Mass Spectrometry based identification of site-specific proteomic alterations and potential pathways underlying the pathophysiology of schizophrenia.

BACKGROUND: Schizophrenia (SZ) is a complex multifactorial disorder that affects 1% of the population worldwide with no available effective treatment. Although proteomic alterations are reported in SZ however proteomic expression aberrations among different brain regions are not fully determined. Therefore, the present study aimed spatial differential protein expression profiling of three distinct regions of SZ brain and identification of associated affected biological pathways in SZ progression. METHODS AND RESULTS: Comparative protein expression profiling of three distinct autopsied human brain regions (i.e., substantia nigra, hippocampus and prefrontal cortex) of SZ was performed with respective healthy controls. Using two-dimensional electrophoresis (2DE)-based nano liquid chromatography tandem mass spectrometry (Nano-LC MS /MS) analysis, 1443 proteins were identified out of which 58 connote to be significantly dysregulated, representing 26 of substantia nigra,14 of hippocampus and 18 of prefrontal cortex. The 58 differentially expressed proteins were further analyzed using Ingenuity pathway analysis (IPA). The IPA analysis provided protein-protein interaction networks of several proteins including nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kb), extracellular signal regulated kinases 1/2 (ERK1/2), alpha serine / Threonine-protein kinase (AKT1), cellular tumor antigen p53 (TP53) and amyloid precursor protein (APP), holding prime positions in networks and interacts with most of the identified proteins and their closely interacting partners. CONCLUSION: These findings provide conceptual insights of novel SZ related pathways and the cross talk of co and contra regulated proteins. This spatial proteomic analysis will further broaden the conceptual framework for schizophrenia research in future.

Characterization of functional protein complexes from Alzheimer's disease and healthy brain by mass spectrometry-based proteome analysis.

Alzheimer's disease (AD) is a complex neurodegenerative disorder with impaired protein activities. Proteins in the form of complexes have a ubiquitous role in diverse range of cellular functions. The key challenge is to identify novel disease associated protein complexes and their potential role in the progression of AD pathology. Protein complexes were obtained from AD brain prefrontal cortex and age matched controls by Blue Native-Polyacrylamide Gel Electrophoresis. A proteomic analysis was performed using second dimension SDS-PAGE followed by nano LC-MS/MS. Differentially expressed proteins were mapped to existing biological networks by Ingenuity Pathway Analysis (IPA). A total of 13 protein complexes with their interacting proteins were resolved on SDS-PAGE. We identified 34 protein spots and found significant abundance difference between the two experimental samples. IPA analysis revealed degeneration of neurons and cell death as a major consequence of protein dysregulation. Furthermore, focused network analysis suggested an integrated regulation of the identified proteins through APP and MAPT dependent mechanisms. The interacting differentially expressed proteins in AD were found to be part of concomitant signaling cascades terminating in neuronal cell death. The identified protein networks and pathways warrant further research to study their actual contribution to AD pathology.

Author Correction: Association of Cyclin Dependent Kinase 10 and Transcription Factor 2 during Human Corneal Epithelial Wound Healing in vitro model.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Higher DNA methylation of ABO gene promoter is associated with acute myocardial infarction in a hospital-based population in Karachi.

OBJECTIVE: To find out if there is any relationship of methylation status of ABO gene promoter with the risk of acute myocardial infarction (AMI) in a hospital-based Pakistani population in Karachi, Pakistan. METHODS: A case control study comprising of 39 adult AMI patients (both males and females; age range 30-70 years) and 39 normal healthy controls (both males and females and similar age range) nested in a large study (to see the relationship of ABO genotypes with AMI) was designed to investigate the methylation status of ABO gene promoter and its association with AMI. The study was carried out at the Aga Khan University, Karachi during July 2018 to June 2019. DNA isolated from samples of AMI patients and normal healthy controls were converted into bisulphite DNA using a kit method. Methylation specific polymerase chain reaction was carried out to determine the methylation status of ABO gene promoter in both cases and controls. Logistic regression was used to find out any association between increased methylation status of ABO gene promoter and risk of AMI. RESULTS: A significantly higher percentage of DNA methylation of the ABO gene promoter was observed in AMI patients as compared to normal healthy controls (82.1% vs. 35.9%; p value <0.001). This higher methylation status of ABO gene promoter was associated with AMI and the odds of AMI in this population were more than 6-fold in subjects with methylated gene promoter compared to those with unmethylated gene promoter after adjusting with age and waist circumference [AOR (95% CI) = 6.27 (1.76-22.3); p value = 0.005]. CONCLUSION: The ABO gene promoter's hypermethylation appears to be increasing the risk of AMI in a hospital-based Pakistani population in Karachi, Pakistan.

