Molecular Biomarkers, Biodesign Center for (MB)

Research Output 1989 2019

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2019

Loss of SETD2 Induces a Metabolic Switch in Renal Cell Carcinoma Cell Lines toward Enhanced Oxidative Phosphorylation

Liu, J., Hanavan, P. D., Kras, K., Ruiz, Y. W., Castle, E. P., Lake, D., Chen, X., O'Brien, D., Luo, H., Robertson, K. D., Gu, H. & Ho, T. H., Jan 4 2019, In : Journal of Proteome Research. 18, 1, p. 331-340 10 p.

Research output: Contribution to journalArticle

Oxidative Phosphorylation
Renal Cell Carcinoma
Cells
Switches
Cell Line
2018
1 Citation (Scopus)

Behavior of blood plasma glycan features in bladder cancer

Ferdosi, S., Ho, T. H., Castle, E. P., Stanton, M. L. & Borges, C., Jul 1 2018, In : PLoS One. 13, 7, e0201208.

Research output: Contribution to journalArticle

blood plasma
Urinary Bladder Neoplasms
Polysaccharides
Blood
polysaccharides

Evaluation of Virex® II 256 and Virex® Tb as Disinfectants of the Dimorphic Fungi Coccidioides immitis and Coccidioides posadasii

Mitchell, N. M., Magee, D., Grys, T. E. & Lake, D., Jan 1 2018, (Accepted/In press) In : Applied Biosafety.

Research output: Contribution to journalArticle

Coccidioides
Disinfectants
Fungi
fungus
ethanol
5 Citations (Scopus)

Proteogenomic Re-Annotation of Coccidioides posadasii Strain Silveira

Mitchell, N. M., Sherrard, A. L., Dasari, S., Magee, D., Grys, T. E. & Lake, D., Jan 1 2018, In : Proteomics. 18, 1, 1700173.

Research output: Contribution to journalArticle

Coccidioides
Genes
Genome
Coccidioidomycosis
Proteins
1 Citation (Scopus)

Selective Deletion of Heparan Sulfotransferase Enzyme, Ndst1, in Donor Endothelial and Myeloid Precursor Cells Significantly Decreases Acute Allograft Rejection

Chen, H., Ambadapadi, S., Wakefield, D., Bartee, M., Yaron, J. R., Zhang, L., Archer-Hartmann, S. A., Azadi, P., Burgin, M., Borges, C., Zheng, D., Ergle, K., Muppala, V., Morshed, S., Rand, K., Clapp, W., Proudfoot, A. & Lucas, A., Dec 1 2018, In : Scientific Reports. 8, 1, 13433.

Research output: Contribution to journalArticle

Sulfotransferases
Myeloid Cells
Allografts
Tissue Donors
Chemokines
1 Citation (Scopus)

Stage Dependence, Cell-Origin Independence, and Prognostic Capacity of Serum Glycan Fucosylation, β1-4 Branching, β1-6 Branching, and α2-6 Sialylation in Cancer

Ferdosi, S., Rehder, D. S., Maranian, P., Castle, E. P., Ho, T. H., Pass, H. I., Cramer, D. W., Anderson, K., Fu, L., Cole, D. E. C., Le, T., Wu, X. & Borges, C., Jan 5 2018, In : Journal of Proteome Research. 17, 1, p. 543-558 16 p.

Research output: Contribution to journalArticle

Polysaccharides
Plasmas
Serum
Neoplasms
Lung Neoplasms
2017
6 Citations (Scopus)

A spin column-free approach to sodium hydroxide-based glycan permethylation

Hu, Y. & Borges, C., Aug 7 2017, In : Analyst. 142, 15, p. 2748-2759 12 p.

Research output: Contribution to journalArticle

Sodium Hydroxide
hydroxide
Polysaccharides
Sodium
sodium
3 Citations (Scopus)

Bacterial expression, correct membrane targeting and functional folding of the HIV-1 membrane protein Vpu using a periplasmic signal peptide

Deb, A., Johnson, W. A., Kline, A. P., Scott, B. J., Meador, L. R., Srinivas, D., Martin-Garcia, J. M., Dörner, K., Borges, C., Misra, R., Hogue, B., Fromme, P. & Leket-Mor, T., Feb 1 2017, In : PLoS One. 12, 2, e0172529.

