provided here address issues related to the lack of standardization of complex tests, preclinical issues, establishing clinical validity and utility, pharmacogenomics considerations, and knowledge gaps.

Keywords:  Clinical and Translational Science Award; Regulatory science; US Food and Drug Administration; omics; precision medicine

DOI:  https://doi.org/10.1017/cts.2018.330
EMBO Mol Med. 2019 Mar 04. pii: e9695. [Epub ahead of print]

NrCAM is a marker for substrate-selective activation of ADAM10 in Alzheimer's disease.

Tobias Brummer, Stephan A Müller, Francisco Pan-Montojo, Fumiaki Yoshida, Andreas Fellgiebel, Taisuke Tomita, Kristina Endres, Stefan F Lichtenthaler.

  The metalloprotease ADAM10 is a drug target in Alzheimer's disease, where it cleaves the amyloid precursor protein (APP) and lowers amyloid-beta. Yet, ADAM10 has additional substrates, which may cause mechanism-based side effects upon therapeutic ADAM10 activation. However, they may also serve-in addition to APP-as biomarkers to monitor ADAM10 activity in patients and to develop APP-selective ADAM10 activators. Our study demonstrates that one such substrate is the neuronal cell adhesion protein NrCAM ADAM10 controlled NrCAM surface levels and regulated neurite outgrowth in vitro in an NrCAM-dependent manner. However, ADAM10 cleavage of NrCAM, in contrast to APP, was not stimulated by the ADAM10 activator acitretin, suggesting that substrate-selective ADAM10 activation may be feasible. Indeed, a whole proteome analysis of human CSF from a phase II clinical trial showed that acitretin, which enhanced APP cleavage by ADAM10, spared most other ADAM10 substrates in brain, including NrCAM Taken together, this study demonstrates an NrCAM-dependent function for ADAM10 in neurite outgrowth and reveals that a substrate-selective, therapeutic ADAM10 activation is possible and may be monitored with NrCAM.

Keywords:  ADAM10; Alzheimer's disease; NrCAM; acitretin; cerebrospinal fluid proteomics

DOI:  https://doi.org/10.15252/emmm.201809695
Allergy. 2019 Mar 04.

Identification of an Antigenic Determinant of Clavulanic Acid Responsible for IgE-mediated Reactions.

Nekane Barbero, Rubén Fernández-Santamaría, Cristobalina Mayorga, Ángela Martin-Serrano, María Salas, Gador Bogas, Francisco Nájera, Dolores Pérez-Sala, Ezequiel Pérez-Inestrosa, Tahia D Fernandez, María I Montañez, María J Torres.

   BACKGROUND: Selective reactions to clavulanic acid (CLV) account for around 30% of immediate reactions after administration of amoxicillin-CLV. Currently, no immunoassay is available for detecting specific IgE to CLV, and its specific recognition in patients with immediate reactions has only been demonstrated by basophil activation testing, however with sub-optimal sensitivity. The lack of knowledge regarding the structure of the drug that remains bound to proteins (antigenic determinant) is hampering the development of in vitro diagnostics. We aimed to identify the antigenic determinants of CLV as well as to evaluate their specific IgE recognition and potential role for diagnosis.
METHODS: Based on complex CLV degradation mechanisms, we hypothesized the formation of two antigenic determinants for CLV, AD-I (N-protein, 3-oxopropanamide) and AD-II (N-protein, 3-aminopropanamide), and designed different synthetic analogs to each one. IgE recognition of these structures was evaluated in basophils from patients with selective reactions to CLV and tolerant subjects. In parallel, the CLV fragments bound to proteins were identified by proteomic approaches.
RESULTS: Two synthetic analogs of AD-I were found to activate basophils from allergic patients. This determinant was also detected bound to lysines 195 and 475 of CLV-treated human serum albumin. One of these analogs was able to activate basophils in 59% of patients whereas CLV only in 41%. Combining both results led to an increase in basophil activation in 69% of patients, and only in 12% of controls.
CONCLUSION: We have identified AD-I as one CLV antigenic determinant, which is the drug fragment that remains protein-bound. This article is protected by copyright. All rights reserved.

Keywords:  Basophils; IgE; clavulanic acid; drug allergy; immediate reactions; in vitro test

DOI:  https://doi.org/10.1111/all.13761
Mol Cancer. 2019 Mar 04. 18(1): 34

Tumor endothelial cell-derived cadherin-2 promotes angiogenesis and has prognostic significance for lung adenocarcinoma.

