Prem Gurnani - Academia.edu (original) (raw)

Papers by Prem Gurnani

Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06), 2006

Abstract— High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) ... more Abstract— High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry has shown promise as a screening tool for detecting discriminatory protein patterns. The major computational obstacle in analyzing MALDI-TOF data is a ...

Journal of Bioinformatics and Computational Biology, 2006

Ovarian cancer recurs at the rate of 75% within a few months or several years later after therapy... more Ovarian cancer recurs at the rate of 75% within a few months or several years later after therapy. Early recurrence, though responding better to treatment, is difficult to detect. Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry has showed the potential to accurately identify disease biomarkers to help early diagnosis. A major challenge in the interpretation of SELDI-TOF data is the high dimensionality of the feature space. To tackle this problem, we have developed a multi-step data processing method composed of t-test, binning and backward feature selection. A new algorithm, support vector machine-Markov blanket/recursive feature elimination (SVM-MB/RFE) is presented for the backward feature selection. This method is an integration of minimum weight feature elimination by SVM-RFE and information theory based redundant/irrelevant feature removal by Markov Blanket. Subsequently, SVM was used for classification. We conducted the biomarker selec...

PLOS ONE, 2015

Klotho transgenic mice exhibit resistance to oxidative stress as measured by their urinal levels ... more Klotho transgenic mice exhibit resistance to oxidative stress as measured by their urinal levels of 8-hydroxy-2-deoxyguanosine, albeit this anti-oxidant defense mechanism has not been locally investigated in the brain. Here, we tested the hypothesis that the reactive oxygen species (ROS)-sensitive apoptosis signal-regulating kinase 1 (ASK1)/p38 MAPK pathway regulates stress levels in the brain of these mice and showed that: 1) the ratio of free ASK1 to thioredoxin (Trx)-bound ASK1 is relatively lower in the transgenic brain whereas the reverse is true for the Klotho knockout mice; 2) the reduced p38 activation level in the transgene corresponds to higher level of ASK1-bound Trx, while the KO mice showed elevated p38 activation and lower level of-bound Trx; and 3) that 14-3-3ζ is hyper phosphorylated (Ser-58) in the transgene which correlated with increased monomer forms. In addition, we evaluated the in vivo robustness of the protection by challenging the brains of Klotho transgenic mice with a neurotoxin, MPTP and analyzed for residual neuron numbers and integrity in the substantia nigra pars compacta. Our results show that Klotho overexpression significantly protects dopaminergic neurons against oxidative damage, partly by modulating p38 MAPK activation level. Our data highlight the importance of ASK1/p38 MAPK pathway in the brain and identify Klotho as a possible anti-oxidant effector.

2007 IEEE 7th International Symposium on BioInformatics and BioEngineering, 2007

High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spect... more High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry has shown promise as a screening tool for detecting discriminatory peptide/protein patterns. The major computational obstacle in analyzing MALDI-TOF data is the large number of mass/charge peaks (a.k.a. features, data points). With such a huge number of data points for a single sample, efficient feature selection is critical for unequivocal protein pattern discovery. In this paper, we propose a feature selection method and a new biclassification algorithm based on error-correcting output coding (ECOC) in multiclass problems. Our scheme is applied to the analysis of Alzheimer's disease (AD) data. To validate the performance of the proposed algorithm, experiments are performed in comparison with other methods. We show that our proposed framework outperforms not only the standard ECOC framework but also other algorithms.

