• Quantitation of the radiotherapeutic importance of naturally-hypoxic normal tissues from collated experiments with rodents using single doses.

      Hendry, Jolyon H; Paterson Laboratories, Christie Hospital and Holt Radium Institute, Manchester (1979-07)
    • Quantitative analysis of biomarkers by LC-MS/MS.

      Cummings, Jeffrey; Unwin, Richard D; Veenstra, Timothy D; University of Manchester, Manchester, UK. jcummings@picr.man.ac.uk (2009-05-01)
    • Quantitative and qualitative alterations of heparan sulfate in fibrogenic liver diseases and hepatocellular cancer.

      Tátrai, Péter; Egedi, Krisztina; Somorácz, Aron; Van Kuppevelt, Toin H; Ten Dam, Gerdy; Lyon, Malcolm; Deakin, Jon A; Kiss, András; Schaff, Zsuzsa; Kovalszky, Ilona; et al. (2010-05)
      Heparan sulfate (HS), due to its ability to interact with a multitude of HS-binding factors, is involved in a variety of physiological and pathological processes. Remarkably diverse fine structure of HS, shaped by non-exhaustive enzymatic modifications, influences the interaction of HS with its partners. Here we characterized the HS profile of normal human and rat liver, as well as alterations of HS related to liver fibrogenesis and carcinogenesis, by using sulfation-specific antibodies. The HS immunopattern was compared with the immunolocalization of selected HS proteoglycans. HS samples from normal liver and hepatocellular carcinoma (HCC) were subjected to disaccharide analysis. Expression changes of nine HS-modifying enzymes in human fibrogenic diseases and HCC were measured by quantitative RT-PCR. Increased abundance and altered immunolocalization of HS was paralleled by elevated mRNA levels of HS-modifying enzymes in the diseased liver. The strong immunoreactivity of the normal liver for 3-O-sulfated epitope further increased with disease, along with upregulation of 3-OST-1. Modest 6-O-undersulfation of HCC HS is probably explained by Sulf overexpression. Our results may prompt further investigation of the role of highly 3-O-sulfated and partially 6-O-desulfated HS in pathological processes such as hepatitis virus entry and aberrant growth factor signaling in fibrogenic liver diseases and HCC.
    • A quantitative comparison of cytogenetic effects of anti-tumor agents.

      Parkes, D J; Scott, David; Paterson Laboratories, Christie Hospital and Holt Radium Institute, Withington, Manchester, M20 9BX, UK (1982)
      The relative potency of different anti-tumor agents in inducing structural and numerical chromosome abnormalities and SCEs was assessed by making comparisons at equitoxic doses, measured in terms of colony forming ability, in cultured diploid human fibroblasts. At approximately 20% survival the relative potency of X-rays, daunorubicin, nitrogen mustard, adriamycin, and actinomycin D in inducing structural aberrations was 1.0, 0.85, 0.26, 0.22, and zero, respectively. SCE induction was quantitatively unrelated to the induction of chromosome aberrations. No numerical changes were observed. Accurate assessment of the yields of chromosome aberrations requires the use of multiple sampling times in asynchronous populations.
    • A quantitative description of the action of high-dose pulses of radiation on aerated acid solutions containing ferrous and chloride ions

      Bjergbakke, E; Navaratnam, S; Parsons, B; Swallow, A John; Riso National Laboratory, Post Box 49, DK-4000, Roskilde, Denmark (1987)
    • Quantitative development of adherent cell colonies in bone marrow cell culture in vitro.

      Mori, K; Fujitake, H; Okubo, H; Dexter, T Michael; Ito, Y (1979-04)
      Quantification of the formation of adherent cell colonies in bone marrow cell culture was attempted. By secondary transfer of the bone marrow cells as a single cell suspension after 4 days' culture of fine marrow fragments, a linear relationship was obtained between the number of adherent cell colonies developing and the number of cells secondarily inoculated into the culture bottle. This suggests that 4 days' culture of the bone marrow cells with close intercellular interactions is sufficient for the 'conditioning' of the cells to develop adherent cell colonies. Activity of such colonies to support haemopoietic stem cell proliferation was also shown.
    • A quantitative histometric murine in vivo model of radiation-induced oral mucositis.

