bims-prodis 2019-02-10 papers

bims-prodis

Biomed News

on Proteomics in disease

Issue of 2019–02–10
38 papers selected by
Nancy Gough, Bioserendipity

Proteomic analysis of plasma exosomes to differentiate malignant from benign pulmonary nodules.
Univariate and classification analysis reveals potential diagnostic biomarkers for early stage ovarian cancer Type 1 and Type 2.
Advances in the proteomics of amniotic fluid to detect biomarkers for chromosomal abnormalities and fetomaternal complications during pregnancy.
Proteome analysis of non-small cell lung cancer cell line secretomes and patient sputum reveals biofluid biomarker candidates for cisplatin response prediction.
The antimicrobial protein S100A12 identified as a potential autoantigen in a subgroup of atopic dermatitis patients.
Molecular pathways of varicocele and its repair - A paired labelled shotgun proteomics approach.
Serum Proteomic Study of Women With Obsessive-Compulsive Disorder, Washing Subtype.
Urine Haptoglobin and Haptoglobin-Related Protein Predict Response to Spironolactone in Patients With Resistant Hypertension.
Interactome Analysis Of The Differentially Expressed Proteins In Uterine Leiomyoma.
Potential urine biomarkers for gestational hypertension and preeclampsia.
Single Cell Omics of Breast Cancer: An Update on Characterization and Diagnosis.
An integrated proteomic and glycoproteomic study for differences on glycosylation occupancy in rheumatoid arthritis.
Ulcerative colitis: functional analysis of the in-depth proteome.
Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us?
[Features of the proteome of the urine in chronic pyelonephritis.]
The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease.
Platelet-Derived Microparticles From Obese Individuals: Characterization of Number, Size, Proteomics, and Crosstalk With Cancer and Endothelial Cells.
The OMICs Window into Nonalcoholic Fatty Liver Disease (NAFLD).
Oncoproteomic and gene expression analyses identify prognostic biomarkers for second primary malignancy in patients with head and neck squamous cell carcinoma.
Novel protein constituents of pathological ocular pseudoexfoliation syndrome deposits identified with mass spectrometry.
Effects of Caloric Restriction with Protein Supplementation on Plasma Protein Profiles in Middle-Aged Women with Metabolic Syndrome-A Preliminary Open Study.
Proteomic atlas of the human brain in Alzheimer's disease.
Glycoproteomic Profiling Provides Candidate Myocardial Infarction Predictors of Later Progression to Heart Failure.
Antibody Microarray Analysis of Plasma Proteins for the Prediction of Histologic Chorioamnionitis in Women With Preterm Premature Rupture of Membranes.
Proteomic Quantification of Human Blood-Brain Barrier SLC and ABC Transporters in Healthy Individuals and Dementia Patients.
Salivary gland secretome: a novel tool towards molecular stratification of patients with primary Sjögren's syndrome and non-autoimmune sicca.
Dissecting CLL through high dimensional single cell technologies.
Omics Studies in Hemoglobinopathies.
Genetic association in female stress urinary incontinence based on proteomic findings: a case-control study.
Correction: Exploration of Serum Proteomic Profiling and Diagnostic Model That Differentiate Crohn's Disease and Intestinal Tuberculosis.
Proteomics in Pathology: The Special Issue.
Fibroblast growth factor receptor 1 (FGFR1) as a therapeutic target in adenoid cystic carcinoma of the lacrimal gland.
Rheumatoid arthritis reprograms circadian output pathways.
Regional protein expression in human Alzheimer's brain correlates with disease severity.
Neoantigen characteristics in the context of the complete predicted MHC class I self-immunopeptidome.
Role of seminal plasma proteins in effective zygote formation- A success road to pregnancy.
Proteomic-based approaches to cardiac development and disease.
Should 'Omics' education be a part of allied health profession curricula?

Clin Proteomics. 2019 ;16 5

Proteomic analysis of plasma exosomes to differentiate malignant from benign pulmonary nodules.

Muyu Kuang, Xiaoting Tao, Yizhou Peng, Wenjing Zhang, Yafang Pan, Lei Cheng, Chongze Yuan, Yue Zhao, Hengyu Mao, Lingdun Zhuge, Zhenhua Zhou, Haiquan Chen, Yihua Sun.

Background: It is difficult to distinguish benign pulmonary nodules (PNs) from malignant PNs by conventional examination. Therefore, novel biomarkers that can identify the nature of PNs are needed. Exosomes have recently been identified as an attractive alternative approach since tumor-specific molecules can be found in exosomes isolated from biological fluids.
Methods: Plasma exosomes were extracted via the exoEasy reagent method. The major proteins from plasma exosomes in patients with PNs were identified via labelfree analysis and screened for differentially expressed proteins. A GO classification analysis and KEGG pathway analysis were performed on plasma exosomal protein from patients with benign and malignant PNs.
Results: Western blot confirmed that protein expression of CD63 and CD9 could be detected in the exosome extract. Via a search of the human Uniprot database, 736 plasma exosome proteins from patients with PNs were detected using high-confidence peptides. There were 33 differentially expressed proteins in the benign and malignant PNs. Of these, 12 proteins were only expressed in the benign PNs group, while 9 proteins were only expressed in the malignant PNs group. We further obtained important information on signaling pathways and nodal proteins related to differential benign and malignant PNs via bioinformatic analysis methods such as GO, KEGG, and String.
Conclusions: This study provides a new perspective on the identification of novel detection strategies for benign and malignant PNs. We hope our findings can provide clues for the identification of benign and malignant PNs.

DOI: https://doi.org/10.1186/s12014-019-9225-5
J Proteomics. 2019 Jan 30. pii: S1874-3919(19)30025-9. [Epub ahead of print]

Univariate and classification analysis reveals potential diagnostic biomarkers for early stage ovarian cancer Type 1 and Type 2.

Simonas Marcišauskas, Benjamin Ulfenborg, Björg Kristjansdottir, Sofia Waldemarson, Karin Sundfeldt.

  Biomarkers for early detection of ovarian tumors are urgently needed. Tumors of the ovary grow within cysts and most are benign. Surgical sampling is the only way to ensure accurate diagnosis, but often leads to morbidity and loss of female hormones. The present study explored the deep proteome in well-defined sets of ovarian tumors, FIGO stage I, Type 1 (low-grade serous, mucinous, endometrioid; n = 9), Type 2 (high-grade serous; n = 9), and benign serous (n = 9) using TMT-LC-MS/MS. Data are available via ProteomeXchange with identifier PXD010939. We evaluated new bioinformatics tools in the discovery phase. This innovative selection process involved different normalizations, a combination of univariate statistics, and logistic model tree and naive Bayes tree classifiers. We identified 142 proteins by this combined approach. One biomarker panel and nine individual proteins were verified in cyst fluid and serum: transaldolase-1, fructose-bisphosphate aldolase A (ALDOA), transketolase, ceruloplasmin, mesothelin, clusterin, tenascin-XB, laminin subunit gamma-1, and mucin-16. Six of the proteins were found significant (p < .05) in cyst fluid while ALDOA was the only protein significant in serum. The biomarker panel achieved ROC AUC 0.96 and 0.57 respectively. We conclude that classification algorithms complement traditional statistical methods by selecting combinations that may be missed by standard univariate tests. SIGNIFICANCE: In the discovery phase, we performed deep proteome analyses of well-defined histology subgroups of ovarian tumor cyst fluids, highly specified for stage and type (histology and grade). We present an original approach to selecting candidate biomarkers combining several normalization strategies, univariate statistics, and machine learning algorithms. The results from validation of selected proteins strengthen our prior proteomic and genomic data suggesting that cyst fluids are better than sera in early stage ovarian cancer diagnostics.

Keywords:  Biomarker; Cyst fluid; Diagnostics; FIGO stage I; Ovarian cancer; Proteome; Proteomics; Type 1 and Type 2

DOI:  https://doi.org/10.1016/j.jprot.2019.01.017
Expert Rev Proteomics. 2019 Feb 05.

Advances in the proteomics of amniotic fluid to detect biomarkers for chromosomal abnormalities and fetomaternal complications during pregnancy.

Aayushi Vasani, Maushmi S Kumar.

   INTRODUCTION: Amniotic fluid (AF) is a dynamic and complex mixture that reflects the physiological condition of developing fetus. In the last decade, proteomic analysis of AF for 16-18 weeks normal pregnancy has been done for the composition and functions of this fluid. Other body fluids such as urine, sweat, tears, etc. are being used for diagnosis of disease, but an insight into protein biomarkers of amniotic fluid can save the fetus and mother from future complications. Areas covered: We have covered the proteomics of amniotic fluid done since 2000, in order to strengthen the establishment of this techniques as a recognized diagnostic tool in the field. After classifying the diseases based on chromosomal aneuploidies, gestational changes and inflammation caused during pregnancy; we have focused on amniotic fluid to detect various complications during and post pregnancy and its effect on the fetomaternal relationship. Expert comment: The main protein biomarkers responsible for various syndromes, diseases and complications have been summarized. Major proteins identified for gestational conditions are IGFBP-1, fibrinogen, neutrophil defensins like calgranulins A and C, cathelicidin, APOA1, TRFE etc. Validation of particular technique and establishing a single standardized biomarker for the diagnosis to avoid any overlapping for different diseases is required. After certain improvements, proteomics approach can be considered for diagnosis of diseases associated with fetal-maternal health.

