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The differential diagnosis of prostate cancer is problematic due to the lack of markers with high diagnostic accuracy. We previously demonstrated the increased binding of IgG to human plasminogen (PLG) in plasma of patients with prostate cancer (PC) compared to healthy controls. Heavy and light chains of PLG (PLG-H and PLG-L) were immobilized on 96-well plates and the binding of IgG to PLG-H and PLG-L was analyzed in serum from 30 prostate cancer (PC) patients, 30 patients with benign prostatic hyperplasia (BPH) and 30 healthy controls using enzyme-linked immunosorbent assay (ELISA). Our results demonstrate that IgG from PC sera bind to PLG-H but not to PLG-L. This interaction occurred through the free IgG C-terminal lysine (Lys) that becomes exposed as a result of IgG conformational changes associated with proteolysis. Circulating levels of modified IgG with exposed C-terminal Lys (IgG-Lys) were significantly higher in PC patients than in healthy controls and in BPH. We used Receiver Operating Characteristic (ROC) analysis to calculate the sensitivity (SN) and specificity (SP) of circulating IgG-Lys for differentiating PC from BPH as 77% and 90%, respectively. The area under the curve (AUC) was 0.87. We demonstrated that the diagnostic accuracy of circulating levels of IgG-Lys is much higher than diagnostic accuracy of total PSA (tPSA).
Anna Lokshin; Lyudmila M. Mikhaleva; Eugene I. Goufman; Marina N. Boltovskaya; Natalia B. Tikhonova; Irina I. Stepanova; Alexandr A. Stepanov; Natalia V. Potoldykova; Andrey Z. Vinarov; Paul Stemmer; Vasily Iakovlev. Proteolyzed Variant of IgG with Free C-Terminal Lysine as a Biomarker of Prostate Cancer. Biology 2021, 10, 817 .
AMA StyleAnna Lokshin, Lyudmila M. Mikhaleva, Eugene I. Goufman, Marina N. Boltovskaya, Natalia B. Tikhonova, Irina I. Stepanova, Alexandr A. Stepanov, Natalia V. Potoldykova, Andrey Z. Vinarov, Paul Stemmer, Vasily Iakovlev. Proteolyzed Variant of IgG with Free C-Terminal Lysine as a Biomarker of Prostate Cancer. Biology. 2021; 10 (8):817.
Chicago/Turabian StyleAnna Lokshin; Lyudmila M. Mikhaleva; Eugene I. Goufman; Marina N. Boltovskaya; Natalia B. Tikhonova; Irina I. Stepanova; Alexandr A. Stepanov; Natalia V. Potoldykova; Andrey Z. Vinarov; Paul Stemmer; Vasily Iakovlev. 2021. "Proteolyzed Variant of IgG with Free C-Terminal Lysine as a Biomarker of Prostate Cancer." Biology 10, no. 8: 817.
Exosomes are a class of small, secreted extracellular vesicles (EV) that have recently gained considerable attention for their role in normal cellular function, disease processes and potential as biomarkers. Exosomes serve as intercellular messengers and carry molecular cargo that can alter gene expression and the phenotype of recipient cells. Here, we investigated alterations of microRNA cargo in exosomes secreted by epileptogenic tissue in tuberous sclerosis complex (TSC), a multi-system genetic disorder that includes brain lesions known as tubers. Approximately 90% of TSC patients suffer from seizures that originate from tubers, and ~60% are resistant to antiseizure drugs. It is unknown why some tubers cause seizures while others do not, and the molecular basis of drug-resistant epilepsy is not well understood. It is believed that neuroinflammation is involved, and characterization of this mechanism may be key to disrupting the “vicious cycle” between seizures, neuroinflammation, and increased seizure susceptibility. We isolated exosomes from epileptogenic and non-epileptogenic TSC tubers, and we identified differences in their microRNA cargo using small RNA-seq. We identified 12 microRNAs (including miR-142-3p, miR-223-3p and miR-21-5p) that are significantly increased in epileptogenic tubers and contain nucleic acid motifs that activate toll-like receptors (TLR7/8), initiating a neuroinflammatory cascade. Exosomes from epileptogenic tissue caused induction of key pathways in cultured cells, including innate immune signaling (TLR), inflammatory response and key signaling nodes SQSTM1 (p62) and CDKN1A (p21). Genes induced in vitro were also significantly upregulated in epileptogenic tissue. These results provide new evidence on the role of exosomes and non-coding RNA cargo in the neuroinflammatory cascade of epilepsy and may help advance the development of novel biomarkers and therapeutic approaches for the treatment of drug-resistant epilepsy.
Daniela Cukovic; Shruti Bagla; Dylan Ukasik; Paul Stemmer; Bhanu Jena; Akshata Naik; Sandeep Sood; Eishi Asano; Aimee Luat; Diane Chugani; Alan Dombkowski. Exosomes in Epilepsy of Tuberous Sclerosis Complex: Carriers of Pro-Inflammatory MicroRNAs. Non-Coding RNA 2021, 7, 40 .
AMA StyleDaniela Cukovic, Shruti Bagla, Dylan Ukasik, Paul Stemmer, Bhanu Jena, Akshata Naik, Sandeep Sood, Eishi Asano, Aimee Luat, Diane Chugani, Alan Dombkowski. Exosomes in Epilepsy of Tuberous Sclerosis Complex: Carriers of Pro-Inflammatory MicroRNAs. Non-Coding RNA. 2021; 7 (3):40.
Chicago/Turabian StyleDaniela Cukovic; Shruti Bagla; Dylan Ukasik; Paul Stemmer; Bhanu Jena; Akshata Naik; Sandeep Sood; Eishi Asano; Aimee Luat; Diane Chugani; Alan Dombkowski. 2021. "Exosomes in Epilepsy of Tuberous Sclerosis Complex: Carriers of Pro-Inflammatory MicroRNAs." Non-Coding RNA 7, no. 3: 40.
Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample, as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in core facility settings has been slow. The Association of Biomolecular Resource Facilities conducted a large interlaboratory study to evaluate DIA performance in laboratories with various instrumentation. Participants were supplied with generic methods and a uniform set of test samples. The resulting 49 DIA datasets act as benchmarks and have utility in education and tool development. The sample set consisted of a tryptic HeLa digest spiked with high or low levels of four exogenous proteins. Data are available in MassIVE MSV000086479. Additionally, we demonstrate how the data can be analysed by focusing on two datasets using different library approaches and show the utility of select summary statistics. These data can be used by DIA newcomers, software developers, or DIA experts evaluating performance with different platforms, acquisition settings and skill levels.
Benjamin A. Neely; Paul M. Stemmer; Brian C. Searle; Laura E. Herring; Leroy Martin; Mukul K. Midha; Brett S. Phinney; Baozhen Shan; Magnus Palmblad; Yan Wang; Pratik D. Jagtap; Joanna Kirkpatrick. 2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study. 2020, 1 .
AMA StyleBenjamin A. Neely, Paul M. Stemmer, Brian C. Searle, Laura E. Herring, Leroy Martin, Mukul K. Midha, Brett S. Phinney, Baozhen Shan, Magnus Palmblad, Yan Wang, Pratik D. Jagtap, Joanna Kirkpatrick. 2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study. . 2020; ():1.
Chicago/Turabian StyleBenjamin A. Neely; Paul M. Stemmer; Brian C. Searle; Laura E. Herring; Leroy Martin; Mukul K. Midha; Brett S. Phinney; Baozhen Shan; Magnus Palmblad; Yan Wang; Pratik D. Jagtap; Joanna Kirkpatrick. 2020. "2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study." , no. : 1.
The effects of glycyrrhizin (GLY) on multi-drug resistant (MDR) systemic (MDR9) vs. ocular (B1045) Pseudomonas aeruginosa clinical isolates were determined. Proteomes of each isolate with/without GLY treatment were profiled using liquid chromatography mass spectrometry (LC-MS/MS). The effect of GLY on adherence of MDR isolates to immortalized human (HCET) and mouse (MCEC) corneal epithelial cells, and biofilm and dispersal was tested. Both isolates were treated with GLY (0.25 minimum inhibitory concentration (MIC), 10 mg/mL for MDR9 and 3.75 mg/mL for B1045) and subjected to proteomic analysis. MDR9 had a greater response to GLY (51% of identified proteins affected vs. <1% in B1045). In MDR9 vs. controls, GLY decreased the abundance of proteins for: antibiotic resistance, biofilm formation, and type III secretion. Further, antibiotic resistance and type III secretion proteins had higher control abundances in MDR9 vs. B1045. GLY (5 and 10 mg/mL) significantly reduced binding of both isolates to MCEC, and B1045 to HCET. MDR9 binding to HCET was only reduced at 10 mg/mL GLY. GLY (5 and 10 mg/mL) enhanced dispersal for both isolates, at early (6.5 h) but not later times (24–72 h). This study provides evidence that GLY has a greater effect on the proteome of MDR9 vs. B1045, yet it was equally effective at disrupting adherence and early biofilm dispersal.
Nicholas Carruthers; Sharon McClellan; Mallika Somayajulu; Ahalya Pitchaikannu; Denise Bessert; Xudong Peng; Kylie Huitsing; Paul Stemmer; Linda Hazlett. Effects of Glycyrrhizin on Multi-Drug Resistant Pseudomonas aeruginosa. Pathogens 2020, 9, 766 .
AMA StyleNicholas Carruthers, Sharon McClellan, Mallika Somayajulu, Ahalya Pitchaikannu, Denise Bessert, Xudong Peng, Kylie Huitsing, Paul Stemmer, Linda Hazlett. Effects of Glycyrrhizin on Multi-Drug Resistant Pseudomonas aeruginosa. Pathogens. 2020; 9 (9):766.
Chicago/Turabian StyleNicholas Carruthers; Sharon McClellan; Mallika Somayajulu; Ahalya Pitchaikannu; Denise Bessert; Xudong Peng; Kylie Huitsing; Paul Stemmer; Linda Hazlett. 2020. "Effects of Glycyrrhizin on Multi-Drug Resistant Pseudomonas aeruginosa." Pathogens 9, no. 9: 766.
Psychological war trauma among displaced refugees is an established risk factor for mental health disorders, especially post-traumatic stress disorder (PTSD). Persons with trauma-induced disorders have heightened neuroplastic restructuring of limbic brain circuits (e.g., amygdala and hippocampus), which are critical factors in the pathophysiology of PTSD. Civilians in war are exposed to both psychological trauma and environmental hazards, such as metals. Little is known about the possible mental health impact from such environmental exposures, alone or in combination with trauma. It is of special interest to determine whether war exposures contribute to dysfunctional neuroplasticity; that is, an adverse outcome from sustained stress contributing to mental health disorders. The current study examined Middle Eastern refugees in the United States to determine the relationships among pre-displacement trauma and environmental exposures, brain derived neurotrophic growth factor (BDNF) and nerve growth factor (NGF)—two neurotrophins reported to mediate neuroplasticity responses to stress-related exposures—and mental health. Middle Eastern refugees (n = 64; 33 men, 31 women) from Syria (n = 40) or Iraq (n = 24) were assessed 1 month after arrival to Michigan, US. Participants were interviewed in Arabic using a semi-structured survey to assess pre-displacement trauma and environmental exposure, PTSD, depression, anxiety, and self-rated mental health. Whole blood was collected, and concentrations of six heavy metals as well as BDNF and NGF levels were determined. Because these two neurotrophins have similar functions in neuroplasticity, we combined them to create a neuroplasticity index. Linear regression tested whether psychosocial trauma, environmental exposures and biomarkers were associated with mental health symptoms. The neuroplasticity index was associated with PTSD (standardized beta, β = 0.25, p < 0.05), depression (0.26, < 0.05) and anxiety (0.32, < 0.01) after controlling for pre-displacement trauma exposures. In addition, pre-displacement environmental exposure was associated with PTSD (0.28, < 0.05) and anxiety (0.32, < 0.05). Syrian refugees and female gender were associated with higher scores on depression (0.25, < 0.05; 0.30, < 0.05) and anxiety scales (0.35, < 0.01; 0.27, < 0.05), and worse on self-rated mental health (0.32, < 0.05; 0.34, < 0.05). In bivariate analysis, the neuroplasticity index was related to blood lead levels (r = 0.40; p < 0.01). The current study confirms the adverse effects of war trauma on mental health. Higher levels of biomarkers of neuroplasticity correlated with worse mental health and higher blood lead levels. Higher neurotrophin levels in refugees might indicate dysfunctional neuroplasticity with increased consolidation of adverse war memories in the limbic system. Such a process may contribute to psychiatric symptoms. Further research is needed to clarify the pathobiological mechanisms linking war trauma and environmental exposures to adverse mental health.
