Articles

Proteomic analysis of purified protein derivative of Mycobacterium tuberculosis

Purified protein derivative (PPD) has been used for more than half a century as an antigen for the diagnosis of tuberculosis infection based on delayed type hypersensitivity. Although designated as “purified,”...

Authors: Thottethodi Subrahmanya Keshava Prasad, Renu Verma, Satish Kumar, Raja Sekhar Nirujogi, Gajanan J Sathe, Anil K Madugundu, Jyoti Sharma, Vinuth N Puttamallesh, Anjali Ganjiwale, Vithal P Myneedu, Aditi Chatterjee, Akhilesh Pandey, HC Harsha and Jayasuryan Narayana

Technology platform development for targeted plasma metabolites in human heart failure

Heart failure is a multifactorial disease associated with staggeringly high morbidity and motility. Recently, alterations of multiple metabolites have been implicated in heart failure; however, the lack of an ...

Authors: CY X’avia Chan, Anjum A Khan, JH Howard Choi, CM Dominic Ng, Martin Cadeiras, Mario Deng and Peipei Ping

Protein expression profiling of nuclear membrane protein reveals potential biomarker of human hepatocellular carcinoma

Complex molecular events lead to development and progression of liver cirrhosis to HCC. Differentially expressed nuclear membrane associated proteins are responsible for the functional and structural alteratio...

Authors: Rizma Khan, Saadia Zahid, Yu-Jui Yvonne Wan, Jameson Forster, A-Bashar Abdul Karim, Atta M Nawabi, Abid Azhar, M Ataur Rahman and Nikhat Ahmed

Semiquantitative proteomic analysis of human hippocampal tissues from Alzheimer’s disease and age-matched control brains

Alzheimer’s disease (AD) is the most common type of dementia affecting people over 65 years of age. The hallmarks of AD are the extracellular deposits known as amyloid β plaques and the intracellular neurofibr...

Authors: Ilijana Begcevic, Hari Kosanam, Eduardo Martínez-Morillo, Apostolos Dimitromanolakis, Phedias Diamandis, Uros Kuzmanov, Lili-Naz Hazrati and Eleftherios P Diamandis

Potential tumor biomarkers identified in ovarian cyst fluid by quantitative proteomic analysis, iTRAQ

Epithelial-derived ovarian adenocarcinoma (EOC) is the most deadly gynecologic tumor, and the principle cause of the poor survival rate is diagnosis at a late stage. Screening and diagnostic biomarkers with ac...

Authors: Björg Kristjansdottir, Kristina Levan, Karolina Partheen, Elisabet Carlsohn and Karin Sundfeldt

Quantitative proteomics for identifying biomarkers for Rabies

Rabies is a fatal acute viral disease of the central nervous system, which is a serious public health problem in Asian and African countries. Based on the clinical presentation, rabies can be classified into e...

Authors: Abhilash K Venugopal, S Sameer Kumar Ghantasala, Lakshmi Dhevi N Selvan, Anita Mahadevan, Santosh Renuse, Praveen Kumar, Harsh Pawar, Nandini A Sahasrabhuddhe, Mooriyath S Suja, Yarappa L Ramachandra, Thottethodi S Keshava Prasad, Shampur N Madhusudhana, Harsha HC, Raghothama Chaerkady, Parthasarathy Satishchandra, Akhilesh Pandey…

Quantitative proteomic analysis of amniocytes reveals potentially dysregulated molecular networks in Down syndrome

Down syndrome (DS), caused by an extra copy of chromosome 21, affects 1 in 750 live births and is characterized by cognitive impairment and a constellation of congenital defects. Currently, little is known abo...

Authors: Chan-Kyung J Cho, Andrei P Drabovich, George S Karagiannis, Eduardo Martínez-Morillo, Shawn Dason, Apostolos Dimitromanolakis and Eleftherios P Diamandis

Proteomic analysis of ERK1/2-mediated human sickle red blood cell membrane protein phosphorylation

In sickle cell disease (SCD), the mitogen-activated protein kinase (MAPK) ERK1/2 is constitutively active and can be inducible by agonist-stimulation only in sickle but not in normal human red blood cells (RBC...

