A functional annotation of subproteomes in human plasma

Ping, Peipei; Vondriska, Thomas M.; Creighton, Chad J.; Gandhi, Tejas; Yang, Zixu; Menon, Rajasree; Kwon, Minseok; Cho, Sang Yun; Drwal, Garry; Kellmann, Markus; Peri, Suraj; Suresh, Shubha; Grønborg, Mads; Molina, Henrik; Chaerkady, Raghothama; Rekha, B.; Shet, Arun S.; Gerszten, Robert E.; Wu, Haifeng; Raftery, Mark J.; Wasinger, Valerie C.; Schulz‐Knappe, Peter; Hanash, Samir M.; Paik, Young Ki; Hancock, William S.; States, David J.; Omenn, Gilbert S.; Pandey, Akhilesh

doi:10.1002/9783527609482.ch16

Cited by 14 publications

(21 citation statements)

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“…Proteiner som albumin og immunglobuliner finnes i høye konsentrasjoner, mens det er svaert lave nivåer av proteiner som skyldes lekkasje fra celler (figur 1). Ett gen kan gi opphav til mange forskjellige genprodukter samtidig som modifikasjoner av proteinet etter at det er syntetisert (posttranslasjonelle modifikasjoner) ytterligere øker variabiliteten av proteomet (5). Et anslag er at det finnes ca.…”

Section: Innledningunclassified

Påvisning av nye biomarkører i plasma-proteomet

Berg¹,

Henninge²,

Lund³

2009

Nor J Epidemiol

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SAMMENDRAGSvar på laboratorieanalyser er av avgjørende betydning for ressursbruk i helsevesenet i forbindelse med utredning, behandling og oppfølgning av pasienter. Undersøkelser fra USA viser at ca. 70% av alle beslutninger som foretas i helsevesenet i stor grad er basert på resultater fra laboratoriene (1). Størst betydning for bruk av ressurser og folkehelse har laboratorieanalyser som kan brukes til å identifisere personer med økt risiko for sykdom som kan forebygges eller kureres. De mest dramatiske eksempler på dette finner man for noen dominant arvelige kreftformer hvor en enkelt genetisk undersøkelse kan påvise personer som trenger ekstra oppfølgning og i enkelte tilfeller profylaktisk kirurgisk behandling.Blod utgjør det viktigste materialet for laboratorieundersøkelser. I denne artikkelen vil vi beskrive noen av mulighetene som finnes i letingen etter nye biomarkører i form av proteiner og peptider i plasmaproteomet som betegner det totale uttrykket av proteiner i plasma. Utviklingen av immunometriske og massespektrometriske metoder har åpnet nye muligheter til å finne nye sykdomsmarkører både som "nye" proteiner og i form av modifikasjoner som er dannet etter at proteinet er syntetisert (post-translasjonelle modifikasjoner). Effektiv testing av kombinasjoner av flere titalls markører gjør det mulig å lete etter sykdomsspesifikke "fingeravtrykk" i proteomet. Plasma-proteomet karakteriseres imidlertid også av at bare noen få proteiner utgjør kvantitativt det meste av proteomet og av store konsentrasjonsforskjeller mellom de ulike proteinene. God tilgang på godt karakteriserte kliniske materialer er helt nødvendig for å kunne validere nytten av en ny biomarkør. Et effektivt samarbeid mellom metode-utviklere og biobanker er derfor av avgjørende betydning for hvor raskt en ny biomarkør kan bli en diagnostisk eller prognostisk faktor. ENGLISH SUMMARYDecision making and use of health care resources depend to a large extent on data from in vitro diagnostic procedures. Laboratory results may have its largest impact on diseases that can be prevented or cured. Most dramatically a single genetic analysis can in certain dominantly inherited diseases differentiate between subjects who are at high risk of developing cancer and subjects who have a risk comparable to the general population. Ultimately, the test may identify individuals eligible for curative prophylactic surgery. Blood is the most important specimen for laboratory investigations. This paper describes some of the possibilities that are emerging in the search for new protein and peptide biomarkers in the plasma proteome, which is the total expression of proteins in plasma. The development of new immunometric and mass spectrometric methods has opened new strategies to identify disease markers both as novel proteins and differences in their post-translational modifications. Efficient testing of combinations of tens of markers simultaneously makes it technically possible to search for fingerprints of specific diseases in the proteome. However, a few plasma...