Huiqin Zhuo, Yan Zhao, Xiao Cheng, Mao Xu, Lin Wang, Lingyun Lin, Zhi Lyu, Xuehui Hong, Jianchun Cai.

  In lung cancer, antiangiogenic strategies targeting tumor-derived endothelial cells (TECs) afford a survival advantage, but the characteristics of TECs have not been comprehensively elucidated. Herein, high-purity (> 98%) TECs were obtained, and these cells retained expression of EC markers and exhibited high viability. ITRAQ-2DLC-MS/MS was performed to profile the proteome and the heterogeneity of ECs. Only 31 of 1820 identified proteins were differentially expressed between adenocarcinoma (ADC)- and squamous cell carcinoma (SCC)-derived TECs (TEC-A and TEC-S, respectively), and cadherin-2 (CDH2) was the most significantly upregulated protein in TEC-A samples. Positive immunostaining for CDH2 (score > 3) was significantly more frequent in the endothelium of ADC tissues than in that of SCC tissues. Loss- or gain-of-function analysis showed that CDH2 significantly promoted in vitro and in vivo angiogenesis and sensitivity to the antagonist exherin. The MAPK/ERK and MAPK/JNK signaling pathways may play crucial roles in CDH2-induced HIF-1α/VEGF-mediated angiogenesis. Moreover, high CDH2 expression in TECs was significantly associated with tumor stage, visceral pleural metastasis, and decreased overall survival in patients with ADC but not SCC. Together, these data indicate the importance of CDH2 in angiogenesis and highlight its potential both for antiangiogenic therapy and as a candidate prognostic marker for ADC.

Keywords:  CDH2 expression; EC proteome profile; Heterogeneity; Non-small cell lung carcinoma; Tumor-derived endothelial cell

DOI:  https://doi.org/10.1186/s12943-019-0987-1
Sci Rep. 2019 Mar 05. 9(1): 3433

Discovery and Validation of a Novel Neutrophil Activation Marker Associated with Obesity.

Yue Pan, Jeong-Hyeon Choi, Huidong Shi, Liwen Zhang, Shaoyong Su, Xiaoling Wang.

Obesity is accompanied by low-grade systemic inflammation that etiologically contributes to obesity-induced cardiovascular disease (CVD). Growing evidence supports that neutrophil, the most abundant type of leukocytes in human, is most likely to be the target peripheral leukocyte subtype initiating the inflammatory cascade in obesity. However, few studies have systematically assessed the genome wide changes in neutrophils associated with obesity. In this study, a hypothesis-free OMIC approach (i.e. the discovery phase) and a target approach (i.e. the validation phase) were used to identify obesity related neutrophil activation markers and their roles on CVD risks. In the discovery phase, genome wide DNA methylation, RNA-sequencing and quantitative proteomics were obtained from purified neutrophils (12 obese vs. 12 lean). In the validation phase, gene expression levels of the promising genes from the OMIC platforms were measured in 81 obese cases vs. 83 lean controls, and the association between the expression levels and CVD risks were evaluated. Significant difference was found for one gene, alkaline phosphatase, liver/bone/kidney (ALPL), across 3 OMIC platforms. In the validation phase, the gene expression levels of ALPL in leukocytes were significantly higher in obese compared with lean subjects (p < 0.05). Within the obese population, we observed that ALPL expression level showed significantly positive association with CVD risk factors (p < 0.05) including systolic blood pressure, diastolic blood pressure, mean arterial pressure, carotid intima-media thickness and borderline significance with fasting insulin (p = 0.08). This study identified one novel marker ALPL of neutrophil activation in response to obesity and provided evidence that obesity induced change in ALPL expression was associated with CVD risk factors.

DOI: https://doi.org/10.1038/s41598-019-39764-4
PeerJ. 2019 ;7 e6543

An interpretable machine learning model for diagnosis of Alzheimer's disease.

Diptesh Das, Junichi Ito, Tadashi Kadowaki, Koji Tsuda.