Association of Cyclin Dependent Kinase 10 and Transcription Factor 2 during Human Corneal Epithelial Wound Healing in vitro model.

Proper wound healing is dynamic in order to maintain the corneal integrity and transparency. Impaired or delayed corneal epithelial wound healing is one of the most frequently observed ocular defect and difficult to treat. Cyclin dependen kinase (cdk), a known cell cycle regulator, required for proper proliferating and migration of cell. We therefore investigated the role of cell cycle regulator cdk10, member of cdk family and its functional association with transcriptional factor (ETS2) at active phase of corneal epithelial cell migration. Our data showed that cdk10 was associated with ETS2, while its expression was upregulated at the active phase (18 hours) of cell migration and gradually decrease as the wound was completely closed. Topical treatment with anti-cdk10 and ETS2 antibodies delayed the wound closure time at higest concentration (10 µg/ml) compared to control. Further, our results also showed increased mRNA expression of cdk10 and ETS2 at active phase of migration at approximately 2 fold. Collectively, our data reveals that cdk10 and ETS2 efficiently involved during corneal wound healing. Further studies are warranted to better understand the mechanism and safety of topical cdk10 and ETS2 proteins in corneal epithelial wound-healing and its potential role for human disease treatment.

Bax, Bcl-2, and Bax/Bcl-2 as prognostic markers in acute myeloid leukemia: are we ready for Bcl-2-directed therapy?

PURPOSE: Many anticancer drugs induce apoptosis in malignant cells, and resistance to apoptosis could lead to suboptimal or no therapeutic benefit. Two cytoplasmic proteins, B-cell lymphoma protein 2 (Bcl-2)-associated X (Bax) and Bcl-2, act as a promoter and an inhibitor of apoptosis, respectively. Both Bax and Bcl-2 as well as their ratio have been regarded as prognostic markers in various cancers. However, conflicting results have been reported. A clear understanding of apoptosis has also become crucial due to reports about anti-Bcl-2 chemotherapy. We explored the relationship of Bax and Bcl-2 gene expression and their ratio with the therapeutic response in acute myeloid leukemia (AML) patients. PATIENTS AND METHODS: Bone marrow and/or blood samples from 90 AML patients treated with cytarabine and daunorubicin were included. Expression of Bax and Bcl-2 was determined through real-time polymerase chain reaction by using ΔΔCt method of relative expression. RESULTS: Bax and Bcl-2 expression among marrow and blood samples correlated with each other (rs=0.5, p<0.01). Although bone marrow expression of Bax and Bcl-2 tended to remain higher among responders (median 1.01 and 0.29, respectively) as compared to non-responders (median 0.66 and 0.24, respectively), the difference failed to reach statistical significance (U=784.5 and 733; p=0.68 and 0.28, respectively). Conversely, Bax/Bcl-2 ratio was higher among poor responders (median 3.07 vs 1.78), though again failed to reach statistical significance (U=698.5, p=0.07). CONCLUSION: Expression of Bax and Bcl-2 does not differ significantly among AML patients treated with cytarabine and daunorubicin in terms of remission, relapse, resistance, overall survival, and disease-free survival, thus questioning the utility of emerging anti-Bcl-2 therapy.

Clinical presentation of acute myeloid leukaemia - A decade-long institutional follow-up.