      Wardley, Andrew M; Booth, Dawn; Roberts, Stephen A; Scarffe, J Howard; Potten, Christopher S; CRC Epithelial Biology Group, UK. (1998-07)
      Gastrointestinal toxicity is a limiting factor in the effectiveness of cancer therapy. This toxicity is most visible in the mouth. There is considerable interest in developing strategies involving growth-factor manipulation of the epithelial stem cells to afford protection to these cells during treatment and/or to speed up the regenerative process following treatment. In order for this to be achieved, studies have to be undertaken in animal systems to demonstrate the proof of principle and determine optimal protocols. Here, a murine model for oral mucositis based on measurements of tissue cellularity at various times after exposure to radiation was used to investigate cytotoxicity. Several sites in the mouth were analysed and the pronounced circadian rhythm in these various epithelial sites determined. The circadian rhythm is important in that it would determine the timing of administration of growth factors. A microscope with an interactive computer was used to define areas of epithelium and lengths of basal layer, within which, and along which, the total number of cell nuclei was determined over a range of times following exposure to 10, 20 and 30 Gy of X-rays. For various practical reasons, the ventral surface of the tongue was identified as the most appropriate tissue to analyse. Here, measurements of cellularity reached minimum values between 6 and 8 days following 20 Gy. Labelling of S-phase cells demonstrated foci of regeneration and a burst of proliferative regeneration that commenced at about 5 days and reached peak values at 8 days after irradiation. This burst of regenerative proliferation was coincident with the minimum in tissue cellularity on about day 8. The lower dose of radiation (10 Gy) had minimal effects on cellularity: after the higher dose (30 Gy), there was clearly a more severe level of cellular depletion. This quantitative model of oral mucositis could be used to study the effects of other cytotoxics, including combinations of agents, and the potential role of growth factors to reduce the severity of the cellular depletion and to speed up the kinetics of regeneration.
    • Quantitative imaging biomarkers in the clinical development of targeted therapeutics: current and future perspectives.

      O'Connor, James P B; Jackson, Alan; Asselin, Marie-Claude; Buckley, David L; Parker, Geoff J M; Jayson, Gordon C; Imaging Science and Biomedical Engineering, University of Manchester, Manchester, UK. james.o'connor@manchester.ac.uk (2008-08)
      Targeted therapeutics have challenged how imaging techniques assess tumour response to treatment because many new agents are thought to cause cytostasis rather than cytotoxicity. Advanced tracer development, image acquisition, and image analysis have been used to produce quantitative biomarkers of pathophysiology, with particular focus on measurement of tumour vascular characteristics. Here, we critically appraise strategies available to generate imaging biomarkers for use in development of targeted therapeutics. We consider important practical and technical features of data acquisition and analysis because these factors determine the precise physiological meaning of every biomarker. We discuss the merits of volume-based and other size-based metrics for assessment of targeted therapeutics, and we examine the strengths and weaknesses of CT, MRI, and PET biomarkers derived from conventional clinical data. We review imaging biomarkers of tumour microvasculature and discuss imaging strategies that probe other physiological processes including cell proliferation, apoptosis, and tumour invasion. We conclude on the need to develop comprehensive compound-specific imaging biomarkers that are appropriate for every class of targeted therapeutics, and to investigate the complementary information given in multimodality imaging studies of targeted therapeutics.
    • Quantitative mass spectrometry-based techniques for clinical use: biomarker identification and quantification.

      Simpson, Kathryn L; Whetton, Anthony D; Dive, Caroline; Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester, M20 4BX, United Kingdom. KSimpson@PICR.man.ac.uk (2009-05-01)
      The potential for development of personalised medicine through the characterisation of novel biomarkers is an exciting prospect for improved patient care. Recent advances in mass spectrometric (MS) techniques, liquid phase analyte separation and bioinformatic tools for high throughput now mean that this goal may soon become a reality. However, there are challenges to be overcome for the identification and validation of robust biomarkers. Bio-fluids such as plasma and serum are a rich source of protein, many of which may reflect disease status, and due to the ease of sampling and handling, novel blood borne biomarkers are very much sought after. MS-based methods for high throughput protein identification and quantification are now available such that the issues arising from the huge dynamic range of proteins present in plasma may be overcome, allowing deep mining of the blood proteome to reveal novel biomarker signatures for clinical use. In addition, the development of sensitive MS-based methods for biomarker validation may bypass the bottleneck created by the need for generation and usage of reliable antibodies prior to large scale screening. In this review, we discuss the MS-based methods that are available for clinical proteomic analysis and highlight the progress made and future challenges faced in this cutting edge area of research.
    • Quantitative multiplexed quantum dot immunohistochemistry.