Bengt B. Arnetz; Sukhesh Sudan; Judith E. Arnetz; Jolin B. Yamin; Mark A. Lumley; John S. Beck; Paul M. Stemmer; Paul Burghardt; Scott E. Counts; Hikmet Jamil. Dysfunctional neuroplasticity in newly arrived Middle Eastern refugees in the U.S.: Association with environmental exposures and mental health symptoms. PLOS ONE 2020, 15, e0230030 .
AMA StyleBengt B. Arnetz, Sukhesh Sudan, Judith E. Arnetz, Jolin B. Yamin, Mark A. Lumley, John S. Beck, Paul M. Stemmer, Paul Burghardt, Scott E. Counts, Hikmet Jamil. Dysfunctional neuroplasticity in newly arrived Middle Eastern refugees in the U.S.: Association with environmental exposures and mental health symptoms. PLOS ONE. 2020; 15 (3):e0230030.
Chicago/Turabian StyleBengt B. Arnetz; Sukhesh Sudan; Judith E. Arnetz; Jolin B. Yamin; Mark A. Lumley; John S. Beck; Paul M. Stemmer; Paul Burghardt; Scott E. Counts; Hikmet Jamil. 2020. "Dysfunctional neuroplasticity in newly arrived Middle Eastern refugees in the U.S.: Association with environmental exposures and mental health symptoms." PLOS ONE 15, no. 3: e0230030.
Identifying single amino acid variants (SAAVs) in cancer is critical for precision oncology. Several advanced algorithms are now available to identify SAAVs but attempts to combine different algorithms and optimize them on large datasets to achieve a more comprehensive coverage of SAAVs have not been implemented. Herein we report an expanded detection of SAAVs in the PANC-1 cell line using three different strategies, which results in identification of 540 SAAVs in the mass spectrometry data. Among the set of 540 SAAVs, 79 are evaluated as deleterious SAAVs based on analysis using novel AssVar software in which one of the driver mutations found in each protein of KRAS, TP53 and SLC37A4 is further validated using independent selected reaction monitoring (SRM) analysis. Our study represents the most comprehensive discovery of SAAVs to date and the first large-scale detection of deleterious SAAVs in the PANC-1 cell line. This work may serve as the basis for future research in pancreatic cancer and personal immunotherapy and treatment.
Zhijing Tan; Jianhui Zhu; Paul M. Stemmer; Liangliang Sun; Zhichang Yang; Kendall Schultz; Matthew J. Gaffrey; Anthony J. Cesnik; Xinpei Yi; Xiaohu Hao; Michael R. Shortreed; Tujin Shi; David M. Lubman. Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line. Journal of Proteome Research 2020, 19, 1635 -1646.
AMA StyleZhijing Tan, Jianhui Zhu, Paul M. Stemmer, Liangliang Sun, Zhichang Yang, Kendall Schultz, Matthew J. Gaffrey, Anthony J. Cesnik, Xinpei Yi, Xiaohu Hao, Michael R. Shortreed, Tujin Shi, David M. Lubman. Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line. Journal of Proteome Research. 2020; 19 (4):1635-1646.
Chicago/Turabian StyleZhijing Tan; Jianhui Zhu; Paul M. Stemmer; Liangliang Sun; Zhichang Yang; Kendall Schultz; Matthew J. Gaffrey; Anthony J. Cesnik; Xinpei Yi; Xiaohu Hao; Michael R. Shortreed; Tujin Shi; David M. Lubman. 2020. "Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line." Journal of Proteome Research 19, no. 4: 1635-1646.
Methicillin-resistant S aureus (MRSA) contributes to patient mortality and extended hospital stays. 3-O-alpha-L-(2″,3″-di-p-coumaroyl)rhamnoside (KCR) is a natural product antibiotic that is effective against MRSA but has no known mechanism of action (MOA). We used proteomics to identify the MOA for KCR. Methicillin sensitive S aureus and a mixture of four KCR stereoisomers were tested. A time-kill assay was used to choose a 4 h treatment using KCR at 5× its MIC for proteomic analysis. S aureus was treated in triplicate with KCR, oxacillin or vehicle and quantitative proteomic analysis was carried out using isobaric tags and mass spectrometry. 1190 proteins were identified and 552 were affected by KCR (q < 0.01). Ontology analysis identified 6 distinct translation-related categories that were affected by KCR (PIANO, 10% false-discovery rate) including structural constituent of ribosome, translation, rRNA binding, tRNA binding, tRNA processing and aminoacyl-tRNA ligase activity. Median fold changes (KCR vs Control) for small and large ribosomal components were 1.46 and 1.43 respectively. KCR inhibited the production of luciferase protein in an in vitro assay (IC50 39.6 μg/ml). Upregulation of translation-related proteins in response to KCR indicates that KCR acts to disrupt S aureus protein synthesis. This was confirmed with an in vitro transcription/translation assay. SIGNIFICANCE: Methicillin-resistant S aureus (MRSA) contributes to patient mortality and extended hospital stays. 3-O-alpha-L-(2″,3″-di-p-coumaroyl)rhamnoside (KCR) is a natural product antibiotic that is effective against MRSA but has no known mechanism of action (MOA). Using proteomic analysis we determined that KCR acts by inhibiting protein synthesis. KCR is an exciting novel antibiotic and this work represents an important step in its development towards clinical use.
