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Wang L, Dehm SM, Hillman DW, Sicotte H, Tan W, Gormley M, Bhargava V, Jimenez R, Xie F, Yin P, Qin S, Quevedo F, Costello BA, Pitot HC, Ho T, Bryce AH, Ye Z, Li Y, Eiken P, Vedell PT, Barman P, McMenomy BP, Atwell TD, Carlson RE, Ellingson M, Eckloff BW, Qin R, Ou F, Hart SN, Huang H, Jen J, Wieben ED, Kalari KR, Weinshilboum RM, Wang L, Kohli M. A prospective genome-wide study of prostate cancer metastases reveals association of wnt pathway activation and increased cell cycle proliferation with primary resistance to abiraterone acetate-prednisone. Ann Oncol 2019; 29:352-360. [PMID: 29069303 DOI: 10.1093/annonc/mdx689] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background Genomic aberrations have been identified in metastatic castration-resistant prostate cancer (mCRPC), but molecular predictors of resistance to abiraterone acetate/prednisone (AA/P) treatment are not known. Patients and methods In a prospective clinical trial, mCRPC patients underwent whole-exome sequencing (n = 82) and RNA sequencing (n = 75) of metastatic biopsies before initiating AA/P with the objective of identifying genomic alterations associated with resistance to AA/P. Primary resistance was determined at 12 weeks of treatment using criteria for progression that included serum prostate-specific antigen measurement, bone and computerized tomography imaging and symptom assessments. Acquired resistance was determined using the end point of time to treatment change (TTTC), defined as time from enrollment until change in treatment from progressive disease. Associations of genomic and transcriptomic alterations with primary resistance were determined using logistic regression, Fisher's exact test, single and multivariate analyses. Cox regression models were utilized for determining association of genomic and transcriptomic alterations with TTTC. Results At 12 weeks, 32 patients in the cohort had progressed (nonresponders). Median study follow-up was 32.1 months by which time 58 patients had switched treatments due to progression. Median TTTC was 10.1 months (interquartile range: 4.4-24.1). Genes in the Wnt/β-catenin pathway were more frequently mutated and negative regulators of Wnt/β-catenin signaling were more frequently deleted or displayed reduced mRNA expression in nonresponders. Additionally, mRNA expression of cell cycle regulatory genes was increased in nonresponders. In multivariate models, increased cell cycle proliferation scores (≥ 50) were associated with shorter TTTC (hazard ratio = 2.11, 95% confidence interval: 1.17-3.80; P = 0.01). Conclusions Wnt/β-catenin pathway activation and increased cell cycle progression scores can serve as molecular markers for predicting resistance to AA/P therapy.
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Affiliation(s)
- L Wang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, USA
| | - S M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, USA; Department of Urology, University of Minnesota, Minneapolis, USA
| | - D W Hillman
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - H Sicotte
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - W Tan
- Department of Medicine, Mayo Clinic, Jacksonville, USA
| | - M Gormley
- Janssen Research and Development, Spring House, Philadelphia, USA
| | - V Bhargava
- Janssen Research and Development, Spring House, Philadelphia, USA
| | - R Jimenez
- Department of Pathology and Lab Medicine, Mayo Clinic, Rochester, USA
| | - F Xie
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, USA
| | - P Yin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, USA
| | - S Qin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, USA
| | - F Quevedo
- Department of Oncology, Mayo Clinic, Rochester, USA
| | - B A Costello
- Department of Oncology, Mayo Clinic, Rochester, USA
| | - H C Pitot
- Department of Oncology, Mayo Clinic, Rochester, USA
| | - T Ho
- Department of Medicine, Mayo Clinic, Scottsdale, USA
| | - A H Bryce
- Department of Medicine, Mayo Clinic, Scottsdale, USA
| | - Z Ye
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, USA
| | - Y Li
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - P Eiken
- Department of Radiology, Mayo Clinic, Rochester, USA
| | - P T Vedell
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - P Barman
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - B P McMenomy
- Department of Radiology, Mayo Clinic, Rochester, USA
| | - T D Atwell
- Department of Radiology, Mayo Clinic, Rochester, USA
| | - R E Carlson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - M Ellingson
- Medical Genetics, Mayo Clinic, Rochester, USA
| | - B W Eckloff
- Medical Genome Facility, Mayo Clinic, Rochester, USA
| | - R Qin
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - F Ou
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - S N Hart
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - H Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, USA
| | - J Jen
- Medical Genome Facility, Mayo Clinic, Rochester, USA; Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, USA
| | - E D Wieben
- Medical Genome Facility, Mayo Clinic, Rochester, USA
| | - K R Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - R M Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, USA
| | - L Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, USA.
| | - M Kohli
- Department of Oncology, Mayo Clinic, Rochester, USA.