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Section: Innledningunclassified

Påvisning av nye biomarkører i plasma-proteomet

Berg¹,

Henninge²,

Lund³

2009

Nor J Epidemiol

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“…Our approach, which is based on the understanding that the serum glycoproteome originates from a wide range of tissues and proteins can be annotated to various biological pathways (19 ), clusters glycoproteins on the basis of their GO attributes to allow direct comparison of the ranking of such groupings in control and disease samples. A concern in the use of these associations is that some GO assignments are based on computerized sequence similarity searches on data that are not well curated.…”

Section: Go Annotationmentioning

confidence: 99%

Multilectin Affinity Chromatography for Characterization of Multiple Glycoprotein Biomarker Candidates in Serum from Breast Cancer Patients

et al. 2006

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Background:Glycoproteins are often associated with cancer and are important in serum studies, for which glycosylation is a common posttranslational modification. Methods: We used multilectin affinity chromatography (M-LAC) to isolate glycoproteins from the sera of breast cancer patients and controls. The proteins were identified by HPLC-tandem mass spectrometry (MS/MS) analysis of the corresponding tryptic digests. We used the FuncAssociate Gene Ontology program for association analysis of the identified proteins. Biomarker candidates in these groups were comparatively quantitated by use of peak area measurements, with inclusion of an internal standard. We analyzed data for concordance within the ontology association groups for vector of change with the development of breast cancer. Results: Detection of the known low-concentration biomarker HER-2 (8 -24 g/L) enabled us to establish a dynamic range of 10 6 , relative to the amount of albumin, for the depletion step. We then used ELISA to confirm this range. Proteins associated with lipid transport and metabolism, cell growth and maintenance, ion homeostasis, and protease inhibition were found to be differentially regulated in serum from women with breast cancer compared with serum from women without breast cancer.

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“…Large numbers of candidate biomarkers for malignant (Etzioni et al, 2003), autoimmune (Prince, 2005), infectious (Zhang et al, 2002), neurological (Carrette et al, 2003), metabolic (Roelofsen et al, 2004;Schwegler et al, 2005) and cardiovascular (Kittleson and Hare, 2005) diseases have been generated using various high-throughput platforms Ping et al, 2005), but the production of high affinity antibodies necessary for biomarker validation remains slow and costly. New methods such as high-throughput screening by flow sorting of recombinant antibodies (scFv) displayed by yeast (Feldhaus et al, 2003) can accelerate the identification of antigen-specific scFv.…”

Section: Introductionmentioning

confidence: 99%

Method for generation of in vivo biotinylated recombinant antibodies by yeast mating

Scholler

Garvik

Quarles

et al. 2006

Journal of Immunological Methods

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We describe here a novel method for generation of yeast-secreted, in vivo biotinylated recombinant antibodies, or biobodies. Biobodies are secreted by diploid yeast resulting from the fusion of two haploid yeast of opposite mating type. One yeast carries a cDNA encoding an antibody recognition sequence fused to an IgA1 hinge and a biotin acceptor site (BCCP) at the C-terminus; the other carries a cDNA encoding an E. Coli biotin ligase (BirA) fused to KEX2 golgi-localization sequences, so that BirA can catalyze the biotin transfer to the recognition sequence-fused BCCP within the yeast secretory compartment. We illustrate this technology with biobodies against HE4, a biomarker for ovarian carcinoma. Anti-HE4 biobodies were derived from clones or pools of anti-HE4-specific yeast-display scFv, constituting respectively monoclonal (mBb) or polyclonal (pBb) biobodies. Anti-HE4 biobodies were secreted directly biotinylated thus bound to labeled-streptavidin and streptavidin-coated surfaces without Ni-purification. Anti-HE4 biobodies demonstrated specificity and sensitivity by ELISA assays, flow cytometry analysis and western blots prior to any maturation; dissociation equilibrium constants as measured by surface plasmon resonance sensor were of K d = 4.8×10 -9 M and K d =5.1×10 -9 M before and after Ni-purification respectively. Thus, yeast mating permits cost-effective generation of biotinylated recombinant antibodies of high affinity.

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A functional annotation of subproteomes in human plasma

Cited by 14 publications

References 0 publications

Påvisning av nye biomarkører i plasma-proteomet

Påvisning av nye biomarkører i plasma-proteomet

Multilectin Affinity Chromatography for Characterization of Multiple Glycoprotein Biomarker Candidates in Serum from Breast Cancer Patients

Method for generation of in vivo biotinylated recombinant antibodies by yeast mating

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