European Urology Supplements - EUR UROL SUPPL, 2007

Computer Methods and Programs in Biomedicine, 2009

Prostate-specific antigen (PSA) is the most widely used serum biomarker for early detection of pr... more Prostate-specific antigen (PSA) is the most widely used serum biomarker for early detection of prostate cancer (PCA). Nevertheless, PSA level can be falsely elevated due to prostatic enlargement, inflammation or infection, which limits the PSA test specificity. The objective of this study is to use a machine learning approach for the analysis of mass spectrometry data to discover more reliable biomarkers that distinguish PCA from benign specimens. Serum samples from 179 prostate cancer patients and 74 benign patients were analyzed. These samples were processed using ProXPRESSION Biomarker Enrichment Kits (PerkinElmer). Mass spectra were acquired using a prOTOF 2000 matrix-assisted laser desorption/ionization orthogonal time-of-flight (MALDI-O-TOF) mass spectrometer. In this study, we search for potential biomarkers using our feature selection method, the Extended Markov Blanket (EMB). From the new marker selection algorithm, a panel of 26 peaks achieved an accuracy of 80.7%, a sensitivity of 83.5%, a specificity of 74.4%, a positive predictive value (PPV) of 87.9%, and a negative predictive value (NPV) of 68.2%. On the other hand, when PSA alone was used (with a cutoff of 4.0ng/ml), a sensitivity of 66.7%, a specificity of 53.6%, a PPV of 73.5%, and a NPV of 45.4% were obtained.

Methods in molecular biology (Clifton, N.J.), 2007

Reverse-phase protein microarrays (RPPMAs) enable heterogeneous mixtures of proteins from cellula... more Reverse-phase protein microarrays (RPPMAs) enable heterogeneous mixtures of proteins from cellular extracts to be directly spotted onto a substrate (such as a protein biochip) in minute volumes (nanoliter-to-picoliter volumes). The protein spots can then be probed with primary antibodies to detect important posttranslational modifications such as phosphorylations that are important for protein activation and the regulation of cellular signaling. Previously, we relied on chromogenic signals for detection. However, quantum dots (QDs) represent a more versatile detection system because the signals can be time averaged and the narrow-emission spectra enable multiple protein targets to be quantified within the same spot. We found that commercially available pegylated, streptavidin-conjugated QDs are effective detection agents, with low-background binding to heterogeneous protein mixtures. This type of test, the RPPMAs, is at the forefront of an exciting, clinically-oriented discipline th...

Biomedicine & Pharmacotherapy, 2007

For Alzheimer&amp... more For Alzheimer's disease (AD), the most common neurodegenerative disease, there is no simple, cost-effective biomarker for disease identification. Using novel mass spectrometry (MS)-based techniques, and analysis of the albumin-enriched low molecular weight proteome, minute amounts of human serum were analyzed for the measurement of thousands of peptides and proteins in parallel. The mass spectrograms were then evaluated with a novel computer algorithm to identify spectral peaks that discriminate between samples from patients with and without AD. There are four peaks that distinguish AD from control subjects and AD subjects from those with Parkinson's disease (PD). Additionally, after analyzing data from a recently published study of AD and control subjects, we found three discriminating peaks in common with the four from our patient serum samples. The identification of these peptides/proteins, and their direct measurement in patient serum, may allow the development of a simple, cost-effective test for AD.

American Journal of Obstetrics and Gynecology, 2007

Journal of Biological Chemistry, 2005

klotho is an aging suppressor gene and extends life span when overexpressed in mice. Klotho prote... more klotho is an aging suppressor gene and extends life span when overexpressed in mice. Klotho protein was recently demonstrated to function as a hormone that inhibits insulin/insulin-like growth factor-1 (IGF-1) signaling. Here we show that Klotho protein increases resistance to oxidative stress at the cellular and organismal level in mammals. Klotho protein activates the FoxO forkhead transcription factors that are negatively regulated by insulin/IGF-1 signaling, thereby inducing expression of manganese superoxide dismutase. This in turn facilitates removal of reactive oxygen species and confers oxidative stress resistance. Thus, Klotho-induced inhibition of insulin/IGF-1 signaling is associated with increased resistance to oxidative stress, which potentially contributes to the anti-aging properties of klotho.