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Hu G, Dasari S, Asmann YW, Greipp PT, Knudson RA, Benson HK, Li Y, Eckloff BW, Jen J, Link BK, Jiang L, Sidhu JS, Wellik LE, Witzig TE, Bennani NN, Cerhan JR, Boddicker RL, Feldman AL. Targetable fusions of the FRK tyrosine kinase in ALK-negative anaplastic large cell lymphoma. Leukemia 2017; 32:565-569. [PMID: 29026208 PMCID: PMC5803446 DOI: 10.1038/leu.2017.309] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- G Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - S Dasari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Y W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - P T Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - R A Knudson
- Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - H K Benson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Y Li
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - B W Eckloff
- Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - J Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - B K Link
- Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - L Jiang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL, USA
| | - J S Sidhu
- Department of Pathology and Laboratory Medicine, United Health Services Hospitals, Johnson City/Binghamton, NY, USA
| | - L E Wellik
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - T E Witzig
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - N N Bennani
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - J R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - R L Boddicker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - A L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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Wu TY, Peng Y, Pelleymounter LL, Moon I, Eckloff BW, Wieben ED, Yee VC, Weinshilboum RM. Pharmacogenetics of the mycophenolic acid targets inosine monophosphate dehydrogenases IMPDH1 and IMPDH2: gene sequence variation and functional genomics. Br J Pharmacol 2011; 161:1584-98. [PMID: 20718729 DOI: 10.1111/j.1476-5381.2010.00987.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND AND PURPOSE Inosine monophosphate dehydrogenases, encoded by IMPDH1 and IMPDH2, are targets for the important immunosuppressive drug, mycophenolic acid (MPA). Variation in MPA response may result, in part, from genetic variation in IMPDH1 and IMPDH2. EXPERIMENTAL APPROACH We resequenced IMPDH1 and IMPDH2 using DNA from 288 individuals from three ethnic groups and performed functional genomic studies of the sequence variants observed. KEY RESULTS We identified 73 single nucleotide polymorphisms (SNPs) in IMPDH1, 59 novel, and 25 SNPs, 24 novel, in IMPDH2. One novel IMPDH1 allozyme (Leu275) had 10.2% of the wild-type activity as a result of accelerated protein degradation. Decreased activity of the previously reported IMPDH2 Phe263 allozyme was primarily due to decreased protein quantity, also with accelerated degradation. These observations with regard to the functional implications of variant allozymes were supported by the IMPDH1 and IMPDH2 X-ray crystal structures. A novel IMPDH2 intron 1 SNP, G > C IVS1(93), was associated with decreased mRNA quantity, possibly because of altered transcription. CONCLUSIONS AND IMPLICATIONS These results provide insight into the nature and extent of sequence variation in the IMPDH1 and IMPDH2 genes. They also describe the influence of gene sequence variation that alters the encoded amino acids on IMPDH function and provide a foundation for future translational studies designed to correlate sequence variation in these genes with outcomes in patients treated with MPA.