Authors: Erik J Soderblom, J Will Thompson, Evan A Schwartz, Edward Chiou, Laura G Dubois, M Arthur Moseley and Rahima Zennadi

Ovarian cyst fluid is a rich proteome resource for detection of new tumor biomarkers

We aimed to investigate the use of ovarian cyst fluid as a source for biomarker discovery and to find novel biomarkers for use in the diagnosis of epithelial ovarian tumors.

Authors: Björg Kristjansdottir, Karolina Partheen, Eric T Fung, Janusz Marcickiewicz, Christine Yip, Mats Brännström and Karin Sundfeldt

Urine proteome of autosomal dominant polycystic kidney disease patients

Autosomal dominant polycystic kidney disease (ADPKD) is responsible for 10% of cases of the end stage renal disease. Early diagnosis, especially of potential fast progressors would be of benefit for efficient ...

Authors: Magda Bakun, Mariusz Niemczyk, Dominik Domanski, Radek Jazwiec, Anna Perzanowska, Stanislaw Niemczyk, Michal Kistowski, Agnieszka Fabijanska, Agnieszka Borowiec, Leszek Paczek and Michal Dadlez

Quantitative proteomics for identifying biomarkers for tuberculous meningitis

Tuberculous meningitis is a frequent extrapulmonary disease caused by Mycobacterium tuberculosis and is associated with high mortality rates and severe neurological sequelae. In an earlier study employing DNA mic...

Authors: Ghantasala S Sameer Kumar, Abhilash K Venugopal, Anita Mahadevan, Santosh Renuse, H C Harsha, Nandini A Sahasrabuddhe, Harsh Pawar, Rakesh Sharma, Praveen Kumar, Sudha Rajagopalan, Keith Waddell, Yarappa L Ramachandra, Parthasarathy Satishchandra, Raghothama Chaerkady, T S Keshava Prasad, K Shankar…

Unique and differential protein signatures within the mononuclear cells of HIV-1 and HCV mono-infected and co-infected patients

Pathogenesis of liver damage in patients with HIV and HCV co-infection is complex and multifactorial. Although global awareness regarding HIV-1/HCV co-infection is increasing little is known about the pathophy...

Authors: Nawal M Boukli, Vivekananda Shetty, Luis Cubano, Martha Ricaurte, Jordana Coelho-dos-Reis, Zacharie Nickens, Punit Shah, Andrew H Talal, Ramila Philip and Pooja Jain

Investigation of ovarian cancer associated sialylation changes in N-linked glycopeptides by quantitative proteomics

In approximately 80% of patients, ovarian cancer is diagnosed when the patient is already in the advanced stages of the disease. CA125 is currently used as the marker for ovarian cancer; however, it lacks spec...

Authors: Vivekananda Shetty, Julie Hafner, Punit Shah, Zacharie Nickens and Ramila Philip

Development of protein biomarkers in cerebrospinal fluid for secondary progressive multiple sclerosis using selected reaction monitoring mass spectrometry (SRM-MS)

Multiple sclerosis (MS) is a chronic inflammatory disorder of the central nervous system (CNS). It involves damage to the myelin sheath surrounding axons and to the axons themselves. MS most often presents with a...

Authors: Yan Jia, Tianxia Wu, Christine A Jelinek, Bibiana Bielekova, Linda Chang, Scott Newsome, Sharmilee Gnanapavan, Gavin Giovannoni, Dawn Chen, Peter A Calabresi, Avindra Nath and Robert J Cotter

The human proteome – a scientific opportunity for transforming diagnostics, therapeutics, and healthcare

A National Institutes of Health (NIH) workshop was convened in Bethesda, MD on September 26–27, 2011, with representative scientific leaders in the field of proteomics and its applications to clinical settings...