Keywords:  Edward’s syndrome; Klinefelter’s syndrome; LC-MS; MALDI-TOF-MS; down syndrome; fetal alcoholic syndrome; gestational diabetes mellitus; intra uterine growth restriction; isotope coded affinity tag strategy; mass restricted score

DOI:  https://doi.org/10.1080/14789450.2019.1578213
J Proteomics. 2019 Jan 30. pii: S1874-3919(19)30026-0. [Epub ahead of print]

Proteome analysis of non-small cell lung cancer cell line secretomes and patient sputum reveals biofluid biomarker candidates for cisplatin response prediction.

Franziska Böttger, Tieneke B M Schaaij-Visser, Inge de Reus, Sander R Piersma, Thang V Pham, Remco Nagel, Ruud H Brakenhoff, Erik Thunnissen, Egbert F Smit, Connie R Jimenez.

  Molecular markers are urgently needed to select non-small cell lung cancer (NSCLC) patients most likely to benefit from platinum-based chemotherapies. Of particular interest are proteins that can be found in biofluids like sputum for non-invasive detection. Therefore, we profiled the secretomes of 6 NSCLC cell lines with varying IC50-values for cisplatin, using label-free GeLC-MS/MS-based proteomics. Out of a total dataset of 2610 proteins, 304 proteins showed significant differences in expression levels between cisplatin sensitive and insensitive cell lines. Functional data mining revealed that the secretion of typically extracellular factors was associated with a higher sensitivity towards cisplatin, while cisplatin insensitivity correlated with increased secretion of theoretically intra-cellular proteins. Stringent statistical analysis and quantitative filtering yielded 58 biomarker candidates, 34 of which could be detected in clinical biofluids of lung cancer patients such as sputum using label-free LC-MS/MS-based proteomics. To assess performance of these biofluid biomarker candidates, we correlated protein expression with patient survival using a publically available clinical gene expression data set (GSE14814). We thus identified 3 top candidates with potential predictive value in determining cisplatin response (UGGT1, COL6A1 and MAP4) for future development as non-invasive biomarkers to guide treatment decisions. SIGNIFICANCE: Platinum-based chemotherapies are still the standard of care for NSCLC and other lung cancer types in the clinic today. However, due to chemoresistance, many patients suffer from the toxic side effects of this treatment without gaining any benefit in terms of survival. To date, no molecular biomarkers are available to predict clinical outcome of platinum-based chemotherapy. Because proteins present the functional read-out of genetic, epigenetic and translational events in the cell, a protein test is likely to be particularly suitable for response prediction. Of high relevance are proteins that are shed or secreted from cells, for example at primary tumor sites, and can be found in easily accessible biofluids like sputum for non-invasive detection. Here, we report the proteome profiling of the conditioned media (secretomes) of a panel of NSCLC cell lines in relation to cisplatin IC50 values, as a pre-clinical model, and of patient sputum as a clinical, lung cancer relevant biofluid. Using this approach in conjunction with exploration of the predictive potential in a transcriptome lung cancer patient dataset, we reveal biofluid biomarker candidates that, with further validation, may be used for non-invasive cisplatin response prediction in the future.

Keywords:  Biomarkers; Cisplatin sensitivity and resistance; Label-free GeLC-MS/MS; Non-small cell lung cancer (NSCLC); Secretome; Sputum

DOI:  https://doi.org/10.1016/j.jprot.2019.01.018
Clin Transl Allergy. 2019 ;9 6

The antimicrobial protein S100A12 identified as a potential autoantigen in a subgroup of atopic dermatitis patients.

Maria Mikus, Catharina Johansson, Nathalie Acevedo, Peter Nilsson, Annika Scheynius.

   Background: Atopic dermatitis (AD) is a complex heterogeneous chronic inflammatory skin disease. Specific IgE antibodies against autoantigens have been observed in a subgroup of AD patients, however, little is known about IgG-auto-reactivity in AD. To investigate the presence of autoreactive IgG antibodies, we performed autoantibody profiling of IgG in patients with AD of different severities and in healthy controls (HC).
Methods: First, we performed an untargeted screening in plasma samples from 40 severe AD (sAD) patients and 40 HC towards 1152 protein fragments on planar antigen microarrays. Next, based on the findings and addition of more fragments, a targeted antigen suspension bead array was designed to profile a cohort of 50 sAD patients, 123 patients with moderate AD (mAD), and 84 HC against 148 protein fragments representing 96 unique proteins.
Results: Forty-nine percent of the AD patients showed increased IgG-reactivity to any of the four antigens representing keratin associated protein 17-1 (KRTAP17-1), heat shock protein family A (Hsp70) member 4 (HSPA4), S100 calcium binding proteins A12 (S100A12), and Z (S100Z). The reactivity was more frequent in the sAD patients (66%) than in those with mAD (41%), whereas only present in 25% of the HC. IgG-reactivity to S100A12, a protein including an antimicrobial peptide, was only observed in AD patients (13/173).
Conclusions: Autoantibody profiling of IgG-reactivity using microarray technology revealed an autoantibody-based subgroup in patients with AD. The four identified autoantigens and especially S100A12 could, if characterized further, increase the understanding of different pathogenic mechanisms behind AD and thereby enable better treatment.

Keywords:  Affinity proteomics; Antimicrobial protein; Atopic dermatitis/eczema; Autoantibody profiling; Autoantigen; Autoimmunity; Co-morbidity; IgG; Protein microarrays; Suspension bead array

DOI:  https://doi.org/10.1186/s13601-019-0240-4
J Proteomics. 2019 Jan 30. pii: S1874-3919(19)30027-2. [Epub ahead of print]196 22-32

Molecular pathways of varicocele and its repair - A paired labelled shotgun proteomics approach.

M Camargo, P Intasqui, L B Belardin, M P Antoniassi, K H M Cardozo, V M Carvalho, R Fraietta, R P Bertolla.

  Varicocelectomy is associated to improved semen quality and sperm functional quality, but individual response is highly variable. Thus, a prospective study was performed including 25 men who collected a semen sample before and 12 months after subinguinal microsurgical varicocelectomy. Semen analysis, sperm functional analysis, and seminal plasma proteomic analysis was performed before and 12 months after varicocelectomy, and according to improvement or not of semen quality (positive and negative outcome). Varicocelectomy led to an increase in semen volume and sperm count, morphology, and mitochondrial activity. In the pre- vs. post-samples, 698 proteins were quantified - 91 differentially expressed after varicocelectomy. In the positive vs. negative outcome analysis, 647 proteins were identified - 151 differentially expressed in the negative outcome group and 30 differentially expressed in the positive outcome group. Tripeptidyl peptidase-1 offered a predictive value for outcome, with an area under a ROC curve of 84.5%. It seems TPP1 is an outcome predictor for varicocelectomy in adults. More importantly, this study demonstrates that the seminal plasma proteome is different in men with varicocele when compared to post-treatment samples from the same individuals. Understanding and monitoring the molecular mechanisms of semen may further establish therapeutic options for these men. SIGNIFICANCE: Although several large-scale studies have demonstrated varicocele is unequivocally associated to male infertility, these same studies have also demonstrated that varicocele is not a determinant of male infertility. We have yet to answer the question of why don't all men with varicocele present with infertility. Varicocele treatment improves semen quality, but its results are variable, and one cannot know who will and who will not benefit from surgical treatment. Results from this study strongly advance a concept that our previous studies have shown: that men with varicocele present an inflammatory semen profile. We have further demonstrated that men operated for varicocele present a decrease in this inflammatory profile, and that when they do not, semen quality remains unaltered. Trypeptidil peptidase-1, a seminal protein, was 3-fold higher in men with a positive outcome after the procedure, when compared to men with a negative outcome. Therefore, inflammation seems to be a central point to varicocele-derived male infertility.

Keywords:  Proteomics; Seminal plasma; Varicocele; Varicocelectomy

DOI:  https://doi.org/10.1016/j.jprot.2019.01.019
Basic Clin Neurosci. 2018 Sep-Oct;9(5):9(5): 337-346

Serum Proteomic Study of Women With Obsessive-Compulsive Disorder, Washing Subtype.

Mona Zamanian-Azodi, Mostafa Rezaei-Tavirani, Mohammad Mahboubi, Mohsen Hamidpour, Majid Rezaei Tavirani, Mostafa Hamdieh, Mohammad Rostami-Nejad, Naser Nejadi, Mohammad Kamran Derakhshan.