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Affiliation(s)
- T-Y Wu
- Division of Clinical Pharmacology, Department of Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
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Hildebrandt MAT, Carrington DP, Thomae BA, Eckloff BW, Schaid DJ, Yee VC, Weinshilboum RM, Wieben ED. Genetic diversity and function in the human cytosolic sulfotransferases. Pharmacogenomics J 2006; 7:133-43. [PMID: 16801938 DOI: 10.1038/sj.tpj.6500404] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Amino-acid substitutions, which result from common nonsynonymous (NS) polymorphisms, may dramatically alter the function of the encoded protein. Gaining insight into how these substitutions alter function is a step toward acquiring predictability. In this study, we incorporated gene resequencing, functional genomics, amino-acid characterization and crystal structure analysis for the cytosolic sulfotransferases (SULTs) to attempt to gain predictability regarding the function of variant allozymes. Previously, four SULT genes were resequenced in 118 DNA samples. With additional resequencing of the remaining eight SULT family members in the same DNA samples, a total of 217 polymorphisms were revealed. Of 64 polymorphisms identified within 8785 bp of coding regions from SULT genes examined, 25 were synonymous and 39 were NS. Overall, the proportion of synonymous changes was greater than expected from a random distribution of mutations, suggesting the presence of a selective pressure against amino-acid substitutions. Functional data for common variants of five SULT genes have been previously published. These data, together with the SULT1A1 variant allozyme data presented in this paper, showed that the major mechanism by which amino acid changes altered function in a transient expression system was through decreases in immunoreactive protein rather than changes in enzyme kinetics. Additional insight with regard to mechanisms by which NS single nucleotide polymorphisms alter function was sought by analysis of evolutionary conservation, physicochemical properties of the amino-acid substitutions and crystal structure analysis. Neither individual amino-acid characteristics nor structural models were able to accurately and reliably predict the function of variant allozymes. These results suggest that common amino-acid substitutions may not dramatically alter the protein structure, but affect interactions with the cellular environment that are currently not well understood.
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Affiliation(s)
- M A T Hildebrandt
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN 55985, USA
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Martin YN, Salavaggione OE, Pelleymounter LL, Eckloff BW, Wieben ED, Weinshilboum RM. 31 HUMAN METHYLENETETRAHYDROFOLATE REDUCTASE PHARMACOGENOMICS: GENE RESEQUENCING AND FUNCTIONAL GENOMIC STUDIES. J Investig Med 2005. [DOI: 10.2310/6650.2005.00206.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Shield AJ, Thomae BA, Eckloff BW, Wieben ED, Weinshilboum RM. Human catechol O-methyltransferase genetic variation: gene resequencing and functional characterization of variant allozymes. Mol Psychiatry 2004; 9:151-60. [PMID: 14966473 DOI: 10.1038/sj.mp.4001386] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Catechol O-methyltransferase (COMT) plays an important role in the metabolism of catecholamines, catecholestrogens and catechol drugs. A common COMT G472A genetic polymorphism (Val108/158Met) that was identified previously is associated with decreased levels of enzyme activity and has been implicated as a possible risk factor for neuropsychiatric disease. We set out to 'resequence' the human COMT gene using DNA samples from 60 African-American and 60 Caucasian-American subjects. A total of 23 single nucleotide polymorphisms (SNPs), including a novel nonsynonymous cSNP present only in DNA from African-American subjects, and one insertion/deletion were observed. The wild type (WT) and two variant allozymes, Thr52 and Met108, were transiently expressed in COS-1 and HEK293 cells. There was no significant change in level of COMT activity for the Thr52 variant allozyme, but there was a 40% decrease in the level of activity in cells transfected with the Met108 construct. Apparent K(m) values of the WT and variant allozymes for the two reaction cosubstrates differed slightly, but significantly, for 3,4-dihydroxybenzoic acid but not for S-adenosyl-L-methionine. The Met108 allozyme displayed a 70-90% decrease in immunoreactive protein when compared with WT, but there was no significant change in the level of immunoreactive protein for Thr52. A significant decrease in the level of immunoreactive protein was also observed in hepatic biopsy samples from patients homozygous for the allele encoding Met108. These observations represent steps toward an understanding of molecular genetic mechanisms responsible for variation in COMT level and/or properties, variation that may contribute to the pathophysiology of neuropsychiatric disease.