Alzheimer's & Dementia, 2005

microglia in the brain. In AD, microglia show also increased expression of the M-CSF receptor (M-... more microglia in the brain. In AD, microglia show also increased expression of the M-CSF receptor (M-CSFR). We previously showed that increasing expression of the M-CSFR on cultured microglia dramatically upregulates microglia M-CSF and IL-1␣ expression. Objectives: To determine if knockdown of microglial interleukin-1␣ and M-CSF expression affects NMDA-induced neurotoxicity in a co-culture system. Methods: We used a co-culture model consisting of microglia overexpressing the M-CSFR and hippocampal organotypic cultures treated with the neurotoxin NMDA. To test the importance of microglial IL-1␣ and M-CSF on neuronal survival, we used an shRNA gene-targeted approach in which we selectively and without toxicity deleted microglial IL-1␣ or M-CSF expression prior to co-culture assembly. Transfections were performed with the hairpin RNA expression plasmid pGSU6-GFP-shRNA. To quantify neuronal injury, we used propidium iodide as well as FluoroJade staining. Results: We found that when microglia overexpressing the M-CSFR were cocultured with organotypic slices, there was complete protection of neurons from NMDA-induced injury. However, after knockdown of either microglial IL-1␣ or M-CSF, neuroprotection was abolished. Using TaqMan real-time RT-PCR, we confirmed that the shRNA constructs resulted in a Ͼ75% knockdown of cytokine expression. Both M-CSF and IL-1␣ were necessary for microglial proliferation, but only IL-1␣ removal also suppressed chemotactic migration of microglia toward the NMDA-injured organotypic culture. Conclusions: These results demonstrate that IL-1␣ and M-CSF are essential for M-CSFR-induced microglial neuroprotection in a microglial-organotypic hippocampal co-culture system. In AD, increased IL-1␣ and M-CSF expression by M-CSFR-activated microglia could actually serve to protect, rather than harm neurons. It may be that some inflammatory factors expressed early in AD could be beneficial, so that suppressing inflammation might accelerate rather than prevent disease progression. (Supported by an Alzheimer's Association New Investigator Award to O.M. and NIH award MH57833).

Clinical Chemistry, 2007

Background: Most cases of ovarian cancer are detected at later stages when the 5-year survival is... more Background: Most cases of ovarian cancer are detected at later stages when the 5-year survival is ϳ15%, but 5-year survival approaches 90% when the cancer is detected early (stage I). To use mass spectrometry (MS) of serum proteins for early detection, a seamless workflow is needed that provides an opportunity for rapid profiling along with direct identification of the underpinning ions. Methods: We used carrier protein-bound affinity enrichment of serum samples directly coupled with MALDI orthagonal TOF MS profiling to rapidly search for potential ion signatures that contained discriminatory power. These ions were subsequently directly subjected to tandem MS for sequence identification. Results: We discovered several biomarker panels that enabled differentiation of stage I ovarian cancer from unaffected (age-matched) patients with no evidence of ovarian cancer, with positive results in >93% of samples from patients with disease-negative results and in 97% of disease-free controls. The carrier protein-based approach identified additional protein fragments, many from low-abundance proteins or proteins not previously seen in serum. Conclusions: This workflow system using a highly reproducible, high-resolution MALDI-TOF platform enables rapid enrichment and profiling of large numbers of clinical samples for discovery of ion signatures and integration of direct sequencing and identification of the ions without need for additional offline, timeconsuming purification strategies.

Biomed Pharmacotherapy, 2007

For Alzheimer&amp... more For Alzheimer's disease (AD), the most common neurodegenerative disease, there is no simple, cost-effective biomarker for disease identification. Using novel mass spectrometry (MS)-based techniques, and analysis of the albumin-enriched low molecular weight proteome, minute amounts of human serum were analyzed for the measurement of thousands of peptides and proteins in parallel. The mass spectrograms were then evaluated with a novel computer algorithm to identify spectral peaks that discriminate between samples from patients with and without AD. There are four peaks that distinguish AD from control subjects and AD subjects from those with Parkinson's disease (PD). Additionally, after analyzing data from a recently published study of AD and control subjects, we found three discriminating peaks in common with the four from our patient serum samples. The identification of these peptides/proteins, and their direct measurement in patient serum, may allow the development of a simple, cost-effective test for AD.

Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06), 2006

Abstract— High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) ... more Abstract— High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry has shown promise as a screening tool for detecting discriminatory protein patterns. The major computational obstacle in analyzing MALDI-TOF data is a ...

Bioconjugate Chemistry, 2005

Protein microarray technologies provide a means of investigating the proteomic content of clinica... more Protein microarray technologies provide a means of investigating the proteomic content of clinical biopsy specimens in order to determine the relative activity of key nodes within cellular signaling pathways. A particular kind of protein microarray, the reverse-phase microarray, is being evaluated in clinical trials because of its potential to utilize limited amounts of cellular material obtained through biopsy. Using this approach, cellular lysates are arrayed in dilution curves on nitrocellulose substrates for subsequent probing with antibodies. To improve the sensitivity and utility of reverse-phase microarrays, we tested whether a new reporter technology as well as a new detection instrument could enhance microarray performance. We describe the use of an inorganic fluorescent nanoparticle conjugated to streptavidin, Qdot 655 Sav, in a reverse-phase protein microarray format for signal pathway profiling. Moreover, a pegylated form of this bioconjugate, Qdot 655 Sav, is found to have superior detection characteristics in assays performed on cellular protein extracts over the nonpegylated form of the bioconjugate. Hyperspectral imaging of the quantum dot microarray enabled unamplified detection of signaling proteins within defined cellular lysates, which indicates that this approach may be amenable to multiplexed, high-throughput reverse-phase protein microarrays in which numerous analytes are measured in parallel within a single spot.

Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry data ha... more Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry data has been increasingly analyzed for identifying biomarkers to help early detection of the disease. Ovarian cancer commonly recurs at the rate of 75% within a few months or several years later after standard treatment. Since recurrent ovarian cancer is relatively difficult to be diagnosed and small tumors generally respond better to treatment, new methods for the detection of early relapse in ovarian cancer are urgently needed. Here, we propose a new algorithm SVM-MB/RFE (SVM-Markov Blanket/Recursive Feature Elimination) based on SVM-RFE, which identifies biomarkers for predicting the early recurrence of ovarian cancer. In this approach, we first apply t-test for feature pruning and then binning using 5-fold cross validation. Finally, 58 peaks are obtained from 27,000 of the raw data. Such dramatically reduced features relax the computational burden in the next step of our algorithm. We compare the performance of three feature selection algorithms and demonstrate that SVM-MB/RFE outperforms other methods.

Journal of Bioinformatics and Computational Biology, Dec 1, 2006

Ovarian cancer recurs at the rate of 75% within a few months or several years later after therapy... more Ovarian cancer recurs at the rate of 75% within a few months or several years later after therapy. Early recurrence, though responding better to treatment, is difficult to detect. Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry has showed the potential to accurately identify disease biomarkers to help early diagnosis. A major challenge in the interpretation of SELDI-TOF data is the high dimensionality of the feature space. To tackle this problem, we have developed a multi-step data processing method composed of t-test, binning and backward feature selection. A new algorithm, support vector machine-Markov blanket/recursive feature elimination (SVM-MB/RFE) is presented for the backward feature selection. This method is an integration of minimum weight feature elimination by SVM-RFE and information theory based redundant/irrelevant feature removal by Markov Blanket. Subsequently, SVM was used for classification. We conducted the biomarker selection algorithm on 113 serum samples to identify early relapse from ovarian cancer patients after primary therapy. To validate the performance of the proposed algorithm, experiments were carried out in comparison with several other feature selection and classification algorithms.

