bims-prodis Biomed News
on Proteomics in disease
Issue of 2019‒04‒14
twenty papers selected by
Nancy Gough
Bioserendipity
  1. Proteomic manifestations of genetic defects in autosomal recessive congenital ichthyosis.
  2. Polycystic Ovary Syndrome and Insulin Physiology: An Observational Quantitative Serum Proteomics Study in adolescent, Normal-Weight Females.
  3. Proteomics derived biomarker panel improves diagnostic precision to classify endometrioid and high-grade serous ovarian carcinoma.
  4. Detection of BDNF-Related Proteins in Human Perilymph in Patients With Hearing Loss.
  5. Use of extracellular vesicles from lymphatic drainage as surrogate markers of melanoma progression and BRAF V600E mutation.
  6. Sputum proteomic signature of gastro-oesophageal reflux in patients with severe asthma.
  7. Redox regulation & sperm function: A proteomic insight.
  8. Rab5C enhances resistance to ionizing radiation in rectal cancer.
  9. Proteomics evidence of specific IGKV1-8 association with cystic lung light chain deposition disease.
  10. Plasma FGF-19 Levels are Increased in Patients with Post-Bariatric Hypoglycemia.
  11. Proteomics insights into the pathology and prognosis of chronic lymphocytic leukemia.
  12. Trends in mass spectrometry imaging for cardiovascular diseases.
  13. Biochemical pathways mediated by KLK6 protease in breast cancer.
  14. A plasma protein derived TGFβ signature is a prognostic indicator in triple negative breast cancer.
  15. Integrated tear proteome and metabolome reveal panels of inflammatory-related molecules via key regulatory pathways in dry eye syndrome.
  16. The plaque-aortic ring assay: a new method to study human atherosclerosis-induced angiogenesis.
  17. Large-scale proteomic analysis of human brain identifies proteins associated with cognitive trajectory in advanced age.
  18. Biomarkers of post-discharge mortality among children with complicated severe acute malnutrition.
  19. AIRE expression controls the peripheral selection of autoreactive B cells.
  20. Immunoproteomic Lessons for Human Respiratory Syncytial Virus Vaccine Design.
  1. J Proteomics. 2019 Apr 09. pii: S1874-3919(19)30117-4. [Epub ahead of print]
    Proteomic manifestations of genetic defects in autosomal recessive congenital ichthyosis.
    Noreen Karim, Blythe Durbin-Johnson, David M Rocke, Michelle Salemi, Brett S Phinney, Muhammad Naeem, Robert H Rice.
      Numerous genetic conditions give rise to a scaly skin phenotype as a result of impaired barrier function. Present work investigates the degree to which the departure from normal of ichthyosis corneocytes on the skin surface depends upon the basic defect as judged by proteomic profiling. Analyzing autosomal recessive congenital ichthyosis arising from defects in the genes PNPLA1, SDR9C7 and TGM1 revealed that profiles of PNPLA1 samples displayed the greatest degree of departure from normal control epidermis, with SDR9C7 samples nearly as divergent, and TGM1 the least divergent. Although the profiles were distinctive, each displaying a set of altered protein levels, they exhibited alterations in 20 proteins in common, of which 15 were expressed consistently at higher and 5 at lower levels. Departure from the normal profile was examined at three different anatomic sites (forearm, forehead, leg). Reflecting that the normal protein profile differed at these sites, comparing profiles from afflicted subjects revealed that the degree of alteration in profile was site-dependent. These results suggest proteomic profiling can provide a quantitative measure of departure from the normal state of epidermis. Further development may help characterize consequences of the genetic defects, including perturbation of signaling pathways, and supplement visual evaluation of treatment. SIGNIFICANCE: ARCI are rare cornification disorders caused by mutations in at least 14 different genes leading to perturbed metabolism and organization of constituent biomolecules of cornified envelope. The phenotypic manifestations of the disorder vary among individuals with the same as well as different genetic defect and even at different anatomic sites within the same individual. The present study investigates the proteomic disturbances at three anatomic sites in patients carrying mutations in three different genes. Our findings provide a basis for elucidating genotype to proteome relationships for ARCI, further investigation of which may help to delineate the underlying pathways as well as to identify new drug targets.
    DOI:  https://doi.org/10.1016/j.jprot.2019.04.007
  2. Proteomics Clin Appl. 2019 Apr 09. e1800184
    Polycystic Ovary Syndrome and Insulin Physiology: An Observational Quantitative Serum Proteomics Study in adolescent, Normal-Weight Females.
    Antigoni Manousopoulou, Nasser M Al-Daghri, Shaun Sabico, Diana J Garay-Baquero, Jie Teng, Amal Alenad, Majed S Alokail, Nikos Athanasopoulos, Efthymios Deligeoroglou, George P Chrousos, Flora Bacopoulou, Spiros D Garbis.