  We present an interpretable machine learning model for medical diagnosis called sparse high-order interaction model with rejection option (SHIMR). A decision tree explains to a patient the diagnosis with a long rule (i.e., conjunction of many intervals), while SHIMR employs a weighted sum of short rules. Using proteomics data of 151 subjects in the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset, SHIMR is shown to be as accurate as other non-interpretable methods (Sensitivity, SN = 0.84 ± 0.1, Specificity, SP = 0.69 ± 0.15 and Area Under the Curve, AUC = 0.86 ± 0.09). For clinical usage, SHIMR has a function to abstain from making any diagnosis when it is not confident enough, so that a medical doctor can choose more accurate but invasive and/or more costly pathologies. The incorporation of a rejection option complements SHIMR in designing a multistage cost-effective diagnosis framework. Using a baseline concentration of cerebrospinal fluid (CSF) and plasma proteins from a common cohort of 141 subjects, SHIMR is shown to be effective in designing a patient-specific cost-effective Alzheimer's disease (AD) pathology. Thus, interpretability, reliability and having the potential to design a patient-specific multistage cost-effective diagnosis framework can make SHIMR serve as an indispensable tool in the era of precision medicine that can cater to the demand of both doctors and patients, and reduce the overwhelming financial burden of medical diagnosis.

Keywords:  ADNI; Alzheimer’s disease (AD); Classification with rejection option; Computer-aided diagnosis (CAD) model; Cost-effective framework; Dementia; Interpretable model; Machine learning model; SHIMR; Sparse high-order interaction

DOI:  https://doi.org/10.7717/peerj.6543
Rom J Morphol Embryol. 2018 ;59(4): 1021-1032

Occupational exposure to urinary bladder carcinogens - risk factors, molecular mechanisms and biomarkers.

Marina Ruxandra Oţelea, Viorel Jinga, Alexandru Ştefan Cătălin Raşcu, Iancu Emil Pleşea, Amelia Nicoleta Petrescu, Luminiţa Elena Mitrache, Mihai Olteanu, Dan Bondari, Agripina Raşcu.

Bladder cancer (BC) is one of the most frequent forms of cancer, particularly in Caucasian population. Many environmental factors are recognized as carcinogenic in humans for this form of neoplasia and some of them are related to occupation. In order to illustrate these effects, we have selected several relevant cases with smoking and occupational exposure to carcinogens and their histopathological findings. We reviewed the most important research published in the field of environmental-genomic interaction in relation with the oncogenesis of BC. Three main directions have been identified and described in the article: the environmental factors involved in BC pathogenesis and evolution, the molecular mechanisms involved in cell mitosis control and xenobiotic metabolism related to the qualitative and quantitative exposure and, finally, the possible biomarkers of the tumor evolution. From the genomic and proteomic research, new biomarkers emerged that are in the validation process. Immunohistochemical methods open also new perspectives to the diagnostic algorithms and could serve as prognosis biomarkers.
Sci Rep. 2019 Mar 05. 9(1): 3611

Differential miRNA expression profile and proteome in plasma exosomes from patients with paroxysmal nocturnal hemoglobinuria.

Raúl Teruel-Montoya, Ginés Luengo-Gil, Fernando Vallejo, José Enrique Yuste, Nataliya Bohdan, Nuria García-Barberá, Salvador Espín, Constantino Martínez, Juan Carlos Espín, Vicente Vicente, Irene Martínez-Martínez.

Paroxysmal Nocturnal Hemoglobinuria (PNH) is a clonal disease of blood cells caused by the lack of glycosyl phosphatidyl inositol anchored proteins bound to the cell membrane. In consequence, erythrocytes lead to intravascular hemolysis upon complement activation, which promotes high risk of thrombosis, intravascular hemolytic anemia, and bone marrow failure in patients. The mechanisms of thrombosis in PNH are still poorly understood. Treatment with eculizumab reduces intravascular hemolysis and thrombotic risk, but not in all cases. Exosomes are extracellular vesicles released by cells and whose secretion is closely related to the inflammatory status. They participate in cell communication by activating signaling pathways and transferring genetic material and proteins to host cells. In consequence, exosomes may serve as surrogate biomarkers for the prognosis and/or diagnosis of a disease. Isolation of exosomes was carried out from healthy controls and from three groups of PNH patients, i.e. i) with no eculizumab treatment; ii) under treatment with eculizumab that have not suffered thrombosis; and iii) under treatment with eculizumab but that have suffered thrombosis. The miRNAome and proteome was analyzed using plasma focus miRNAs PCR panel and LC-MS analysis respectively. We found differential expression of miRNAs miR-148b-3p, miR-423-3p, miR29b-3p, miR15b-5p, let-7e-5p, miR126-3p, miR-125b-5p and miR-376c-3p as well as hemoglobin, haptoglobin, protein S and C4-binding protein in healthy controls vs PNH patients. Our results warrant further research and provide new information on the content of exosomes that could play a role in the hypercoagulable state in this disease.

DOI: https://doi.org/10.1038/s41598-019-40453-5