Data Revues 07533322 00610007 07001138, Mar 21, 2008

Amer J Obstet Gynecol, 2007

Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06), 2006

Abstract— High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) ... more Abstract— High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry has shown promise as a screening tool for detecting discriminatory protein patterns. The major computational obstacle in analyzing MALDI-TOF data is a ...

Journal of Bioinformatics and Computational Biology, 2006

Ovarian cancer recurs at the rate of 75% within a few months or several years later after therapy... more Ovarian cancer recurs at the rate of 75% within a few months or several years later after therapy. Early recurrence, though responding better to treatment, is difficult to detect. Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry has showed the potential to accurately identify disease biomarkers to help early diagnosis. A major challenge in the interpretation of SELDI-TOF data is the high dimensionality of the feature space. To tackle this problem, we have developed a multi-step data processing method composed of t-test, binning and backward feature selection. A new algorithm, support vector machine-Markov blanket/recursive feature elimination (SVM-MB/RFE) is presented for the backward feature selection. This method is an integration of minimum weight feature elimination by SVM-RFE and information theory based redundant/irrelevant feature removal by Markov Blanket. Subsequently, SVM was used for classification. We conducted the biomarker selec...

PLOS ONE, 2015

Klotho transgenic mice exhibit resistance to oxidative stress as measured by their urinal levels ... more Klotho transgenic mice exhibit resistance to oxidative stress as measured by their urinal levels of 8-hydroxy-2-deoxyguanosine, albeit this anti-oxidant defense mechanism has not been locally investigated in the brain. Here, we tested the hypothesis that the reactive oxygen species (ROS)-sensitive apoptosis signal-regulating kinase 1 (ASK1)/p38 MAPK pathway regulates stress levels in the brain of these mice and showed that: 1) the ratio of free ASK1 to thioredoxin (Trx)-bound ASK1 is relatively lower in the transgenic brain whereas the reverse is true for the Klotho knockout mice; 2) the reduced p38 activation level in the transgene corresponds to higher level of ASK1-bound Trx, while the KO mice showed elevated p38 activation and lower level of-bound Trx; and 3) that 14-3-3ζ is hyper phosphorylated (Ser-58) in the transgene which correlated with increased monomer forms. In addition, we evaluated the in vivo robustness of the protection by challenging the brains of Klotho transgenic mice with a neurotoxin, MPTP and analyzed for residual neuron numbers and integrity in the substantia nigra pars compacta. Our results show that Klotho overexpression significantly protects dopaminergic neurons against oxidative damage, partly by modulating p38 MAPK activation level. Our data highlight the importance of ASK1/p38 MAPK pathway in the brain and identify Klotho as a possible anti-oxidant effector.

2007 IEEE 7th International Symposium on BioInformatics and BioEngineering, 2007

High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spect... more High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry has shown promise as a screening tool for detecting discriminatory peptide/protein patterns. The major computational obstacle in analyzing MALDI-TOF data is the large number of mass/charge peaks (a.k.a. features, data points). With such a huge number of data points for a single sample, efficient feature selection is critical for unequivocal protein pattern discovery. In this paper, we propose a feature selection method and a new biclassification algorithm based on error-correcting output coding (ECOC) in multiclass problems. Our scheme is applied to the analysis of Alzheimer's disease (AD) data. To validate the performance of the proposed algorithm, experiments are performed in comparison with other methods. We show that our proposed framework outperforms not only the standard ECOC framework but also other algorithms.