      BACKGROUND: Polycystic ovary syndrome (PCOS) is a common endocrine disorder associated with insulin resistance, even in the absence of overweight/obesity. The aim of the present study was to examine the global serum proteomic profile of adolescent, normal-weight females with PCOS in order to gain novel insight in the association of this endocrine disorder with insulin physiology but also identify novel circulating markers that can guide intervention protocols.METHODS: Non-depleted serum from normal-weight (BMI: 18-23 kg/m2 ), adolescent females (13 to 21 years old) with PCOS (n = 20) was compared to BMI- and age-matched healthy controls (n = 20) using our three-dimensional quantitative proteomics methodology. Serum samples from study participants were randomly pooled to form four biological replicates of females with PCOS and four of healthy controls (n = 5 per sample pool).
    RESULTS: One-hundred and twenty-six proteins were differentially expressed in females with PCOS compared to controls. Gene ontology analysis showed significant enrichment for terms related to inflammatory | immune response, metabolism and insulin-like growth factor receptor signalling pathway. Circulating levels of IGF-1 and -2 and IGFBP-2, -3 and -4 were found to be lower in females with PCOS compared to healthy controls.
    CONCLUSIONS: The present serum proteomics study provides insight into the pro- inflammatory status and insulin dysregulation in young females with PCOS and identifies potential serological markers that can guide early intervention protocols. This article is protected by copyright. All rights reserved.
    Keywords:  PCOS; iTRAQ; inflammation; insulin resistance; non-depleted serum; proteomics
    DOI:  https://doi.org/10.1002/prca.201800184
  3. Clin Cancer Res. 2019 Apr 12. pii: clincanres.3818.2018. [Epub ahead of print]
    Proteomics derived biomarker panel improves diagnostic precision to classify endometrioid and high-grade serous ovarian carcinoma.
    Lynne-Marie Postovit, Dylan Z Dieters-Castator, Peter F Rambau, Linda E Kelemen, Gabrielle M Siegers, Gilles A Lajoie, Martin Köbel.
      PURPOSE: Ovarian carcinomas are a group of distinct diseases classified by histotypes. As histotype-specific treatment evolves, accurate classification will become critical for optimal precision medicine approaches.EXPERIMENTAL DESIGN: To uncover differences between the two most common histotypes - high-grade serous (HGSC) and endometrioid carcinoma (EC) - we performed label-free quantitative proteomics on freshly frozen tumour tissues (HGSC, n=10; EC, n=10). Eight candidate protein biomarkers specific to EC were validated by immunohistochemistry using tissue microarrays representing 361 cases of either EC or HGSC.
    RESULTS: Over 500 proteins were differentially expressed (p<0.05) between EC and HGSC tumour proteomes. A ranked set of 106 proteins were sufficient to correctly discriminate 90% of samples. Immunohistochemistry validated KIAA1324 as the most discriminatory novel biomarker for EC. An 8-marker panel was found to exhibit superior performance for discriminating EC from HGSC compared to the current standard of WT1 plus TP53 alone, improving the classification rate for HGSC from 90.7% to 99.2%. EC specific diagnostic markers such as PLCB1, KIAA1324, and SCGB2A1 were also significantly associated with favorable prognosis within EC suggesting biological heterogeneity within this histotype. Pathway analysis of proteomic data revealed differences between EC and HGSC pertaining to estrogen and interferon signalling.
    CONCLUSIONS: In summary, these findings support the use of multi-marker panels for the differential diagnosis of difficult cases resembling EC and HGSC.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-18-3818
  4. Front Neurosci. 2019 ;13 214
    Detection of BDNF-Related Proteins in Human Perilymph in Patients With Hearing Loss.
    Ines de Vries, Heike Schmitt, Thomas Lenarz, Nils Prenzler, Sameer Alvi, Hinrich Staecker, Martin Durisin, Athanasia Warnecke.