OBJECTIVE: To analyse a decade-long pattern of clinical presentation of acute myeloid leukaemia patients and compare it with contemporary data. METHODS: The retrospective cohort study was conducted at the National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, and comprised of medical record of acute myeloid leukaemia patients from March 2006 to October 2016. Data noted age at presentation, gender, medical history, physical examination, blood and bone marrow investigations such as, haemoglobin levels, blood cell count myeloperoxidase activity, periodic acid-Schiff and reticulin staining as well as final diagnosis. Comparison, where possible, was done with contemporary literature. SPSS 19 was used for data analysis. RESULTS: Of the 626 subjects, 248(39.6%) were females and 378(60.4%) males. The overall mean age was 35.3±17.1 years. The most common age group was 15-40 years with 354(56.5%) patients. The most common subtype was acute myeloid leukaemia with maturation 183(33.6%). Myeloperoxidase activity was positive for the majority of the acute myeloid leukaemia patients. Periodic acid-Schiff test, done on only selected patients, was mostly negative. Reticulin staining was positive for 113(65.3%) patients. The most common presenting complaints were fever 266(71.9%) and weakness 168(45.4%). Mean haemoglobin and red blood cell count were 8.3 ± 2.4 g/dL and 2.9 ± 1.2 1012/L, respectively. CONCLUSIONS: Acute myeloid leukaemia was found to be a highly variable disease that presented with non-specific signs and symptoms.

Recent advances in diagnostic and prognostic aspects of acute myeloid leukaemia.

Acute myeloid leukaemia (AML) is a group of haematological malignant disorders. Although not a new disease, many studies have been conducted to explore AML etiology, pathogenesis and prognosis at molecular level over the past two decades. A meticulous and continuous review of the available literature is still required to contemplate currently discovered information. We searched Google Scholar and PubMed by using different key word such as: updates in diagnostic criteria of AML, WHO classification of AML, new prognostic factors and risk stratification of AML. Mostly articles are referred from international sources published during last five years. Some older articles were only used when pivotal information required could not be surpassed by newer articles. Initially 50 relevant articles were included which were subsequently reduced to 36 by excluding articles with similar information. In this review an attempt is made to approach the subject in the light of currently available literature.

Differential expression of proteins in brain regions of Alzheimer's disease patients.

Alzheimer's disease (AD), a progressive neurodegenerative disorder and the most common form of dementia and cognitive impairment is usually characterized by neuritic amyloid plaques, cerebrovascular amyloidosis and neurofibrillary tangles. In order to find out the pathological protein expression, a quantitative proteome analysis of AD hippocampus, substantia nigra and cortex was performed and the extent of protein expression variation not only in contrast to age-matched controls but also among the understudied regions was analyzed. Expression alterations of 48 proteins were observed in each region along with significant co/contra regulation of malate dehydrogenase, lactate dehydrogenase B chain, aconitate hydratase, protein NipSnap homolog 2, actin cytoplasmic 1, creatine kinase U-type and glyceraldehyde-3-phosphate dehydrogenase. These differentially expressed proteins are mainly involved in energy metabolism, cytoskeleton integration, apoptosis and several other potent cellular/molecular processes. Interaction association network analysis further confirms the close interacting relationship between the co/contra regulated differentially expressed proteins among all the three regions. Elucidation of co/contra regulation of differentially expressed proteins will be helpful to understand disease progression and functional alterations associated with AD.

