16 research outputs found
Study of ischemia-reperfusion induced metabolite changes in porcine kidney model and their potential role in acute kidney injury
Acute kidney injury (AKI) is a common and serious complication in patients undergoing surgery, chronic treatment or kidney transplantation. In AKI patients, the normal functioning of kidneys are suddenly compromised leading to morbidity and mortality. It is reported that annually more than 40,000 inpatient deaths and expenditure of one billion pounds by National Health Service (NHS) in England are associated with AKI. There is a critical need to understand the pathophysiology of ischemia-reperfusion induced acute kidney injury and develop biomarkers useful for clinical management of AKI.
In the present study, mass spectrometry based metabolomics approach was employed to investigate the metabolite changes in the kidney tissues of porcine AKI model. To ischemia or reperfusion induced porcine kidneys, two step solvent extraction followed by chromatography separation of metabolites was done prior to mass spectrometric analysis. The mass spectrometric data was generated and processed using IDEOM or Progenesis CoMet software algorithms. Further multivariate and univariate statistical analysis was done using SIMCA or Metaboanalyst software to identify key metabolites associated with Ischemia or reperfusion. Comparative analysis between control, ischemia and reperfusion kidneys revealed altered levels of several metabolites and majority of them belongs to amino acid, lipid and carbohydrate metabolisms. Degradation of several glucogenic and ketogenic amino acids was observed implicating their potential role in ischemia-reperfusion induced acute kidney injury. The combination of high throughput mass spectrometry, bioinformatics and statistical tools resulted in high confidence identification of metabolites and pathways associated with AKI and provide an opportunity for clinical intervention that may help prevent acute kidney injury
Quantitative tissue proteome profile reveals neutrophil degranulation and remodeling of extracellular matrix proteins in early stage gallbladder cancer
Gallbladder cancer (GBC) is an aggressive malignancy of the gastrointestinal tract with a poor prognosis. It is important to understand the molecular processes associated with the pathogenesis of early stage GBC and identify proteins useful for diagnostic and therapeutic strategies. Here, we have carried out an iTRAQ-based quantitative proteomic analysis of tumor tissues from early stage GBC cases (stage I, n=7 and stage II, n=5) and non-tumor controls (n=6) from gallstone disease (GSD). We identified 357 differentially expressed proteins (DEPs) based on ≥ 2 unique peptides and ≥ 2 fold change with p value < 0.05. Pathway analysis using the STRING database showed, ‘neutrophil degranulation’ to be the major upregulated pathway that includes proteins such as MPO, PRTN3, S100A8, MMP9, DEFA1, AZU, and ‘ECM organization’ to be the major downregulated pathway that includes proteins such as COL14A1, COL1A2, COL6A1, COL6A2, COL6A3, BGN, DCN. Western blot and/or IHC analysis confirmed the elevated expression of MPO, PRTN3 and S100A8 in early stage of the disease. Based on the above results, we hypothesize that there is an increased neutrophil infiltration in tumor tissue and neutrophil degranulation leading to degradation of extracellular matrix (ECM) proteins promoting cancer cell invasion in the early stage GBC. Some of the proteins (MPO, MMP9, DEFA1) associated with ‘neutrophil degranulation’ showed the presence of ‘signal sequence’ suggesting their potential as circulatory markers for early detection of GBC. Overall, the study presents a protein dataset associated with early stage GBC
Study of ischemia-reperfusion induced metabolite changes in porcine kidney model and their potential role in acute kidney injury
Acute kidney injury (AKI) is a common and serious complication in patients undergoing surgery, chronic treatment or kidney transplantation. In AKI patients, the normal functioning of kidneys are suddenly compromised leading to morbidity and mortality. It is reported that annually more than 40,000 inpatient deaths and expenditure of one billion pounds by National Health Service (NHS) in England are associated with AKI. There is a critical need to understand the pathophysiology of ischemia-reperfusion induced acute kidney injury and develop biomarkers useful for clinical management of AKI.