      Sweeney, Elizabeth; Ward, Timothy H; Gray, N; Womack, C; Jayson, Gordon C; Hughes, Andrew; Dive, Caroline; Byers, Richard J; Clinical and Experimental Pharmacology, Paterson Institute for Cancer Research, Wilmslow Road, Manchester, 420 4BX, UK. (2008-09-19)
      Quantum dots are photostable fluorescent semiconductor nanocrystals possessing wide excitation and bright narrow, symmetrical, emission spectra. These characteristics have engendered considerable interest in their application in multiplex immunohistochemistry for biomarker quantification and co-localisation in clinical samples. Robust quantitation allows biomarker validation, and there is growing need for multiplex staining due to limited quantity of clinical samples. Most reported multiplexed quantum dot staining used sequential methods that are laborious and impractical in a high-throughput setting. Problems associated with sequential multiplex staining have been investigated and a method developed using QDs conjugated to biotinylated primary antibodies, enabling simultaneous multiplex staining with three antibodies. CD34, Cytokeratin 18 and cleaved Caspase 3 were triplexed in tonsillar tissue using an 8h protocol, each localised to separate cellular compartments. This demonstrates utility of the method for biomarker measurement enabling rapid measurement of multiple co-localised biomarkers on single paraffin tissue sections, of importance for clinical trial studies.
    • Quantitative phosphoproteome analysis of embryonic stem cell differentiation toward blood.

      Piazzi, M; Williamson, Andrew J K; Lee, Chia-Fang; Pearson, Stella; Lacaud, Georges; Kouskoff, Valerie; McCubrey, James A; Cocco, L; Whetton, Anthony D; Cell Signaling Laboratory, Department of Biomedical Science (DIBINEM), University of Bologna, Italy (2015-03-26)
      Murine embryonic stem (ES) cells can differentiate in vitro into three germ layers (endodermic, mesodermic, ectodermic). Studies on the differentiation of these cells to specific early differentiation stages has been aided by an ES cell line carrying the Green Fluorescent Protein (GFP) targeted to the Brachyury (Bry) locus which marks mesoderm commitment. Furthermore, expression of the Vascular Endothelial Growth Factor receptor 2 (Flk1) along with Bry defines hemangioblast commitment. Isobaric-tag for relative and absolute quantification (iTRAQTM) and phosphopeptide enrichment coupled to liquid chromatography separation and mass spectrometry allow the study of phosphorylation changes occurring at different stages of ES cell development using Bry and Flk1 expression respectively. We identified and relatively quantified 37 phosphoentities which are modulated during mesoderm-induced ES cells differentiation, comparing epiblast-like, early mesoderm and hemangioblast-enriched cells. Among the proteins differentially phosphorylated toward mesoderm differentiation were: the epigenetic regulator Dnmt3b, the protein kinase GSK3b, the chromatin remodeling factor Smarcc1, the transcription factor Utf1; as well as protein specifically related to stem cell differentiation, as Eomes, Hmga2, Ints1 and Rif1. As most key factors regulating early hematopoietic development have also been implicated in various types of leukemia, understanding the post-translational modifications driving their regulation during normal development could result in a better comprehension of their roles during abnormal hematopoiesis in leukemia.
    • Quantitative proteomic analysis reveals maturation as a mechanism underlying glucocorticoid resistance in B lineage ALL and re-sensitization by JNK inhibition.