   Introduction: Many genetic studies are conducted on Obsessive-Compulsive Disorder (OCD). however, a high-throughput examination of proteome profile of this severe disease has not been performed yet.
Methods: Here, the proteomic study of OCD patients' serum samples was conducted by the application of Two-Dimensional Electrophoresis (2DE) followed by Mass Spectrometry (MALDI-TOF-TOF).
Results: A total of 240 protein spots were detected and among them, five significant differentially expressed protein spots with the fold change of ≥1.5 were considered for further evaluations. These proteins include IGKC, GC, HPX, and two isoforms of HP. While IGKC and HP show down-regulation, GC and HPX indicate up-regulation. Moreover, a validation study of overall HP levels in patients' serum via nephelometric quantification confirmed the lower levels of this protein in the serum of OCD patients. Additionally, enrichment analysis and validation test revealed that inflammation is one of most dominant processes in OCD.
Conclusion: It is suggested that these candidate proteins and their underlying processes (especially, inflammation) may be linked to OCD pathophysiology and can promise a clinical use after extensive validation studies.

Keywords:  Biomarkers; Obsessive Compulsive Disorder; Protein interaction maps; Proteomics

DOI:  https://doi.org/10.32598/bcn.9.5.337
Hypertension. 2019 Feb 04. HYPERTENSIONAHA11812242

Urine Haptoglobin and Haptoglobin-Related Protein Predict Response to Spironolactone in Patients With Resistant Hypertension.

Marta Martin-Lorenzo, Paula J Martinez, Montserrat Baldan-Martin, Juan A Lopez, Pablo Minguez, Aranzazu Santiago-Hernandez, Jesus Vazquez, Julian Segura, Gema Ruiz-Hurtado, Fernando Vivanco, Maria G Barderas, Luis M Ruilope, Gloria Alvarez-Llamas.

  Resistant hypertension prevalence is progressively increasing, and prolonged exposure to suboptimal blood pressure control results in higher cardiovascular risk and end-organ damage. Among various antihypertensive agents, spironolactone seems the most effective choice to treat resistant hypertension once triple therapy including a diuretic fails. However success in blood pressure control is not guaranteed, adverse effects are not negligible, and no clinical tools are available to predict patient's response. Complementary to our previous study of resistant hypertension metabolism, here we investigated urinary proteome changes with potential capacity to predict response to spironolactone. Twenty-nine resistant hypertensives were included. A prospective study was conducted and basal urine was collected before spironolactone administration. Patients were classified in responders or nonresponders in terms of blood pressure control. Protein quantitation was performed by liquid chromatography-mass spectrometry; ELISA and target mass spectrometry analysis were performed for confirmation. Among 3310 identified proteins, HP (haptoglobin) and HPR (haptoglobin-related protein) showed the most significant variations, with increased levels in nonresponders compared with responders before drug administration (variation rate, 5.98 and 7.83, respectively). Protein-coordinated responses were also evaluated by functional enrichment analysis, finding oxidative stress, chronic inflammatory response, blood coagulation, complement activation, and regulation of focal adhesions as physiopathological mechanisms in resistant hypertension. In conclusion, protein changes able to predict patients' response to spironolactone in basal urine were here identified for the first time. These data, once further confirmed, will support clinical decisions on patients' management while contributing to optimize the rate of control of resistant hypertensives with spironolactone.

Keywords:  blood pressure; haptoglobin; human; proteomics; resistant hypertension; spironolactone

DOI:  https://doi.org/10.1161/HYPERTENSIONAHA.118.12242
Anticancer Agents Med Chem. 2019 Feb 06.

Interactome Analysis Of The Differentially Expressed Proteins In Uterine Leiomyoma.

Tahreem Sahar, Aruna Nigam, Shadab Anjum, Farheen Waziri, Shipie Biswas, Swatantra K Jain, Saima Wajid.

   BACKGROUND: Recent advances in proteomics present enormous opportunities to discover proteome related disparities and thus understanding the molecular mechanisms related to a disease. Uterine leiomyoma is a benign monoclonal tumor, located in the pelvic region, and affecting 40% of reproductive aged female.
OBJECTIVE: Identification and characterization of the differentially expressed proteins associated with leiomyogenesis by comparing uterine leiomyoma and normal myometrium.
METHOD: Paired samples of uterine leiomyoma and adjacent myometrium retrieved from twenty-five females suffering from uterine leiomyoma (n=50) were submitted to two-dimensional electrophoresis (2-DE), matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and to reverse transcription polymerase chain reaction (RT-PCR).
RESULTS: Comparison of protein patterns revealed seven proteins with concordantly increased spot intensities in leiomyoma samples. E3 ubiquitin-protein ligase MIB2 (MIB2), Mediator of RNA polymerase II transcription subunit 10 (MED10), HIRA-interacting protein (HIRP3) and Fatty acid binding protein brain (FABP7) were found to be upregulated. While, Biogenesis of lysosome-related organelles complex 1 subunit 2 (BL1S2), Shadow of prion protein (SPRN) and RNA binding motif protein X linked like 2 (RMXL2) were found to be exclusively present in leiomyoma sample. The expression modulations of the corresponding genes were further validated which corroborated with the 2-DE result showing significant upregulation in leiomyoma. We have generated a master network showing the interactions of the experimentally identified proteins with their close neighbors and further scrutinized the network to prioritize the routes leading to cell proliferation and tumorigenesis.
CONCLUSION: This study highlights the importance of identified proteins as potential targets for therapeutic purpose. This work provides an insight into the mechanism underlying the overexpression of the proteins but warrants further investigations.

Keywords:  2-DE; MALDI-TOF MS; Monoclonal tumor; leiomyoma; myometrium; proteomics; real-time PCR.

DOI:  https://doi.org/10.2174/1871520619666190206143523
Mol Med Rep. 2019 Jan 30.

Potential urine biomarkers for gestational hypertension and preeclampsia.

Hong-Xia Guo, Yan-Bin Zhu, Cui-Ping Wu, Mei Zhong, Shui-Wang Hu.

Differential proteomic technology was used to identify urine proteomic profile of gestational hypertension and preeclampsia. Urine samples were collected from 10 patients with gestational hypertension, 10 patients with mild preeclampsia, 10 patients with severe preeclampsia and 10 normal pregnancies and analyzed by 2‑D difference gel electrophoresis, then matrix assisted laser desorption ionization mass spectrometry was used to identify differential proteins. Subsequently, ELISA was used to verify the content variation of the identified proteins in 200 urine samples. In total, 30 differential proteins were identified. For prostaglandin‑H2 D‑isomerase (L‑PGDS), perlecan and other 15 proteins, the contents in patients with gestational hypertension were higher than that of normal pregnancies, but lower in mild and severe preeclampsia. By contrast, serum albumin and α‑1‑antitrypsin was lower in samples from patients with gestational hypertension and higher in patients with mild and severe preeclampsia compared with normal pregnancies. ELISA verified that the urinary concentration of L‑PGDS and perlecan were significantly lower in patients with preeclampsia than in normal pregnancies (P<0.05). Urine proteomics is a useful tool to identify potential biomarkers to distinguish between different types of hypertensive disorders in pregnancy. L‑PGDS and perlecan could potentially be used as markers to reflect the state of renal function, and may participate in the genesis and development of renal injury during preeclampsia.

DOI: https://doi.org/10.3892/mmr.2019.9911
Indian J Clin Biochem. 2019 Jan;34(1): 3-18

Single Cell Omics of Breast Cancer: An Update on Characterization and Diagnosis.

Shailendra Dwivedi, Purvi Purohit, Radhieka Misra, Malavika Lingeswaran, Jeewan Ram Vishnoi, Puneet Pareek, Sanjeev Misra, Praveen Sharma.

  Breast cancer is recognized for its different clinical behaviors and patient outcomes, regardless of common histopathological features at diagnosis. The heterogeneity and dynamics of breast cancer undergoing clonal evolution produces cells with distinct degrees of drug resistance and metastatic potential. Presently, single cell analysis have made outstanding advancements, overshadowing the hurdles of heterogeneity linked with vast populations. The speedy progression in sequencing analysis now allow unbiased, high-output and high-resolution elucidation of the heterogeneity from individual cell within a population. Classical therapeutics strategies for individual patients are governed by the presence and absence of expression pattern of the estrogen and progesterone receptors and human epidermal growth factor receptor 2. However, such tactics for clinical classification have fruitfulness in selection of targeted therapies, short-term patient responses but unable to predict the long-term survival. In any phenotypic alterations, like breast cancer disease, molecular signature have proven its implication, as we aware that individual cell's state is regulated at diverse levels, such as DNA, RNA and protein, by multifaceted interplay of intrinsic biomolecules pathways existing in the organism and extrinsic stimuli such as ambient environment. Thus for complete understanding, complete profiling of single cell requires a synchronous investigations from different levels (multi-omics) to avoid incomplete information produced from single cell. In this article, initially we briefed on novel updates of various methods available to explore omics and then we finally pinpointed on various omics (i.e. genomics, transcriptomics, epigenomics, proteomics and metabolomics) data and few special aspects of circulating tumor cells, disseminated tumor cells and cancer stem cells, so far available from various studies that can be used for better management of breast cancer patients.