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Affiliation(s)
- A J Shield
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Medical School, Mayo Clinic, Mayo Foundation, Rochester, MN 55905, USA
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Thomae BA, Eckloff BW, Freimuth RR, Wieben ED, Weinshilboum RM. Human sulfotransferase SULT2A1 pharmacogenetics: genotype-to-phenotype studies. Pharmacogenomics J 2002; 2:48-56. [PMID: 11990382 DOI: 10.1038/sj.tpj.6500089] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
SULT2A1 catalyzes the sulfate conjugation of dehydroepiandrosterone (DHEA) as well as other steroids. As a step toward pharmacogenetic studies, we have 'resequenced' SULT2A1 using 60 DNA samples from African-American and 60 samples from Caucasian-American subjects. All exons, splice junctions and approximately 370 bp located 5' of the site of transcription initiation were sequenced. We observed 15 single nucleotide polymorphisms (SNPs), including three non-synonymous coding SNPs (cSNPs) that were present only in DNA from African-American subjects. Linkage analysis revealed that two of the nonsynonymous cSNPs were tightly linked. Expression constructs were created for all nonsynonymous cSNPs observed, including a 'double variant' construct that included the two linked cSNPs, and those constructs were expressed in COS-1 cells. SULT2A1 activity was significantly decreased for three of the four variant allozymes. Western blot analysis demonstrated that decreased levels of immunoreactive protein appeared to be the major mechanism responsible for decreases in activity, although apparent Km values also varied among the recombinant allozymes. In addition, the most common of the nonsynonymous cSNPs disrupted the portion of SULT2A1 involved with dimerization, and this variant allozyme behaved as a monomer rather than a dimer during gel filtration chromatography. These observations indicate that common genetic polymorphisms for SULT2A1 can result in reductions in levels of both activity and enzyme protein. They also raise the possibility of ethnic-specific pharmacogenetic variation in SULT2A1-catalyzed sulfation of both endogenous and exogenous substrates for this phase II drug-metabolizing enzyme.
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Affiliation(s)
- B A Thomae
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Medical School-Mayo Clinic-Mayo Foundation, Rochester, MN 55905, USA
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8
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Eckloff BW, Podzorski RP, Kline BC, Cockerill FR. A comparison of 16S ribosomal DNA sequences from five isolates of Helicobacter pylori. Int J Syst Bacteriol 1994; 44:320-3. [PMID: 8186097 DOI: 10.1099/00207713-44-2-320] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Other workers have found that clinical isolates of Helicobacter pylori exhibit very extensive DNA sequence polymorphisms when they are examined by ribotyping or some other genomic sequence characterization technique. In fact, it is rare to find similar clones, much less identical ones, among isolates. We found that the levels of divergence between the 16S ribosomal DNA sequences of individual organisms and the consensus sequence of the five isolates which we examined ranged from 0.2 to 0.5%. In contrast, other workers have shown that levels of divergence between the 16S ribosomal DNA sequence of H. pylori and the 16S ribosomal DNA sequences of four other Helicobacter species range from 2.7 to 8.0%. Our results show that the H. pylori 16S ribosomal DNA is not very polymorphic and support the conclusion that H. pylori is a unique species.
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Affiliation(s)
- B W Eckloff
- Department of Biochemistry and Molecular Biology, Mayo Clinic and Foundation, Rochester, Minnesota 55905
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Kline BC, Sandhu GS, Eckloff BW, Aleff RA. Site-specific proteolysis of mini-F plasmid replication protein RepE destroys initiator function and generates an incompatibility substance. J Bacteriol 1992; 174:3004-10. [PMID: 1569028 PMCID: PMC205955 DOI: 10.1128/jb.174.9.3004-3010.1992] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Plasmid F replication is controlled by a plasmid-specified Rep protein with both autorepressor and initiator functions. The mechanism by which these two functions of a Rep protein are balanced to achieve stable replication is unknown; however, we speculated in prior work that Rep protein modification could be involved. We report here that naturally proteolyzed F RepE protein has been detected and characterized. The processed molecule lost the first 17 N-terminal aminoacyl residues and initiator function but acquired increased specific DNA-binding affinity in the presence of Escherichia coli chromosomal DNA. When supplied in trans, the altered protein acts as an incompatibility substance and eliminates maintenance of F'lac. These findings indicate that protein processing has the potential to contribute to the overall control of DNA replication.
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Affiliation(s)
- B C Kline
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota 55905
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Sandhu GS, Eckloff BW, Kline BC. Chemiluminescent substrates increase sensitivity of antigen detection in western blots. Biotechniques 1991; 11:14-6. [PMID: 1954010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Replacement of colorimetric substrates in Western blots by chemiluminescent reagents enhances the sensitivity of detection by more than an order of magnitude. Protein levels beyond the detection limit of colorimetric substrates can be consistently detected without modifying pre-existing laboratory protocols.
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Affiliation(s)
- G S Sandhu
- Dept. of Biochemistry and Molecular Biology, Mayo Clinic and Foundation, Rochester, MN 55905
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