Research output: Contribution to journalArticle

viral proteins
Viral Proteins
Protein Sorting Signals
Human immunodeficiency virus 1
signal peptide
1 Citation (Scopus)

Chicken albumin exhibits natural resistance to glycation

Zuck, J., Borges, C., Braun, E. J. & Sweazea, K., Jan 1 2017, In : Comparative Biochemistry and Physiology Part - B: Biochemistry and Molecular Biology. 203, p. 108-114 7 p.

Research output: Contribution to journalArticle

Innate Immunity
Albumins
Chickens
Glucose
Temperature
2 Citations (Scopus)

Ex vivo instability of glycated albumin: A role for autoxidative glycation

Jeffs, J. W., Ferdosi, S., Yassine, H. N. & Borges, C., Sep 1 2017, In : Archives of Biochemistry and Biophysics. 629, p. 36-42 7 p.

Research output: Contribution to journalArticle

Temperature
Albumins
Bearings (structural)
Atmospheric composition
Plasmas

Insights on the HLA-Binding Peptidome in Cancer

Lake, D., 2017, (Accepted/In press) In : Enzymes.

Research output: Contribution to journalArticle

Oligopeptides
Tumors
Proteasome Endopeptidase Complex
T-cells
T-Lymphocytes
Raptors
Strigiformes
Birds
Blood Proteins
Antioxidants
2016
5 Citations (Scopus)

Development of quantitative mass spectrometric immunoassay for serum amyloid A

Trenchevska, O., Yassine, H. N., Borges, C., Nelson, R. W. & Nedelkov, D., Jul 22 2016, (Accepted/In press) In : Biomarkers. p. 1-9 9 p.

Research output: Contribution to journalArticle

Serum Amyloid A Protein
Immunoassay
Proteins
17 Citations (Scopus)

Disialylated apolipoprotein C-III proteoform is associated with improved lipids in prediabetes and type 2 diabetes1

Koska, J., Yassine, H., Trenchevska, O., Sinar, S., Schwenke, D. C., Yen, F. T., Billheimer, D., Nelson, R. W., Nedelkov, D. & Reaven, P. D., May 1 2016, In : Journal of Lipid Research. 57, 5, p. 894-905 12 p.

Research output: Contribution to journalArticle

Apolipoprotein C-III
Apolipoproteins C
Prediabetic State
Lipids
pioglitazone
21 Citations (Scopus)

Dynamic reprogramming of DNA methylation in SETD2-deregulated renal cell carcinoma

Tiedemann, R. L., Hlady, R. A., Hanavan, P. D., Lake, D., Tibes, R., Lee, J. H., Choi, J. H., Ho, T. H. & Robertson, K. D., 2016, In : Oncotarget. 7, 2, p. 1927-1946 20 p.

Research output: Contribution to journalArticle

DNA Methylation
Renal Cell Carcinoma
Developmental Genes
Phenotype
Cell Line
7 Citations (Scopus)

Electronic single-molecule identification of carbohydrate isomers by recognition tunnelling

Im, J. O., Biswas, S., Liu, H., Zhao, Y., Sen, S., Biswas, S., Ashcroft, B., Borges, C., Wang, X., Lindsay, S. & Zhang, P., Dec 21 2016, In : Nature Communications. 7, 13868.

Research output: Contribution to journalArticle

carbohydrates
sugars
Sugars
Isomers
Polysaccharides
8 Citations (Scopus)

EUS-guided portal injection chemotherapy for treatment of hepatic metastases: Feasibility in the acute porcine model

Faigel, D. O., Lake, D., Landreth, T. L., Kelman, C. C. & Marler, R. J., Feb 1 2016, In : Gastrointestinal Endoscopy. 83, 2, p. 444-446 3 p.

Research output: Contribution to journalArticle

irinotecan
Swine
Neoplasm Metastasis
Drug Therapy
Injections
6 Citations (Scopus)

Glycan node analysis: A bottom-up approach to glycomics

Zaare, S., Aguilar, J. S., Hu, Y., Ferdosi, S. & Borges, C., May 22 2016, In : Journal of Visualized Experiments. 2016, 111, e53961.