Keywords:  Genomics; Molecular sub-typing of breast cancer; Proteomics; Single cell omics; Transcriptomics

DOI:  https://doi.org/10.1007/s12291-019-0811-0
Anal Bioanal Chem. 2019 Feb 07.

An integrated proteomic and glycoproteomic study for differences on glycosylation occupancy in rheumatoid arthritis.

Xu Li, Lang Ding, Xue Li, He Zhu, Ebtesam A Gashash, Zhanguo Li, Peng George Wang, Cheng Ma.

  Rheumatoid arthritis (RA) is an autoimmune disease in which certain immune cells are dysfunctional and attack their own healthy tissues. There has been great difficulty in finding an accurate and efficient method for the diagnosis of early-stage RA. The present shortage of diagnostic methods leads to the rough treatments of the patients in the late stages, such as joint removing. Nowadays, there is an increasing focus on glyco-biomarkers discovery for malicious disease via MS-based strategy. In this study, we present an integrated proteomics and glycoproteomics approach to uncover the pathological changes of some RA-related glyco-biomarkers and glyco-checkpoints involved in the RA onset. Among 39 distinctly expressive N-glycoproteins, 27 N-glycoproteins were discovered with over twofold expression significances. On the other hand, 13 proteins have been distinguished with significant differences in 53 distinctly expressed proteins identified in this study. Such an integrated approach will provide a comprehensive strategy for new potential glyco-biomarkers and checkpoints discovery in rheumatoid arthritis.

Keywords:  Biomarker; Label-free quantification; Mass spectrometry; Rheumatoid arthritis

DOI:  https://doi.org/10.1007/s00216-018-1543-3
Clin Proteomics. 2019 ;16 4

Ulcerative colitis: functional analysis of the in-depth proteome.

Armin Schniers, Rasmus Goll, Yvonne Pasing, Sveinung Wergeland Sørbye, Jon Florholmen, Terkel Hansen.

   Background: Ulcerative colitis (UC) is one major form of inflammatory bowel disease. The cause and the pathophysiology of the disease are not fully understood and we therefor aim in this study to identify important pathophysiological features in UC from proteomics data.
Methods: Colon mucosa biopsies from inflamed tissue of untreated UC patients at diagnosis and from healthy controls were obtained during colonoscopy. Quantitative protein data was acquired by bottom-up proteomics and furthermore processed with MaxQuant. The quantitative proteome data was analyzed with Perseus and enrichment data was analyzed by ClueGO for Cytoscape.
Results: The generated proteome dataset is to-date the deepest from colon mucosa biopsies with 8562 identified proteins whereof 6818 were quantified in > 70% of the samples. We report abundance differences between UC and healthy controls and the respective p values for all quantified proteins in the supporting information. From this data set enrichment analysis revealed decreased protein abundances in UC for metallothioneins, PPAR-inducible proteins, fibrillar collagens and proteins involved in bile acid transport as well as metabolic functions of nutrients, energy, steroids, xenobiotics and carbonate. On the other hand increased abundances were enriched in immune response and protein processing in the endoplasmic reticulum, e.g. unfolded protein response and signal peptidase complex proteins.
Conclusions: This explorative study describes the most affected functions in UC tissue. Our results complemented previous findings substantially. Decreased abundances of signal peptidase complex proteins in UC are a new discovery.

Keywords:  Calprotectin; Inflammatory bowel disease; Signal peptidase complex; Ulcerative colitis

DOI:  https://doi.org/10.1186/s12014-019-9224-6
Bioessays. 2019 Feb 08. e1800042

Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us?

Anjali Arora, Kumaravel Somasundaram.

  While mass spectrometry (MS)-based quantification of small molecules has been successfully used for decades, targeted MS has only recently been used by the proteomics community to investigate clinical questions such as biomarker verification and validation. Targeted MS holds the promise of a paradigm shift in the quantitative determination of proteins. Nevertheless, targeted quantitative proteomics requires improvisation in making sample processing, instruments, and data analysis more accessible. In the backdrop of the genomic era reaching its zenith, certain questions arise: is the proteomic era about to come? If we are at the beginning of a new future for protein quantification, are we prepared to incorporate targeted proteomics at the benchside for basic research and at the bedside for the good of patients? Here, an overview of the knowledge required to perform targeted proteomics as well as its applications is provided. A special emphasis is placed on upcoming areas such as peptidomics, proteoform research, and mass spectrometry imaging, where the utilization of targeted proteomics is expected to bring forth new avenues. The limitations associated with the acceptance of this technique for mainstream usage are also highlighted. Also see the video abstract here https://youtu.be/mieB47B8gZw.

Keywords:  MRM; PRM; SRM; mass spectrometry; targeted proteomics

DOI:  https://doi.org/10.1002/bies.201800042
Klin Lab Diagn. 2018 ;63(7): 397-402

[Features of the proteome of the urine in chronic pyelonephritis.]

L Kh Pastyshkova, N B Zakharova, D N Kashirina, A G Brzhozovsky, R V Lyakh, A N Ponukalin, I M Larina.

  Clinical observation and examination of 12 patients with chronic pyelonephritis (CPN) were performed. The first group (GI) included patients with exacerbation of the disease. In the comparison group (GII)- the same patients after 1.5-3 months after completion of treatment, without clinical manifestations of exacerbation of CPN. Laboratory signs of acute renal damage were not revealed in all examined patients. Additionally, urine was collected in the afternoon after Breakfast, in the form of a freely separated 2nd fraction and its sample preparation, consisting of the stages: recovery, alkylation, protein deposition and proteolysis using trypsin. The resulting polypeptide mixture was separated by liquid chromatography in three repetitions and analyzed on a system consisting of Agilent 1100 chromatograph and ltq-FT ultra hybrid mass spectrometer. A list of proteins was obtained, indicating the number of peptides by which they were identified, and the parameters of its reliability. Most of the information about the obtained proteins was obtained from UniProt databases. Identified and analyzed 10 proteins that differ significantly in occurrence in the clinical group of patients in the period of exacerbation of PN. The appearance of these proteins in urine in 1patients with exacerbation of chronic PH allows us to consider them as potential biomarkers directly associated with inflammation and damage to the epithelial lining of the renal tubules.

Keywords:  mass spectrometry; proteomics; pyelonephritis; urinary biomarkers

DOI:  https://doi.org/10.18821/0869-2084-2018-63-7-397-402
Therap Adv Gastroenterol. 2019 ;12 1756284818822250

The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease.

Jonathan P Segal, Benjamin H Mullish, Mohammed Nabil Quraishi, Animesh Acharjee, Horace R T Williams, Tariq Iqbal, Ailsa L Hart, Julian R Marchesi.

  The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient's genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn's disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD. With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingly also the alterations in microbiota function that accompany these. Technologies such as metagenomics, metataxomics, metatranscriptomics, metaproteomics and metabonomics are therefore allowing us a deeper understanding of the role of the microbiota in IBD. Furthermore, the integration of these systems biology technologies through advancing computational and statistical techniques are beginning to understand the microbiome interactions that both contribute to health and diseased states in IBD. This review aims to explore how such systems biology technologies are advancing our understanding of the gut microbiota, and their potential role in delineating the aetiology, development and clinical care of IBD.

Keywords:  bioinformatics; genomics; gut microbiota; inflammatory bowel diseases; interactome; metagenomics; metatranscriptomics metabonomics; proteomics

DOI:  https://doi.org/10.1177/1756284818822250
Front Pharmacol. 2019 ;10 7

Platelet-Derived Microparticles From Obese Individuals: Characterization of Number, Size, Proteomics, and Crosstalk With Cancer and Endothelial Cells.

Rosalia Grande, Melania Dovizio, Simone Marcone, Paulina B Szklanna, Annalisa Bruno, H Alexander Ebhardt, Hilary Cassidy, Fionnuala Ní Áinle, Anna Caprodossi, Paola Lanuti, Marco Marchisio, Geltrude Mingrone, Patricia B Maguire, Paola Patrignani.