In the present study, mass spectrometry based metabolomics approach was employed to investigate the metabolite changes in the kidney tissues of porcine AKI model. To ischemia or reperfusion induced porcine kidneys, two step solvent extraction followed by chromatography separation of metabolites was done prior to mass spectrometric analysis. The mass spectrometric data was generated and processed using IDEOM or Progenesis CoMet software algorithms. Further multivariate and univariate statistical analysis was done using SIMCA or Metaboanalyst software to identify key metabolites associated with Ischemia or reperfusion. Comparative analysis between control, ischemia and reperfusion kidneys revealed altered levels of several metabolites and majority of them belongs to amino acid, lipid and carbohydrate metabolisms. Degradation of several glucogenic and ketogenic amino acids was observed implicating their potential role in ischemia-reperfusion induced acute kidney injury. The combination of high throughput mass spectrometry, bioinformatics and statistical tools resulted in high confidence identification of metabolites and pathways associated with AKI and provide an opportunity for clinical intervention that may help prevent acute kidney injury
Transcriptomic and Proteomic Data Integration and Two-Dimensional Molecular Maps with Regulatory and Functional Linkages: Application to Cell Proliferation and Invasion Networks in Glioblastoma
Glioblastoma multiforme (GBM), the
most aggressive primary brain
tumor, is characterized by high rates of cell proliferation, migration,
and invasion. New therapeutic strategies and targets are being continuously
explored with the hope for better outcome. By overlaying transcriptomic
and proteomic data from GBM clinical tissues, we identified 317 differentially
expressed proteins to be concordant with the messenger RNAs (mRNAs).
We used these entities to generate integrated regulatory information
at the level of microRNAs (miRNAs) and their mRNA and protein targets
using prediction programs or experimentally verified miRNA target
mode in the miRWalk database. We observed 60% or even more of the
miRNA–target pairs to be consistent with experimentally observed
inverse expression of these molecules in GBM. The integrated view
of these regulatory cascades in the contexts of cell proliferation
and invasion networks revealed two-dimensional molecular interactions
with regulatory and functional linkages (miRNAs and their mRNA–protein
targets in one dimension; multiple miRNAs associated in a functional
network in the second dimension). A total of 28 of the 35 differentially
expressed concordant mRNA–protein entities represented in the
proliferation network, and 51 of the 59 such entities represented
in the invasion network, mapped to altered miRNAs from GBM and conformed
to an inverse relationship in their expression. We believe the two-dimensional
maps of gene expression changes enhance the strength of the discovery
datasets derived from omics-based studies for their applications in
GBM as well as tumors in general
Tissue proteome analysis for profiling proteins associated with lymph node metastasis in gallbladder cancer
Abstract Lymph node (LN) metastasis is the earliest sign of metastatic spread and an established predictor of poor outcome in gallbladder cancer (GBC). Patients with LN positive GBC have a significantly worse survival (median survival- 7 months) than patients with LN negative disease (median survival- ~ 23 months) in spite of standard treatment which includes extended surgery followed by chemotherapy, radiotherapy and targeted therapy. This study aims at understanding the underlying molecular processes associated with LN metastasis in GBC. Here, we used iTRAQ-based quantitative proteomic analysis using tissue cohort comprising of primary tumor of LN negative GBC (n = 3), LN positive GBC (n = 4) and non-tumor controls (Gallstone disease, n = 4), to identify proteins associated with LN metastasis. A total of 58 differentially expressed proteins (DEPs) were found to be specifically associated with LN positive GBC based on the criteria of p value ≤ 0.05, fold change ≥ 2 and unique peptides ≥ 2. These include the cytoskeleton and associated proteins such as keratin, type II cytoskeletal 7 (KRT7), keratin type I cytoskeletal 19 (KRT19), vimentin (VIM), sorcin (SRI) and nuclear proteins such as nucleophosmin Isoform 1 (NPM1), heterogeneous nuclear ribonucleoproteins A2/B1 isoform X1 (HNRNPA2B1). Some of them are reported to be involved in promoting cell invasion and metastasis. Bioinformatic analysis of the deregulated proteins in LN positive GBC using STRING database identified ‘neutrophil degranulation’ and ‘HIF1 activation’ to be among the top deregulated pathways. Western blot and IHC analysis showed a significant overexpression of KRT7 and SRI in LN positive GBC in comparison to LN negative GBC. KRT7, SRI and other proteins may be further explored for their diagnostics and therapeutic applications in LN positive GBC