      The outcome of cochlear implantation depends on multiple variables including the underlying health of the cochlea. Brain derived neurotrophic factor (BDNF) has been shown to support spiral ganglion neurons and to improve implant function in animal models. Whether endogenous BDNF or BDNF-regulated proteins can be used as biomarkers to predict cochlear health and implant outcome has not been investigated yet. Gene expression of BDNF and downstream signaling molecules were identified in tissue of human cochleae obtained from normal hearing patients (n = 3) during skull base surgeries. Based on the gene expression data, bioinformatic analysis was utilized to predict the regulation of proteins by BDNF. The presence of proteins corresponding to these genes was investigated in perilymph (n = 41) obtained from hearing-impaired patients (n = 38) during cochlear implantation or skull base surgery for removal of vestibular schwannoma by nanoscale liquid chromatography coupled to tandem mass spectrometry (nano LC-MS/MS). Analyzed by mass spectrometry were 41 perilymph samples despite three patients undergoing bilateral cochlear implantation. These particular BDNF regulated proteins were not detectable in any of the perilymph samples. Subsequently, targeted analysis of the perilymph proteome data with Ingenuity Pathway Analysis (IPA) identified further proteins in human perilymph that could be regulated by BDNF. These BDNF regulated proteins were correlated to the presence of residual hearing (RH) prior to implantation and to the performance data with the cochlear implant after 1 year. There was overall a decreased level of expression of BDNF-regulated proteins in profoundly hearing-impaired patients compared to patients with some RH. Phospholipid transfer protein was positively correlated to the preoperative hearing level of the patients. Our data show that combination of gene expression arrays and bioinformatic analysis can aid in the prediction of downstream signaling proteins related to the BDNF pathway. Proteomic analysis of perilymph may help to identify the presence or absence of these molecules in the diseased organ. The impact of such prediction algorithms on diagnosis and treatment needs to be established in further studies.
    Keywords:  BDNF; bioinformatic analysis; cochlear implant; diagnostics; inner ear; neurotrophin; perilymph; proteomics
    DOI:  https://doi.org/10.3389/fnins.2019.00214
  5. J Exp Med. 2019 Apr 11. pii: jem.20181522. [Epub ahead of print]
    Use of extracellular vesicles from lymphatic drainage as surrogate markers of melanoma progression and BRAF V600E mutation.
    Susana García-Silva, Alberto Benito-Martín, Sara Sánchez-Redondo, Alberto Hernández-Barranco, Pilar Ximénez-Embún, Laura Nogués, Marina S Mazariegos, Kay Brinkmann, Ana Amor López, Lisa Meyer, Carlos Rodríguez, Carmen García-Martín, Jasminka Boskovic, Rocío Letón, Cristina Montero, Mercedes Robledo, Anna Szumera-Ciećkiewicz, Iwona Kalinowska, Johan Skog, Mikkel Noerholm, Javier Muñoz, Pablo L Ortiz-Romero, Yolanda Ruano, José L Rodríguez-Peralto, Piotr Rutkowski, Héctor Peinado.
      Liquid biopsies from cancer patients have the potential to improve diagnosis and prognosis. The assessment of surrogate markers of tumor progression in circulating extracellular vesicles could be a powerful non-invasive approach in this setting. We have characterized extracellular vesicles purified from the lymphatic drainage also known as exudative seroma (ES) of stage III melanoma patients obtained after lymphadenectomy. Proteomic analysis showed that seroma-derived exosomes are enriched in proteins resembling melanoma progression. In addition, we found that the BRAFV600E mutation can be detected in ES-derived extracellular vesicles and its detection correlated with patients at risk of relapse.
    DOI:  https://doi.org/10.1084/jem.20181522
  6. Respir Med. 2019 Apr;pii: S0954-6111(19)30044-7. [Epub ahead of print]150 66-73
    Sputum proteomic signature of gastro-oesophageal reflux in patients with severe asthma.
    K Tariq, J P R Schofield, B L Nicholas, D Burg, J Brandsma, A T Bansal, S J Wilson, R Lutter, S J Fowler, Bakke, M Caruso, B Dahlen, I Horváth, N Krug, P Montuschi, M Sanak, T Sandström, T Geiser, I Pandis, A R Sousa, I M Adcock, D E Shaw, C Auffray, P H Howarth, P J Sterk, K F Chung, P J Skipp, B Dimitrov, R Djukanović, .
      Gastro-oesophageal reflux disease (GORD) has long been associated with poor asthma control without an established cause-effect relationship. 610 asthmatics (421 severe/88 mild-moderate) and 101 healthy controls were assessed clinically and a subset of 154 severe asthmatics underwent proteomic analysis of induced sputum using untargeted mass spectrometry, LC-IMS-MSE. Univariate and multiple logistic regression analyses (MLR) were conducted to identify proteins associated with GORD in this cohort. When compared to mild/moderate asthmatics and healthy individuals, respectively, GORD was three- and ten-fold more prevalent in severe asthmatics and was associated with increased asthma symptoms and oral corticosteroid use, poorer quality of life, depression/anxiety, obesity and symptoms of sino-nasal disease. Comparison of sputum proteomes in severe asthmatics with and without active GORD showed five differentially abundant proteins with described roles in anti-microbial defences, systemic inflammation and epithelial integrity. Three of these were associated with active GORD by multiple linear regression analysis: Ig lambda variable 1-47 (p = 0·017) and plasma protease C1 inhibitor (p = 0·043), both in lower concentrations, and lipocalin-1 (p = 0·034) in higher concentrations in active GORD. This study provides evidence which suggests that reflux can cause subtle perturbation of proteins detectable in the airways lining fluid and that severe asthmatics with GORD may represent a distinct phenotype of asthma.