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

BACKGROUND: 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 alteration during the progression from cirrhosis to carcinoma. Although alterations/ post translational modifications in protein expression have been extensively quantified, complementary analysis of nuclear membrane proteome changes have been limited. Deciphering the molecular mechanism that differentiate between normal and disease state may lead to identification of biomarkers for carcinoma. RESULTS: Many proteins displayed differential expression when nuclear membrane proteome of hepatocellular carcinoma (HCC), fibrotic liver, and HepG2 cell line were assessed using 2-DE and ESI-Q-TOF MS/MS. From the down regulated set in HCC, we have identified for the first time a 15 KDa cytochrome b5A (CYB5A), ATP synthase subunit delta (ATPD) and Hemoglobin subunit beta (HBB) with 11, 5 and 22 peptide matches respectively. Furthermore, nitrosylation studies with S-nitrosocysteine followed by immunoblotting with anti SNO-cysteine demonstrated a novel and biologically relevant post translational modification of thiols of CYB5A in HCC specimens only. Immunofluorescence images demonstrated increased protein S-nitrosylation signals in the tumor cells and fibrotic region of HCC tissues. The two other nuclear membrane proteins which were only found to be nitrosylated in case of HCC were up regulated ATP synthase subunit beta (ATPB) and down regulated HBB. The decrease in expression of CYB5A in HCC suggests their possible role in disease progression. Further insight of the functional association of the identified proteins was obtained through KEGG/ REACTOME pathway analysis databases. String 8.3 interaction network shows strong interactions with proteins at high confidence score, which is helpful in characterization of functional abnormalities that may be a causative factor of liver pathology. CONCLUSION: These findings may have broader implications for understanding the mechanism of development of carcinoma. However, large scale studies will be required for further verification of their critical role in development and progression of HCC.

Phosphoproteome profiling of substantia nigra and cortex regions of Alzheimer's disease patients.

Alzheimer's disease (AD) is the most common form of dementia and cognitive impairment usually characterized by widespread neurodegeneration throughout the association cortex, limbic system and hippocampus. Aberrant protein phosphorylation is a defining pathological hallmark of AD and implicated in the dysregulation of major cellular processes through highly dynamic and complex signaling pathways. Here in, we demonstrate 81 proteins, of 600 spots selected, unambiguously identified as phosphorylated, providing a partial phosphoproteome profile of AD substantia nigra and cortex and respective control brain regions. More importantly, abnormal phosphorylation signal intensity of nine physiologically important proteins observed can profoundly affect cell metabolism, signal transduction, cytoskeleton integration, and synaptic function and accounts for biological and morphological alterations. Our studies employed two-dimensional gel electrophoresis for protein separation, Pro-Q(®) Diamond phosphoprotein staining and electrospray ionization quadrupole time of flight tandem MS for protein identification. NetPhosk 1.0 is used for the confirmation of protein modification status as well known/putative phosphoproteins. A further insight into the links among the identified phosphoproteins and functional roles STRING 8.3, KEGG and REACTOME pathway databases were applied. The present quantitative phosphoproteomic analysis can be supportive in establishing a broad database of potential protein targets of abnormal phosphorylation in AD brain.

Albumin precursor and Hsp70 modulate corneal wound healing in an organ culture model.

In order to investigate the role of albumin precursor and Hsp70 in corneal wound healing, we have analyzed the distribution of these proteins in wounded and non-wounded corneas of rabbits and the effects of topical applications of anti-albumin precursor and anti-Hsp70 antibodies on wound healing. Anti-albumin precursor and anti-Hsp70 antibodies were topically applied in healing corneal epithelium of rabbit eyes in organ culture. Corneas were allowed to heal in vitro for up to 120 h in serum-free medium with 5 and 10 µg/ml or without (migrating control) anti-albumin precursor/ or anti-Hsp70 antibodies. Fibronectin (Fb) (5 µg/ml) was used as a positive control. Immunofluorescence labelling was used to detect proteins in corneal epithelium at various time intervals following an epithelial defect. Delay in wound healing (p<0.005) was observed with 10 µg/ml anti-albumin antibody labelling. A similar pattern was observed when anti-fibronectin antibody (5 µg/ml) alone and in combination with anti-albumin (10 µg/ml) was ectopically added with wound closure occurring at 120 h. However with anti-Hsp70 antibody (5 µg/ml) slightly delayed (p<0.005) wound closure was observed at 96 h and considerable retardation >120 h with 10 µg/ml. Additionally, immunofluoresence showed a strong co-localization of Hsp70 and albumin precursor during the active phase of wound healing. The presence of albumin precursor and Hsp70 in the epithelial compartment of the cornea indicates a role for these proteins in modulating cell behavior such as epithelial growth, adhesion or regeneration, thus contributing to corneal epithelial wound healing.