European Urology Supplements - EUR UROL SUPPL, 2007

Computer Methods and Programs in Biomedicine, 2009

Prostate-specific antigen (PSA) is the most widely used serum biomarker for early detection of pr... more Prostate-specific antigen (PSA) is the most widely used serum biomarker for early detection of prostate cancer (PCA). Nevertheless, PSA level can be falsely elevated due to prostatic enlargement, inflammation or infection, which limits the PSA test specificity. The objective of this study is to use a machine learning approach for the analysis of mass spectrometry data to discover more reliable biomarkers that distinguish PCA from benign specimens. Serum samples from 179 prostate cancer patients and 74 benign patients were analyzed. These samples were processed using ProXPRESSION Biomarker Enrichment Kits (PerkinElmer). Mass spectra were acquired using a prOTOF 2000 matrix-assisted laser desorption/ionization orthogonal time-of-flight (MALDI-O-TOF) mass spectrometer. In this study, we search for potential biomarkers using our feature selection method, the Extended Markov Blanket (EMB). From the new marker selection algorithm, a panel of 26 peaks achieved an accuracy of 80.7%, a sensitivity of 83.5%, a specificity of 74.4%, a positive predictive value (PPV) of 87.9%, and a negative predictive value (NPV) of 68.2%. On the other hand, when PSA alone was used (with a cutoff of 4.0ng/ml), a sensitivity of 66.7%, a specificity of 53.6%, a PPV of 73.5%, and a NPV of 45.4% were obtained.

Methods in molecular biology (Clifton, N.J.), 2007

Reverse-phase protein microarrays (RPPMAs) enable heterogeneous mixtures of proteins from cellula... more Reverse-phase protein microarrays (RPPMAs) enable heterogeneous mixtures of proteins from cellular extracts to be directly spotted onto a substrate (such as a protein biochip) in minute volumes (nanoliter-to-picoliter volumes). The protein spots can then be probed with primary antibodies to detect important posttranslational modifications such as phosphorylations that are important for protein activation and the regulation of cellular signaling. Previously, we relied on chromogenic signals for detection. However, quantum dots (QDs) represent a more versatile detection system because the signals can be time averaged and the narrow-emission spectra enable multiple protein targets to be quantified within the same spot. We found that commercially available pegylated, streptavidin-conjugated QDs are effective detection agents, with low-background binding to heterogeneous protein mixtures. This type of test, the RPPMAs, is at the forefront of an exciting, clinically-oriented discipline th...

Biomedicine & Pharmacotherapy, 2007

For Alzheimer&amp... more For Alzheimer's disease (AD), the most common neurodegenerative disease, there is no simple, cost-effective biomarker for disease identification. Using novel mass spectrometry (MS)-based techniques, and analysis of the albumin-enriched low molecular weight proteome, minute amounts of human serum were analyzed for the measurement of thousands of peptides and proteins in parallel. The mass spectrograms were then evaluated with a novel computer algorithm to identify spectral peaks that discriminate between samples from patients with and without AD. There are four peaks that distinguish AD from control subjects and AD subjects from those with Parkinson's disease (PD). Additionally, after analyzing data from a recently published study of AD and control subjects, we found three discriminating peaks in common with the four from our patient serum samples. The identification of these peptides/proteins, and their direct measurement in patient serum, may allow the development of a simple, cost-effective test for AD.

American Journal of Obstetrics and Gynecology, 2007

Journal of Biological Chemistry, 2005

klotho is an aging suppressor gene and extends life span when overexpressed in mice. Klotho prote... more klotho is an aging suppressor gene and extends life span when overexpressed in mice. Klotho protein was recently demonstrated to function as a hormone that inhibits insulin/insulin-like growth factor-1 (IGF-1) signaling. Here we show that Klotho protein increases resistance to oxidative stress at the cellular and organismal level in mammals. Klotho protein activates the FoxO forkhead transcription factors that are negatively regulated by insulin/IGF-1 signaling, thereby inducing expression of manganese superoxide dismutase. This in turn facilitates removal of reactive oxygen species and confers oxidative stress resistance. Thus, Klotho-induced inhibition of insulin/IGF-1 signaling is associated with increased resistance to oxidative stress, which potentially contributes to the anti-aging properties of klotho.