Nicholas J. Carruthers; Paul M. Stemmer; Joe Media; Ken Swartz; Xiaojuan Wang; Nicholas Aube; Mark T. Hamann; Frederick Valeriote; Jiajiu Shaw. The anti-MRSA compound 3-O-alpha-L-(2″,3″-di-p-coumaroyl)rhamnoside (KCR) inhibits protein synthesis in Staphylococcus aureus. Journal of Proteomics 2019, 210, 103539 .
AMA StyleNicholas J. Carruthers, Paul M. Stemmer, Joe Media, Ken Swartz, Xiaojuan Wang, Nicholas Aube, Mark T. Hamann, Frederick Valeriote, Jiajiu Shaw. The anti-MRSA compound 3-O-alpha-L-(2″,3″-di-p-coumaroyl)rhamnoside (KCR) inhibits protein synthesis in Staphylococcus aureus. Journal of Proteomics. 2019; 210 ():103539.
Chicago/Turabian StyleNicholas J. Carruthers; Paul M. Stemmer; Joe Media; Ken Swartz; Xiaojuan Wang; Nicholas Aube; Mark T. Hamann; Frederick Valeriote; Jiajiu Shaw. 2019. "The anti-MRSA compound 3-O-alpha-L-(2″,3″-di-p-coumaroyl)rhamnoside (KCR) inhibits protein synthesis in Staphylococcus aureus." Journal of Proteomics 210, no. : 103539.
Microcystins are potent hepatotoxins that have become a global health concern in recent years. Their actions in at-risk populations with pre-existing liver disease is unknown. We tested the hypothesis that the No Observed Adverse Effect Level (NOAEL) of Microcystin-LR (MC-LR) established in healthy mice would cause exacerbation of hepatic injury in a murine model (Leprdb/J) of Non-alcoholic Fatty Liver Disease (NAFLD). Ten-week-old male Leprdb/J mice were gavaged with 50 μg/kg, 100 μg/kg MC-LR or vehicle every 48 h for 4 weeks (n = 15–17 mice/group). Early mortality was observed in both the 50 μg/kg (1/17, 6%), and 100 μg/kg (3/17, 18%) MC-LR exposed mice. MC-LR exposure resulted in significant increases in circulating alkaline phosphatase levels, and histopathological markers of hepatic injury as well as significant upregulation of genes associated with hepatotoxicity, necrosis, nongenotoxic hepatocarcinogenicity and oxidative stress response. In addition, we observed exposure dependent changes in protein phosphorylation sites in pathways involved in inflammation, immune function, and response to oxidative stress. These results demonstrate that exposure to MC-LR at levels that are below the NOAEL established in healthy animals results in significant exacerbation of hepatic injury that is accompanied by genetic and phosphoproteomic dysregulation in key signaling pathways in the livers of NAFLD mice.
Apurva Lad; Robin C. Su; Joshua D. Breidenbach; Paul M. Stemmer; Nicholas J. Carruthers; Nayeli K. Sanchez; Fatimah K. Khalaf; Shungang Zhang; Andrew L. Kleinhenz; Prabhatchandra Dube; Chrysan J. Mohammed; Judy A. Westrick; Erin L. Crawford; Dilrukshika Palagama; David Baliu-Rodriguez; Dragan Isailovic; Bruce Levison; Nikolai Modyanov; Amira F. Gohara; Deepak Malhotra; Steven T. Haller; David J. Kennedy. Chronic Low Dose Oral Exposure to Microcystin-LR Exacerbates Hepatic Injury in a Murine Model of Non-Alcoholic Fatty Liver Disease. Toxins 2019, 11, 486 .
AMA StyleApurva Lad, Robin C. Su, Joshua D. Breidenbach, Paul M. Stemmer, Nicholas J. Carruthers, Nayeli K. Sanchez, Fatimah K. Khalaf, Shungang Zhang, Andrew L. Kleinhenz, Prabhatchandra Dube, Chrysan J. Mohammed, Judy A. Westrick, Erin L. Crawford, Dilrukshika Palagama, David Baliu-Rodriguez, Dragan Isailovic, Bruce Levison, Nikolai Modyanov, Amira F. Gohara, Deepak Malhotra, Steven T. Haller, David J. Kennedy. Chronic Low Dose Oral Exposure to Microcystin-LR Exacerbates Hepatic Injury in a Murine Model of Non-Alcoholic Fatty Liver Disease. Toxins. 2019; 11 (9):486.
Chicago/Turabian StyleApurva Lad; Robin C. Su; Joshua D. Breidenbach; Paul M. Stemmer; Nicholas J. Carruthers; Nayeli K. Sanchez; Fatimah K. Khalaf; Shungang Zhang; Andrew L. Kleinhenz; Prabhatchandra Dube; Chrysan J. Mohammed; Judy A. Westrick; Erin L. Crawford; Dilrukshika Palagama; David Baliu-Rodriguez; Dragan Isailovic; Bruce Levison; Nikolai Modyanov; Amira F. Gohara; Deepak Malhotra; Steven T. Haller; David J. Kennedy. 2019. "Chronic Low Dose Oral Exposure to Microcystin-LR Exacerbates Hepatic Injury in a Murine Model of Non-Alcoholic Fatty Liver Disease." Toxins 11, no. 9: 486.