      Nicholson, L; Evans, Caroline A; Matheson, E; Minto, L; Keilty, C; Sanichar, M; Case, M; Schwab, C; Williamson, D; Rainer, J; et al. (2015-08-27)
      Glucocorticoid (GC) resistance is a continuing clinical problem in childhood acute lymphoblastic leukaemia (ALL) but the underlying mechanisms remain unclear. A proteomic approach was used to compare profiles of the B-lineage ALL GC-sensitive cell line, PreB 697, and its GC-resistant sub-line, R3F9, pre- and post-dexamethasone exposure. PAX5, a transcription factor critical to B-cell development was differentially regulated in the PreB 697 compared to the R3F9 cell line in response to GC. PAX5 basal protein expression was less in R3F9 compared to its GC-sensitive parent and confirmed to be lower in other GC-resistant sub-lines of Pre B 697 and was associated with a decreased expression of the PAX5 transcriptional target, CD19. Gene set enrichment analysis showed that increasing GC-resistance was associated with differentiation from preB-II to an immature B-lymphocyte stage. GC-resistant sub-lines were shown to have higher levels of phosphorylated JNK compared to the parent line and JNK inhibition caused re-sensitization to GC. Exploiting this maturation may be key to overcoming GC resistance and targeting signalling pathways linked to the maturation state, such as JNK, may be a novel approach.
    • Quantitative proteomic analysis using isobaric protein tags enables rapid comparison of changes in transcript and protein levels in transformed cells.

      Unwin, Richard D; Pierce, Andrew; Watson, Rod B; Sternberg, David W; Whetton, Anthony D; Department of Faculty of Medical and Human Sciences, University of Manchester, Christie Hospital, Withington, Manchester, M20 9BX, United Kingdom. (2005-07)
      Isobaric tags for relative and absolute quantitation, an approach to concurrent, relative quantification of proteins present in four cell preparations, have recently been described. To validate this approach using complex mammalian cell samples that show subtle differences in protein levels, a model stem cell-like cell line (FDCP-mix) in the presence or absence of the leukemogenic oncogene TEL/PDGFRbeta has been studied. Cell lysates were proteolytically digested, and peptides within each sample were labeled with one of four isobaric, isotope-coded tags via their N-terminal and/or lysine side chains. The four labeled samples are mixed and peptides separated by two-dimensional liquid chromatography online to a mass spectrometer (LC-MS). Upon peptide fragmentation, each tag releases a distinct mass reporter ion; the ratio of the four reporters therefore gives relative abundances of the given peptide. Relative quantification of proteins is derived using summed data from a number of peptides. TEL/PDGFRbeta leukemic oncogene-mediated changes in protein levels were compared with those seen in microarray analysis of control and transfected FDCP-mix cells. Changes at the protein level in most cases reflected those seen at the transcriptome level. Nonetheless, novel differences in protein expression were found that indicate potential mechanisms for effects of this oncogene.
    • Quantitative proteomics analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis.

      Williamson, Andrew J K; Smith, Duncan L; Blinco, David; Unwin, Richard D; Pearson, Stella; Wilson, Claire L; Miller, Crispin J; Lancashire, Lee J; Lacaud, Georges; Kouskoff, Valerie; et al. (2008-03)
      Embryonic stem (ES) cells can differentiate in vitro to produce the endothelial and hematopoietic precursor, the hemangioblasts, which are derived from the mesoderm germ layer. Differentiation of Bry(GFP/+) ES cell to hemangioblasts can be followed by the expression of the Bry(GFP/+) and Flk1 genes. Proteomic and transcriptomic changes during this differentiation process were analyzed to identify mechanisms for phenotypic change during early differentiation. Three populations of differentiating Bry(GFP) ES cells were obtained by flow cytometric sorting, GFP-Flk1- (epiblast), GFP+Flk1- (mesoderm), and GFP+Flk1+ (hemangioblast). Microarray analyses and relative quantification two-dimensional LCLC-MS/MS on nuclear extracts were performed. We identified and quantified 2389 proteins, 1057 of which were associated to their microarray probe set. These included a variety of low abundance transcription factors, e.g. UTF1, Sox2, Oct4, and E2F4, demonstrating a high level of proteomic penetrance. When paired comparisons of changes in the mRNA and protein expression levels were performed low levels of correlation were found. A strong correlation between isobaric tag-derived relative quantification and Western blot analysis was found for a number of nuclear proteins. Pathway and ontology analysis identified proteins known to be involved in the regulation of stem cell differentiation, and proteins with no described function in early ES cell development were also shown to change markedly at the proteome level only. ES cell development is regulated at the mRNA and protein level.
    • Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells.