Research output: Contribution to journalArticle

Glycomics
Sugar Alcohols
Polysaccharides
Glycosyltransferases
Hexoses
3 Citations (Scopus)

Glycan structure of Gc Protein-derived Macrophage Activating Factor as revealed by mass spectrometry

Borges, C. & Rehder, D. S., Sep 15 2016, In : Archives of Biochemistry and Biophysics. 606, p. 1-13 13 p.

Research output: Contribution to journalArticle

Macrophage-Activating Factors
Mass spectrometry
Polysaccharides
Mass Spectrometry
Galactosidases
3 Citations (Scopus)

Prolonged exposure of primary human muscle cells to plasma fatty acids associated with obese phenotype induces persistent suppression of muscle mitochondrial ATP synthase β subunit

Tran, L., Hanavan, P. D., Campbell, L. E., Filippis, E. D., Lake, D., Coletta, D. K., Roust, L. R., Mandarino, L. J., Carroll, C. C. & Katsanos, C., Aug 1 2016, In : PLoS One. 11, 8, e0160057.

Research output: Contribution to journalArticle

Mitochondrial Proton-Translocating ATPases
primary contact
H-transporting ATP synthase
Proton-Translocating ATPases
myocytes
8 Citations (Scopus)

The association of plasma cystatin C proteoforms with diabetic chronic kidney disease

Yassine, H. N., Trenchevska, O., Dong, Z., Bashawri, Y., Koska, J., Reaven, P. D., Nelson, R. W. & Nedelkov, D., Mar 25 2016, In : Proteome Science. 14, 1, 7.

Research output: Contribution to journalArticle

Cystatin C
Diabetic Nephropathies
Chronic Renal Insufficiency
Plasmas
Glomerular Filtration Rate
2 Citations (Scopus)

Total and Lectin-Binding Proteome of Spherulin from Coccidioides posadasii

Grys, T. E., Kaushal, S., Chowdhury, Y., Dasari, S., Mitchell, N. M., Magee, D., Blair, J. E., Colby, T. V. & Lake, D., Oct 7 2016, In : Journal of Proteome Research. 15, 10, p. 3463-3472 10 p.

Research output: Contribution to journalArticle

Coccidioides
Proteome
Lectins
Griffonia
Glycoproteins
17 Citations (Scopus)
Microfluidics
Mass spectrometry
Labeling
Proteins
Apoptosis
6 Citations (Scopus)

Universal Readers Based on Hydrogen Bonding or π-π Stacking for Identification of DNA Nucleotides in Electron Tunnel Junctions

Biswas, S., Sen, S., Im, J. O., Biswas, S., Krstic, P., Ashcroft, B., Borges, C., Zhao, Y., Lindsay, S. & Zhang, P., Dec 27 2016, In : ACS Nano. 10, 12, p. 11304-11316 13 p.

Research output: Contribution to journalArticle

Tunnel junctions
nucleotides
readers
Nucleotides
tunnel junctions
2015
6 Citations (Scopus)

A multidisciplinary biospecimen bank of renal cell carcinomas compatible with discovery platforms at Mayo Clinic, Scottsdale, Arizona

Ho, T. H., Nateras, R. N., Yan, H., Park, J., Jensen, S., Borges, C., Lee, J. H., Champion, M. D., Tibes, R., Bryce, A. H., Carballido, E. M., Todd, M. A., Joseph, R. W., Wong, W. W., Parker, A. S., Stanton, M. L. & Castle, E. P., Jul 16 2015, In : PLoS One. 10, 7, e0132831.

Research output: Contribution to journalArticle

kidney cells
Renal Cell Carcinoma
carcinoma
Cells
RNA
2 Citations (Scopus)

Characterization of additional vitamin D binding protein variants

Fu, L., Borges, C., Rehder, D. S., Wong, B. Y. L., Williams, R., Carpenter, T. O. & Cole, D. E. C., Jun 15 2015, (Accepted/In press) In : Journal of Steroid Biochemistry and Molecular Biology.