    DOI:  https://doi.org/10.1016/j.rmed.2019.02.008
  7. Indian J Med Res. 2018 Dec;148(Supplement): S84-S91
    Redox regulation & sperm function: A proteomic insight.
    Gayatri Mohanty, Luna Samanta.
      Infertility affects nearly 15 per cent of all couples within the reproductive age worldwide, with about 50 per cent being exhibited in the male, called male factor infertility. Successful reproduction is dependent on sperm chromatin integrity. Spermatozoa are highly specialized cells that aim to transmit the paternal genomic blueprint to the oocyte. The spermatozoon is regulated by redox mechanisms during its epididymal transit to acquire fertilizing ability. While, at physiological levels, the production of reactive oxygen species (ROS) supports the spermatozoon to acquire its fertilizing ability, at high concentrations, it affects sperm function leading to infertility. Emerging proteomic technologies provide an opportunity to address these key issues that may solve many fertility-associated problems resulting from oxidative stress (OS). This review highlights the need for an efficient therapeutic approach to male infertility with the application of high-throughput OS-mediated proteomic technology, and also addresses the question as to whether targeting these altered sperm-specific proteins may help in designing an efficient and reversible male contraceptive.
    Keywords:  Male contraception; male infertility; proteomics; reactive oxygen species
    DOI:  https://doi.org/10.4103/ijmr.IJMR_242_18
  8. J Mol Med (Berl). 2019 Apr 09.
    Rab5C enhances resistance to ionizing radiation in rectal cancer.
    Antuani Rafael Baptistella, Michele Christine Landemberger, Marcos Vinicios Salles Dias, Fernanda Salgueiredo Giudice, Bruna Roz Rodrigues, Petrus Paulo Combas Eufrazio da Silva, Edson Kuatelela Cassinela, Tonielli Cristina Lacerda, Fabio Albuquerque Marchi, Adriana Franco Paes Leme, Maria Dirlei Begnami, Samuel Aguiar, Vilma Regina Martins.
      Rectal cancer represents one third of the colorectal cancers that are diagnosed. Neoadjuvant chemoradiation is a well-established protocol for rectal cancer treatment reducing the risk of local recurrence. However, a pathologic complete response is only achieved in 10-40% of cases and the mechanisms associated with resistance are poorly understood. To identify potential targets for preventing therapy resistance, a proteomic analysis of biopsy specimens collected from stage II and III rectal adenocarcinoma patients before neoadjuvant treatment was performed and compared with residual tumor tissues removed by surgery after neoadjuvant therapy. Three proteins, Ku70, Ku80, and Rab5C, exhibited a significant increase in expression after chemoradiation. To better understand the role of these proteins in therapy resistance, a rectal adenocarcinoma cell line was irradiated to generate a radiotherapy-resistant lineage. These cells overexpressed the same three proteins identified in the tissue samples. Furthermore, radiotherapy resistance in this in vitro model was found to involve modulation of epidermal growth factor receptor (EGFR) internalization by Rab5C in response to irradiation, affecting expression of the DNA repair proteins, Ku70 and Ku80, and cell resistance. Taken together, these findings indicate that EGFR and Rab5C are potential targets for the sensitization of rectal cancer cells and they should be further investigated. KEY MESSAGES: • Rab5C orchestrates a mechanism of radioresistance in rectal adenocarcinoma cell. • Rab5C modulates EGFR internalization and its relocalization to the nucleus. • In the nucleus, EGFR can modulate the expression of the DNA repair proteins, Ku70 and Ku80. • Rab5C, Ku70, and Ku80 are overexpressed in tumor tissues that contain tumor cells that are resistant to chemoradiation treatment.
    Keywords:  DNA repair; EGF receptor; Neoadjuvant treatment; Rab5C protein; Rectal cancer; Therapy resistance
    DOI:  https://doi.org/10.1007/s00109-019-01760-6
  9. Blood. 2019 Apr 09. pii: blood.2019898577. [Epub ahead of print]
    Proteomics evidence of specific IGKV1-8 association with cystic lung light chain deposition disease.
    Mylène Camus, Sandrine Hirschi, Grégoire Prevot, Marie-Pierre Chenard, Hervé Mal, Marc Stern, Martine Reynaud-Gaubert, Julia Gilhodes, Odile Burlet-Schiltz, Pierre Brousset, Magali Colombat.