Authors: Marc Vidal, Daniel W Chan, Mark Gerstein, Matthias Mann, Gilbert S Omenn, Danilo Tagle and Salvatore Sechi

Nm23/nucleoside diphosphate kinase-A as a potent prognostic marker in invasive pancreatic ductal carcinoma identified by proteomic analysis of laser micro-dissected formalin-fixed paraffin-embedded tissue

Pancreatic cancer is among the most lethal malignancies worldwide. This study aimed to identify a novel prognostic biomarker, facilitating treatment selection, using mass spectrometry (MS)-based proteomic anal...

Authors: Tatsuyuki Takadate, Tohru Onogawa, Kiyonaga Fujii, Fuyuhiko Motoi, Sayaka Mikami, Tetsuya Fukuda, Makoto Kihara, Takashi Suzuki, Taro Takemura, Takashi Minowa, Nobutaka Hanagata, Kengo Kinoshita, Takanori Morikawa, Keiichi Shirasaki, Toshiki Rikiyama, Yu Katayose…

Overexpression of ribosome binding protein 1 (RRBP1) in breast cancer

The molecular events that lead to malignant transformation and subsequent metastasis of breast carcinoma include alterations in the cells at genome, transcriptome and proteome levels. In this study, we used pu...

Authors: Deepthi Telikicherla, Arivusudar Marimuthu, Manoj Kumar Kashyap, Y L Ramachandra, Sujatha Mohan, Juan Carlos Roa, Jagadeesha Maharudraiah and Akhilesh Pandey

Selected Reaction Monitoring (SRM) Analysis of Epidermal Growth Factor Receptor (EGFR) in Formalin Fixed Tumor Tissue

Analysis of key therapeutic targets such as epidermal growth factor receptor (EGFR) in clinical tissue samples is typically done by immunohistochemistry (IHC) and is only subjectively quantitative through a na...

Authors: Todd Hembrough, Sheeno Thyparambil, Wei-Li Liao, Marlene M Darfler, Joseph Abdo, Kathleen M Bengali, Paul Taylor, Jiefei Tong, Humberto Lara-Guerra, Thomas K Waddell, Michael F Moran, Ming-Sound Tsao, David B Krizman and Jon Burrows

Detection of BK virus in urine from renal transplant subjects by mass spectrometry

The diagnosis and management of BK virus (BKV) reactivation following renal transplantation continues to be a significant clinical problem. Following reactivation of latent virus, impaired cellular immunity en...

Authors: Rebecca Konietzny, Roman Fischer, Nicola Ternette, Cynthia A Wright, Ben W Turney, Aron Chakera, David Hughes, Benedikt M Kessler and Chris W Pugh

The cerebrospinal fluid proteome in HIV infection: change associated with disease severity

Central nervous system (CNS) infection is a nearly universal feature of untreated systemic HIV infection with a clinical spectrum that ranges from chronic asymptomatic infection to severe cognitive and motor d...

Authors: Thomas E Angel, Jon M Jacobs, Serena S Spudich, Marina A Gritsenko, Dietmar Fuchs, Teri Liegler, Henrik Zetterberg, David G Camp II, Richard W Price and Richard D Smith

Characterization of the seminal plasma proteome in men with prostatitis by mass spectrometry

Prostatitis is an inflammation of the prostate gland which affects approximately 10% of men. Despite its frequency, diagnosing prostatitis and monitoring patient response to treatment remains frustrating. As t...

Authors: Daniel Kagedan, Irene Lecker, Ihor Batruch, Christopher Smith, Ilia Kaploun, Kirk Lo, Ethan Grober, Eleftherios P Diamandis and Keith A Jarvi

Virtual screening and evaluation of Ketol-Acid Reducto-Isomerase (KARI) as a putative drug target for Aspergillosis

Aspergillus is a leading causative agent for fungal morbidity and mortality in immuno-compromised patients. To identify a putative target to design or identify new antifungal drug, against Aspergillus is requi...

Authors: Vivek K Morya, Shalini Kumari and Eun-ki Kim

Desmin expression in colorectal cancer stroma correlates with advanced stage disease and marks angiogenic microvessels

Biomarkers that improve stratification of colorectal cancer patients for adjuvant therapy versus resection alone, or that are predictive of response to therapeutic agents, have the potential to greatly improve...