  Rationale: Obesity is a risk factor for atherothrombosis and various cancers. However, the mechanisms are not yet completely clarified. Objectives: We aimed to verify whether the microparticles (MPs) released from thrombin-activated platelets differed in obese and non-obese women for number, size, and proteomics cargo and the capacity to modulate in vitro the expression of (i) genes related to the epithelial to mesenchymal transition (EMT) and the endothelial to mesenchymal transition (EndMT), and (ii) cyclooxygenase (COX)-2 involved in the production of angiogenic and inflammatory mediators. Methods and Results: MPs were obtained from thrombin activated platelets of four obese and their matched non-obese women. MPs were analyzed by cytofluorimeter and protein content by liquid chromatography-mass spectrometry. MPs from obese women were not different in number but showed increased heterogeneity in size. In obese individuals, MPs containing mitochondria (mitoMPs) expressed lower CD41 levels and increased phosphatidylserine associated with enhanced Factor V representing a signature of a prothrombotic state. Proteomics analysis identified 44 proteins downregulated and three upregulated in MPs obtained from obese vs. non-obese women. A reduction in the proteins of the α-granular membrane and those involved in mitophagy and antioxidant defenses-granular membrane was detected in the MPs of obese individuals. MPs released from platelets of obese individuals were more prone to induce the expression of marker genes of EMT and EndMT when incubated with human colorectal cancer cells (HT29) and human cardiac microvascular endothelial cells (HCMEC), respectively. A protein, highly enhanced in obese MPs, was the pro-platelet basic protein with pro-inflammatory and tumorigenic actions. Exclusively MPs from obese women induced COX-2 in HCMEC. Conclusion: Platelet-derived MPs of obese women showed higher heterogeneity in size and contained different levels of proteins relevant to thrombosis and tumorigenesis. MPs from obese individuals presented enhanced capacity to cause changes in the expression of EMT and EndMT marker genes and to induce COX-2. These effects might contribute to the increased risk for the development of thrombosis and multiple malignancies in obesity. Clinical Trial Registration: www.ClinicalTrials.gov, identifier NCT01581801.

Keywords:  cellular cross-talk; microparticles; obesity; platelets; proteomics

DOI:  https://doi.org/10.3389/fphar.2019.00007
Metabolites. 2019 Feb 01. pii: E25. [Epub ahead of print]9(2):

The OMICs Window into Nonalcoholic Fatty Liver Disease (NAFLD).

Lucia Carulli, Giulia Zanca, Filippo Schepis, Erica Villa.

  Nonalcoholic fatty liver disease (NAFLD) is a common cause of hepatic abnormalities worldwide. Nonalcoholic steatohepatitis (NASH) is part of the spectrum of NAFLD and leads to progressive liver disease, such as cirrhosis and hepatocellular carcinoma. In NASH patient, fibrosis represents the major predictor of liver-related mortality; therefore, it is important to have an early and accurate diagnosis of NASH. The current gold standard for the diagnosis of NASH is still liver biopsy. The development of biomarkers able to predict disease severity, prognosis, as well as response to therapy without the need for a biopsy is the focus of most up-to-date genomic, transcriptomic, proteomic, and metabolomic research. In the future, patients might be diagnosed and treated according to their molecular signatures. In this short review, we discuss how information from genomics, proteomics, and metabolomics contribute to the understanding of NAFLD pathogenesis.

Keywords:  Fibrosis; Genomics; Liver biopsy; Metabolomics; Proteomics; Transcriptomics; nonalcoholic fatty liver disease; nonalcoholic steatohepatitis

DOI:  https://doi.org/10.3390/metabo9020025
Mod Pathol. 2019 Feb 08.

Oncoproteomic and gene expression analyses identify prognostic biomarkers for second primary malignancy in patients with head and neck squamous cell carcinoma.

Sacarin Bunbanjerdsuk, Nutchavadee Vorasan, Thammakorn Saethang, Tanjitti Pongrujikorn, Duangjai Pangpunyakulchai, Narongsak Mongkonsiri, Lalida Arsa, Nintita Thokanit, Warut Pongsapich, Tauangtham Anekpuritanang, Nuttapong Ngamphaiboon, Artit Jinawath, Somkiat Sunpaweravong, Trairak Pisitkun, Bhoom Suktitipat, Natini Jinawath.

Patients with head and neck squamous cell carcinoma are at increased risk of developing a second primary malignancy, which is associated with poor prognosis and early death. To help improve clinical outcome, we aimed to identify biomarkers for second primary malignancy risk prediction using the routinely obtained formalin-fixed paraffin-embedded tissues of the index head and neck cancer. Liquid chromatography-tandem mass spectrometry was initially performed for candidate biomarker discovery in 16 pairs of primary cancer tissues and their matched normal mucosal epithelia from head and neck squamous cell carcinoma patients with or without second primary malignancy. The 32 candidate proteins differentially expressed between head and neck cancers with and without second primary malignancy were identified. Among these, 30 selected candidates and seven more from literature review were further studied using NanoString nCounter gene expression assay in an independent cohort of 49 head and neck cancer patients. Focusing on the p16-negative cases, we showed that a multivariate logistic regression model comprising the expression levels of ITPR3, KMT2D, EMILIN1, and the patient's age can accurately predict second primary malignancy occurrence with 88% sensitivity and 75% specificity. Furthermore, using Cox proportional hazards regression analysis and survival analysis, high expression levels of ITPR3 and DSG3 were found to be significantly associated with shorter time to second primary malignancy development (log-rank test P = 0.017). In summary, we identified a set of genes whose expressions may serve as the prognostic biomarkers for second primary malignancy occurrence in head and neck squamous cell carcinomas. In combination with the histopathologic examination of index tumor, these biomarkers can be used to guide the optimum frequency of second primary malignancy surveillance, which may lead to early diagnosis and better survival outcome.

DOI: https://doi.org/10.1038/s41379-019-0211-2
Mol Vis. 2018 ;24 801-817

Novel protein constituents of pathological ocular pseudoexfoliation syndrome deposits identified with mass spectrometry.

Shiwani Sharma, Tim Chataway, Sonja Klebe, Kim Griggs, Sarah Martin, Nusha Chegeni, Alpana Dave, Tiger Zhou, Maurizio Ronci, Nicolas H Voelcker, Richard A Mills, Jamie E Craig.

Purpose: Pseudoexfoliation (PEX) syndrome is an age-related progressive disease of the extracellular matrix with ocular manifestations. PEX is clinically diagnosed by the presence of extracellular exfoliative deposits on the anterior surface of the ocular lens. PEX syndrome is a major risk factor for developing glaucoma, the leading cause of irreversible blindness in the world, and is often associated with the development of cataract. PEX reportedly coexists with Alzheimer disease and increases the risk of heart disease and stroke. PEX material deposited on the anterior surface of the ocular lens is highly proteinaceous, complex, and insoluble, making deciphering the protein composition of the material challenging. Thus, to date, only a small proportion of the protein composition of PEX material is known. The aim of this study was to decipher the protein composition of pathological PEX material deposited on the ocular lens in patients and advance the understanding of pathophysiology of PEX syndrome.
Methods: Liquid-chromatography and tandem mass spectrometry (LC-MS/MS) was employed to discover novel proteins in extracts of neat PEX material surgically isolated from patients (n = 4) with PEX syndrome undergoing cataract surgery. A sub-set of the identified proteins was validated with immunohistochemistry using lens capsule specimens from independent patients (n=3); lens capsules from patients with cataract but without PEX syndrome were used as controls (n=4). Expression of transcripts of the validated proteins in the human lens epithelium was analyzed with reverse transcription PCR (RT-PCR). Functional relationships among the proteins identified in this study and genes and proteins previously implicated in the disease were bioinformatically determined using InnateDB.
Results: Peptides corresponding to 66 proteins, including ten proteins previously known to be present in PEX material, were identified. Thirteen newly identified proteins were chosen for validation. Of those proteins, 12 were found to be genuine components of the material. The novel protein constituents include apolipoproteins (APOA1 and APOA4), stress response proteins (CRYAA and PRDX2), and blood-related proteins (fibrinogen and hemoglobin subunits), including iron-free hemoglobin. The gene expression data suggest that the identified stress-response proteins and hemoglobin are contributed by the lens epithelium and apolipoproteins and fibrinogen by the aqueous humor to the PEX material. Pathway analysis of the identified novel protein constituents and genes or proteins previously implicated in the disease reiterated the involvement of extracellular matrix organization and degradation, elastic fiber formation, and complement cascade in PEX syndrome. Network analysis suggested a central role of fibronectin in the pathophysiology of the disease. The identified novel protein constituents of PEX material also shed light on the molecular basis of the association of PEX syndrome with heart disease, stroke, and Alzheimer disease.
Conclusions: This study expands the understanding of the protein composition of pathological PEX material deposited on the ocular lens in patients with PEX syndrome and provides useful insights into the pathophysiology of this disease. This study together with the previous study by our group (Sharma et al. Experimental Eye Research 2009;89(4):479-85) demonstrate that using neat PEX material, devoid of the underlying lens capsule, for proteomics analysis is an effective approach for deciphering the protein composition of complex and highly insoluble extracellular pathological ocular deposits present in patients with PEX syndrome.
J Clin Med. 2019 Feb 06. pii: E195. [Epub ahead of print]8(2):

Effects of Caloric Restriction with Protein Supplementation on Plasma Protein Profiles in Middle-Aged Women with Metabolic Syndrome-A Preliminary Open Study.