      We previously reported a new form of LCDD presenting as diffuse cystic lung disorder that differs from the usual systemic form, with respect to the age, the male/female ratio, the involved organs, and the hematologic characteristics. We also demonstrated that the light chains were produced by an intrapulmonary B-cell clone and, that this clone shared a stereotyped antigen receptor IGHV4-34/IGKV1. However, we analyzed only 3 patients. Herein, we conducted a retrospective study including lung tissue samples from 24 patients with pulmonary LCDD (pLCDD) matched with samples from 13 patients with pulmonary AL kappa amyloidosis used as controls. Mass spectrometry-based proteomics identified immunoglobulin kappa peptides as the main protein component of the tissue deposits in all patients. Interestingly, in pLCDD, IGKV1 was the most common kappa family detected (86.4%) and, IGKV1-8 was overrepresented compared with pulmonary AL kappa amyloidosis (75% vs 11.1%, p=0.0033). Furthermore, IGKV1-8 was predominantly associated with a diffuse cystic pattern (94%) in pLCDD. In conclusion, high frequency of IGKV1-8 usage in cystic pLCDD constitutes an additional feature arguing for a specific entity distinct from the systemic form that uses preferentially IGKV4-1.
    DOI:  https://doi.org/10.1182/blood.2019898577
  10. Obes Surg. 2019 Apr 11.
    Plasma FGF-19 Levels are Increased in Patients with Post-Bariatric Hypoglycemia.
    Christopher M Mulla, Allison B Goldfine, Jonathan M Dreyfuss, Sander Houten, Hui Pan, David M Pober, Nicolai J Wewer Albrechtsen, Maria S Svane, Julie B Schmidt, Jens Juul Holst, Colleen M Craig, Tracey L McLaughlin, Mary-Elizabeth Patti.
      BACKGROUND: Hypoglycemia is an increasingly recognized complication of bariatric surgery. Mechanisms contributing to glucose lowering remain incompletely understood. We aimed to identify differentially abundant plasma proteins in patients with post-bariatric hypoglycemia (PBH) after Roux-en-Y gastric bypass (RYGB), compared to asymptomatic post-RYGB.METHODS: Proteomic analysis of blood samples collected after overnight fast and mixed meal challenge in individuals with PBH, asymptomatic RYGB, severe obesity, or overweight recruited from outpatient hypoglycemia or bariatric clinics.
    RESULTS: The top-ranking differentially abundant protein at 120 min after mixed meal was fibroblast growth factor 19 (FGF-19), an intestinally derived hormone regulated by bile acid-FXR signaling; levels were 2.4-fold higher in PBH vs. asymptomatic post-RYGB (mean + SEM, 1094 ± 141 vs. 428 ± 45, P < 0.001, FDR < 0.01). FGF-19 ELISA confirmed 3.5-fold higher concentrations in PBH versus asymptomatic (360 ± 70 vs. 103 ± 18, P = 0.025). To explore potential links between increased FGF-19 and GLP-1, residual samples from other human studies in which GLP-1 was modulated were assayed. FGF-19 levels did not change in response to infusion of GLP-1 and PYY in overweight/obese individuals. Infusion of the GLP-1 receptor antagonist exendin 9-39 in recently operated asymptomatic post-RYGB did not alter FGF-19 levels after mixed meal. By contrast, GLP-1 receptor antagonist infusion yielded a significant increase in FGF-19 levels after oral glucose in individuals with PBH. While plasma bile acids did not differ between PBH and asymptomatic post-RYGB, these data suggest unique interrelationships between GLP-1 and FGF-19 in PBH.
    CONCLUSIONS: Taken together, these data support FGF-19 as a potential contributor to insulin-independent pathways driving postprandial hypoglycemia in PBH.
    Keywords:  Bile acids; FGF-19; Gastric bypass; Hypoglycemia
    DOI:  https://doi.org/10.1007/s11695-019-03845-0
  11. Saudi Med J. 2019 Apr;40(4): 317-327
    Proteomics insights into the pathology and prognosis of chronic lymphocytic leukemia.
    Suliman A Alsagaby, Fahad A Alhumaydhi.
      Chronic lymphocytic leukemia (CLL) is an incurable malignant disease of B-lymphocytes characterized by drastically heterogeneous clinical courses. Proteomics is an advanced approach that allows a global profiling of protein expression, providing a valuable chance for the discovery of disease-related proteins. In the last 2 decades, several proteomics studies were conducted on CLL to identify aberrant protein expression underpinning the malignant transformation and progression of the disease. Overall, these studies provided insights into the pathology and prognosis of CLL and reveal protein candidates with the potential to serve as biomarkers and/or therapeutic targets of the tumor. The major findings reported in these studies are discussed here.
    DOI:  https://doi.org/10.15537/smj.2019.4.23598
  12. Anal Bioanal Chem. 2019 Apr 12.
    Trends in mass spectrometry imaging for cardiovascular diseases.
    Stephanie T P Mezger, Alma M A Mingels, Otto Bekers, Berta Cillero-Pastor, Ron M A Heeren.