Mineral dust-induced gene (mdig) encodes a member of the evolutionarily conserved JmjC family proteins that play fundamental roles in regulating chromatin-based processes as well as transcription of the genes in eukaryotic cells. This gene is also named as myc-induced nuclear antigen 53 (MINA), nucleolar protein 52 (NO52) and ribosomal oxygenase 2 (RIOX2). Increased expression of mdig had been noted in a number of human cancers, esp. lung cancer. Emerging evidence suggests that the oncogenic activity of mdig is most likely achieved through its regulation on the demethylation of histone proteins, despite it lacks the structural identities of the demethylases. Here, we discuss the latest discoveries on the characteristics of the mdig protein and its roles in a wide variety of normal and carcinogenic processes. We will also provide perspectives on how mdig is involved in the maintenance and differentiation of the embryonic stem cells, somatic stem cells and cancer stem cells.
Qian Zhang; Chitra Thakur; Junwei Shi; Jiaying Sun; Yao Fu; Paul Stemmer; Fei Chen. New discoveries of mdig in the epigenetic regulation of cancers. Seminars in Cancer Biology 2019, 57, 27 -35.
AMA StyleQian Zhang, Chitra Thakur, Junwei Shi, Jiaying Sun, Yao Fu, Paul Stemmer, Fei Chen. New discoveries of mdig in the epigenetic regulation of cancers. Seminars in Cancer Biology. 2019; 57 ():27-35.
Chicago/Turabian StyleQian Zhang; Chitra Thakur; Junwei Shi; Jiaying Sun; Yao Fu; Paul Stemmer; Fei Chen. 2019. "New discoveries of mdig in the epigenetic regulation of cancers." Seminars in Cancer Biology 57, no. : 27-35.
Objective To identify whether factors toxic to oligodendrocytes (OLs), released by B cells from patients with MS, are found in extracellular microvesicles enriched in exosomes. Methods Conditioned medium (Sup) was obtained from cultures of blood B cells of patients with MS and normal controls (NCs). Exosome-enriched (Ex-En) fractions were prepared by solvent precipitation from Sup containing bovine serum and from serum-free Sup by ultracentrifugation (UC) or immunoprecipitation (IP) with antibodies to CD9. Ex-En fractions were diluted 1:4 with OL culture medium and screened for toxic effects on cultured rat OLs as measured by trypan blue uptake. Proteomic analysis was performed on Sup fractions. Results MS B cell–derived Ex-En fractions prepared from Sup by solvent extraction, UC, or IP induced OL death, whereas corresponding Ex-En fractions from NC showed little toxicity. Proteomic analysis of Sup demonstrated enrichment of proteins characteristic of exosomes from both NC and MS B-cell Sup. Ontology enrichment analysis suggested differences in the types and cargo of exosomes from MS Sup compared with NC, with proteins related to cell surface, extracellular plasma membrane, and gliogenesis enriched in MS. Conclusions Much of the in vitro toxicity of Sup from B cells of patients with relapsing-remitting MS is found in Ex-En fractions, as confirmed by 3 methods. Proteomic analysis of B-cell Sup indicates multiple differences between MS and NC.
Joyce A. Benjamins; Liljana Nedelkoska; Hanane Touil; Paul M. Stemmer; Nicholas J. Carruthers; Bhanu P. Jena; Akshata R. Naik; Amit Bar-Or; Robert P. Lisak. Exosome-enriched fractions from MS B cells induce oligodendrocyte death. Neurology - Neuroimmunology Neuroinflammation 2019, 6, e550 .
AMA StyleJoyce A. Benjamins, Liljana Nedelkoska, Hanane Touil, Paul M. Stemmer, Nicholas J. Carruthers, Bhanu P. Jena, Akshata R. Naik, Amit Bar-Or, Robert P. Lisak. Exosome-enriched fractions from MS B cells induce oligodendrocyte death. Neurology - Neuroimmunology Neuroinflammation. 2019; 6 (3):e550.
Chicago/Turabian StyleJoyce A. Benjamins; Liljana Nedelkoska; Hanane Touil; Paul M. Stemmer; Nicholas J. Carruthers; Bhanu P. Jena; Akshata R. Naik; Amit Bar-Or; Robert P. Lisak. 2019. "Exosome-enriched fractions from MS B cells induce oligodendrocyte death." Neurology - Neuroimmunology Neuroinflammation 6, no. 3: e550.
Akshata R. Naik; Sebastian Pernal; Kenneth T. Lewis; Yaobin Wu; Hongkai Wu; Nicholas J. Carruthers; Paul M. Stemmer; Bhanu P. Jena. Human Skeletal Muscle Cells on Engineered 3D Platform Express Key Growth and Developmental Proteins. ACS Biomaterials Science & Engineering 2018, 5, 970 -976.
AMA StyleAkshata R. Naik, Sebastian Pernal, Kenneth T. Lewis, Yaobin Wu, Hongkai Wu, Nicholas J. Carruthers, Paul M. Stemmer, Bhanu P. Jena. Human Skeletal Muscle Cells on Engineered 3D Platform Express Key Growth and Developmental Proteins. ACS Biomaterials Science & Engineering. 2018; 5 (2):970-976.
Chicago/Turabian StyleAkshata R. Naik; Sebastian Pernal; Kenneth T. Lewis; Yaobin Wu; Hongkai Wu; Nicholas J. Carruthers; Paul M. Stemmer; Bhanu P. Jena. 2018. "Human Skeletal Muscle Cells on Engineered 3D Platform Express Key Growth and Developmental Proteins." ACS Biomaterials Science & Engineering 5, no. 2: 970-976.