Research output: Contribution to journalArticle

Vitamin D-Binding Protein
Mutant Proteins
Exons
Screening
Cysteine
6 Citations (Scopus)

Click Addition of a DNA Thread to the N-Termini of Peptides for Their Translocation through Solid-State Nanopores

Biswas, S., Song, W., Borges, C., Lindsay, S. & Zhang, P., Sep 12 2015, In : ACS Nano. 9, 10, p. 9652-9664 13 p.

Research output: Contribution to journalArticle

Nanopores
threads
Peptides
peptides
DNA
28 Citations (Scopus)

Development of multiplex mass spectrometric immunoassay for detection and quantification of apolipoproteins C-I, C-II, C-III and their proteoforms

Trenchevska, O., Schaab, M. R., Nelson, R. W. & Nedelkov, D., Jun 15 2015, In : Methods. 81, p. 86-92 7 p.

Research output: Contribution to journalArticle

Apolipoprotein C-I
Apolipoprotein C-III
Immunoassay
Assays
Apolipoproteins C
18 Citations (Scopus)

Ebselen inhibits QSOX1 enzymatic activity and suppresses invasion of pancreatic and renal cancer cell lines

Hanavan, P. D., Borges, C., Katchman, B. A., Faigel, D. O., Ho, T. H., Ma, C. T., Sergienko, E. A., Meurice, N., Petit, J. L. & Lake, D., 2015, In : Oncotarget. 6, 21, p. 18418-18428 11 p.

Research output: Contribution to journalArticle

Kidney Neoplasms
Pancreatic Neoplasms
Cell Line
Neoplasms
Heterografts
13 Citations (Scopus)

Gamma-carboxylation and fragmentation of osteocalcin in human serum defined by mass spectrometry

Rehder, D. S., Gundberg, C. M., Booth, S. L. & Borges, C., Jun 1 2015, In : Molecular and Cellular Proteomics. 14, 6, p. 1546-1555 10 p.

Research output: Contribution to journalArticle

Carboxylation
Osteocalcin
Mass spectrometry
Mass Spectrometry
Vitamin K
4 Citations (Scopus)

Posttranslational modifications of apolipoprotein A-II proteoforms in type 2 diabetes

Azizkhanian, I., Trenchevska, O., Bashawri, Y., Hu, J., Koska, J., Reaven, P. D., Nelson, R. W., Nedelkov, D. & Yassine, H. N., Nov 3 2015, (Accepted/In press) In : Journal of Clinical Lipidology.

Research output: Contribution to journalArticle

Apolipoprotein A-II
Post Translational Protein Processing
Type 2 Diabetes Mellitus
HDL Lipoproteins
Immunoassay
13 Citations (Scopus)

Quantitative mass spectrometric immunoassay for the chemokine RANTES and its variants

Trenchevska, O., Sherma, N. D., Oran, P. E., Reaven, P. D., Nelson, R. W. & Nedelkov, D., Feb 6 2015, In : Journal of Proteomics. 116, p. 15-23 9 p.

Research output: Contribution to journalArticle

Chemokine CCL5
Chemokines
Immunoassay
Assays
Pulse time modulation
15 Citations (Scopus)

Serum amyloid A truncations in type 2 diabetes mellitus

Yassine, H. N., Trenchevska, O., He, H., Borges, C., Nedelkov, D., Mack, W., Kono, N., Koska, J., Reaven, P. D. & Nelson, R. W., Jan 1 2015, In : PLoS One. 10, 1, e0115320.

Research output: Contribution to journalArticle

Serum Amyloid A Protein
amyloid
Medical problems
noninsulin-dependent diabetes mellitus
Type 2 Diabetes Mellitus
13 Citations (Scopus)

The association of human apolipoprotein C-III sialylation proteoforms with plasma triglycerides

Yassine, H. N., Trenchevska, O., Ramrakhiani, A., Parekh, A., Koska, J., Walker, R. W., Billheimer, D., Reaven, P. D., Yen, F. T., Nelson, R. W., Goran, M. I. & Nedelkov, D., Dec 1 2015, In : PLoS One. 10, 12, e0144138.

Research output: Contribution to journalArticle

apolipoprotein C-III
Apolipoproteins C
Apolipoprotein C-III
Triglycerides
triacylglycerols
2014
13 Citations (Scopus)

Delineation of concentration ranges and longitudinal changes of human plasma protein variants

Trenchevska, O., Phillips, D. A., Nelson, R. W. & Nedelkov, D., Jun 23 2014, In : PLoS One. 9, 6, e100713.