The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate-washed membrane standard.

The Asia Oceania Human Proteome Organisation (AOHUPO) has embarked on a Membrane Proteomics Initiative with goals of systematic comparison of strategies for analysis of membrane proteomes and discovery of membrane proteins. This multilaboratory project is based on the analysis of a subcellular fraction from mouse liver that contains endoplasmic reticulum and other organelles. In this study, we present the strategy used for the preparation and initial characterization of the membrane sample, including validation that the carbonate-washing step enriches for integral and lipid-anchored membrane proteins. Analysis of 17 independent data sets from five types of proteomic workflows is in progress.

Changes in albumin precursor and heat shock protein 70 expression and their potential role in response to corneal epithelial wound repair.

Many proteins displayed differential expression (either up- or down-regulation) when proteome of migrating and non-migrating epithelium was assessed using 2-DE and ESI-Q-TOF MS/MS. From the up-regulated set, we have identified for the first time a 69-kDa albumin precursor protein with four peptides sequences and 70-kDa heat shock protein (hsp70) with one peptide in the active phase of cell migration (48 h) during the healing process. Western blot analysis was used to further characterize these proteins at different phases (24, 48 and 72 h) of healing. An increase in the mRNA expression (measured using RT-PCR) in the active migration phase (48 h) for albumin precursor and hsp70 was also observed. Furthermore, co-immunoprecipitation studies with anti-albumin precursor and anti-hsp70 antibodies, followed by immunoblotting with anti-fibronectin antibody demonstrated a novel and biologically relevant interaction between albumin precursor protein and fibronectin in corneal epithelial wound healing but not with hsp70. The increased gene and protein expression of albumin and hsp70 during the active phase of cell migration (48 h) in the corneal epithelium suggests their possible role in corneal wound healing. These findings may have broader implications for developing therapeutic strategies for treating wound healing disorders.

Clozapine induced neutrophil cytotoxicity in rats.

OBJECTIVE: The study was carried out to understand the pathogenesis of hematological dyscrasias and cytotoxicity following administration of both purified and commercially available form of Clozapine in an animal model. METHODS: The Albino Sprague Dawley rats (n=30) with an average weight of 180g were taken and divided into three groups. Haematological parameters including haemoglobin, haematocrit, RBC and differential counts, absolute indices, Red cell Distribution Width (RDW) and morphological features of RBCs by peripheral blood smear were performed by standard laboratory methods. Additionally Serum Iron Concentration (SIC), Total Iron Binding Capacity (TIBC) (Roche Ltd.) and the serum ferritin level (Randox Ltd.) were also determined in each group. All statistical analysis was performed using graph pad prism. RESULTS: Clozapine induced neutrophil toxicity was manifested in both experimental groups, with condensation and subsequent breakdown of chromatin material. CONCLUSION: Our data, raised concerns about haematological safety and the potential mechanisms of neutrophil cytotoxicity related to the use of this drug.

Hemoglobinopathies among five major ethnic groups in Karachi, Pakistan.

A brief survey of abnormal hemoglobin variants among the major ethnic groups of Karachi was conducted; 202,600 subjects were studied. Patients with low hemoglobin (Hb), low mean cell volume (MCV) and mean cell hemoglobin (MCH) including anemia, microcytosis, hypochromic hemolysis and target cells, were refered for the identification of hemoglobinopathy by molecular methods. Population screening showed that 60% had iron-deficiency anemia and 40% had hemolytic anemia, of which 20.6% was due to beta-thalassemia major, 13% beta-thalassemia trait, 5.1% sickle cell disease, 0.76% hemoglobin D Punjab (HbD Punjab), 0.32% hemoglobin C (HbC), and 0.22% hereditary persistence of fetal hemoglobin (HPFH).