We have performed deep proteomic profiling down to as few as 9 Panc-1 cells using sample fractionation, TMT multiplexing and a carrier/reference strategy. Off line fractionation of the TMT-labeled sample pooled with TMT-labeled carrier Panc-1 whole cell proteome was achieved using alkaline reversed phase spin columns. The fractionation in conjunction with the carrier/reference (C/R) proteome allowed us to detect 47,414 unique peptides derived from 6,261 proteins which provided a sufficient coverage to search for single amino acid variants (SAAVs) related to cancer. This high sample coverage is essential in order to detect a significant number of SAAVs. In order to verify genuine SAAVs versus false SAAVs, we used the SAVControl pipeline and found a total of 79 SAAVs from the 9-cell Panc-1 sample and 174 SAAVs from the 5000-cell Panc-1 C/R proteome. The SAAVs as sorted into high confidence and low confidence SAAVs were checked manually. All the high confidence SAAVs were found to be genuine SAAVs while half of the low confidence SAAVs were found to be false SAAVs mainly related to PTMs. We identified several cancer-related SAAVs including KRAS which is an important oncoprotein in pancreatic cancer. In addition, we were able to detect sites involved in loss or gain of glycosylation due to the enhanced coverage available in these experiments where we can detect both sites of loss and gain of glycosylation
Zhijing Tan; Xinpei Yi; Nicholas J. Carruthers; Paul M. Stemmer; David M. Lubman. Single Amino Acid Variant Discovery in Small Numbers of Cells. Journal of Proteome Research 2018, 18, 417 -425.
AMA StyleZhijing Tan, Xinpei Yi, Nicholas J. Carruthers, Paul M. Stemmer, David M. Lubman. Single Amino Acid Variant Discovery in Small Numbers of Cells. Journal of Proteome Research. 2018; 18 (1):417-425.
Chicago/Turabian StyleZhijing Tan; Xinpei Yi; Nicholas J. Carruthers; Paul M. Stemmer; David M. Lubman. 2018. "Single Amino Acid Variant Discovery in Small Numbers of Cells." Journal of Proteome Research 18, no. 1: 417-425.
The prediction of calmodulin-binding (CaM-binding) proteins plays a very important role in the fields of biology and biochemistry, because the calmodulin protein binds and regulates a multitude of protein targets affecting different cellular processes. Computational methods that can accurately identify CaM-binding proteins and CaM-binding domains would accelerate research in calcium signaling and calmodulin function. Short-linear motifs (SLiMs), on the other hand, have been effectively used as features for analyzing protein-protein interactions, though their properties have not been utilized in the prediction of CaM-binding proteins. We propose a new method for the prediction of CaM-binding proteins based on both the total and average scores of known and new SLiMs in protein sequences using a new scoring method called sliding window scoring (SWS) as features for the prediction module. A dataset of 194 manually curated human CaM-binding proteins and 193 mitochondrial proteins have been obtained and used for testing the proposed model. The motif generation tool, Multiple EM for Motif Elucidation (MEME), has been used to obtain new motifs from each of the positive and negative datasets individually (the SM approach) and from the combined negative and positive datasets (the CM approach). Moreover, the wrapper criterion with random forest for feature selection (FS) has been applied followed by classification using different algorithms such as k-nearest neighbors (k-NN), support vector machines (SVM), naive Bayes (NB) and random forest (RF). Our proposed method shows very good prediction results and demonstrates how information contained in SLiMs is highly relevant in predicting CaM-binding proteins. Further, three new CaM-binding motifs have been computationally selected and biologically validated in this study, and which can be used for predicting CaM-binding proteins.
Yixun Li; Mina Maleki; Nicholas J. Carruthers; Paul M. Stemmer; Alioune Ngom; Luis Rueda. The predictive performance of short-linear motif features in the prediction of calmodulin-binding proteins. BMC Bioinformatics 2018, 19, 410 .
AMA StyleYixun Li, Mina Maleki, Nicholas J. Carruthers, Paul M. Stemmer, Alioune Ngom, Luis Rueda. The predictive performance of short-linear motif features in the prediction of calmodulin-binding proteins. BMC Bioinformatics. 2018; 19 (14):410.
Chicago/Turabian StyleYixun Li; Mina Maleki; Nicholas J. Carruthers; Paul M. Stemmer; Alioune Ngom; Luis Rueda. 2018. "The predictive performance of short-linear motif features in the prediction of calmodulin-binding proteins." BMC Bioinformatics 19, no. 14: 410.
Intracellular signaling is controlled to a large extent by the phosphorylation status of proteins. To determine how human breast cells can be reprogrammed during tumorigenic progression, we profiled cell lines in the MCF10A lineage by phosphoproteomic analyses. A large cluster of proteins involved in RNA splicing were hypophosphorylated as cells progressed to a hyperplastic state, and then hyperphosphorylated after progression to a fully metastatic phenotype. A comprehensive transcriptomic approach was used to determine whether alterations in splicing factor phosphorylation status would be reflected in changes in mRNA splicing. Results indicated that the degree of mRNA splicing trended with the degree of tumorigenicity of the 4 cell lines tested. That is, highly metastatic cell cultures had the greatest number of genes with splice variants, and these genes had greater fluctuations in expression intensities. Genes with high splicing indices were mapped against gene ontology terms to determine whether they have known roles in cancer. This group showed highly significant associations for angiogenesis, cytokine-mediated signaling, cell migration, programmed cell death and epithelial cell differentiation. In summary, data from global profiling of a human model of breast cancer development suggest that therapeutics should be developed which target signaling pathways that regulate RNA splicing.
Joseph A. Caruso; Nicholas J. Carruthers; Bryan Thibodeau; Timothy J. Geddes; Alan A. Dombkowski; Paul M. Stemmer. Global Signaling Profiling in a Human Model of Tumorigenic Progression Indicates a Role for Alternative RNA Splicing in Cellular Reprogramming. International Journal of Molecular Sciences 2018, 19, 2847 .