Authors: Georgia Arentz, Tim Chataway, Timothy J Price, Zaipul Izwan, Gemma Hardi, Adrian G Cummins and Jennifer E Hardingham

The Clinical Proteomics editorial team would like to announce a change in the volume listings for the journal

Authors:

Morphological changes in diabetic kidney are associated with increased O-GlcNAcylation of cytoskeletal proteins including α-actinin 4

The objective of the present study is to identify proteins that change in the extent of the modification with O-linked N-acetylglucosamine (O-GlcNAcylation) in the kidney from diabetic model Goto-Kakizaki (GK) ra...

Authors: Yoshihiro Akimoto, Yuri Miura, Tosifusa Toda, Margreet A Wolfert, Lance Wells, Geert-Jan Boons, Gerald W Hart, Tamao Endo and Hayato Kawakami

A simpler method of preprocessing MALDI-TOF MS data for differential biomarker analysis: stem cell and melanoma cancer studies

Raw spectral data from matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) with MS profiling techniques usually contains complex information not readily providing biological insight into dis...

Authors: Dong L Tong, David J Boocock, Clare Coveney, Jaimy Saif, Susana G Gomez, Sergio Querol, Robert Rees and Graham R Ball

Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery

Early diagnosis of Oral Squamous Cell Carcinoma (OSCC) increases the survival rate of oral cancer. For early diagnosis, molecular biomarkers contained in samples collected non-invasively and directly from at-r...

Authors: Joel A Kooren, Nelson L Rhodus, Chuanning Tang, Pratik D Jagtap, Bryan J Horrigan and Timothy J Griffin

Drug metabolizing enzyme activities versus genetic variances for drug of clinical pharmacogenomic relevance

Enzymes are critically important in the transportation, metabolism, and clearance of most therapeutic drugs used in clinical practice today. Many of these enzymes have significant genetic polymorphisms that af...

Authors: Alan H B Wu

Functional proteomics can define prognosis and predict pathologic complete response in patients with breast cancer

To determine whether functional proteomics improves breast cancer classification and prognostication and can predict pathological complete response (pCR) in patients receiving neoadjuvant taxane and anthracycl...

Authors: Ana M Gonzalez-Angulo, Bryan T Hennessy, Funda Meric-Bernstam, Aysegul Sahin, Wenbin Liu, Zhenlin Ju, Mark S Carey, Simen Myhre, Corey Speers, Lei Deng, Russell Broaddus, Ana Lluch, Sam Aparicio, Powel Brown, Lajos Pusztai, W Fraser Symmans…

Immobilized pH gradient-driven paper-based IEF: a new method for fractionating complex peptide mixtures before MS analysis

The vast difference in the abundance of different proteins in biological samples limits the determination of the complete proteome of a cell type, requiring fractionation of proteins and peptides before MS ana...

Authors: Beerelli Seshi, Kumaraguru Raja and KH Chandramouli

The ADAMs family of proteases: new biomarkers and therapeutic targets for cancer?

The ADAMs are transmembrane proteins implicated in proteolysis and cell adhesion. Forty gene members of the family have been identified, of which 21 are believed to be functional in humans. As proteases, their...

Authors: Michael J Duffy, Maeve Mullooly, Norma O'Donovan, Sumainizah Sukor, John Crown, Aisling Pierce and Patricia M McGowan

Aberrant glycosylation associated with enzymes as cancer biomarkers

One of the new roles for enzymes in personalized medicine builds on a rational approach to cancer biomarker discovery using enzyme-associated aberrant glycosylation. A hallmark of cancer, aberrant glycosylatio...

Authors: Danni L Meany and Daniel W Chan

Challenges in implementing individualized medicine illustrated by antimetabolite therapy of childhood acute lymphoblastic leukemia

Predicting the response to medical therapy and subsequently individualizing the treatment to increase efficacy or reduce toxicity has been a longstanding clinical goal. Not least within oncology, where many pa...