      Mass spectrometry imaging (MSI) is a widely established technology; however, in the cardiovascular research field, its use is still emerging. The technique has the advantage of analyzing multiple molecules without prior knowledge while maintaining the relation with tissue morphology. Particularly, MALDI-based approaches have been applied to obtain in-depth knowledge of cardiac (dys)function. Here, we discuss the different aspects of the MSI protocols, from sample handling to instrumentation used in cardiovascular research, and critically evaluate these methods. The trend towards structural lipid analysis, identification, and "top-down" protein MSI shows the potential for implementation in (pre)clinical research and complementing the diagnostic tests. Moreover, new insights into disease progression are expected and thereby contribute to the understanding of underlying mechanisms related to cardiovascular diseases.
    Keywords:  Cardiovascular diseases; Lipids; MALDI; Mass spectrometry imaging; Proteins; SIMS
    DOI:  https://doi.org/10.1007/s00216-019-01780-8
  13. Mol Oncol. 2019 Apr 13.
    Biochemical pathways mediated by KLK6 protease in breast cancer.
    Georgios Pampalakis, Eleni Zingkou, Konstantinos Gus Sidiropoulos, Eleftherios P Diamandis, Vassilis Zoumpourlis, George M Yousef, Georgia Sotiropoulou.
      KLK6 is a serine protease normally expressed in mammary tissue, and aberrantly regulated in breast cancer. At physiological levels, KLK6 functions as a suppressor of breast cancer, while its aberrant overexpression (>50-fold higher than normal) is characteristic of a subset of breast cancers and has been linked to accelerated growth of primary breast tumors in SCID mice (Pampalakis et al. Cancer Res 2009). Here, we investigated the molecular mechanisms underlying the concentration-dependent functions of KLK6 by comparing MDA-MB-231 stable transfectants expressing increasing levels of KLK6 in in vitro and in vivo tumorigenicity assays (soft agar, xenograft growth, tail vein metastasis). Quantitative proteomics was applied to identify proteins that are altered upon re-expression of KLK6 in MDA-MB-231 at normal or constitutive levels. Overexpression of KLK6 is associated with increased metastatic ability of breast cancer cells into lungs, increased expression of certain S100 proteins (S100A4, S100A11) and keratins, and downregulation of the apoptosis-related proteases CASP7 and CASP8, and RABs. On the other hand, KLK6 re-expression at physiological levels leads to inhibition of lung metastases associated with suppression of S100 proteins (S100A4, S100A10, S100A13, S100A16) and induced CASP7 and CASP8 expression. As this is the first report that KLK6 expression is associated with S100 proteins, caspases, RABs and keratins, we validated this finding in clinical datasets. By integrating proteomics and microarray data from breast cancer patients, we generated two composite scores, (KLK6+S100B-S100A7) and (KLK6+S100B-S100A14-S100A16), to predict long-term survival of breast cancer patients. We present previously unknown pathways implicating KLK6 in breast cancer. The findings promise to aid our understanding of the functional roles of KLK6 in breast cancer and may yield new biomarkers for the cancer types in which KLK6 is known to be aberrantly up-regulated.
    Keywords:  KLK6; S100A; apoptosis; proteomics; triple negative breast cancer
    DOI:  https://doi.org/10.1002/1878-0261.12493
  14. NPJ Precis Oncol. 2019 ;3 10
    A plasma protein derived TGFβ signature is a prognostic indicator in triple negative breast cancer.
    Hiroyuki Katayama, Peiling Tsou, Makoto Kobayashi, Michela Capello, Hong Wang, Francisco Esteva, Mary L Disis, Samir Hanash.
      We investigated the potential of in-depth quantitative plasma proteome analysis to uncover proteins predictive of progression and metastasis in triple negative breast cancer (TNBC). Analysis of samples from 24 pre-menopausal and 24 post-menopausal women with newly diagnosed TNBC who subsequently developed metastasis or remained metastasis free were utilized in the proteomic discovery set, which resulted in 43 proteins associated with tumor progression. These proteins were found to form a hierarchical network with TGFβ. The signature was further confirmed and refined by integrating plasma protein data from a murine TNBC model that encompassed mice with rapid- versus slow-growing tumors. Three genes consisting of CLIC1, MAPRE1, and SERPINA3 in the refined TGFβ signature significantly stratified overall survival (log-rank p = 0.0141) in a larger validation cohort irrespective of menopausal status, tumor stage, grade, and size.
    DOI:  https://doi.org/10.1038/s41698-019-0082-5
  15. J Proteome Res. 2019 Apr 09.
    Integrated tear proteome and metabolome reveal panels of inflammatory-related molecules via key regulatory pathways in dry eye syndrome.