AMA StyleJoseph A. Caruso, Nicholas J. Carruthers, Bryan Thibodeau, Timothy J. Geddes, Alan A. Dombkowski, Paul M. Stemmer. Global Signaling Profiling in a Human Model of Tumorigenic Progression Indicates a Role for Alternative RNA Splicing in Cellular Reprogramming. International Journal of Molecular Sciences. 2018; 19 (10):2847.
Chicago/Turabian StyleJoseph A. Caruso; Nicholas J. Carruthers; Bryan Thibodeau; Timothy J. Geddes; Alan A. Dombkowski; Paul M. Stemmer. 2018. "Global Signaling Profiling in a Human Model of Tumorigenic Progression Indicates a Role for Alternative RNA Splicing in Cellular Reprogramming." International Journal of Molecular Sciences 19, no. 10: 2847.
Although the increased incidence of type 2 diabetes since the 1950s is thought to be primarily due to coincident alterations in lifestyle factors, another potential contributing factor in industrialized countries is exposure of the population to environmental pollutants and industrial chemicals. Exposure levels of many environmental toxicants have risen in the same time-frame as the disease incidence. Of particular interest in this regard is the metal lead. Although overall lead exposure levels have diminished in recent decades, there is an under-recognized but persistent occurrence of lead exposure in poor underserved urban populations. Although the neural developmental pathologies induced by lead exposures have been well documented, very little is known about the effect of lead exposure on the incidence of chronic metabolic diseases such as type 2 diabetes. Although our understanding of the metabolic health effects of lead exposure is incomplete, there are studies in model systems and a small amount of epidemiological data that together suggest a deleterious effect of environmental lead exposure on metabolic health. This article reviews the human, animal and in vitro studies that have examined the effects of lead exposure on the development of diabetes and related metabolic conditions.
Todd Leff; Paul Stemmer; Jannifer Tyrrell; Ruta Jog. Diabetes and Exposure to Environmental Lead (Pb). Toxics 2018, 6, 54 .
AMA StyleTodd Leff, Paul Stemmer, Jannifer Tyrrell, Ruta Jog. Diabetes and Exposure to Environmental Lead (Pb). Toxics. 2018; 6 (3):54.
Chicago/Turabian StyleTodd Leff; Paul Stemmer; Jannifer Tyrrell; Ruta Jog. 2018. "Diabetes and Exposure to Environmental Lead (Pb)." Toxics 6, no. 3: 54.
Chemokine signaling regulates cell migration and tumor metastasis. CXCL12, a member of the chemokine family, and its receptor, CXCR4, a G protein coupled receptor (GPCR), are key mediators of prostate-cancer (PC) bone metastasis. In PC cells androgens activate CXCR4 gene expression and receptor signaling on lipid rafts, which induces protease expression and cancer cell invasion. To identify novel lipid-raft-associated CXCR4 regulators supporting invasion/metastasis, we performed a SILAC-based quantitative proteomic analysis of lipid-rafts derived from PC3 stable cell lines with overexpression or knockdown of CXCR4. This analysis identified the evolutionarily conserved phosphatidylinositol 4-kinase IIIα (PI4KIIIα), and SAC1 phosphatase that dephosphorylates phosphatidylinositol-4-phosphate as potential candidate CXCR4 regulators. CXCR4 interacted with PI4KIIIα membrane targeting machinery recruiting them to the plasma membrane for PI4P production. Consistent with this interaction, PI4KIIIα was found tightly linked to the CXCR4 induced PC cell invasion. Thus, ablation of PI4KIIIα in CXCR4-expressing PC3 cells reduced cellular invasion in response to a variety of chemokines. Immunofluorescence microscopy in CXCR4-expressing cells revealed localized production of PI4P on the invasive projections. Human tumor studies documented increased PI4KIIIα expression in metastatic tumors vs. the primary tumor counterparts, further supporting the PI4KIIIα role in tumor metastasis. Furthermore, we also identified an unexpected function of PI4KIIIα in GPCR signaling where CXCR4 regulates PI4KIIIα activity and mediate tumor metastasis. Altogether, our study identifies a novel cross-talk between PI4KIIIα and CXCR4 in promoting tumor metastasis and suggests that PI4KIIIα pharmacological targeting may have therapeutic benefit for advanced prostate cancer patients.
Diego Sbrissa; Louie Semaan; Barani Govindarajan; Yanfeng Li; Nicholas J. Caruthers; Paul M. Stemmer; Michael L. Cher; Seema Sethi; Ulka Vaishampayan; Assia Shisheva; Sreenivasa R. Chinni. A novel cross-talk between CXCR4 and PI4KIIIα in prostate cancer cells. Oncogene 2018, 38, 332 -344.
AMA StyleDiego Sbrissa, Louie Semaan, Barani Govindarajan, Yanfeng Li, Nicholas J. Caruthers, Paul M. Stemmer, Michael L. Cher, Seema Sethi, Ulka Vaishampayan, Assia Shisheva, Sreenivasa R. Chinni. A novel cross-talk between CXCR4 and PI4KIIIα in prostate cancer cells. Oncogene. 2018; 38 (3):332-344.
Chicago/Turabian StyleDiego Sbrissa; Louie Semaan; Barani Govindarajan; Yanfeng Li; Nicholas J. Caruthers; Paul M. Stemmer; Michael L. Cher; Seema Sethi; Ulka Vaishampayan; Assia Shisheva; Sreenivasa R. Chinni. 2018. "A novel cross-talk between CXCR4 and PI4KIIIα in prostate cancer cells." Oncogene 38, no. 3: 332-344.