Research output: Contribution to journalArticle

blood proteins
Blood Proteins
Proteins
proteins
Polymorphism
6 Citations (Scopus)

Distance from construction site and risk for coccidioidomycosis, Arizona, USA

Blair, J. E., Chang, Y. H. H., Ruiz, Y., Duffy, S., Heinrich, B. E. & Lake, D., 2014, In : Emerging Infectious Diseases. 20, 9, p. 1464-1471 8 p.

Research output: Contribution to journalArticle

Coccidioidomycosis
Soil
Southwestern United States
Coccidioides
Infection
12 Citations (Scopus)

Elevated plasma albumin and apolipoprotein A-I oxidation under suboptimal specimen storage conditions

Borges, C., Rehder, D. S., Jensen, S., Schaab, M. R., Sherma, N. D., Yassine, H., Nikolova, B. & Breburda, C., 2014, In : Molecular and Cellular Proteomics. 13, 7, p. 1890-1899 10 p.

Research output: Contribution to journalArticle

Apolipoprotein A-I
Serum Albumin
Albumins
Oxidation
Methionine
19 Citations (Scopus)

Mass Spectrometric Immunoassay for the qualitative and quantitative analysis of the cytokine Macrophage Migration Inhibitory Factor (MIF)

Sherma, N. D., Borges, C., Trenchevska, O., Jarvis, J. W., Rehder, D. S., Oran, P. E., Nelson, R. W. & Nedelkov, D., 2014, In : Proteome Science. 12, 1, 52.

Research output: Contribution to journalArticle

Macrophage Migration-Inhibitory Factors
Immunoassay
Assays
Cytokines
Chemical analysis
8 Citations (Scopus)

Oxidative protein folding: Nature's knotty challenge

Borges, C. & Lake, D., Jul 20 2014, In : Antioxidants and Redox Signaling. 21, 3, p. 392-395 4 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Disulfides
Oxidation-Reduction
Proteins
26 Citations (Scopus)

Parallel workflow for high-throughput (>1,000 samples/day) quantitative analysis of human insulin-like growth factor 1 using mass spectrometric immunoassay

Oran, P. E., Trenchevska, O., Nedelkov, D., Borges, C., Schaab, M. R., Rehder, D. S., Jarvis, J. W., Sherma, N. D., Shen, L., Krastins, B., Lopez, M. F., Schwenke, D. C., Reaven, P. D. & Nelson, R. W., Mar 24 2014, In : PLoS One. 9, 3, e92801.

Research output: Contribution to journalArticle

Workflow
somatomedins
Somatomedins
immunoassays
Immunoassay
26 Citations (Scopus)

Selective trapping of single mammalian breast cancer cells by insulator-based dielectrophoresis

Bhattacharya, S., Chao, T. C., Ariyasinghe, N., Ruiz, Y., Lake, D., Ros, R. & Ros, A., 2014, In : Analytical and Bioanalytical Chemistry. 406, 7, p. 1855-1865 11 p.

Research output: Contribution to journalArticle

Electrophoresis
Cells
Breast Neoplasms
Microfluidics
Lab-On-A-Chip Devices
86 Citations (Scopus)

Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling

Zhao, Y., Ashcroft, B., Zhang, P., Liu, H., Sen, S., Song, W., Im, J., Gyarfas, B., Manna, S., Biswas, S., Borges, C. & Lindsay, S., 2014, In : Nature Nanotechnology. 9, 6, p. 466-473 8 p.

Research output: Contribution to journalArticle

Peptides
peptides
amino acids
Amino acids
Spectroscopy
10 Citations (Scopus)

Techniques for the analysis of cysteine sulfhydryls and oxidative protein folding

Borges, C. & Sherma, N. D., Jul 20 2014, In : Antioxidants and Redox Signaling. 21, 3, p. 511-531 21 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Disulfides
Cysteine
Proteins
13 Citations (Scopus)

The application of multiple reaction monitoring and multi-analyte profiling to HDL proteins

Yassine, H. N., Jackson, A. M., Borges, C., Billheimer, D., Koh, H., Smith, D., Reaven, P., Lau, S. S. & Borchers, C. H., Jan 8 2014, In : Lipids in Health and Disease. 13, 1, 8.