Authors: Jacob Nersting, Louise Borst and Kjeld Schmiegelow

Spectral counting assessment of protein dynamic range in cerebrospinal fluid following depletion with plasma-designed immunoaffinity columns

In cerebrospinal fluid (CSF), which is a rich source of biomarkers for neurological diseases, identification of biomarkers requires methods that allow reproducible detection of low abundance proteins. It is th...

Authors: Jacques Borg, Alex Campos, Claudio Diema, Núria Omeñaca, Eliandre de Oliveira, Joan Guinovart and Marta Vilaseca

Down-regulation of kallikrein-related peptidase 5 (KLK5) expression in breast cancer patients: a biomarker for the differential diagnosis of breast lesions

Kallikrein-related peptidase 5 (KLK5) is a secreted trypsin-like protease of the KLK family, encoded by the KLK5 gene. KLK5 has been found to cleave various extracellular matrix components, as well as to activate...

Authors: Margaritis Avgeris, Georgia Papachristopoulou, Athanasios Polychronis and Andreas Scorilas

Two-dimensional difference gel electrophoresis (DIGE) analysis of sera from visceral leishmaniasis patients

Visceral leishmaniasis is a parasitic infection caused by Lesihmania donovani complex and transmitted by the bite of the phlebotomine sand fly. It is an endemic disease in many developing countries with more than...

Authors: Lokesh A Rukmangadachar, Jitender Kataria, Gururao Hariprasad, Jyotish C Samantaray and Alagiri Srinivasan

Exciting news from Clinical Proteomics

Authors: Daniel W Chan

Plasma proteomic profile of sulfur mustard exposed lung diseases patients using 2-dimensional gel electrophoresis

Sulfur mustard "bis (2-chlroethyl) sulphide" (SM) is a chemical warfare agent that remains a threat to human health. The aim of this study was to identify protein expression signature or biomarkers that reflec...

Authors: Hossein Mehrani, Mostafa Ghanei, Jafar Aslani and Zahra Tabatabaei

Proteomic profiling of the mesenteric lymph after hemorrhagic shock: Differential gel electrophoresis and mass spectrometry analysis

Experiments show that upon traumatic injury the composition of mesenteric lymph changes such that it initiates an immune response that can ultimately result in multiple organ dysfunction syndrome (MODS). To id...

Authors: Ashley Zurawel, Ernest E Moore, Erik D Peltz, Janeen R Jordan, Sagar Damle, Monika Dzieciatkowska, Anirban Banerjee and Kirk C Hansen

A Technical Assessment of the Utility of Reverse Phase Protein Arrays for the Study of the Functional Proteome in Non-microdissected Human Breast Cancers

The lack of large panels of validated antibodies, tissue handling variability, and intratumoral heterogeneity potentially hamper comprehensive study of the functional proteome in non-microdissected solid tumor...

Authors: Bryan T. Hennessy, Yiling Lu, Ana Maria Gonzalez-Angulo, Mark S. Carey, Simen Myhre, Zhenlin Ju, Michael A. Davies, Wenbin Liu, Kevin Coombes, Funda Meric-Bernstam, Isabelle Bedrosian, Mollianne McGahren, Roshan Agarwal, Fan Zhang, Jens Overgaard, Jan Alsner…

Membrane Protein Profiling of Human Islets of Langerhans Using Several Extraction Methods

Proteomic characterization of the human pancreatic islets, containing the insulin producing beta-cells, is likely to be of great importance for improved treatment and understanding of the pathophysiology of di...

Authors: Sara F. Hansson, Åsa Henriksson, Lars Johansson, Olle Korsgren, Jan W. Eriksson, Hans Tornqvist and Pia Davidsson

Comparative Proteomic Analysis of Candida albicans and Candida glabrata

Candida albicans and Candida glabrata are the two most common opportunistic pathogens which are part of the normal flora in humans. Clinical diagnosis of infection by these organisms is still largely based on cul...