Alzheimer's & Dementia, 2005

microglia in the brain. In AD, microglia show also increased expression of the M-CSF receptor (M-... more microglia in the brain. In AD, microglia show also increased expression of the M-CSF receptor (M-CSFR). We previously showed that increasing expression of the M-CSFR on cultured microglia dramatically upregulates microglia M-CSF and IL-1␣ expression. Objectives: To determine if knockdown of microglial interleukin-1␣ and M-CSF expression affects NMDA-induced neurotoxicity in a co-culture system. Methods: We used a co-culture model consisting of microglia overexpressing the M-CSFR and hippocampal organotypic cultures treated with the neurotoxin NMDA. To test the importance of microglial IL-1␣ and M-CSF on neuronal survival, we used an shRNA gene-targeted approach in which we selectively and without toxicity deleted microglial IL-1␣ or M-CSF expression prior to co-culture assembly. Transfections were performed with the hairpin RNA expression plasmid pGSU6-GFP-shRNA. To quantify neuronal injury, we used propidium iodide as well as FluoroJade staining. Results: We found that when microglia overexpressing the M-CSFR were cocultured with organotypic slices, there was complete protection of neurons from NMDA-induced injury. However, after knockdown of either microglial IL-1␣ or M-CSF, neuroprotection was abolished. Using TaqMan real-time RT-PCR, we confirmed that the shRNA constructs resulted in a Ͼ75% knockdown of cytokine expression. Both M-CSF and IL-1␣ were necessary for microglial proliferation, but only IL-1␣ removal also suppressed chemotactic migration of microglia toward the NMDA-injured organotypic culture. Conclusions: These results demonstrate that IL-1␣ and M-CSF are essential for M-CSFR-induced microglial neuroprotection in a microglial-organotypic hippocampal co-culture system. In AD, increased IL-1␣ and M-CSF expression by M-CSFR-activated microglia could actually serve to protect, rather than harm neurons. It may be that some inflammatory factors expressed early in AD could be beneficial, so that suppressing inflammation might accelerate rather than prevent disease progression. (Supported by an Alzheimer's Association New Investigator Award to O.M. and NIH award MH57833).

Clinical Chemistry, 2007

Background: Most cases of ovarian cancer are detected at later stages when the 5-year survival is... more Background: Most cases of ovarian cancer are detected at later stages when the 5-year survival is ϳ15%, but 5-year survival approaches 90% when the cancer is detected early (stage I). To use mass spectrometry (MS) of serum proteins for early detection, a seamless workflow is needed that provides an opportunity for rapid profiling along with direct identification of the underpinning ions. Methods: We used carrier protein-bound affinity enrichment of serum samples directly coupled with MALDI orthagonal TOF MS profiling to rapidly search for potential ion signatures that contained discriminatory power. These ions were subsequently directly subjected to tandem MS for sequence identification. Results: We discovered several biomarker panels that enabled differentiation of stage I ovarian cancer from unaffected (age-matched) patients with no evidence of ovarian cancer, with positive results in >93% of samples from patients with disease-negative results and in 97% of disease-free controls. The carrier protein-based approach identified additional protein fragments, many from low-abundance proteins or proteins not previously seen in serum. Conclusions: This workflow system using a highly reproducible, high-resolution MALDI-TOF platform enables rapid enrichment and profiling of large numbers of clinical samples for discovery of ion signatures and integration of direct sequencing and identification of the ions without need for additional offline, timeconsuming purification strategies.

Biomed Pharmacotherapy, 2007

For Alzheimer&amp... more For Alzheimer's disease (AD), the most common neurodegenerative disease, there is no simple, cost-effective biomarker for disease identification. Using novel mass spectrometry (MS)-based techniques, and analysis of the albumin-enriched low molecular weight proteome, minute amounts of human serum were analyzed for the measurement of thousands of peptides and proteins in parallel. The mass spectrograms were then evaluated with a novel computer algorithm to identify spectral peaks that discriminate between samples from patients with and without AD. There are four peaks that distinguish AD from control subjects and AD subjects from those with Parkinson's disease (PD). Additionally, after analyzing data from a recently published study of AD and control subjects, we found three discriminating peaks in common with the four from our patient serum samples. The identification of these peptides/proteins, and their direct measurement in patient serum, may allow the development of a simple, cost-effective test for AD.

Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06), 2006

Abstract— High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) ... more Abstract— High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry has shown promise as a screening tool for detecting discriminatory protein patterns. The major computational obstacle in analyzing MALDI-TOF data is a ...

Bioconjugate Chemistry, 2005

Protein microarray technologies provide a means of investigating the proteomic content of clinica... more Protein microarray technologies provide a means of investigating the proteomic content of clinical biopsy specimens in order to determine the relative activity of key nodes within cellular signaling pathways. A particular kind of protein microarray, the reverse-phase microarray, is being evaluated in clinical trials because of its potential to utilize limited amounts of cellular material obtained through biopsy. Using this approach, cellular lysates are arrayed in dilution curves on nitrocellulose substrates for subsequent probing with antibodies. To improve the sensitivity and utility of reverse-phase microarrays, we tested whether a new reporter technology as well as a new detection instrument could enhance microarray performance. We describe the use of an inorganic fluorescent nanoparticle conjugated to streptavidin, Qdot 655 Sav, in a reverse-phase protein microarray format for signal pathway profiling. Moreover, a pegylated form of this bioconjugate, Qdot 655 Sav, is found to have superior detection characteristics in assays performed on cellular protein extracts over the nonpegylated form of the bioconjugate. Hyperspectral imaging of the quantum dot microarray enabled unamplified detection of signaling proteins within defined cellular lysates, which indicates that this approach may be amenable to multiplexed, high-throughput reverse-phase protein microarrays in which numerous analytes are measured in parallel within a single spot.

Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry data ha... more Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry data has been increasingly analyzed for identifying biomarkers to help early detection of the disease. Ovarian cancer commonly recurs at the rate of 75% within a few months or several years later after standard treatment. Since recurrent ovarian cancer is relatively difficult to be diagnosed and small tumors generally respond better to treatment, new methods for the detection of early relapse in ovarian cancer are urgently needed. Here, we propose a new algorithm SVM-MB/RFE (SVM-Markov Blanket/Recursive Feature Elimination) based on SVM-RFE, which identifies biomarkers for predicting the early recurrence of ovarian cancer. In this approach, we first apply t-test for feature pruning and then binning using 5-fold cross validation. Finally, 58 peaks are obtained from 27,000 of the raw data. Such dramatically reduced features relax the computational burden in the next step of our algorithm. We compare the performance of three feature selection algorithms and demonstrate that SVM-MB/RFE outperforms other methods.

Journal of Bioinformatics and Computational Biology, Dec 1, 2006

Ovarian cancer recurs at the rate of 75% within a few months or several years later after therapy... more Ovarian cancer recurs at the rate of 75% within a few months or several years later after therapy. Early recurrence, though responding better to treatment, is difficult to detect. Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry has showed the potential to accurately identify disease biomarkers to help early diagnosis. A major challenge in the interpretation of SELDI-TOF data is the high dimensionality of the feature space. To tackle this problem, we have developed a multi-step data processing method composed of t-test, binning and backward feature selection. A new algorithm, support vector machine-Markov blanket/recursive feature elimination (SVM-MB/RFE) is presented for the backward feature selection. This method is an integration of minimum weight feature elimination by SVM-RFE and information theory based redundant/irrelevant feature removal by Markov Blanket. Subsequently, SVM was used for classification. We conducted the biomarker selection algorithm on 113 serum samples to identify early relapse from ovarian cancer patients after primary therapy. To validate the performance of the proposed algorithm, experiments were carried out in comparison with several other feature selection and classification algorithms.

Data Revues 07533322 00610007 07001138, Mar 21, 2008

Amer J Obstet Gynecol, 2007