Chia-Yu Chang, Yu-Tang Tung, Yen-Kuang Lin, Chen-Chung Liao, Ching-Feng Chiu, Te-Hsuan Tung, Amalina Shabrina, Shih-Yi Huang.

   BACKGROUND: Clinical studies have demonstrated that higher protein intake based on caloric restriction (CR) alleviates metabolic abnormalities. However, no study has examined the effects of plasma protein profiles on caloric restriction with protein supplementation (CRPS) in metabolic syndrome (MetS). Therefore, using a proteomic perspective, this pilot study investigated whether CRPS ameliorated metabolic abnormalities associated with MetS in middle-aged women.
METHODS: Plasma samples of middle-aged women with MetS in CR (n = 7) and CRPS (n = 6) groups for a 12-week intervention were obtained and their protein profiles were analysed. Briefly, blood samples from qualified participants were drawn before and after the dietary treatment. Anthropometric, clinical, and biochemical variables were measured and correlated with plasma proteomics.
RESULTS: In results, we found that body mass index, total body fat, and fasting blood glucose decreased significantly after the interventions but were not different between the CR and CRPS groups. After liquid chromatography⁻tandem mass spectrometry analysis, the relative plasma levels of alpha-2-macroglobulin (A2M), C4b-binding protein alpha chain (C4BPA), complement C1r subcomponent-like protein (C1RL), complement component C6 (C6), complement component C8 gamma chain (C8G), and vitamin K-dependent protein S (PROS) were significantly different between the CRPS and CR groups. These proteins are involved in inflammation, the immune system, and coagulation responses. Moreover, blood low-density lipoprotein cholesterol levels were significantly and positively correlated with C6 plasma levels in both groups.
CONCLUSIONS: These findings suggest that CRPS improves inflammatory responses in middle-aged women with MetS. Specific plasma protein expression (i.e., A2M, C4BPA, C1RL, C6, C8G, and PROS) associated with the complement system was highly correlated with fasting blood glucose (FBG), blood lipids (BLs), and body fat.

Keywords:  caloric restriction; metabolic syndrome; plasma proteomics; protein supplementation

DOI:  https://doi.org/10.3390/jcm8020195
J Proteome Res. 2019 Feb 08.

Proteomic atlas of the human brain in Alzheimer's disease.

Justin McKetney, Rosie Runde, Alexander S Hebert, Shahriar Salamat, Subhojit Roy, Joshua J Coon.

The brain represents one of the most divergent and critical organs in the human body. Yet, it can be afflicted by a variety of neurodegenerative diseases specifically linked to aging, about which we lack a full biomolecular understanding of onset and progression, such as Alzheimer's Disease (AD). Here we provide a proteomic resource comprising nine functionally distinct sections from three individuals clinically diagnosed with AD, across a spectrum of disease progression. Using state-of-the-art mass spectrometry, we identify a core brain proteome that exhibits only small variance in expression, accompanied by a group of proteins that are highly differentially expressed in individual sections and broader regions. AD affected tissue exhibited slightly elevated levels of tau protein with similar relative expression to factors associated with the AD pathology. Substantial differences were identified between previous proteomic studies of mature adult brains and our aged cohort. Our findings suggest considerable value in examining specifically the brain proteome of aged human populations from a multiregional perspective. This resource can serve as a guide, as well as a point of reference for how specific regions of the brain are affected by aging and neurodegeneration.

DOI: https://doi.org/10.1021/acs.jproteome.9b00004
ACS Omega. 2019 Jan 31. 4(1): 1272-1280

Glycoproteomic Profiling Provides Candidate Myocardial Infarction Predictors of Later Progression to Heart Failure.

Kristine Y Deleon-Pennell, Osasere K Ero, Yonggang Ma, Rugmani Padmanabhan Iyer, Elizabeth R Flynn, Ingrid Espinoza, Solomon K Musani, Ramachandran S Vasan, Michael E Hall, Ervin R Fox, Merry L Lindsey.

We hypothesized that identifying plasma glycoproteins that predict the development of heart failure following myocardial infarction (MI) could help to stratify subjects at risk. Plasma collected at visit 2 (2005-2008) from an MI subset of Jackson Heart Study participants underwent glycoproteomics and was grouped by the outcome: (1) heart failure hospitalization after visit 2 (n = 15) and (2) without hospitalization by 2012 (n = 45). Proteins were mapped for biological processes and functional pathways using Ingenuity Pathway Analysis and linked to clinical characteristics. A total of 198 glycopeptides corresponding to 88 proteins were identified (data available via ProteomeXchange with identifier PXD009870). Of these, 14 glycopeptides were significantly different between MI and MI + HF groups and corresponded to apolipoprotein (Apo) F, transthyretin, Apo C-IV, prostaglandin-D2 synthase, complement C9, and CD59 (p < 0.05 for all). All proteins were elevated in the MI + HF group, except CD59, which was lower. Four canonical pathways were upregulated in the MI + HF group (p < 0.05 for all): acute phase response, liver X receptor/retinoid X receptor, and macrophage reactive oxygen species generation. The coagulation pathway was significantly downregulated in the MI + HF group (p < 0.05). Even after adjustment for age and sex, Apo F was associated with the increased risk for heart failure (OR = 21.84; 95% CI 3.20-149.14). In conclusion, glycoproteomic profiling provided candidate early MI predictors of later progression to heart failure.

DOI: https://doi.org/10.1021/acsomega.8b02207
Reprod Sci. 2019 Feb 06. 1933719119828043

Antibody Microarray Analysis of Plasma Proteins for the Prediction of Histologic Chorioamnionitis in Women With Preterm Premature Rupture of Membranes.

Jeong Woo Park, Kyo Hoon Park, Ji Eun Lee, Yu Mi Kim, Se Jin Lee, Dong Huey Cheon.

  We aimed to identify maternal blood biomarkers predictive of histologic chorioamnionitis (HCA) in the plasma of women with preterm premature rupture of membranes (PPROM) and to determine whether the combination of these biomarkers with conventional clinical variables can improve the prediction of HCA. This retrospective cohort study included 82 consecutive women with PPROM (23-34 gestational weeks) who delivered within 96 hours of blood sampling. A membrane-based human antibody microarray was used to analyze the plasma proteome. The validation of 5 candidate biomarkers of interest was performed by enzyme-linked immunosorbent assay (ELISA) in the final cohort (n = 82). Serum C-reactive protein (CRP) levels were measured at sampling. Seventy-nine molecules studied exhibited intergroup differences. Validation by ELISA confirmed higher levels of plasma matrix metalloproteinase-9 (MMP-9), interleukin-6 (IL-6), S100 A8/A9, and insulin-like growth factor-binding protein 1 (IGFBP-1), but not tissue inhibitor of metalloproteinase 1 (TIMP-1), in women with HCA than in women without HCA. Using a stepwise regression analysis, a combined prediction model was developed, which included the plasma MMP-9, serum CRP levels, and gestational age (area under the curve [AUC], 0.932). The AUC for this model was significantly greater than that for any single variable included in the predictive model. Protein-antibody microarray technology can be useful in identifying plasma-based predictors for HCA. This study suggests that plasma MMP-9, IL-6, IGFBP-1, and S100 A8/A9 are important noninvasive predictors for HCA in women with PPROM and that the best predictive model, which combined these biomarkers with conventional clinical factors, can significantly improve the predictability for HCA.

Keywords:  antibody microarray; biomarkers; histologic chorioamnionitis; plasma; preterm premature rupture of membranes

DOI:  https://doi.org/10.1177/1933719119828043
Mol Pharm. 2019 Feb 08.

Proteomic Quantification of Human Blood-Brain Barrier SLC and ABC Transporters in Healthy Individuals and Dementia Patients.

Zubida M Al-Majdoub, Hajar Al Feteisi, Brahim Achour, Stacey Warwood, Sibylle Neuhoff, Amin Rostami-Hodjegan, Jill Barber.

  The blood-brain barrier (BBB) maintains brain homeostasis by controlling traffic of molecules from the circulation into the brain. This function is predominantly dependent on proteins expressed at the BBB, especially transporters and tight junction proteins. Alterations to the level and function of BBB proteins can impact the susceptibility of the central nervous system to exposure to xenobiotics in the systemic circulation with potential consequent effects on brain function. In this study, expression profiles of drug transporters and solute carriers in the BBB were assessed in tissues from healthy individuals ( n = 12), Alzheimer's patients ( n = 5), and dementia with Lewy bodies patients ( n = 5), using targeted, accurate mass retention time (AMRT) and global proteomic methods. A total of 53 transporters were quantified, 19 for the first time in the BBB. A further 20 novel transporters were identified but not quantified. The global proteomic method identified another 3333 BBB proteins. Transporter abundances, taken together with the scaling factor, microvessel protein content per unit tissue (BMvPGB also measured here), can be used in quantitative systems pharmacology models predicting drug disposition in the brain and permitting dose adjustment (precision dosing) in special populations of patients, such as those with dementia. Even in this small study, we see differences in transporter profile between healthy and diseased brain tissue.