Research output: Contribution to journalArticle

Monitoring
Proteins
Medical problems
Cardiovascular Diseases
Throughput
19 Citations (Scopus)

The application of multiple reaction monitoring to assess ApoA-I methionine oxidations in diabetes and cardiovascular disease

Yassine, H. N., Jackson, A. M., Reaven, P. D., Nedelkov, D., Nelson, R. W., Lau, S. S. & Borchers, C. H., 2014, In : Translational Proteomics. 4-5, p. 18-24 7 p.

Research output: Contribution to journalArticle

Apolipoprotein A-I
Medical problems
Methionine
Cardiovascular Diseases
Chemical vapor deposition
2013
22 Citations (Scopus)

Expression of quiescin sulfhydryl oxidase 1 is associated with a highly invasive phenotype and correlates with a poor prognosis in Luminal B breast cancer

Katchman, B. A., Ocal, I. T., Cunliffe, H. E., Chang, Y. H., Hostetter, G., Watanabe, A., LoBello, J. & Lake, D., Mar 28 2013, In : Breast Cancer Research. 15, 2, R28.

Research output: Contribution to journalArticle

Breast Neoplasms
Phenotype
Estrogen Receptors
Informatics
sulfhydryl oxidase
35 Citations (Scopus)

Mass spectrometric immunoassay and MRM as targeted MS-based quantitative approaches in biomarker development: Potential applications to cardiovascular disease and diabetes

Yassine, H., Borges, C., Schaab, M. R., Billheimer, D., Stump, C., Reaven, P., Lau, S. S. & Nelson, R., Aug 2013, In : Proteomics - Clinical Applications. 7, 7-8, p. 528-540 13 p.

Research output: Contribution to journalArticle

Biomarkers
Medical problems
Immunoassay
Type 2 Diabetes Mellitus
Cardiovascular Diseases
6 Citations (Scopus)

Multiplexed surrogate analysis of glycotransferase activity in whole biospecimens

Borges, C., Rehder, D. S. & Boffetta, P., Mar 5 2013, In : Analytical Chemistry. 85, 5, p. 2927-2936 10 p.

Research output: Contribution to journalArticle

Polysaccharides
alpha-1,3-mannosylglycoprotein beta-1,4-N-acetylglucosaminyltransferase
Plasmas
Methylation
Monosaccharides
72 Citations (Scopus)

Rapid development of sensitive, high-throughput, quantitative and highly selective mass spectrometric targeted immunoassays for clinically important proteins in human plasma and serum

Krastins, B., Prakash, A., Sarracino, D. A., Nedelkov, D., Niederkofler, E. E., Kiernan, U. A., Nelson, R., Vogelsang, M. S., Vadali, G., Garces, A., Sutton, J. N., Peterman, S., Byram, G., Darbouret, B., Pérusse, J. R., Seidah, N. G., Coulombe, B., Gobom, J., Portelius, E., Pannee, J. & 5 othersBlennow, K., Kulasingam, V., Couchman, L., Moniz, C. & Lopez, M. F., Apr 2013, In : Clinical Biochemistry. 46, 6, p. 399-410 12 p.

Research output: Contribution to journalArticle

Plasma (human)
Immunoassay
Throughput
Assays
Serum
2012
9 Citations (Scopus)

Cancer of the ampulla of Vater: Analysis of the whole genome sequence exposes a potential therapeutic vulnerability

Demeure, M. J., Craig, D. W., Sinari, S., Moses, T. M., Christoforides, A., Dinh, J., Izatt, T., Aldrich, J., Decker, A., Baker, A., Cherni, I., Watanabe, A., Koep, L., Lake, D., Hostetter, G., Trent, J. M., Von Hoff, D. D. & Carpten, J. D., Jul 4 2012, In : Genome Medicine. 4, 7, 56.

Research output: Contribution to journalArticle

Ampulla of Vater
Genome
Neoplasms
Bile Duct Neoplasms
Common Bile Duct