Petroleum coke (PC) is a coal-like product that is produced during the refinement of crude oil and bituminous sand. Fugitive dust from open storage of PC in urban areas is a potential human health concern. Animal inhalation studies suggest that PC leads to an adverse pulmonary histopathology, including areas of fibrosis and chronic inflammation; however, little is known about its impact on human health. In order to identify biomarkers and cellular pathways that are associated with exposure, we performed two-dimensional liquid chromatography–mass spectrometric analyses on secreted proteins from two human lung culture models. A total of 2795 proteins were identified and relatively quantified from an immortalized cell line and 2406 proteins from primary cultures that were either mock treated or exposed to particulate matter with a diameter of 2.5–10 μm PC or filtered urban air particulates for 16 h. Pathway analysis on secretomes from primary lung cultures indicated that PC exposure suppressed the secretion of proteins involved in the organization of the extracellular matrix and epithelial differentiation. Because these cellular processes could facilitate fibrosis, we performed chronic 12-day exposure studies on three-dimensional human lung cultures consisting of epithelia and stromal fibroblasts. Relative to mock-treated cells, matrix metallopeptidase 9 levels in the conditioned media were lower by 4 days postexposure and remained suppressed for the duration of the experiment. Immunocytochemical staining of collagen III, a marker associated with fibrosis, showed increased accumulation in the epithelial layer and at the air–liquid interface.
Ja Caruso; Pm Stemmer. Petroleum coke exposure leads to altered secretome profiles in human lung models. Human & Experimental Toxicology 2018, 37, 1215 -1232.
AMA StyleJa Caruso, Pm Stemmer. Petroleum coke exposure leads to altered secretome profiles in human lung models. Human & Experimental Toxicology. 2018; 37 (11):1215-1232.
Chicago/Turabian StyleJa Caruso; Pm Stemmer. 2018. "Petroleum coke exposure leads to altered secretome profiles in human lung models." Human & Experimental Toxicology 37, no. 11: 1215-1232.
Nicholas J. Carruthers; Allen J. Rosenspire; Joseph A. Caruso; Paul M. Stemmer. Low level Hg 2+ exposure modulates the B-cell cytoskeletal phosphoproteome. Journal of Proteomics 2018, 173, 107 -114.
AMA StyleNicholas J. Carruthers, Allen J. Rosenspire, Joseph A. Caruso, Paul M. Stemmer. Low level Hg 2+ exposure modulates the B-cell cytoskeletal phosphoproteome. Journal of Proteomics. 2018; 173 ():107-114.
Chicago/Turabian StyleNicholas J. Carruthers; Allen J. Rosenspire; Joseph A. Caruso; Paul M. Stemmer. 2018. "Low level Hg 2+ exposure modulates the B-cell cytoskeletal phosphoproteome." Journal of Proteomics 173, no. : 107-114.
A. Rosenspire; Paul Stemmer. Antigen-Specific Signal Transduction. Comprehensive Toxicology 2018, 282 -305.
AMA StyleA. Rosenspire, Paul Stemmer. Antigen-Specific Signal Transduction. Comprehensive Toxicology. 2018; ():282-305.
Chicago/Turabian StyleA. Rosenspire; Paul Stemmer. 2018. "Antigen-Specific Signal Transduction." Comprehensive Toxicology , no. : 282-305.
Epidemiological evidence and animal models suggest that exposure to low and non-neurotoxic concentrations of mercury may contribute to idiosyncratic autoimmune disease. Since defects in function and signaling in B cells are often associated with autoimmunity, we investigated whether mercury exposure might alter B cell responsiveness to self-antigens by interfering with B cell receptor (BCR) signal transduction. In this study we determined the effects of mercury on the protein tyrosine kinase SYK, a critical protein involved in regulation of the BCR signaling pathway. Phosphorylation sites of murine SYK were mapped before and after treatment of WEHI cell cultures with mercury, or with anti-IgM antibody (positive control) or pervanadate (a potent phosphatase inhibitor). Phosphopeptides were enriched by either titanium dioxide chromatography or anti-phosphotyrosine immunoaffinity, and analyzed by liquid chromatography-mass spectrometry. Select SYK phosphosite cluster regions were profiled for responsiveness to treatments using multiple reaction monitoring (MRM) methodology. A total of 23 phosphosites were identified with high probability in endogenous SYK, including 19 tyrosine and 4 serine residues. For 10 of these sites phosphorylation levels were increased following BCR activation. Using MRM to profile changes in phosphorylation status we found that 4 cluster regions, encompassing 8 phosphosites, were activated by mercury and differentially responsive to all 3 treatments. Phosphorylation of tyrosine-342 and -346 residues were most sensitive to mercury exposure. This cluster is known to propagate normal BCR signal transduction by recruiting adaptor proteins such as PLC-γ and Vav-1 to SYK during formation of the BCR signalosome. Our data shows that mercury alters the phosphorylation status of SYK on tyrosine sites known to have a role in promoting BCR signals. Considering the importance of SYK in the BCR signaling pathway, these data suggest that mercury can alter BCR signaling in B cells, which might affect B cell responsiveness to self-antigen and have implications with respect to autoimmunity and autoimmune disease.
Joseph A. Caruso; Nicholas Carruthers; Namhee Shin; Randal Gill; Paul M. Stemmer; Allen Rosenspire. Mercury alters endogenous phosphorylation profiles of SYK in murine B cells. BMC Immunology 2017, 18, 37 -37.
AMA StyleJoseph A. Caruso, Nicholas Carruthers, Namhee Shin, Randal Gill, Paul M. Stemmer, Allen Rosenspire. Mercury alters endogenous phosphorylation profiles of SYK in murine B cells. BMC Immunology. 2017; 18 (1):37-37.
Chicago/Turabian StyleJoseph A. Caruso; Nicholas Carruthers; Namhee Shin; Randal Gill; Paul M. Stemmer; Allen Rosenspire. 2017. "Mercury alters endogenous phosphorylation profiles of SYK in murine B cells." BMC Immunology 18, no. 1: 37-37.