Keywords:  Alzheimer’s disease (AD); blood−brain barrier (BBB); dementia with Lewy bodies (DLB); solute carrier (SLC) and ATP-binding cassette (ABC) transporters

DOI:  https://doi.org/10.1021/acs.molpharmaceut.8b01189
RMD Open. 2019 ;5(1): e000772

Salivary gland secretome: a novel tool towards molecular stratification of patients with primary Sjögren's syndrome and non-autoimmune sicca.

Sofie L M Blokland, Maarten R Hillen, Fréderique M van Vliet-Moret, Angela Bikker, Wilco de Jager, Aridaman Pandit, Aike A Kruize, Timothy R D J Radstake, Joel A G van Roon.

   Objective: To explore the potential of salivary gland biopsy supernatants (the secretome) as a novel tool to aid in stratification of patients with sicca syndrome and to study local immunopathology in Sjögren's syndrome.
Methods: Labial salivary gland biopsies were incubated in saline for 1 hour. In these tissue supernatants from a discovery cohort (n=16) of patients with primary Sjögren's syndrome (pSS) and non-Sjögren's sicca (nSS), 101 inflammatory mediators were measured by Luminex. Results were validated in a replication cohort (n=57) encompassing patients with pSS, incomplete SS and nSS.
Results: The levels of 23 cytokines were significantly increased in patients with pSS versus nSS in the discovery cohort. These 23 and 3 additional cytokines were measured in a second cohort. Elevated concentrations of 11 cytokines were validated and the majority correlated with clinical parameters. Classification tree analysis indicated that the concentrations of CXCL13, IL-21, sIL-2R and sIL-7Rα could be used to classify 95.8% of patients with pSS correctly.
Conclusion: Labial salivary gland secretomes can be used to reliably assess mediators involved in immunopathology of patients with pSS, potentially contributing to patient classification. As such, this method represents a novel tool to identify therapeutic targets and markers for diagnosis, prognosis and treatment response.

Keywords:  chemokines; cytokines; multi-cytokine analysis; proteomics; salivary gland; sjögren’s syndrome

DOI:  https://doi.org/10.1136/rmdopen-2018-000772
Blood. 2019 Feb 06. pii: blood-2018-09-835389. [Epub ahead of print]

Dissecting CLL through high dimensional single cell technologies.

Satyen Gohil, Catherine J Wu.

We now have the potential to undertake detailed analysis of the inner workings of thousands of cancer cells, one cell at a time, through the emergence of a range of techniques probing the genome, transcriptome and proteome, combined with the development of bioinformatics pipelines that enable their interpretation. This provides an unprecedented opportunity to better understand the heterogeneity of the disease and how mutations, activation states and protein expression at a single-cell level impact disease course, response to treatment and outcomes. Herein, we review the emerging application of these new techniques to chronic lymphocytic leukemia and examine the fresh insights already attained through this transformative technology.

DOI: https://doi.org/10.1182/blood-2018-09-835389
Mol Diagn Ther. 2019 Feb 02.

Omics Studies in Hemoglobinopathies.

Eleni Katsantoni.

Hemoglobinopathies include all genetic diseases of hemoglobin and are grouped into thalassemia syndromes and structural hemoglobin variants. The β-thalassemias constitute a group of severe anemias with monogenic inheritance, caused by β-globin gene mutations. This review is focused on omics studies in hemoglobinopathies and mainly β-thalassemia, and discusses genomic, epigenomic, transcriptomic, proteomic and metabolomic findings. Omics analyses have identified various disease modifiers with an impact on disease severity and efficacy of treatments. These modifiers have contributed to the understanding of globin genes regulation/hemoglobin switching and the development of novel therapies. How omics data and their integration can contribute to efficient patient stratification, therapeutic management, improvements in existing treatments and application of novel personalized therapies is discussed.

DOI: https://doi.org/10.1007/s40291-019-00386-1
Int Urogynecol J. 2019 Feb 04.

Genetic association in female stress urinary incontinence based on proteomic findings: a case-control study.

Theresa Reischer, Sukirthini Balendran-Braun, Sandra Liebmann-Reindl, Berthold Streubel, Wolfgang Umek, Heinz Koelbl, Marianne Koch.

   INTRODUCTION AND HYPOTHESIS: Previous studies have indicated a hereditary component of stress urinary incontinence; however, evidence on candidate genes or single-nucleotide polymorphisms (SNPs) is scarce. We hypothesize a genetic association of female stress urinary incontinence based on significant differences of the urinary and serum proteomic pattern in the identical study population.
METHODS: Case-control study of 19 patients and 19 controls. We searched for known SNPs of SUI candidate genes (COL1A1, MMP1, SERPINA5, UMOD) in the database of short genetic variations and PubMed. Genomic DNA was isolated using QIAamp DNA Blood Midi Kit (Qiagen). We performed Sanger sequencing of selected exons and introns.
RESULTS: The rs885786 SNP of the SERPINA5 gene was identified in 15 cases and 10 controls (p = 0.09). The rs6113 SNP of the SERPINA5 gene was present in 4 controls compared to 0 cases (p = 0.105). The rs4293393, rs13333226 and rs13335818 SNPs of the UMOD gene were identified in five cases and two controls (p = 0.20), the rs1800012 SNP of the COL1A1 gene in five cases versus four controls (p = 0.24) and the homozygous rs1799750 SNP of the MMP1 gene in eight cases versus five controls (p = 0.18). The combination of the rs885786 SNP of the SERPINA5 gene and rs179970 SNP of the MMP1 gene was detected in ten cases versus five controls (p = 0.072).
CONCLUSIONS: We found nonsignificant trends toward associations of SNPs on the SERPINA5, UMOD and MMP1 gene and SUI.

Keywords:  COL1A1; Genetic association; MMP1; SERPINA5; Serum proteome; Stress urinary incontinence; UMOD; Urinary proteome

DOI:  https://doi.org/10.1007/s00192-019-03878-0
PLoS One. 2019 ;14(2): e0212300

Correction: Exploration of Serum Proteomic Profiling and Diagnostic Model That Differentiate Crohn's Disease and Intestinal Tuberculosis.

Fenming Zhang, Chengfu Xu, Longgui Ning, Fengling Hu, Guodong Shan, Hongtan Chen, Ming Yang, Wenguo Chen, Jiekai Yu, Guoqiang Xu.

[This corrects the article DOI: 10.1371/journal.pone.0167109.].

DOI: https://doi.org/10.1371/journal.pone.0212300
Proteomics Clin Appl. 2019 Jan;13(1): e1800167

Proteomics in Pathology: The Special Issue.

Rémi Longuespée, Rita Casadonte, Kristina Schwamborn, Mark Kriegsmann.

DOI: https://doi.org/10.1002/prca.201800167
Oncotarget. 2019 Jan 11. 10(4): 480-493

Fibroblast growth factor receptor 1 (FGFR1) as a therapeutic target in adenoid cystic carcinoma of the lacrimal gland.

Ravi Doddapaneni, Wensi Tao, Andrea Naranjo, Neda Nikpoor, David T Tse, Daniel Pelaez.

  Identification of molecular targets is the first step in developing efficacious therapeutic strategies for tumors. A tumors' biological response to perturbagens yields important information on the molecular determinants for tumor growth. The aim of this study was to characterize the response of adenoid cystic carcinoma of the lacrimal gland (LGACC) to intra-arterial cytoreductive chemotherapy (IACC) in order to identify novel targets to enhance therapy. We performed high-throughput proteomic analysis on paired samples from pre-IACC diagnostic biopsies and post-IACC excised tumor samples from 6 LGACC patients. This proteomic analysis provides a comprehensive landscape of the cellular compartments contained within the excised tumors. Interestingly, we found a strong upregulation across the fibroblast growth factor (FGF) signaling pathway, with FGF receptor 1 (FGFR1) exhibiting a consistent and significant upregulation in all post-IACC samples. We thus evaluated the therapeutic efficacy of a novel FGFR1 selective inhibitor, AZD4547, in combination with cisplatin on LGACC cells in-vitro. The combination index (CI) value (<0.895) demonstrated synergistic effect of AZD4547 and cisplatin in inhibiting cell growth and viability (p<0.02), with a differential response seen in post-IACC cultures when compared to pre-IACC cultures. The combination approach showed synergy of the drugs in the migration assay. Western blot analysis indicated a significant upregulation of cleaved caspase-3 and downregulation the expression of FGFR1 (p<0.05) with the combination treatment as compared to either agent independently. Our findings demonstrate that FGFR1 inhibition potentiates the cytoreductive effects of cisplatin and suggest a potential therapeutic benefit of using AZD4547 in the management of LGACC.