      Unwin, Richard D; Smith, Duncan L; Blinco, David; Wilson, Claire L; Miller, Crispin J; Evans, Caroline A; Jaworska, Ewa; Baldwin, Stephen A; Barnes, Kay; Pierce, Andrew; et al. (2006-06-15)
      The proteome is determined by rates of transcription, translation, and protein turnover. Definition of stem cell populations therefore requires a stem cell proteome signature. However, the limit to the number of primary cells available has restricted extensive proteomic analysis. We present a mass spectrometric method using an isobaric covalent modification of peptides for relative quantification (iTRAQ), which was employed to compare the proteomes of approximately 1 million long-term reconstituting hematopoietic stem cells (Lin(-)Sca(+)Kit(+); LSK(+)) and non-long-term reconstituting progenitor cells (Lin(-)Sca(+)Kit(-); LSK(-)), respectively. Extensive 2-dimensional liquid chromatography (LC) peptide separation prior to mass spectrometry (MS) enabled enhanced proteome coverage with relative quantification of 948 proteins. Of the 145 changes in the proteome, 54% were not seen in the transcriptome. Hypoxia-related changes in proteins controlling metabolism and oxidative protection were observed, indicating that LSK(+) cells are adapted for anaerobic environments. This approach can define proteomic changes in primary samples, thereby characterizing the molecular signature of stem cells and their progeny.
    • Quantitative replicon analysis of DNA synthesis in cancer-prone conditions and the defects in Bloom's syndrome.

      Ockey, Charles H; Paterson Laboratories, Christie Hospital and Holt Radium Institute, Manchester (1979-12)
      A quantitative method of replicon analysis of DNA fibre autoradiographs has been used to study the relationship between mean rate of DNA chain growth (R) and distance between adjacent replicons (ID) in fibroblasts from cancer-prone conditions. Results are expressed in terms of the mean linear regression R = delta +(K.ID)10-2. When replicon behaviour was examined in cells from patients with ataxia telangiectasia, basal cell naevus and Bloom's syndromes grown at high density after 48 h in culture, no significant differences could be found in replicon behaviour between these syndromes and normal cultures. However when Bloom's cells were grown at low density and examined 24 h earlier, the mean rate of chain growth R was reduced compared to normal cells at the same density. Both cell types at high densities at 24 h showed equal but lower R values than at 48 h after plating the cultures. The lower rate of chain growth in Bloom's was accompanied by a longer S-period and cell cycle. Studies of cell proliferation kinetics using consecutive mitoses after bromodeoxyuridine (BUdR) incorporation and harlequin banding showed that Bloom's cells at low cell density require a longer period to recover a normal cell cycle length after plating than do normal cells at the same density. Plating densities and using conditioned media shorten the recovery period in Bloom's cells, and when foetal calf serum/MEM is replaced by human AB serum/McCoy 5a medium as the growth media, cell cycle behaviour of low density Bloom's and normal cells are equal at a much earlier time. It is concluded that the slow rate of DNA chain growth in Bloom's cells is an artefact introduced by culture conditions and also may be present in normal cells at an earlier period. The behaviour of replicons during this recovery period appears to be similar in Bloom's and normal cells except for the time lag. As recovery proceeds, the DNA chain growth in the associated replicon pairs recover progressively. This alters both the mean R value from 0.4 to 0.8 micron/min, the slope of the regression K from less than 1.0 to approximately 1.0 while the distance between initiation sites (ID) remains constant throughout. Pretreatment of all cultures with fluorodeoxyuridine (FUdR) produced the same differential effect on release from DNA synthesis inhibition, that is a similar increase in the activation of normally inactive replicons and a slightly slower rate of chain growth over all replicons. No evidence of a substance released by Bloom's cells in culture capable of increasing the sister-chromatid frequency in normal cells could be found. Since SCE frequencies were found to increase with fixation time after BUdR introduction it is concluded that some of the reported changes could be due to differences in cell cycle kinetics brought about by the different media conditions.
    • Quantitative trait locus analysis reveals two intragenic sites that influence O6-alkylguanine-DNA alkyltransferase activity in peripheral blood mononuclear cells.