    Xueli Chen, Jun Rao, Zhi Zheng, Yan Yu, Shang Lou, Liping Liu, Qinsi He, Luhua Wu, Xinghuai Sun.
      Dry eye syndrome (DES) is a growing public health concern with a high global prevalence; however, the fundamental processes involved in its pathogenic mechanisms remain poorly understood. In the present study, we applied nanoscale liquid chromatography and quadrupole time-of-flight tandem mass spectrometry (nanoLC/Q-TOF-MS/MS) and ultra-performance LC/Q-TOF-MS/MS technologies on tear samples obtained from 18 dry eye patients and 19 healthy controls for integrated proteomic and metabolomic analyses. Overall, 1,031 tear proteins were detected, while 190 proteins were determined to be significantly expressed in dry eye patients. Further functional analysis suggested various biological processes were highly expressed and involved in the pathogenesis of DES, especially immune and inflammatory processes. Totally, 156 named metabolites were identified, among which 34 were found to be significantly changed in dry eye patients. The results highlighted the key elements, especially inflammatory-related proteins and metabolites that played important roles in the development of DES. Further, the regulatory roles of primary pathways, including complement and coagulation cascades, glycolysis/gluconeogenesis, and amino acid metabolism, were also identified as processes involved in DES. Collectively, our work not only provided insight into the potential biomarkers of DES for diagnostic and prognostic purposes, but extended our knowledge of the physiopathology of this syndrome.
    DOI:  https://doi.org/10.1021/acs.jproteome.9b00149
  16. Angiogenesis. 2019 Apr 09.
    The plaque-aortic ring assay: a new method to study human atherosclerosis-induced angiogenesis.
    Alfred C Aplin, Roberto F Nicosia.
      Progression of atherosclerotic plaques into life-threatening lesions is associated with angiogenesis which contributes to intraplaque hemorrhages and plaque instability. The lack of adequate models for the study of human plaque-induced angiogenesis has limited progress in this field. We describe here a novel ex vivo model which fills this gap. Plaques obtained from 15 patients who underwent endarterectomy procedures were co-cultured in collagen gels with rat aorta rings which served as read-out of human plaque angiogenic activity. The majority of plaque fragments markedly stimulated angiogenic sprouting from the aortic rings while concurrently promoting the outgrowth of resident macrophages from the aortic adventitia. This stimulatory activity correlated with the presence of intraplaque macrophages. Proteomic analysis of plaque secretomes revealed heterogeneity of macrophage-stimulatory cytokine and angiogenic factor production by different plaques. VEGF was identified in some of the plaque secretomes. Antibody-mediated blockade of VEGF had significant but transient inhibitory effect on angiogenesis, which suggested redundancy of plaque-derived angiogenic stimuli. Pharmacologic ablation of adventitial macrophages permanently impaired the angiogenic response of aortic rings to plaque stimuli. Our results show that human plaque-induced angiogenesis can be reproduced ex vivo using rat aortic rings as read-out of plaque angiogenic activity. This model can be used to identify key cellular and molecular mechanisms responsible for the neovascularization of human plaques.
    Keywords:  Assay; Atherosclerosis; Collagen; Endothelial cells; Neovascularization
    DOI:  https://doi.org/10.1007/s10456-019-09667-z
  17. Nat Commun. 2019 04 08. 10(1): 1619
    Large-scale proteomic analysis of human brain identifies proteins associated with cognitive trajectory in advanced age.
    Aliza P Wingo, Eric B Dammer, Michael S Breen, Benjamin A Logsdon, Duc M Duong, Juan C Troncosco, Madhav Thambisetty, Thomas G Beach, Geidy E Serrano, Eric M Reiman, Richard J Caselli, James J Lah, Nicholas T Seyfried, Allan I Levey, Thomas S Wingo.
      In advanced age, some individuals maintain a stable cognitive trajectory while others experience a rapid decline. Such variation in cognitive trajectory is only partially explained by traditional neurodegenerative pathologies. Hence, to identify new processes underlying variation in cognitive trajectory, we perform an unbiased proteome-wide association study of cognitive trajectory in a discovery (n = 104) and replication cohort (n = 39) of initially cognitively unimpaired, longitudinally assessed older-adult brain donors. We find 579 proteins associated with cognitive trajectory after meta-analysis. Notably, we present evidence for increased neuronal mitochondrial activities in cognitive stability regardless of the burden of traditional neuropathologies. Furthermore, we provide additional evidence for increased synaptic abundance and decreased inflammation and apoptosis in cognitive stability. Importantly, we nominate proteins associated with cognitive trajectory, particularly the 38 proteins that act independently of neuropathologies and are also hub proteins of protein co-expression networks, as promising targets for future mechanistic studies of cognitive trajectory.