Keywords:  FGFR; adenoid cystic carcinoma; lacrimal gland; precision medicine; targeted therapy

DOI:  https://doi.org/10.18632/oncotarget.26558
Arthritis Res Ther. 2019 Feb 06. 21(1): 47

Rheumatoid arthritis reprograms circadian output pathways.

Toryn M Poolman, Julie Gibbs, Amy L Walker, Suzanna Dickson, Laura Farrell, James Hensman, Alexandra C Kendall, Robert Maidstone, Stacey Warwood, Andrew Loudon, Magnus Rattray, Ian N Bruce, Anna Nicolaou, David W Ray.

   OBJECTIVE: We applied systems biology approaches to investigate circadian rhythmicity in rheumatoid arthritis (RA).
METHODS: We recruited adults (age 16-80 years old) with a clinical diagnosis of RA (active disease [DAS28 > 3.2]). Sleep profiles were determined before inpatient measurements of saliva, serum, and peripheral blood mononuclear leukocytes (PBML). Transcriptome and proteome analyses were carried out by RNA-SEQ and LC-MS/MS. Serum samples were analysed by targeted lipidomics, along with serum from mouse collagen induced-arthritis (CIA). Bioinformatic analysis identified RA-specific gene networks and rhythmic processes differing between healthy and RA.
RESULTS: RA caused greater time-of-day variation in PBML gene expression, and ex vivo stimulation identified a time-of-day-specific RA transcriptome. We found increased phospho-STAT3 in RA patients, and some targets, including phospho-ATF2, acquired time-of-day variation in RA. Serum ceramides also gained circadian rhythmicity in RA, which was also seen in mouse experimental arthritis, resulting from gain in circadian rhythmicity of hepatic ceramide synthases.
CONCLUSION: RA drives a gain in circadian rhythmicity, both in immune cells, and systemically. The coupling of distant timing information to ceramide synthesis and joint inflammation points to a systemic re-wiring of the circadian repertoire. Circadian reprogramming in response to chronic inflammation has implications for inflammatory co-morbidities and time-of-day therapeutics.

Keywords:  Arthritis; Ceramide; Circadian; Immune cell; Rheumatoid arthritis

DOI:  https://doi.org/10.1186/s13075-019-1825-y
Commun Biol. 2019 ;2 43

Regional protein expression in human Alzheimer's brain correlates with disease severity.

Jingshu Xu, Stefano Patassini, Nitin Rustogi, Isabel Riba-Garcia, Benjamin D Hale, Alexander M Phillips, Henry Waldvogel, Robert Haines, Phil Bradbury, Adam Stevens, Richard L M Faull, Andrew W Dowsey, Garth J S Cooper, Richard D Unwin.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that currently affects 36 million people worldwide with no effective treatment available. Development of AD follows a distinctive pattern in the brain and is poorly modelled in animals. Therefore, it is vital to widen the spatial scope of the study of AD and prioritise the study of human brains. Here we show that functionally distinct human brain regions display varying and region-specific changes in protein expression. These changes provide insights into the progression of disease, novel AD-related pathways, the presence of a gradient of protein expression change from less to more affected regions and a possibly protective protein expression profile in the cerebellum. This spatial proteomics analysis provides a framework which can underpin current research and open new avenues to enhance molecular understanding of AD pathophysiology, provide new targets for intervention and broaden the conceptual frameworks for future AD research.

DOI: https://doi.org/10.1038/s42003-018-0254-9
Oncoimmunology. 2019 ;8(3): 1556080

Neoantigen characteristics in the context of the complete predicted MHC class I self-immunopeptidome.

Scott D Brown, Robert A Holt.

  The self-immunopeptidome is the repertoire of all self-peptides that can be presented by the combination of MHC variants carried by an individual, defined by their HLA genotype. Each MHC variant presents a distinct set of self-peptides, and the number of peptides in a set is variable. Subjects carrying MHC variants that present fewer self-peptides should also present fewer mutated peptides, resulting in decreased immune pressure on tumor cells. To explore this, we predicted peptide-MHC binding values using all unique 8-11mer human peptides in the human proteome and all available HLA class I allelic variants, for a total of 134 billion unique peptide--MHC binding predictions. From these predictions, we observe that most peptides are able to be presented by relatively few (< 250) MHC, while some can be presented by upwards of 1,500 different MHC. There is substantial overlap among the repertoires of peptides presented by different MHC and no relationship between the number of peptides presented and HLA population frequency. Nearly 30% of self-peptides are presentable by at least one MHC, leaving 70% of the human peptidome unsurveyed by T cells. We observed similar distributions of predicted self-immunopeptidome sizes in cancer subjects compared to controls, and within the pan-cancer population, predicted self-immunopeptidome size combined with mutational load to predict survival. Self-immunopeptidome analysis revealed evidence for tumor immunoediting and identified specific peptide positions that most influence immunogenicity. Because self-immunopeptidome size is defined by HLA genotypes and approximates neoantigen load, HLA genotyping could offer a rapid predictive biomarker for response to immunotherapy.

Keywords:  Self-immunopeptidome; cancer; immunogenicity; immunopeptidome; immunotherapy; neoantigen; peptide-MHC; predictions

DOI:  https://doi.org/10.1080/2162402X.2018.1556080
Protein Pept Lett. 2019 Feb 07.

Role of seminal plasma proteins in effective zygote formation- A success road to pregnancy.

Archana Kumar, T B Sridharn, Kamini A Rao.

  Seminal plasma proteins contributed by secretions of accessory glands plays a copious role in fertilization. Their role is overlooked for decades and even now, as Artificial Reproduction Techniques (ART) excludes the plasma components in the procedures. Recent evidences suggest the importance of these proteins starting from imparting fertility status to men, fertilization and till successful implantation of the conceptus in the female uterus. Seminal plasma is rich in diverse proteins, but a major part of the seminal plasma is constituted by very lesser number of proteins. This makes isolation and further research on non abundant protein a tough task. With the advent of much advanced proteomic techniques and bio informatics tools, studying the protein component of seminal plasma has become easy and promising. This review is focused on the role of seminal plasma proteins on various walks of fertilization process and thus, the possible exploitation of seminal plasma proteins for understanding the etiology of male related infertility issues. In addition, a compilation of seminal plasma proteins and their functions has been done.

Keywords:  Accessory reproductive glands; Immunomodulatory seminal proteins; Male infertility

DOI:  https://doi.org/10.2174/0929866526666190208112152
Curr Opin Chem Biol. 2019 Jan 31. pii: S1367-5931(18)30138-8. [Epub ahead of print]48 150-157

Proteomic-based approaches to cardiac development and disease.

Kerry M Dorr, Frank L Conlon.

Congenital malformations, or structural birth defects, are now the leading cause of infant mortality in the United States and Europe (Dolk et al., 2010; Heron et al., 2009). Of the congenital malformations, congenital heart disease (CHD) is the most common (Dolk et al., 2010; Heron et al., 2009). Thus, a molecular understanding of heart development is an essential goal for improving clinical approaches to CHD. However, CHDs are commonly a result of genetic defects that manifest themselves in a spatial and temporal manner during the early stages of embryogenesis, leaving them mostly intractable to mass spectrometry-based analysis. Here, we describe the technologies and advancements in the field of mass spectrometry over the past few years that have begun to provide insights into the molecular and cellular basis of CHD and prospects for these types of approaches in the future.

DOI: https://doi.org/10.1016/j.cbpa.2019.01.001
Genomics. 2019 Feb 05. pii: S0888-7543(18)30697-9. [Epub ahead of print]

Should 'Omics' education be a part of allied health profession curricula?

Hadley D Brown, Kittipong Boonme, Victorine Imrhan, Shanil Juma, Parakat Vijayagopal, Chandan Prasad.

  Sequencing of human genome followed by monumental progress in omics sciences within last two decades has made personalized nutrition for better health is a reality for near future. The complexity of underlying science in making personalized nutrition recommendation has led to the need for training of health care providers. The International Society of Nutrigenetics/Nutrigenomics (ISNN) has mission to increase the understanding among both professionals and the general public of the role of genetic variation and nutrients in gene expression. To bring this mission to fruition, we need trained healthcare professionals ready to educate public. With this in mind, we have surveyed allied health students for their omics knowledge, desire to learn more and their perception of the need of omics education. The results show a need for training in omics in all allied health disciplines and desire of the students to learn more.

Keywords:  Foodomics; Metabolomics; Nutrigenomics; Personalized nutrition; Proteomics

DOI:  https://doi.org/10.1016/j.ygeno.2019.01.009