Heterogeneous Nuclear Ribonucleoproteins and Their Interactors Are a Major Class of Deregulated Proteins in Anaplastic Astrocytoma: A Grade III Malignant Glioma
Anaplastic
astrocytoma is a high grade malignant glioma (WHO grade
III) of the central nervous system which arises from a low grade II
tumor and invariably progresses into lethal glioblastoma (WHO grade
IV). We have studied differentially expressed proteins from the microsomal
fraction of the clinical specimens of these tumors, using iTRAQ and
high-resolution mass spectrometry followed by immunohistochemistry
for representative proteins on tissue sections. A total of 2642 proteins
were identified, 266 of them with minimum 2 peptide signatures and
2-fold change in expression. The major groups of proteins revealed
to be differentially expressed were associated with key cellular processes
such as post transcriptional processing, protein translation, and
acute phase response signaling. A distinct inclusion among these important
proteins is 10 heterogeneous nuclear ribonucleoproteins (hnRNPs) and
their interacting partners which have regulatory functions in the
cell. hnRNP-mediated post transcriptional events are known to play
a major role in mRNA processing, stability, and distribution. Their
altered levels have also been observed by us in lower (diffused astrocytoma)
and higher (glioblastoma) grades of gliomas, and membrane localization
of hnRNPs has also been documented in the literature. hnRNPs may thus
be major factors underlying global gene expression changes observed
in glial tumors while their differential presence in the microsomal
fraction suggests yet additional and unknown roles in tumorigenesis
Heterogeneous Nuclear Ribonucleoproteins and Their Interactors Are a Major Class of Deregulated Proteins in Anaplastic Astrocytoma: A Grade III Malignant Glioma
Anaplastic
astrocytoma is a high grade malignant glioma (WHO grade
III) of the central nervous system which arises from a low grade II
tumor and invariably progresses into lethal glioblastoma (WHO grade
IV). We have studied differentially expressed proteins from the microsomal
fraction of the clinical specimens of these tumors, using iTRAQ and
high-resolution mass spectrometry followed by immunohistochemistry
for representative proteins on tissue sections. A total of 2642 proteins
were identified, 266 of them with minimum 2 peptide signatures and
2-fold change in expression. The major groups of proteins revealed
to be differentially expressed were associated with key cellular processes
such as post transcriptional processing, protein translation, and
acute phase response signaling. A distinct inclusion among these important
proteins is 10 heterogeneous nuclear ribonucleoproteins (hnRNPs) and
their interacting partners which have regulatory functions in the
cell. hnRNP-mediated post transcriptional events are known to play
a major role in mRNA processing, stability, and distribution. Their
altered levels have also been observed by us in lower (diffused astrocytoma)
and higher (glioblastoma) grades of gliomas, and membrane localization
of hnRNPs has also been documented in the literature. hnRNPs may thus
be major factors underlying global gene expression changes observed
in glial tumors while their differential presence in the microsomal
fraction suggests yet additional and unknown roles in tumorigenesis
Heterogeneous Nuclear Ribonucleoproteins and Their Interactors Are a Major Class of Deregulated Proteins in Anaplastic Astrocytoma: A Grade III Malignant Glioma
Anaplastic
astrocytoma is a high grade malignant glioma (WHO grade
III) of the central nervous system which arises from a low grade II
tumor and invariably progresses into lethal glioblastoma (WHO grade
IV). We have studied differentially expressed proteins from the microsomal
fraction of the clinical specimens of these tumors, using iTRAQ and
high-resolution mass spectrometry followed by immunohistochemistry
for representative proteins on tissue sections. A total of 2642 proteins
were identified, 266 of them with minimum 2 peptide signatures and
2-fold change in expression. The major groups of proteins revealed
to be differentially expressed were associated with key cellular processes
such as post transcriptional processing, protein translation, and
acute phase response signaling. A distinct inclusion among these important
proteins is 10 heterogeneous nuclear ribonucleoproteins (hnRNPs) and
their interacting partners which have regulatory functions in the
cell. hnRNP-mediated post transcriptional events are known to play
a major role in mRNA processing, stability, and distribution. Their
altered levels have also been observed by us in lower (diffused astrocytoma)
and higher (glioblastoma) grades of gliomas, and membrane localization
of hnRNPs has also been documented in the literature. hnRNPs may thus
be major factors underlying global gene expression changes observed
in glial tumors while their differential presence in the microsomal
fraction suggests yet additional and unknown roles in tumorigenesis