    DOI:  https://doi.org/10.1038/s41467-019-09613-z
  18. Sci Rep. 2019 Apr 12. 9(1): 5981
    Biomarkers of post-discharge mortality among children with complicated severe acute malnutrition.
    James M Njunge, Agnes Gwela, Nelson K Kibinge, Moses Ngari, Lydia Nyamako, Emily Nyatichi, Johnstone Thitiri, Gerard Bryan Gonzales, Robert H J Bandsma, Judd L Walson, Evelyn N Gitau, James A Berkley.
      High mortality after discharge from hospital following acute illness has been observed among children with Severe Acute Malnutrition (SAM). However, mechanisms that may be amenable to intervention to reduce risk are unknown. We performed a nested case-control study among HIV-uninfected children aged 2-59 months treated for complicated SAM according to WHO recommendations at four Kenyan hospitals. Blood was drawn from 1778 children when clinically judged stable before discharge from hospital. Cases were children who died within 60 days. Controls were randomly selected children who survived for one year without readmission to hospital. Untargeted proteomics, total protein, cytokines and chemokines, and leptin were assayed in plasma and corresponding biological processes determined. Among 121 cases and 120 controls, increased levels of calprotectin, von Willebrand factor, angiotensinogen, IL8, IL15, IP10, TNFα, and decreased levels of leptin, heparin cofactor 2, and serum paraoxonase were associated with mortality after adjusting for possible confounders. Acute phase responses, cellular responses to lipopolysaccharide, neutrophil responses to bacteria, and endothelial responses were enriched among cases. Among apparently clinically stable children with SAM, a sepsis-like profile is associated with subsequent death. This may be due to ongoing bacterial infection, translocated bacterial products or deranged immune response during nutritional recovery.
    DOI:  https://doi.org/10.1038/s41598-019-42436-y
  19. Sci Immunol. 2019 Apr 12. pii: eaav6778. [Epub ahead of print]4(34):
    AIRE expression controls the peripheral selection of autoreactive B cells.
    Joel Sng, Burcu Ayoglu, Jeff W Chen, Jean-Nicolas Schickel, Elise M N Ferre, Salomé Glauzy, Neil Romberg, Manfred Hoenig, Charlotte Cunningham-Rundles, Paul J Utz, Michail S Lionakis, Eric Meffre.
      Autoimmune regulator (AIRE) mutations result in autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) syndrome characterized by defective central T cell tolerance and the production of many autoantibodies targeting tissue-specific antigens and cytokines. By studying CD3- and AIRE-deficient patients, we found that lack of either T cells or AIRE function resulted in the peripheral accumulation of autoreactive mature naïve B cells. Proteomic arrays and Biacore affinity measurements revealed that unmutated antibodies expressed by these autoreactive naïve B cells recognized soluble molecules and cytokines including insulin, IL-17A, and IL-17F, which are AIRE-dependent thymic peripheral tissue antigens targeted by autoimmune responses in APECED. AIRE-deficient patients also displayed decreased frequencies of regulatory T cells (Tregs) that lacked common TCRβ clones found instead in their conventional T cell compartment, thereby suggesting holes in the Treg TCR repertoire of these patients. Hence, AIRE-mediated T cell/Treg selection normally prevents the expansion of autoreactive naïve B cells recognizing peripheral self-antigens.
    DOI:  https://doi.org/10.1126/sciimmunol.aav6778
  20. J Clin Med. 2019 Apr 10. pii: E486. [Epub ahead of print]8(4):
    Immunoproteomic Lessons for Human Respiratory Syncytial Virus Vaccine Design.
    Daniel López, Alejandro Barriga, Elena Lorente, Carmen Mir.
      Accurate antiviral humoral and cellular immune responses require prior recognition of antigenic peptides presented by human leukocyte antigen (HLA) class I and II molecules on the surface of antigen-presenting cells. Both the helper and the cytotoxic immune responses are critical for the control and the clearance of human respiratory syncytial virus (HRSV) infection, which is a significant cause of morbidity and mortality in infected pediatric, immunocompromised and elderly populations. In this article we review the immunoproteomics studies which have defined the general antigen processing and presentation rules that determine both the immunoprevalence and the immunodominance of the cellular immune response to HRSV. Mass spectrometry and functional analyses have shown that the HLA class I and II cellular immune responses against HRSV are mainly focused on three viral proteins: fusion, matrix, and nucleoprotein. Thus, these studies have important implications for vaccine development against this virus, since a vaccine construct including these three relevant HRSV proteins could efficiently stimulate the major components of the adaptive immune system: humoral, helper, and cytotoxic effector immune responses.
    Keywords:  Antigen processing; HLA; T cells; immune response; immunoproteomics; mass spectrometry; respiratory infectious disease; vaccine
    DOI:  https://doi.org/10.3390/jcm8040486
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