      Margison, Geoffrey P; Heighway, Jim; Pearson, Steven J; McGown, Gail; Thorncroft, Mary R; Watson, Amanda J; Harrison, Kathryn L; Lewis, Sarah J; Rohde, Klaus; Barber, Philip V; et al. (2005-08)
      The repair of specific types of DNA alkylation damage by O6-alkylguanine-DNA alkyltransferase (MGMT) is a major mechanism of resistance to the carcinogenic and chemotherapeutic effects of certain alkylating agents. MGMT expression levels vary widely between individuals but the underlying causes of this variability are not known. To address this, we used an expressed single nucleotide polymorphism (SNP) and demonstrated that the MGMT alleles are frequently expressed at different levels in peripheral blood mononuclear cells (PBMC). This suggests that there is a genetic component of inter-allelic variation of MGMT levels that maps close to or within the MGMT locus. We then used quantitative trait locus (QTL) analysis using intragenic SNPs and found that there are at least two sites influencing inter-individual variation in PBMC MGMT activity. One is characterized by an SNP at the 3' end of the first intron and the second by two SNPs in the last exon. The latter are in perfect disequilibrium and both result in amino acid substitutions-one of them, Ile143Val, affecting an amino acid close to the Cys145 residue at the active site of MGMT. Using in vitro assays, we further showed that while the Val143 variant did not affect the activity of the protein on methylated DNA substrate, it was more resistant to inactivation by the MGMT pseudosubstrate, O6-(4-bromothenyl)guanine. These findings suggest that further investigations of the potential epidemiological and clinical significance of inherited differences in MGMT expression and activity are warranted.
    • Quantum dots brighten biological imaging.

      Byers, Richard J; Hitchman, Elizabeth R; School of Cancer and Enabling Sciences, University of Manchester, Manchester, UK. richard.byers@cmft.nhs.uk (2011-02)
      Quantum dots (QDs) are novel photostable semiconductor nanocrystals possessing wide excitation spectra and narrow, symmetrical emission spectra and can be conjugated to a wide range of biological targets, including proteins, antibodies and nucleic acid probes. These characteristics have provoked considerable interest in their use for bioimaging. Much investigation has been performed into their use for multiplex immunohistochemistry and in situ hybridisation which, when combined with multispectral imaging, has enabled quantitation and colocalisation of gene expression in clinical tissue. Many advances have recently been made using QDs for live cell and in vivo imaging, in which QD-labelled molecules can be tracked and visualised in 3-D. This review aims to outline the beneficial properties presented by QDs along with important advances in their biological application.
    • Quantum dots light up pathology.

      Tholouli, E; Sweeney, Elizabeth; Barrow, E; Clay, V; Hoyland, Judith A; Byers, Richard J; Department of Clinical Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, UK. (2008-11)
      Quantum dots (QDs) are novel nanocrystal fluorophores with extremely high fluorescence efficiency and minimal photobleaching. They also possess a constant excitation wavelength together with sharp and symmetrical tunable emission spectra. These unique optical properties make them near-perfect fluorescent markers and there has recently been rapid development of their use for bioimaging. QDs can be conjugated to a wide range of biological targets, including proteins, antibodies, and nucleic acid probes, rendering them of particular interest to pathology researchers. They have been used in multiplex immunohistochemistry and in situ hybridization, which when combined with multispectral imaging, has enabled quantitative measurement of gene expression in situ. QDs have also been used for live in vivo animal imaging and are now being applied to an ever-increasing range of biological problems. These are detailed in this review, which also acts to outline the important advances that have been made in their range of applications. The relative novelty of QDs can present problems in their practical use and guidelines for their application are given.
    • QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

      Boehm, U.; Nelson, G.; Brown, C. M.; Bagley, Steven; Bajcsy, P.; Bischof, J.; Dauphin, A.; Dobbie, I. M.; Eriksson, J. E.; Faklaris, O.; et al. (2021)