Authors: Thottethodi Subrahmanya Keshava Prasad, Shivakumar Keerthikumar, Raghothama Chaerkady, Kumaran Kandasamy, Santosh Renuse, Arivusudar Marimuthu, Abhilash Karavattu Venugopal, Joji Kurian Thomas, Harrys K. C. Jacob, Renu Goel, Harsh Pawar, Nandini A. Sahasrabuddhe, Venkatarangaiah Krishna, Bipin G. Nair, Marjan Gucek, Robert N. Cole…

Urine Peptidomic and Targeted Plasma Protein Analyses in the Diagnosis and Monitoring of Systemic Juvenile Idiopathic Arthritis

Systemic juvenile idiopathic arthritis is a chronic pediatric disease. The initial clinical presentation can mimic other pediatric inflammatory conditions, which often leads to significant delays in diagnosis ...

Authors: Xuefeng B. Ling, Kenneth Lau, Chetan Deshpande, Jane L. Park, Diana Milojevic, Claudia Macaubas, Chris Xiao, Viorica Lopez-Avila, John Kanegaye, Jane C. Burns, Harvey Cohen, James Schilling and Elizabeth D. Mellins

Specific Investigation of Sample Handling Effects on Protease Activities and Absolute Serum Concentrations of Various Putative Peptidome Cancer Biomarkers

In the search for novel cancer biomarkers, various proteolytically derived peptides have been proposed to exhibit cancer or cancer-type specificity. As these peptides are presumably also generated after sample...

Authors: Irene van den Broek, Rolf W. Sparidans, Jan H. M. Schellens and Jos H. Beijnen

Serum Proteome Pool Changes in Type 2 Diabetic Patients Treated with Anakinra

High glucose concentrations induce the production of IL-1β in human pancreatic beta cells leading to impaired insulin secretion, decreased cell proliferation and apoptosis. Blockade of IL-1 signalling with the...

Authors: Mette Koefoed, Claus M. Larsen, Mirjam V. Faulenbach, Allan Vaag, Jan A. Ehses, Marc Y. Donath, James Norton McGuire, Flemming Pociot and Thomas Mandrup-Poulsen

Quantitative iTRAQ-Based Proteomic Identification of Candidate Biomarkers for Diabetic Nephropathy in Plasma of Type 1 Diabetic Patients

As part of a clinical proteomics programme focused on diabetes and its complications, it was our goal to investigate the proteome of plasma in order to find improved candidate biomarkers to predict diabetic ne...

Authors: Anne Julie Overgaard, Tine E. Thingholm, Martin R. Larsen, Lise Tarnow, Peter Rossing, James N. McGuire and Flemming Pociot

Decoding the Folding Patterns of Serum Proteins: An Alternative Strategy for Cancer Biomarker Validation?

Authors: Dai J. Li and Daniel W. Chan

Proteomic Analysis of the Systemic Response to Radiographic Contrast Media

Radiographic contrast media (RCM) have numerous effects on the hemostatic system, inflammatory pathways, and vascular endothelium. Given the increasing number of high-risk patients undergoing radiographic proc...

Authors: Juan Martinez, Warren K. Laskey, Cheri Wells, Armin Foghi, Sarah Rohde, Mark Ricciardi and Charlotte Mobarak

The Quest for Renal Disease Proteomic Signatures: Where Should We Look?

Renal diseases are prevalent and important. However, despite significant strides in medicine, clinical nephrology still relies on nonspecific and inadequate markers such as serum creatinine and total urine pro...

Authors: Ana Konvalinka, James W. Scholey and Eleftherios P. Diamandis

A Targeted Proteomics Approach for Biomarker Discovery Using Bilateral Matched Nipple Aspiration Fluids

The objective of this study was to identify cancer-associated protein expression patterns in bilateral matched nipple aspiration fluids using nanoscale reciprocal Cy3/Cy5 labeling and high-content antibody mic...

Authors: Jinong Li, Junma Zhou, Bruce Trock, Theodore N. Tsangaris, Neil B. Friedman, Deanna Shapiro, Michelle Brotzman and Daniel W. Chan